Ecology: Fine-scale environmental specialization of reef-building corals might be limiting reef recovery in the Florida Keys by Carly D. Kenkel, Albert T. Almanza, and Mikhail V. Matz

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Volume 96, Issue 12 (December) 2015
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Volume 96, Issue 12 (December 2015)

Carly D. Kenkel, Albert T. Almanza, and Mikhail V. Matz 2015. Fine-scale environmental specialization of reef-building corals might be limiting reef recovery in the Florida Keys. Ecology 96:3197–3212. Department of Integrative Biology, The University of Texas, 1 University Station C0990, Austin, Texas 78712 USA

Despite decades of monitoring global reef decline, we are still largely unable to explain patterns of reef deterioration at local scales, which precludes the development of effective management strategies. Offshore reefs of the Florida Keys, USA, experience milder temperatures and lower nutrient loads in comparison to inshore reefs yet remain considerably more degraded than nearshore patch reefs. A year-long reciprocal transplant experiment of the mustard hill coral (Porites astreoides) involving four source and eight transplant locations reveals that corals adapt and/or acclimatize to their local habitat on a <10-km scale. Surprisingly, transplantation to putatively similar environmental types (e.g., offshore corals moved to a novel offshore site, or along-shore transplantation) resulted in greater reductions in fitness proxies, such as coral growth, than cross-channel transplantation between inshore and offshore reefs. The only abiotic factor showing significantly greater differences between along-shore sites was daily temperature range extremes (rather than the absolute high or low temperatures reached), providing a possible explanation for this pattern. Offshore-origin corals exhibited significant growth reductions at sites with greater daily temperature ranges, which explained up to 39% of the variation in their mass gain. In contrast, daily temperature range explained at most 9% of growth variation in inshore-origin corals, suggesting that inshore corals are more tolerant of high-frequency temperature fluctuations. Finally, corals incur trade-offs when specializing to their native reef. Across reef locations the coefficient of selection against coral transplants was 0.07 ± 0.02 (mean ± SE). This selection against immigrants could hinder the ability of corals to recolonize devastated reefs, whether through assisted migration efforts or natural recruitment events, providing a unifying explanation for observed patterns of coral decline in this reef system. Key words:  acclimatization, adaptation, fitness trade-offs, inshore, offshore, Porites astreoides, reef-building corals, selection Received: December 3, 2014; Received: May 13, 2015; Accepted: May 19, 2015 1 Present address: Australian Institute of Marine Science, PMB Number 3, Townsville MC, Queensland, Australia. E-mail: Corresponding Editor: J. F. Bruno.

Coral-list: NOAA: Coral Bleaching Threat in Western Atlantic and Pacific

Coral Bleaching rising While corals can recover from mild bleaching, severe or long-term bleaching kills corals. Even if corals recover, they are more susceptible to disease. Once corals die, it usually takes decades for the reef to recover — but recovery is only possible if the reefs are undisturbed. After corals die, reefs degrade and the structures corals build are eroded away, providing less shoreline protection and less habitat for fish and shellfish.
“The bleaching that started in June 2014 has been really bad for corals in the western Pacific,” said Mark Eakin, NOAA Coral Reef Watch coordinator. “We are worried that bleaching will spread to the western Atlantic and again into Hawaii.”

Earlier this year, NOAA’s Coral Reef Watch four-month Coral Bleaching Outlook accurately predicted coral bleaching in the South Pacific, including the Solomon Islands, Papua New Guinea, Nauru, Fiji, and American Samoa. It also recently predicted the coral bleaching in the Indian Ocean, including the British Indian Ocean Territory and the Maldives.

In fall 2014, Hawaii saw widespread coral bleaching for the first time since 1996. If corals in Hawaii bleach again this year, it would be the first time it happened in consecutive years in the archipelago.

Warmer ocean temperatures in 2014 also dealt a blow to coral nurseries in the Florida Keys, where scientists are growing threatened coral species to transplant onto local reefs. Coral reefs in Florida and the Caribbean have weathered repeated and worsening coral bleaching events for the past thirty years. The NOAA Coral Reef Watch monitoring team says that more bleaching so soon could spell disaster for corals that have yet to recover from last year’s stress.

“Many healthy, resilient coral reefs can withstand bleaching as long as they have time to recover,” Eakin said. “However, when you have repeated bleaching on a reef within a short period of time, it’s very hard for the corals to recover and survive. This is even worse where corals are suffering from other environmental threats, like pollution or overfishing.”

NOAA’s bleaching prediction for the upcoming months supports the findings of a paper published in the journal Science last week that examined the threat to marine ecosystems and ecosystem services under two different carbon dioxide emission pathways.

“The paper reports that even if humans limit the Earth’s warming to two degrees C (3.8 degrees F), many marine ecosystems, including coral reefs, are still going to suffer,” said Eakin, an author on the paper. “The increase we are seeing in the frequency and severity of bleaching events is part of why the climate models in that paper predict a dire future for coral reefs.”

The NOAA Coral Reef Watch program’s satellite data provide current reef environmental conditions to quickly identify areas at risk for coral bleaching , while its climate model-based outlooks provide managers with information on potential bleaching months in advance. The Coral Reef Watch mission is to utilize remote sensing and in situ tools for near-real-time and long term monitoring, modeling and reporting of physical environmental conditions of coral reef ecosystems.

The four-month Coral Bleaching Outlooks , based on NOAA’s operational Climate Forecast System, use NOAA’s vast collection of environmental data to provide resource managers and the general public with the necessary tools to help reduce effects of climate change and other environmental and human caused stressors.

The outlook is produced by NOAA’s Satellite and Information Service and funded by the Coral Reef Conservation Program, Climate Program Office , and National Centers for Environmental Prediction .

For more information on coral bleaching and these products, visit: .
NOAA’s mission is to understand and predict changes in the Earth’s environment, from the depths of the ocean to the surface of the sun, and to conserve and manage our coastal and marine resources. Join us on Facebook , Twitter , Instagram and our other social media channels .

C. Mark Eakin, Ph.D.
Coordinator, NOAA Coral Reef Watch
National Oceanic and Atmospheric Administration
Center for Satellite Applications and Research
Satellite Oceanography & Climate Division

NOAA Center for Weather and Climate Prediction (NCWCP)
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“We have many advantages in the fight against global warming, but time is not one of them. Instead of idly debating the precise extent of global warming, or the precise timeline of global warming, we need to deal with the central facts of rising temperatures, rising waters, and all the endless troubles that global warming will bring. We stand warned by serious and credible scientists across the world that time is short and the dangers are great. The most relevant question now is whether our own government is equal to the challenge.”
Senator John McCain, December 5 2008

Benthic Macroalgal Blooms as Indicators of Nutrient Loading from Aquifer-Injected Sewage Effluent in Environmentally Sensitive Near-Shore Waters Associated with the South Florida Keys

Journal of Geography and Geology; Vol. 6, No. 4; 2014
ISSN 1916-9779 E-ISSN 1916-9787
Published by Canadian Center of Science and Education

by: Sydney T. Bacchus1, Sergio Bernardes1, Thomas Jordan1 & Marguerite Madden1
1 Center for Geospatial Research, Department of Geography, University of Georgia, Athens, Georgia
30602-2502 USA
Correspondence: Marguerite Madden, Center for Geospatial Research, Department of Geography, University of
Georgia, Athens, Georgia 30602-2502, USA. E-mail:

JGG Bacchus et al fracture SGD paper1214

PLOS ONE: RNA-seq Profiles of Immune Related Genes in the Staghorn Coral Acropora cervicornis Infected with White Band Disease by Silvia Libro mail, Stefan T. Kaluziak, Steven V. Vollmer

Published: Nov 21, 2013
DOI: 10.1371/journal.pone.0081821


Coral diseases are among the most serious threats to coral reefs worldwide, yet most coral diseases remain poorly understood. How the coral host responds to pathogen infection is an area where very little is known. Here we used next-generation RNA-sequencing (RNA-seq) to produce a transcriptome-wide profile of the immune response of the Staghorn coral Acropora cervicornis to White Band Disease (WBD) by comparing infected versus healthy (asymptomatic) coral tissues. The transcriptome of A. cervicornis was assembled de novo from A-tail selected Illumina mRNA-seq data from whole coral tissues, and parsed bioinformatically into coral and non-coral transcripts using existing Acropora genomes in order to identify putative coral transcripts. Differentially expressed transcripts were identified in the coral and non-coral datasets to identify genes that were up- and down-regulated due to disease infection. RNA-seq analyses indicate that infected corals exhibited significant changes in gene expression across 4% (1,805 out of 47,748 transcripts) of the coral transcriptome. The primary response to infection included transcripts involved in macrophage-mediated pathogen recognition and ROS production, two hallmarks of phagocytosis, as well as key mediators of apoptosis and calcium homeostasis. The strong up-regulation of the enzyme allene oxide synthase-lipoxygenase suggests a key role of the allene oxide pathway in coral immunity. Interestingly, none of the three primary innate immune pathways – Toll-like receptors (TLR), Complement, and prophenoloxydase pathways, were strongly associated with the response of A. cervicornis to infection. Five-hundred and fifty differentially expressed non-coral transcripts were classified as metazoan (n = 84), algal or plant (n = 52), fungi (n = 24) and protozoans (n = 13). None of the 52 putative Symbiodinium or algal transcript had any clear immune functions indicating that the immune response is driven by the coral host, and not its algal symbionts.

Citation: Libro S, Kaluziak ST, Vollmer SV (2013) RNA-seq Profiles of Immune Related Genes in the Staghorn Coral Acropora cervicornis Infected with White Band Disease. PLoS ONE 8(11): e81821. doi:10.1371/journal.pone.0081821

Editor: Kenneth Söderhäll, Uppsala University, Sweden

Received: August 22, 2013; Accepted: October 24, 2013; Published: November 21, 2013

Copyright: © 2013 Libro et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

Funding: Grant funding was provided by the NSF to Steve Vollmer (NSF-OCE 0751666). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

Competing interests: The authors have declared that no competing interests exist.


The global rise in disease epidemics linked to climate change has taken a heavy toll on tropical reef-building corals and the diverse ecosystems they support [1-4]. A prime example is White Band Disease (WBD), which beginning in the late 1970s [5], caused unprecedented Caribbean-wide die-offs of two species of Acropora corals, the Staghorn coral A. cervicornis and the Elkhorn coral A. palmata [6-8]. As a result, both species are now listed as threatened on the US Endangered Species Act [9] and as critically endangered under the International Union for the Conservation of Nature (IUCN) Red List criteria [4]. Despite the devastating impacts of coral diseases on reefs world-wide, little is known about the basic etiology and ecology of most coral diseases [10-12] including basic information about how corals fight diseases [2,12,13], even though information about the coral immune response may be crucial to understanding the future resiliency of reef corals [2].

Genetic surveys indicate that corals and other cnidarians possess the genetic architecture underlying common innate immune pathways, including Toll-like receptors (TLR) as well as components of the complement and prophenoloxidase (PO) pathways [10,14,15]. PO activity and melanization responses have been elicited in corals exposed to pathogens [16-18] and components of the TLR pathway were differentially expressed in corals infected with non-host specific Symbiodinium types [19]. Elements of the complement pathway, such as mannose-binding lectins, appear to be involved in pathogen, symbiont, and self/nonself recognition in Acropora millepora [20]. Although cnidaria lack specialized immune cells, such as macrophages, cnidaria possess mobile amebocytes that are activated upon pathogen exposure or tissue damage [21-24]. Phagocytosis activity in cnidarians is commonly observed in flagellate gastrodermal cells during food uptake [25]. However, several studies have demonstrated that, upon immune stimulation, different populations of amebocytes can exhibit phagocitic activity directed toward wound healing and removal of necrotic tissue, as well as encapsulation of foreign particles [26,27].

Relatively few studies have studied the genetic response of corals infected with disease [28,29]. A microarray study of Pocillopora damicornis infected with Vibrio identified six candidate immune genes including three lectins and three putative antimicrobial proteins [28]. Exposure of A. millepora to bacterial and viral pathogen associated molecular patterns (PAMPs) resulted in up-regulation of few immune related genes including three GTPase of immunity associated proteins (GiMAP) [29], a family of conserved small GTPases involved in the antibacterial response of plants and mammals [30].

White Band Disease represents a good system to investigate the immune response of a reef-building coral. It is one of the few coral diseases that is highly transmissible [31] and host-specific [5,11]. WBD is characterized by an interface of white dying tissue that advances rapidly along the coral colony (Figure 1). Current evidence suggests that the pathogen is bacterial [31-36], but Henle-Koch postulates have not been satisfied. To date, multiple bacteria have been associated with WBD infections, including Vibrio harveyi [33,37] as well as a marine Rickettsia CAR1α [34]. In situ transmission experiments have identified naturally resistant and susceptible genotypes of A. cervicornis [31], indicating that the immune response to WBD varies among individuals.

Figure 1

Figure 1. White Band Disease on Acropora cervicornis.

A colony of the Staghorn coral A. cervicornis infected with White Band Disease showing the characteristic white band of dying and necrotic coral tissue.

Here we used next-generation RNA-sequencing to produce a transcriptome-wide profile of the immune response of A. cervicornis to WBD by comparing infected versus healthy (asymptomatic) coral tissues. The transcriptome of A. cervicornis was assembled de novo from A-tail selected mRNA-seq data from whole coral tissues, and parsed bioinformatically into coral and non-coral transcripts using existing Acropora genomes in order to identify putative coral transcripts. Differentially expressed transcripts were identified in the coral and non-coral datasets to identify which genes were up- and down-regulated due to disease infection and characterize the immune response of the coral.

A de novo assembly of the A. cervicornis transcriptome was assembled from 436.5 million Illumina RNA-sequencing reads from 45 coral samples of A. cervicornis and A. palmata. The total reads were de novo assembled using Trinity [38], resulting in 95,389 transcripts, with a N50 of 363 and N75 of 696. A total of 47,748 transcripts mapped against the existing Acropora genomes [39,40] and were classified as putative coral transcripts while the remaining 47,641 were classified as non-coral transcripts (Table 1).

Table 1. Summary of coral and non-coral transcripts.
Total number of transcripts (n), significantly differentially expressed transcripts (adj p-val<0.05) (DE), number of up-regulated (up) and down-regulated (down) transcripts among the entire dataset and annotated transcripts only (E-val<10-5). First row refers to putative coral transcripts, second row to non-coral transcripts. For this study, five diseased (i.e. infected) and six healthy corals were used to profile the immune response of Staghorn corals infected with WBD. The average number of putative coral reads (±SE) was 4,076,829 (± 898,542) in the diseased coral samples compared to 4,199,946 (±761,894) in the healthy samples. In total, 20,503 coral transcripts (43 %) and 14,253 (30%) non-coral transcripts had strong protein annotations (Blastx e-value < 10-5) (Table 1). Differentially expressed coral transcripts Statistical analysis in DEseq [41] identified 1,805 differentially expressed (DE) transcripts (adj p-value < 0.05) between healthy and WBD coral samples (Table 1, Table S1); 559 of these DE transcripts had reliable protein annotations (Blastx e-values < 10-5) that could be used to characterize the immune response of A. cervicornis infected with WBD (Figure 2a, Figure 3). Annotated transcripts were characterized by gene ontology (GO) and grouped into manually curated categories based on literature searches highlighting immune functions (Table 2). WBD-infected corals exhibited strong gene expression responses for genes related to immunity (n = 72), apoptosis (n = 18) and arachidonic acid metabolism (n = 5). Calcification (n = 14) and calcium homeostasis (n = 21) were also perturbed, as well as cell growth and remodeling (n = 134), cellular processes (n = 188) and general metabolism (n = 43). figure 2

Figure 2. Volcano plots displaying differential gene expression between healthy and disease A. cervicornis.

Figure a. plots gene expression values of the putative coral transcripts, figure b. plots putative non coral transcripts. Each point represents an individual gene transcript. Red points represent significantly differentially expressed transcripts (adj p-value < 0.05). doi:10.1371/journal.pone.0081821.g002 figure 3

Figure 3. Heatmap of immune-related differentially expressed coral transcripts.

Table 2
Table 2. Summary of the main pathways involved in A.cervicornis response to WBD.
Number (N) of differentially expressed (DE) transcripts per category. Function defined by GO terms and manually curated categories. Expression values reported as log2fold change of WBD infected corals relative to healthy corals.

Immune-related processes

Sixty-nine DE transcripts were associated with immunity. Three C-type lectins receptors, C- type mannose receptor 2 (MRC2), macrophage lectin 2 (CLEC10A) and collectin-12 (COLEC12) were up-regulated in infected corals. Two mediators of phagocytosis were up-regulated – the macrophage receptor multiple epidermal growth factor-like domains protein 10 (MEGF10) and actin-22 (act22), which is involved in the phagosome formation. All three subunits of NADPH oxidase (NOX) involved in reactive oxygen species (ROS) production were up-regulated, including cytochrome b-245 heavy chain (CYBB), NADPH oxidase 3 (NOX3) and neutrophil cytosol factor 2 (p67-phox). Other DE immune related genes included nine antioxidants participating in the detoxification of ROS such as peroxidasin (PXDN, n=3) and glutaredoxin (GLRX), and 12 transcripts associated to response to stress such as golgi-associated plant pathogenesis-related protein 1 (GAPR-1, n = 3) and universal stress protein A-like protein (UspA, n = 2).

Little or no differential expression was detected in the three primary innate immune pathways – Toll/TLR, complement and prophenoloxidase (PO) pathways. In the Toll/TLR pathway, two TLR2 homologs and the adaptor molecule TNF receptor-associated factor 3 (TRAF3) were up-regulated in WBD corals. In the complement pathway, two transcripts encoding macrophage-expressed gene protein 1 (MPEG1) were differentially expressed, but they were down regulated in WBD corals. No differentially expressed transcripts were detected in the PO pathway.
Arachidonic acid metabolism

Six DE transcripts participating to the metabolism of arachidonic acid (AA) were up-regulated in diseased corals. Five matched coral allene oxide synthase-lipoxygenase (AOSL), a catalase related hemoprotein that catalyzes the biosynthesis of allene oxide, a precursor of marine eicoesanoids. The sixth transcript matched the enzyme phospholipase A2 (PLA2), involved formation of AA from membrane phospholipids.

Eighteen DE transcripts were associated with apoptosis, including both pro- and anti-apoptotic regulators such as the extracellular matrix protein thrombospondin 2 and fibroblast growth factor receptor 2 (n = 2), respectively. Tumor necrosis factor receptor superfamily member 1A (TNFRSF1A) and caspase 3 (CASP-3) were up-regulated while caspase 8 (CASP-8) was down-regulated in WBD corals.
Calcification and calcium homeostasis

DE transcripts in this category included 14 proteins participating to carbon dioxide transport, biomineralization and skeletal growth. Two carbonic anhydrases were up-regulated (CA2 and CA3) and one was down-regulated (CA2) in WBD corals. Mediators of calcium homeostasis included 27 DE transcripts participating in calcium ion binding and transport such as calmodulin (CaM, n = 3), calumenin (CALU) and calsequestrin-2 (CASQ2) and were all up-regulated.
Cell growth and remodeling

Among the 138 DE transcripts related to cell growth and remodeling we identified 17 metallopeptidases (15 up, 2 down), 29 cytoskeletal proteins (all up-regulated) and 14 angiogenesis mediators (11 up, 3 down). A large group of DE transcripts were cell adhesion proteins (n = 29), including four up-regulated transcripts encoding sushi, von Willebrand factor type A, EGF and pentraxin domain-containing protein 1 (polydom/SVEP1).
Cell metabolism

Forty-two DE transcripts were associated with cell metabolism. These included 14 mediators of lipid metabolism, in particular, five lipases involved in lipid and phospholipid catabolism (n = 5, all up), such as pancreatic triacylglycerol lipase (PL), pancreatic lipase-related protein 2 (PL-RP2) and phospholipase DDHD1 (DDHD1). Four transcripts participating in fatty acid biosynthesis, such as fatty acid synthase (FASN), acetyl-CoA carboxylase (ACC) and acetyl-CoA carboxylase 1 (ACC1), were all down-regulated in WBD corals, and five transcripts involved in the breakdown of fatty acids such as long-chain-fatty-acid–CoA ligase 1 (LACS1) and 5 (LACS5) were up-regulated.
Non-coral transcripts

Out of the 47,641 putative non-coral transcripts in the dataset, 550 were differentially expressed in WBD infected corals (Table 1, Table S2). Of these 550 DE transcripts, 251 were well-annotated and were all up-regulated (Figure 2b). About 33 % were metazoan, the remaining were putative zooxanthellae (23%), fungi (10%) and protozoa (5%). A small number of transcripts matched bacteria (4%) and viruses (0.1%), while the remaining 23 % were unknown.

Metazoan transcripts (n = 84) included mediators of cell growth and remodeling (n = 16), metabolism (n = 4), cellular processes (n = 61) and two uncharacterized transcripts. Only two immune-related transcripts were identified and were the antioxidant peroxiredoxin-2 (PRDX2) and the metallopeptidase aminopeptidase O (AP-O), which may be involved in leukotrienes synthesis from AA.

Fifty-nine transcripts had plant, algae or Alveolata protein IDs and are presumed or putative Symbiodinum transcripts. Based on GO terms, these Symbiodinium transcripts were associated with cell growth and remodeling (n = 8), cellular processes (n= 38) and metabolism (n = 10), while two were uncharacterized. One transcript matched cysteine proteinase RD21a (RD21), a peptidase involved in defense against fungi. Fungal transcripts (n = 24) belonged to cell processes (n = 20) and metabolism (n = 3) plus one uncharacterized protein. Out of the 14 transcripts matching protozoa, 13 were associated to cellular processes, two to metabolism and one to cell growth and remodeling.

Nine transcripts matched bacterial proteins, six of them were involved in cellular processes (n = 3), metabolism (n = 3) and three were uncharacterized. Two transcripts shared protein IDs annotating to virus proteins (glycoprotein gp2 and one uncharacterized), while the remaining 59 transcripts did not have functional annotations.

Our study demonstrates that Acropora cervicornis mounts a vigorous immune response against White Band Disease (WBD) pathogen(s) involving dramatic changes in gene expression across 4% of the coral transcriptome. The identities of the differentially expressed (DE) coral transcripts indicate that the response of A. cervicornis to WBD infection is driven by phagocytosis of apoptotic cells (Figure 3, Table 2). Corals infected with WBD exhibited strong differential expression of transcripts involved in macrophage-mediated pathogen recognition and ROS production, two hallmarks of phagocytosis, as well as key mediators of apoptosis and calcium homeostasis. The strong up-regulation of transcripts involved in arachidonic acid (AA) metabolism and allene oxide synthesis suggests their key role in coral immunity.

The primary signature of phagocytosis activity in WBD infected corals was the up-regulation of four macrophage receptors that recognize and bind to conserved motifs on the surface of target cells. Three of these receptors, MRC2, CLEC10A and COLEC12 belong to the C-type lectin family of proteins that include several Pathogen Recognition Receptors (PRRs). MRC2 recognizes mannose and fucose on glycoproteins of bacteria, viruses and fungi [42] while CLEC10A recognizes galactose and N-acetyl-galactosamine residues [43]. COLEC12is a scavenger receptor that shares structural similarity with macrophage scavenger receptor class A type I (SR-AI), a surface membrane receptor that mediates binding and phagocytosis of gram-positive, gram-negative bacteria and yeasts [44]. The fourth receptor, MEGF10, is membrane protein that promotes the clearance of apoptotic cells by causing macrophages to adhere and engulf them [45]. The stronger up-regulation of the three macrophage PRRs (2.2, 5.4 and 4.1 fold) compared to the one apoptotic cell recognizing receptor MEGF10 (2.17 fold) suggests the response is primarily driven by phagocytosis of microbes. A second signature of phagocytosis was the up-regulation of transcripts linked to ROS production, including three subunits of the enzymatic complex NADPH oxidase (NOX). ROS production is a general and highly conserved response to invading pathogens and stress and the release of ROS from the mitochondria can induce apoptosis in metazoan and yeasts [46,47]. During phagocytosis, ROS are generated in mature phagosomes (i.e. specialized vacuoles in phagocytic cells) [48] to kill engulfed cells [49]. In cnidarians, ROS production has been observed in the hydroid Hydra vulgaris exposed to the immune stimulant lipopolysaccaride (LPS) [50] and in reef corals during thermal and UV-induced bleaching [51,52], possibly due to the breakdown of the mitochondrial and photosynthetic membranes [53,54].

In WBD infected corals, it is possible that phagocytosis is aimed either at the removal of invading pathogens and/or used to clear damaged apoptotic cells [55]. The genetic signature of phagocytosis in WBD infected corals raises questions about the identity of these phagocytic immune cells in A. cervicornis. Cnidaria lack specialized immune cells, but do possess mobile amebocytes. Aggregations of amebocytes have been observed in the gorgonian coral Gorgonia ventalina infected with pathogenic fungi [24] and near wounded tissues in the soft coral Plexaurella fusifera [26]. Histological examination revealed that amebocytes exhibited phagocytic and PO activity [27] as well as antimicrobial activity against Gram-negative bacteria and ROS production [56]. Interestingly, certain populations of ameboid cells always show phagocytic activity, while others only acquire it upon immune activation [27]. These findings indicate that cnidaria, traditionally considered “simple” animals, are able to mount an innate immune response by employing the functional plasticity of amebocytes, which seem to represent the primary immune population of phagocytic cells.

Increased apoptosis in WBD infected corals was indicated by the differential expression of TNFRSF1A and CASP-3. During apoptosis, TNFRSF1A binds to tumor necrosis factor (TNF), which then recruits CASP-8 initiating the downstream activation of CASP-3, the main effector caspase of the apoptotic pathway [57,58]. While both TNFRSF1A and CASP-3 are up-regulated, CASP-8 is down-regulated which may suggest that CASP-3 is activated by some alternative pathway. Active programmed cell death was also suggested by disruption of calcium homeostasis as indicated by the strong up-regulation of CaM and other calcium binding proteins. In both plants and animals [59,60], apoptosis can be triggered by LPS from gram-negative bacteria via alteration of TNFRSF1A expression [61]. Some bacterial pathogens are also able to induce or inhibit apoptosis in their host [60,62,63] via alteration of membrane permeability and disruption of Ca2+ homeostasis [64], direct activation of TNF-α [65], TLR2 [66,67]or CASP-3 [68]. In corals, apoptosis occurs normally during metamorphosis [69] and the onset of symbiosis [70], but it has also been observed during bleaching as a possible mechanism to expel zooxanthellae in response to thermal stress [71-73]. Apoptosis has also been detected in the lesions of three Pacific species of Acropora infected by White Syndrome (WS), suggesting that it is a mechanism of tissue loss in WS [74].

Another key, yet unexpected, finding of this study is the potential role of the arachidonic acid (AA) pathway in the coral immune response. Genes involved in AA synthesis increased dramatically in WBD infected corals. The role of AA as an inflammation regulator is well-known in metazoans [75] , but has not been described in Cnidaria or in association with any coral disease. In metazoans, AA is released by apoptotic cells as chemotactic factor to promote clearance by phagocytes [76], but it can also induce apoptosis via rapid increase of calcium concentration and activation of CASP-3 in a CASP-8-independent way [77]. These findings are consistent with our data showing up-regulation of CASP-3, but not CASP-8, suggesting that AA may act similarly as immunomodulator in A. cervicornis. The five transcripts matching allene oxide synthase-lypoxigenases (AOSL) from the soft coral Plexaura homomalla, on the other hand, indicated that AA is converted into allene oxide, an intermediate compound of prostanoid synthesis in plants and soft corals [78-82].

Allene oxide has received considerable attention as a putative precursor of clavulones [83], a class of unique marine prostanoids known for their anti-viral and anti-cancer activity [84,85]. The link between the AOSL pathway and clavulones synthesis in corals, although still under debate, was suggested by the similarities with the biosynthetic pathway of jasmonic acid [83] a plant hormone that is produced via an allene oxide intermediate upon mechanical injury [86] and herbivore attack [87]. Although further study is needed to understand the role allene oxide in corals, our data represent the first evidence implicating AOSL in coral immunity and suggest that AOSL may be involved in controlling levels of free AA produced by apoptotic cells.

Several other immune related genes exhibited altered expression in infected corals. The majority were anti-oxidants including PXDN, peroxidasin-like proteins and GLRX – a glutathione-dependent enzyme. PXDN has been shown to be DE in some thermally stressed corals, but not in a consistent manner. For example, in Montastraea faveolata, PXDN was up-regulated in thermally-stressed larvae [88], but was down-regulated in thermally-bleached adult colonies [89]. Active cell remodeling and cell matrix degradation was indicated by several DE cytoskeletal proteins, metalloproteases and cell adhesion proteins, probably associated with cellular and cytoskeletal rearrangements linked to phagocytosis and apoptosis. CASP-3 activation, in particular, initiates apoptosis by altering the expression of metalloproteases and hydrolytic enzymes such as cathepsins that degrade extracellular matrix components [90]. Interestingly, WBD infected corals up-regulated three transcripts encoding polydom, a cell adhesion protein belonging to the pentraxin family of lectins. Recent studies suggest an immune function for polydom based on its similarities in its protein domains to complement proteins and C-type lectins with antimicrobial activity [91]. In cnidarians, the potential immune role for polydom is bolstered by its up-regulation in the hydroid Hydractinia symbiolongicarpus after fungal and bacterial exposure [92].

Surprisingly, none of the three main innate immune pathways – TLR, complement and PO – played a prominent role in the immune signature of A. cervicornis infected with WBD, even though transcripts from these pathways are well-represented in our transcriptome. Only three transcripts in the TLR pathway were differentially expressed: two TLRs matching to human TLR2 and TRAF3. In the lectin complement pathway, the only two DE transcripts were two proteins matching MPEG1, a MAC/PF (membrane attack complex/perforin) containing protein that is involved in the response against Gram negative bacteria in sponges and is up-regulated upon LPS exposure [93]. None of the transcripts belonging to the PO pathway were differentially expressed during WBD infection, even though in other corals PO activity acts as an important defense against invading pathogens and tissue damage [16-18].
Non-coral transcripts

The taxonomic distribution of non-coral transcripts highlighted the presence of several members of the coral holobiont, i.e. the coral host and associated symbiotic microorganisms, including zooxanthellae, fungi and protozoa. The majority of these non-coral transcripts matched metazoan and putative zooxanthaellae proteins, while the remaining transcripts matched fungi, protozoa and bacteria. GO term analysis revealed that most of these non-coral transcripts encoded mediators of cell homeostasis and general metabolism. Transcripts with metazoan identities were likely coral transcripts that did not have identities in the coral reference genomes and may thus represent transcripts unique to A. cervicornis. Putative zooxanthellae transcripts were identified as transcripts annotating to Viridiplantae, Heterokontophyta (i.e. algae), cyanobacteria and the superphylum Alveolata. Interestingly, no genetic signature of immune activity from the algal symbionts was evident in our transcriptome. Instead, our data suggest drastic changes in photosynthesis and cell metabolism of the zooxanthellae; this is consistent with a previous study showing that Symbiodinum undergo major alteration of carbon metabolism in response to stress [94].

Our data reveal that the coral host, but not its algal symbionts, undergoes dramatic alterations in gene expression during response to WBD infection. Transcriptional changes affected mediators of innate immunity, in particular receptors on the surface of phagocytic cells, enzymes involved in ROS production and modulators of apoptosis. Taken together, our data suggest that WBD infection in A. cervicornis is associated with apoptosis, and that WBD pathogen triggers a powerful immune response driven by phagocytic cells that encapsulate and degrade apoptotic cells. This study also indicates a key role for arachidonic acid and in particular the enzyme AOSL in A. cervicornis immunity.
Materials and Methods

Total RNA was extracted from diseased and healthy Acropora cervicornis sampled from Crawl Cay reef in Bocas del Toro, Panama under Autoridad Nacional del Ambiente (ANAM) Collecting permit SE/A-71-08. For the diseased samples, corals with active mobile WBD interfaces were identified by monitoring the mobility of disease interfaces for two days, and then sampling a 2 cm region of tissue at and above the disease interface. A comparably sized and located tissue sample was taken from healthy (i.e. asymptomatic) corals. The coral tissues were flash frozen in liquid nitrogen and stored at -80°C. Total RNA was extracted in TriReagent (Molecular Research Center, Inc.) following the manufacturer’s protocol. Total RNA quality was assessed using the RNA Pico Chips on an Agilent Bioanalyzer 2100, and only extractions showing distinctive 28S and 18S bands and RIN values of 6 or higher were prepped for RNA sequencing.

RNA sequencing was performed on five diseased and six healthy coral samples using a multiplexed Illumina mRNA-seq protocol [95] with the following modifications. Instead of fragmenting the mRNA prior to cDNA synthesis, we obtained much better success fragmenting the double stranded cDNA using DNA fragmentase (New England Biolabs) for 30 minutes at 37°C. RNA-seq libraries were then prepared using next-generation sequencing modules (New England Biolabs) and custom paired-end adapters with 4bp barcodes. Multiplexed samples were run (2-3 samples per lane) on the Illumina GAII platform (Illumina, Inc, San Diego, California, USA) at the FAS Center for System Biology at Harvard University. Barcoded samples were de-multiplexed and raw sequencing reads were quality trimmed to remove sequences and regions with a Phred score of less than 30 and a read length less than 15bp long using custom Perl Scripts in the FASTX-Toolkit (http://hannonlab.

A de novo transcriptome was assembled using Trinity [38] from 463.5 million single-end Illumina RNA-Seq reads from 39 A. cervicornis and 6 A. palmata samples, including the 11 A. cervicornis samples included in this paper. The assembled transcriptome produced 95,389 transcripts with a N50 of 363 and N75 of 696. RNA-seq data were produced using whole coral tissue, which putatively contains sequences from the coral host, its algal symbiont Symbiodinium, and other members of the coral holobiont (e.g. fungi, bacteria, and viruses).

In order to resolve the holobiont, and putatively classify the source of the transcripts that were assembled as either coral or non-coral, we utilized a multistep pipeline leveraging the existing genomes of two congener species – A. digitifera [39] and A. millepora [40]. RNA-seq reads were mapped against both Acropora reference genomes using Bowtie [96] to produce two exomes. Transcripts from our de novo assembly were aligned using BLAST [97] against each exome. Transcripts were assigned as putatively coral if they matched either exome with an e-value of less than 10-10. Transcripts without significant coral hits were assigned as non-coral and could potentially include novel coral and/or algal symbiont Symbiodinium transcripts, as well as other associated eukaryotes, like endolithic fungi. Bacterial and viral transcripts are possible, but less likely given that A-tail selection to isolate eukaryotic mRNAs was performed prior to cDNA synthesis.

Putative gene identities for each transcript were identified by performing homology searches against the Swiss-Prot and TReMBLE protein databases [98], using tBLASTx. Matches with an e-value of less than10-5 were considered homologous protein-coding genes. Subsequently, GenBank Flat Files corresponding to the hits’ Accession ID’s were downloaded and used to extract taxonomic data for each used as a second method to identify the putative source of the transcripts. GO terms and gene functions were obtained for the annotated transcripts on UniProt. The reference transcriptome sequences are available on Bioproject (accession number PRJNA222758).

Differences in gene expression between healthy and disease A.cervicornis specimens were estimated using the R package DESeq [38]. First, all contigs were separated into two datasets –i.e. coral and non-coral- based on their matches to the Acropora genomes. Size factor estimation and normalization were then performed separately on each dataset using the functions estimateSizeFactors and estimateDispersions, respectively. Differentially expressed contigs were detected by running a negative binomial test using the function nbinomTest. Only differentially expressed transcripts (adjusted p-value < 0.05) that were also annotated (e-values < 10-5) were used for this study. Supporting Information Table_S1.xlsx Table_S1

Table S2.

Dataset of annotated (E-val<10-5 ) non-coral transcripts exhibiting differential expression between healthy and diseased samples (adj p-val<0.05). Table s2


The authors would like to thank Elizabeth Hemond for helping with sample collection and library preparation, Laura Geyer and the Smithsonian Tropical Research Institute and the for field and logistical support and the members of the Vollmer lab for valuable comments. Collection permits were provided by Autoridad Nacional del Ambiente (ANAM) SE/A-71-08.
Author Contributions

Conceived and designed the experiments: SV. Performed the experiments: SL. Analyzed the data: SL STK. Contributed reagents/materials/analysis tools: SV. Wrote the manuscript: SL SV.

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91. Gilgès D, Vinit MA, Callebaut I, Coulombel L, Cacheux V et al. (2000) Polydom: a secreted protein with pentraxin, complement control protein, epidermal growth factor and von Willebrand factor A domains. Biochem J 352: 49-59. doi:. PubMed: 11062057. doi: 10.1042/0264-6021:3520049.
92. Schwarz RS, Bosch TC, Cadavid LF (2008) Evolution of polydom-like molecules: identification and characterization of cnidarian polydom (Cnpolydom) in the basal metazoan Hydractinia. Dev Comp Immunol 32: 1192-1210. doi:. PubMed: 18466971. doi: 10.1016/j.dci.2008.03.007.
93. Wiens M, Korzhev M, Krasko A, Thakur NL, Perović-Ottstadt S et al. (2005) Innate immune defense of the sponge Suberites domuncula against bacteria involves a MyD88-dependent signaling pathway. Induction of a perforin-like molecule. J Biol Chem 280: 27949-27959. doi:. PubMed: 15923643. doi: 10.1074/jbc.m504049200.
94. Leggat W, Seneca F, Wasmund K, Ukani L, Yellowlees D et al. (2011) Differential Responses of the Coral Host and Their Algal Symbiont to Thermal Stress. PLOS ONE 6: e26687. doi:. doi: 10.1371/journal.pone.0026687.
95. Craig DW, Pearson JV, Szelinger S, Sekar A, Redman M, et al. (2008) Identification of genetic variants using bar-coded multiplexed sequencing. Nat Methods 5(10): 887-893. doi:. PubMed: 18794863. doi: 10.1038/nmeth.1251.
96. Langmead B, Trapnell C, Pop M, Salzberg SL (2009) Ultrafast and memory-efficient alignment of short DNA sequences to the human genome.
97. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215: 403-410. doi:. PubMed: 2231712. doi: 10.1016/s0022-2836(05)80360-2.
98. Consortium U (2012). Reorganizing the Protein Space at The Universal Protein Resource (UniProt). doi: 10.1093/nar/gkr981. BP spill money funds Fla. snapper project

11:36 AM, Nov 24, 2013 |

A $3 million, five-year project to expand data collection on red snapper and other reef fish stocks in the northern and eastern Gulf of Mexico is being hailed by Ocean Conservancy as a major milestone in the recovery of the marine resources affected by the 2010 BP oil spill disaster.

The Enhanced Assessment for Recovery of Gulf of Mexico Fisheries is one of six Florida projects funded by $15.7 million of BP and Transocean criminal fine money that addresses high priority conservation needs, ?according to the National Fish and Wildlife Foundation that’s administering the money.

“This is a good investment of BP fine money in the sustainability of the fisheries,” said ?Elizabeth Fetherston, a marine restoration strategist for Ocean Conservancy based in St. ?Petersburg.

It’s the first project funded by oil spill recovery money targeting fisheries and, more importantly, for red snapper stocks that “are incredibly important to the Gulf of Mexico and Pensacola’s fishing, ?tourism and seafood industry,” Fetherston said.

The Florida Fish and Wildlife Conservation Commission is managing the project.

Gil McRae, director of the agency’s research institute, said the findings from the project will fill critical gaps in data collection.

Gulf fisheries are managed by both state and federal agencies, and at times there’s confusion over harvest estimates, he said.

That system, based on the estimates of pounds caught a season, is very difficult to track accurately and leads to unpredictable regulations on the length and times of fishing seasons, McRea said. This has created discontent among commercial and recreational fishing communities, he said.

McRae’s team will put researchers on commercial and recreational fishing boats that volunteer for the program to more accurately document first hand what’s being caught, what’s being released and how many of the released fish are surviving.

“What we hope is the information will improve the predictability of the season and prevent wide swings in regulations of size limits and bag limits,” he said. “The project is all about getting better data to better manage offshore fisheries, especially red snapper.”

Another highlight of the project is developing smartphone apps that would allow anglers to record their catches in a central computer.

Enhanced assessment of the fisheries stock will lead to greater ability to sustain the populations, McRea said.

Will Patterson, a University of South Florida marine sciences biology professor who has been studying the impacts of the oil spill on fish populations, said more detailed studies of this scope have been conducted in the western Gulf, but there’s never been a study of this caliber east of Pensacola.

“The information that’s going to be collected will be based on what fish are living here, how fast they grow, where they live and how much they eat. That’s information we’ve not had.”
Charter boat captain Baz Yelverton of Gulf Breeze runs snapper trips into the Gulf.

He said he believes the assessment is a step in the right direction in better managing the fisheries.

“But what I’d really like to see happen is effort put into finding ways to (harmlessly) repel dolphins from where you’re fishing,” he said. “They’re a real problem. They wait until you throw your snapper back in the water, and they’re right there eating them. Let a snapper have a chance of getting back in the water.”

Pensacola News Journal, Kim Blair
Special thanks to Richard Charter

NFW: Artificial Reefs of the Gulf of Mexico: A Review of Gulf State Programs & Key Considerations


New National Wildlife Federation white paper encourages decision-makers to take environmental considerations into account when developing new artificial reefs.
11-08-2013 // Ryan Fikes

ArtificialReef_UnivofFL Over the past few decades the five Gulf States have built artificial reefs both inshore and offshore with the aim of enhancing recreational fishing and diving opportunities. State and local governments on the Gulf Coast have expressed interest in creating additional artificial reefs with some of the money from the federal penalties resulting from the BP oil disaster.

This white paper, Artificial Reefs of the Gulf of Mexico: A Review of Gulf State Programs & Key Considerations, encourages decision-makers to take environmental considerations into account when developing new artificial reefs. The paper provides a review of existing programs and offers key recommendations as governments consider creating additional artificial reefs.

Artificial reefs are materials placed on the sea floor to attract fish or otherwise influence physical or biological processes related to living marine resources. Artificial reefs attract certain species of fish and therefore have high recreational value for both fishing and diving activities.

The Northern Gulf of Mexico has somewhat limited natural reefs; these habitats include rock banks, oyster reefs, and coral reefs. Oyster reefs are a particularly valuable type of natural reef habitat that provide food and habitat for many different species of fish, birds, and other wildlife. Unfortunately, over half of the historic oyster reefs in the estuaries of the Gulf Coast have been lost. Decision-makers should prioritize replacing lost natural habitats such as oyster reefs when considering construction of new reef structures.

The paper provides considerations for maximizing the potential habitat value of any new artificial reefs. More research is needed in order to effectively compare the functionality of artificial reefs and their impacts on fish and wildlife to their natural counterparts.
Related Resources

Special thanks to Richard Charter

Sea Change: The Pacific’s Perilous Turn–Ocean acidification, the lesser-known twin of climate change, threatens to scramble marine life on a scale almost too big to fathom.

This incredible multi-media report, with links to scientific studies, should be read by all. DV

Story by Craig Welch

Photographs by Steve Ringman

“Sea Change” was produced, in part, with funding from the Pulitzer Center on Crisis Reporting.

Increased Stray Gas Abundance in a Subset of Drinking Water Wells Near Marcellas Shale Gas Extraction


Robert B. Jacksona,b,1, Avner Vengosha, Thomas H. Darraha, Nathaniel R. Warnera, Adrian Downa,b, Robert J. Poredac,
Stephen G. Osbornd, Kaiguang Zhaoa,b, and Jonathan D. Karra,b
aDivision of Earth and Ocean Sciences, Nicholas School of the Environment and
bCenter on Global Change, Duke University, Durham, NC 27708;
cDepartment of Earth and Environmental Sciences, University of Rochester, Rochester, NY 14627; and
dGeological Sciences Department, California State Polytechnic University, Pomona, CA 91768

Edited by Susan E. Trumbore, Max Planck Institute for Biogeochemistry, Jena, Germany, and approved June 3, 2013 (received for review December 17, 2012)

Horizontal drilling and hydraulic fracturing are transforming energy production, but their potential environmental effects remain controversial. We analyzed 141 drinking waterwells across the Appalachian Plateaus physiographic province of northeastern Pennsylvania, examining natural gas concentrations and isotopic signatures with proximity to shale gas wells. Methane was detected in 82% of drinking water samples, with average concentrations six times higher for homes <1 km from natural gas wells (P = 0.0006). Ethane was 23 times higher in homes <1 km from gas wells (P =0.0013); propane was detected in 10 water wells, all within approximately 1 km distance (P = 0.01). Of three factors previously proposed to influence gas concentrations in shallow groundwater (distances to gas wells, valley bottoms, and the Appalachian Structural Front, a proxy for tectonic deformation), distance to gas wells was highly significant for methane concentrations (P = 0.007; multiple regression), whereas distances to valley bottoms and the Appalachian Structural Front were not significant (P = 0.27 and P = 0.11, respectively). Distance to gas wells was also the mostsignificant factor for Pearson and Spearman correlation analyses (P < 0.01). For ethane concentrations, distance to gas wells was the only statistically significant factor (P < 0.005). Isotopic signatures (δ13C-CH4, δ13C-C2H6, and δ2H-CH4), hydrocarbon ratios (methane to ethane and propane), and the ratio of the noble gas 4He to CH4in groundwater were characteristic of a thermally postmature Marcellus-like source in some cases. Overall, our data suggest that some homeowners living <1 km from gas wells have drinking water contaminated with stray gases.

Seaweb via Coral-list: Marine Science Review Contaminants and Pollution – Ocean Acidification

Ahh, the power of the internet and open sources. For anyone studying ocean acidification, this is a nirvana of resources. DV

From: SeaWeb
Date: Wed, Jun 12, 2013 at 9:01 AM

June 11, 2013

OA indicates an open access article or journal.

– *Ocean acidification limits temperature-induced poleward expansion of coral habitats around Japan.
**Biogeosciences* 9(12): 4955-4968, 2012. *OA*

– *Observed acidification trends in North Atlantic water masses. **
Biogeosciences* 9(12): 5217-5230, 2012. *OA*

– *Spatiotemporal variability and long-term trends of ocean acidification in the California Current System.
**Biogeosciences*10(1): 193-216, 2013.*OA*

– *High tolerance of microzooplankton to ocean acidification in an Arctic coastal plankton community.
**Biogeosciences* 10(3): 1471-1481, 2013. *OA*

– *Short- and long-term consequences of larval stage exposure to constantly and ephemerally elevated carbon dioxide for
marine bivalve populations. **Biogeosciences* 10(4): 2241-2253, 2013. *OA*

– *Influence of ocean warming and acidification on trace metal biogeochemistry.
**Marine Ecology Progress Series* 470: 191-205, 2012. *OA*

– *Responses of marine primary producers to interactions between ocean acidification, solar radiation, and warming.
**Marine Ecology Progress Series* 470: 167-189, 2012. *OA*

– *Marine life on acid. **BioScience* 63(5): 322-328, 2013.

– *Red coral extinction risk enhanced by ocean acidification. **Scientific Reports* 3: art. 1457, 2013. *OA*

– *Dolomite-rich coralline algae in reefs resist dissolution in acidified conditions.
**Nature Climate Change* 3(3): 268-272, 2013.

– *Variation in plastic responses of a globally distributed picoplankton species to ocean acidification.
**Nature Climate Change* 3(3): 298-302, 2013.

– *Effects of ocean acidification on the embryos and larvae of red king crab, Paralithodes camtschaticus.
**Marine Pollution Bulletin* 69(1-2): 38-47, 2013.

– *Temperature and CO2 additively regulate physiology, morphology and genomic responses of larval sea urchins,
Strongylocentrotus purpuratus. **Proceedings of the Royal Society of London [B]* 280(1759): art. 20130155, 2013.

– *Addressing ocean acidification as part of sustainable ocean development. **Ocean Yearbook* 27: 29-46, 2013.

– *The marine inorganic carbon system along the Gulf of Mexico and Atlantic coasts of the United States: Insights from a
transregional coastal carbon study. **Limnology and Oceanography* 58(1): 325-342, 2013. *OA*

– *The responses of eight coral reef calcifiers to increasing partial pressure of CO2 do not exhibit a tipping point.
**Limnology and Oceanography* 58(1): 388-398, 2013. *OA*

– *Concentration boundary layers around complex assemblages of macroalgae: Implications for the effects of ocean
acidification on understory coralline algae. **Limnology and Oceanography* 58(1):121-130, 2013.

– *Interactive effects of elevated temperature and CO2 levels on metabolism and oxidative stress in two common marine
bivalves (Crassostrea virginica and Mercenaria mercenaria).
**Comparative Biochemistry and Physiology Part A: Molecular and Integrative Physiology* 164(4):545-553, 2013.

– *CO2-driven seawater acidification differentially affects development and molecular plasticity along life history of fish
(Oryzias latipes). *
*Comparative Biochemistry and Physiology Part A: Molecular and Integrative Physiology* 165(2): 119-130, 2013.

– *Preparing to manage coral reefs for ocean acidification: lessons from coral bleaching.
**Frontiers in Ecology and the Environment* 11(1): 20-27, 2013.

– *Marine fungi may benefit from ocean acidification. **Aquatic Microbial Ecology* 69(1): 59-67, 2013.

– *Effects of ocean acidification on early life-history stages of the intertidal porcelain crab Petrolisthes cinctipes.
**Journal of Experimental Biology* 216(8): 1405-1411, 2013.

– *Impact of ocean acidification on metabolism and energetics during early life stages of the intertidal porcelain crab
Petrolisthes cinctipes. **Journal of Experimental Biology* 216(8): 1412-1422, 2013.

– *Response to ocean acidification in larvae of a large tropical marine fish, Rachycentron canadum. **Global Change Biology*
19(4): 996-1006, 2013.

– *Interacting effects of ocean acidification and warming on growth and DMS-production in the haptophyte coccolithophore
Emiliania huxleyi.
**Global Change Biology* 19(4): 1007-1016, 2013.

– *Food availability outweighs ocean acidification effects in juvenile Mytilus edulis: laboratory and field experiments.
**Global Change Biology*19(4): 1017-1027, 2013.

– *Anthropogenic changes to seawater buffer capacity combined with natural reef metabolism induce extreme future coral reef
CO2 conditions. **Global Change Biology *19(5): 1632-1641, 2013.

– *Impacts of ocean acidification on marine organisms: quantifying sensitivities and interaction with warming.
**Global Change Biology*19(6): 1884-1896, 2013.*OA*

– *Detrimental effects of ocean acidification on the economically important Mediterranean red coral (Corallium rubrum).
**Global Change Biology* 19(6): 1897-1908, 2013.

– *Ocean acidification and warming scenarios increase micro-bioerosion of coral skeletons.
**Global Change Biology* 19(6):1919-1929, 2013.

– *Vulnerability of the calcifying larval stage of the Antarctic sea urchin Sterechinus neumayeri to near-future ocean
acidification and warming. **Global Change Biology *19(7): 2264-2275, 2013.

– *Does elevated pCO2 affect reef octocorals? **Ecology and Evolution*3(3): 465-473, 2013. *OA*

– *One-year experiment on the physiological response of the Mediterranean crustose coralline alga, Lithophyllum cabiochae, to
elevated pCO2 and temperature. **Ecology and Evolution* 3(3): 676-693, 2013. *OA*

– *Meta-analysis reveals complex marine biological responses to the interactive effects of ocean acidification and warming.
**Ecology and Evolution* 3(4): 1016-1030, 2013. *OA*

– *Near-future ocean acidification causes differences in microbial associations within diverse coral reef taxa.
**Environmental Microbiology Reports* 5(2): 243-251, 2013.

– *Consequences of increased temperature and acidification on bacterioplankton community composition during a mesocosm spring
bloom in the Baltic Sea. **Environmental Microbiology Reports* 5(2): 252-262, 2013.

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research at so that we can highlight your work. Why rare species found in coral reefs, tropical forests and alpine meadows could determine how our planet survives global disasters

Researchers from the University of Montpellier in France analysed the role rare species play within coral reefs, tropical forests and alpine meadows

The findings suggest that rare species play a more important part in maintaining ecosystems than was first thought and this ‘calls into question many current strategies’

By Victoria Woollaston

PUBLISHED: 16:03 EST, 28 May 2013 | UPDATED: 16:03 EST, 28 May 2013

Rare species perform unique roles in the way the world functions, claims new research, contradicting what was previously thought.

A study from a team of researchers at the University of Montpellier in France has discovered that rare species perform tasks that more common species can’t.

Using data from three different ecosystems – coral reefs, tropical forests and alpine meadows – the researchers found that these unique functions are essential for maintaining balance within current ecosystems.
Researchers from the University of Montpellier in France have discovered that rare species, such as the giant moray eel, play a much more vital role in the balance of their ecosystems than was first thought.

Rare species, such as the giant moray eel found in coral reefs in the Red Sea, play a much more vital role in the balance of their ecosystems than was first thought

Coral reefs are underwater structures made from calcium carbonate released by corals.

Reefs grow best in warm, shallow, clear, sunny and agitated waters.

Often called ‘rainforests of the sea’, coral reefs form some of the most diverse ecosystems on Earth.

They take up less than 0.1% of the world’s ocean surface, yet are home to 25% of all marine species, including fish, mollusks, worms, crustaceans, echinoderms and sponges.

The annual global economic value of coral reefs was estimated at US$ 375 billion in 2002.

However, coral reefs are fragile ecosystems because they are very sensitive to water temperature.

And if these rare species disappear, our ecosystems could fail – or struggle to rebuild in the event of a global disaster.

Lead researcher Dr David Mouillot said: ‘These unique features are irreplaceable, as they could be important for the functioning of ecosystems if there is major environmental change.’
sea turtle

As rare species and the biodiversity of these regions decline, the unique traits and features these animals bring to the areas are vulnerable to extinction because rare species are likely to disappear first.

Biodiverse environments are known by their large number of rare species.

These rare species contribute to the diversity of an area but, up until now, their functional importance within these ecosystems has been largely unknown.

Because there are fewer rare species within a region, they were traditionally thought to have little bearing on how other species interact and how the ecosystem functions, compared with more common species.
If rare species seen in places such as coral reefs and rainforests die out, the carefully balanced ecosystems of those regions could fail and be damaged.

If rare species seen in places such as coral reefs and rainforests die out, the carefully balanced ecosystems of those regions could fail or be damaged. This is because rare species perform unique functions within these areas, say the researchers
The rare pyramidal saxifrage, an alpine plant, is an important resource for pollinators in the mountain regions of Europe

The rare pyramidal saxifrage, an alpine plant, is an important resource for pollinators in the mountain regions of Europe

It was previously assumed that rare species play the same roles within an ecosystem as their common neighbours, yet have less impact because of their low numbers.

This phenomenon is known as ‘functional redundancy’.

The redundancy suggests that rare species merely serve as an ‘insurance’ policy for the ecosystem, in the event of an ecological loss.

To test this, the researchers analysed the extent to which rarer species in the three different ecosystems performed the same ecological functions as the most common ones.

They examined biological and bio-geographical information from 846 reef fish, 2,979 alpine plants and 662 tropical trees and found that most of the unique and vulnerable functions, carried out via a combination of traits, were associated with rare species.

Examples of rare species that were found by the researchers to perform vulnerable functions include the giant moray, a predatory fish that hunts at night in the labyrinths of coral reefs and the pyramidal saxifrage, an alpine plant that is an important resource for pollinators.

Another was the Pouteria maxima, a huge tree in the rainforest of Guyana, which is particularly resilient to fire and drought.

Not only are these species rare, they also have few functional equivalents among the more common species in their respective ecosystems, according to the research published in the journal PLOS Biology.
The Kaieteur National Park in Guyana.

The Kaieteur National Park in Guyana. The rainforest in Guyana is a biodiverse environment because of the large number of species that live in relatively close proximity. Researchers have found that rare species, including the Guyanan tree Pouteria maxima, are fundamental to maintaining balance in biodiverse ecosystems

Dr Mouillot said: ‘Our results suggest that the loss of these species could heavily impact upon the functioning of their ecosystems.

‘This calls into question many current conservation strategies.’

The work emphasises the importance of the conservation of rare species, even in diverse ecosystems.

Dr Mouillot said rare species are more vulnerable and serve irreplaceable functions, the preservation of biodiversity as a whole – not just the most common species, but all those who perform vulnerable functions – appears to be crucial for the resilience of ecosystems.

He added: ‘Rare species are not just an ecological insurance – they perform additional ecological functions that could be important during rapid transitions experienced by ecosystems.

‘The vulnerability of these functions, in particular biodiversity loss caused by climate change, highlights the underestimated role of rare species in the functioning and resilience of ecosystems.

‘Our results call for new experiments to explicitly test the influence of species rarity and the uniqueness of combinations of traits on ecological processes.’

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Coral-list: Scott Woolridge: A new explanation for the how? and why? of coral calcification

Scott Wooldridge via

6:40 AM (3 hours ago) Thursday, May 2, 2013

to coral-list
For both the geologist and biologist alike, the extending dimension of coral skeletal growth (i.e. skeletal extension) is often considered a good indicator of the efficient functioning of the coral-algae symbiosis. In a new manuscript in Biogeosciences I outline why this conceptualisation can be misleading. This new explanation provides insight into: (i) why fast growth at optimal temperatures is often a reliable indicator of ‘bleaching sensitivity’ under thermal stress, (ii) why the gross skeletal morphology of a coral changes with variable environmental conditions (nutrients, pco2, light, SST, flow), and (iii) why this challenges the development of reliable paleo-climate proxies based on coral skeletons.
Wooldridge, S (2013) A new conceptual model of coral biomineralisation: hypoxia as the physiological driver of skeletal extension, Biogeosciences, 10, 2867-2884.

The manuscript builds upon ideas and concepts developed in another recently published Biogeosciences manuscript which explains why enlarged and fast-growing endosymbiont populations – as permitted by the modern envelope of seawater conditions (characterised by elevated temperatures, rising pCO2, and enriched nutrient levels) – are conspiring to lower the thermal ‘breakpoint’ of the coral-algae symbiosis.
Wooldridge, S (2013) Breakdown of the coral-algae symbiosis: towards formalising a linkage between warm-water bleaching thresholds and the growth rate of the intracellular zooxanthellae, Biogeosciences, 10, 1647-1658.

In their separate ways, the two papers support the case that the optimal (stable) pCO2-SST-light-nutrient envelope for the coral-algae symbiosis was transgressed for most global reef sites long before the first ‘visual’ recordings of mass bleaching in the early 1980’s. For those interested, I have previously outlined in another Biogeosciences manuscript the available evidence to suggest that the interglacial pCO2 threshold (<260ppm) is a key stability threshold for the coral-algae symbiosis. Wooldridge, S (2012) A hypothesis linking sub-optimal seawater pCO2 conditions for cnidarians-Symbiodinium symbioses with the exceedence of the interglacial threshold (>260ppmv), Biogeosciences, 9, 1709-1723.

Scott Wooldridge
Research Scientist
Climate Change and Ocean Acidification Team
Australian Institute of Marine Science

Common Dreams: Health groups call for urgent action to address health risks from coal and coal seam gas

Please find attached and below an overview of the outcomes of the Health and Energy Policy Roundtable and Workshop in Canberra last week. You will see there has been a decision to form a new collaborative network of health groups to work together to raise awareness of the health implication of current energy and minerals policy in Australia. This includes the development of a joint Position Statement on Health and Energy and a campaign featuring health professional clean safe renewable energy and highlighting the risks to health from coal and coal seam gas.

Signatories to this work so far include over 70 health groups, with two umbrella groups represented (Climate and Health Alliance and National Rural Health Alliance).

If you would like to also sign the statement and participate in this work, please contact Fiona Armstrong, CAHA Convenor or 0438900005.


Health groups call for urgent action to address health risks from coal and coal seam gas

A new collaborative network of health organisations has agreed to joint action to raise awareness of the adverse health effects of Australia’s current minerals and energy policy at a meeting in Canberra this week.

Hosted by five national health organisations, the Public Health Association of Australia (PHAA), Climate and Health Alliance (CAHA), National Rural Health Alliance (NRHA), Climate Change Health Research Network (NCCARF-ARN), Australian Healthcare and Hospitals Association (AHHA), the Health and Energy Roundtable was attended by energy experts, community activists and health professionals, including doctors, physicians, nurses, physiotherapists and GPs, from dozen of organisations around the country.

A statement from the groups at the meeting, including the lead groups and joined by Cancer Council Australia, Heart Foundation, Australian Research Alliance for Children and Youth (ARACY), National Toxics Network (NTN), Australian Physiotherapy Association (APA), and New South Wales Nurses and Midwives Association (NSWNMA), signalled an intention to work together collaboratively to highlight the adverse health impacts and environmental damages associated with current minerals energy policy, particularly those relating to coal and coal seam gas.

“The risks to human health from energy and resources policy are not being well accounted for in current policy decisions,” the joint statement said.

“Significant policy reform is needed to ensure health and wellbeing is not compromised by policy decisions in other sectors. Recognising the importance of the social and environmental determinants of health is an important part of that.

“The overriding concern is that climate change is being driven by energy choices and minerals policies that privilege and prioritise the extraction and combustion of fossil fuels over safer, healthier, lower emissions, renewable energy resources.

“The local health impacts from coal mining, transportation and combustion are also a significant concern, and communities living in proximity to these activities are experiencing adverse social impacts, such as loss of amenity, displacement, and loss of social capital as well as facing increased risks of respiratory disease, heart disease, and lung cancer.

“The rapid expansion of the fossil fuel (coal and unconventional gas) industries in Australia demands these issues be urgently addressed.

There were also serious concerns raised about the availability of data and support for health research on the issue.

“A lack of monitoring and inadequate investment in research means there is grossly insufficient data available in Australia on health impacts to inform policy decisions. Research from international sources suggests major cause for concern in terms of exposure to pollution of water and air – these impacts need to be evaluated here in Australia.

“The health impacts of minerals and energy policy must be an area of research priority that is given significant levels of independent funding, and there needs to be greatly increased surveillance and monitoring to ensure sufficient data collection on which to base this research.”

The meeting identified a need for education for health professionals and the community more broadly around the health implications of energy policy choices, and encouraged health professionals across all disciplines to advocate for minerals, energy and climate policies on the basis of health.

“Health professionals have an important role to play in educating decision makers and the community about the health implications of energy choices and the health implications of climate change.”

The joint statement calls for precautionary approaches to policy and for the intergenerational consequences of decisions made now to be considered.

“The local and global effect of fossil fuel use on health and wellbeing is an immediate problem as well as an issue of intergenerational equity, with the exploitation of these resources causing irreversible harm to Earth’s systems, compromising the health and security of future generations.”

The groups have committed to work together and develop a framework for joint advocacy and announced plans for a campaign featuring health professionals calling for an urgent transition to safe, clean, renewable energy supply systems that do not contribute to global warming or harm human health and wellbeing.

The groups also announced an intention to develop a joint position statement on the health effects of Australia’s minerals and energy policies to inform public discussion about balancing the benefits and harms of our mineral and energy choices, specifically issues such as unconventional gas, coal exports and renewable energy.

For further information, contact Fiona Armstrong, CAHA Convenor or 0438900005.

Convenor, Climate and Health Alliance
M: 0438 900 005
T: @healthy_climate

CNews-Canada: Damning new study links toxin increase directly to oil sands

By Jessica Hume, Parliamentary Bureau

The Athabasca river runs through the city of Fort McMurray, Alta., in this file photo. REUTERS/Todd Korol

OTTAWA – A new study suggests aquatic toxins close to the Athabasca River have increased dramatically and simultaneously with oilsands development there, contradicting earlier government assertions the contamination was naturally occurring.
Calling the data a “smoking gun”, lead scientist and Queens University professor John Smol explained that, unlike previous studies that relied on insufficient historical data and so produced mere “snapshots” of contaminants in a given area at a given time, the new research used core samples of lake sediment from before oilsands development in the area began.

“The sediment is like a history book, and what it shows clearly is that the rise in PAH (polycyclic aromatic hydrocarbons) started in the ’60s in lockstep with oilsands development,” Smol said. “But it also shows undeniably that the contamination is not natural and that it’s showing up as far as 90 km away.”

Special thanks to Richard Charter

Science Magazine: Coral Reefs Could Be Decimated by 2100

by Eli Kintisch on 20 December 2012, 1:15 PM | 1 Comment

Barrier falling. Oceanographers have blamed bleaching of Porites coral from Australia’s Great Barrier Reef on warming water temperatures, ocean acidification, and pollution.
Credit: Louis Wray/Creative Commons

Nearly every coral reef could be dying by 2100 if current carbon dioxide emission trends continue, according to a new review of major climate models from around the world. The only way to maintain the current chemical environment in which reefs now live, the study suggests, would be to deeply cut emissions as soon as possible. It may even become necessary to actively remove carbon dioxide from the atmosphere, say with massive tree-planting efforts or machines.

The world’s open-ocean reefs are already under attack by the combined stresses of acidifying and warming water, overfishing, and coastal pollution. Carbon emissions have already lowered the pH of the ocean a full 0.1 unit, which has harmed reefs and hindered bivalves’ ability to grow. The historical record of previous mass extinctions suggests that acidified seas were accompanied by widespread die-offs but not total extinction.

To study how the world’s slowly souring seas would affect reefs in the future, scientists with the Carnegie Institution for Science in Palo Alto, California, analyzed the results of computer simulations performed by 13 teams around the world. The models include simulations of how ocean chemistry would interact with an atmosphere with higher carbon dioxide levels in the future. This so-called “active biogeochemistry” is a new feature that is mostly absent in the previous generation of global climate models.

Using the models’ predictions for future physical traits such as pH and temperature in different sections of the ocean, the scientists were able to calculate a key chemical measurement that affects coral. Corals make their shells out of the dissolved carbonate mineral known as aragonite. But as carbon dioxide pollution steadily acidifies the ocean, chemical reactions change the extent to which the carbonate is available in the water for coral. That availability is known as its saturation, and is generally thought to be a number between 3 and 3.5.

No precise rule of thumb exists to link that figure and the health of reefs. But the Carnegie scientists say paleoclimate data suggests that the saturation level during preindustrial times—before carbon pollution began to accumulate in the sky and seas—was greater than 3.5.

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The models that the Carnegie scientists analyzed were prepared for the major global climate report coming out next year: the Intergovernmental Panel on Climate Change report. The team compared the results of those simulations to the location of 6000 reefs for which there is data, two-thirds of the world total. That allowed them to do what amounted to a chemical analysis of future reef habitats.

In a talk reviewing the study at the fall meeting of the American Geophysical Union earlier this month, senior author and Carnegie geochemist Ken Caldeira showed how the amount of carbon emitted in the coming decades could have huge impacts on reefs’ fates. In a low-emissions trajectory in which carbon pollution rates were slashed and carbon actively removed from the air by trees or machines, between 77% and 87% of reefs that they analyzed stay in the safe zone with the aragonite saturation above 3.

“If we are on the [business as usual] emissions trajectory, then the reefs are toast,” Caldeira says. In that case, all the reefs in the study were surrounded by water with Aragonite saturation below 3, dooming them. In that scenario, Caldeira says, “details about sensitivity of corals are just arguments about when they will die.”

“In the absence of deep reductions in CO2 emissions, we will go outside the bounds of the chemistry that surrounded all open ocean coral reefs before the industrial revolution,” says Carnegie climate modeler Katharine Ricke, the first author on the new study.

Greg Rau, a geochemist at Lawrence Livermore National Laboratory in California, says the work sheds new light onto the future of aragonite saturation levels in the ocean, also known as “omega.” “There is a very wide coral response to omega—some are able to internally control the [relevant] chemistry,” says Rau, who has collaborated with Caldeira in the past but did not participate in this research. Those tougher coral species could replace more vulnerable ones “rather than a wholesale loss” of coral. “[But] an important point made by [Caldeira] is that corals have had many millions of years of opportunity to extend their range into low omega waters. With rare exception they have failed. What are the chances that they will adapt to lowering omega in the next 100 years?”

Special thanks to Doug Fenner and the NOAA Coral-list.

Conservation Letters: Long-term trends of coral imports into the United States indicate future opportunities for ecosystem and societal benefits by Andrew L. Rhyne, Michael F. Tlusty, Les Kaufman

Article first published online: 26 JUL 2012

DOI: 10.1111/j.1755-263X.2012.00265.x

Volume 5, Issue 6, pages 478–485, December 2012


Aquarium trade;
coral trade;
curio trade;
coral triangle;
marine policy
Author Information

1 New England Aquarium, John H. Prescott Marine Laboratory, Boston, MA, USA
2 Roger Williams University, Department of Biology and Marine Biology, Bristol, RI, USA
3 Boston University Marine Program, Department of Biology, Boston University, Boston, MA, USA
4 Conservation International, Arlington, VA, USA

*Andrew L Rhyne, Department of Biology and Marine Biology, Roger Williams University, One Old Ferry Road, Bristol, RI 02809, USA. Tel: 401 254-5750; Fax: 401 254-3310. E-mail:

Editor  Dirk Roux

Publication History

Issue published online: 11 DEC 2012
Article first published online: 26 JUL 2012
Accepted manuscript online: 2 JUL 2012 03:52PM EST
Received 5 March 2012, Accepted 12 June 2012


The international trade in corals used to be primarily a curio trade of dried skeletons, but now focuses on live corals for the marine reef aquarium trade. The trade is still rapidly evolving, creating challenges including the addition of new species that outpace effective management strategies. New species in the live coral trade initially command high prices, but as they become common the price radically decreases with feedback effects to the trade. To understand these trends, 21 years of live coral import data for the United States were assessed. Trade increased over 8% per year between 1990 until the mid-2000s, and has since decreased by 9% annually. The timing of the peak and decline varies among species, and is a result of the rising popularity of mini-reef ecosystem aquariums, the global financial crisis, and an increase in aquaculture production. The live coral trade offers opportunities for coral reef ecosystem conservation and sustainable economic benefits to coastal communities, but realization of these externalities will require effective data tracking.

Special thanks to Coral-list

Summit County Voice: Environment: Traces of Deepwater Horizon oil cause deformities, swimming deficiencies in Gulf fish

Posted on December 10, 2012 by Bob Berwyn

An explosion and subsequent fire on BP’s Deepwater Horizon drilling platform in the Gulf of Mexico led to the biggest oil spill on recornd in U.S. coastal waters. Photo courtesy U.S. Coast Guard.

Study shows that sunlight intensifies the impacts of PAHs
By Summit Voice

FRISCO – In yet another sign that BP’s spilled Deepwater Horizon may have long-lasting impacts on Gulf ecosystems, a team of researchers said last week that even low-level, short-term exposure to traces of oil remnants causes deformities and impairs the swimming ability of fish.

The research was led by scientists with the University of Miami Rosenstiel School of Marine & Atmospheric Science. The school is a leader in the field of marine toxicology and used a state of the art hatchery to study the effect of polycyclic aromatic hydrocarbons (PAHs) on various species of fish, including cobia and mahi mahi.

PAH’s are toxic components of oil that are released from oil into the water column. The team also studied the effects of photo-enhanced toxicity, or the impact of sunlight on the potency of the toxic compounds found in the oil from the DWH spill.

A previous study by Smith University scientists showed similar impacts to fish during embryonic stages of development.

“We found that in more sensitive species the photo-enhanced toxicity could account for up to a 20-fold higher sensitivity,” said Dr. Martin Grosell, professor and associate dean of graduate studies for the Rosenstiel School. “This is an important part of the equation because it means that traditional toxicity testing performed under laboratory conditions will tend to underestimate the toxicity that might have occurred in the natural environment under the influence of sunlight,” he added.

The team collected freshly fertilized eggs from mahi mahi made available via UM’s Aquaculture Program, and exposed the embryos to low levels of different types of water mixed with DWH oil. In species like mahi mahi just 2 to 6 micrograms of total PAHs per liter of seawater were observed to reduce hatch rates and survival, and to result in impaired cardiac development.

The lab also tested newly hatched fish, observing them for deformities resulting from exposure to oiled seawater. Many hatchlings showed subtle heart abnormalities after only trace oil exposures in the egg that lasted only a day or so. After a month of raising these fish in clean water, the team put the resulting juveniles through the paces on their “fish treadmill” and they could only swim about 70 percent as fast as those that had never been exposed to oil.

“The severely reduced swimming performance we saw could impact the ability of these fish to catch sufficient prey, avoid predation, or travel the long distances that some migratory species require for survival,” Grosell said.

Other researchers included Andrew Esbaugh, Ed Mager, Charlotte Bodinier, as well as UM Professor and Aquaculture Program Director Dr. Daniel Benetti, Hatchery Manager Ron Hoenig and Graduate Student John Stieglitz, along with collaborators from NOAA’s Northwest Fisheries Science Center and the University of North Texas.

Special thanks to Richard Charter

Coral-list: Coral Thermal Tolerance: Tuning Gene Expression to Resist Thermal Stress by Bellatuono, Granados-Cifuentes, Miller, Hoegh-Guldberg and Rodriguez-Lanetty

A new publication from our group has been recently published online, which
you might find of interest.

*”Coral Thermal Tolerance: Tuning Gene Expression to Resist Thermal Stress”*

Anthony J. Bellantuono, Camila Granados-Cifuentes, David J. Miller, Ove
Hoegh-Guldberg, Mauricio Rodriguez-Lanetty*

PLoS ONE: Research Article, published 30 Nov 2012.

Abstract Top

The acclimatization capacity of corals is a critical consideration in the persistence of coral reefs under stresses imposed by global climate change. The stress history of corals plays a role in subsequent response to heat stress, but the transcriptomic changes associated with these plastic changes have not been previously explored. In order to identify host transcriptomic changes associated with acquired thermal tolerance in the scleractinian coral Acropora millepora, corals preconditioned to a sub-lethal temperature of 3°C below bleaching threshold temperature were compared to both non-preconditioned corals and untreated controls using a cDNA microarray platform. After eight days of hyperthermal challenge, conditions under which non-preconditioned corals bleached and preconditioned corals (thermal-tolerant) maintained Symbiodinium density, a clear differentiation in the transcriptional profiles was revealed among the condition examined. Among these changes, nine differentially expressed genes separated preconditioned corals from non-preconditioned corals, with 42 genes differentially expressed between control and preconditioned treatments, and 70 genes between non-preconditioned corals and controls. Differentially expressed genes included components of an apoptotic signaling cascade, which suggest the inhibition of apoptosis in preconditioned corals. Additionally, lectins and genes involved in response to oxidative stress were also detected. One dominant pattern was the apparent tuning of gene expression observed between preconditioned and non-preconditioned treatments; that is, differences in expression magnitude were more apparent than differences in the identity of genes differentially expressed. Our work revealed a transcriptomic signature underlying the tolerance associated with coral thermal history, and suggests that understanding the molecular mechanisms behind physiological acclimatization would be critical for the modeling of reefs in impending climate change scenarios.

Best regards,


Dr. Mauricio Rodriguez-Lanetty
Assistant Professor
Department of Biological Sciences
Florida International University
11200 SW 8th st.
Miami, FL 33199
Ph: 305-3484922
Coral-List mailing list

MSNBC: Dispersant makes oil from spills 52 times more toxic & Environmental Pollution: Synergistic toxicity of Macondo crude oil and dispersant Corexit 9500A® to the Brachionus plicatilis species complex (Rotifera)

As in 2010 Gulf of Mexico disaster, it makes petroleum less visible, but much more harmful

This is important: I don’t think Corexit should EVER be used again in U.S. ocean waters. DV

By Douglas Main
updated 11/30/2012 6:46:08 PM ET

For microscopic animals living in the Gulf of Mexico, even worse than the toxic oil released during the 2010 Deepwater Horizon disaster may be the very oil dispersants used to clean it up, a new study finds.

More than 2 million gallons (7.5 million liters) of oil dispersants called Corexit 9527A and 9500A were dumped into the gulf in an effort to prevent oil from reaching shore and to help it degrade more quickly.

However, when oil and Corexit are combined, the mixture becomes up to 52 times more toxic than oil alone, according to a study published online this week in the journal Environmental Pollution.

“There is a synergistic interaction between crude oil and the dispersant that makes it more toxic,” said Terry Snell, a study co-author and biologist at Georgia Tech. Using dispersants breaks up the oil into small droplets and makes it less visible, but, “on the other hand, makes it more toxic to the planktonic food chain,” Snell told LiveScience.

Toxic mixture
That mixture of dispersant and oil in the gulf would’ve wreaked havoc on rotifers, which form the base of the marine food web, and their eggs in seafloor sediments, Snell said.

In the study, Snell and colleagues tested ratios of oil and dispersant found in the gulf in 2010, using actual oil from the well that leaked in the Deepwater Horizon oil spill and the dispersant. The mixture was similarly toxic at the various ratios tested, the study found. His group exposed several varieties of rotifers to concentrations of the oil-dispersant mixture likely seen over a large area of the gulf.

“The levels in the gulf were toxic, and seriously toxic,” Snell said. “That probably put a big dent in the planktonic food web for some extended period of time, but nobody really made the measurements to figure out the impact.” [ Deepwater Horizon: Images of the Impact ]

The dispersant makes the oil more deadly by decreasing the size of the droplets, making it more “bio-available” to small organisms, said Ian MacDonald, a researcher at Florida State University. “The effect is specifically a toxic synergy – the sum is worse than the parts,” said MacDonald, who was not involved in the research.

A cautionary tale
This is one of the first studies to look at the impact of the oil-dispersant mixture on plankton. A decline in populations of plankton could impact larger animals all the way up to whales, he said. In general, plankton can rebound quickly, although the toxicity to larvae in sediments is concerning, since it reduces the size of the next generation. This ocean-bottom oil slurry could also have impacted other species that spend part of their life cycles here like algae and crustaceans.

“This is an important study that adds badly needed data to help us better understand the effects of oil spills and oil spill remediation strategies, such as the use of dispersants,” said Stephen Klaine, an environmental toxicologist at Clemson University who wasn’t involved in the research. “Species’ differences in the sensitivity to any toxic compounds, including the ones in this discussion, can be huge.”

The results contrast with those released by the Environmental Protection Agency in August 2010. That study found that a mixture of oil and Corexit isn’t more toxic than oil alone to both a species of shrimp and species of fish. However, several studies have found the mixture is more toxic than oil to the embryos of several fish species. The EPA could not immediately be reached for comment.

“To date, EPA has done nothing but congratulate itself on how Corexit was used and avow they would do it the same way again,” MacDonald said.

However, Snell said the dispersant should not be used. It would be better to let the oil disperse on its own to minimize ecological damage, he said.

“This is a cautionary tale that we need to do the science before the emergency happens so we can make decisions that are fully informed,” Snell said. “In this case, the Corexit is simply there to make the oil disperse and go out of sight. But out of sight doesn’t mean it’s safe in regard to the food web.”

“It’s hard to sit by and not do something,” Snell said. “But in this case, doing something actually made it more toxic.”

Reach Douglas Main at


This photograph shows windrows of emulsified oil (bright orange) sprayed with dispersant. The photo was taken on April 26, 2010 as part of an aerial observation overflight.


Environmental Pollution

Volume 173, February 2013, Pages 5-10

Synergistic toxicity of Macondo crude oil and dispersant Corexit 9500A® to the Brachionus plicatilis species complex (Rotifera)
Roberto Rico-Martíneza, , , Terry W. Snellb, Tonya L. Shearerb
a Universidad Autónoma de Aguascalientes, Centro de Ciencias Básicas, Departamento de Química, Avenida Universidad 940, Aguascalientes, Ags., C.P. 20131, Mexico
b Georgia Institute of Technology, School of Biology, Atlanta, Georgia 30332-0230, USA, How to Cite or Link Using DOI
Permissions & Reprints
Special thanks to Richard Charter

Caribbean Coral Reef Ecosystems Program — Smithsonian Marine Station Belize 2012 Annual Report

The Caribbean Coral Reef Ecosystems (CCRE) Program is a long term field study dedicated to investigations of coral reefs and associated mangroves, seagrass meadows, and sandy bottoms. Field operations are based at the Carrie Bow Cay Field Station on the Meso-American Barrier Reef in Belize, while logistical and administrative operations are based at the Smithsonian Marine Station at Fort Pierce, Florida. Follow the link for the 2012 Annual Report.

SI NMNH Caribbean Coral Reef Ecosystems Home

Nature Climate Change | Letter : Nutrient enrichment can increase the susceptibility of reef corals to bleaching

Similar to findings of Dr. James Cervino about ten years ago, yet we are still debating the human impacts that trigger climate change instead of implementing policies to address them. DV

Jörg Wiedenmann,
Cecilia D’Angelo,
Edward G. Smith,
Alan N. Hunt,
François-Eric Legiret,
Anthony D. Postle
& Eric P. Achterberg

Nature Climate Change (2012)

Received 20 April 2012
Accepted 11 July 2012
Published online 19 August 2012

Mass coral bleaching, resulting from the breakdown of coral–algal symbiosis has been identified as the most severe threat to coral reef survival on a global scale1. Regionally, nutrient enrichment of reef waters is often associated with a significant loss of coral cover and diversity2. Recently, increased dissolved inorganic nitrogen concentrations have been linked to a reduction of the temperature threshold of coral bleaching3, a phenomenon for which no mechanistic explanation is available. Here we show that increased levels of dissolved inorganic nitrogen in combination with limited phosphate concentrations result in an increased susceptibility of corals to temperature- and light-induced bleaching. Mass spectrometric analyses of the algal lipidome revealed a marked accumulation of sulpholipids under these conditions. Together with increased phosphatase activities, this change indicates that the imbalanced supply of dissolved inorganic nitrogen results in phosphate starvation of the symbiotic algae. Based on these findings we introduce a conceptual model that links unfavourable ratios of dissolved inorganic nutrients in the water column with established mechanisms of coral bleaching. Notably, this model improves the understanding of the detrimental effects of coastal nutrient enrichment on coral reefs, which is urgently required to support knowledge-based management strategies to mitigate the effects of climate change.


Shallow-water coral reefs owe their success to the symbiosis of the cnidarian host with dinoflagellates of the genus Symbiodinium (zooxanthellae)4. Recent reports predict that most coral reefs will be lost in the near future as a result of an average surface ocean temperature rise of 1–2 °C and an increased frequency of strong short-term temperature anomalies1. Thermal stress is considered to induce a malfunctioning of the photosynthetic apparatus of the algal symbiont and contribute to a breakdown of the symbiosis manifested by the loss of zooxanthellae and the often fatal bleaching of the corals5. In addition to other factors, anthropogenic eutrophication of coastal waters has been linked to coral reef degradation1. Recently, a connection between terrestrially sourced dissolved inorganic nitrogen (DIN) loading and the upper thermal bleaching thresholds of inshore reefs on the Great Barrier Reef was established3. However, the view that nutrient enrichment is responsible for coral reef decline has been challenged as corals can thrive in high-nutrient water and several experimental studies using increased nutrient levels did not find obvious negative impacts on the physiology of corals6, 7, 8. The lack of consensus can potentially lead to confusion over policy development, government inaction and continued environmental degradation2. Therefore, understanding of the nutrient-dependent processes needs to be urgently improved to promote coral reef resilience by knowledge-based management efforts.

Anthropogenic nutrification often results not only in an increase of dissolved inorganic nutrients such as ammonium, nitrate and phosphate but it also usually modifies the ratio of their concentrations9. In different phytoplankton species, growth becomes chemically unbalanced when the availability of a specific type of nutrient decreases relative to the cellular demand10. This condition is defined as nutrient starvation and results in detrimental effects such as reduced photosynthetic efficiency, measurable as a decrease in fluorescence-based maximum quantum yield of photosystem II photochemistry (Fv/Fm; ref. 10).

Among other factors, phosphate limitation plays a potentially important role in the control of zooxanthellae numbers in the host tissue11. However, several studies have reported an increase in algal cell densities in response to increased concentrations of DIN in the water2, 12, indicating a strong influence of the external nitrogen levels on the proliferation rates of zooxanthellae.

Despite the nutrient limitation that zooxanthellae experience in hospite, the steady-state population of algal cells remains functional because of their full acclimation to this condition. In fact, the limited access to nutrients allows the zooxanthellae to transfer a substantial amount of their photosynthetically fixed carbon to the host cells4 and is therefore of high importance for the functioning of the symbiosis. Recycling of nutrients derived from feeding of the host supports the maintenance of the standing crop of zooxanthellae, but is not sufficient to account for their growth under reef conditions where the supply with food tends to be low4, 13.

In analogy to the findings in phytoplankton10, we hypothesize that an increased concentration of DIN in the water can be expected to accelerate proliferation of zooxanthellae2, resulting in phosphate starvation when phosphate availability is low. This scenario might apply particularly to symbiotic algae in corals from coastal regions where the naturally low phosphate and DIN concentrations are altered by anthropogenic inputs14. Here, we tested whether increased DIN levels in combination with limiting phosphate concentrations increases the susceptibility of corals to temperature- and light-induced bleaching.

Using our multicompartment mesocosm15, we cultured seven species of scleractinian corals under a photonflux of ~90 μmol m−2 s−1 in artificial sea water with low nutrient (low DIN/low phosphate; LN/LP); nutrient-replete (high DIN/high phosphate; HN/HP) and imbalanced nutrient (high DIN/ambient phosphate; HN/AP) levels as detailed in the Methods. Over a period of 12 weeks, the low nutrient conditions resulted in pronounced paling of the corals caused by a strong decrease in the density of algal cells (Fig. 1a,b and Supplementary Fig. S1). However, Fv/Fm determined as a measure of the photosynthetic efficiency of zooxanthellae16 was high (>0.5) in nutrient-replete and low nutrient conditions (Fig. 1b and Supplementary Fig. S1). These findings are in close agreement with studies on phytoplankton that demonstrated that Fv/Fm is high and insensitive to nutrient limitation as long as the cells are fully acclimated to this condition10. Montipora foliosa cultured for >five weeks under imbalanced nutrient levels showed higher zooxanthellae densities compared with corals from the nutrient-limited conditions (Fig. 1a,b). In the red- and a purple–green-colour morphs of this species and four other species exposed to imbalanced nutrient levels, however, Fv/Fm dropped below values of zooxanthellae from low nutrient and nutrient-replete conditions, in most cases below the healthy values >0.5 (Fig. 1b,h and Supplementary Fig. S1), indicating a common response among corals from a broad taxonomic range. When corals incubated at imbalanced nutrient levels were exposed to light levels >180 μmol m−2 s−1 they showed strong signs of bleaching, particularly in the light-exposed parts of the colony (Fig. 1c–g). This resembled bleaching patterns often observed during natural bleaching events17. The bleached colonies died partially or completely (Fig. 1g), whereas specimens exposed to lower light levels survived (Fig. 1a and Supplementary Fig. S1). We incubated replicate samples of Euphyllia paradivisia under a photonflux of ~80 μmol m−2 s−1 in replete and imbalanced nutrient conditions to further investigate the role of light in nutrient-mediated bleaching. After four weeks, individuals from both treatments exhibited healthy Fv/Fm values (>0.5) and no visible signs of bleaching. At this point, the light intensity was doubled, reaching a level known to saturate photosynthesis in other shade-acclimated corals18. After 14 days, the samples experiencing imbalanced nutrient levels showed a steep drop in Fv/Fm, suggesting severe photo-inhibition of the zooxanthellae (Fig. 1h). In contrast, photosynthetic competence of algae in the control samples remained essentially unaltered. After three weeks, the corals from imbalanced nutrient conditions lost ~ 50% of their zooxanthellae and also the chlorophyll a content of the algal cells was reduced by >50% (Fig. 1i,j). Increased light levels can cause a reduction in Fv/Fm associated with photodamage of zooxanthellae, stimulate the production of reactive oxygen species and contribute to coral bleaching, particularly if the photosynthetic apparatus was impaired by other factors including temperature stress18, 19. In our experiments, corals in the different treatments were exposed to the same quantity and quality of light, hence the reduction in Fv/Fm and the loss of algal cells suggest that the imbalanced nutrient levels in the water rendered the zooxanthellae more sensitive to light stress.
Figure 1: Bleaching patterns of corals at different nutrient concentrations.
Bleaching patterns of corals at different nutrient concentrations.

a, Representative replicate colonies of M. foliosa cultured under photonfluxes of ~90 μmol m−2 s−1 and HN/HP, LN/LP or HN/AP conditions. b, Fv/Fm and zooxanthellae densities of colonies exposed to different nutrient concentrations. c–g, Bleaching of corals from HN/AP conditions under photonfluxes >180 μmol m−2 s−1. c–e, Pronounced bleaching of light-exposed areas in A. microphthalma (c) and M. foliosa (d). Arrows indicate the direction of the incident light the corals experienced during the treatment. e, Replicate colonies of E. paradivisia exposed to ~90 μmol m−2 s−1 (left colony) and ~180 μmol m−2 s−1 (right colony). f, Acropora valida. g, Bleaching of Porites lobata colonies resulted in complete or partial mortality. h–j, Effects of increased light intensity on E. paradivisia incubated under HN/HP or HN/AP conditions. h, Fv/Fm is strongly reduced in corals from HN/AP after the doubling of the light intensity. i,j, Bleaching of these samples is caused by loss of zooxanthellae and reduced chlorophyll a content per algal cell. The horizontal dashed line in b and h signifies the level above which Fv/Fm values are considered to be in a healthy range. Colour scales are provided in a and g to facilitate the comparison of coral colours. Asterisks indicate statistically significant differences (*p<0.05; **p<0.01) as detailed in the Supplementary Information. We evaluated whether this reduced photosynthetic efficiency could be caused by phosphate starvation of a proliferating symbiont population. First, we allowed M. foliosa colonies to adjust for six weeks in low-nutrient sea water to photonfluxes of ~30 μmol m−2 s−1. This acclimation was necessary to prevent a light-stress-driven loss of zooxanthellae after the transfer to sea water with imbalanced nutrient levels. Within 14 days after this transfer, the symbiont densities doubled, reporting an accordingly increased nutrient demand (Supplementary Fig. S2). Accordingly, zooxanthellae from corals kept under imbalanced nutrient conditions and a photonflux of ~90 μmol m−2 s−1 showed increased acidic and alkaline phosphatase activity indicating an increased demand for phosphorus20 (Fig. 2a). a, Increased activity of acidic and alkaline phosphatases in zooxanthellae from HN/AP treatments. b, Mass spectrometric analysis of the algal lipid content revealed a strong increase in SQDG in phosphate-starved zooxanthellae as determined by a precursor scan of the characteristic fragment of a mass of 225 under positive ionization (225+) c, Under phosphate starvation, the ratios of the zooxanthellae lipids, SQDG, PG and PC, are disturbed by the strong increase of SQDGs. Asterisks indicate statistically significant differences (*p<0.05; **p<0.01) as detailed in the Supplementary Information. Photosynthetic organisms respond to LP stress by substituting phospholipids such as phosphatidylglycerol (PG) with sulpholipids, in particular with sulphoquinovosyldiacylglycerol (SQDG), to maintain the functionality of photosynthetic membranes and the embedded photosystems21. We observed a marked increase of SQDGs by one order of magnitude in zooxanthellae of M. foliosa kept under imbalanced nutrient conditions (Fig. 2b,c). These findings demonstrate that the stress symptoms observed under increased light intensities resulted indeed from phosphate starvation of the algal cells in hospite. The changes in the algal lipid complement offer potential explanations for the detrimental effects of phosphate starvation. The increase in SQDGs results in a shift in lipid ratios that will presumably alter the normal ionic character of photosynthetic membranes required for maintaining the proper assembly and functioning of the photosynthetic apparatus21. Most interestingly, malfunctioning photosystems and increased oxidative stress associated with photoinhibition of zooxanthellae have been shown to promote coral bleaching5, 22. Moreover, Tchernov and colleagues found that the specific lipid composition of different zooxanthellae strains is correlated with their susceptibility to thermal bleaching23. Taken together, our results allow to link the effects of phosphate starvation conveniently with established downstream processes of coral bleaching5, 19. As temperature stress is the main cause of mass coral bleaching on the global scale, we tested the impact of increased temperatures and the influence of additional light stress on phosphate-starved corals. After incubation (>five weeks) at ambient temperatures under a photonflux of ~90 μmol m−2 s−1 and imbalanced nutrient levels, Acropora polystoma showed a reduction in photosynthetic efficiency (Fig. 3a). The Fv/Fm values, though, were still in the healthy range of >0.5. Photosynthetic efficiency diminished slightly with increasing temperature. A subsequent increment in light intensity resulted in a remarkable decrease in Fv/Fm, which dropped earlier below critical levels (<0.5) in phosphate-starved individuals compared with nutrient-replete controls (Fig. 3a). A similarly pronounced decrease of Fv/Fm was observed when higher light levels were followed by an increase in temperatures, suggesting that light and temperature act together to promote bleaching in phosphate-starved corals (Fig. 3c). These results are in agreement with reports that bleaching of the fire coral Millepora alcicornis from a high-light habitat occurred one week earlier compared with a low-light habitat during the period of heat stress in 1998 (ref. 24). Over the full duration of our experiments, Fv/Fm of phosphate-starved zooxanthellae was always lower compared with the controls and at the end their density reached only ~ 40% of the nutrient-replete counterparts (Fig. 3b,d), resulting in a bleached appearance of the corals from imbalanced nutrient levels (Supplementary Fig. S3). The changes in light and temperature conditions over time are indicated by the labels of the abscissas. a,c, Time courses of combined stress experiments indicate that phosphate starvation, temperature and light stress result in reduced Fv/Fm values in zooxanthellae of A. polystoma. The horizontal dashed line in a and c indicates the threshold above which Fv/Fm values are considered to be in a healthy range. b,d, The lower photosynthetic efficiency is associated with reduced zooxanthellae numbers determined at the end of the respective experiment. e, Survival rates of replicate colonies of A. microphthalma from HN/HP or HN/AP sea water exposed to light and temperature stress. Asterisks indicate statistically significant differences (*p<0.05; **p<0.01) as detailed in the Supplementary Information. In a combined light- and temperature-stress experiment we tested whether phosphate starvation also affects survival rates of corals. After a three-week treatment period, 100% mortality was observed among phosphate-starved Acropora microphthalma (Fig. 3e). In contrast, all control samples were visibly bleached, but survived the treatment. In phosphate-starved M. foliosa, the cover of the skeleton with living tissue was reduced by ~ 70% (Supplementary Fig. S4). Our findings indicate that phosphate starvation lowers the threshold of corals to suffer from light- and temperature-driven bleaching. We propose a new conceptual model of nutrient effects on coral bleaching (Fig. 4). This model assumes that a transition of zooxanthellae from a nutrient-limited to a nutrient-starved (here: phosphate) state leads to changes in the lipid composition of the algal membranes. Under thermal stress and in combination with light exposure, the altered photosynthetic membranes and embedded photosystems would show the previously described malfunctions of photosynthesis23, 25 that ultimately result in the breakdown of the coral–algal symbiosis and loss of zooxanthellae. Stress from low nutrient concentrations can arise owing to increased cellular demand during chemically unbalanced growth, but also may occur in waters in which specific nutrients become exhausted over time. Our findings suggest that the most severe impact on coral health might actually not arise from the over-enrichment with one group of nutrients (for example, DIN) but from the resulting relative depletion of other types (for example, phosphate) that is caused by the increased demand of proliferating zooxanthellae populations. This view is substantiated by the finding that the photosynthetic efficiency of zooxanthellae is reduced under a combination of limited iron availability and high temperatures26. Figure 4: Conceptual model of nutrient-starvation stress in zooxanthellae using the example of phosphate starvation. Conceptual model of nutrient-starvation stress in zooxanthellae using the example of phosphate starvation. a, Nutrient limitation in a steady-state population where the growth rate is determined by the rate of nutrient supply. Cells are fully acclimated and show no signs of stress. b, Phosphate starvation of zooxanthellae is induced by the transition from a nutrient-limited (a), to nutrient-starved state (b), owing to an increased cellular P demand caused by growth rates being accelerated through an increased DIN supply. The prioritized distribution of phosphate resources by the algae results in an altered composition of (thylakoid) membranes and a reduced threshold for light- and heat-induced bleaching. Our results have strong implications for coastal management. They suggest that reef resilience could benefit from considering local nutrient profiles and adjusting agricultural and tertiary wastewater-treatment practices in the proximity of coral reefs to reach favourable nutrient ratios in reef waters while working towards overall lower nutrient loadings. Finally, our findings support the view that local management of nutrient enrichment could reduce the effects of global climate change on coral reefs2, 3 and should help the design of functioning marine reserves. Methods The experiments were conducted in the coral mesocosm of the coral reef laboratory at the National Oceanography Centre Southampton. A detailed description of the experimental set-up is provided in ref. 15. This aquarium system has been running since 2007 and comprises three identical units. Each unit consists of two reservoir bins containing heating and filtration equipment and several experimental tanks. In the connected mode, a body of 2,250 l of artificial sea water circulates through the system. The artificial sea water was prepared by dissolving PRO-REEF salt mixture (Tropic Marin) in demineralized water. Five per cent of the water is changed on a weekly basis and an iron supplement is added daily. For the present experiment, phosphate levels were kept at low levels (<0.07 μM) by the application of Rowaphos phosphate-removal matrix (Rowa) and the addition of ethanol (2.5 ml per 1,000 l per day; ref. 15). Phosphate and nitrate levels were increased or maintained by continuous low-level dosing of sodium nitrate or disodium hydrogen phosphate solutions using peristaltic pumps. Corals were fed with frozen rotifers (Tropical Marine Centre) at a density of 0.5 g (frozen weight) per 135 l twice a week. If not stated otherwise, the temperature of the system was kept constant at 24 °C. Temperature-stress treatments were conducted in experimental tanks (40 l) equipped with precision heaters (Jaeger). These tanks were supplied with water from the connected unit with a flow rate of 80 l h−1. Current inside the experimental tanks (flow rate: 1,800 l h−1) was generated by Nanostream 6015 (Tunze). Corals were illuminated with metal halide lamps fitted with Aqualine 10000 burners (Aqua Medic) on a 10 hr/14 hr light/dark cycle. Changes in light intensity were achieved by altering the distance of the lamps to the samples. The corals used here were kept in our system for at least 2.5 years. For experimental purposes, the mother colonies were fragmented and the fragments were glued on tiles. They were allowed to regenerate and grow for at least two months before entering an experiment. Diagnostic restriction digests of the polymerase chain reaction-amplified small subunit ribosomal DNA gene of zooxanthellae of the corals under study revealed clade C as the dominant symbiont strain in the brown-, red- and purple–green-colour morphs of Montipora spp. (foliosa) and A. microphthalma27. Using the same approach, we found a prevalence of clade C also in E. paradivisia; Porites lobata and in the encrusting Montipora species. The zooxanthellae complement of A. polystoma consisted of a combination of clade C (~ 40%) with a yet unidentified strain (~ 60%). A detailed description of the methods is provided in the Supplementary Information. Briefly, nitrate, nitrite and phosphate at micromolar concentrations were determined using standard colourimetric techniques with a nutrient autoanalyser (Seal Analytical)28. Nanomolar levels of phosphate were determined with a colourimetric method using a 2 m liquid waveguide capillary cell with a miniaturized detector (Ocean Optics)29. Ammonium measurements were undertaken following a modified version of the method by Holmes using a FP-2020 Fluorescence Detector (Jasco). Ammonium levels found in our mesocosm were very low (<0.7% of total DIN) compared with the combined nitrite (~10%) and nitrate concentrations (~ 90%). Therefore, here DIN was considered to be represented by nitrite+nitrate values. Different units of the tank system were adjusted to low-nutrient (DIN ~0.7 μM/phosphate ~0.006 μM), nutrient-replete (DIN ~6.5 μM/phosphate ~0.3 μM) and imbalanced-nutrient (DIN >3 μM/phosphate ~0.07 μM) conditions15.

Zooxanthellae were counted using a haemocytometer and their pigment content was determined by spectrophotometric analysis of acetone extracts as described previously30. The maximum quantum yield of photosystem II photochemistry of zooxanthellae was measured with a submersible pulse-amplitude modulated fluorometer (Diving-PAM) according to previous recommendations16. The hydrolysis of para-nitrophenyl phosphate was determined colourimetrically as measure of alkaline and acidic phosphatase activity in zooxanthellae as described20. Specific lipids of interest for these studies, SQDG, PG and phosphatidylcholine (PC) molecular species, were analysed in detail using a Waters Micromass Quattro Ultima triple quadrupole mass spectrometer (Micromass) equipped with an electrospray ionization interface. To quantify the loss of tissue, coral fluorescence was documented and analysed for live tissue quantification using ImageJ ( and MATLAB (MathWorks).

Hughes, T. P. et al. Climate change, human impacts, and the resilience of coral reefs. Science 301, 929–933 (2003).

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Dubinsky, Z. & Jokiel, P. L. Ratio of energy and nutrient fluxes regulates symbiosis between zooxanthellae and corals. Pacif. Sci. 48, 313–324 (1994).

Tchernov, D. et al. Apoptosis and the selective survival of host animals following thermal bleaching in zooxanthellate corals. Proc. Natl Acad. Sci. USA 108, 9905–9909 (2011).

Szmant, A. M. Nutrient enrichment on coral reefs: Is it a major cause of coral reef decline? Estuaries 25, 743–766 (2002).

Atkinson, M. J., Carlson, B. & Crow, G. L. Coral growth in high-nutrient, low-pH seawater: A case study of corals cultured at the Waikiki Aquarium, Honolulu, Hawaii. Coral Reefs 14, 215–223 (1995).

Bongiorni, L., Shafir, S., Angel, D. & Rinkevich, B. Survival, growth and gonad development of two hermatypic corals subjected to in situ fish-farm nutrient enrichment. Mar. Ecol. Prog. Ser. 253, 137–144 (2003).

Brodie, J., Devlin, M., Haynes, D. & Waterhouse, J. Assessment of the eutrophication status of the Great Barrier Reef lagoon (Australia). Biogeochemistry 106, 281–302 (2011).

Parkhill, J-P., Maillet, G. & Cullen, J. J. Fluorescence-based maximal quantum yield for PSII as a diagnostic of nutrient stress. J. Phycol. 37, 517–529 (2001).

Miller, D. J. & Yellowlees, D. Inorganic nitrogen uptake by symbiotic marine cnidarians: A critical review. Proc. R. Soc. Lond. B 237, 109–125 (1989).

Muscatine, L., Falkowski, P. G., Dubinsky, Z., Cook, P. A. & McCloskey, L. R. The effect of external nutrient resources on the population dynamics of zooxanthellae in a reef coral. Proc. R. Soc. Lond. B 236, 311–324 (1989).

Rahav, O., Dubinsky, Z., Achituv, Y. & Falkowski, P. G. Ammonium metabolism in the zooxanthellate coral, stylophora pistillata. Proc. R. Soc. Lond. B 236, 325–337 (1989).

Berkelmans, R. & Willis, B. L. Seasonal and local spatial patterns in the upper thermal limits of corals on the inshore Central Great Barrier Reef. Coral Reefs 18, 219–228 (1999).

D’Angelo, C. & Wiedenmann, J. An experimental mesocosm for long-term studies of reef corals. J. Mar. Biol. Assoc. UK 92, 769–775 (2012).

Warner, M. E., Lesser, M. P. & Ralph, P. J. in Chlorophyll Fluorescence in Aquatic Sciences: Methods and Applications (eds Suggett, D. J., Prasil, O. & Borowitzka, M.) (Springer, 2010).

Hoegh-Guldberg, O. Climate change, coral bleaching and the future of the world’s coral reefs. Mar. Freshwat. Res. 50, 839–866 (1999).

Jones, R. J. & Hoegh-Guldberg, O. Diurnal changes in the photochemical efficiency of the symbiotic dinoflagellates (Dinophyceae) of corals: Photoprotection, photoinactivation and the relationship to coral bleaching. Plant Cell Environ. 24, 89–99 (2001).

Smith, D. J., Suggett, D. J. & Baker, N. R. Is photoinhibition of zooxanthellae photosynthesis the primary cause of thermal bleaching in corals? Glob. Change Biol. 11, 1–11 (2005).

Annis, E. R. & Cook, C. B. Alkaline phosphatase activity in symbiotic dinoflagellates (zooxanthellae) as a biological indicator of environmental phosphate exposure. Mar. Ecol. Prog. Ser. 245, 11–20 (2002).

Frentzen, M. Phosphatidylglycerol and sulphoquinovosyldiacylglycerol: Anionic membrane lipids and phosphate regulation. Curr. Opin. Plant Biol. 7, 270–276 (2004).

Warner, M. E., Fitt, W. K. & Schmidt, G. W. Damage to photosystem II in symbiotic dinoflagellates: A determinant of coral bleaching. Proc. Natl Acad. Sci. USA 96, 8007–8012 (1999).

Tchernov, D. et al. Membrane lipids of symbiotic algae are diagnostic of sensitivity to thermal bleaching in corals. Proc. Natl Acad. Sci. USA 101, 13531–13535 (2004).

Banaszak, A. T., Ayala-Schiaffino, B. N., Rodriguez-Roman, A., Enriquez, J. & Iglesias-Prieto, R. Response of Millepora alcicornis (Milleporina : Milleporidae) to two bleaching events at Puerto Morelos reef, Mexican Caribbean. Rev. Biol. Trop. 51, 57–66 (2003).

Lesser, M. P. Oxidative stress in marine environments: Biochemistry and physiological ecology. Annu. Rev. Physiol. 68, 253–278 (2006).

Shick, J. M., Iglic, K., Wells, C. G., Trick, J. D. & Dunlap, W. C. Responses to iron limitation in two colonies of Stylophora pistillata exposed to high temperature: Implications for coral bleaching. Limnol. Oceanogr. 56, 813–828 (2011).

Hartle-Mougiou, K. et al. Diversity of zooxanthellae from corals and sea anemones after long-term aquarium culture. J. Mar. Biol. Assoc. UK 92, 687–691 (2012).

Gordon, L. I., Jennings, J. C. J., Ross, A. A. & Krest, J. M. A suggested protocol for continuous flow automated analysis of seawater nutrients in the WOCE Hydrographic Program and the Joint Global Ocean Fluxes Study. OSU Coll. of Oc. Descr. Chem. Oc. Grp. Tech. Rpt. 92-1 (1992).

Patey, M. D. et al. Determination of nitrate and phosphate in seawater at nanomolar concentrations. Trends Anal. Chem. 27, 169–182 (2008).

D’Angelo, C. et al. Blue light regulation of host pigment in reef-building corals. Mar. Ecol. Prog. Ser. 364, 97–106 (2008).

Special thanks to Coral-list Crown of Thorns is a symptom of reef decline: let’s address the cause

3 October 2012, 2.39pm AEST

A recent report on coral loss from the Great Barrier Reef has pointed the finger at cyclones and Crown of Thorns starfish. The real culprit is human activity, and until we reduce port activity and pollution, coral will be unable to bounce back. Three recent studies, published in 2004, 2007 and this…

Terry Hughes
Terry Hughes

Federation Fellow, ARC Centre of Excellence for Coral Reef Studies at James Cook University

Disclosure Statement

Terry Hughes does not work for, consult to, own shares in or receive funding from any company or organisation that would benefit from this article, and has no relevant affiliations.

The Conversation provides independent analysis and commentary from academics and researchers.

We are funded by CSIRO, Melbourne, Monash, RMIT, UTS, UWA, Canberra, CDU, Deakin, Flinders, Griffith, La Trobe, Murdoch, QUT, Swinburne, UniSA, UTAS, UWS and VU.
Articles by This Author
14 June 2012 New marine reserves won’t address UNESCO’s Reef concerns
Rn7jm488-1349228774 Killing starfish one by one is no long-term solution. Paul Cizek

A recent report on coral loss from the Great Barrier Reef has pointed the finger at cyclones and Crown of Thorns starfish. The real culprit is human activity, and until we reduce port activity and pollution, coral will be unable to bounce back.

Three recent studies, published in 2004, 2007 and this week, have shown that at least 50% of the corals on the Great Barrier Reef have disappeared in recent decades.

Last year, another report claimed the declines were more modest and the result of a natural cycle. But the latest report, from the Australian Institute of Marine Science, confirms earlier studies – the Great Barrier Reef is in trouble.

Corals are the backbone of the reef, providing habitat for many other species. Measuring coral cover on a reef is the simplest way to monitor its condition. But other metrics – like counts of sharks, dugongs and turtles – also show alarming downward trajectories. The decline in coral cover highlights UNESCO’s concerns about the dwindling Universal Heritage Values of the Barrier Reef.

The key question now is, what are we going to do about these losses?
Storms do affect coral, but cyclone activity has been reduced in the last 100 years. NASA
Click to enlarge

First, we need to consider why coral cover changes. The amount of coral goes down when they reproduce less, grow more slowly or die more frequently. Even under ideal conditions, about one-quarter to one-third of a coral population dies each year from background mortality. They can die from old age, disease, predation, competition with a neighbour, erosion of their skeleton, smothering by sediment, severe coral bleaching, and from storms.

On a healthy reef, loss of cover is balanced by new recruitment of young corals and by new growth. It’s just like a human population – we measure births, deaths and net migration to track demographic changes. Measuring mortality alone won’t help us to plan for schools or new roads.

Next consider where the loss of coral cover is greatest. The 50% decline in coral cover is averaged over the whole Great Barrier Reef (GBR). However, there has been no net loss of coral cover in the remote north beyond Cooktown or on reefs far from shore. Consequently, most reefs that are close to the coast (and to people) have lost far more than 50% of their cover.

Coastal reefs have been obliterated by runoff of sediment, dredging and pollution. Once-thriving corals have been replaced by mud and seaweed (see Figure 1).

Figure 1. Dramatic loss of coral cover on Queensland’s coastal reefs. Both photographs are from the same site, indicated by the hilly backdrop. Modern photo taken by David Wachenfeld
Click to enlarge

The latest study attributed 100% of the loss of coral cover solely to higher mortality, due to just three causes – cyclones (48%), crown-of-thorns starfish (42%) and coral bleaching due to climate change (10%). However, reefs have coped with cyclones for millions of years, and – despite some claims to the contrary – the number of cyclones per decade has actually dropped slightly in the past 100 years. Too many starfish is a symptom of the decline of the Great Barrier Reef, not the direct cause.

In reality, we are responsible for the loss of corals, not storms and starfish. Before people, corals recovered from routine shocks like recurrent cyclones, and now they don’t (except in the most remote places).

The rush by many reef scientists to focus solely on climate change research has distracted attention from other ongoing threats to the reef that, so far at least, have been much more destructive. Four outbreaks of crown-of-thorns starfish have occurred on the Great Barrier Reef since the 1960s, and widespread damage from the first two of them led to the initiation of formal monitoring of corals in the 1980s.

There are two plausible but unproven theories about the causes of outbreaks of crown-of-thorns starfish. One suggests that dredging and runoff of nutrient pollution from land promotes blooms of phytoplankton which speeds up the development of starfish larvae, contributing to outbreaks. The other surmises that the changes we have made to the structure of foodwebs have resulted in fewer juvenile starfish being eaten.

Planned marine parks could help reduce damage to coral. Matt Kieffer

The best way to restore foodwebs and rebuild fish stocks is to create a network of no-take fishing reserves. The success of the GBR green zones in rebuilding depleted fish stocks bolsters the Commonwealth’s plan for a national system of marine reserves.

There is no shortage of crackpot solutions being proposed to fix the problems of the Great Barrier Reef – like covering corals with shade cloth to prevent bleaching, moving corals out of harm’s way, or killing millions of starfish one at a time with a syringe. There is a new outbreak of crown-of-thorns underway, the fourth in 50 years, and it is far too late to stop it. Direct intervention to kill starfish is expensive and time consuming. At best, it just might help to control numbers adjacent to a tourist pontoon, but it won’t change the trajectory of the current outbreak.

To increase coral cover, we need to improve the conditions that help them reproduce, survive and grow. The capacity for coral recovery is impaired on a reef that is muddy, polluted or overfished. The ongoing decline of corals demonstrates that the Great Barrier Reef is very poorly positioned to recover from future bouts of coral bleaching. Governments need to focus on controlling pollution and dredging, reducing carbon emissions, and placing a ban on new coal ports.

Special thanks to Terry Hughes,

The Ocean Foundation: Deadly Serious: Acid Oceans and What We Must Do

by Mark J. Spalding, President of The Ocean Foundation
A magnified image of the coccolithophore, Gephyrocapsa oceanica Kamptner. Coccolithophores are single-celled algae, protists, and phytoplankton and considered especially vulnerable to ocean acidification due to their calcium carbonate shells. (Image: Gephyrocapsa oceanica Kamptner from Mie Prefecture, Japan. SEM:JEOL JSM-6330F. Scale bar = 1.0 micron. Licensed under the Creative Commons Attribution-Share Alike 2.5 Generic license.)

Last week I was in Monterey, California for the 3rd International Symposium on the Ocean in a High CO2 World, which was simultaneous to the BLUE Ocean Film Festival at the hotel next door (but that is a whole other story to tell). At the symposium, I joined hundreds of other attendees in learning about the current state of knowledge and potential solutions to address the effects of elevated carbon dioxide (CO2) on the health of our oceans and the life within. We call the consequences ocean acidification because the pH of our oceans is getting lower and thus more acidic, with significant potential harm to ocean systems as we know them.


The 2012 High CO2 meeting was a huge leap from the 2nd meeting in Monaco in 2008. Over 500 attendees and 146 speakers, representing 37 nations, were gathered to discuss the issues at hand. It included a first major inclusion of socio-economic studies. And, while the primary focus was still on marine life organism responses to ocean acidification and what that means for ocean system, everyone was in agreement that our knowledge about effects and potential solutions has greatly advanced in the last four years.

For my part, I sat in rapt amazement as one scientist after another gave a history of the science around ocean acidification (OA), information on the current state of science knowledge about OA, and our first inklings of specifics about the ecosystem and economic consequences of a warmer ocean that is more acidic and has lower oxygen levels.

As Dr. Sam Dupont of The Sven Lovén Centre for Marine Sciences – Kristineberg, Sweden said:

What do we know?

Ocean Acidification is real
It is directly coming from our carbon emissions
It is happening fast
Impact is certain
Extinctions are certain
It is already visible in the systems
Change will happen

Hot, sour and breathless are all symptoms of the same disease.

Especially when combined with other diseases, OA becomes a major threat.

We can expect lots of variability, as well as positive and negative carry over effects.

Some species will alter behavior under OA.

We know enough to act

We know a major catastrophic event is coming

We know how to prevent it

We know what we don’t know

We know what we need to do (in science)

We know what we will focus on (bringing solutions)

But, we should be prepared for surprises; we have so completely perturbed the system.

Dr. Dupont closed his comments with a photo of his two children with a powerful and striking two sentence statement:

I am not an activist, I am a scientist. But, I am also a responsible father.

The first clear statement that CO2 accumulation in the sea could have “possible catastrophic biological consequences” was published in 1974 (Whitfield, M. 1974. Accumulation of fossil CO2 in the atmosphere and in the sea. Nature 247:523-525.). Four years later, in 1978, the direct linkage of fossil fuels to CO2 detection in the ocean was established. Between 1974 and 1980, numerous studies began to demonstrate the actual change in ocean alkalinity. And, finally, in 2004, the spectre of ocean acidification (OA) became accepted by the scientific community at large, and the first of the high CO2 symposia were held.

The following spring, the marine funders were briefed at their annual meeting in Monterey, including a field trip to see some cutting edge research at Monterey Bay Aquarium Research Institute (MBARI). I should note that most of us had to be reminded of what the pH scale means, although everyone seemed to recollect using the litmus paper to test liquids in middle school science classrooms. Fortunately, the experts were willing to explain that the pH scale is from 0 to 14, with 7 being neutral. The lower the pH, means lower alkalinity, or more acidity.

At this point, it has become clear that the early interest in ocean pH has produced some concrete results. We have some credible scientific studies, which tell us that as ocean pH falls, some species will thrive, some survive, some are replaced, and many go extinct (the expected result is loss of biodiversity, but a maintenance of biomass). This broad conclusion is the result of lab experiments, field exposure experiments, observations at naturally high CO2 locations, and studies focused on fossil records from previous OA events in history.


While we can see changes in ocean chemistry and ocean sea surface temperature over the 200 some years since the industrial revolution, we need to go back further in time for a control comparison (but not too far back). So the Pre-Cambrian period (the first 7/8s of Earth’s geological history) has been identified as the only good geological analog (if for no other reason than similar species) and includes some periods with lower pH. These previous periods experienced a similar high CO2 world with lower pH, lower oxygen levels, and warmer sea surface temperatures.

However, there is nothing in the historical record that equals our current rate of change of pH or temperature.

The last dramatic ocean acidification event is known as PETM, or the Paleocene–Eocene Thermal Maximum, which took place 55 million years ago and is our best comparison. It happened rapidly (over about 2,000 years) it lasted for 50,000 years. We have strong data/evidence for it – and thus scientists use it as our best available analog for a massive carbon release.

However, it is not a perfect analog. We measure these releases in petagrams. PgC are Petagrams of carbon: 1 petagram = 1015 grams = 1 billion metric tons. The PETM represents a period when 3,000 PgC were released over a few thousand years. What matters is the rate of change in the last 270 years (the industrial revolution), as we have pumped 5,000 PgC of carbon into our planet’s atmosphere. This means the release then was 1 PgC y-1 compared to the industrial revolution, which is 9 PgC y-1. Or, if you are just an international law guy like me, this translates to the stark reality that what we have done in just under three centuries is 10 times worse than what caused the extinction events in the ocean at PETM.

The PETM ocean acidification event caused big changes in the global ocean systems, including some extinctions. Interestingly, the science indicates that total biomass stayed about even, with dinoflagellate blooms and similar events offsetting the loss of other species. In total, the geological record shows a wide range of consequences: blooms, extinctions, turnovers, calcification changes, and dwarfism. Thus, OA causes a significant biotic reaction even when the rate of change is much slower than our current rate of carbon emissions. But, because it was much slower, the “future is uncharted territory in the evolutionary history of most modern organisms.”

Thus, this anthropogenic OA event will easily top PETM in impact. AND, we should expect to see changes in how change occurs because of we have so disturbed the system. Translation: Expect to be surprised.

Brilliant shades of blue and green explode across the Barents Sea just north of the Scandinavian peninsula in this natural-color image, created by a massive bloom of phytoplankton that are common in the area each August. The milky blue color strongly suggests that the bloom contains coccolithophores, microscopic plankton that are plated with white calcium carbonate. When viewed through ocean water, a coccolithophore bloom tends to be bright blue. The species is most likely Emiliana huxleyi, whose blooms tend to be triggered by high light levels during the 24-hour sunlight of Arctic summer. Ocean acidifications impact on plankton species is of particular concern given the potential to undermine the base of the ocean food chain. (Image: NASA Earth Observatory)

Brilliant shades of blue and green explode across the Barents Sea just north of the Scandinavian peninsula in this natural-color image, created by a massive bloom of phytoplankton that are common in the area each August. The milky blue color strongly suggests that the bloom contains coccolithophores, microscopic plankton that are plated with white calcium carbonate. When viewed through ocean water, a coccolithophore bloom tends to be bright blue. The species is most likely Emiliana huxleyi, whose blooms tend to be triggered by high light levels during the 24-hour sunlight of Arctic summer. Ocean acidifications impact on plankton species is of particular concern given the potential to undermine the base of the ocean food chain. (Image: NASA Earth Observatory)

Ocean acidification and temperature change both have carbon dioxide (CO2) as a driver. And, while they can interact, they are not running in parallel. Changes in pH are more linear, with smaller deviations, and are more homogenous in different geographical spaces. Temperature is far more variable, with wide deviations, and is substantially variable spatially.

Temperature is the dominant driver of change in the ocean. Thus, it is not a surprise that change is causing a shift in distribution of species to the extent they can adapt. And we have to remember that all species have limits to acclimation capacity. Of course, some species remain more sensitive than others because they have narrower boundaries of temperature in which they thrive. And, like other stressors, temperature extremes increase sensitivity to the effects of high CO2.

The pathway looks like this:

CO2 emissions → OA → biophysical impact → loss of ecosystem services (e.g. a reef dies, and no longer stops storm surges) → socio-economic impact (when the storm surge takes out the town pier)

Noting at the same time, that demand for ecosystem services is rising with population growth and increasing income (wealth)

To look at the effects, scientists have examined various mitigation scenarios (different rates of pH change) compared to maintaining the status quo which risks:

Simplification of diversity (up to 40%), and thus a reduction of ecosystem quality
There is little or no impact on abundance
Average size of various species decreases by 50%
OA causes shift away from dominance by calcifiers (organisms whose structure is formed of calcium-based material):
No hope for survival of corals which are utterly dependent on water at a certain pH to survive (and for cold water corals, warmer temperatures will exacerbate the problem);
Gastropods (thin-shelled sea snails) are the most sensitive of the mollusks;
There is a big impact on exoskeleton-bearing aquatic invertebrates, including various species of mollusks, crustaceans, and echinoderms (think clams, lobsters and urchins)
Within this category of species, arthropods (such as shrimp) are not as bad off, but there is a clear signal of their decline
Other invertebrates adapt faster (such as jellyfish or worms)
Fish, not so much, and fish may also have no place to migrate to (for example in SE Australia)
Some success for marine plants that may thrive on consuming CO2
Some evolution can occur on relatively short time scales, which may mean hope
Evolutionary rescue by less sensitive species or populations within species from standing genetic variation for pH tolerance (we can see this from breeding experiments; or from new mutations (which are rare))

So, the key question remains: Which species will be affected by OA? We have a good idea of the answer: bivalves, crustaceans, predators of calcifiers, and top predators in general. It is not difficult to envision how severe the financial consequences will be for the shellfish, seafood, and dive tourism industries alone, much less others in the network of suppliers and service. And in the face of the enormity of the problem, it can be hard to focus on solutions.


Rising CO2 is the root cause (of the disease) [but like smoking, getting the smoker to quit is very hard]

We must treat the symptoms [high blood pressure, emphysema]
We must reduce other stressors [cut back on drinking and over-eating]

Reducing the sources of ocean acidification requires sustained source reduction efforts at both the global and the local scale. Global carbon dioxide emissions are the biggest driver of ocean acidification at the scale of the world’s ocean, so we must reduce them. Local additions of nitrogen and carbon from point sources, nonpoint sources, and natural sources can exacerbate the effects of ocean acidification by creating conditions that further accelerate pH reductions. Deposition of local air pollution (specifically carbon dioxide, nitrogen and sulfur oxide) can also contribute to reduced pH and acidification. Local action can help slow the pace of acidification. So, we need to quantify key anthropogenic and natural processes contributing to acidification.

The following are priority, near-term action items for addressing ocean acidification.

Quickly and significantly reduce global emissions of carbon dioxide to mitigate and reverse the acidification of our oceans.
Limit nutrient discharges entering marine waters from small and large on-site sewage systems, municipal wastewater facilities, and agriculture, thus limiting the stressors on ocean life to support adaptation and survival.
Implement effective clean water monitoring and best management practices, as well as revise existing and/or adopt new water quality standards to make them relevant to ocean acidification.
Investigate selective breeding for ocean acidification tolerance in shellfish and other vulnerable marine species.
Identify, monitor and manage the marine waters and species in potential refuges from ocean acidification so they may endure concurrent stresses.
Understand the association between water chemistry variables and shellfish production and survival in hatcheries and in the natural environment, promoting collaborations between scientists, managers, and shellfish growers. And, establish an emergency warning and response capacity when monitoring indicates a spike in low pH water that threatens sensitive habitat or shellfish industry operations.
Restore seagrass, mangroves, marsh grass etc. that will take up and fix dissolved carbon in marine waters and locally prevent (or slow) changes in the pH of those marine waters
Educate the public about the problem of ocean acidification and its consequences for marine ecosystems, economy, and cultures

The good news is that progress is being made on all of these fronts. Globally, tens of thousands of people are working to reduce greenhouse gas emissions (including CO2) at the international, national and local levels (Item 1). And, in the USA, item 8 is the primary focus of a coalition of NGOs coordinated by our friends at Ocean Conservancy. For item 7, TOF hosts our own effort to restore damaged seagrass meadows. But, in an exciting development for items 2-7, we are working with key state decision-makers in four coastal states to develop, share and introduce legislation designed to address OA. The existing effects of ocean acidification on shellfish and other marine life in Washington and Oregon’s coastal waters have inspired action in a number of ways.

All of the speakers at the conference made it clear that more information is needed—especially about where pH is changing rapidly, which species will be able to thrive, survive, or adapt, and local and regional strategies that are working. At the same time, the takeaway lesson was that even though we do not know everything we want to know about ocean acidification, we can and should be taking steps to mitigate its effects. We will continue to work with our donors, advisors, and other members of the TOF community to support the solutions.

Special thanks to Mark Spalding, The Ocean Foundation

The Ocean Foundation: Ignorance is Not Bliss: New Study on the Status of Unassessed Fish Stocks Underscores Global Threat Posed By Overfishing

Date: October 4, 2012 5:53:29 PM EDT

by Kenneth Stump, Ocean Policy Fellow at The Ocean Foundation

Photo courtesy of John Surrick-Chesapeake Bay Foundation/Marine Photobank

Overfishing (and the use of destructive fishing gear) is often cited as one of the two greatest threats to animals in the ocean. Overfishing occurs when a fishery removes fish from a population faster than the population can replenish itself – in a word, overfishing is overkill. If not quickly controlled, overfishing leads to the eventual decimation of a fish stock and the collapse of the fishery. Scientists and fishery managers strive to identify how big the population of any given species should be to say that it is not overfished.

For well-studied stocks that have been scientifically assessed, it is possible to evaluate the status of the stock relative to overfishing criteria that are based on the ability of a given stock to produce maximum sustainable yield (MSY). Using these conventional measures of fisheries sustainability, Dr. Boris Worm et al. (2009) found that 63% of assessed fished stocks worldwide have a breeding stock size (“biomass,” denoted as “B”) below the level that is estimated to produce MSY (B/Bmsy <1), while a separate study by the FAO (2010) concluded that 32% of globally assessed stocks are overfished (B/Bmsy < 0.5). In short, most of the world’s assessed fish stocks are fully or overexploited. But only ~20% of the global fish catch (reported landings) comes from assessed species. What about the status of the thousands of data-poor, unassessed fish stocks which account for 80% or more of the global seafood catch every year? UC Santa Barbara’s Christopher Costello and colleagues have just published a new study of the status of the world’s data-poor stocks in an online edition of Science (September 27, 2012). Using available landings records and indirect evaluation methods, the authors of the new study conclude that most of these fish stocks are likely to be considerably depleted and in serious decline: 64% of unassessed fisheries stocks have a stock biomass less than Bmsy (B/Bmsy <1), which is tantamount to a depletion rate on the order of 60-70% for most stocks. 18% of unassessed stocks are collapsed (B/Bmsy < 0.2) – a level of depletion so severe that a fish population may be only a tiny fraction of its natural, unfished size. The depleted status of so many fish populations (low B/Bmsy) has consequences for food security: fishery yields are far below their potential if stocks were allowed to recover to the level that will, in theory, produce MSY. Since many of these unassessed fisheries are in poor and developing countries, management approaches to rebuilding stocks that rely on strong governance and monitoring capabilities are not likely to work. But Costello and colleagues also hold out the hope that innovative strategies combining territorial user rights (TURFs), fishing cooperatives, and no-take marine protected areas can restore these populations to healthier, more productive levels – if swift action is taken to reverse the declines. In the U.S., reforms to the national fisheries law in 1996 and 2006 have reduced overfishing on assessed stocks by about half since the National Marine Fisheries Service began issuing annual status reports in the late 1990s, as shown in Fig. 1. In 2011, U.S. commercial fisheries recorded the highest catch in 17 years, which suggests that efforts to curb overfishing and rebuild overfished stocks are starting to pay off in many (but not all) regions of the country. Fig. 1: Of the U.S. fish stocks that could be assessed for overfishing and overfished status in 2011, 14% were subject to overfishing and 21% were overfished - an improvement over past years. While encouraging, the fact that overfishing persists at all testifies to the difficulty of preventing it even when the governance system prohibits it and when substantial investments in management are made to monitor compliance with catch limits. Political and economic pressure to keep catch limits high can undermine efforts to prevent overfishing and rebuild overfished stocks as quickly as possible. Fig. 1: Of the U.S. fish stocks that could be assessed for overfishing and overfished status in 2011, 14% were subject to overfishing and 21% were overfished – an improvement over past years. While encouraging, the fact that overfishing persists at all testifies to the difficulty of preventing it even when the governance system prohibits it and when substantial investments in management are made to monitor compliance with catch limits. Political and economic pressure to keep catch limits high can undermine efforts to prevent overfishing and rebuild overfished stocks as quickly as possible. But about half of all managed stocks in U.S. waters are still unassessed and the study by Costello et al. finds that some of these data-poor stocks are likely to be in as bad a shape as those in developing countries. For instance, numerous reef fish such as groupers in the South Atlantic and Gulf of Mexico, many species of sharks, halibut in New England, to name a few, are known to be historically depleted even though they have not been formally assessed. The effects of overfishing are not limited to the decline of individual species of fish. Depletion of commercially valuable species in rapid succession can trigger trophic cascades that change the structure of the food web over time, creating unintended consequences,. The ecological consequences of overfishing rarely receive much consideration in the conventional calculus of overfishing, but one recent analysis by NOAA’s Northeast Fisheries Science Center concluded that the New England region has experienced ecosystem overfishing as a consequence of widespread overfishing and species-selective harvesting patterns that have caused a shift in the fish community composition from a system dominated by species such as cod to one increasingly dominated by lower-value small pelagic fishes such as herring and elasmobranch species (small sharks and skates). Similar effects have been observed in other heavily fished marine ecosystems, such as Europe’s North Sea or the coral reefs of the Caribbean. As the new study by Costello et al. shows, literally thousands of species are affected by fishing worldwide and most appear to be in decline. The unintended consequences of such widespread impacts on marine ecosystems are not fully known, but ignorance is not bliss. Overfishing threatens food security and local fishing economies, but efforts to sustain the production of wild fish as food for humans will fail if we ignore the functional roles that all these species play in the ecosystem. . As fisheries scientists and managers grapple with ways to end the scourge of overfishing, they must factor these ecological considerations into their calculations of how much fishing is too much. It may mean catching fewer fish, but the alternative may be catching no fish at all. Sources: Christopher Costello, Daniel Ovando, Ray Hilborn, Steven D. Gaines, Olivier Deschenes, and Sarah E. Lester (2012), Status and Solutions for the World’s Unassessed Fisheries, Science Online, September 27, 2012. NOAA Northeast Fisheries Science Center (2009), Ecosystem Status Report for the NE Continental Shelf Large Marine Ecosystem. Boris Worm et al. (2009), Rebuilding Global Fisheries, Science 325: 578-585. Special thanks to Mark Spalding, The Ocean Foundation

Summit Voice: Environment: Excess nutrients speed up ocean acidification

Posted on October 7, 2012 by Bob Berwyn

Shellfish are expected to be hit hard by ocean acidification in the coming decades.

Bob Berwyn photo.

CO2 from decaying algae blooms adds to ocean woes

By Summit Voice

SUMMIT COUNTY — Runoff from agricultural and urban areas is speeding up ocean acidification in some coastal areas, adding to the woes resulting from increased concentration of atmospheric carbon dioxide.

A new study by researchers with the National Oceanic and Atmospheric Administration and the University of Georgia found that CO2 released from decaying algal blooms intensifies acidification, which is already taking a toll on shellfish populations in some areas.

Ocean acidification occurs when the ocean absorbs carbon dioxide from the atmosphere or from the breakdown of organic matter, causing a chemical reaction to make it more acidic. Species as diverse as scallops and corals are vulnerable to ocean acidification, which can affect the growth of their shells and skeletons.

The study suggests that, given current atmospheric CO2 concentrations and projected CO2 released from organic matter decay, seawater acidity could nearly double in waters with higher salinity and temperature, and could rise as much as 12 times current levels in waters with lower salinity and lower temperature.

The study found that, that, given current atmospheric CO2 concentrations and projected CO2 released from organic matter decay, seawater acidity could nearly double in waters with higher salinity and temperature, and could rise as much as 12 times current levels in waters with lower salinity and lower temperature.

NOAA’s William G. Sunda and Wei-jun Cai of the University of Georgia found that eutrophication — the production of excess algae from increased nutrients, such as, nitrogen and phosphorus — is large, often overlooked source of CO2 in coastal waters. When combined with increasing CO2 in the atmosphere, the release of CO2 from decaying organic matter is accelerating the acidification of coastal seawater.

The effects of ocean acidification on the nation’s seafood industry are seen in the Pacific Northwest oyster fishery. According to NOAA, ocean acidification is affecting oyster shell growth and reproduction, putting this multi-million dollar industry at risk. Annually, the Pacific Northwest oyster fishery contributes $84 million to $111 million to the West Coast’s economy. According to an earlier NOAA study ocean acidification could put more than 3,000 jobs in the region at risk.

Sunda and Cai used a new chemical model to predict the increase in acidity of coastal waters over a range of salinities, temperatures and atmospheric CO2 concentrations. They found that the combined interactive effects on acidity from increasing CO2 in the atmosphere and CO2 released from the breakdown of organic matter were quite complex, and varied with water temperature, salinity and with atmospheric CO2.

“These interactions have important biological implications in a warming world with increasing atmospheric CO2,” said Sunda. “The combined effects of the two acidification processes, along with increased nutrient loading of nearshore waters, are reducing the time available to coastal managers to adopt approaches to avoid or minimize harmful impacts to critical ecosystem services such as fisheries and tourism.”

These model predictions were verified with measured acidity data from the northern Gulf of Mexico and the Baltic Sea, two eutrophic coastal systems with large temperature and salinity differences, which experience large-scale algal blooms. The observed and modeled increases in acidity from eutrophication and algal decay are well within the range that can harm marine organisms.

Funding support for the research came from the National Science Foundation, NASA and NOAA. The study can be found in this month’s edition of the American Chemical Society’s Environmental Science and Technology journal.

Special thanks to Craig Quirolo

Reuters: Storms to Starfish: Great Barrier Reef is rapidly losing coral; coral cover could fall to ~5% in the next decade
Storms to starfish: Great Barrier Reef faces rapid coral loss-study

Mon Oct 1, 2012 2:59pm EDT

* Great Barrier Reef suffers unprecedented coral loss

* Study says storms, starfish, bleaching cause most damage

* Risk of rapid decline unless world adopts tough CO2 goals

By David Fogarty

SINGAPORE, Oct 2 (Reuters) – The world’s largest coral reef – under threat from Australia’s surging coal and gas shipments, climate change and a destructive starfish – is declining faster than ever and coral cover could fall to just 5 percent in the next decade, a study shows.

Researchers from the Australian Institute of Marine Science (AIMS) in the northeastern city of Townsville say Australia’s Great Barrier Reef has lost half of its coral in little more than a generation. And the pace of damage has picked up since 2006.

Globally, reefs are being assailed by myriad threats, particularly rising sea temperatures, increased ocean acidity and more powerful storms, but the threat to the Great Barrier Reef is even more pronounced, the AIMS study published on Tuesday found.

“In terms of geographic scale and the extent of the decline, it is unprecedented anywhere in the world,” AIMS chief John Gunn told Reuters.

AIMS scientists studied data from more than 200 individual reefs off the Queensland coast covering the period 1985-2012. They found cyclone damage caused nearly half the losses, crown-of-thorns starfish more than 40 percent and coral bleaching from spikes in sea temperatures 10 percent.

The starfish are native and prey on the reefs. But plagues are occurring much more frequently.

Ordinarily, reefs can recover within 10 to 20 years from storms, bleachings or starfish attacks but climate change impacts slow this down. Rising ocean acidification caused by seas absorbing more carbon dioxide is disrupting the ability of corals to build their calcium carbonate structures. Hotter seas stress corals still further.

Greens say the 2,000 km (1,200 mile) long reef ecosystem, the centre-piece of a multi-billion tourism industry, also faces a growing threat from shipping driven by the planned expansion of coal and liquefied natural gas projects.

Those concerns have put pressure on the authorities to figure out how to protect the fragile reef.


The researchers say the pace of coral loss has increased since 2006 and if the trend continues, coral cover could halve again by 2022, with the southern and central areas most affected.

Between 1985 and 2012, coral cover of the reef area fell from 28 percent to 13.8 percent.

“Coral cover on the reef is consistently declining, and without intervention, it will likely fall to 5 to 10 percent within the next 10 years,” say the researchers in the study published in the Proceedings of the National Academy of Sciences journal. They called for tougher curbs on greenhouse gas emissions as a crucial way to stem the loss.

Shipping and new ports on the Queensland coast are another major threat, Greenpeace says.

Coal is one of Australia’s top export earners and the state of Queensland is the country’s largest coal-producer. It also has a rapidly growing coal-seam gas industry for LNG exports.

Earlier this year, Greenpeace estimated port expansion could more than triple Queensland’s coal export capacity by 2020 from 257 million tonnes now. That would mean as many as 10,000 coal ships per year could make their way through the Great Barrier Reef area by 2020, up 480 percent from 1,722 ships in 2011, according to the group.

The Queensland and national governments, which jointly manage the reef, have launched a major review of managing the risks facing the UNESCO-listed reef and its surrounding marine area. The review will look at managing the threats from increased shipping to urban development.

Gunn said better management was all about buying time and improving the reef’s resilience to climate change. A key area was improving water quality from rivers flowing into the reef area, with studies suggesting fertiliser-rich waters help the crown-of-thorns starfish larvae rapidly multiply. (Editing by Jeremy Laurence).

Special thanks to Coral-list

Scientists Uncover Hotbed of Marine Life in New Caledonia’s Reefs; Coextinction of reefs exhibited

4 September 2012

South Australian Museum parasite expert Ian Whittington is one of several international scientists whose study in New Caledonia is today published in the journal Aquatic Biosystems.

New Caledonia is home to the biggest coral reef lagoon and the second biggest coral reef on the planet. Coral reefs, essential to the world’s ecosystems, are home to more than 25% of global marine biodiversity but comprise less than 0.1% of the Earth’s ocean surface. They are considered biological “hotspots” because they are especially rich in marine species. Parasites play a major role in species evolution and the maintenance of populations and ecosystems. However the role of parasites is little known or appreciated.

South Australian Museum Scientist, Associate Professor Ian Whittington, and Honorary Research Associate at the Museum, Professor Ian Beveridge (University of Melbourne) are among an international research team of eight scientists from Australia, Britain, Czech Republic, and France. Directed by Jean-Lou Justine at the National Museum of Natural History in Paris, the team are embarking on an eight year study investigating parasite biodiversity on fish living in New Caledonia’s tropical lagoon.

Their study found that the number of fish parasites is at least ten times the number of fish species in coral reefs (for fish of similar or greater size to the species in the four families studied). Therefore extinction of a fish species on this coral reef would very likely lead to the co-extinction at least ten parasite species associated with it. The disappearance of these parasites, although insignificant at first glance, would result in a biodiversity loss ten times higher. The consequences of such extinctions for the balance of coral reefs and species evolution in general are incalculable.

Associate Professor Ian Whittington and his team in New Caledonia. Photo by Jean-Lou Justine, National Museum of Natural History, Paris.

The Director of the South Australian Museum, Professor Suzanne Miller, says “the findings of this study provide a key insight into the aquatic biodiversity of the Pacific region. Associate Professor Whittington and his colleagues have effectively illustrated the complex relationships between marine organisms and their fragility in the face of climate change and other environmental disturbances.”

The team’s investigation primarily focused on traditional parasite morphology – with an emphasis on crustaceans, external and internal flukes, tapeworms and roundworms. The aim was to estimate the number of parasite species from reef fish and the number of host-parasite combinations possible, and give a clear picture of marine biodiversity in the region. The results of this study are published this week in the online open access journal Aquatic Biosystems.

Parasitic isopod (Anilocra gigantea), photographed alive on an ornate snapper (Pristipomoides argyrogrammicus). Jean-Lou Justine, National Museum of Natural History, Paris.

The parasite and certain fish material collected and studied is held in several natural history museums across the world including the South Australian Museum’s Australian Helminthological Collection in Adelaide. This collection is an internationally renowned collection of parasitic worms established with support from the Australian Society for Parasitology. The material is also held in the Czech Republic, France, UK and USA. All these collections are available to the scientific community for further studies. This emphasises the importance of preserving and increasing the collections of natural history museums. Scientists’ pioneering work in this area and the collections will serve as a reference for similar studies on other coral reefs.

The team:

Jean-Lou Justine, UMR 7138 Systematics, Adaptation, Evolution, Muséum National d’Histoire Naturelle, Paris, France
Ian Beveridge, Department of Veterinary Science, University of Melbourne, Australia
Geoffrey A. Boxshall, Department of Zoology, Natural History Museum, London, UK
Rod A. Bray, Department of Zoology, Natural History Museum, London, UK
Terrence L. Miller, Biodiversity Program, Queensland Museum, Queensland, Australia
František Moravec, Institute of Parasitology, Biology Centre, Academy of Sciences of the Czech Republic, Branišovská, Czech Republic
John Paul Trilles, Team ecophysiological adaptations and Ontogeny, UMR 5119 (CNRS-IRD-UM1-UM2-IFREMER), Université Montpellier 2, France
Ian D. Whittington, Monogenean Research Laboratory, The South Australian Museum & Marine Parasitology Laboratory, & Australian Centre for Evolutionary Biology and Biodiversity, The University of Adelaide, Australia

Header image: Associate Professor Ian Whittington and his team studying specimens. Photo by Jean-Lou Justine, National Museum of Natural History, Paris.

03 September 2012

Coral-list: Terry Hughes provides Summary of Outcomes for 12th International Coral Reef Symposium

A 4-page summary of outcomes of the 12th International Coral Reef Symposium is now online at:

The Symposium website will remain operational indefinitely. Here are some useful direct links:, 1500 talk and poster abstracts, uploaded posters, videos of all the 12ICRS Plenary talks and the Darwin Medal address, a collection of beautiful images, an hour-long panel discussion on the Future of Coral Reefs, where you can still join more than 3,100 coral reef scientists by endorsing the Consensus Statement on the future of coral reefs.

It has been a great privilege to host 12ICRS, and we hope everyone enjoyed contributing to it, either onsite in Cairns or online. A special thanks to Eliza Glasson, for an amazing job.

Cheers, Terry
Prof. Terry Hughes FAA
Director, ARC Centre of Excellence for Coral Reef Studies
James Cook University
Townsville, QLD 4811, AUSTRALIA
Fax: 61 (0) 4781-6722
tel: 61 (0)7-4781-4000

“Scientists can help by undertaking solution-focused research, by participating more vigorously in policy debates to improve coral reef legislation and implementation, and by sending the clear message that reefs can still be saved if we try harder.” Hughes et al. 2010. Trends in Ecology and Evolution 25: 619-680.

Special thanks to Terry Hughes via the Coral-list

Huffington Post: Climate Change: Coral Reefs Expected To Suffer Greatly, Study Finds

Reuters | Posted: 09/16/2012 1:00 pm Updated: 09/16/2012 8:34 pm

* 70 pct of corals will suffer degradation by 2030

* To protect half of reefs, temperature rise must be under 1.5C

By Nina Chestney

LONDON, Sept 16 (Reuters) – The chance to save the world’s coral reefs from damage caused by climate change is dwindling as man-made greenhouse gas emissions continue to rise, scientists said in a study released on Sunday.

Around 70 percent of corals are expected to suffer from long-term degradation by 2030, even if strict emission cuts are enforced, according to the study.

“The window of opportunity to preserve the majority of coral reefs, part of the world’s natural heritage, is small,” said Malte Meinshausen, co-author of the report published in the journal Nature Climate Change.

“We close this window if we follow another decade of ballooning global greenhouse-gas emissions.”

Coral reefs are home to almost a quarter of the world’s ocean species, they provide coastal protection and can support tourism and fishing industries for millions of people worldwide.

The rise of global average temperatures, warmer seas and the spread of ocean acidification due to greenhouse gas emissions, however, pose major threats to coral ecosystems.

The scientists from the Potsdam Institute for Climate Impact Research, the University of British Columbia and the universities of Melbourne and Queensland in Australia used climate models to calculate the effects of different emissions levels on 2,160 reefs worldwide.

World carbon dioxide emissions increased by more than 3 percent last year and global average temperatures have risen by about 0.8 degrees Celsius over the past century.

Coral reefs face serious threats even if global warming is restricted to a 2 degrees Celsius limit, which is widely viewed as a safe threshold to avert the most devastating effects of climate change, such as drought, sea level rise or crop failure.

Warmer sea surface temperatures are likely to trigger more frequent and more intense mass coral bleaching, which is when reefs turn pale, the study said.

Although corals can survive bleaching, if the heat persists they can die. This happened in 1998 when 16 percent of corals were lost in a single, prolonged period of warmth worldwide.

Ocean acidification can put even more stress on corals.

As more and more carbon dioxide is absorbed from the atmosphere, sea water turns more acidic which can hinder calcification which is crucial for corals’ growth.

“Thus, the threshold to protect at least half of the coral reefs worldwide is estimated to be below 1.5 degrees Celsius mean temperature increase,” the study said.

A separate report last week said Caribbean corals were under immediate threat and urgent action was needed to limit pollution and aggressive fishing practices.

Average live coral cover on Caribbean reefs has declined to just 8 percent today compared to more than 50 percent in the 1970s, according to the report by the International Union for Conservation of Nature. (Editing by Rosalind Russell)

Special thanks to Desiree Barbazon

IUCN: Crunch time for Caribbean corals

07 September 2012 | International news release

Jeju Island, Republic of Korea, 7 September 2012 (IUCN) – Time is running out for corals on Caribbean reefs. Urgent measures must be taken to limit pollution and regulate aggressive fishing practices that threaten the existence of Caribbean coral reef ecosystems, according to a new IUCN (International Union for Conservation of Nature) report.

Average live coral cover on Caribbean reefs has declined to just 8% of the reef today, compared with more than 50% in the 1970s according to the report’s findings. Furthermore, rates of decline on most reefs show no signs of slowing, although the deterioration of live coral cover on more remote reefs in the Netherlands Antilles, Cayman Islands and elsewhere is less marked—with up to 30% cover still surviving. These areas are less exposed to human impact as well as to natural disasters such as hurricanes.

Special thanks to Paul Hoetjes via Coral-list

Journal of Indonesian Coral Reefs available online

Dear All,
We proudly announce that our first volume of Journal of Indonesian Coral Reefs is finally available on line
( incres). It is free download for full-text pdf format. More numbers and Volumes coming on line soon. Please distribute this information and link to our friends and colleagues who might be interested to know more various issues about Indonesian Coral Reefs. We also encourage you all to share your information by submitting your manuscript (please refer to Guide for Author on the above link).

We also welcome any suggestions to improve the quality of this journal. Thanks for your kind attention and cooperation,

Best Regards,
Jamal Jompa
Editor in Chief
Coral-List mailing list

Important International Coral Reef Symposium 2012 Info

From: Hughes, Terry
Sent: Friday, 11 May 2012 3:37 PM

Two months in advance of the 12th International Coral Reef Symposium (ICRS 2012) in Cairns, Australia from 9-13 July, the draft Scientific Program is now available online, at

Close to 2,000 people from 75 countries have registered to attend so far, and over 1,500 oral and poster presentations have been scheduled.

Prior to the Symposium, we will also place the finalized Book of Abstracts online to help delegates plan their trip, and to make this information available more broadly. Immediately after ICRS 2012, the Symposium Proceedings, uploaded posters, and videos of the Plenary talks will be freely available online.

We look forward to providing broad internet access to the Symposium’s outputs to the coral reef research community. You can still register to attend, and we very much look forward to welcoming those of you who coming to Cairns in just a few week’s time.

Terry Hughes
ICRS 2012 Convenor

Special thanks to Coral-list

In Tech: Long-Term Impacts of Non-Sustainable Tourism and Urban Development in Small Tropical Islands Coastal Habitats in a Changing Climate: Lessons Learned from Puerto Rico Edwin A. Hernández- Delgado1, Carlos E. Ramos-Scharrón2, Carmen R. Guerrero-Pérez3, Mary Ann Lucking4, Ricardo Laureano5, Pablo A. Méndez-Lázaro6 and Joel O. Meléndez-Díaz7 1Center for Applied Tropical Ecology and Conservation, University of Puerto Rico-Río Piedras 2Island Resources Foundation & Department of Geography and the Environment, University of Texas at Austin 3 Instituto para un Desarrollo Sustentable 4Coralations, Inc. 5Vegabajeños Impulsando Desarrollo Ambiental Sustentable, Inc. 6Department of Environmental Health, University of Puerto Rico-Medical Sciences Campus 7Department of Environmental Sciences, University of Puerto Rico-Río Piedras 1,3,4,5,6,7Puerto Rico 2USA


Fox News: Whales sensed Deepwater Horizon oil rig disaster

By Peter Gwynne
Published April 08, 2012
Inside Science News Service

A technique that monitors whales through the sounds they emit has answered a key issue raised by the explosion of the Deepwater Horizon oil rig in the Gulf of Mexico two years ago this month.

The sound-monitoring technique revealed that sperm whales retreated from the immediate area around the spill caused by the explosion.

“There’s obvious evidence of relocation,” said team member Azmy Ackleh, professor and head of mathematics at the University of Louisiana at Lafayette.

The discovery is important because it provides information about a species almost hunted to extinction for its valuable oil in the 19th century.

Sperm whales are listed as endangered under the terms of the United States Endangered Species Act, and estimates of their population vary between 200,000 and 1.5 million worldwide.

However, said Vassili Papastavrou, lead whale biologist for the International Fund for Animal Welfare who did not work on the study, “sperm whales are difficult animals to count, because they spend so much of their lives beneath the surface. The overall population estimates are so uncertain that it is not possible to determine trends.”

The discovery of their relocation also indicates the value of “passive” acoustic technology, which quietly listens for things instead of actively bouncing sounds off objects to find them.

This approach, first tried in the 1980s, uses hydrophones mounted on buoys to detect “clicks,” the powerful sounds emitted by the sperm whales. The University of Louisiana team, led by Natalia Sidorovskaia, associate professor and chair of the physics department, has extended the technology to localize and track sperm whales and to estimate their populations, and to do the same for other marine mammals, including other types of whales and dolphins.

Traditionally, zoologists have measured the location and size of whale populations by spotting them from boats or tagging individual whales with radio transmitters. While visual surveys are often inaccurate, tagging is very expensive.

The use of sound overcomes both problems.

“The usefulness of passive acoustics is generally under-appreciated, and the effort to develop it as a long-term monitor tool is timely,” said Donald Baltz, professor and chair of the department of oceanography and coastal sciences at Louisiana State University, who was not involved with the study.

“As long as we can hear the whales, we can count them,” Sidorovskaia said. “Passive acoustic measurements are not dependent on weather or light conditions and are much cheaper.”

Sperm whales transmit three types of sound, Sidorovskaia said. An echolocation signal is used in the way humans use radar, which helps the whales locate the ocean bottom and identify prey. A second signal serves as communication between whales. And the third is a short-range echolocation signal emitted when they are very close to their prey. Sidorovskaia said it’s probably “for more accurate short-range prey tracking.”

The range of frequencies in the sound signals, otherwise known as bandwidth, differentiates sperm whales from other whales, in much the same way that different cell-phone providers use different parts of the radio-frequency spectrum for managing communications.

“Each animal has a particular bandwidth,” Ackleh explained. “It’s a low bandwidth for sperm whales.”

By using enough hydrophones, the team can determine more than the density of sperm whales in any part of the sea.

“We can determine the range and depth of the whales,” Sidorovskaia said. “We can even track whales’ diving patterns based on the signals they produce.”

The team used passive acoustics to monitor a “resident population” of female sperm whales and their calves off the Louisiana coast in 2001, 2002 and 2007.

After the Deepwater Horizon explosion and spill, team members realized that the hydrophones they used for those recordings had been placed nine, 25, and 50 miles from the ill-fated oil rig.

So they set up fresh hydrophones in the same locations, collected acoustic signals characteristic of sperm whales, and applied statistical methods to compare the species’ population before and after the spill.

“A comparison of the 2007 and the 2010 recordings shows a decrease in acoustic activity and abundance of sperm whales at the nine-mile site by a factor of two, whereas acoustic activity and abundance at the 25-mile site has clearly increased,” the team wrote in the Journal of the Acoustical Society of America.

Just why the sperm whales moved away from the site is unclear. One possibility is that they followed their food sources out of the spill area. Sperm whales feed on giant squid, for which they dive about half a mile below the sea surface. They are also known to follow fishing boats and snag fish off their lines.

The team has garnered other firsts in applying passive acoustics. For example, it is building a library of whales’ “voiceprints” based on the sounds they make, which they can then use to locate and track single whales.

“This is very new,” Sidorovskaia asserted. “Our group would claim the initial idea.”Other research involves listening for beaked whales and refining the technology for more precise location of marine mammals. “We’re looking at a two-dimensional circle in the water now,” Ackleh said. “We hope eventually to detect animals in three-dimensional spheres.”

Read more:

Special thanks to Richard Charter

Scientific American: Phytoplankton Population Drops 40 Percent Since 1950

News | Energy & Sustainability

Researchers find trouble among phytoplankton, the base of the food chain, which has implications for the marine food web and the world’s carbon cycle

By Lauren Morello and ClimateWire | July 29, 2010 | 49

The microscopic plants that form the foundation of the ocean’s food web are declining, reports a study published July 29 in Nature.

The tiny organisms, known as phytoplankton, also gobble up carbon dioxide to produce half the world’s oxygen output—equaling that of trees and plants on land.

But their numbers have dwindled since the dawn of the 20th century, with unknown consequences for ocean ecosystems and the planet’s carbon cycle.

Researchers at Canada’s Dalhousie University say the global population of phytoplankton has fallen about 40 percent since 1950. That translates to an annual drop of about 1 percent of the average plankton population between 1899 and 2008.

The scientists believe that rising sea surface temperatures are to blame.

“It’s very disturbing to think about the potential implications of a century-long decline of the base of the food chain,” said lead author Daniel Boyce, a marine ecologist.

They include disruption to the marine food web and effects on the world’s carbon cycle. In addition to consuming CO2, phytoplankton can influence how much heat is absorbed by the world’s oceans, and some species emit sulfate molecules that promote cloud formation.

A continuing mystery story
“In some respect, these findings are the beginning of the story, not the end,” Boyce said. “The first question is what will happen in the future. We looked at these trends over the past century but don’t know what will happen 10 years down the road.”

The study “makes a sorely needed contribution to our knowledge of historical changes in the ocean biosphere,” said David Siegel of the University of California, Santa Barbara, and Bryan Franz of NASA in an essay, also published in Nature.

“Their identification of a connection between long-term global declines in phytoplankton biomass and increasing ocean temperatures does not portend well for [ocean] ecosystems in a world that is likely to be warmer,” they wrote. “Phytoplankton productivity is the base of the food web, and all life in the sea depends on it.”

Boyce said he and his co-authors began their study in an attempt to get a clearer picture of how phytoplankton were faring, given that earlier studies that relied on satellite measurements produced conflicting results.

Biggest declines at the poles
The scientists dug back into the historical record, well past 1997, the year continuous satellite measurements began. They examined a half-million data points collected using a tool called a Secchi disk, as well as measurements of chlorophyll—a pigment produced by the plankton.

The Secchi disk was developed in the 19th century by a Jesuit astronomer, Father Pietro Angelo Secchi, when the Papal navy asked him to map the transparency of the Mediterranean Sea.

What Secchi produced was a dinner plate-sized white disk that is lowered into ocean water until it cannot be seen anymore. The depth it reaches before disappearing gives a measure of water clarity.

That can be used as a proxy for phytoplankton population in a given area, since the tiny organisms live close to the ocean’s surface, where they are exposed to sunlight they use to produce energy.

Data gathered with a Secchi disk are roughly as accurate as observations collected by satellites, Boyce said, although satellites have greater global reach.

The researchers found the most notable phytoplankton declines in waters near the poles and in the tropics, as well as the open ocean.

They believe that rising sea temperatures are driving the decline. As surface water warms, it tends to form a distinct layer that does not mix well with cooler, nutrient-rich water below, depriving phytoplankton of some of the materials they need to turn CO2 and sunlight into energy.

Special thanks to Marine Life Health Reports

ScienceDaily: Viral Disease — Particularly from Herpes — Gaining Interest as Possible Cause of Coral Decline

ScienceDaily (Mar. 28, 2012) — As corals continue to decline in abundance around the world, researchers are turning their attention to a possible cause that’s almost totally unexplored — viral disease.

It appears the corals that form such important parts of marine ecosystems harbor many different viruses — particularly herpes. And although they don’t get runny noses or stomach upset, corals also are home to the adenoviruses and other viral families that can cause human colds and gastrointestinal disease.

In a research review published in the Journal of Experimental Marine Biology and Ecology, scientists point out that coral declines are reaching crisis proportions but little has been done so far to explore viral disease as one of the mechanisms for this problem.

“Coral abundance in the Caribbean Sea has gone down about 80 percent in the past 30-40 years, and about one-third of the corals around the world are threatened with extinction,” said Rebecca Vega-Thurber, an assistant professor of microbiology at Oregon State University.

“We’ve identified 22 kinds of emerging disease that affect corals, but still don’t know the pathogens that cause most of them,” Vega-Thurber said. “Most researchers have looked only at bacteria. But we suspect viruses may play a role in this as well, and it’s important to learn more about what is causing this problem. Corals are the building blocks of the tropical seas.”

A research program at OSU, one of only two of its type in the world, is studying viral “metagenomics” in corals, meaning the analysis of multiple genomes at the same time. It may help explain one of the underlying causes of coral decline, Vega-Thurber said, and is one of the most comprehensive analyses yet done on the types of viruses in a marine animal. It may also shed light on the broader range of viruses that affect not only corals but many other animals, including humans.

One of the surprises from recent research was the predominance in corals of herpes viruses — similar but not identical to the herpes virus that can infect humans. Herpes viruses appear to constitute a majority of the viruses found in corals, and one experiment showed that herpes-like viral sequences were produced in coral tissues after acute episodes of stress.

“We were shocked to find that so many coral viruses were in the herpes family,” Vega-Thurber said. “But corals are one of the oldest animal life forms, evolving around 500 million years ago, and herpes is a very old family of viruses that can infect almost every kind of animal. Herpes and corals may have evolved together.”

It’s not yet certain, researchers say, whether the viruses being found on corals are actually causing diseases.

“Just because you harbor a virus doesn’t mean you are getting sick from it,” Vega-Thurber said. “This is part of what we have to pin down with further research.”

Some of the possible causes of coral decline that have been identified so far include global warming that causes coral bleaching, loss of symbiotic algae that help nourish corals, pollution such as sewage runoff, and human-coral interactions.

A “mucus” sometimes found on corals can harbor human-borne viruses, and levels of these viruses have been correlated with terrestrial human population density.

“We have found that nutrient increases from pollution can cause increased levels of viral infection, as do warmer water and physical handling,” Vega-Thurber said. “Now we have to determine if those increases in infection cause actual diseases that are killing the coral.”

Corals are often a major component of marine ecosystems and biodiversity, especially in the tropics. They host thousands of species of fish and other animals. And whether or not viruses are implicated in coral disease, it may also be that they are passing diseases along to fish.

Research is “likely to reveal that viruses have numerous and profound roles on coral reefs,” the scientists wrote in their study. “As the diversity, distribution and function of reef-associated viruses becomes increasingly well defined, so will our ability to predict, prevent and/or mitigate disease epizootics on coral reefs.”

Special thanks to Robert Bolland PhD via Coral-list

Coral-list: Judy Lang provides new aids for identifying corals and fishes in AGRRA surveys for wider Caribbean

Judith Lang via

10:33 AM (7 hours ago) March 14th, 2012

Dear All,
New aids for identifying the species of corals and fishes in the wider Caribbean that can occur in AGRRA surveys are now available for downloading at:

Many new photographs and, for the corals, a few taxonomic revisions are included in these materials.

Additional AGRRA datafiles will be posted online in the near future.

Kind regards,

Special thanks to:
Coral-List mailing list

Science Now: Some Corals May Adapt to Warmer Seas
by Dennis Normile on 12 March 2012, 12:25 PM |

Pictures of ghostly white coral colonies bleached by elevated sea temperatures have become symbols of the effects of global warming. Now there is a glimmer of hope that at least some corals may be more resilient than previously thought. A study suggests that certain kinds of corals subjected to bleaching adapt to endure higher water temperatures.

Corals rely on symbiotic algae, called zooxanthellae, for their color and to produce nutrients through photosynthesis. Above a tipping point, warm seawater typically upsets this delicate symbiotic balance and corals expel the algae, turning white and eventually dying if high temperatures persist. Such bleaching events are becoming more frequent as periodic hot spells exacerbate the sea temperature rise due to global warming. This raises concerns about the long-term survival of coral reefs, which are refuges for marine biodiversity.

Yet corals may be hardier than biologists have thought. During a 2010 bleaching episode, an international team studied three coral reef sites. At one in Indonesia that had not bleached previously, corals responded typically to warmer water. There, fast-growing branching coral species—such as Acropora—suffered severe die-offs. But at two sites in Singapore and Malaysia that had bleached in 1998, this pattern was reversed, with normally susceptible Acropora colonies appearing healthy while massive slow-growing corals, such as Porites were heavily damaged. The group concluded that “the effects of bleaching will not be as uniform as anticipated” and fast-growing corals such as Acropora and Pocillopora may be able to survive more frequent rises in water temperature. Marine biologist James Guest, previously at the National University of Singapore and now at University of New South Wales in Sydney, Australia, and colleagues reported their findings online on 9 March at PLoS One.

The report “is very interesting and hopeful,” says Mikhail Matz, a coral biologist at University of Texas, Austin. Matz says it appears natural selection led to the evolution of higher bleaching resistance in just one coral generation, “which would be awesome news indeed.” He would like to see additional evidence to clarify the mechanism involved.

Guest agrees additional work is needed. “We don’t know whether the unusual resistance in the branching corals was due to the host coral or the symbionts or both,” he says. They are starting additional studies to learn more about the specific type of zooxanthellae inhabiting the coral that adapted and to try to study the phenomenon in the laboratory. He also cautions that higher water temperatures could still affect the composition and health of reefs. Finding evidence of adaptation “does not mean that the global threat to reefs from climate change has lessened,” he says.

Special thanks to Doug Fenner, posted on Contrasting Patterns of Coral Bleaching Susceptibility in 2010 Suggest an Adaptive Response to Thermal Stress

James R. Guest1¤*, Andrew H. Baird2, Jeffrey A. Maynard3, Efin Muttaqin4, Alasdair J. Edwards5, Stuart J. Campbell4, Katie Yewdall6, Yang Amri Affendi7, Loke Ming Chou1

1 Marine Biology Laboratory, Department of Biological Sciences, National University of Singapore, Singapore, Singapore, 2 Australian Research Council Centre of Excellence for Coral Reef Studies, James Cook University of North Queensland, Townsville, Australia, 3 Centre National de la Recherche Scientifique, Centre de Recherches Insulaires et Observatoire de l’Environnement, Moorea, French Polynesia, 4 The Wildlife Conservation Society, Indonesian Marine Program, Bogor, Indonesia, 5 School of Biology, Newcastle University, Newcastle-upon-Tyne, United Kingdom, 6 Blue Ventures, Aberdeen Centre, London, United Kingdom, 7 Institute of Biological Sciences, Faculty of Science, Universiti Malaya, Kuala Lumpur, Malaysia
Abstract Top

Coral bleaching events vary in severity, however, to date, the hierarchy of susceptibility to bleaching among coral taxa has been consistent over a broad geographic range and among bleaching episodes. Here we examine the extent of spatial and temporal variation in thermal tolerance among scleractinian coral taxa and between locations during the 2010 thermally induced, large-scale bleaching event in South East Asia.
Methodology/Principal Findings

Surveys to estimate the bleaching and mortality indices of coral genera were carried out at three locations with contrasting thermal and bleaching histories. Despite the magnitude of thermal stress being similar among locations in 2010, there was a remarkable contrast in the patterns of bleaching susceptibility. Comparisons of bleaching susceptibility within coral taxa and among locations revealed no significant differences between locations with similar thermal histories, but significant differences between locations with contrasting thermal histories (Friedman = 34.97; p<0.001). Bleaching was much less severe at locations that bleached during 1998, that had greater historical temperature variability and lower rates of warming. Remarkably, Acropora and Pocillopora, taxa that are typically highly susceptible, although among the most susceptible in Pulau Weh (Sumatra, Indonesia) where respectively, 94% and 87% of colonies died, were among the least susceptible in Singapore, where only 5% and 12% of colonies died. Conclusions/Significance The pattern of susceptibility among coral genera documented here is unprecedented. A parsimonious explanation for these results is that coral populations that bleached during the last major warming event in 1998 have adapted and/or acclimatised to thermal stress. These data also lend support to the hypothesis that corals in regions subject to more variable temperature regimes are more resistant to thermal stress than those in less variable environments. Citation: Guest JR, Baird AH, Maynard JA, Muttaqin E, Edwards AJ, et al. (2012) Contrasting Patterns of Coral Bleaching Susceptibility in 2010 Suggest an Adaptive Response to Thermal Stress. PLoS ONE 7(3): e33353. doi:10.1371/journal.pone.0033353 Editor: Mikhail V. Matz, University of Texas, United States of America Received: November 17, 2011; Accepted: February 13, 2012; Published: March 9, 2012 Copyright: © 2012 Guest et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Funding: Funding was provided by a Singapore Ministry of Education Academic Research Fund Tier 1 FRC Grant (Grant number: R-154-000-432-112). The funder had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Competing interests: The authors have declared that no competing interests exist. * E-mail: ¤ Current address: Centre for Marine Bio-innovation, University of New South Wales, Sydney, Australia Introduction Top Coral reefs are critically important for the ecosystem goods and services they provide to maritime tropical and subtropical nations [1]. However, major coral bleaching events – caused by a breakdown in the relationship between scleractinian corals and their algal symbionts – have led to widespread coral mortality on reefs in recent decades [2]. Global warming poses a particularly significant threat to the future of coral reef ecosystems because large-scale coral bleaching episodes are strongly correlated with elevated sea temperatures [3], [4]. Indeed, among Earth's ecosystems, coral reefs are one of the most severely threatened by global warming [5]. Coral bleaching severity varies in space and time as a consequence of the magnitude of thermal stress [6], levels of irradiance [7], [8], symbiont types [9], the species composition of the coral assemblage [10], [11], [12] and thermal history of the site [13], [14]. Species composition is one of the strongest drivers of this variation due to a predictable hierarchy of susceptibility among coral taxa [10], [11], [12]. Fast growing branching taxa, such as Acropora and Pocillopora, are normally highly susceptible to thermal stress; they bleach rapidly and experience high rates of whole colony mortality [15]. In contrast, massive taxa such as Porites and some faviids are more resistant to bleaching, they take longer to bleach, and although they may stay bleached for longer, few entire colonies die [15]. This consistency has led to the prediction that hardier, slow-growing massive species will replace less hardy, fast-growing branching species on reefs in the future [10], [16]. The thermal history of a site may also play an important role in determining bleaching severity. For example, on reefs with naturally higher temperature fluctuations, corals are frequently exposed to stressful temperatures for short periods, and this may lead to greater tolerance during episodes of more prolonged thermal stress [14], [17]. Scleractinian corals are the major framework builders of reefs and provide most of the structural complexity in reef ecosystems. Therefore, the capacity of coral species to adapt and acclimatise to increasing episodes of thermal stress will greatly influence rates of reef degradation [5]. Several studies cite repeated bleaching episodes in the same coral assemblages, the increasing scale and frequency of coral bleaching and the low overall evolutionary potential of scleractinians as evidence that corals have exhausted their capacity to adapt to rising sea temperatures [18], [19]. In contrast, other studies show considerable spatial and temporal variation in bleaching susceptibility within scleractinian taxa, suggesting an underappreciated capacity for corals to adapt and/or acclimatise to thermal stress [20]. If the hypothesis that corals still have the capacity to adapt to elevated sea temperatures is correct, we would expect to find increases in thermal tolerance on reefs that have previously experienced major bleaching with the most susceptible species exhibiting the greatest increases in thermal tolerance [21]. Furthermore, we would expect reefs in more thermally variable environments to bleach less severely during episodes of elevated sea temperatures [14]. Here we examine the bleaching and mortality responses of corals at sites with contrasting thermal histories during a large-scale bleaching event in 2010. Our data provide evidence in support of both hypotheses as we documented an unprecedented reversal in the susceptibility of coral genera, but only at sites where bleaching occurred in 1998. Furthermore we show that corals generally bleached less severely at locations where temperature variability has been greater and warming rates lower over the last 60 years. Results Top Coral bleaching and mortality response A major thermal anomaly that began in May 2010 led to extensive coral bleaching on reefs at sites in South East Asia (​/index.html). In Pulau Weh, north Sumatra, in May and June 2010 we observed patterns of susceptibility that were similar to the last major bleaching episode in the Indo-West Pacific in 1998, with severe bleaching and mortality of Acropora and Pocillopora (Figure 1A). However, at sites in Malaysia and Singapore in July 2010 we found these taxa were surprisingly, largely unaffected by bleaching whereas massive taxa bleached severely, as expected given the level of thermal stress (Figure 1B, C). thumbnail Figure 1. Contrasting coral bleaching patterns during 2010. Extensive stands of bleached Acropora colonies from (A) Pulau Weh, north Sumatra, Indonesia where patterns in bleaching susceptibility were normal. Reversals in bleaching susceptibility gradients were observed in (B) Singapore and (C) Tioman Island, Malaysia, where healthy Acropora colonies were found adjacent to bleached encrusting, foliose and massive colonies: corals which are usually relatively resistant to bleaching. The inset map shows the three study locations. doi:10.1371/journal.pone.0033353.g001 Analysis of the bleaching and mortality response (BMI) of coral genera [12] (and see methods) carried out at the three locations in 2010 and the Great Barrier Reef (GBR) in 1998 revealed a significant difference in bleaching susceptibility among locations (Friedman test = 34.97, p<0.0001). Dunn's post-hoc multiple comparisons revealed that there were no significant differences between Pulau Weh in 2010 and the GBR in 1998 [11] (Table 1). Similarly, there were no significant differences between the two South China Sea locations in 2010 (Table 1). However, bleaching susceptibilities of coral taxa at both Singapore and Tioman Island were significantly different from Pulau Weh (p<0.001, Table 1). The coral taxa Acropora and Pocillopora were the most susceptible in Pulau Weh but among the least susceptible in Singapore. In Pulau Weh, 94% of Acropora and 87% of Pocillopora colonies were recorded as recently dead, compared to only 5% of Acropora and 12% of Pocillopora in Singapore (Table 2, Figure 2). In Tioman Island, Acropora and Pocillopora were much less affected than at Pulau Weh, with 28% and 36% respectively of colonies recently dead, however these taxa still ranked among the most susceptible at this location (Table 2, Figure 2). thumbnail Figure 2. Comparison of bleaching and mortality indices among locations during 2010. Graphs compare the bleaching and mortality indices (BMI) of 15 coral genera that had >5 colonies recorded during surveys at each location for (A) Pulau Weh, (B) Singapore and (C) Tioman Island in 2010. Data used to estimate BMI are from Table 2.

Table 1. Results of Friedman test and Dunn’s multiple comparisons of bleaching and mortality response within taxa and among locations.

Table 2. Bleaching and mortality response of coral genera from three study locations.

In addition to the reversal in the hierarchy of susceptibility among taxa between Singapore and Pulau Weh, most genera in Pulau Weh in 2010 were more severely affected than at the other two sites. In Pulau Weh, 44.7±5.04%, (mean ± SE) of colonies were recently dead during surveys whereas in Singapore and Tioman Island only 4.2±0.71% and 15.4±2.47% (mean ± SE) of colonies were recently dead (Table 2). Several taxa in Pulau Weh had a high proportion of dead colonies (i.e. >50% of colonies recently dead) relative to the other locations. For example, in Pulau Weh, 53% of Hydnophora and 57% of Echinopora colonies were recently dead, whereas in Singapore only 6% of Hydnophora colonies were dead and in Tioman Island no colonies of either genera were found dead (Table 2). The massive faviid genera Cyphastrea, Favia and Platygyra, although less severely affected than other taxa, were also more severely affected in Pulau Weh compared to Singapore and Tioman Island with 15% to 25% of colonies recently dead in Pulau Weh compared to <2% of colonies in the South China Sea sites (Table 2). Conversely branching Porites were severely affected in all locations with the proportion of recently dead colonies being 60% in Pulau Weh, 50% in Singapore and 46% in Tioman Island; whereas four massive coral taxa (Diploastrea, massive Porites, Montastraea and Goniastrea) had similar, but less severe, responses at all three locations with between 0% and 8% of colonies recently dead (Table 2). Short-term thermal history of study sites Coral bleaching occurs when sea surface temperatures (SST) exceed climatological maximum monthly mean (MMM) for prolonged periods and the extent of thermal stress is typically expressed in terms of degree heating weeks (DHW) [22]. Remotely sensed data from Pulau Weh, (the location most severely affected by bleaching in 2010), showed that SST and DHW rarely exceeded the MMM in 1998 (Figure 3A), whereas in both Singapore and Tioman Island they did for prolonged periods (Figure 3B, C). Total DHW above MMM were 5 and 7 times higher in Tioman Island and Singapore than in Pulau Weh in 1998. In contrast, thermal stress was high and similar at all locations in 2010, with maximum DHW above MMM ranging from 12.02 to 15.44°C-weeks (Figure 3). thumbnail Figure 3. Comparison of sea temperatures and thermal stress during 1998 and 2010. Weekly mean sea surface temperatures (°C) and maximum monthly mean (MMM) temperatures (top row) and thermal stress in degree heating weeks (DHW) (°C-weeks) above MMM in 1998 and 2010 (bottom row) for (A) Pulau Weh; (B) Singapore; and (C) Tioman Island. Blue lines are SST and DHW from 1998, red lines are from 2010 and the gray line is MMM. Values for maximum degree DHW > MMM in 1998 and 2010 are shown.
Long-term thermal history of study sites

Long-term thermal histories for each location, determined by examining monthly mean SST data for the 1° longitude–latitude squares that encompassed each study location, indicate that despite similar mean temperatures in Singapore (mean 28.89 ± SD 0.83°C), Tioman Island (mean 28.72 ± SD 0.90°C) and Pulau Weh (mean 28.74 ± SD 0.59°C), only the thermal histories of the two South China Sea locations are similar (Figure 4). For example, annual variability (standard deviation) at the South China Sea locations is 41–52% higher than that of Pulau Weh. Furthermore, the decadal rates of warming over the last 60 years for Singapore (0.08°C decade−1) and Tioman Island (0.09°C decade−1) are close to half the rate for Pulau Weh (0.16°C decade−1).

Figure 4. Comparison of long-term thermal histories.

Monthly mean sea surface temperatures from January 1951 to December 2010 for (A) Pulau Weh; (B) Singapore and (C) Tioman Island. The linear regression is shown by the straight black line and the equation shows the average rate of temperature increase.
Discussion Top

Fast growing branching coral taxa, such as Acropora and Pocillopora, are normally highly susceptible to thermal stress and to date there has been a predictable hierarchy of bleaching susceptibility that was consistent over a wide geographic range and among bleaching events [10], [11], [12]. The hierarchy of susceptibility in Pulau Weh in 2010 was typical of previous bleaching episodes, for example the 1998 event on the GBR [11], but was in marked contrast with the patterns of susceptibility observed in Singapore and Tioman Island (see Figure 1). Comparisons of the BMI of taxa among locations revealed significantly different patterns between Pulau Weh and the South China Sea locations and confirmed a reversal in the normal patterns of susceptibility between Singapore and Pulau Weh. This is the first time such a reversal has been reported during a major warming-induced bleaching event. The remotely sensed temperature data corroborate reports indicating that corals in Singapore and Tioman Island bleached in 1998 but those in Pulau Weh did not. Extensive bleaching was documented in Singapore, in several nearby Indonesian sites [23] and Tioman Island [24] during 1998; whereas there are no reports of bleaching from Pulau Weh prior to 2010 despite numerous reports from elsewhere in the Indonesian archipelago ( Local dive operators have not witnessed mass bleaching in the area in the last 30 years and in nearby Andaman Sea sites, severe bleaching was not observed during 1997–1998 [8]. A parsimonious explanation for the contrasting bleaching responses among locations, therefore, is that removal of susceptible individuals from populations that bleached during 1998 in Singapore and Tioman Island, followed by reproduction and successful recruitment of the remaining, more thermally tolerant individuals, has led to adaptation through natural selection within an ecological time frame [13], [25].

Recurring bleaching episodes of increasing magnitude and frequency within coral assemblages have been cited as evidence that corals have exhausted their capacity to adapt and it is often stated that the generation times of corals are too long to allow rapid adaptation to a changing climate [18], [19]. In contrast, a growing body of evidence indicates that the capacity for adaptation and acclimatisation in corals has been underestimated [13], [21], [26]. Even for highly susceptible coral species, variation in specific characteristics of the symbiotic zooxanthellae [27] and the coral host [28] lead to different bleaching responses among colonies. Selective mortality among individuals within populations suggests there is sufficient genetic variability upon which natural selection can act [29]. Several studies have documented increasing thermal tolerance and declining rates of bleaching induced mortality over successive bleaching episodes [21], [30]. Similarly, thermal history and previous exposure to thermal stress have been shown to determine bleaching responses to contemporary thermal stress [13]. The most compelling evidence of an adaptive response at our study locations is that the taxa that showed the greatest contrast in response (Acropora and Pocillopora), have life history traits most likely to lead to rapid adaptation. For example, these taxa become sexually mature within 2 to 3 years [31], [32] and typically experience high rates of whole colony mortality following thermal stress [15].

Most taxa bleached much less severely and far fewer corals died in Singapore and at Tioman Island than in Pulau Weh in 2010. The 2010 episode in Pulau Weh was greater in magnitude compared to previous major bleaching episodes, such as that on the GBR in 1998 [11], and surveys from other sites in the Andaman Sea indicate that the 2010 event is the most severe for this region on record [8], [33]. The differences in overall bleaching severity among the three study locations in 2010 are not readily explained by differences in the magnitude of the thermal anomaly but may have been influenced by long-term differences in thermal histories at each location. In environments with naturally higher temperature fluctuations, the coral holobiont is frequently exposed to stressful temperatures for short durations, and this may lead to greater tolerance during episodes of prolonged thermal stress [14], [17], [34]. Consequently, acclimatisation of corals driven by greater thermal variability and facilitated by slower warming rates may also have led to overall differences in the severity of bleaching responses among locations. If our findings apply more generally then locations that are more resistant to bleaching can be identified from their thermal histories. Such knowledge can be used to inform protected area planning by aiding in the identification of sites with lower relative vulnerability to global warming [35], [36].

It is often stated that corals have exhausted their capacity to adapt to thermal stress [18], [19]. Here we provide evidence in support of the alternative hypothesis, i.e., taxa that, to date, have been consistently the most thermally susceptible possess an underappreciated capacity for adaptation to thermal stress [26]. Identification of genes that respond to thermal stress and are under selection, followed by studies to quantify changes in gene expression and gene frequency among coral populations are required to assess the likelihood that adaptation has driven the response seen in these populations [37]. Our study also highlights the critical importance of comparing rates of bleaching induced mortality within coral populations and spanning repeated bleaching episodes; indeed, such data are essential if we hope to assess the capacity of coral populations to adapt to rising temperatures. We cannot rule out the possibility that differences in irradiance [8], turbidity and thermal stress among locations also contributed to the spatial variation in the severity of bleaching in 2010. For example lower bleaching severity in Singapore may in part be explained by lower thermal stress and higher turbidity relative to the other sites – however, the differences in environmental stress do not explain the reversal in the hierarchy of susceptibility among taxa.

An adaptive response in certain taxa at a few locations does not mean that the global threat to reefs from climate change has lessened. There are likely to be limits to thermal adaptation and acclimatisation, and these may incur costs in life history traits such as growth, fecundity and competitive ability [20]. In addition, reefs continue to be threatened by numerous other factors including overfishing, pollution, disease, acidification, and severe storms [16]. The results of the present study do indicate however that the effects of bleaching will not be as uniform as anticipated [20] and fast-growing branching taxa such as Acropora and Pocillopora are likely to persist in some locations despite increases in the frequency of thermal stress events.
Materials and Methods Top
Coral bleaching and mortality response surveys

Surveys to assess the bleaching and mortality response were carried out on reefs at three locations: around Pulau Weh, northwest Sumatra, Indonesia (5°50′N, 95°20′E); southeast of Singapore (1°10′N, 103°50E); and at Tioman Island, off the east coast of Peninsular Malaysia (2°49′N, 104°08′E) (Figure 1). The marked contrast in hierarchy of taxa susceptibility was first noted during visits to the three locations during May, June and July 2010 (Figure 1). Subsequently, surveys of the bleaching and mortality responses (BMI) [12] of corals were carried out at 13 sites in Pulau Weh between 26 and 31 July 2010, four sites southeast of Singapore between 4 and 13 October 2010 and five sites at Tioman Island between 9 and 11 of October 2010. In relation to the time of the onset of the thermal anomaly, surveys were +21 weeks (Pulau Weh) and +25 weeks (Singapore and Tioman Island) after sea temperatures exceeded the climatological MMM. Depth at the survey sites ranged from 1 to 6 m. Two-metre radius survey plots were selected by swimming in a haphazardly chosen direction and for a random number of fin-kicks between 3 and 20. All colonies within the survey plot were included and this process was repeated for between 40 min and 2 h at each site. Each colony within the survey plot was identified to genus and bleaching status [11] was recorded as follows: 1, healthy = no bleaching; 2, moderately bleached = colony pale or less than 50% of surface area bleached; 3, severe = colony greater than 50% bleached; and 4, recently dead. An index of the susceptibility to the bleaching event for each taxon and location was calculated [12]. A bleaching and mortality index (BMI) based on the four coral status categories described above and was calculated as follows:

where c1 to c4 are the four coral status categories expressed as the proportion of colonies (%) surveyed arranged in order from normal (unbleached) to recently dead. The sum of the four categories is divided by 3 to produce an index that is on a scale from 0 to 100 [12]. A non-parametric Friedman test, followed by Dunn’s post-hoc multiple comparison test was carried out to compare BMI within taxa and among the three study locations. In addition, to compare the bleaching and mortality response between Pulau Weh in 2010 and previous major bleaching episodes, BMI data from Pulau Weh were compared with data from the GBR in 1998. The BMI of coral genera from the GBR during the 1998 bleaching event were calculated from data taken from Table 2 in Marshall and Baird [11].
Short-term thermal history of study sites

Historical records of the temperature regime used to develop climatologies and estimate thermal stress at each location were obtained using remotely sensed SST. These were measured by Advanced Very High Resolution Radiometer from the satellite platforms of the US National Oceanic and Atmospheric Administration. Weekly mean SSTs were obtained from the Pathfinder dataset [38] for the centroid of the pixel closest to each study site for a 4 km2 grid from 1985 [39] until 2008 and a 50 km2 grid from 2009 to 2010 [40]. Data from 1985 to 1996 were used to establish SST climatologies and the MMM temperatures for each location. DHW above MMM for each location between March and August in 1998 and 2010 were estimated by summing thermal anomalies (i.e. weeks where temperatures (°C) were greater than MMM) for the preceding twelve week period. Maximum DHW above MMM was the highest value that occurred during the bleaching event. The method used here differs from the most commonly used DHW method [22] where thermal anomalies only begin to accumulate at temperatures ≥1°C above MMM. Using that approach DHW values ≥4°C-weeks typically result in significant bleaching and DHW values ≥8°C-weeks result in widespread bleaching and significant mortality [40]. We found this approach to severely under-estimate thermal stress at our locations, for example, yielding maximum DHW of only 2.7°C-weeks in Pulau Weh in 2010 despite severe bleaching and mortality (Figures 1 & 2) (Table 2).
Long-term thermal history of study sites

Long-term thermal histories for each location were determined by examining monthly mean SST data for the 1° longitude–latitude squares that encompassed each study location (5°–6°N & 95°–96°E for Pulau Weh; 1°–2°N and 103°–104°E for Singapore; and 2°–3°N & 104°–105°E for Tioman Island). Data were obtained from HadISST1.1 (Met Office Hadley Centre for Climate Change Global Ocean Surface Temperature dataset; for 1951 to 2010 [41]_ENREF_26. SST variability was estimated from the standard deviation of the mean of all monthly mean SST values from January 1951 to December 2010. The long term SST trend (decadal warming rate) was estimated from the regression equation following removal of seasonality using seasonal decomposition (Minitab v. 16).
Acknowledgments Top

We are grateful to Rudolf Meier, Pete Mumby, Peter Todd, Richard Corlett and Morgan Pratchett for suggestions that greatly improved the manuscript. We also thank Toh Tai Chong, Tioman Dive Centre and Henry Singer at Banyan Tree Resorts for field support.
Author Contributions Top

Conceived and designed the experiments: JG AB JM AE. Performed the experiments: JG AB EM SC KY YAA LMC. Analyzed the data: JG AB JM AE. Wrote the paper: JG AB JM AE SC EM KY YAA LMC.
References Top

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Special thanks to Doug Fenner, posted on

Marine Ecology Progress Series: Ongoing global biodiversity loss and the need to move beyond protected areas: a review of the technical and practical shortcomings of protected areas on land and sea Camilo Mora1, 3,*, Peter F. Sale2
doi: 10.3354/meps09214 Published July 28, 2011
Contribution to the Theme Section ‘Biodiversity, ecosystems and coastal zone management’

1Department of Biology, Dalhousie University, Halifax, Nova Scotia B3H 4J1, Canada
2Institute for Water, Environment and Health, United Nations University, Port Carling, Ontario P0B 1J0, Canada
3Present address: Department of Geography, University of Hawaii, Honolulu, Hawaii 96822, USA

ABSTRACT: A leading strategy in international efforts to reverse ongoing losses in biodiversity is the use of protected areas. We use a broad range of data and a review of the literature to show that the effectiveness of existing, and the current pace of the establishment of new, protected areas will not be able to overcome current trends of loss of marine and terrestrial biodiversity. Despite local successes of well-designed and well-managed protected areas proving effective in stemming biodiversity loss, there are significant shortcomings in the usual process of implementation of protected areas that preclude relying on them as a global solution to this problem. The shortcomings include technical problems associated with large gaps in the coverage of critical ecological processes related to individual home ranges and propagule dispersal, and the overall failure of such areas to protect against the broad range of threats affecting ecosystems. Practical issues include budget constraints, conflicts with human development, and a growing human population that will increase not only the extent of anthropogenic stressors but the difficulty in successfully enforcing protected areas. While efforts towards improving and increasing the number and/or size of protected areas must continue, there is a clear and urgent need for the development of additional solutions for biodiversity loss, particularly ones that stabilize the size of the world’s human population and our ecological demands on biodiversity.

KEY WORDS: Land protected areas · Marine protected areas · Effectiveness · Conservation ·
Biodiversity loss · Human population · Human consumption

AFP: Ocean acidification may be worst in 300 million years: study & NYTImes Editorial: Changing the Chemistry of the Earth’s Oceans

(AFP) – 5 days ago March 1, 2012

WASHINGTON — High levels of pollution may be turning the planet’s oceans acidic at a faster rate than at any time in the past 300 million years, with unknown consequences for future sea life, researchers said Thursday.

The acidification may be worse than during four major mass extinctions in history when natural pulses of carbon from asteroid impacts and volcanic eruptions caused global temperatures to soar, said the study in the journal Science.

An international team of researchers from the United States, Britain, Spain, Germany and the Netherlands examined hundreds of paleoceanographic studies, including fossils wedged in seafloor sediment from millions of years ago.

They found only one time in history that came close to what scientists are seeing today in terms of ocean life die-off — a mysterious period known as the Paleocene-Eocene Thermal Maximum about 56 million years ago.

Though the reason for the carbon upsurge back then remains a source of debate, scientists believe that the doubling of harmful emissions drove up global temperatures by about six degrees Celsius and caused big losses of ocean life.

Oceans are particularly vulnerable because they soak up excess carbon dioxide from the air which turns the waters more acidic, a state that can kill corals, mollusks and other forms of reef and shell organisms.

“We know that life during past ocean acidification events was not wiped out — new species evolved to replace those that died off,” said lead author Barbel Honisch, a paleoceanographer at Columbia University’s Lamont-Doherty Earth Observatory.

“But if industrial carbon emissions continue at the current pace, we may lose organisms we care about — coral reefs, oysters, salmon.”

Honish and colleagues said the current rate of ocean acidification is at least 10 times faster than it was 56 million years ago.

“The geological record suggests that the current acidification is potentially unparalleled in at least the last 300 million years of Earth history, and raises the possibility that we are entering an unknown territory of marine ecosystem change,” said co-author Andy Ridgwell of Bristol University.

The UN Environment Program released a report in 2010 that warned carbon emissions from fossil fuels may bear a greater risk for the marine environment than previously thought.

Rising acidity levels have an impact on calcium-based lifeforms, ranging from tiny organisms called ptetropods that are the primary food source, to crabs, fish, lobsters and coral, it said.

The UN report called for cuts in human-made CO2 emissions to reduce acidification and support for further work to quantify the risk and identify species that could be most in peril.

Special thanks to Craig Quirolo.

New York Times

Changing the Chemistry of Earth’s Oceans
Published: March 9, 2012

The oceans have always served as a sink for carbon dioxide, but the burning of fossil fuels since the beginning of the industrial revolution, especially over the last 40 years, has given them more than they can safely absorb. The result is acidification – a change in the chemical balance that threatens the oceans’ web of life.

In earth’s history, there have been many episodes of acidification, mainly from prolonged volcanic eruptions. According to a new research review by paleoceanographers at Columbia University, published in Science, the oceans may be turning acid far faster than at any time in the past 300 million years.

Changing something as fundamental as the pH of seawater – a measurement of how acid or alkaline it is – has profound effects. Increased acidity attacks the shells of shellfish and the skeletal foundation of corals, dissolving the calcium carbonate they’re made of. Coral reefs are among the most diverse ecosystems on the planet. Ocean acidification threatens the corals and every other species that makes its living on the reefs.

The authors tried to determine which past acidification events offer the best comparison to what is happening now. The closest analogies are catastrophic events, often associated with intense volcanic activity resulting in major extinctions. The difference is that those events covered thousands of years. We have acidified the oceans in a matter of decades, with no signs that we have the political will to slow, much less halt, the process.

A version of this editorial appeared in print on March 10, 2012, on page A18 of the New York edition with the headline: Changing the Chemistry of Earth’s Oceans.

Special thanks to Richard Charter

UC Davis: Stinging and Seeing

View this story on the Web at

University of California, Davis
March 5, 2012

New research from the University of California shows how the ability
to detect light could have evolved before anything like an eye.

As published today (March 5) in the journal BMC Biology, the research
is based on the stinging mechanism in the tiny, brainless and eyeless
freshwater polyp Hydra magnipapillata. Part of a group of animals
called cnidarians that includes sea anemones, corals and jellyfish, a
hydra is essentially a mouth surrounded by tentacles armed with
stinging cells, or cnidocytes.

The researchers — David Plachetzki, now a postdoctoral researcher at
UC Davis, working with undergraduate Caitlin Fong and Professor Todd
Oakley in the Department of Ecology, Evolution and Marine Biology at
UC Santa Barbara — discovered a simple nervous system linking the
stinging cells and nerve cells that detect light using a process
similar to the human eye’s.

The nerve cells express a set of genes including opsin, a
light-sensitive pigment; cyclic nucleotide gated ion channels; and
arrestin. These components are basically the same as those in the
light-detecting pathway in animals with eyes, including people.

The hydra fire their stingers less in bright than in dim light, the
researchers found. When they blocked one of the pathway’s components,
the hydra acted as if they were in dim light and fired their stingers

Most of the hydra’s cnidarian relatives lack eyes. But all cnidarians
have cnidocyte stinging cells.

“This capacity for stinging cell regulation by light-sensitive
neurons could have predated the evolution of eyes in cnidarians,”
Plachetzki said. Future work will be aimed at how these findings
relate to the evolution of eyes in other groups of animals.

The National Science Foundation funded the work.

Media contact(s):
* David Plachetzki, Center for Population Biology,
* Andy Fell, UC Davis News Service, (530) 752-4533,

Special thanks to Craig Quirolo

NOAA Fisheries announces the release of the *2012 Deep Sea Coral Research and Technology Program Report to Congress (with focus on SE Florida)

This report highlights the exciting discovery of deep-sea coral habitats as well as progress made in our nationwide research.

* *

Featured in the report is an overview of the program’s first three-year field study, focused on the Southeast U.S., which revealed new and currently unprotected deep-sea coral communities off the eastern and southern coasts of Florida. These fragile habitats are home to a wide variety of species, many of which are commercially important. NOAA’s deep-water coral investigations have been instrumental in providing data and documentation on the distribution and ecological significance of these resources.

In addition to the discoveries off the southeastern U.S., scientists are exploring deep-sea coral and sponge habitats off the West Coast, documenting their importance for fish, and providing key information to fishery and National Marine Sanctuary managers.

The report is complemented by descriptions all the program’s activities on our website:

NOAA’s *Deep Sea Coral Research and Technology Program *provides scientific information needed to conserve and manage deep-sea coral habitats. We are committed to increasing the scientific understanding of these rich and valuable communities and making it available to ocean resource managers to inform conservation actions. The Program’s work is made possible through partnerships with other federal agencies, academic scientists and non-governmental organizations. I thank the many of you who have participated in making this a successful Program.

Tom Hourigan

Chief Scientist, Deep Sea Coral Research and Technology Program
Special thanks to:

Coral-List mailing list

Earthjustice, Center for Biological Diversity: Lawsuit Aims to Protect Endangered Caribbean Corals from Overfishing; Elkhorn and staghorn corals need parrotfish to survive

For Immediate Release: January 30, 2012


Andrea Treece, Earthjustice, (415) 217-2089

Miyoko Sakashita, Center for Biological Diversity, (415) 632-5308

Washington, D.C. – A lawsuit was filed today in federal district court seeking greater protections from fishing for threatened coral reefs in the Caribbean. The
lawsuit asserts that the National Marine Fisheries Service ignored science showing that parrotfish and other grazing fish play a key role in promoting the health of coral reefs; the government’s authorization of targeted fishing for parrotfish poses a risk to elkhorn and staghorn corals, protected under the Endangered Species Act.

“The Caribbean’s coral reefs are already in deep trouble, and reducing the parrotfish that help them stay healthy only makes matters worse,” said Miyoko Sakashita, oceans director at the Center for Biological Diversity. “If we don’t take steps now to safeguard the creatures that keep these vital reefs alive, we risk losing all of it.”

According to the lawsuit, the National Marine Fisheries Service violated the Endangered Species Act by finding that the targeted fishing for parrotfish would not jeopardize already imperiled corals or “adversely modify,” (i.e. damage) their critical habitat.

Excessive algal growth threatens the health of Caribbean reefs, choking out corals and degrading the habitat that other reef creatures-such as fish, sea turtles and lobsters-depend on. Fish, especially parrotfish, which graze on algae around coral reefs, play a key function in providing suitable habitat for corals to settle and build those reefs. Fish populations in the
Caribbean have been overfished, including the parrotfish that are the subject of this lawsuit; managing the overfishing of parrotfish will help corals recover and become more resilient to other threats, including global warming and ocean acidification.

“Restoring healthy populations of elkhorn and staghorn coral is critical to restoring the health of Caribbean reefs as a whole,” said Andrea Treece, an attorney with Earthjustice. “These corals provide shelter, nursery grounds, and hunting grounds for an incredible array of fish, lobsters, sea turtles and other species. Without better protection, we risk losing the entire reef community.”

“Corals are competing with algae, and without a robust population of parrotfish, the algae are going to win,” said Sakashita. “But wise management of our reefs can keep algae in check and promote both healthy corals and healthy fish.”

Elkhorn and staghorn corals were once the dominant reef-building corals in the Caribbean but they are perilously close to extinction. Corals suffer from a variety of threats, including pollution, global warming and ocean acidification. A key threat to corals, however, continues to be overfishing and competition with algae. The corals have declined by more than 90 percent
since the 1970s. In 2006, the two corals were protected under the Endangered Species Act in response to a petition by the Center for Biological Diversity.

Learn more:
* Parrotfish to aid reef repair
– BBC (video)
* Read the complaint.

Special thanks to Andrew Baker/ Coral-list ‘Other CO2 problem’ research shows that fish won’t be OK

Posted Sun, 11 Dec 2011 18:00:00 GMT by Colin Ricketts

It’s the ‘other CO2 problem’, global warming’s little brother, and ocean acidification could be even more damaging than had previously been thought according to new research on how fish are affected. As the amount of carbon dioxide in the atmosphere rises, more of it is dissolved into the sea, forming carbonic acid, making the sea more acidic.

While negative effects have been recorded for many simple marine creatures – coral reefs, shellfish, urchins and plankton for example – no research had shown that fish were damaged, until now.

Research published in Nature Climate Change by a team from Stony Brook University in New York dismisses the so-called ‘fish are OK’ theory.

According to the new research, the belief that fish were relatively unaffected by more acidic oceans ignored the effect of CO2 on fish larvae and even eggs.

Christopher Gobler and Hannes Baumann, both professors at the Stony Brook University School of Marine and Atmospheric Science (SoMAS) studied how higher concentrations of CO2 impacted on the eggs of the inland silverside – a common river estuary fish.

Gobler and Baumann examined levels of CO2 concentration which are predicted for later this century. At the moment the level is 400 parts per cubic metre (ppm3), which is expected to rise to 600ppm3 by the middle of the century and 1,000ppm3 by the 2200.

They found a terrible toll. Eggs and larvae of the inland silverside were very sensitive to rises in CO2 levels and at the levels predicted for the end of the century, CO2 was killing 70% of the fish within a week of their hatching. Those larvae that did survive were significantly smaller than under current conditions.

“We knew from the study of other ocean animals, such as scallops and clams, that earliest life stages such as larvae are most sensitive to CO2 and thus targeted the same life stage during our investigation of fish,” said Professor Gobler.

Brad Warren, Science Director of Sustainable Fisheries Partnerships warned of the possible damage to the fishing industry.

He said: “This study is a shot across the bow and shows that some important fish stocks may be eroded by high CO2 levels. And keep in mind, as estuarine fish, inland silversides are likely to be adapted to higher levels of CO2 than many fish found in the open ocean, where chemistry is much more stable. This suggests that many commercially harvested marine fish stocks may be vulnerable too. Pelagic spawners, such as albacore, bigeye, yellowfin, and bluefin tuna, whose larvae are not adapted to acidified waters, could be particularly vulnerable.”

The researchers now intend to carry out more research across a range of fish species.

Environmental Science & Technology: Connecting the Dots: Responses of Coastal Ecosystems to Changing Nutrient Concentrations

Jacob Carstensen,*,† María Sanchez-Camacho,‡ Carlos M. Duarte,‡,§ Dorte Krause-Jensen,† and Nuria Marba‡
†Department of Bioscience, Aarhus University, Frederiksborgvej 399, DK-4000 Roskilde, Denmark
‡Department of Global Change Research, IMEDEA (CSIC-UIB), Instituto Mediterraneo de Estudios Avanzados, Miquel Marques 21,
07190 Esporles (Illes Balears), Spain
§The UWA Oceans Institute, University of Western Australia, 35 Stirling Highway, Crawley 6009, Australia

ABSTRACT: Empirical relationships between phytoplankton biomass and nutrient concentrations established across a wide range of different ecosystems constitute fundamental quantitative tools for predicting effects of nutrient management plans. Nutrient management plans based on such relationships, mostly established over trends of increasing rather than decreasing nutrient concentrations, assume full reversibility of coastal eutrophication. Monitoring data from 28 ecosystems located in four well-studied regions were analyzed to study the generality of chlorophyll a versus nutrient relationships and their
applicability for ecosystem management. We demonstrate significant differences across regions as well as between specific coastal ecosystems within regions in the response of chlorophyll a to changing nitrogen concentrations. We also show that the chlorophyll a versus nitrogen relationships over time constitute convoluted trajectories rather than simple unique relationships. The ratio of
chlorophyll a to total nitrogen almost doubled over the last 3040 years across all regions. The uniformity of these trends, or shifting baselines, suggest they may result from large-scale changes, possibly associated with global climate change and increasing human stress on coastal ecosystems. Ecosystem management must, therefore, develop adaptation strategies to face shifting baselines and maintain ecosystem services at a sustainable level rather than striving to restore an ecosystem state of the past.

University of Florida: Beneficial bacteria can help keep Florida coral healthy, UF researchers report

Filed under Business, Economic Impact, Environment, Florida, Research on Tuesday, October 11, 2011.

GAINESVILLE, Fla. — Bacteria that could potentially help corals resist the devastating disease white pox have been found by researchers at the University of Florida and Mote Marine Laboratory.

The findings could help maintain the health of Florida’s coral reefs, which bring in billions of dollars to the state annually and are important for tourism, fisheries, shoreline protection and pharmaceutical research.

“Coral reefs are a major attraction for tourists in Florida,” said Max Teplitski, a microbiologist and an associate professor at UF’s Institute of Food and Agricultural Sciences. “They support the economies of South Florida, and they’re also important for fisheries and, in general, healthy ecosystems.”

“Unfortunately, in the past 20 years, corals have been degrading due to global environmental changes and direct human impacts, like overfishing and other pressures,” he said. “And also, diseases have been wiping out stressed corals in South Florida.”

White pox is caused by Serratia marcescens, a bacterium that commonly occurs in feces of animals and is capable of attacking a variety of animals and plants.

To combat white pox, Teplitski and a team of researchers began studying the interactions between the pathogen that causes the malady and other microorganisms that live on corals.

Their findings are detailed in a study Teplitski co-authored in this month’s issue of The ISME Journal: Multidisciplinary Journal of Microbial Ecology.

Corals are ancient creatures that recruit microorganisms such as bacteria to protect themselves from disease. Their characteristic structure is built by animals known as polyps.

In the study, the researchers screened several hundred bacteria isolated from coral and non-coral polyps for the ability to help ward off white pox.

The researchers found four bacteria that stopped white pox disease progression under controlled laboratory conditions and, to some degree, protected the polyps from getting sick.

They also noted that polyps containing the bacteria survived white pox infection, whereas those without the bacteria died.

Based on these results, scientists may begin checking individual polyps for the presence of beneficial bacteria before introducing them into a reef system as part of coral reef restoration.

Kim Ritchie, senior scientist and manager for the marine microbiology program at Mote Marine Laboratory in Sarasota, said Florida’s coral reefs are some of the sickest in the world.

“They seem to be in the worst shape,” said Ritchie, a co-author of the study. “But the more we can learn about the balance of beneficial bacteria and pathogenic bacteria, the easier it will be to help the coral reefs in the Keys become healthier.”

The research was funded by sales of Protect Our Reefs specialty license plates, a statewide program administered by Mote Marine Laboratory Inc.

Study authors also include Ali Alagely, a former UF undergraduate student, and Cory Krediet, a doctoral student in the interdisciplinary ecology program at UF’s School of Natural Resources and Environment.

The University of Florida is one of the nation’s largest public universities. A member of the Association of American Universities, UF received $619 million in sponsored research funding in 2010-11. Through its research and other activities, UF contributes more than $8.76 billion a year to Florida’s economy and is responsible for generating more than 100,000 jobs statewide. University of Florida Research; Working for Florida.

Robert H. Wells,, 352-273-3569
Max Teplitski,, 352-273-8189
Kim Ritchie,, 941-388-4441

Special thanks to Carolyn Baker Kitchener biologist studying effects of Gulf oil spill–kitchener-biologist-studying-effects-of-gulf-oil-spill

By Mirko Petricevic, Record staff

Galvez Kitchener native Fernando Galvez is an assistant professor in the biology department at Louisiana State University in Baton Rouge, LA.

A Kitchener biologist studying the effects of last year’s sprawling oil spill in the Gulf of Mexico isn’t worried about eating fish hauled from the contaminated region.
But he’s concerned the spill could starve future generations of wildlife in the area.

“I’m not a big seafood guy,” said Fernando Galvez, assistant professor of biological sciences at Louisiana State University in Baton Rouge, La. “(But) I would eat the fish in Louisiana.”

Galvez, a Kitchener native and graduate of the former St. Jerome’s high school, was part of a team of scientists whose research was published online Tuesday in Proceedings of the National Academy of Sciences, the journal for the National Academy of Sciences based in Washington, D.C.

While the team didn’t detect abnormally high levels of toxins in the fish they studied, Galvez observed a surprising amount of biological damage to the fish.

“I was surprised by the level of change,” Galvez said in a telephone interview Friday. “Especially during the height of exposure there was massive damage on the gills – very inflamed. Also, there was a lot of damage to the intestines.”

The worst offshore oil spill in U.S. history started April 20, 2010, after the Deepwater Horizon drilling rig exploded, killing 11 workers and eventually spewing 757 million litres of oil throughout the Gulf.

The disaster caused billions of dollars in damage to hundreds of kilometres of coastline.
Galvez started taking samples in various Louisiana marshes about 10 days after the spill began, but before the oil drifted into those areas. The sampling lasted for four months.
In some regions, the surface of the water was a colourful swirling mass of crude oil.
“It looked like the surface of Jupiter,” Galvez said.

Fish collected from those areas showed “no noticeable accumulation” of toxins, he said. But there were signs of biological damage triggered by the contamination, he said.
The fish’s bodies naturally metabolized the toxins, so there was no buildup. But their bodies were damaged as a result of the biological process that metabolizes the toxins, Galvez said.

He suspects small fish, as well as other species that live in the marshes, will suffer problems reproducing and that their numbers will be depleted in the long-term.
“I think the problem is in terms of population level collapses that may have effects on fisheries because of the fact that there’s less food,” he said.

He said he expects the damage will continue long-term because oil is still soaked in sediment and it’s not breaking down. Occasionally wind and waves stir up blobs of oil and work crews continue to clean up the mess.

It’s a process that can continue to contaminate wildlife for decades, he said.

The population levels of some species of fish and birds in Alaska are still depleted two decades after the 1989 Exxon Valdez oil spill, Galvez said.

Gilbert T. Rowe, a marine ecologist at Texas A&M University at Galveston, said examining the small fish, known as killifish, was a good choice because they are so abundant. “It’s like studying a mouse” to figure out effects on humans, he said.

Bernard Rees, a fish physiologist at the University of New Orleans, said the researchers had found an important link between oil contamination and possible physiological effects. He said the most troubling possibility for the long-term health of killifish was the chance that oil contamination harmed reproduction.

But Rees said that it was too early to know the long-term effects. “Nature has the capacity to rebound, so we’ll have to wait and see if there are any long lasting population effects.”

The research team’s article is available online at
Special thanks to Richard Charer

National Wildlife Federation: Alarming New Study Documents BP Oil’s Impact on Gulf Ecosystem “Genomic and physiological footprint of the Deepwater Horizon oil spill on resident marsh fishes”

Alarming New Study Documents BP Oil’s Impact on Gulf Ecosystem

Washington, DC (September 26, 2011) – A study published today in the Proceedings of the National Academy of Sciences documents the effect of BP oil on the Gulf killifish. The minnow-like wetlands resident, also known as bull minnow or cacahoe, is a critical part of the Gulf’s food chain and was chosen for study by a team of researchers because of its abundance and sensitivity to any effects of toxic pollution. The study finds that oil exposure has altered the killifish’s cellular function in ways that are known to be predictive of developmental abnormalities, decreased hatching success, and decreased embryo and larval survival.

Doug Inkley, senior scientist with the National Wildlife Federation, said today:

“This study is alarming because similar health effects seen in fish, sea otters, and harlequin ducks following the Exxon Valdez spill in Alaska were predictive of population impacts, from decline to outright collapse. While up to 210 million gallons of oil were involved in the Gulf oil disaster, the study is a reminder that even small amounts of oil can have a large and lasting impact on individual fish and wildlife. Wherever oil continues to be found in the Gulf, it should be removed if doing so won’t cause more environmental harm than good.

“The Gulf killifish provides us with a reminder that oil’s impacts on wildlife can’t be separated from its impacts on people. Not only are Gulf killifish a food source for sport fish like redfish and speckled trout, but killifish eat mosquitoes, helping to keep the pest population in check.

“The study is also a reminder that Congress has yet to act to protect the Gulf’s people and wildlife by passing comprehensive response legislation. Action is urgently needed, both to improve oil and gas drilling safety regulations so this doesn’t happen again, and to dedicate fines and penalties to Gulf Coast restoration.”

Learn more about the National Wildlife Federation’s response to the Gulf oil disaster at and visit the National Wildlife Federation Media Center at

Celebrating 75 years of inspiring Americans to protect wildlife for our children’s future.

Miles Grant
Online Communications Manager
National Wildlife Federation
202-797-6855 (office) – 703-864-9599 (cell)

Genomic and physiological footprint of the Deepwater Horizon oil spill on resident marsh fishes

by Andrew Whiteheada,1, Benjamin Dubanskya, Charlotte Bodiniera, Tzintzuni I. Garciab, Scott Milesc, Chet Pilleyd, Vandana Raghunathane, Jennifer L. Roacha, Nan Walkere, Ronald B. Walterb, Charles D. Ricef, and Fernando Galveza Departments of a Biological Sciences, c Environmental Sciences, and e Oceanography and Coastal Sciences, and d Coastal Studies Institute, Louisiana State University, Baton Rouge, LA 70803; b Department of Chemistry and Biochemistry, Texas State University, San Marcos, TX 78666; and f Department of Biological Sciences, Clemson University, Clemson, SC 29634

Edited by Paul G. Falkowski, Rutgers, The State University of New Jersey, New Brunswick, NJ, and approved September 1, 2011 (received for review June 13, 2011)

The biological consequences of the Deepwater Horizon oil spill are unknown, especially for resident organisms. Here, we report results from a field study tracking the effects of contaminating oil across space and time in resident killifish during the first 4 mo of the spill event. Remote sensing and analytical chemistry identified exposures, which were linked to effects in fish characterized by genome expression and associated gill immunohistochemistry, despite very low concentrations of hydrocarbons
remaining in water and tissues. Divergence in genome expression coincides with contaminating oil and is consistent with genome responses that are predictive of exposure to hydrocarbon-like chemicals and indicative of physiological and reproductive impairment.

Oil-contaminated waters are also associated with aberrant protein expression in gill tissues of larval and adult fish. These data suggest that heavily weathered crude oil from the spill imparts significant biological impacts in sensitive Louisiana marshes, some of which remain for over 2 mo following initial exposures.

ecological genomics | ecotoxicology | microarray | RNA-seq |vtoxicogenomics

Following the Deepwater Horizon (DWH) drilling disaster on
April 20, 2011, in the Gulf of Mexico, acute oiling and the
resulting mortality of marine wildlife were evident. In contrast,
the sublethal effects, critically important for predicting longterm
population-level impacts of oil pollution (1), have not
been well described following the DWH disaster. Here, we report
the results of a 4-mo field study monitoring the biological
effects of oil exposure on fish resident in Gulf of Mexico coastal
marsh habitats.
Gulf killifish (Fundulus grandis) were used as our model species
because they are among the most abundant vertebrate animals
in Gulf of Mexico-exposed marshes (2–4). Furthermore, the
Atlantic-distributed sister species to F. grandis (Fundulus heteroclitus)
has a narrow home range and high site fidelity, especially
during the summer (5, 6), and, among fishes, it is relatively
sensitive to the toxic effects of organic pollutants (7). Although
home range and toxicology studies are lacking for F. grandis, we
infer that F. grandis is also relatively sensitive to pollutants and
exhibits high site fidelity, such that the biology of this species is
likely affected primarily by the local environment, given the recent
shared ancestry of F. grandis with F. heteroclitus (8) and
similar physiology, life history, and habitat (9–13). We sampled
from populations resident in Gulf of Mexico-exposed marshes
before oil landfall (May 1–9, 2010), during the peak of oil
landfall (June 28–30, 2010), and after much of the surface oil was
no longer apparent 2 mo later (August 30–September 1, 2010) at
six field sites from Barataria Bay, Louisiana, east to Mobile Bay,
Alabama (Fig. 1 and Dataset S1).
Results and Discussion
Remote sensing and analytical chemistry were used to characterize
exposure to DWH oil, where remote sensing data are
spatially and temporally comprehensive but of low resolution
and chemistry data are of high resolution but patchy in space and
time. Ocean surface oil was remotely detected through the
analysis of images from synthetic aperture radar (SAR) (14).
Proximity of the nearest oil slick to each field site (e.g., Fig. S1)
was measured for each day that SAR data were available, from
May 11 through August 13, 2010, to approximate the location,
timing, and duration of coastal oiling (Fig. 1C). Although surface
oil came close to many of our field sites in mid-June, only the
Grande Terre (GT) site was directly oiled (Fig. 1 B and C).
Although the GT site had been clearly contaminated with crude
oil for several weeks before our sampling (Fig. 1C and Fig. S2)
and retained much oil in sediments (Dataset S2), only trace
concentrations of oil components were detected in subsurface
water samples collected from the GT site on June 28, 2010, and
tissues did not carry abnormally high burdens of oil constituents
at any site or time point (Dataset S2). Despite a low chemical
signal for oil in the water column and tissues at the time of
sampling, we detected significant biological effects associated
with the GT site postoil.
We sampled multiple tissues from adult Gulf killifish (average
weight of 3.5 g) from each of six field sites for each of three time
points [only the first two time points for the Mobile Bay (MB)
site] spanning the first 4 mo of the spill event (Fig. 1C). We
compared biological responses across time (before, at the peak,
and after oiling) and across space (oiled sites and sites not oiled)
and integrated responses at the molecular level using genome
expression profiling with complimentary protein expression and
tissue morphology. Genome expression profiles, using microarrays
and RNAseq, were characterized for livers because the
organ is internal and integrates xenobiotic effects from multiple
routes of entry (gill, intestine, and skin), and because liver is the
primary tissue for metabolism of toxic oil constituents. Tissue
morphology and expression of CYP1A protein, a common biomarker
for exposure to select polycyclic aromatic hydrocarbons
(PAHs), was characterized for gills, the organ that provides the
greatest surface area in direct contact with the surrounding
aquatic environment. In addition, we exposed developing
embryos to field-collected water samples to document bioavailability
and bioactivity of oil contaminants for this sensitive
early life stage.
Author contributions: A.W. and F.G. designed research; A.W., B.D., C.B., T.I.G., S.M., C.P.,
V.R., J.L.R., N.W., R.B.W. and F.G. performed research; C.D.R. contributed new reagents/
analytic tools; A.W., B.D., C.B., T.I.G., S.M., C.P., V.R., N.W., R.B.W. and F.G. analyzed data;
and A.W., B.D., C.B., and F.G. wrote the paper.
The authors declare no conflict of interest.
This article is a PNAS Direct Submission.
Data deposition: Microarray data have been deposited to ArrayExpress (accession no.
1To whom correspondence should be addressed. E-mail:
This article contains supporting information online at
1073/pnas.1109545108/-/DCSupplemental. PNAS Early Edition | 1 of 5
The oiling of the GT site at the end of June 2010 is associated
with a clear functional genomic footprint. Of the 3,296 genes
included in our analysis, expression of 1,600 and 1,257 genes
varied among field sites and throughout the time course, respectively
(P < 0.01) (Dataset S3). For the 646 genes that varied in expression only among sites (no significant time effect or siteby- time interaction), site variation followed a pattern of population isolation by distance, which is consistent with neutral evolutionary divergence (Fig. 2A) and population genetic expectations (15). Most importantly, 1,500 genes indicated a pattern of site-dependent time course expression (significant interaction, false discovery rate <0.01), where the trajectory of genome expression through time was divergent at the GT site compared with all other sites (Fig. 2 B and C), particularly at the second time point, which coincides with oil contamination (Fig. 1C). Previous studies have identified genes that are transcriptionally responsive to planar polychlorinated biphenyl (PCB) exposures in killifish (16). Planar PCBs, dioxins, and PAHs (the primary toxic constituents in crude oil) are all mechanistically related insofar as they exert biological effects, in whole or in part, through aryl-hydrocarbon receptor (AHR) signaling pathways; indeed, morpholino knockdown of the AHR is protective of the toxic effects of PAHs and PCBs in killifish (17), and exposures to PCBs and PAHs induce common genome expression responses in flounder (18). Of the genes that were transcriptionally responsive to PCB exposures (16), 380 were included in the current analysis. Expression of this subset of genes is predictive of transcriptional divergence in fish from the GT site coincident with oil contamination compared with other field sites (Fig. S3), especially for the top 10% of PCB-responsive genes (Fig. 2D). Transcriptional activation of these planar PCB-responsive genes in developing killifish embryos is predictive of induction of developmental abnormalities, decreased hatching success, and decreased embryonic and larval survival (16, 19). This set of genes includes members of the canonical battery of genes that are transcriptionally induced by ligand-activated AHR signaling, such as cytochrome P450s, cytochrome B5, and UDP-glucuronosyltransferase (Fig. 2F, set 1), for which increased transcription is particularly diagnostic of exposure to select hydrocarbons (20). Indeed, many genes that are transcriptionally induced or repressed by AHR activators (dioxins, PCBs, and PAHs) show induction or repression at the GT site coincident with crude oil contamination (Fig. 2F, set 1). An independent measure of genome expression, RNAseq, also indicates AHR activation in GT fish from June 28, 2010, compared with reference RNA (e.g., upregulation of cytochrome P450s, UDP-glucuronosyltransferase (UGT), and AHR itself; Fig. 2E). In parallel, up-regulation of CYP1A protein was detected in gills from GT fish sampled postoil and in early life-stage fish following controlled exposures to GT waters (Figs. 3 and 4). These data appear to be diagnostic of exposure to the toxic constituents in contaminating oil (PAHs) at a sufficient concentration and duration to induce biological responses in resident fish. Sustained activation of the CYP1A gene (Figs. 2F and 3) was predictive of persistent exposure to sublethal concentrations of crude oil components and negative population-level impacts in fish, sea otters, and harlequin ducks following the Exxon Valdez oil spill (reviewed in 1), although PAH toxicity may be mediated through AHR-independent pathways as well (21). Transcriptional responses in other sets of coexpressed genes offer insights into the potential biological consequences of contaminating oil exposure at the GT site. Several gene ontology (GO) categories were enriched in the subset of genes that showed GT-specific expression divergence coincident with siteand time-specific oil contamination (Dataset S4). GO enrichment indicates activation of the ubiquitin-proteasome system (Fig. 2F, set 2), which, among diverse functions, is important for cellular responses to stress, cell cycle regulation, regulation of DNA repair, apoptosis, and immune responses (22). The AHR protein itself plays a role as a unique ligand-dependent E3 ubiquitin ligase that targets sex steroid (estrogen and androgen) receptor proteins for proteasomal destruction, thereby impairing Fig. 1. Location of field study sites and incidence of oil contamination. (A) Location of field sampling sites, which include Grand Terre (GT), Bay St. Louis (BSL), Belle Fontaine Point (BFP), Bayou La Batre (BLB), Mobile Bay (MB), and Fort Morgan (FMA). Color coding is consistent with other figures. The red star indicates the DWH spill site. (B) Photograph (by A.W.) of the GT field site on June 28, 2010, showing contaminating oil and minnow traps in the marsh. (C) Proximity of nearest surface oil to each field site was determined by SAR, where rows are field sites and columns are days. Light gray represents no data, and black represents the nearest surface oil at a distance of >4 km; the increasing intensity of red indicates closer proximity of oil. Three field sampling trips are
highlighted (blue boxes). BSL; BFP; FMA.
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normal cellular responses to sex hormones in reproductive tissues,
and this response can be activated by planar PAHs (23).
Significant down-regulation of transcripts for egg envelope proteins
zona pellucida (ZP3 and ZP4) and choriogenin (ChgHm
and ChgH) that we detect at the GT site coincident with oil
exposure (Fig. 2F, set 1) may be linked to this AHR-dependent
proteolytic pathway because their transcription is estrogen-dependent
(24, 25) and is down-regulated by exposure to PAHs in
fish (25–27). In corroboration, RNAseq detects dramatically
down-regulated ZP, ChgH, and vitellogenin transcripts in GT
fish (Fig. 2E). Although the transcriptional response that we
detect is in male fish, these proteins are synthesized in male livers
(reviewed in 25, 27) and down-regulation is consistent with
antiestrogenic effects from exposure to PAHs (28). Possible
impacts on reproduction merit attention because water only
from the GT site induced CYP1A protein in the gills of developing
killifish (Fig. 3) at low concentrations of total aromatics
and alkanes (Dataset S2) and more than 2 mo after initial oiling,
indicating persistent bioavailability of PAHs. Marsh contamination
with DWH oil coincided with the spawning season for many
marsh animals, including killifish (29), and reproductive effects are
predictive of long-term population-level impacts from oil spills (1).
Controlled exposures of developing killifish to water collected
from GT on June 28 and August 30, 2010, induced CYP1A protein
expression in larval gills relative to fish exposed to GT water
preoil and exposed to Bayou La Batre (BLB) site water that was
not oiled (Fig. 3). This response is consistent with the location and
timing of oil contamination, and it indicates that the remaining oil
constituents dissolved at very low concentrations at GT after
landfall (Dataset S2) were bioavailable and bioactive to developing
fish. Although exposures to PAHs stereotypically induce
cardiovascular system abnormalities in developing fish at relatively
high concentrations (e.g., 21), none were observed in these
animals. However, even very low-concentration exposures during
development, insufficient to induce cardiovascular abnormalities
in embryos, can impair cardiac performance in adulthood (30).
The adult fish sampled in situ from the oil-contaminated GT site
showed divergent regulation of several genes involved in blood
vessel morphogenesis and heme metabolism coincident with oil
contamination (Fig. 2F, set 3). Multigeneration field studies are
necessary to confirm cardiovascular effects from DWH oil contamination
of marshes that coincided with spawning.
Fig. 3. CYP1A protein expression (dark red staining) in larval killifish gills
(24 d postfertilization) exposed to waters collected from GT (oiled) and BLB
(not oiled) during development. (Magnification 40×, scale bars = 10 μm.)
CYP1A expression is elevated in the lamellae of larvae exposed during development
to waters collected from GT postoil (trips 2 and 3) compared with
background levels of CYP1A expression in larvae exposed to GT water preoil
(trip 1), compared with CYP1A in fish exposed to waters collected from BLB
(which was not directly oiled), and compared with CYP1A in fish reared in
laboratory control water. Nuclei were stained using hematoxylin (blue).
Analytical chemistry of exposure waters is reported in Dataset S2.
Fig. 2. Genome expression between field sites and across time. Field sites include Grand Terre (GT), Bay St. Louis (BSL), Belle Fontaine Point (BFP), Bayou La
Batre (BLB), Mobile Bay (MB), and Fort Morgan (FMA). GT was the only site to be directly oiled, which occurred between the first and second sampling times
(Fig. 1 and Dataset S2). (A) For genes that vary only among sites (no expression change with time or interaction), pairwise site-specific transcriptome divergence
along principal component (PC) 1, as a function of pairwise geographical distance, shows a pattern consistent with isolation by distance. (B) Trajectory
of genome expression responses through time for each of six field sites from the preoil sample time (dot at base of arrow) through the peak-oil sample
time (middle dot), to the latest postevent sample time (dot at head of arrow) following PC analysis of genes showing statistically significant main effects (site
and time) and interaction terms. (C) Divergence along PC1 is isolated, where bars for each site from left to right represent sampling times from the earliest to
the latest. (D) Expression divergence along PC1 for the subset of genes that is dose-responsive to PCB exposure (top 10% of PCB-responsive genes). (E) RNAseq
data showing genes up- and down-regulated (x axis positive and negative, respectively) in fish from GT sample time 2 (coincident with oil) compared with
reference RNA, where select genes are identified. (Inset) Genes are dramatically down-regulated at GT (detailed RNAseq data are presented in Dataset S5). (F)
Expression levels for specific genes (rows) and treatments (columns), where cell color indicates up-regulation (yellow) or down-regulation (blue) scaled
according to site-specific expression level at the preoil sample time, for genes with divergent expression at the GT site. Genes are grouped into functional
categories, and scale bars indicate N-fold up- or down-regulation.
Whitehead et al. PNAS Early Edition | 3 of 5
Coastal salt marsh habitats are dynamic and stressful, where
changes in environmental parameters, such as temperature,
hypoxia, and salinity, can continuously challenge resident wildlife.
Regulation of ion transport in fish is particularly important
for facilitating homeostasis in response to the salinity fluctuations
that are common in estuaries. We found altered regulation
of multiple ion transport genes in fish from the GT site coincident
with oil contamination (Fig. 2F, set 4). For example, Vtype
proton ATPases are up-regulated and Na+,K+-ATPase
subunits and tight-junction proteins are down-regulated, coincident
with oiling at the GT site, in the absence of substantial
changes in environmental salinity (Dataset S2). Other genes
important for osmotic regulation in killifish (31) are also divergently
down-regulated at the GT site, including type II
iodothyronine deiodinase (DIO2), transcription factor jun-B
(JUNB), and arginase 2 (ARG2). In corroboration, RNAseq
data show down-regulation of DIO2, JUNB, and ARG2 in GT
fish compared with reference fish (Fig. 2E). Although the physiological
consequences of oil exposures are typically studied in
isolation, it is reasonable to predict that exposure to oil may
compromise the ability of resident organisms to adjust physiologically
to natural stressors.
Induction of CYP1A protein expression is a hallmark of AHR
signaling pathway activation, making it a sensitive biomarker of
exposure to select planar PAHs and other hydrocarbons (20).
Although the liver is the key organ for CYP1A-mediated metabolism
of these substrates, gill tissues represent the most
proximate site of exposure to PAHs. As a result of direct contact
with the environment and the nature of the gill as a transport
epithelium, the gill may be a more sensitive indicator of exposure
to contaminants than the liver (32). CYP1A protein was markedly
elevated in GT fish postoil compared with GT fish preoil
and compared with fish from other field sites that were not directly
oiled (Fig. 4). CYP1A induction was localized predominantly
to pillar cells of the gill lamellae and within
undifferentiated cells underlying the interlamellar region, which
may have contributed to the filamental and lamellar hyperplasia
observed during trips 2 and 3, as well as the gross proliferation of
the interlamellar region observed during trip 2 in GT fish (Fig.
4). These effects imply a decrease in the effective surface area of
the gill, a tissue that supports critical physiological functions,
such as ion homeostasis, respiratory gas exchange, systemic acidbase
regulation, and nitrogenous waste excretion (33). Currently,
the degree to which oil-induced effects may interact with commonly
encountered challenges, such as fluctuations in hypoxia
and salinity, to compromise physiological resilience is unclear.
By integrating remote sensing and in situ chemical measures of
exposure, and linking these with integrated measures of biological
effect (genome expression and tissue morphology), we
provide evidence that links biological impacts with exposure to
contaminating oil from the DWH spill within coastal marsh
habitats. Although body burdens of toxins are not high, consistent
with reports indicating that seafood from the Gulf of Mexico
is safe for consumption (34), this does not mean that negative
biological impacts are absent. Our data reveal biologically relevant
sublethal exposures causing alterations in genome expression and
tissue morphology suggestive of physiological impairment persisting
for over 2 mo after initial exposures. Sublethal effects were
predictive of deleterious population-level impacts that persisted
over long periods of time in aquatic species following the Exxon
Valdez spill (1) and must be a focus of long-term research in
the Gulf of Mexico, especially because high concentrations of
hydrocarbons in sediments (Dataset S2) may provide a persistent
source of exposures to organisms resident in Louisiana marshes.
The locations (latitude and longitude) of our field sampling sites and dates for
sampling at each site are summarized in Dataset S1. Gulf killifish (F. grandis)
were caught by minnow trap, and tissues were excised immediately. Liver
was preserved in RNAlater (Ambion, Inc.) for genome expression (microarray
and RNAseq) analysis. Gill tissues were fixed in situ in buffered zinc-based
formalin Z-Fix (Anatech LTD). Succinct methods follow, and more detailed
methods are available online.
Satellite imagery (SAR) was analyzed to provide estimation of the timing,
location, and duration of coastal oil contamination. The calculated distance
from each field sampling site to the nearest oil slick was calculated from the
“straight-line” distance from the global positioning system position of the
station (Dataset S1) to that of the observed oil across any and all intervening
geographical barriers (e.g., Fig. S1).
Fig. 4. CYP1A protein expression in adult killifish gills (dark red staining)
sampled in situ from all sampling times (columns) and locations (rows).
Locations include Grand Terre (GT), Bay St. Louis (BSL), Belle Fontaine Point
(BFP), Bayou La Batre (BLB), Mobile Bay (MB), and Fort Morgan (FMA).
(Magnification 40×, scale bars = 10 μm.) The MB site was only sampled on
trips 1 and 2, and gills from trip 1 at the BLB site were not available for
processing. Fish gills from the GT site during trips 2 and 3 showed high CYP1A
expression and an elevated incidence of hyperplasia of the lamellae and
interlamellar space on the gill filaments coincident with oil contamination.
CYP1A protein was elevated at the GT site postoil (trips 2 and 3) compared
with GT preoil (trip 1) as well as with other field sites, none of which were
directly oiled. Nuclei were stained using hematoxylin (blue). Exact site locations
and sampling dates are reported in Dataset S1.
4 of 5 | Whitehead et al.
Analytical chemistry of water, tissue, and sediment samples was performed
to offer detailed characterization of exposure to contaminating oil (data
reported in Dataset S2). Sample dates and locations are summarized in
Dataset S1. All sample extracts were analyzed using GC interfaced to an MS
detector system. Spectral data were processed by Chemstation Software
(Agilent Technologies), and analyte concentrations were calculated based
on the internal standard method.
Genome expression across sites and time was characterized using custom
oligonucleotide microarrays. Genome expression was measured in liver tissues
from five replicate individual male fish per site-time treatment (5 biological
replicates) hybridized in a loop design, including a dye swap. Data
were lowess-normalized and then mixed model-normalized using linear
mixed models to account for fixed (dye) effects and random (array) effects.
Normalized data were then analyzed using mixed model ANOVA, with
“site” [Grand Terre (GT), Bay St. Louis (BSL), Belle Fontaine Point (BFP),
Bayou La Batre (BLB), Mobile Bay (MB), and Fort Morgan (FMA)] and
“sampling time” (sampling trips 1, 2, and 3) (Dataset S1) as main effects,
including an interaction (site-by-time) term. The false discovery rate was
estimated using Q-value (35). Principal components analysis was performed
using MeV (36). GO enrichment was tested using DAVID (37).
For RNAseq, transcript abundance was compared between liver mRNA
from three replicate fish (RNA was not pooled) from the GT site from June 28,
2010, and mRNA from two control samples. All RNA samples were sequenced
on the Illumina Gene Analyzer platform (Expression Analysis, Inc.). Following
quality control filtering, quantitative transcript abundance analysis was
performed by mapping sequence reads to target sequences (6,810 unique F.
heteroclitus target EST sequences, Dataset S5) using the Bowtie short read
alignment software (38). A custom Perl script determined the number of
fragments mapped to each target sequence. The Bioconductor package
DESeq (version 2.8) (39) was used to determine the statistical significance of
each differentially expressed target using a negative binomial method with
P values adjusted by the Benjamini–Hochberg procedure.
Gill tissues were sampled from all field sites for morphological analysis and
immunohistochemical analysis of CYP1A protein expression. Gill tissues from
the first and second gill arches were sectioned along the longitudinal axis at
a thickness of 4 μm and probed with mAb C10-7 against fish CYP1A (40).
Sections were counterprobed using the Vectastain ABC immunoperoxidase
system (Vector Laboratories), utilizing the ImmPACT Nova RED peroxidase
substrate kit (Vector Laboratories) to visualize the CYP1A protein in red.
Tissue sections were counterstained with Vector Hematoxylin QS (Vector
F. grandis embryos obtained from parents not exposed to oil (collected
from Cocodrie, LA) were exposed to water samples from the GT and BLB
sites collected subsurface on the dates indicated in Dataset S1. Following
fertilization, 20 embryos were randomly transferred in triplicate to one of
the six field-collected waters (2 field sites × 3 time points) at 3 h postfertilization.
Embryos were also exposed to a laboratory control consisting
of artificial 17 parts per thousand (ppt) water. Larvae were sampled at 24
d postfertilization and fixed in Z-Fix solution. Sectioning and staining were
as described in the previous section.
ACKNOWLEDGMENTS. K. Carman helped facilitate early field studies. The
authors thank R. Brennan, D. Roberts, E. McCulloch, Y. Meng, A. Rivera,
C. Elkins, H. Graber, R. Turner, D. Crawford, and M. Oleksiak, for technical
assistance. Funding was from the National Science Foundation (Grants DEB-
1048206 and DEB-1120512 to A.W., Grant EF-0723771 to A.W. and F.G., and
Grant DEB-1048241 to R.B.W.), the National Institutes of Health (R15-
ES016905-01 to C.D.R.), and the Gulf of Mexico Research Initiative (A.W.,
F.G., and N.W.).
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Whitehead et al. PNAS Early Edition | 5 of 5
Supporting Information
Whitehead et al. 10.1073/pnas.1109545108
SI Methods
The locations (latitude and longitude) of our field sampling sites
and dates for sampling at each site are summarized in Dataset S1.
Gulf killifish (Fundulus grandis) were caught by minnow trap, and
tissues were excised immediately. Liver was preserved in RNAlater
(Ambion, Inc.) for genome expression (microarray and
RNAseq) analysis. Gill tissues were fixed in situ in buffered zincbased
formalin Z-Fix (Anatech LTD).
Satellite Imagery. Satellite imagery was analyzed to provide
a coarse but spatially and temporally comprehensive estimation of
the timing, location, and duration of coastal oil contamination.
Surface oil from the DWH oil spill was detected through the
analysis of SAR images, which offer the most effective means of
detecting oil remotely. This active radar system operates over
large spatial scales in all weather and at all times of day (1, 2). Oil
dampens the ocean’s smallest capillary waves (3–5 cm in length),
yielding black regions in the image attributable to the total lack
of microwave backscatter from the sea surface to the sensor,
compared with higher backscatter from surrounding regions with
waves (Fig. S1). False-positive results are possible from areas
with low wind (<3 m/s) and from algal blooms; thus, the use of another satellite sensor or “sea truth” (e.g., wind measurements) is advisable for confirmation of the SAR signal. Only SAR images with distinct signatures, unrelated to these potential artifacts, were used in this study, although even thin oil sheens would potentially yield a dark return because SAR data yield no information about oil thickness. We used SAR measurements from multiple satellites (TerraSARX; ERS-2; CosmoSkymed-1, -2, and -3; Radarsat-1 and -2; Palsar; and Envisat-2). Data were received and processed in real time at the University of Miami Center for Southeastern Tropical Advanced Remote Sensing (CSTARS) laboratory and were further processed at the Louisiana State University Earth Scan Laboratory. The calculated distance from each field sampling site to the nearest oil slick was calculated from the “straight-line” distance from the global positioning system position of the station (Dataset S1) to that of the observed oil across any and all intervening geographical barriers (e.g., Fig. S1). Therefore, calculated distances do not necessarily represent the overall distance oil would have traveled to reach a sample station, although as the calculated distance approaches zero, these two distances (straight line vs. travel distance) become extensionally equivalent. Analytical Chemistry. Analytical chemistry of water, tissue, and sediment samples was performed to offer detailed characterization of exposure to contaminating oil (data reported in Dataset S2). Sample dates and locations are summarized in Dataset S1. Two liters of water was collected subsurface in 1-L amber-glass jars from each sample site and date, and it was kept at 4 °C until extraction, which was performed within 1 wk of collection. Tissues (whole fish) were collected from each of the field sites from the second (June 2010) and third (August 2010) sampling time points and frozen at −20 °C until extraction. Sediment was collected from each of the field sites after the final sampling time point (September 2010) in 8-oz glass jars and frozen at −20 °C until extraction. The sediment extraction procedure is as follows. Approximately 30 g of sediment/soil was accurately weighed (to the nearest 0.01 g) into a precleaned 500-mL beaker. The material was homogenized with anhydrous sodium sulfate sample until a “dry” sand-like matrix was created. One milliliter of surrogate standard was spiked into the sample, followed by the addition of 100 mL of pesticide-grade dichloromethane (DCM). The sample mixture was sonicated (60% intensity) for ∼10 min and allowed to settle for 15 min. The solvent was poured over a sodium sulfate funnel to remove any water and drained into 500-mL flat-bottomed flasks. The extraction process was repeated two more times, followed by rinsing the funnel with 25 mL of DCM. The flask was placed on a Buchi evaporative system and reduced to a final volume of 5–10 mL of DCM. The DCM concentrate was pipetted from the flask, placed into a 10- mL microextraction thimble, and reduced to a final volume of 1 mL using a nitrogen blow-down system. The 1-mL extract was transferred to a 2-mL autosampler vial and spiked with 10 μL of internal standard solution. Autosampler vials were stored at 4 °C until ready for analysis. The water extraction procedure is as follows. Approximately 1,000 mL of water was accurately weighed (to the nearest 1.0 mL) into a precleaned 20,000-mL separatory funnel. One milliliter of surrogate standard was spiked into the sample, followed by the addition of 100 mL of pesticide-grade DCM. The sample mixture was hand-shaken for ∼10 min and allowed to settle for 15 min. The solvent in the bottom of the funnel was drained through a sodium sulfate funnel to remove any water and drained into a 500-mL flat-bottomed flask. The extraction process was repeated two more times, followed by rinsing the funnel with 25 mL of DCM. The flask was placed on a Buchi evaporative system and reduced to a final volume of 5–10 mL of DCM. The DCM concentrate was pipetted from the flask, placed into a 10-mL microextraction thimble, and reduced to a final volume of 1 mL using a nitrogen blow-down system. The 1-mL extract was transferred to a 2-mL autosampler vial and spiked with 10 μL of internal standard solution. Autosampler vials were stored at 4 °C until ready for analysis. The tissue extraction procedure is as follows. Approximately 5– 10 g of tissue was accurately weighed to the nearest 0.01 g into a precleaned 500-mL beaker. The material was homogenized with anhydrous sodium sulfate sample until a dry sand-like matrix was created. One milliliter of surrogate standard was spiked into the sample, followed by the addition of 50 mL of pesticidegrade DCM. The sample mixture was sonicated (60% intensity) for ∼10 min and allowed to settle for 15 min. The solvent was poured over a sodium sulfate funnel to remove any water and drained into a 250-mL flat-bottomed flask. The extraction process was repeated two more times, followed by rinsing the funnel with 25 mL of DCM. The flask was placed on a Buchi evaporative system and reduced to a final volume of 3–5 mL of DCM. The DCM extract was exchanged to hexane with ∼25 mL of pesticide-grade hexane. The flask was returned to the evaporation system and evaporated down to a final volume of 2–5 mL of hexane. The sample was fractionated on an alumina/silica gel column by placing the 2- to 5-mL hexane aliquot on the aluminum/ silica gel column, which was then rinsed with high-purity hexane. The flow of hexane was stopped before exposing the silica gel to air. This fraction, which contained alkanes, was collected in a graduated thimble. The alumina/silica gel column was then rinsed with 50% DCM and 50% hexane. The solvents were allowed to elute completely in a separate extraction thimble. This fraction contained the PAHs. The alkane and PAH fractions were combined and concentrated to 1.0 mL under a gentle stream of nitrogen and stored in a 2-mL autosampler vial (4 °C) until GC/MS analysis. All sample extracts were analyzed using an Agilent 7890A Gas Chromatography system (Agilent Technologies, Inc.) config- Whitehead et al. 1 of 4 ured with a 5% diphenyl/95% (vol/vol) dimethyl polysiloxane high-resolution capillary column (30 m, 0.25-mm inner diameter, 0.25-μm film) directly interfaced to an Agilent 5975 inert XL MS detector system (Agilent Technologies, Inc.). An Agilent 7638B series Auto Injector (Agilent Technologies, Inc.) was used for sample introduction into the GC/MS system. The GC flow rates were optimized to provide a required degree of separation, which includes near-baseline resolution of n-C17 and pristine, and baseline resolution of n-C18 and phytane. The injection temperature was set at 250 °C, and only high-temperature and low-thermal bleed septa were used in the GC inlet. GC was performed in the temperature program mode with an initial column temperature of 55 °C for 3 min, which was then increased to 280 °C at a rate of 5 °C/min and held for 3 min. The oven was then heated from 280 °C to 300 °C at a rate of 1.5 °C/min and held at 300 °C for 2 min. Total run time was 66.33 min per sample. The interface to the MS was maintained at 280 °C. Ultra-high-purity helium was the carry gas for the GC/MS system. Spectral data were processed by Chemstation Software (Agilent Technologies, Inc.). Analyte concentrations were calculated based on the internal standard method. Therefore, an internal standard mixture composed of naphthalene-d8, acenaphthened10, chrysene-dl2, and perylene-dl2 (usually at a concentration of 10 ng/μL) was spiked into the sample extracts just before analysis. The concentration of specific target oil analytes was determined by a five-point calibration and internal standard method. Standards containing parent (nonalkylated) hydrocarbons were used in the calibration curve. Alkylated homologs were quantified using the response factor of the parent, and were therefore semiquantitative. This was the standard procedure, because alkylated standards were not available. Genome Expression: Microarrays. Genome expression across sites and time was characterized using custom oligonucleotide microarrays. Genome expression was measured in liver tissues from five replicate individual male fish per site-time treatment (5 biological replicates). Male fish were chosen for genome expression analysis because sampling was conducted during spawning season, when female reproductive condition (and associated liver genome expression) can be highly variable. Microarray probes (60-mer) were designed from contigs constructed from F. heteroclitus-expressed sequence tags. F. heteroclitus is the Atlantic coast-distributed sister species of Gulf coastdistributed F. grandis (3). Microarrays included probes for 6,800 unique EST sequences, each printed in duplicate on 15,000 element custom Agilent microarrays (design ID no. 027999) (Agilent Technologies, Inc.). Total RNA was extracted using TRIzol reagent, antisense RNA (aRNA) prepared using the amino allyl aRNA amplification kit (Ambion, Inc.), and purified aRNA coupled to Alexa Fluor dyes (Alexa Fluor 555 and 647; Molecular Probes, Inc.), and it was hybridized to custom microarrays for 18 h at 60 °C in a balanced loop design. Microarray images were captured using a Packard Bioscience ScanArray Express (PerkinElmer, Inc.) microarray scanner, and images were processed using Imagene (Biodiscovery, Inc.). Spots that were too bright (saturated) or too faint (below 2 SDs above background intensity) were excluded from normalization, resulting in a final set of 3,296 probes included for normalization and statistical analysis (Dataset S3). Data were lowess-normalized and then mixed model-normalized using linear mixed models to account for fixed (dye) effects and random (array) effects. Normalized data were then analyzed using mixed model ANOVA, with “site” [Grand Terre (GT), Bay St. Louis (BSL), Belle Fontaine Point (BFP), Bayou La Batre (BLB), Mobile Bay (MB), and Fort Morgan (FMA)] and “sampling time” (sampling trips 1, 2, and 3) (Dataset S1) as main effects, including an interaction (site-bytime) term. “Dye” was considered a fixed effect, and “array” and “replicate individual within site-time treatment” (n = 5) were treated as random effects. The false discovery rate was estimated using Q-value (4). Principal components analysis was performed using MeV (5). GO enrichment was tested using DAVID (6). Genome Expression: RNAseq. Transcript abundance was compared between liver mRNA from three replicate fish (RNA was not pooled) from the GT site from June 28, 2010, and mRNA from two control samples. The two control samples are composed of pooled liver mRNA from six and eight individuals, respectively, collected in April 2008. The individuals for one control sample were collected (2 each) from three sites west of the Mississippi river, including Port Aransas, Texas; Cocodrie, Louisiana; and LeeVille, Louisiana. The individuals for the second control sample were collected (2 each) from four sites west of the Mississippi River, including Dauphin Island, Alabama; Weeks Bay, Alabama; Santa Rosa Island, Florida; and St. Teresa, Florida. All RNA samples were sequenced on the Illumina Gene Analyzer platform (Expression Analysis, Inc.), and the resulting short-read data were summarized in fastq format. Short reads with more than two uncalled bases were removed. Each read was cut whenever a position fell below a minimum quality score of 10 or if the average of the qualities of a position and its two neighbors fell below 20, and the largest remaining fragment was used. Quantitative transcript abundance analysis was initiated by mapping filtered short reads to target sequences (6,810 unique F. heteroclitus target EST sequences, Dataset S5) using the Bowtie short read alignment software (7). A custom Perl script determined the number of fragments mapped to each target sequence. The Bioconductor package DESeq (version 2.8) (8) was then used to determine statistical significance of each differentially expressed target using a negative binomial method with P values adjusted by the Benjamini–Hochberg procedure. The three GT site samples were identified as a single “Exposed” class to DESeq, and the two pooled samples were identified as a single “Control” class. Gill Morphology and Protein Expression: Field Study. Male and female fish were sampled from all field sites for analysis of CYP1A protein expression in the gills. Tissues were fixed immediately in ZFix, stored on ice, and held at room temperature before further processing. Gill tissues from at least three fish per site per sampling time were dehydrated in ascending grades of histology-grade ethanol. Tissues were then transferred to a t-butanol bath before clearing in Histochoice Clearing Agent (Amersco) and embedding in Paraplast (Sigma). Tissues were cut along the longitudinal axis at a thickness of 4 μmusing an American Optical 820 microtome and transferred onto poly-L-lysine–coated microscope slides. After rehydration, tissues were processed for antigen retrieval by microwave in Tris-buffered saline (pH 9.0) and blocked. Tissues were then probed with mAb C10-7 against fish CYP1A (9). Sections were counterprobed using the Vectastain ABC immunoperoxidase system (Vector Laboratories), utilizing the ImmPACT Nova RED peroxidase substrate kit (Vector Laboratories) to visualize the CYP1A protein in red. Tissue sections were counterstained with Vector Hematoxylin QS (Vector Laboratories). Slides were then observed with a Leica DM RXA2 microscope (Leica Microsystems), and images were captured with a Spot Insight 4 megapixel camera (Diagnostic Instruments). Representative images were captured at a magnification of 40×. Early Life-Stage Experiments. Approximately 20 L of water was collected (in coordination with collection of water for analytical chemistry; Dataset S2) subsurface from field sites on the dates indicated in Dataset S1. Water was stored in airtight stainlesssteel soda kegs and kept at 4 °C until experiments were conducted. Water samples from GT and BLB were utilized in laboratory exposures of F. grandis embryos obtained by in vitro Whitehead et al. 2 of 4 fertilization using ova and spermatozoa collected from a brood stock of unexposed adult F. grandis derived from Cocodrie, Lousiana before oiling. Cocodrie parental stock fish were maintained at Louisiana State University, where they were held in the aquatics facility at the Department of Biological Sciences in 400-L tanks maintained at 17 parts per thousand (ppt) water (Instant Ocean) under recirculating conditions. Following fertilization, 20 embryos were randomly transferred in triplicate to one of the six field-collected waters (2 field sites × 3 time points) at 3 h postfertilization. Embryos were also exposed to a laboratory control consisting of artificial 17 ppt water. Larvae at 24 d postfertilization were sampled and fixed in Z-Fix solution. After fixation, tissues were prepared, sectioned, and stained with the mAb C10-7, as described in the previous section. 1. Brekke C, Solberg AHS (2005) Oil spill detection by satellite remote sensing. Remote Sensing of Environment 95:1e13. 2. Fingas MF, Brown CE (1997) Review of oil spill remote sensing. Spill Science and Technology Bulletin 4:199e208. 3. Whitehead A (2010) The evolutionary radiation of diverse osmotolerant physiologies in killifish (Fundulus sp.). Evolution 64:2070e2085. 4. Storey JD, Tibshirani R (2003) Statistical significance for genomewide studies. Proc Natl Acad Sci USA 100:9440e9445. 5. Saeed AI, et al. (2006) TM4 microarray software suite. Methods Enzymol 411:134e193. 6. Huang W, Sherman BT, Lempicki RA (2009) Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc 4:44e57. 7. Langmead B, Trapnell C, Pop M, Salzberg SL (2009) Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10:R25. 8. Anders S, Huber W (2010) Differential expression analysis for sequence count data. Genome Biol 11:R106. 9. Rice CD, Schlenk D, Ainsworth J, Goksoyr A (1998) Cross-reactivity of monoclonal antibodies against peptide 277-294 of rainbow trout CYP1A1 with hepatic CYP1A among fish. Mar Environ Res 46:87e91. Fig. S1. Representative measurements of the distance from field sites to ocean surface oil according to the CosmoSkymed2 SAR image captured May 13, 2010, at 11:56 UTC (Coordinated Universal Time). Field sites include Grand Terre (GT), Bay St. Louis (BSL), Belle Fontaine Point (BFP), Bayou La Batre (BLB), and Fort Morgan (FMA). Fig. S2. Oil contaminating the marsh at the GT field site on June 16, 2010 (photograph by B.D.). Whitehead et al. 3 of 4 Dataset S1. Sites, precise locations, and sampling dates for three field sampling trips Dataset S1 Dataset S2. Analytical chemistry of subsurface water samples, tissue samples (whole fish), and sediment samples Dataset S2 Fig. S3. Expression divergence along principal component 1 (PC1) across consecutive sampling times for the subset of 380 genes that was dose-responsive to PCB exposure in a study by Whitehead et al. (1). Field sites include Grand Terre (GT), Bay St. Louis (BSL), Belle Fontaine Point (BFP), Bayou La Batre (BLB), and Fort Morgan (FMA). Dataset S3. Genome expression microarray data: All probes included in the analysis, including the target EST sequence, probe sequence, annotation, average expression within each treatment (average of n = 5 replicate samples within each site-by-time treatment), and results from statistical analyses Dataset S3 Dataset S4. Results of GO enrichment analysis using DAVID for the subset of genes that were divergently expressed at the GT site coincident with oil contamination Dataset S4 Dataset S5. Genome expression RNAseq data: All gene targets included in the analysis, including the target EST sequence, annotation, fold difference in transcript abundance between the average of three replicate fish from GT sample time 2 (June 28, 2010) and two replicate reference RNA pools, and adjusted P values Dataset S5 1. Whitehead A, Pilcher W, Champlin D, Nacci D (2011) Common mechanism underlies repeated evolution of extreme pollution tolerance. Proc R Soc B, 10.1098/rspb.2011.0847. Whitehead et al. 4 of 4

ScienceNOW: Human Excrement to Blame for Coral Decline

Reef Relief Founder Craig Quirolo first observed white pox disease and alerted Dr. Porter to it; Reef Relief worked for years to encourage the City of Key West to adopt advanced wastewater treatment, despite a sea of denial. So glad we succeeded! DV

by Gisela Telis on 17 August 2011, 5:00 PM

Coral killer. Bacteria found in human excrement cause white pox disease, which bares coral skeletons and kills their tissue.
Credit: James W. Porter/University of Georgia

Coral reef ecologists have laid a persistent and troubling puzzle to rest. The elkhorn coral, named for its resemblance to elk antlers and known for providing valuable marine habitat, was once the Caribbean’s most abundant reef builder. But the “redwood of the coral forest” has declined 90% over the past decade, in part due to highly contagious white pox disease, which causes large lesions that bare the coral’s white skeleton and kill its tissue. Now, after nearly a decade of data collection and analysis, researchers have fingered the cause of the affliction: human excrement. The finding represents the first example of human-to-invertebrate disease transmission and suggests a practical approach for halting the disease’s spread.

“This is a really important bit of work,” says coral researcher Thomas Goreau of the Global Coral Reef Alliance in Cambridge, Massachusetts. “I would say they’ve now proven their case beyond any doubt.”

Nine years ago, a research team led by coral reef ecologists Kathryn Sutherland, now of Rollins College in Winter Park, Florida, and James Porter of the University of Georgia, Athens, linked white pox to a bacterium called Serratia marcescens, which is found in the intestines of humans and a handful of other animals. In humans, Serratia can cause respiratory and urinary tract infections. But although Sutherland and her team strongly suspected human waste—stemming from septic tanks that leak sewage into the Florida Keys’s porous bedrock—was the culprit, they had no proof that the disease didn’t start with Key deer, cats, seagulls, or any of the Caribbean’s other Serratia-harboring wildlife. “There was considerable skepticism—it was too easy to blame other things,” Porter says.

The duo and colleagues spent years collecting Serratia samples from healthy and diseased corals, from humans via a wastewater treatment facility in Key West, and from other animals. To obtain each sample’s genetic fingerprint, they added an enzyme that breaks up the bacterium’s genome wherever a specific gene sequence is found.

Because every strain’s genome differs slightly, each one yields a unique pattern of breaks. Comparing the patterns among all their samples, the team found only two that matched each other exactly: the Serratia strain found in white pox-afflicted coral and the one drawn from human waste.

To dispel any remaining doubt, the researchers cultivated small fragments of healthy, Serratia-free coral in the lab, and then exposed these to the human-specific strain. Within as little as 4 days, the healthy coral showed signs of white pox infection, they report today in PLoS ONE.

In the Florida Keys and the Caribbean, where sea-based tourism and recreation pump billions into the economy each year, the discovery has significant implications, Porter says.

Sutherland and Porter hope their new evidence will encourage communities throughout the Caribbean to upgrade their waste management facilities, replacing septic tanks ill-suited for the region’s geography and geology with wastewater treatment plants. Key West has not seen a single new case of white pox since its transition to an advanced wastewater treatment facility in 2001, the researchers say.

Special thanks to Thomas Goreau *Study of coral may lead to sunburn pill*

see also Mother Nature Network article at:

A study of underwater coral reefs by researchers of King’s College London may lead to the development of a pill to prevent sunburn. The research team hope within the next two years to test a compound based on one which shields coral against harmful ultraviolet rays.

“We already knew that coral and some algae can protect themselves from the harsh UV rays in tropical climates by producing their own sunscreens but, until now, we didn’t know how,” said Dr Paul Long, head of the team.

“What we have found is that the algae living within the coral makes a compound that we think is transported to the coral, which then modifies it into a sunscreen for the benefit of both the coral and the algae.

“Not only does this protect them both from UV damage, but we have seen that fish that feed on the coral also benefit from this sunscreen protection, so it is clearly passed up the food chain,” the King’s team leader added.

“This led us to believe that if we can determine how this compound is created and passed on, we could biosynthetically develop it in the laboratory to create a sunscreen for human use, perhaps in the form of a tablet, which would work in a similar way.

“We are very close to being able to reproduce this compound in the lab, and if all goes well we would expect to test it within the next two years,” Long said. “There would have to be a lot of toxicology tests done first but I imagine a sunscreen tablet might be developed in five years or so,” he said.

“After taking the tablet you’d find the compound in your skin and eyes. Nothing like it exists at the moment.”

This month, as part of the three-year project funded by the Biotechnology and Biological Sciences Research Council, the King?s team collected coral samples for analysis from Australia’s Great Barrier Reef, in collaboration with Dr Walter Dunlap from the Australian Institute for Marine Science and Professor Malcolm Shick from the University of Maine USA.

A long-term goal of the King’s study is to look at whether the same processes could help sustainable agriculture in developing countries by using the natural sunscreen compounds found in coral to produce UV-tolerant crop plants capable of withstanding harsh tropical UV light.

“The part algae play in protecting itself and coral against UV is thought to be a biochemical pathway called the shikimate pathway, found only in microbes and plants,” Long said. “If we could take the part of the pathway that the coral generates, and put this into plants, we could potentially also utilise their shikimate pathway to make these natural sunscreens.

“If we do this in crop plants that have been bred in temperate climates for high yield, but that at present would not grow in the tropics because of high exposure to sunlight, this could be a way of providing a sustainable nutrient-rich food source, particularly in need for Third World economies.”

Coral is an animal which has a unique symbiotic partnership with algae that lives inside it — the algae use photosynthesis to make food for the coral and the coral waste products are used by the algae for photosynthesis. Because photosynthesis needs sunlight to work, corals must live in shallow water, which means they are vulnerable to sunburn.

Long’s team is also looking for clues as to how climate change is leading to coral bleaching, which can lead to coral death.
Bleaching occurs when a rise in sea temperature (by 2-3 degrees more than the summer average) means the algae is lost from the coral tissues, and if the relationship between algae and coral is not re-established, the coral may die.

In 1998, world-wide temperature anomalies resulted in a global bleaching event causing major coral mortality on 16 percent of the world’s coral reefs. As coral reefs provide a habitat for many forms of sea life, this can lead to significant loss.

Following the recent collection of samples from the Great Barrier Reef, the King’s team is looking at the genetic and biochemical changes that occur when coral is exposed to light at higher water temperatures. It is thought that this study will contribute vital knowledge for management and conservation of reef biodiversity in the context of global warming.

Special thanks to Coral-list EPA Denies Petition to Curb River Pollution While Gulf Dead Zone Rages

Blog – Healthy Waters / Dead Zone
Thursday, 04 August 2011 14:35
New Orleans, LA—EPA has denied a petition to implement a clean-up plan for an aquatic Dead Zone in the Gulf of Mexico, despite heavy economic losses to the U.S. fishing industry and continued research that shows the Dead Zone has doubled in size since 1985. This week, scientists from the Louisiana Universities Marine Consortium completed their annual measurement of the Gulf Dead Zone, which measured 6,765 square miles and is larger than the state of Connecticut. Members of The Mississippi River Collaborative had petitioned the EPA to set numeric limits on the discharge of pollutants that feed the Dead Zone. However, last week EPA declined to take responsibility for setting regulations that would address the problem of lackluster and hodge-podge individual states’ water pollution regulation.

The Dead Zone in the Gulf of Mexico is an area where there is not enough oxygen in the water to support marine life. It forms every summer, caused by high levels of nitrogen and phosphorus pollution draining from the Mississippi River watershed. The pollution stimulates excessive growth of algae, or blooms. When the dying algae decays it uses up most of the oxygen in the water, which chokes marine life. The pollution comes from chemical fertilizer escaping farm fields, sewage treatment plant discharges, and polluted runoff from cities. These sources of pollution are along the entire length of the Mississippi River.

“Just days before the announcement that the measured size of the Dead Zone is larger-than-average, the EPA declined to take actions to limit Dead Zone-causing pollution and to implement a clean-up plan,” said Matt Rota, Science and Water Policy Director for the Gulf Restoration Network. “The Dead Zone is detrimental to Gulf sea life and the coastal residents’ way of life, and yet EPA continues to rely on the states to do things they have failed to do for well over a decade.”

Despite the fact that the Dead Zone has ballooned over the past thirty years, EPA denied the petition, filed in 2008 by members of the Mississippi River Collaborative, which asked for immediate action to set numeric limits on Dead Zone-causing pollution in the Mississippi River and Gulf, as well as create an enforceable clean-up plan for the Dead Zone.

The petition showed that EPA has neglected its responsibility under the federal Clean Water Act to limit pollution in the Mississippi River and the Gulf of Mexico. Through the petition, the Mississippi River Collaborative also showed that the Dead Zone will continue to grow unless EPA sets numeric standards for nitrogen and phosphorus pollution and requires all states in the river basin to meet those standards. Efforts now in Congress to cut funds for Farm Bill conservation programs—designed to prevent both cropland erosion and fertilizer run-off pollution—will exacerbate the pollution in the river and the Dead Zone.

Not only does the Dead Zone threaten the $2.8 billion Gulf fishing industry, nitrogen and phosphorus pollution cause environmental problems throughout the entire Mississippi River Basin. For example, toxic algae blooms result in fish kills, the death of livestock and pets, and damage to drinking water supplies. The Mississippi River Collaborative believes that because of the basin-wide implications of nitrogen and phosphorus pollution, it is the EPA’s responsibility to take a leadership role in preventing further pollution.

“It’s distressing that the EPA will allow the decade of delay by the states along the Mississippi River to continue,” said Kris Sigford, Water Quality Director for the Minnesota Center for Environmental Advocacy. “So there is effectively no one to tackle the pollution that causes green, gunky lakes, toxic algae blooms, unsafe drinking water supplies and the wipeout of marine life in the Gulf.”

The EPA called on states in 1998 to adopt specific limits on nitrogen and phosphorus pollution, threatening to enact its own limits if states had not complied by 2003. Every state along the Mississippi River has ignored that and other deadlines set by EPA, but so far, the federal government has failed to supply urgently needed protections. As a result, inland water pollution problems have multiplied while the Dead Zone makes its annual appearance—each time bringing with it damage to the coastal residents and their livelihood.

Special thanks to Gulf Restoration Network.

Coral-list: Dave Vaughan of Mote Marine reports Elkhorn corals spawning in July at Looe Key

Just a note that /A. palmata/ (i.e. Elkhorn coral) colonies were observed to spawn Tuesday night July 19th.(Looe Key- Florida Keys National Marine Sanctuary, Special Protected Area), at about 2 hours after sunset. This is one month earlier than usual (3-4 days after full moon in August). Could this be a new trend with warmer seawater temperatures? It seams that corals may have spawned earlier these past two years as well. It seams apparent that some corals think its August or September.

Are there any other early spawning observations taking place?

Dave Vaughan,
Coral Reef Research Center Director
Mote Tropical Research Lab
Summerland Key, Florida,

TG Mississippi runoff expands Gulf ‘dead zone’
Posted on Jul 19th 2011 by Kate Taylor

The so-called Gulf Dead Zone is looking set to be the biggest ever this year.

It’s currently about 3,300 square miles, or roughly the size of Delaware and Rhode Island combined, but researchers at Texas A & M University say it’s likely to become much larger.

The dead zone is caused by hypoxia, whereby oxygen levels in seawater drop to dangerously low levels. Severe hypoxia can potentially result in widespread fish kills.

During the past five years, the Gulf dead zone has averaged about 5,800 square miles and has been predicted to exceed 9,400 square miles this year.

More changes are expected because large amounts of water are still flowing into the Gulf of Mexico from the Mississippi River.

“This was the first-ever research cruise conducted to specifically target the size of hypoxia in the month of June,” says oceanography professor Steve DiMarco.

“We found three distinct hypoxic areas. One was near the Barataria and Terrebonne region off the Louisiana coast, the second was south of Marsh Island (also Louisiana) and the third was off the Galveston coast. We found no hypoxia in the 10 stations we visited east of the Mississippi delta.”

The largest areas of hypoxia are still around the Louisiana coast, he says, thanks to the huge amounts of fresh water still coming down from the Mississippi River. The hypoxic area extends about 50 miles off the coast.

The Mississippi is the US’ largest river, draining 40 percent of the land area of the country. It also accounts for almost 90 percent of the freshwater runoff into the Gulf of Mexico.

Special thanks to Craig Quirolo

Conservation Letters: Underestimating the damage: interpreting cetacean carcass recoveries in the context of the Deepwater Horizon/BP incident Rob Williams1, Shane Gero2, Lars Bejder3, John Calambokidis4, Scott D. Kraus5, David Lusseau6, Andrew J. Read7, & Jooke Robbins8

Conservation Letters 4 (2011) 228–233

cetacean carcasses and oil spills 1

Author affiliations:
1Marine Mammal Research Unit, University of British Columbia, Vancouver, Canada
2Department of Biology, Dalhousie University, Halifax, Canada
3Centre for Fish and Fisheries Research, Cetacean Research Unit, Murdoch University, Western Australia
4Cascadia Research Collective, Olympia, WA, USA
5New England Aquarium, Boston, MA, USA
6School of Biology, Aberdeen University, Aberdeen, Scotland, UK
7Nicholas School of the Environment, Duke University, Beaufort, NC, USA
8Humpback Whale Studies Program, Provincetown Center for Coastal Studies, Provincetown, MA, USA

Anthropogenic impacts; dolphin; Deepwater
Horizon; Gulf of Mexico; mortality; oil;

Rob Williams, Current address: Sea Mammal
Research Unit, Scottish Oceans Institute,
St Andrews Fife KY16 8LB. Tel: +44 (0)1334
462630; Fax: +44 (0)1334 463443.

Received 23 September 2010
Accepted 15 February 2011
Editor Leah Gerber
doi: 10.1111/j.1755-263X.2011.00168.x

Evaluating impacts of human activities on marine ecosystems is difficult when effects occur out of plain sight. Oil spill severity is often measured by the number of marine birds and mammals killed, but only a small fraction of carcasses
are recovered. The Deepwater Horizon/BP oil spill in the Gulf of Mexico was the largest in the U.S. history, but some reports implied modest environmental impacts, in part because of a relatively low number (101) of observed marine mammal mortalities. We estimate historical carcass-detection rates for 14 cetacean species in the northern Gulf of Mexico that have estimates of abundance,
survival rates, and stranding records. This preliminary analysis suggests that carcasses are recovered, on an average, from only 2% (range: 0–6.2%) of cetacean deaths. Thus, the true death toll could be 50 times the number of carcasses recovered, given no additional information. We discuss caveats to this estimate, but present it as a counterpoint to illustrate the magnitude of
misrepresentation implicit in presenting observed carcass counts without similar qualification. We urge methodological development to develop appropriate multipliers. Analytical methods are required to account explicitly for low probability of carcass recovery from cryptic mortality events (e.g., oil spills, ship strikes, bycatch in unmonitored fisheries and acoustic trauma).

Special thanks to Richard Charter The Guardian/UK: Climate Skeptic Willie Soon Received $1m from Oil Companies, Papers Show

Published on Tuesday, June 28, 2011
Documents obtained by Greenpeace show prominent opponent of climate change was funded by ExxonMobil, among others
by John Vidal

One of the world’s most prominent scientific figures to be skeptical about climate change has admitted to being paid more than $1m in the past decade by major US oil and coal companies.

Willie Soon received over $1m from oil companies including ExxonMobil, documents reveal. (Photograph: Donna Williams/AP) Dr Willie Soon, an astrophysicist at the Solar, Stellar and Planetary Sciences Division of the Harvard-Smithsonian Centre for Astrophysics, is known for his view that global warming and the melting of the arctic sea ice is caused by solar variation rather than human-caused CO2 emissions, and that polar bears are not primarily threatened by climate change.

But according to a Greenpeace US investigation, he has been heavily funded by coal and oil industry interests since 2001, receiving money from ExxonMobil, the American Petroleum Institute and Koch Industries along with Southern, one of the world’s largest coal-burning utility companies. Since 2002, it is alleged, every new grant he has received has been from either oil or coal interests.

In addition, freedom of information documents suggest that Soon corresponded in 2003 with other prominent climate skeptics to try to weaken a major assessment of global warming being conducted by the UN’s leading climate science body, the Nobel prize-winning Intergovernmental Panel on Climate Change.

Soon, who had previously disclosed corporate funding he received in the 1990s, was today reportly unapologetic, telling Reuters that he agreed that he had received money from all of the groups and companies named in the report but denied that any group would have influenced his studies.

“I have never been motivated by financial reward in any of my scientific research,” he said. “I would have accepted money from Greenpeace if they had offered it to do my research.” He did not respond to a request from the Guardian to comment.

Documents provided to Greenpeace by the Smithsonian under the US Freedom of Information Act (FoIA) show that the Charles G Koch Foundation, a leading provider of funds for climate sceptic groups, gave Soon two grants totalling $175,000 (then roughly £102,000) in 2005/6 and again in 2010. In addition the American Petroleum Institute (API), which represents the US petroleum and natural gas industries, gave him multiple grants between 2001 and 2007 totalling $274,000, oil company Exxon Mobil provided $335,000 between 2005 and 2010, and Soon received other grants from coal and oil industry sources including the Mobil Foundation, the Texaco Foundation and the Electric Power Research Institute.

As one of very few scientists to publish in peer-reviewed literature denying climate change, Soon is widely regarded as one of the leading skeptical voices. His scientific position and the vehemence of his views has made him a central figure in a heated political debate that has informed the US right wing and helped to undermine public trust in the science of global warming and UN negotiations.

“A campaign of climate change denial has been waged for over 20 years by big oil and big coal,” said Kert Davies, a research director at Greenpeace US. “Scientists like Dr Soon, who take fossil fuel money and pretend to be independent scientists, are pawns.”

Soon has strongly argued that the 20th century was not a uniquely extreme climatic period. His most famous work challenged the “hockey stick” graph of temperature records published by Michael Mann, which showed a relatively sharp rise in temperatures during the second half of the 20th century. A paper published with Sallie Baliunas in 2003 in the journal Climate Research which attacked the hockey stick on flimsy evidence led to a group of leading climate scientists including Mann deciding to boycott the journal. In a letter to the Guardian in February 2004, Soon wrote that the authors had been open about their sources of funding. “All sources of funding for our research were fully disclosed in our manuscript. Most of our funding came from federal agencies, including the Air Force Office of Scientific Research and Nasa,” he wrote.

He has also questioned the health risks of mercury emissions from coal and in 2007 co-wrote a paper that down-played the idea that polar bears are threatened by human-caused climate change

The investigation is likely to embarrass Exxon, the world’s largest oil company, which for many years funded climate sceptics but in 2008 declared it would cut funds to lobby groups that “divert attention” from the need to find new sources of clean energy. According to the documents, Exxon provided $55,000 for Soon to study Arctic climate change in 2007 and 2008, and another $76,106 for research into solar variability between 2008 and 2010.

Exxon spokesman Alan Jeffers said this week the company did not fund Soon last year, and that it funds hundreds of organisations to do research on climate and the environment.

Southern gave Soon $120,000 starting in 2008 to study the Sun’s relation to climate change, according to the FIA documents. Spokeswoman Stephanie Kirijan said the company has spent about $500m on funding environmental research and development ,and that it did not fund Soon last year.

In one 2003 email released to Greenpeace, that Soon sent, it is believed, to four other leading skeptics, he writes: “Clearly [the fourth assessment report] chapters may be too much for any one of us to tackle them all … But as a team, we may give it our best shot to try to anticipate and counter some of the chapters …” He adds: “I hope we can … see what we can do to weaken the fourth assessment report.”

In 2003 Soon said at a US senate hearing that he had “not knowingly been hired by, nor employed by, nor received grants from any organisation that had taken advocacy positions with respect to the Kyoto protocol or the UN Framework Convention on Climate Change.” DILUTION CANNOT BE ASSUMED THE SOLUTION FOR AQUACULTURE POLLUTION by S. K. Venayagamoorthy, H.Ku, O.B. Fringer, A. Chiu, R.L. Naylor, & J.R. Koseff

Venayagamoorthy, S.K., H. Ku, O.B. Fringer, A. Chiu, R.L. Naylor and J.R. Koseff. 2011. Numerical modeling of
aquaculture dissolved waste transport in a coastal embayment. Environmental Fluid Mechanics.

A recent scientific study published in the journal Environmental Fluid Mechanics shows that the location of
coastal and offshore aquaculture pens can dramatically influence the extent to which dissolved fish farm
waste disperses from its source and reaches coastlines. This study is the first detailed look at how real
world factors influence the flow of wastewater from fish farms and provides a further basis for understanding
the impact of aquaculture fish-pens on coastal water quality.

Marine aquaculture, or fish farming, is viewed as a means to supplement declining wild fisheries and to
help meet the rising global demand for seafood; however it can cause environmental degradation. For
example, water quality can be significantly impacted because farmed fish excrete much of the nutrients
contained in their feed, including nitrogen and phosphorous. In excess, these nutrients, can trigger
eutrophication and depleted oxygen levels. Nutrients discharges are a particular concern when fish are
grown in open net pens because nutrient-laden feces, undigested feed, and other fish wastes flow freely
into the surrounding environment, some settling to the bottom and other waste products dissolving into
the water column. The concentrations of dissolved waste from net pens are often assumed to decline
continuously in all directions as the discharge moves further from the pens, diluting the environmental
impacts as the distance from the pens increases.

Dr. Venayagamoorthy and colleagues, supported by the Lenfest Ocean Program, explored the influence
of local currents and flow conditions on the concentration and dispersal of dissolved wastes from
marine aquaculture net pens. In order to test the assumption that waste products are consistently
diluted as distance from the net pens increases, the scientists developed an idealized computational
model and performed simulations of dissolved pollutant plumes in variable coastal and offshore marine
environments. The simulations included representations of the local physical environment (i.e., the
shape and depth of the embayment containing the pens), flow conditions (i.e., tides and wind-induced
currents), and the physical locale of the pens relative to the coasts and freshwater discharges.
The scientists showed that specific flow conditions around the aquaculture pens, such as tidal flow, the
earth’s rotation, local river discharges and the drag introduced by the pens, can lead to pockets of
concentrated pollution traveling considerable distances from the source, potentially affecting coastal
waters and the coastlines far from the aquaculture pens themselves.

The results of this study show that producers, regulators and other stakeholders cannot simply assume
that fish waste discharge will be diluted consistently as it moves away from the net pens, or that dilution
is necessarily the solution for aquaculture wastes. Instead, they need to consider how factors such as
tides, river outflows, shape of embayments and other factors will influence the concentration and spread
of dissolved wastewater plumes. Thus, the effluent model created in this exercise can be a useful tool
for predicting a site’s ability to meet water quality standards before aquaculture facilities are built.

Lenfest Ocean Program: Protecting Ocean Life Through Marine Science
The Lenfest Ocean Program supports scientific research aimed at forging
solutions to the challenges facing the global marine environment.

Huffington Post: State Of The Ocean: ‘Shocking’ Report Warns Of Mass Extinction From Current Rate Of Marine Distress

by Travis Donovan

If the current actions contributing to a multifaceted degradation of the world’s oceans aren’t curbed, a mass extinction unlike anything human history has ever seen is coming, an expert panel of scientists warns in an alarming new report.

The preliminary report from the International Programme on the State of the Ocean (IPSO) is the result of the first-ever interdisciplinary international workshop examining the combined impact of all of the stressors currently affecting the oceans, including pollution, warming, acidification, overfishing and hypoxia.

“The findings are shocking,” Dr. Alex Rogers, IPSO’s scientific director, said in a statement released by the group. “This is a very serious situation demanding unequivocal action at every level. We are looking at consequences for humankind that will impact in our lifetime, and worse, our children’s and generations beyond that.”

The scientific panel concluded that degeneration in the oceans is happening much faster than has been predicted, and that the combination of factors currently distressing the marine environment is contributing to the precise conditions that have been associated with all major extinctions in the Earth’s history.

According to the report, three major factors have been present in the handful of mass extinctions that have occurred in the past: an increase of both hypoxia (low oxygen) and anoxia (lack of oxygen that creates “dead zones”) in the oceans, warming and acidification. The panel warns that the combination of these factors will inevitably cause a mass marine extinction if swift action isn’t taken to improve conditions.

The report is the latest of several published in recent months examining the dire conditions of the oceans. A recent World Resources Institute report suggests that all coral reefs could be gone by 2050 if no action is taken to protect them, while a study published earlier this year in BioScience declares oysters as “functionally extinct”, their populations decimated by over-harvesting and disease. Just last week scientists forecasted that this year’s Gulf “dead zone” will be the largest in history due to increased runoff from the Mississippi River dragging in high levels of nitrates and phosphates from fertilizers.

A recent study in the journal Nature, meanwhile, suggests that not only will the next mass extinction be man-made, but that it could already be underway. Unless humans make significant changes to their behavior, that is.
Travis Donovan
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State Of The Ocean: ‘Shocking’ Report Warns Of Mass Extinction From Current Rate Of Marine Distress
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First Posted: 06/20/11 05:19 PM ET Updated: 06/21/11 09:09 AM ET
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If the current actions contributing to a multifaceted degradation of the world’s oceans aren’t curbed, a mass extinction unlike anything human history has ever seen is coming, an expert panel of scientists warns in an alarming new report.

The preliminary report from the International Programme on the State of the Ocean (IPSO) is the result of the first-ever interdisciplinary international workshop examining the combined impact of all of the stressors currently affecting the oceans, including pollution, warming, acidification, overfishing and hypoxia.

“The findings are shocking,” Dr. Alex Rogers, IPSO’s scientific director, said in a statement released by the group. “This is a very serious situation demanding unequivocal action at every level. We are looking at consequences for humankind that will impact in our lifetime, and worse, our children’s and generations beyond that.”

The scientific panel concluded that degeneration in the oceans is happening much faster than has been predicted, and that the combination of factors currently distressing the marine environment is contributing to the precise conditions that have been associated with all major extinctions in the Earth’s history.

According to the report, three major factors have been present in the handful of mass extinctions that have occurred in the past: an increase of both hypoxia (low oxygen) and anoxia (lack of oxygen that creates “dead zones”) in the oceans, warming and acidification. The panel warns that the combination of these factors will inevitably cause a mass marine extinction if swift action isn’t taken to improve conditions.

The report is the latest of several published in recent months examining the dire conditions of the oceans. A recent World Resources Institute report suggests that all coral reefs could be gone by 2050 if no action is taken to protect them, while a study published earlier this year in BioScience declares oysters as “functionally extinct”, their populations decimated by over-harvesting and disease. Just last week scientists forecasted that this year’s Gulf “dead zone” will be the largest in history due to increased runoff from the Mississippi River dragging in high levels of nitrates and phosphates from fertilizers.

A recent study in the journal Nature, meanwhile, suggests that not only will the next mass extinction be man-made, but that it could already be underway. Unless humans make significant changes to their behavior, that is.

The IPSO report calls for such changes, recommending actions in key areas: immediate reduction of CO2 emissions, coordinated efforts to restore marine ecosystems, and universal implementation of the precautionary principle so “activities proceed only if they are shown not to harm the ocean singly or in combination with other activities.” The panel also calls for the UN to swiftly introduce an “effective governance of the High Seas.”

“The challenges for the future of the ocean are vast, but unlike previous generations we know what now needs to happen,” Dan Laffoley of the International Union for Conservation of Nature and Natural Resources (IUCN) and co-author of the report said in a press release for the new report. “The time to protect the blue heart of our planet is now, today and urgent.”

Special thanks to Lynn Davidson. USA Today reports Record ‘Dead Zone’ Predicted in Gulf of Mexico

Published on Wednesday, June 15, 2011

by Doyle Rice

The “Dead Zone” in the Gulf of Mexico – a region of oxygen-depleted water off the Louisiana and Texas coasts that is harmful to sea life and the commercial fishing industry – is predicted to be the largest ever recorded this year, federal scientists announced Tuesday.

The majority of land in the Mississippi’s watershed is farm land (in green). Each spring, as farmers fertilize their land in preparation for crop season, rain washes fertilizer off the land and into streams, rivers, and then the Gulf of Mexico. This leads to a Dead Zone in the Gulf. (NOAA)

The majority of land in the Mississippi’s watershed is farm land (in green). Each spring, as farmers fertilize their land in preparation for crop season, rain washes fertilizer off the land and into streams, rivers, and then the Gulf of Mexico. This leads to a Dead Zone in the Gulf. (NOAA) The unusually large size of the zone is due to the extreme flooding of the Mississippi River this spring.

The Dead Zone occurs when there is not enough oxygen in the water to support marine life. Also known as “hypoxia,” it is created by nutrient runoff, mostly from over-application of fertilizer on agricultural fields. It flows into streams, then rivers and eventually the Gulf.

Forty-one percent of the contiguous USA drains into the Mississippi River and then out to the Gulf of Mexico. The majority of the land in Mississippi’s watershed is farm land.

Excess nutrients such as nitrogen can spur the growth of algae, and when the algae die, their decay consumes oxygen faster than it can be brought down from the surface, according to NOAA. As a result, fish, shrimp and crabs can suffocate, threatening the region’s commercial fishing industry.

Scientists say the area could measure between 8,500 and 9,421 square miles, or an area about the size of New Hampshire. If it does reach those levels, it would be the largest since mapping of the Gulf Dead Zone began in 1985.

The largest Dead Zone on record occurred in 2002 and encompassed more than 8,400 square miles. On average, the Dead Zone size is estimated to be 6,000 square miles. The Guardian/UK: Explosion in Jellyfish Numbers May Lead to Ecological Disaster, Warn Scientists

Published on Monday, June 13, 2011 by The Guardian/UK

by Tracy McVeigh

Global warming has long been blamed for the huge rise in the world’s jellyfish population. But new research suggests that they, in turn, may be worsening the problem by producing more carbon than the oceans can cope with.

Dr Carol Turley, a scientist at Plymouth University’s Marine Laboratory, said the research highlighted the growing problem of ocean acidification, the so-called “evil twin” of global warming. (Image: wiki commons) Research led by Rob Condon of the Virginia Institute of Marine Science in the US focuses on the effect that the increasing numbers of jellyfish are having on marine bateria, which play an important role by recycling nutrients created by decaying organisms back into the food web. The study, published in the journal Proceedings of the National Academy of Sciences, finds that while bacteria are capable of absorbing the constituent carbon, nitrogen, phosphorus and other chemicals given off by most fish when they die, they cannot do the same with jellyfish. The invertebrates, populating the seas in ever-increasing numbers, break down into biomass with especially high levels of carbon, which the bacteria cannot absorb well. Instead of using it to grow, the bacteria breathe it out as carbon dioxide. This means more of the gas is released into the atmosphere.

Dr Carol Turley, a scientist at Plymouth University’s Marine Laboratory, said the research highlighted the growing problem of ocean acidification, the so-called “evil twin” of global warming. “Oceans have been taking up 25% of the carbon dioxide that man has produced over the last 200 years, so it’s been acting as a buffer for climate change. When you add more carbon dioxide to sea water it becomes more acidic. And already that is happening at a rate that hasn’t occurred in 600 million years.”

The acidification of the oceans is already predicted to have such a corrosive effect that unprotected shellfish will dissolve by the middle of the century.”

Condon’s research also found that the spike in jellyfish numbers is also turning the marine food cycle on its head. The creatures devour huge quantities of plankton, thus depriving small fish of the food they need. “This restricts the transfer of energy up the food chain because jellyfish are not readily consumed by other predators,” said Condon.

The increase in the jellyfish population has been attributed to factors including climate change, over-fishing and the runoff of agricultural fertilisers. The rise in sea temperature and the elimination of predators such as sharks and tuna has made conditions ideal, and “blooms” – when populations explode in great swarms, sparking regular panics on beaches around the world– are being reported in ever-increasing size and frequency. Last year scientists at the University of British Columbia found that global warming was causing 2,000 different jellyfish species to appear earlier each year and expanding their number.

The proliferation of jellyfish has caused problems for seaside power and desalination plants in Japan, the Middle East and Africa. The blooms are also perilous to swimmers; the effects of a jellyfish sting range across the species from painless to tingling to agony and death. Climate Change: Losers and winners in coral reefs acclimatized to elevated carbon dioxide concentrations by Katharina E. Fabricius, et. al.

The link to the original article is

by Katharina E. Fabricius, Chris Langdon, Sven Uthicke, Craig Humphrey, Sam Noonan, Glenn De’ath, Remy Okazaki, Nancy Muehllehner, Martin S. Glas & Janice M. Lough

Reference: Fabricius KE, Langdon C, Uthicke S, Humphrey C, Noonan S, De’ath G, Okazaki R, Muehllehner N, Glas M, Lough JM (2011) Losers and winners in coral reefs acclimatized to elevated carbon dioxide concentrations. Nature Climate Change 1: 165-169

Published online 29 May 2011

Experiments have shown that ocean acidification due to rising atmospheric carbon dioxide concentrations has deleterious effects on the performance of many marine organisms1, 2, 3, 4. However, few empirical or modelling studies have addressed the long-term consequences of ocean acidification for marine ecosystems5, 6, 7. Here we show that as pH declines from 8.1 to 7.8 (the change expected if atmospheric carbon dioxide concentrations increase from 390 to 750 ppm, consistent with some scenarios for the end of this century) some organisms benefit, but many more lose out. We investigated coral reefs, seagrasses and sediments that are acclimatized to low pH at three cool and shallow volcanic carbon dioxide seeps in Papua New Guinea. At reduced pH, we observed reductions in coral diversity, recruitment and abundances of structurally complex framework builders, and shifts in competitive interactions between taxa. However, coral cover remained constant between pH 8.1 and ~7.8, because massive Porites corals established dominance over structural corals, despite low rates of calcification. Reef development ceased below pH 7.7. Our empirical data from this unique field setting confirm model predictions that ocean acidification, together with temperature stress, will probably lead to severely reduced diversity, structural complexity and resilience of Indo-Pacific coral reefs within this century.


Australian Institute of Marine Science, PMB 3, Townsville, Queensland 4810, Australia
Katharina E. Fabricius,
Sven Uthicke,
Craig Humphrey,
Sam Noonan,
Glenn De’ath &
Janice M. Lough
University of Miami Rosenstiel School of Marine and Atmospheric Science, 4600 Rickenbacker Causeway, Florida 33149, USA
Chris Langdon,
Remy Okazaki &
Nancy Muehllehner
Max-Planck Institute for Marine Microbiology, Department of Biogeochemistry, Celsiusstr. 1, 28395 Bremen, Germany
Martin S. Glas


All authors were involved with either fieldwork or data analyses. K.E.F. initiated and designed the study and wrote the manuscript, with contributions from all others. C.L. and R.O. analysed the seawater chemistry, C.H., S.N., K.E.F. and J.M.L. collected and analysed the Porites data, C.L. the in situ coral growth data, K.E.F. and S.N. the reef community data, S.U. the sediments and foraminifera, N.M. and S.U. the seagrass and epibiont data, and G.D. and K.E.F. conducted the statistical analyses.
Competing financial interests

The authors declare no competing financial interests.

Correspondence to: Katharina E. Fabricius

Conservation International: Coral Health Index: Measuring Community Coral Reef Health

by Kaufman L, Sandin S, Sala E, Obura D, Rohwer F, and Tschirky T (2011)
Coral Health Index (CHI): measuring coral community health.
Science and Knowledge Division, Conservation International, Arlington, VA, USA.

There is a new tool for assessing coral healthwhich has just been released by Conservation International (CI) and is available for download free on an IUCN website (International Union for the Conservation of Nature). I find it very easy to read and understand, and this appears to me to have widespread potential for applicability and use around the world to get a much better idea of how our reefs are doing. I can’t wait to try it out on reefs near me and see how they rate (I have a guess, but still it will be fascinating to see). Cheers, Doug Fenner

Special thanks to Doug Fenner, coral-list

BBC News: Acid oceans turn ‘Finding Nemo’ fish deaf

31 May 2011 Last updated at 19:47 ET

By Richard Black Environment correspondent, BBC News

Clownfish, the spectacular tropical species featured in the movie Finding Nemo, appear to lose their hearing in water slightly more acidic than normal.

At levels of acidity that may be common by the end of the century, the fish did not respond to the sounds of predators.

The oceans are becoming more acidic because they absorb much of the CO2 that humanity puts into the atmosphere.

Scientists write in the journal Biology Letters that failing to move away from danger would hurt the fish’s survival.

“Avoiding coral reefs during the day is very typical behaviour of fish in open water,” said research leader Steve Simpson from the School of Biological Sciences at the UK’s Bristol University.

“They do this by monitoring the sounds of animals on the reef, most of which are predators to something just a centimetre in length.

“But sounds are also important for mate detection, pack hunting, foraging – so if any or all of those capacities are gone, you’d have a very lost fish,” he told BBC News.

Previous research has shown that fish also lose their capacity to scent danger in slightly more acidic seawater.
Experimental chamber The fish were put in a “choice chamber” that allowed them to swim away, or not, on hearing the noise

The team raised baby clownfish in tanks containing water at different levels of acidity.

One resembled the seawater of today, with the atmosphere containing about 390 parts per million (ppm) of carbon dioxide.

The other tanks were set at levels that could be reached later this century – 600, 700 and 900 ppm.

The more CO2 there is in the atmosphere, the more the oceans absorb – and the more they absorb, the more acidic the water becomes.

In this experiment, the fish could decide whether to swim towards or away from an underwater loudspeaker replaying the sounds of predators recorded on a reef, with shrimps and fish that would take a small clownfish.

In water with today’s levels of CO2, the fish spent three-quarters of the time at the opposite end of the tube from the loudspeaker.

But at higher concentrations, they showed no preference. This suggests they could not hear, could not decipher or did not act on the warning signals.

“The reef has been described as ‘a wall of mouths’ waiting to receive the clownfish,” said Dr Simpson.
Continue reading the main story
Ocean pH levels (Image: BBC)

The oceans are thought to have absorbed about half of the extra CO2 put into the atmosphere in the industrial age
This has lowered its pH by 0.1
pH is the measure of acidity and alkalinity
Liquids lie between pH 0 (very acidic) and pH 14 (very alkaline); 7 is neutral
Seawater is mildly alkaline with a “natural” pH of about 8.2
The IPCC forecasts that ocean pH will fall by “between 0.14 and 0.35 units over the 21st Century, adding to the present decrease of 0.1 units since pre-industrial times”

“What we have done here is put today’s fish in tomorrow’s environment, and the effects are potentially devastating.”

If it takes several decades for the oceans to reach these more acidic levels, there is a chance, the team says, that fish could adapt.

Whether that can happen is one of the outstanding questions from this research. Another is whether other species are similarly affected.

A third question is why the fish are affected by these slight changes in acidity.

There appears to be no physical damage to their ears; the team suggests there could be some effect on nerves, or maybe they are stressed by the higher acidity and do not behave as they otherwise would.

Further experiments are in train that may answer those questions.

Concern about ocean acidification has arisen considerably more recently than alarm over global warming; but already there is ample evidence that it could bring significant changes to ocean life.

The organisms most directly affected appear to be corals and those that make shells, such as snails.

Just this weekend, another team of researchers published findings from a “natural laboratory” in the seas off Papua New Guinea, where carbon dioxide bubbles into the water from the slopes of a dormant volcano.

This local acidity is too much for most corals; instead, an alternative ecosystem based on seagrasses thrives.

With carbon emissions continuing to rise, researchers predicted most reefs around the world would be in serious trouble before the end of the century.
More on This Story
Related Stories

Fish ‘at risk’ in acidified ocean 21 NOVEMBER 2009, SCI/TECH
Bubbling sea signals coral threat 29 MAY 2011, SCIENCE & ENVIRONMENT
Coral reefs heading into crisis 23 FEBRUARY 2011, SCIENCE & ENVIRONMENT
Recipe for rescuing our reefs 05 NOVEMBER 2008, SCI/TECH

Special thanks to Doug Fenner, Coral-list. The Observer/UK: Ocean Acidification Is Latest Manifestation of Global Warming

Published on Sunday, May 29, 2011

Carbon dioxide pollution adds to threat to world’s oceans and marine species
by Robin McKie, science editor

The infernal origins of Vulcano Island are easy to pinpoint. Step off the hydrofoil from Sicily and the rotten-egg smell of hydrogen sulphide strikes you immediately. Beside the quay, there are piles of yellow sulphurous rocks and chunks of pumice; the beach is made of thick, black volcanic sand; while the huge caldera that dominates the bay emits a constant stream of smoke and steam.

By the middle of the century there will probably be only a few pockets of coral left, in the North Sea and the Pacific. Millions of species of marine life will be wiped out. (Photo: Vladimir Levantovsky/Alamy) According to legend, this was the lair of the Roman god of fire, Vulcan, who gave his name to the island and subsequently to all other volcanoes. An early eruption here also provided history with one of the first recorded descriptions of a volcano in action.

But Vulcano’s importance today has nothing to do with the rock and lava it has spewed out for millennia. It is the volcano’s output of invisible carbon dioxide – about 10 tonnes a day – that now interests scientists. They have found that the gas is bubbling through underground vents and is making the island’s coastal waters more and more acidic. The consequences for sea life are grim with dozens of species having been eliminated.

That discovery is highly revealing, and worrying, because Vulcano’s afflictions are being repeated today on a global scale, in every ocean on the planet – not from volcanic sources but from the industrial plants, power stations, cars and planes that are pumping out growing amounts of carbon dioxide and which are making our seas increasingly acidic. Millions of marine species are now threatened with extinction; fisheries face eradication; while reefs that protect coastal areas are starting to erode.

Ocean acidification is now one of the most worrying threats to the planet, say marine biologists. “Just as Vulcano is pumping carbon dioxide into the waters around it, humanity is pouring more and more carbon dioxide into the atmosphere,” Dr Jason Hall-Spencer, a marine biologist at Plymouth University, told a conference on the island last week.

“Some of the billions of tonnes of carbon dioxide we emit each year lingers in the atmosphere and causes it to heat up, driving global warming. But about 30% of that gas is absorbed by the oceans where it turns to carbonic acid. It is beginning to kill off coral reefs and shellfish beds and threaten stocks of fish. Very little can live in water that gets too acidic.”

Hence science’s renewed interest in Vulcano. Its carbon dioxide springs – which bubble up like burst water mains below the shallow seabed – provide researchers with a natural laboratory for testing the global impact of ocean acidification. “These vents and the carbonic acid they generate tell us a great deal about how carbon dioxide is going to affect the oceans and marine life this century,” said Hall-Spencer. “And we should be worried. This problem is a train coming straight at us.”

Scientists estimate that oceans absorb around a million tonnes of carbon dioxide every hour and our seas are 30% more acidic than they were last century. This increased acidity plays havoc with levels of calcium carbonate, which forms the shells and skeletons of many sea creatures, and also disrupts reproductive activity.

Among the warning signs recently noted have been the failures of commercial oyster and other shellfish beds on the Pacific coasts of the US and Canada. In addition, coral reefs – already bleached by rising global temperatures – have suffered calamitous disintegration in many regions. And at the poles and high latitudes, where the impact of ocean acidification is particularly serious, tiny shellfish called pteropods – the basic foodstuff of fish, whales and seabirds in those regions – have suffered noticeable drops in numbers. In each case, ocean acidification is thought to be involved.

The problem was recently highlighted by the head of the US National Oceanic and Atmospheric Administration, Dr Jane Lubchenco. She described ocean acidification as global warming’s “equally evil twin”. It is a powerful comparison, though it is clear that of the two, the crisis facing our seas has received far less attention. The last UN climate assessment report was more than 400 pages long but had only two pages on ocean acidification – mainly because studies of the phenomenon are less well advanced than meteorological and atmospheric research in general.

The workshop, held last week on Vulcano, is part of the campaign to understand the likely impact of ocean acidification. Dozens of young oceanographers, geologists and ecologists gathered for the meeting run by the Mediterranean Sea Acidification (MedSeA) programme. Dr Maoz Fine, of Bar-Ilan University in Israel, reported work on coral reef organisms that had been exposed to waters of different levels of acidity, temperature and light in his laboratory.

“We found that species of coral reef respond differently to rising carbon dioxide levels,” he said. “Bigger corals suffer but survive while smaller, branching varieties become less able to fight disease and die off. That sort of thing just makes it even more difficult to predict exactly what is going to happen to our oceans.”

Few scientists doubt that the impact on reefs will be anything short of devastating, however. The Caribbean has already lost about 80% of its coral reefs to bleaching caused by rising temperatures and by overfishing which removes species that normally aid coral growth. Acidification threatens to do the same for the rest of the world’s coral reefs.

“By the middle of the century there will probably be only a few pockets – in the North Sea and the Pacific. Millions of species of fish, shellfish and micro-organisms will be wiped out,” said Fine.

Acidification has affected the oceans in the past. However, these prehistoric events occurred at a far slower rate, said Dr Jerry Blackford of Plymouth Marine Laboratory. “The waters of the world take around 500 years to circulate the globe,” he said. “If carbon dioxide was rising slowly, in terms of thousands of years, natural factors could then compensate. Sediments could buffer the carbonic acid, for example.”

But levels of carbon dioxide are rising much faster today. By the end of the century, surface seawater will be 150% more acidic than it was in 1800. “There is simply not enough time for buffering to come into effect and lessen the impact,” said Blackford. “The result will be significant acid build-up in the upper parts of the oceans which, of course, are the parts that are of greatest importance to humans.”

A vision of the seas we are now creating can be seen at Vulcano. On the eastern side of its main bay, beyond an open-air thermal spa filled with elderly bathers wallowing in volcanically heated mud, there is a long stretch of black sand.

Just offshore, in about four feet of water, silver beads of carbon dioxide stream up from stones that lie over an underground vent. The water, although cold, looks like a huge, frothing Jacuzzi. Water here is highly acidic and there is no marine life around the vent – not even seaweed.

“The acidity here is far greater than even the worst ocean scenario for 2100, so we have to be careful about making comparisons,” said Dr Marco Milazzo, of Palermo University. “However, currents carry that acid water round the bay and it becomes more and more dilute. We can then study waters which reflect the kind of acidity we are likely to get at the end of the century.”

Milazzo and his colleagues have placed open boxes containing coral and other forms of marine life in the waters round the bay and monitor the effects of the different levels of acidity in the sea water on these samples and also on the bay’s natural marine life. “When I look one way, out to sea, where there is little acidity, the plant life is rich in reds, whites, greens and other colours. There is abundance and variety in the habitat,” said Milazzo.

“However, when I look the other way – back towards the carbon dioxide vent – that habitat gets less and less varied as the water gets more acidic. It is reduced to a dark brown bloom of macro-algae. There is no richness or variety here. In effect I am looking at the oceans of tomorrow. It is profoundly depressing.”

Acidity is measured by its pH (power of hydrogen) value. Fresh water has a pH reading of 7. Readings below that are considered to be acidic. Those above 7 are alkaline. Surface sea water had a reading of 8.2 a century ago. Today it has dropped to 8.1 because so much carbon dioxide has been absorbed by the world’s oceans. That may seem a small amount but the pH scale is logarithmic which means that 0.1 difference actually represents an increase in acidity of 30%. By the end of the century, the pH of surface sea water could have dropped to 7.8, which represents a decrease in alkalinity – or an increase in acidity, depending on your viewpoint – of around 150%.

Science Daily: Un. of New Hampshire: Deepwater Horizon Spill Threatens More Species Than Legally Protected, Study Finds

ScienceDaily (May 11, 2011) —Marine species facing threats from the 2010 BP Deepwater Horizon oil spill in the Gulf of Mexico far exceed those under legal protection in the United States, a new paper in the journal BioScience finds. University of New Hampshire professor Fred Short and others found 39 additional marine species beyond the 14 protected by federal law that are at an elevated risk of extinction. These species, which range from whale sharks to seagrass, should receive priority for protection and restoration efforts, the authors advocate.

“A lot of species in the Gulf of Mexico are going to be damaged by this oil spill but aren’t on the U.S. radar screen, although they’re threatened globally,” says Short, who is a research professor of natural resources and the environment at UNH. Along with lead author Claudio Campagna of the Wildlife Conservation Society and others, Short was a major contributor to the paper, “Gulf of Mexico Oil Blowout Increases Risks to Globally Threatened Species,” which appears in the Roundtable section of the May 2011 issue of BioScience.

“It is imperative to understand the global consequences of environmental disasters, as a local perspective under emphasizes the incidence on widely distributed species,” says the Wildlife Conservation Society’s Campagna.”The IUCN Red List data has an unmatched, so far neglected potential to inform policy decisions at a regional level.”

The researchers consulted the extensive species database of the International Union for Conservationof Nature’s (IUCN) Red List, which assesses species’ global survival status via a rigorous scientific process. They found 53 species with a distribution that overlaps the area of the oil spill that are categorized as critically endangered, endangered, or vulnerable by the IUCN Red List. Of these, only 14 receive legal protection in the United States under the Endangered Species Act, the Migratory Bird Treaty Act, or the Marine Mammal Protection Act.

“There are species that are surely threatened that could be driven to extinction because of this oil spill,” says Short.

Among the Red List species that are not protected by U.S. law are the commercially valuable Atlantic bluefin tuna (western stock), 16 species of sharks, and eight corals. Many species are particularly vulnerable because they return to the Gulf of Mexico to spawn, and the oil spill coincided with peak spawning periods. The researchers also write that the whale shark, the largest fish in the world, is uniquely at risk from oil and oil dispersants because of its filter-feeding behavior; its long lifespan and slow reproductive rate compound the threat to its recovery. It is listed as vulnerable on the IUCN Red List but not protected by the Endangered Species Act.

“Threatened species not yet listed in national legislation should nevertheless be the subject of damage assessments, targeted research, and monitoring, as well as recovery efforts when needed,” the authors write. The U.S.Natural Resource Damage Assessment, which is the primary legal authority for assessing damages and providing for recovery of coastal and marine species, may not account for injury to these globally threatened species.

Further, the authors advocate that environmental impact assessments conducted for future offshore oil and gas development should incorporate available data on globally threatened species, including species on the IUCN Red List.

“Next time this happens — and we know there will be a next time — we need to take this broader list into consideration,” says Short.

The above story is reprinted(with editorial adaptations by ScienceDaily staff) from materials provided by University of New Hampshire.

Journal Reference:

1. Claudio Campagna, Frederick T. Short, Beth A. Polidoro, Roger McManus, Bruce B. Collette, Nicolas J. Pilcher, Yvonne Sadovy de Mitcheson, Simon N. Stuart, Kent E. Carpenter. Gulf of Mexico Oil Blowout Increases Risks to Globally Threatened Species. BioScience, 2011; 61 (5): 393 DOI: 10.1525/bio.2011.61.5.8

University of New Hampshire (2011,May 11). Deepwater Horizon spill threatens more species than legally protected, study finds. ScienceDaily. Retrieved May 11, 2011,from°© /releases/2011/05/110511134221.htm

Disclaimer: Views expressedi n this article do not necessarily reflect those of ScienceDaily or its staff.

Special thanks to Richard Charter

Seeking Relief for Bali’s Reefs: Fishing Community at Serangan Island in Bali Working on Decades-Long Project to Restore Reef Destroyed by Developer in Mid-1990s


5 hectares of coral surrounding Serangan island near Sanur in Bali have been destroyed by beach reclamations work done at the location in 1996. According to, an estimated 20 years is now needed to rehabilitate the reef.

Wayan Patut, who is a an environmental activist and the head of the Sari Mertasegara fishing group, said: “When the reclamation was done in 1996 the reef, which is the breeding areas for a wide variety of sea life, was badly damaged. The original island measuring 112 hectares was expanded to become 481 hectares. You can just imagine how much coral reef was consumed in the process of creating new land areas.”

Patut told the press 5 hectares of coral reef was destroyed causing losses to local fishermen who live on Serangan island. “There’s no more fish that can be caught there due to the demolition of the reef by reclamation.”

In 2003 efforts began to rehabilitate the reef surrounding Serangan island. Fishermen who once contributed to the destruction of the reef are now working to rebuild coral through activities organized by the Sari Mertasegera fishing group.

Explained Patut: “Thus far, the fishing group at Serangan island has managed to plant 1.5 hectares of new coral from a targeted area of 10 hectares. The rehabilitation process will continue until the environment of Serangan island can be restored. This will take 20 years for the coral reef to regain its former status.”

© Bali Discovery Tours. Articles may be quoted and reproduced if attributed to All images and graphics are copyright protected.

Coral-list: IUCN Report “Coral Community Decline at Bonaire, Southern Caribbean”

Dear colleagues,
Following up on the IUCN report of the Bonaire Marine Park, I would like to draw your attention to a recently published article in Bulletin of Marine Science:

“Coral community decline at Bonaire, Southern Caribbean”


We assessed the status of coral reef benthic communities at Bonaire, Netherlands Antilles, in December 2008 and January 2009 through aprox 5 km of photo transects taken at depths of 5, 10, and 20 m at 14 locations around the island. Univariate and multivariate analyses detected significant variation in benthic communities among depths and locations, as well as between leeward and windward sides of the island. Mean percentage cover of scleractinian corals ranged between 0.2 percent and 43.6 percent at the study sites and tended to be lowest at 5-m depth. The survey recorded 40 scleractinian coral species from 19 genera, within 10 families. Faviidae were by far the most abundant scleractinian family at all depths (predominantly Montastraea spp.), followed by Agariciidae at 20 and 10 m, and by Astrocoeniidae at 5-m depth. Macroalgal cover exceeded scleractinian coral cover at nearly all sites, averaging 34.9 percent (all samples pooled), compared with a pooled mean coral cover of 15.4 percent. Windward reefs were characterized by prolific growth of the brown algae Sargassum spp., and leeward reefs by growth of turf algae, Dictyota spp., Trichogloeopsis pedicellata (Howe) I. A. Abbott and Doty, and Lobophora variegata (Lamouroux) Womersley ex Oliveira. Damage from recent hurricanes was evident from the presence of toppled and fragmented corals, the movement of sand, and exposure of cemented Acropora cervicornis (Lamarck, 1816) rubble on the shallow reef platform. The combination of algal dominance and low to moderate coral cover are symptomatic of partly degraded reef systems, particularly as they coincide with elevated nutrients and reduced herbivory.


Dr Sander Scheffers

Lecturer & Senior Research Fellow Southern Cross University
Honorary Research Fellow University of Queensland
Deputy Director Southern Cross Marine Science,
Associate Researcher Caribbean Research Institute for Management of Biodiversity (CARMABI), Curaçao (Netherlands Antilles)

Southern Cross University
PO Box 157, Lismore, NSW 2480, Australia

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William and Mary: VIMS study: propeller turbulence may affect marine food webs

by David Malmquist | April 25, 2011

A new study by researchers at the Virginia Institute of Marine Science shows that turbulence from boat propellers can and does kill large numbers of copepods-tiny crustaceans that are an important part of marine food webs.

The study-by VIMS graduate student Samantha Bickel, VIMS professor Kam Tang, and Hampton University undergraduate Joseph Malloy Hammond- appears in the March issue of the Journal of Experimental Marine Biology and Ecology.

The researchers don’t expect their findings to lead to any new “NoWake” signs in local waterways; their interest instead is to better understand how significant levels of propeller-induced mortality among copepods might affect local food webs in Chesapeake Bay and other highly trafficked waterways.

“Non-predatory mortality such as this is rarely considered in the literature,” says Bickel, “but it could be important for properly understanding zooplankton ecology and food-web dynamics in coastal and estuarine waters, particularly during summer months when recreational boating increases.”

Zooplankton are small drifting animals that consume algae and other microscopic floating plants. Copepods-shrimp-like crustaceans about the size of a rice grain-typically make up a major part of the zooplankton community and serve an important role by moving energy upthe marine food chain-from microscopic plants that are too small for most fish to eat up to larger game-fish and, ultimately,humans.

“If turbulence from boat propellers is killing off large numbers of copepods,” says Bickel, “it could be reducing the supply of food energy available to fish, and reducing zooplankton grazing of algal blooms.” “It’s like cutting down the number of zebras in a herd,” she adds. “That would affect not only the zebras, but also the grass they eat and the lions that eat them.”

This type of shift could potentially have a noticeable impact on marine food webs and water quality. “If a large portion of copepods are being killed, and if they sink down to the bottom, you could have additional high-quality organic material available for bottom-dwelling organisms to eat,” says Bickel. “If the amount is high enough, microbial decomposition could even perhaps contribute to development of localized low-oxygen ‘dead zones.'”

The researchers caution that there are untold millions of zooplankton in the world’s aquatic systems, so that when viewed at a global scale, the portion of copepods killed by boat-generated turbulence is probably minimal.

“The importance of turbulence as a source of mortality among copepods would be of much greater importance at a local scale,” saysBickel, “including highly trafficked areas near harbors and marinas, and within closed freshwater systems such as lakes.”

The research team studied propeller-induced mortality both in the field and laboratory. During the spring of 2010, they sampled copepods at three sites near the mouth of the Hampton River, a tributary of Chesapeake Bay. One site was a marina with numerous boats but minimal turbulence due to an imposed speed limit. The second was in a high-traffic area of a nearby navigational channel, where fast-moving boats generated considerable turbulence in their wakes. The third site was a tranquil shoreline opposite from the marina, with few boats and little or no boat-generated turbulence.

They compared the percentage of live and dead copepods collected from these sites using a dye that is only taken up by living copepods. The results of their comparison showed a much higher fraction of dead copepods in the channel (34%) than in the marina (5.9% dead) or along the shoreline (5.3%).

A field experiment in the York River near the VIMS campus confirmed the results of the Hampton River study. Here, they sampled copepods from within the wakes of passing boats, and again found a link between turbulence and mortality: the percentage of copepod carcasses increased from 7.7% outside the wakes to 14.3% inside the wakes.

The researchers were careful in both cases to minimize turbulence from their own vessel, using a rowboat for the Hampton River study and maintaining an idle during sampling in the York.

The team’s final experiment took place in the laboratory, where they exposed copepods to turbulence from a small motor calibrated to mimic the effects of different boat propellers. Their results again confirmed their earlier findings, with a clear link between mortality and increasing levels of turbulent energy.

Their experiments also show that natural turbulence from tides, currents, and waves is unlikely to stress or kill copepods other thanperhaps during an extreme storm event such as a hurricane ornor’easter.

Special thanks to Richard Charter

Nature: Biodiversity of wetlands may help keep water clean by Bradley Cardinale

8 April 2011 | EN

New Zealand wetlandsBiodiversity of wetlands may help keep water clean

Flickr/Brenda Anderson

Conserving biodiversity could help shield waterways against nitrogen pollution, says a study that showed how streams with more species are better at removing excess nutrients from water.

The findings imply that developing countries that keep rivers and lakes species-rich could save money on water treatment, Bradley Cardinale, author of the study and an aquatic ecologist from the University of Michigan, United States, told SciDev.Net.

The study, published in Nature yesterday (7 April), is the first rigorous analysis of how biodiversity improves water quality, Cardinale said.

Mopping up nitrogen compounds — a major cause of water pollution — released from agricultural fertilisers and waste, human sewage, and fossil fuel burning, is an important goal for environmental policy.

Scientists have long known that ecosystems with more biodiversity are better at mopping up pollutants like nitrogen. But there was little experimental evidence for why this happens. A leading theory is that different species make maximum use of nutrients because they each fill a unique biological habitat — niche.

Cardinale tested this theory in a laboratory experiment on algae.

He grew one to eight species of common algae in 150 artificial river channels. Some artificial streams had a single habitat, whilst others mimicked several natural habitats created by differences and disturbances in water flow in the streams.

Cardinale found that nitrogen uptake increased in more biodiverse streams, as long as there were varied habitats available in the stream. One stream with eight species removed nitrogen 4.5 times faster than the average for a single species stream, implying also “that biodiversity may help to buffer natural ecosystems against the ecological impacts of nutrient pollution”.

“Nature is much like a sports team. Each member has a different, but complementary, role to play,” Cardinale said. “And, as each of the players becomes better, they make for a more efficient team.”

He said it was difficult to know how far to extend the conclusions from this laboratory study but added that these results would probably apply to any habitat with partitioned niches.

Emily Stanley, a freshwater ecologist from the University of Wisconsin-Madison, United States, said: “These sorts of controlled lab experiments are important tools for suggesting how nature might work.  Cardinale has challenged us to see if this is the way things actually work in real world settings.”

And John Matthews, director of freshwater and adaptation at the non-governmental organisation Conservation International, said: “This study strengthens the arguments for how protecting biodiversity can be used to promote sustainable development”.

But he added that these findings will probably not be enough to prompt more action on conservation of biodiversity.

Link to full paper in Nature


Nature doi: 10.1038/nature09904 (2011)

Special thanks to Alfredo Quarto

Science Magazine: Organic Aerosol Formation Downwind from the Deepwater Horizon Oil Spill by J.A. de Gouw, A.M. Middlebrook, C. Warneke, et. al.
Science 11 March 2011:
Vol. 331 no. 6022 pp. 1295-1299
DOI: 10.1126/science.1200320

A large fraction of atmospheric aerosols are derived from organic compounds with various volatilities. A National Oceanic and Atmospheric Administration (NOAA) WP-3D research aircraft made airborne measurements of the gaseous and aerosol composition of air over the Deepwater Horizon (DWH) oil spill in the Gulf of Mexico that occurred from April to August 2010. A narrow plume of hydrocarbons was observed downwind of DWH that is attributed to the evaporation of fresh oil on the sea surface. A much wider plume with high concentrations of organic aerosol (>25 micrograms per cubic meter) was attributed to the formation of secondary organic aerosol (SOA) from unmeasured, less volatile hydrocarbons that were emitted from a wider area around DWH. These observations provide direct and compelling evidence for the importance of formation of SOA from less volatile hydrocarbons.

Special thanks to Richard Charter

Huffington Post: Coral Reefs May Be Gone By 2050: Study

Coral Reef

The Huffington Post  Joanna Zelman  Posted: 02/25/11 08:37 AM


A recent study has found that all of the world’s coral reefs could be gone by 2050. If lost, 500 million people’s livelihoods worldwide would be threatened.

The World Resources Institute report, “Reefs at Risk Revisited,” suggests that by 2030, over 90 percent of coral reefs will be threatened. If action isn’t taken soon, nearly all reefs will be threatened by 2050. Jane Lubchenco, administrator of the National Oceanic and Atmospheric Administration states, “Threats on land, along the coast and in the water are converging in a perfect storm of threats to reefs.”

The AFP suggests that these threats include overfishing, coastal development, pollution, and climate change. Warming sea temperatures lead to coral bleaching, a stress response where corals expose their white skeletons. In 2005, the Caribbean saw the most extensive coral bleaching event ever recorded, often attributed to rising ocean temperatures. CO2 emissions are also making the oceans more acidic. Because of the rising acidity levels, some scientists claim we will see conditions not witnessed since the period of dinosaurs.

Lauretta Burke, one of the report’s lead authors, feels that quick action could help save the reefs. She encourages policymakers to reduce overfishing and cut greenhouse gas emissions. If action is not taken though, millions of people will suffer. Shorelines will lose protection from storms — a Time Magazine post suggests that up to 90 percent of the energy from wind generated waves is absorbed by reef ecosystems. If reefs are lost, coastal communities will lose a source of food security and tourism.

Special thanks to Erika Biddle.

Coral-list: P.L. Harrison: New Coral Global Reproduction Review Available


the following global coral reproduction review chapter has recently
been published in Dubinsky and Stambler’s book:

Harrison, P.L. (2011). Sexual reproduction of scleractinian corals.
In: Z. Dubinsky and N. Stambler (Editors), Coral Reefs: An Ecosystem
in Transition Part 3, 59-85,
DOI: 10.1007/978-94-007-0114-4_6 Springer Publishers.

This new review presents a synthesis of current global knowledge of
coral reproduction and updates aspects of the earlier major review by
Harrison, P.L. and Wallace, C.C. (1990), with particular emphasis on
new data and molecular perspectives that have emerged during the past
two decades.

Some key points that may be of interest:
Information on sexual reproduction is now available for 444
scleractinian coral species (almost double the number of species
compared with the 230 species whose reproductive characteristics had
been studied by the late 1980s).

The global data confirm many of the trends noted previously: the
great majority of species that have been studied are hermaphroditic
broadcast spawers (64.5%) with fewer gonochoric spawners (19.5%) and
relatively few hermaphroditic brooders or gonochoric brooders
recorded. However, there are a number of species for which mixed
sexual patterns/sex change and/or both brooding and spawning modes of
development have been recorded hence these sexual patterns and modes
of development are not simple binary characteristics for all
scleractinian corals.

Biogeographical patterns are even more complex:  multispecific
spawning has been recorded in many reef regions, but the scale of
spawning and degree of reproductive synchrony within and among
populations of different species forms a continuum from largely
asynchronous patterns through to highly synchronised mass spawning

If you want to know more please contact me.  Read the actual paper here. Harrison 2011 Coral Reproduction Review[1]

cheers, Peter

Professor Peter Harrison, PhD
Director of Marine Studies SCU
Director, Marine Ecology Research Centre
Research Leader, Coral Reef and Whale Research Teams
Marine Science and Management Course Coordinator
School of Environmental Science and Management
Southern Cross University, PO Box 157
Lismore NSW 2480   AUSTRALIA
Patron, Banyan Tree Marine Labs, Maldives
SCU Phone: 0266 203774    Fax: 0266 212669
Mobile: 0407456249
International Phone: 61 266 203774   International Fax: 61 266 212669
Special thanks to:

Coral-List mailing list

Global Coral Disease Database: Welcome to the

The GCDD is the result of a collaboration between UNEP-WCMC and NOAA NMFS. The project aims to collate information on the global distribution of coral diseases, in order to contribute to the understanding of coral disease prevalence. The GCDD is a compilation of information from scientific literature gathered before 2007 (archive data), as well as new contributions from users. The content of the database is being continually updated by users, creating a sustainable platform for the dissemination of coral disease data.

Oceana: Ocean Acidification: The Untold Stories

download the entire report at:

November 1, 2010

Our use of fossil fuels, deforestation and land use changes are wreaking havoc on the  oceans. Besides causing global climate change, which could cause catastrophic impacts around the world, the release of carbon dioxide from these activities is also leading to ocean acidification. The oceans ultimately absorb most carbon dioxide from the atmosphere, and thus play a critical role in regulating climate. They also help to mitigate human caused climate change. But the unprecedented amount of carbon dioxide being created by human activity has surpassed what the oceans can healthfully absorb, changing ocean chemistry and making them more acidic.

Acidity is measured on a pH scale, where lower pH indicates more acidic water. Ocean pH has dropped by thirty percent globally during the last two hundred years. Even though the drop in pH appears small (from 8.2 to 8.1), the pH scale is logarithmic, meaning that this change is large enough that it may already be beginning to affect some of the oceans most beloved and biologically important residents, including corals.

The changing acidity of the oceans threatens to throw off the delicate chemical balance upon which marine ife depends for survival. The scant attention this issue has received has focused primarily on corals, which are threatened with extinction within this century unless we change course. Corals are the framework builders of reefs, by far the most diverse ecosystems of our oceans. However, the effects of acidification are not going to stop with reefs, like dominoes, the impacts are going to be far-reaching throughout the oceans.

ArticleSafari: Dolphin DNA Very Close to Human

Seema Kumar, of Discovery Channel Online, writes that scientists have discovered that the genetic make-up of dolphins is amazingly similar to humans. They’re closer to us than cows, horses, or pigs, despite the fact that they live in the water.

The extent of the genetic similarity came as a real surprise to us,” says David Busbee of Texas A&M University. He hopes his research will reveal how long ago humans and dolphins branched off the evolutionary tree. There’s been some speculation that dolphins and whales, who breathe air, may have returned to the water AFTER first evolving into land animals.

Dolphins are marine mammals that swim in the ocean and it was astonishing to learn that we had more in common with the dolphin than with land mammals,” says geneticist Horst Hameister.

Busbee says, “If we can show that humans are similar to dolphins, and anything that endangers dolphins is an equal concern for humans, it may be easier to persuade governments to keep oceans clean.

There are still many mysteries about the beings who share the earth with us. Humans and dolphins may have much more in common than people think, especially when it comes to genetics.

In a Sea Grant-funded project, Texas A&M University veterinarians are comparing human chromosomes to those of dolphins and are finding that the two share many similarities. The scientists hope to use these similarities to identify and map the genes of dolphins.

Genes are organized into segments along the length of a chromosome – a tightly wound spool of DNA. This spool is made up of two, complementary, single strands of DNA bound together. Every living thing has a characteristic number of chromosomes, and each chromosome carries different genes. Dolphins have 44 chromosomes, and humans have 46. Dr. David Busbee and his team applied human “paints,” fluorescently labeled pieces of human chromosomes, to dolphin chromosomes on microscope slides. Scientists broke open dolphin cells, releasing chromosomes onto slides. The dolphin chromosomes were then treated with labled human chromosome pieces, providing the opportunity for complementary DNA strands to match up.

When scientists examined the photos taken with a fluorescence microscope, they found dolphin chromosomes fluorescently tagged with the labeled, or “painted,” pieces of human chromosomes and concluded that dolphins hold many of the same chromosomes as humans. “We started looking at these and it became very obvious to us that every human chromosome had a corollary chromosome in the dolphin,” Busbee said. “We’ve found that the dolphin genome and the human genome basically are the same. It’s just that there’s a few chromosomal rearrangements that have changed the way the genetic material is put together.

Dolphins have been viewed as somehow magical for millennia by humans. They’re one of the only animals that appear to play, leaping out of the water and doing tricks, and the bottlenose dolphin even seems to grin widely at everything. It was inevitable that such a remarkable animal also collected a remarkable mythology that extends through today.

The first documented culture that seems to have mythology associated with the dolphin was the Minoan, a seafaring people in the Mediterranean. They left few written records, but they did leave beautiful murals on the walls of their palaces, murals that show the importance of dolphins in their mythology.

Because they were strongly associated with Poseidon by the later Greeks, this probably explains why the sea god was so often surrounded by dolphins. In one myth about Poseidon, dolphin messengers were sent to bring him a nymph he loved, who he later married. As a reward, he set the dolphin in the sky as a constellation. And he was constantly accompanied by dolphins among other sea creatures.

This wasn’t the last time the Greeks associated dolphins with romance. Aphrodite is often depicted with dolphins, riding them or being accompanied by them. Later, the god Dionysus transformed the way dolphins were perceived in Greek literature. He was set upon while at sea by a band of pirates. Instead of simply destroying the sea raiders, he transformed them into a pod of dolphins, charging them to rescue any distressed sailors in the ocean.


Pirates transforming into dolphins. Drawing from an Etruscan Black Figure Hydria, 510-500 BC


Special thanks to Larry Lawhorn.

Science Mag: Record hot summer wreaks havoc — record high temps, record low ice volume

Science Now reports that NASA says this year so far is the hottest on record in the 131 years of record keeping.  Nearly 0.7 C hotter than the average from 1951 to 1980, and NOAA has found essentially the same thing using different data.  Nightime temperatures hit record highs in 37 states of the US this summer.  The National Snow and Ice Data Center in Boulder, Colorado, has found near-record ice area loss so far this year in the Arctic Ocean, and expects the area to hit a record low this year.  Ice volume is at a record low, 10,000 cubic kilometers lower than the average of the last 30 years.  Ice volume is being lost at 17% per decade.  The open sea surface absorbs much more light energy than the white ice, trapping more heat. Since coral disease outbreaks have been reported following some bleaching events, I’d suggest people keep disease in mind for monitoring as well, if a bleaching event develops in their area.  The diseases can cause a significant proportion of the total mortality.

Doug Fenner, Coral-list 9/21/10

Record Hot Summer Wreaks Havoc

by Eli Kintisch on 15 September 2010, 5:10 PM |

Hot trends.  In the Arctic, the past 4 years have had the four smallest recorded extents of sea ice.   Coral has suffered in warm water temperatures near the equator in 1997 and this year, both due in part to El Niño.

Record-breaking summer temperatures and the warmest year to date in 131 years are wreaking havoc on the global environment, say climate scientists.

The National Snow and Ice Data Center (NSIDC) in Boulder, Colorado, is about to report near-record loss of sea ice this summer, and modelers say total ice volume is at a record low. Meanwhile, the National Oceanic and Atmospheric Administration (NOAA) has issued warnings about coral bleaching throughout the Caribbean, a problem exacerbated by high water temperatures in the Atlantic Ocean.

According to NASA’s Goddard Institute for Space Studies, the first 8 months of 2010 is the warmest such January-to-August period in climate records stretching back 131 years. This period was nearly 0.7˚C warmer than the average temperature from 1951 to 1980. (NOAA announced roughly the same finding today, using many of the same temperature stations but a different analysis method.) Scorching summer temperatures set records across the United States, and nighttime temperatures hit record highs in 37 U.S. states this summer, the Natural Resources Defense Council will announce in a new report tomorrow.

Science has learned that NSIDC expects this summer to yield the third lowest area of ice “extent” in the Arctic. The ice has reached its yearly minimum, which generally occurs in September.

“Extent” means the area of icy water—essentially, areas with more than 15% of the surface covered with ice. The past 4 years have yielded the four smallest extents of sea ice in the Arctic, says NSIDC.

NSIDC climatologist Julienne Stroeve told ScienceNOW that warmer-than-average ocean temperatures were a factor in this summer’s sea-ice losses, but so are circulation patterns that push sea ice toward the pole, opening up water that can be warmed by the sun. In addition, she notes, “there’s a lot less of the old ice” in the Arctic due to its recent formation and relative thinness.

Arctic experts at the University of Washington use temperature, satellite, and weather data in a computer model to estimate the total volume of ice in the area. According to their model, the total ice volume in the Arctic is now at an all-time low, nearly 10,000 cubic kilometers less than the average of the past 30 years. “We think there is a lot of thin ice up there, but there’s little data to validate [that],” says Ron Lindsay of the University of Washington, Seattle. Overall, he says, the model suggests a stunning 17% loss of ice volume per decade.

A moderate El Niño event that began last year and ended earlier this summer has contributed to rising global ocean temperatures. El Niño periods, characterized by a redistribution of heat in the Pacific Ocean, lead to warming on the western and eastern sides of the Pacific and the western Atlantic. A very vigorous 1997–98 El Niño led to record-setting temperatures over the oceans and land. Even though this year’s warming due to El Niño is smaller, trends in ocean temperature have roughly matched 1997–98 thus far due to an overall warmer system. The trend is especially clear in waters near the equator.

The biggest immediate effect of warmer ocean temperatures in the tropics has been the extraordinary death of corals, as Science laid out 3 weeks ago:

Reefs on both sides of the Thai Peninsula were hit, with up to 100% of some coral species bleached, says James True, a coral biologist at Prince of Songkla University in Hat Yai, Thailand. He expects at least 80% of the most sensitive species to die. “A few inshore reefs got so badly damaged, they probably won’t ever come back to the way they were,” he says. Among surviving corals, “disease is rampant,” True says, with two to three times the usual incidence of necrotic lesions and growth anomalies. Similar reports of “quite extensive bleaching” have come from Vietnam and through the heart of the Coral Triangle in Indonesia and the Philippines.

Experts told Al Jazeera that up to 20% of the coral off the shore of Malaysia could die this fall. A dive instructor interviewed there said he had seen neither bleached coral nor 34˚C water in 6 years of working there. The Malaysian government has closed 13 sites to divers and snorkelers to try to mitigate the damage.

Meanwhile, in the Caribbean, according to a new bulletin put out by NOAA last week:

The NOAA Coral Reef Watch (CRW) satellite coral bleaching monitoring shows sea surface temperatures continue to remain above average throughout the wider Caribbean region. Large areas of the southeastern Caribbean Sea are experiencing thermal stress capable of causing coral bleaching. The western Gulf of Mexico and the southern portion of the Bahamas have also experienced significant bleaching thermal stress. The CRW Coral Bleaching Thermal Stress Outlook … indicates that the high stress should continue to develop in the southern and southeast Caribbean until mid-October . Bleaching stress in the western Gulf of Mexico and southern Bahamas should dissipate quickly in the next couple of weeks.

A reprieve from the sweltering temperatures is coming, but it will only be temporary. Columbia University’s Richard Seager says the now-ended El Niño phase has been followed by a La Niña phase, which usually means cooler average global ocean and land temperatures. El Niño will eventually return. More importantly, as the planet’s average temperature warms, Seager says, the El Niño-La Niña cycles “cancel one another out.”

Ohio State Un: PhD Graduate Research Opportunity In Coral Bleaching & Ocean Acidification


Desired (but not required) qualifications:
– MSc in Marine Science, Geology, Biology, or any physical
science.  Exceptional applicants without an MSc will also be considered.
– Experience in isotope biogeochemistry, organic chemistry, or
relevant coursework
– Tropical fieldwork experience or coral aquaculture experience
– The successful candidate must be accepted into the graduate program
in the School of Earth Sciences at The Ohio State University

The position starts in September 2011 and includes four years of
support.  Please submit applications electronically by following the
instructions at
Indicate that you would like to study with Dr. Grottoli in your
application.  In addition, send a complete copy of your application
materials as a single .pdf file to Dr. Andrea G. Grottoli at (Note: File should contain copy of your research
statement, a cover letter, resume, GRE scores, the names and contact
information of three references, and a list of relevant course with
grades).  Please indicate “Graduate student application” in the
subject line.  For more information on Dr. Grottoli’s research
program, please visit
Application deadline is 5 January 2011.  OSU is an equal
opportunity/affirmative action employer.
Andrea G. Grottoli, Associate Professor
Ohio State University
School of Earth Sciences
125 South Oval Mall
Columbus, OH 43210

office:  614-292-5782
lab: 614-292-7415
cell: 215-990-9736
fax: 614-292-7688

Grottoli webpage:
Fieldwork Micro-blog:
Stable Isotope Biogeochemistry Laboratory (SIB Lab):
SES seminars:

Office location: 329 Mendenhall Labs

Special thanks to Coral-list

Institute for Tropical Ecology & Conservation: Field Course in Coral Reef Ecology in Panama

2010 WINTER COURSE ANNOUNCEMENT (December 20th- January 9th)


LOCATION:  The field courses will take place at the Institute for Tropical Ecology and Conservation (ITEC) Bocas del Toro Biological Station, Boca del Drago, Isla Colon, Bocas del Toro, Panama:

The Bocas del Toro (“mouths of the bull”) Biological Station is located on the north end of Isla Colón in an area known as Boca del Drago (“mouth of the dragon”). Isla Colón is the northern-most of five large islands and hundreds of smaller ones that form the Bocas del Toro Archipelago. Set in Almirante Bay on the Caribbean side of western Panama, this collection of islands is sometimes referred to as the “Galapagos of Central America”. This is because, after having been isolated for 10,000 years by geologic activity, each of the islands has evolved its own unique biota. Taking its name from Christopher Columbus who sailed into this region in 1502, Isla Colón is approximately 14 km long and 7 km wide. Isla Colón is composed primarily of limestone, and has a hilly topography supporting primary and secondary tropical rain forest. This island has a 5 km beach (Bluff Beach) on its east side, mangroves on its west side, and caves in the interior. Marine habitats include extensive turtle grass beds, hard and soft coral reefs, beaches, rocky intertidals, mangrove forests and estuaries.

Isla Colón has the highest human population in the archipelago, with most individuals living in the town of Bocas del Toro located on the far side of the island from our facility. Besides being biologically diverse, the region is also culturally diverse with a mix of Latin American, Afro-Caribbean and indigenous Ngöbe. Spanish is the official language but English is spoken. Many Ngöbe speak only their native dialect. There are only two roads on the island, both originating in the town of Bocas. One road travels along the eastern margin of the island to Bluff Beach and the other cuts through the island’s interior to Boca del Drago, where our facility is located.

INSTRUCTOR: Carlos Gustavo A. Ormond, Simon Fraser University; Conservation Science Institute; Coalición por los Tiburones (Shark Coalition), email:; Elizabeth McGinty (TA), University of Texas at Arlington, email:

COURSE LENGTH AND SCHEDULE: Winter field courses are three weeks in length (December 20th- January 9th).

TUITION: $1650 USD. Tuition fee includes all room and board, local transportation and a three-day field trip to the Boquete cloud forest on Panama’s mainland.

REGISTRATION DEADLINE: November 20, 2010. Since registration is limited to 10 students, we recommend those interested to contact the Carlos in order for him to be aware of your application.

COURSE DESCRIPTION: This course is designed to promote the desire for not only discovery and advanced understanding of coral reef ecosystems from an integrated ecological perspective but also an appreciation and understanding of the Latin American and Caribbean (LAC) culture. In addition to learning coral reef ecosystem dynamics, organism identification, and experimental design, this course will also investigate human dimensions in coral reef ecosystems, both past and present. To compliment the course and for the pure enjoyment of learning a new language, students will be taught a “Spanish for Survival” at the beginning of the session.

By taking an integrated multidisciplinary approach, this course will demonstrate the importance of melding traditional approaches to understanding and investigating coral reef ecosystems with the human dimension. A large component of the course will involve field work, complimented by lectures and discussions on daily course readings. The course will require the completion of group assignments, as well as an individual research project that may be as much sociological as it is ecological in theory. Therefore, the course will not only be of interest to those of you in the natural sciences but also those of you from the social sciences.

General Topics
•        Spanish Language
•        Environmental History and Cultural Anthropology of Panama
•        Coral Reef Formation and Oceanography
•        Coral Reef Ecology
•        Sampling Methods
•        Research Design
•        Present State of Coral Reefs
•        Coral Reef Conservation issues
•        Human Rights and the Environment in Latin America
•        Global Environmental Governance

NOTE: Dive certification is not necessary to enroll in this course, but what is required is an attraction to the ocean and a comfort in being in it. All students will require snorkel equipment (mask and fins) and those with SCUBA certification are expected to bring their own BCD, regulator, and most importantly proof of certification. There is the possibility of renting dive equipment as well as receiving dive certification from the local dive shops. If this is something that interests you, please contact Carlos for more information.

COURSE CREDIT: Up to six units of credit will be granted for these courses. Credit must be arranged by the student through his/her academic advisor and university.  Contact ITEC for details.

CONTACT: Institute for Tropical Ecology and Conservation (ITEC); 1023 SW 2nd Ave., Gainesville, FL 32601; phn: 352-367-9128, fax: 352-367-0610,, or Carlos Gustavo A. Ormond  Please visit us on the web at  ITEC is a Non-profit (501c3) organization.

* Aunque esta clase está presentada en inglés, si sos hispanoparlante y estás interesado/a en tomar esta clase sobre los arrecifes de coral por favor comunícate conmigo, Carlos Gustavo A. Ormond

Special thanks to Coral-list

New York Times: Extreme Heat Puts Coral Reefs at Risk, Forecasts Say

Coral bleaching, like that seen in the Flower Garden Banks off the Texas-Louisiana border, is an indicator of heat stress.    By JUSTIN GILLIS

Published: September 20, 2010

>From Thailand to Texas, many corals are reacting to heat stress by shedding their color and going into survival mode, putting the oceans’ richest ecosystems and fisheries at risk.
September 20, 2010
Extreme Heat Puts Coral Reefs at Risk, Forecasts Say
This year’s extreme heat is putting the world’s coral reefs under such severe stress that scientists fear widespread die-offs, endangering not only the richest ecosystems in the ocean but also associated fisheries that feed millions of people.

>From Thailand to Texas, corals are reacting to the heat stress by bleaching, or shedding their color and going into survival mode. Many have already died, and more are expected to do so in coming months. Computer forecasts of water temperature suggest that corals in the Caribbean may undergo drastic bleaching in the next few weeks.

What is unfolding this year is only the second known global bleaching of coral reefs. Scientists are holding out hope that this year will not be as bad, over all, as 1998, the hottest year in the historical record, when an estimated 16 percent of the world’s shallow-water reefs died. But in some places, including Thailand, the situation is looking worse than in 1998.

Scientists say the trouble with the reefs is linked to climate change. For years they have warned that corals, highly sensitive to excess heat, would serve as an early indicator of the ecological distress on the planet caused by the buildup of greenhouse gases.

“I am significantly depressed by the whole situation,” said Clive Wilkinson, director of the Global Coral Reef Monitoring Network, an organization in Australia that is tracking this year’s disaster.

According to the National Oceanic and Atmospheric Administration, the first eight months of 2010 matched 1998 as the hottest January to August period on record. High ocean temperatures are taxing the organisms most sensitive to them, the shallow-water corals that create some of the world’s most vibrant and colorful seascapes.

Coral reefs occupy a tiny fraction of the ocean, but they harbor perhaps a quarter of all marine species, including a profusion of fish. Often called the “rain forests of the sea,” they are the foundation not only of important fishing industries but also of tourist economies worth billions.

Drastic die-offs of coral were seen for the first time in 1983 in the eastern Pacific and the Caribbean, during a large-scale weather event known as El Niño. During an El Niño, warm waters normally confined to the western Pacific flow to the east; 2010 is also an El Niño year.

Serious regional bleaching has occurred intermittently since the 1983 disaster. It is clear that natural weather variability plays a role in overheating the reefs, but scientists say it cannot, by itself, explain what has become a recurring phenomenon.

“It is a lot easier for oceans to heat up above the corals’ thresholds for bleaching when climate change is warming the baseline temperatures,” said C. Mark Eakin, who runs a program called Coral Reef Watch for the National Oceanic and Atmospheric Administration. “If you get an event like El Niño or you just get a hot summer, it’s going to be on top of the warmest temperatures we’ve ever seen.”

Coral reefs are made up of millions of tiny animals, called polyps, that form symbiotic relationships with algae. The polyps essentially act as farmers, supplying the algae with nutrients and a place to live. The algae in turn capture sunlight and carbon dioxide to make sugars that feed the coral polyps.

The captive algae give reefs their brilliant colors. Many reef fish sport fantastical colors and patterns themselves, as though dressing to match their surroundings.

Coral bleaching occurs when high heat and bright sunshine cause the metabolism of the algae to speed out of control, and they start creating toxins. The polyps essentially recoil. “The algae are spat out,” Dr. Wilkinson said.

The corals look white afterward, as though they had been bleached. If temperatures drop, the corals’ few remaining algae can reproduce and help the polyps recover. But corals are vulnerable to disease in their denuded condition, and if the heat stress continues, the corals starve to death.

Even on dead reefs, new coral polyps will often take hold, though the overall ecology of the reef may be permanently altered. The worst-case situation is that a reef dies and never recovers.

In dozens of small island nations and in some coastal areas of Indonesia and the Philippines, people are heavily dependent on reef fish as a source of protein. The death of corals is not immediately lethal to the fish, but if the coral polyps do not recover, scientists say the reef can eventually collapse, and the associated fishery will become far less productive.

Research shows that is already happening in parts of the Caribbean, though people there are not as dependent on fishing as those living on Pacific islands.

It will be months before this year’s toll is known for sure. But scientists tracking the fate of corals say they have already seen widespread bleaching in Southeast Asia and the western Pacific, with corals in Thailand, parts of Indonesia and some smaller island nations being hit especially hard earlier this year.

Temperatures have since cooled in the western Pacific and the immediate crisis has passed there, even as it accelerates in places like the Caribbean where the waters are still warming. Serious bleaching has been seen recently in the Flower Garden Banks, a marine sanctuary off the Texas-Louisiana border.

In Thailand, “there some signs of recovery in places,” said James True, a biologist at Prince of Songkla University. But in other spots, he said, corals were hit so hard that it is not clear young polyps will be available from nearby areas to repopulate dead reefs.

“The concern we have now is that the bleaching is so widespread that potential source reefs upstream have been affected,” Dr. True said.

Even in a hot year, of course, climate varies considerably from place to place. The water temperatures in the Florida Keys are only slightly above normal this year, and the beloved reefs of that region have so far escaped serious harm.

Parts of the northern Caribbean, including the United States Virgin Islands, saw incipient bleaching this summer, but the tropical storms and hurricanes moving through the Atlantic have cooled the water there and may have saved some corals. Farther south, though, temperatures are still remarkably high, putting many Caribbean reefs at risk.

Summer is only just beginning in the Southern Hemisphere, but water temperatures off Australia are also above normal, and some scientists are worried about the single most impressive reef on earth. The best hope now, Dr. Wilkinson said, is for mild tropical storms that would help to cool Australian waters.

“If we get a poor monsoon season,” he said, “I think we’re in for a serious bleaching on the Great Barrier Reef.”

Coral-list: Media and Oil Spill Science; disclosure of conflicts of interest

Reply |Bill Allison to Steve, coral-list
show details August 29, 2010

Good-day Steve:

Disclosure is not a novel concept (e.g., Harding, 1949), and is required by
most journals (e.g., Davidoff and DeAngelis, 2001). Is it unreasonable to
expect it in politically and economically freighted discussions on this
Harding, T. S. (1949). “Vested Interests in Scientific Research.” American
Journal of Economics and Sociology 8(2): 181-192.
A prominent industrialist once spoke of scientific research as being “the
first line of defense of the capitalistic dynamic economy as opposed to a
State-planned economy.” Science thus itself becomes propaganda. Very often
what appears to be an authentic scientific publication is nothing but
disguised propaganda.

Davidoff, F., C. D. DeAngelis, et al. (2001). “Sponsorship, authorship and
accountability.” Canadian Medical Association Journal 165(6): 786-788.

What follows was abstracted from the section on publication ethics from the
“Uniform Requirements for Manuscripts Submitted to Biomedical Journals:
Writing and Editing for Biomedical Publication”. This was adopted as CMAJ
policy on May 11, 2001.

Financial relationships (such as employment, consultancies, stock ownership,
honoraria, paid expert testimony) are the most easily identifiable conflicts
of interest and the most likely to undermine the credibility of the journal,
the authors, and of science itself. p.787

On Sat, Aug 28, 2010 at 11:15 PM, Steve Mussman <>wrote:

> Realizing that there is a spirited consensus (based on remarks
> posted in previous discussions) that we keep this list from becoming
> politically charged, I would like to momentarily step between adversaries
> involved in the discussion on the media and oil spill science.
> My fear is that without modification we may ultimately lose
> the opportunity to candidly discuss issues that are in vital need
> of being aired among members of this forum.
> Considering that there is an obvious call for scientists to communicate
> more directly with the public on so many contemporary issues,
> although fully unauthorized, I would like to make a suggestion.
> When participants are identifying themselves (by citing credentials)
> it might help to avoid undue controversy (and the associated
> animus this sometimes creates) if they would freely reveal any
> affiliations that might reflect even the potential for a conflict of
> interest.
> In this way, perhaps we can assure the continuation of these much needed
> and valued discussions and, at the same time, be able to more accurately
> assess and evaluate the opinions expressed without eliciting resentment.
> Steve Mussman
> Totally void of credentials worthy of mention.
> Just an old diver and self-avowed ocean and marine life advocate.

August 30th, Bill provided this additional information:

Here are my notes on the Davidoff article if the elaboration is useful.
Davidoff, F., C. D. DeAngelis, et al. (2001). “Sponsorship, authorship and accountability.” Canadian Medical Association Journal 165(6): 786-788.
What follows was abstracted from the section on publication ethics from the “Uniform Requirements for Manuscripts Submitted to Biomedical Journals: Writing and Editing for Biomedical Publication”. This was adopted as CMAJ policy on May 11, 2001. The full revised “Uniform Requirements” will be published later.
Financial relationships (such as employment, consultancies, stock ownership, honoraria, paid expert testimony) are the most easily identifiable conflicts of interest and the most likely to undermine the credibility of the journal, the authors, and of science itself. p.787
When authors submit a manuscript, whether an article or a letter, they are responsible for disclosing all financial and personal relationships between themselves and others that might bias their work. To prevent ambiguity, authors must state explicitly whether potential conflicts do or do not exist. Authors should do so in the manuscript on a conflict of interest notification page that follows the title page, providing additional detail, if necessary, in the accompanying cover letter. p.788
Biases potentially introduced when sponsors are directly involved in research are analogous to methodological biases of other sorts; some journals therefore choose to include information about the sponsor’s involvement in the methods section of the published paper. p.788
Editors should avoid selecting external peer reviewers with obvious potential conflicts of interest, for example, those who work in the same department or institution as any of the authors. p.788
If a study is funded by an agency with a proprietary or financial interest in the outcome, editors may ask authors to sign a statement such as, “I had full access to all of the data in this study and I take complete responsibility for the integrity of the data and the accuracy of the data analysis.” Editors should be encouraged to review copies of the protocol and/or contracts associated with project-specific studies before accepting such studies for publication.
Editors who make final decisions about manuscripts must have no personal, professional or financial involvement in any of the issues they might judge. Other members of the editorial staff, if they participate in editorial decisions, must provide editors with a current description of their financial interests (as they might relate to editorial judgments) and disqualify themselves from any decisions where they have a conflict of interest. p.788
Editors should avoid submitting to their own journal reports of original research to which they have contributed as authors. p.788

>Special thanks to Coral-list

Marine Pollution Bulletin: Modeling patterns of coral bleaching at a remote Central Pacific atoll.

Williams GJ, Knapp IS, Maragos JE, Davy SK (2010) Marine Pollution Bulletin 60: 1467-1476
Link to paper through ScienceDirect:
This paper reports on the effects of the late 2009 El Nino on the reefs at Palmyra Atoll National Wildlife Refuge, Northern Line Islands, Central Pacific.

A mild bleaching event occured (9.2% prevalence) in response to the elevated and sustained temperatures and we relate local environmental conditions to spatial patterns of bleaching.

Special thanks to Coral-list and  Gareth J. Williams (on behalf of the authors) who posted this.

NOAA Coral Reef Watch: Analysis of Current Coral Bleaching Thermal Stress & Seasonal Guidance through November 2010

(August 2010)


The Coral Reef Watch (CRW) satellite coral bleaching monitoring shows
sea surface temperatures (SSTs) have been above average throughout the
Caribbean and Gulf of Mexico, and are already above the bleaching
threshold in some areas. The CRW Coral Bleaching Thermal Stress Outlook
indicates that there is a high potential for thermal stress capable of
causing coral bleaching in the Caribbean in 2010. The intensity of the
stress is likely to increase until mid-October.

According to the CRW HotSpot, there is currently bleaching-level thermal
stress around a large region in the northwestern Pacific, with the
highest stress currently centered on the Philippines. Note that clouds
have covered these areas for a prolonged time period, so satellite data
have not been updated regularly at many locations in this region. This
may be causing the CRW products to overestimate the thermal stress. The
outlook shows that the thermal stress in the northeastern Philippines is
expected to linger into September. The potential of high thermal stress
is predicted to spread east into Guam, the Commonwealth of the Northern
Mariana Islands, the Federated States of Micronesia, and the surrounding
areas. Dissipation of this thermal stress may begin in mid- to

The southern hemisphere and the entire Indian Ocean basin are expected
to remain free from significant bleaching thermal stress through
November 2010.

(See full alert message with figures at

*Caribbean Analysis and Outlook: *

/Current conditions:/

The CRW satellite monitoring shows that the development of thermal
stress has already started in the Caribbean, bearing a similar signature
to the thermal stress observed at the same time period in 2005, the year
of a record mass coral bleaching event. SSTs in most of the Caribbean
region and tropical Atlantic Ocean have been significantly above the
normal for most of 2010. Temperatures in the Gulf of Mexico and Florida
Keys increased dramatically in early May, rising nearly 2°C over several
days at some locations. Warming in Florida followed an extreme cold
outbreak in January 2010 that resulted in significant coral mortality..
Two tropical storms (Alex in June and Bonnie in July) and other tropical
depressions have temporarily relieved some thermal stress in the
northern Caribbean, Gulf of Mexico, and Florida Keys. However, the
thermal stress has quickly bounced back in these areas. Bleaching
recently has been reported from parts of Puerto Rico. Degree Heating
Weeks currently show low to medium levels of thermal stress built up in
the northern Bahamas and the central Lesser Antilles island arc,
centered east of Dominica and Guadeloupe. DHWs around 4, high enough to
cause significant bleaching, have been observed on the Caribbean coast
of Panama and Costa Rica.

/Bleaching outlook: /

The CRW Coral Bleaching Thermal Stress Outlook continues to indicate a
high potential for thermal stress capable of causing significant coral
bleaching in the Caribbean in 2010. The region potentially at greatest
risk fills the region east from Nicaragua past the island of Hispaniola
to Puerto Rico and the Lesser Antilles, and south along the Caribbean
coasts of Panama and South America. The intensity of the potential
thermal stress is predicted to increase until mid-October. The Caribbean
typically experiences elevated temperature during the second year of an
El Niño event, with the 2009-2010 El Niño ending in May 2010. The region
described here as having the highest potential to experience
bleaching-levels of thermal stress is the same region that has been
anomalously warm for most of 2010.

/Comparison to the 2005 mass bleaching event: /

In 2005, a record breaking mass coral bleaching event in the Caribbean
along with the most active hurricane season on record in the Atlantic
Ocean followed a similar pre-bleaching season SST anomaly pattern. This
preheating increases the likelihood that temperatures will exceed
bleaching thresholds during the following bleaching season, indicating
high potential for thermal stress above levels required for significant
coral bleaching.

In 2005, the active hurricane season cooled waters in the Florida Keys
and Gulf of Mexico greatly reducing the coral bleaching stress. However,
the lack of tropical cyclones around the Lesser Antilles contributed to
consistently warm temperatures in the epicenter of the 2005 mass coral
bleaching event. This year, two tropical storms (Alex in June and Bonnie
July) and other tropical depressions have temporarily relieved some
thermal stress in the northern Caribbean, Gulf of Mexico, and Florida
Keys. However, the thermal stress has quickly bounced back in these
areas. Given the record-breaking mass coral bleaching in 2005 and the
similarity in the pattern of the thermal stress between this year and
2005, the development of this year’s thermal stress in the Caribbean
needs to be monitored closely.
*Northwestern Pacific Analysis and Outlook: *

/Current conditions: /

The thermal stress that caused bleaching in Southeast Asia has abated,
but stress has moved into the central and northern Philippines.
Temperatures across much of the western tropical Pacific are above
normal at the moment, especially along the west coast of the Philippines
where bleaching has been reported. However, the Alert Level 2 areas seen
in the Gulf of Thailand and the eastern South China Sea may be over
estimated, as three months of persistent cloud cover have prevented
updates to the satellite SST data since May 2010 at some locations.

/Bleaching outlook: /

The high temperatures that have caused mass coral bleaching in the
Philippines may persist in the northern-most Philippines into September.
As the summer continues in the northern hemisphere, our outlook shows
that temperatures in the northwestern Pacific will increase during the
next few months. The outlook indicates that there is a high potential of
thermal stress capable of causing bleaching in Guam, CNMI (Commonwealth
of the Northern Mariana Islands), FSM (Federated States of Micronesia),
and the surrounding areas until late October and early November.
*Indian Ocean 2010 Bleaching Season Retrospective: *

With the 2009-2010 El Niño, the Indian Ocean experienced significant
coral bleaching thermal stress since the beginning of this year in a
spatial pattern similar to that seen in 1998. Most of the northern
Indian Ocean and Southeast Asia regions have been experiencing intensive
thermal stress. Significant bleaching has been reported in the Maldives,
both sides of the Thai Peninsula (Andaman Sea and Gulf of Thailand),
Malaysia, Singapore, Cambodia, parts of Indonesia, and the Anilao region
of the Philippines. Bleaching was observed in southwestern and
northeastern Madagascar earlier this year.

The thermal stress has now dissipated in the Indian Ocean and most of
Southeast Asia. Many areas in this region have been experiencing
persistent cloud cover since early May, which should be favorable for
corals’ recovery from the mass bleaching.

The CRW bleaching outlook has been predicting well the overall high
thermal stress in the Indian Ocean since the beginning of 2010,
indicating an active bleaching season. However, our outlook issued
earlier this year under-predicted the high thermal stress observed in
the Bay of Bengal and over-predicted the thermal stress in the region
off Sumatra where low levels of thermal stress were observed. This is
most likely caused by the relatively low skill level of the LIM model
(the SST prediction model of the CRW outlook system) in the Bay of
Bengal and off Sumatra. Further evaluation and testing of a new scheme
to refine the LIM are underway to improve the skill in this region.
[Note: The Bleaching Outlook discussed below is an experimental product
and should be used as an indicator of potential general patterns rather
than a precise predictor of thermal stress at any location. Actual
conditions may vary due to model uncertainty, subsequent changes in
climatic conditions, extreme localized variability, or weather patterns.]
Current HotSpot and Degree Heating Week charts and data formatted for
HDF and Google Earth can be found at:

Time series graphics for index sites can be found at:

You can sign up for automated bleaching alerts at:

Please report bleaching events (or non-events) at:

NOAA Coral Reef Watch

Special thanks to Coral-list

Coral-list: Marine Reseach & Conservation in the Coral Triangle

Hi all,

       I would like to inform you all of a new peer reviewed book just published titled ‘Marine Research and Conservation in the Coral Triangle: The Wakatobi National Park’. This is now available for purchase on etc (see ) with all royalties going to Indonesian conservation related charities.

This book aims to bring together research about marine resources, their biology and sustainable use in the Wakatobi National Park in Indonesia, and places this information in the context of the wider Coral Triangle region.. This is the culmination of over 10 years research by a range of academic researchers, conservation leaders and students.

I and all the editors and authors hope that this will be well recieved and provide some contribution to conservation policy and management in the region.


Richard Unsworth

Special thanks to Coral-list

Global Change Institute: New Coral Reef Rehabilitation Manual

New Coral Reef Rehabilitation Manual
The Coral Reef Targeted Research (CRTR) Program has recently released a
new Reef Rehabilitation Manual.  The manual is the culmination of
research from the CRTR Program, CRISP and ReefRES projects, and is
intended to complement the Reef Restoration Concepts & Guidelines. 

The Manual captures the experience of international research into reef
rehabilitation and seeks to reduce the proportion of reef rehabilitation
projects that fail. It provides detailed hands-on advice, based on
lessons learned from previous experience, on how to carry out coral reef
rehabilitation in a responsible and cost-effective manner.

Copies of the Manual can be downloaded or ordered from the CRTR Program
website at from the Publications page or enter

Ove Hoegh-Guldberg

Professor and Director

Global Change Institute

University of Queensland

Special thanks to Coral-list

Southeast Florida Coral Reef Initiative published science including just released: “Guidelines & Mngt. Practises for Artificial Reef Sitings, Usage, Construction and Anchoring in Southeast Florida”

This site features links to all the published science of the South East Florida Coral Reef Initiative, hosted by the Florida Department of Environmental Protection, including the following topics:  

* land-based sources of pollution

* awareness and appreciation

*  fishing diving and other uses, and

*  maritime industries and coastal impacts

and including the latest document: 

” Guidelines and Management Practices for Artificial Reef Siting, Usage, Construction and Anchoring in Southeast Florida”

Coral-list: Invasion of a New Scleractinian – Tubastraea micranthus

The Atlantic Lionfish has a New Friend: 

A new species of coral has been discovered on one of the oil platforms just
southwest of the mouth of the Mississippi River.  It is Tubastraea
micranthus, a western Indo-Pacific coral which has now gained a foot-hold in
the Gulf of Mexico.  It has been sighted in the Grand Isle lease area, off
the Louisiana coast, southeast of Port Fourchon.  What makes the sighting
particularly alarming is that its sister species, Tubastraea coccinea, also
invaded the southwestern Atlantic during the 1940s.  Some fifty yrs later,
it had made its way to the northern Gulf of Mexico and has become the single
most abundant coral there.  It has been recorded from the Americas, the
Antilles, the northern Gulf of Mexico (GOM), and on many of oil and gas
platforms in the northern Gulf – inhabiting a stretch from the Florida Keys
to Brazil.  It is particularly successful on artificial substrata (bridges,
oil and gas platforms, breakwaters, etc.).  The northern Gulf of Mexico now
boasts millions of these coral colonies.  The question arises as to whether
this type of expansion will be repeated with Tubastraea micranthus, which
has used a different geographic entry point into the Atlantic than its

Paul Sammarco (Louisiana Universities Marine Consortium – LUMCON), Scott
Porter (same; and EcoLogic Environmental), and Stephen Cairns (Smithsonian
Institution, Washington, DC) have reported the first observation of this new
species – Tubastraea micranthus – in the western Atlantic.  In a recently
released paper published in Aquatic Invasions1, they raise the question as
to whether this new introduction may pose a threat similar to that of its
sister species – Tubatraea coccinea.

Sammarco and Scott, together and independently, surveyed a total of 83
platforms, including deep-water, toppled, “Rigs-to-Reefs” structures, in the
northern Gulf of Mexico for coral colonization between 2000 and 2009.
(“Rigs-to-Reefs” platforms are those platforms which have been donated by
the oil companies to the government and have been toppled either in place or
towed elsewhere to be used as artificial reefs.)  The surveys performed by
SCUBA divers stretched from Matagorda Island, Texas to Mobile, Alabama, USA,
between the depths of 7-37 m.  Five platforms were surveyed by a Remotely
Operated Vehicle (ROV) to depths of up to 117 m.  Tubastraea micranthus was
found on only one platform – Grand Isle 93C (GI-93C), off Port Fourchon,
Louisiana, near the mouth of the Mississippi River.  This location is
particularly important because it occurs at the cross-roads of two major
shipping lanes (safety fairways) transited by large international commercial
ships.  For this species to occur only on this one platform indicates that
the introduction is most likely recent.  The coral probably invaded via
larvae carried in the ballast water of a ship from the Indo-Pacific or from
an adult colony which “hitch-hiked” on the hull of a vessel.

If the growth and reproductive rates of Tubastraea micranthus (sexual and
asexual) are similar to those of Tubastraea coccinea, it is possible that
this species could similarly become a dominant in the western Atlantic.  In
addition, if its ability to out-compete its sister species and other reef
organisms that live on these hard bottoms, it is possible that local species
could be displaced.

In a sister recent study, Sammarco has determined that Tubastraea coccinea
is an “opportunistic species”.  That is, it takes advantage of new,
disturbed, or unusual habitats and does not necessarily have the capability
of dominating natural, mature ecological communities, like well-developed,
well established coral reefs.  This trait has prevented its dominating
natural reefs in western Atlantic.  It is not yet known whether Tubastraea
micranthus is similarly restricted in its growth patterns.

The question is raised as to whether it might be possible to eradicate this
species.  It is known that rapid eradication responses to new species
introductions can be highly effective, as has been the case several times in
California.  On the other hand, it is also known that waiting too long to
respond can result in domination of the new species, as has happened with
Tubastraea coccinea, the fire ant, Nutria, and the Volitan lionfish, are
ineffective.  Attempts at eradication long after integration of the new
species into the community can also cause more disturbance than the original
introduction itself.  This was demonstrated recently by the removal of
thousands of feral cats from the Australian National Heritage Site,
Macquarie Island.  This resulted in a population explosion of rabbits which
had otherwise been kept in check by the cats.  This in turn resulted in the
loss of 40% of the vegetation on the island, which is now having negative
effects on nesting bird populations on the island.  Eradication is more
effective sooner rather than later.

The fate of benthic (hard-bottom) communities in the northern Gulf of Mexico
and the western Atlantic in this case remains to be seen.

July 27, 2010

1Sammarco, P.W., S.A. Porter, and S.D. Cairns.  2010.  New invasive coral
species for the Atlantic Ocean:  Tubastraea micranthus (Cairns and Zibrowius
1997) (Colenterata, Anthozoa, Scleractinia):  A potential major threat?
Aquat. Invasions 5:  131-140.

Paul W. Sammarco                                                 Scott

Louisiana Universities Marine Consortium               Ecologic

(LUMCON)                                                     & LUMCON                    

Stephen D. Cairns

Smithsonian Institution

Paul W. Sammarco, Ph.D.

Executive Director

Association of Marine Laboratories of the Caribbean (AMLC)



Louisiana Universities Marine Consortium (LUMCON)

8124 Hwy. 56

Chauvin, LA  70344


Tel:                1-985-851-2876

FAX:              1-985-851-2874



Coral-list: NOAA 2011 Funding Opportunity–Regional Ecosystem Prediction Program: Understanding Coral Ecosystem Connectivity in the Gulf of Mexico–Pulley Ridge to the Florida Keys


Due Date: Full proposals are due October 21, 2010 at 3 p.m. Eastern Time.


NOAA’s Center for Sponsored Coastal Ocean Research (NOAA/CSCOR), in
partnership with the NOAA Office of National Marine Sanctuaries, Office
of Ocean Exploration and Research (NOAA/OER), National Marine Fisheries
Service Southeast Regional Office, and Gulf of Mexico Regional
Collaboration Team, is soliciting proposals for a project under the
Regional Ecosystem Prediction Program of up to 5 years in duration to
conduct research to improve the understanding of population connectivity
of key species between the southernmost portion of Pulley Ridge on the
West Florida continental shelf and downstream to the coral ecosystems of
the Florida Keys. Coral ecosystems upstream of Pulley Ridge can be
considered if directly relevant to population connectivity or to provide
context to the overall study. This information will be used to improve
the ability of Gulf of Mexico resource managers to proactively develop
strategies to manage and protect poorly understood mesophotic coral
ecosystems, including coastal and marine spatial planning and the siting
of marine protected areas and marine protected area networks for shallow
and mesophotic coral ecosystems.

One project is expected to be supported for up to 5 years, with an
annual budget up to $1,000,000. At no additional cost, up to 15 days per
year for two years of time using the MolaMola/ /AUV will be provided by
the NOAA/OER National Institute for Undersea Science and Technology.

Additionally, NOAA/CSCOR has partnered once again with NOAA/OER to
provide their expertise in administering appropriate technologies for
field-based research to support your proposal such as advanced technical
diving, autonomous underwater vehicles and remotely operated vehicles..
Operational costs for conducting the research must be included in the

The full funding opportunity and information on how to apply can be
found on by clicking on this link
or by searching for CFDA #11.478.

For more information, please contact Kimberly Puglise, NOAA/CSCOR,
301-713-3338 x140 or

<°}}}>>< <°}}}>>< <°}}}>>< <°}}}>>< <°}}}>>< <°}}}>><

Kimberly Puglise
Center for Sponsored Coastal Ocean Research
National Centers for Coastal Ocean Science
NOAA’s National Ocean Service
1305 East-West Highway, N/SCI2
Silver Spring, MD 20910
(301) 713-3338 x140
(301) 713-4044 (Fax)

Coral-list: Links to over 900 pdf publications by members of the ARC Centre of Coral Reef Studies

July 26, 2010

Examples of articles published in the first half of 2010 and added to
the Centre’s publications listing include:

Ainsworth, TD, Thurber, RV and Gates, RD (2010). The future of coral
reefs: a microbial perspective. /Trends in Ecology & Evolution/ 25(4):

Babcock, RC, Shears, NT, Alcala, AC, Barrett, NS, Edgar, GJ, Lafferty,
KD, McClanahan, TR and Russ, GR (2010). Decadal trends in marine
reserves reveal differential rates of change in direct and indirect
effects. /Proceedings of the National Academy of Sciences/: -.
Budd, AF and Pandolfi, JM (2010). Evolutionary novelty is concentrated
at the edge of coral species distributions. /Science/ 328(5985): 1558-1561.
Fabinyi, M (2010). The intensification of fishing and the rise of
tourism: competing coastal livelihoods in the Calamianes Islands,
Philippines. /Human Ecology/ 38(3): 415-427.
McCook, LJ, Ayling, T, Cappo, M, Choat, JH, Evans, RD, De Freitas, DM,
Heupel, M, Hughes, TP, Jones, GP, Mapstone, B, Marsh, H, Mills, M,
Molloy, FJ, Pitcher, CR, Pressey, RL, Russ, GR, Sutton, S, Sweatman, H,
Tobin, R, Wachenfeld, DR and Williamson, DH (2010). Adaptive management
of the Great Barrier Reef: a globally significant demonstration of the
benefits of networks of marine reserves. /Proceedings of the National
Academy of Sciences/.
Mumby, PJ and Harborne, AR (2010). Marine reserves enhance the recovery
of corals on Caribbean Reefs. /PLoS ONE/ 5(1): e8657.
Munday, PL, Dixson, DL, McCormick, MI, Meekan, M, Ferrari, MCO and
Chivers, DP (2010). Replenishment of fish populations is threatened by
ocean acidification. /Proceedings of the National Academy of Sciences/
Pollnac, R, Christie, P, Cinner, JE, Dalton, T, Daw, TM, Forrester, GE,
Graham, NAJ and McClanahan, TR (2010). Marine reserves as linked
social-ecological systems. /Proceedings of the National Academy of
Wilson, SK, Fisher, R, Pratchett, MS, Graham, NAJ, Dulvy, NK, Turner,
RA, Cakacaka, A and Polunin, NVC (2010). Habitat degradation and fishing
effects on the size structure of coral reef fish communities.
/Ecological Applications/ 20(2): 442-451.
Prof. Terry Hughes FAA
Director, ARC Centre of Excellence for Coral Reef Studies
ARC Federation Fellow (2002-2007, 2007-2012)
Fellow of the Beijer Institute of Ecological Economics, Sweden

ARC Centre of Excellence for Coral Reef Studies
James Cook University
Townsville, QLD 4811
Fax: 61 (0) 4781-6722
tel: 61 (0)7-4781-4000
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