CBC News: Algae on coral in UAE ‘gives hope’ against bleaching


Technology & Science

Persian Gulf algae prevents coral bleaching in seawater that can reach 36 Celsius in summer

CBC News Posted: Feb 27, 2015 5:00 AM ET Last Updated: Feb 27, 2015 5:00 AM ET


Algae living on coral in the Persian Gulf appear to protect the host coral from dying off. Seawater in the area gets so warm the same temperatures would kill off reefs elsewhere. (Jorg Wiedenmann, John Burt)

Scientists have discovered a new species of algae in the United Arab Emirates that helps corals survive in the warmest seawater temperatures on the planet.

Researchers from the University of Southampton and the New York University Abu Dhabi described the “heat-tolerant species” in a paper published this week in the journal Scientific Reports.

‘It gives hope to find that corals have more ways to adjust to stressful environmental conditions than we had previously thought.’- Jorg Wiedenmann, Coral Reef Laboratory at University of Southampton. Ocean waters in the Persian Gulf can reach temperatures of up to 36 degrees Celsius at the peak of summer — warm enough to kill off corals found anywhere else in the world.

How Gulf corals manage to thrive in such habitats likely has something to do with the nutrient-rich algae living in their tissue, the researchers believe.

It seems the algae living off Gulf corals in a symbiotic relationship give their coral hosts a heat-resistant edge not found in reefs elsewhere.

Climate change threat

“When analyzed by alternative molecular biological approaches, we found pronounced differences that set this heat-tolerant species clearly aside,” the researchers said in a statement.

In reference to its ability to survive unusually high temperatures, the researchers named the algae Symbiodinium thermophilum.

Higher water temperatures often cause corals to lose their colour and die, a phenomenon known as coral bleaching. (Ove Hoegh-Guldberg/Centre for Marine Studies/The University of Queensland)

Algae are known to deliver nutrition to the coral they inhabit. However, algae are also sensitive to environmental changes, with even slight increases in seawater temperatures putting them at risk.

Loss of algae on corals in the symbiotic relationship often results in “coral bleaching,” in which the white skeletons of corals are left exposed once their algae tissue thins or dies.

“In Gulf corals, both the coral host and the associated algal partners need to withstand the high seawater temperatures,” Jörg Wiedenmann, head of the Coral Reef Laboratory at the University of Southampton Ocean, said in a statement.

John Burt, with NYU Abu Dhabi, said the team confirmed the new type of algae is prevalent year-round across several dominant species found near the coast of Abu Dhabi, the capital of the UAE.

Wiedenmann said more research must be done to better understand how the Gulf’s coral reefs can withstand extreme temperatures, in order to get a better grasp of how reefs elsewhere are dying as a result of climate change.

“It gives hope to find that corals have more ways to adjust to stressful environmental conditions than we had previously thought,” Wiedenmann said. “However, it is not only heat that troubles coral reefs. Pollution and nutrient enrichment, overfishing and coastal development also represent severe threats to their survival.”

Science Daily: New Listing to Protect 21 Species of Sharks and Rays

ScienceDaily: Your source for the latest research news
Featured Research from universities, journals, and other organizations
New listing to protect 21 species of sharks and rays
November 10, 2014
Wildlife Conservation Society
Conservationists are rejoicing at the listing of 21 species of sharks and rays under the Appendices of the Convention on Migratory Species (CMS), made official today in the final plenary session of the Conference of Parties (CoP). With these listings, member countries agreed to grant strict protection to the reef manta, the nine devil rays, and the five sawfishes, and committed to work internationally to conserve all three species of thresher sharks, two types of hammerheads, and the silky shark.

“We are elated by the overwhelming commitment expressed by CMS Parties for safeguarding some of the world’s most imperiled shark and ray species, including the highly endangered sawfishes,” said Sonja Fordham of Shark Advocates International, a project of The Ocean Foundation. “Today’s unprecedented actions more than triple the number of shark and ray species slated for enhanced conservation initiatives.”

The proposal to list the thresher sharks was brought by the EU. Silky shark listing was proposed by Egypt. Ecuador and Costa Rica jointly proposed the two hammerhead species. Kenya put forward the sawfish proposal while both the reef manta and devil rays were proposed by Fiji. Fifty-nine of the 120 CMS Parties participated in this CoP.

“Manta and devil rays are exceptionally vulnerable to overexploitation, usually having just one pup every few years,” explained Ian Campbell from WWF, who served on the delegation of Fiji. “The Appendix I listing obligates CMS Parties to ban fishing for reef manta and all devil ray species, and reflects a responsible, precautionary approach in light of their inherent susceptibility to depletion.”

Listing on CMS Appendix I commits countries to strictly protect species while Appendix II listing encourages international cooperation towards conservation of shared species. The rays (including sawfishes) were listed under both Appendices while the six shark species were added to Appendix II.

“From hammerheads of the Galapagos to threshers in the Philippines, sharks are incredibly popular attractions for divers,” noted Ania Budziak of Project AWARE. “With increasing recognition of the economic benefits of associated tourism, divers’ voices are playing a key role in winning protections for these iconic species.”

While consensus to advance the sawfish, devil ray, hammerhead, and thresher shark proposals was reached in Committee, Peru and Chile at the time expressed opposition to listing silky sharks on CMS Appendix II. In the final plenary session, however, the two countries did not voice resistance, thereby clearing the way for adoption.

“We could not be more pleased that, in the end, all of the proposals to list sharks and rays under CMS were adopted, and yet we stress that the benefits of such listings depend on concrete follow-up action by the Parties,” said Amie Brautigam of the Wildlife Conservation Society. “We urge countries to channel the overwhelming concern for sharks and rays demonstrated at this historic meeting into leadership towards national protections and regional limits on fishing.”

The CMS Parties also agreed a Resolution encouraging improved data collection and fisheries management for sharks and rays.

Story Source:

The above story is based on materials provided by Wildlife Conservation Society. Note: Materials may be edited for content and length.

Cite This Page:


Wildlife Conservation Society. “New listing to protect 21 species of sharks and rays.” ScienceDaily. ScienceDaily, 10 November 2014. .

Special thanks to Robert F. Bolland, Ph.D

Coral list: Paul Hoetjes–Curacao Office of Nature: Final Report of Caribbean Coral Reef Monitoring Workshop, Curacao August 2014

Hi everyone,
Below please find a link to the final report of the Caribbean workshop on Coral Reef Monitoring held in Curaçao last August.

Summarizing very briefly: a steering committee for coral reef monitoring in the Caribbean was agreed and tentatively identified, coordinated by SPAW through its Regional Activity Center (RAC) in Guadeloupe. A set of core data necessary for meaningful monitoring was agreed and recommended methods to collect those data. A set of training materials and, when possible, meetings to exchange knowledge and issues, are planned to support this program.

Paul C. Hoetjes
Policy Coordinator Nature
Ministry of Economic Affairs (EZ)
National Office for the Caribbean Netherlands (RCN)
Visiting address: Kaya International z/n, Kralendijk, Bonaire, Caribbean Netherlands
Mailing address: P.O.Box 357, Kralendijk, Bonaire, Caribbean Netherlands
T (+599) 715 83 08
M (+599) 795 90 86
F (+599) 717 83 30

Dear all,

I am glad to tell you that the final report and the outcomes (ref. annexes) of the Curacao workshop have been finalized and are now available on the SPAW-RAC website. (This page layout will be improved tomorrow!)

Please note that the technical outcomes are still proposals at this stage, and are therefore subject to improvement along the coming months ( in particular the Proposed core set of data & methods , the Network Structure , the Terms of Reference and the Socio-economic guidelines).

As planned during the workshop, a presentation was prepared and presented by Jeremy and Ruben this week at ICRI meeting in Japan.
Results will also be presented in two weeks, during the GCFI meeting in Barbados (by Peter, Ruben and Jeremy)

We encourage you to communicate and circulate this information among your contacts, and to forward us the feedback you will receive.

Thank you again for all your input on the report and hard work on the annexes!

Best regards,

Project coordinator – CAR-SPAW
Regional Activity Centre for Protected Areas and Wildlife

Parc national de la Guadeloupe
97120 Saint-Claude – Guadeloupe
Tél : +590 (0)5 90 41 55 85 – Fax : +590 (0)5 90 41 55 56

Open Journal of Ecology: Community-Based Coral Reef Rehabilitation in a Changing Climate: Lessons Learned from Hurricanes, Extreme Rainfall, and Changing Land Use Impacts

OJE> Vol.4 No.14, October 2014

Edwin A. Hernández-Delgado1,2,3*, Alex E. Mercado-Molina2,3, Pedro J. Alejandro-Camis3, Frances Candelas-Sánchez3, Jaime S. Fonseca-Miranda2,3, Carmen M. González-Ramos1,2,3, Roger Guzmán-Rodríguez3, Pascal Mège2, Alfredo A. Montañez-Acuña1,2,3, Iván Olivo Maldonado3, Abimarie Otaño-Cruz1,3,4, Samuel E. Suleimán-Ramos3

1Center for Applied Tropical Ecology and Conservation, Coral Reef Research Group, University of Puerto Rico, San Juan, Puerto Rico.
2Department of Biology, University of Puerto Rico, San Juan, Puerto Rico.
3Sociedad Ambiente Marino, San Juan, Puerto Rico.
4Department of Environmental Sciences, University of Puerto Rico, San Juan, Puerto Rico.

Coral reefs have largely declined across multiple spatial scales due to a combination of local-scale anthropogenic impacts, and due to regional-global climate change. This has resulted in a significant loss of entire coral functional groups, including western Atlantic Staghorn coral (Acropora cervicornis) biotopes, and in a net decline of coral reef ecosystem resilience, ecological functions, services and benefits. Low-tech coral farming has become one of the most important tools to help restore depleted coral reefs across the Wider Caribbean Region. We tested a community-based, low-tech coral farming approach in Culebra Island, Puerto Rico, aimed at adapting to climate change-related impacts through a two-year project to propagate A. cervicornis under two contrasting fishing management conditions, in coastal areas experimenting significant land use changes. Extreme rainfall events and recurrent tropical storms and hurricanes had major site-and method-specific impacts on project outcome, particularly in areas adjacent to deforested lands and subjected to recurrent impacts from land-based source pollution (LBSP) and runoff. Overall, coral survival rate in “A frame” units improved from 73% during 2011-2012 to 81% during 2012-2013. Coral survival rate improved to 97% in horizontal line nurseries (HLN) incorporated during 2012-2013. Percent tissue cover ranged from 86% to 91% in “A frames”, but reached 98% in HLN. Mean coral skeletal extension was 27 cm/y in “A frames” and 40 cm/y in HLN. These growth rates were up to 545% to 857% faster than previous reports from coral farms from other parts of the Caribbean, and up to 438% faster than wild colonies. Branch production and branchiness index (no. harvestable branches > 6 cm) increased by several orders of magnitude in comparison to the original colonies at the beginning of the project. Coral mortality was associated to hurricane physical impacts and sediment-laden runoff impacts associated to extreme rainfall and deforestation of adjacent lands. This raises a challenging question regarding the impact of chronic high sea surface temperature (SST), in combination with recurrent high nutrient pulses, in fostering increased coral growth at the expense of coral physiological conditions which may compromise corals resistance to disturbance. Achieving successful local management of reefs and adjacent lands is vital to maintain the sustained net production in coral farms and of reef structure, and the provision of the important ecosystem services that they provide. These measures are vital for buying time for reefs while global action on climate change is implemented. Adaptive community-based strategies are critical to strengthen institutional management efforts. But government agencies need to transparently build local trust, empower local stakeholders, and foster co-management to be fully successful. Failing to achieve that could make community-based coral reef rehabilitation more challenging, and could potentially drive rapidly declining, transient coral reefs into the slippery slope to slime.

Acropora cervicornis, Climate Change, Coral Farming, Extreme Weather Events

Cite this paper
Hernández-Delgado, E. , Mercado-Molina, A. , Alejandro-Camis, P. , Candelas-Sánchez, F. , Fonseca-Miranda, J. , González-Ramos, C. , Guzmán-Rodríguez, R. , Mège, P. , Montañez-Acuña, A. , Maldonado, I. , Otaño-Cruz, A. and Suleimán-Ramos, S. (2014) Community-Based Coral Reef Rehabilitation in a Changing Climate: Lessons Learned from Hurricanes, Extreme Rainfall, and Changing Land Use Impacts. Open Journal of Ecology, 4, 918-944. doi: 10.4236/oje.2014.414077.

Coral Morphologic: Bad Year for Coral Bleaching & Sediment on Miami coral reefs

Coral Morphologic

12:09 PM (3 hours ago)

to coral-list
A combination of hot weather and sunny days in summer 2014 has resulted in
very a bad year for coral bleaching in South Florida. Recently, we surveyed
the natural reef (‘first reef tract’) just offshore Fisher Island here in
Miami. Unfortunately, the water has been kept exceptionally silty from the
Army Corps’ ongoing dredging of nearby Government Cut. The water is 10-15
feet deep here, and nearly all of the coral heads on the reef were
bleached. However, the most alarming thing we observed, was the prevalence
of black band disease infecting many of the brain corals. As evidenced from
the video, the dredge silt has settled on the corals, and seems a likely a
culprit in causing this disease outbreak. Prior to this summer, we have
never observed BBD as prevalently on Miami’s corals. Currently, the dredge
ships are operating just outside the mouth of Government Cut jetties,
resulting in plumes of silt that smother corals on the natural reefs in
every direction.

See the video of the bleached and diseased corals here:

Fortunately, the water temperatures have steadily decreased since the start
of September, so we are hopeful that the bleached corals throughout South
Florida will begin to recover soon. However, up here in Miami with the Deep
Dredge ongoing, our corals may be too stressed out, diseased, or smothered
to survive. We will be monitoring the situation closely, and will continue
to update as necessary.

Colin Foord
Co-Founder Coral Morphologic

Huffington Post: 20 New Species Of Coral Listed As Threatened


The Center for Biologic Diversity deserves the credit for starting the process with NOAA to designate these corals. DeeVon

WASHINGTON (AP) — The federal government is protecting 20 types of colorful coral by putting them on the list of threatened species, partly because of climate change.

As with the polar bear, much of the threat to the coral species is because of future expected problems due to global warming, said David Bernhart, an endangered-species official at the National Oceanic and Atmospheric Administration. These coral species are already being hurt by climate change “but not to the point that they are endangered yet,” he said.

Climate change is making the oceans warmer, more acidic and helping with coral diseases like bleaching — and those “are the major threats” explaining why the species were put on the threatened list, Bernhart said in a Wednesday conference call.

Other threats include overfishing, runoff from the land, and some coastal construction, but those are lesser, Bernhart said.

Five species can be found off the Atlantic and Gulf of Mexico coasts of Florida, Puerto Rico and the Virgin Islands. They include pillar coral, rough cactus coral and three species of star coral. The other 15 are in the Pacific Ocean area near Guam and American Samoa, but not Hawaii.

The agency looked at listing 66 species, but Wednesday listed only 20 for various reasons. All are called threatened, not endangered. Two coral species were already listed.

Coral reefs, which are in trouble worldwide, are important fish habitats.

The agency did not create any new rules yet that would prevent coral from being harvested or damaged.

“There is a growing body of expert scientists talking about a risk of mass extinction in the sea and on land,” said Elliott Norse, founder and chief scientist of the Marine Conservation Institute of Seattle. Coral “are organisms on the front line of anything that humans do.”

“I hope this wakes people up and we don’t have to lose more coral,” Norse said.



NOAA: http://www.fisheries.noaa.gov/stories/2014/08/corals_listing.html

Terry Hughes: Dredging on the Great Barrier Reef

Coal mining and natural gas extraction (fracking) in Queensland, Australia are expanding rapidly. Apart from the enormous additional CO2 emissions, the expansion of huge ports and dumping of dredge spoil within the Great Barrier Reef (GBR) World Heritage Area have prompted UNESCO to consider including the GBR on their list of “World Heritage Areas in Danger”. The Australian Federal government and the State of Queensland earn billions of dollars in royalties from mining and they are now fast-tracking new mega-coal mines and the largest coal and gas ports in the world. These officials claim that dredging and dumping >100 million cubic meters of sediment will cause no significant damage to the environment.

However, two new scientific studies from James Cook University prove that dredging is a major threat to marine ecosystems, including coral reefs. A recent study by Pollock et al. shows that dredging-associated sedimentation and turbidity dramatically increase coral disease levels on nearby reefs. Essentially, corals get sick more often when they are stressed by reduced light levels and sedimentation (http://dx.plos.org/10.1371/journal.pone.0102498). A separate study by Burns examines the dispersal of fine particles, and shows that hydrocarbons from coal have already dispersed across the width of the GBR, and are approaching international benchmarks for toxicity in suspended sediments and on the benthos (http://dx.doi.org/10.1016/j.ecss.2014.04.001).
Together these benchmark studies prove that dredging is a major threat to the Great Barrier Reef. I encourage you to read them.
Yesterday, Australia became the first country to repeal legislation that curbs CO2 emissions.

Paper citations:
Pollock FJ, Lamb JB, Field SN, Heron SF, Schaffelke B, Shedrawi G, Bourne DG, Willis BL (2014) Sediment and turbidity associated with offshore dredging increase coral disease prevalence on nearby reefs. PLoS ONE 9(7): e102498. doi:10.1371/journal.pone.0102498
Burns KA (2014) PAHs in the Great Barrier Reef Lagoon reach potentially toxic levels from coal port activities. Estuarine, Coastal and Shelf Science 144:39-45. http://dx.doi.org/10.1016/j.ecss.2014.04.001

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

Special thanks to Coral-list

International Society for Reef Studies publishes “Reef Encounter” again


Special thanks to NOAA Coral-list:

Dear Coral Listers,

Regarding REEF ENCOUNTER, may I take the opportunity to advise those of you who are not yet members of ISRS (International Society for Reef Studies) that the Society’s Council has now agreed to make the re-launched electronic version of the society’s news journal REEF ENCOUNTER available, with a slight delay, to non-members.

As a result a pdf file of the latest edition (Volume 29 No. 1 published in March) can now be downloaded from the society’s membership server free of charge by entering / clicking on the following web address:


This edition contains an interesting variety of news, general articles, opinion pieces, scientific letters and reviews.
Notes for potential contributors are included on the back pages.

Free on-line access to the society’s academic journal CORAL REEFS remains however available only to members.

Chemical defenses and resource trade-offs structure sponge communities on Caribbean coral reefs by T. Loh and J. Pawlik


Proceedings of the National Academy of Sciences of the United States of America PNAS,
vol. 111 no. 11 Tse-Lynn Loh, 4151–4156, doi: 10.1073/pnas.1321626111

by Tse-Lynn Loh1 and Joseph R. Pawlik2

Author Affiliations
Edited* by Jerrold Meinwald, Cornell University, Ithaca, NY, and approved January 22, 2014 (received for review November 19, 2013)


Chemical defenses are known to protect some species from consumers, but it is often difficult to detect this advantage at the community or ecosystem levels because of the complexity of abiotic and biotic factors that influence species abundances. We surveyed the community of sponges and sponge predators (angelfishes and parrotfishes) on coral reefs across the Caribbean ranging from heavily overfished sites to protected marine reserves. High predator abundance correlated with high abundance of chemically defended sponge species, but reefs with few predators were dominated by undefended sponge species, which grow or reproduce faster than defended species. Overfishing may enhance competition between palatable sponge species and reef-building stony corals, further impeding the recovery of Caribbean coral reefs.

Ecological studies have rarely been performed at the community level across a large biogeographic region. Sponges are now the primary habitat-forming organisms on Caribbean coral reefs. Recent species-level investigations have demonstrated that predatory fishes (angelfishes and some parrotfishes) differentially graze sponges that lack chemical defenses, while co-occurring, palatable species heal, grow, reproduce, or recruit at faster rates than defended species. Our prediction, based on resource allocation theory, was that predator removal would result in a greater proportion of palatable species in the sponge community on overfished reefs. We tested this prediction by performing surveys of sponge and fish community composition on reefs having different levels of fishing intensity across the Caribbean. A total of 109 sponge species was recorded from 69 sites, with the 10 most common species comprising 51.0% of sponge cover (3.6–7.7% per species). Nonmetric multidimensional scaling indicated that the species composition of sponge communities depended more on the abundance of sponge-eating fishes than geographic location. Across all sites, multiple-regression analyses revealed that spongivore abundance explained 32.8% of the variation in the proportion of palatable sponges, but when data were limited to geographically adjacent locations with strongly contrasting levels of fishing pressure (Cayman Islands and Jamaica; Curaçao, Bonaire, and Martinique), the adjusted R2 values were much higher (76.5% and 94.6%, respectively). Overfishing of Caribbean coral reefs, particularly by fish trapping, removes sponge predators and is likely to result in greater competition for space between faster-growing palatable sponges and endangered reef-building corals.

chemical ecology
indirect effects
community structure
marine protected areas
trophic dynamics


1Present address: Daniel P. Haerther Center for Conservation and Research, John G. Shedd Aquarium, Chicago, IL 60605.
2To whom correspondence should be addressed. E-mail: pawlikj@uncw.edu.

Author contributions: J.R.P. designed research; T.-L.L. and J.R.P. performed research; T.-L.L. and J.R.P. analyzed data; and T.-L.L. and J.R.P. wrote the paper.

The authors declare no conflict of interest.

*This Direct Submission article had a prearranged editor.

This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10.1073/pnas.1321626111/-/DCSupplemental.

PLOS ONE: Hyperspectral Sensing of Disease Stress in the Caribbean Reef-Building Coral, Orbicella faveolata – Perspectives for the Field of Coral Disease Monitoring by David A. Anderson, Roy A. Armstrong, Ernesto Weil


Published: December 04, 2013
DOI: 10.1371/journal.pone.0081478


The effectiveness of management plans developed for responding to coral disease outbreaks is limited due to the lack of rapid methods of disease diagnosis. In order to fulfill current management guidelines for responding to coral disease outbreaks, alternative methods that significantly reduce response time must be developed. Hyperspectral sensing has been used by various groups to characterize the spectral signatures unique to asymptomatic and bleached corals. The 2010 combined bleaching and Caribbean yellow band disease outbreak in Puerto Rico provided a unique opportunity to investigate the spectral signatures associated with bleached and Caribbean yellow band-diseased colonies of Orbicella faveolata for the first time. Using derivative and cluster analyses of hyperspectral reflectance data, the present study demonstrates the proof of concept that spectral signatures can be used to differentiate between coral disease states. This method enhanced predominant visual methods of diagnosis by distinguishing between different asymptomatic conditions that are identical in field observations and photographic records. The ability to identify disease-affected tissue before lesions become visible could greatly reduce response times to coral disease outbreaks in monitoring efforts. Finally, spectral signatures associated with the poorly understood Caribbean yellow band disease are presented to guide future research on the role of pigments in the etiology.

Oregon State University: Large study shows pollution impact on coral reefs — and offers solution

Contact: Rebecca Vega-Thurber


IMAGE: Diver Andrew Schantz of Florida International University studies the effect of pollution on corals in the Florida Keys.
Click here for more information.

CORVALLIS, Ore. – One of the largest and longest experiments ever done to test the impact of nutrient loading on coral reefs today confirmed what scientists have long suspected – that this type of pollution from sewage, agricultural practices or other sources can lead to coral disease and bleaching.

A three-year, controlled exposure of corals to elevated levels of nitrogen and phosphorus at a study site in the Florida Keys, done from 2009-12, showed that the prevalence of disease doubled and the amount of coral bleaching, an early sign of stress, more than tripled.

However, the study also found that once the injection of pollutants was stopped, the corals were able to recover in a surprisingly short time.

“We were shocked to see the rapid increase in disease and bleaching from a level of pollution that’s fairly common in areas affected by sewage discharge, or fertilizers from agricultural or urban use,” said Rebecca Vega-Thurber, an assistant professor in the College of Science at Oregon State University.

“But what was even more surprising is that corals were able to make a strong recovery within 10 months after the nutrient enrichment was stopped,” Vega-Thurber said. “The problems disappeared. This provides real evidence that not only can nutrient overload cause coral problems, but programs to reduce or eliminate this pollution should help restore coral health. This is actually very good news.”

The findings were published today in Global Change Biology, and offer a glimmer of hope for addressing at least some of the problems that have crippled coral reefs around the world. In the Caribbean Sea, more than 80 percent of the corals have disappeared in recent decades. These reefs, which host thousands of species of fish and other marine life, are a major component of biodiversity in the tropics.


IMAGE: This coral, which was part of a scientific study, is bleached as a result of exposure to elevated levels of nitrogen and phosphorus.
Click here for more information.

Researchers have observed for years the decline in coral reef health where sewage outflows or use of fertilizers, in either urban or agricultural areas, have caused an increase in the loading of nutrients such as nitrogen and phosphorus. But until now almost no large, long-term experiments have actually been done to pin down the impact of nutrient overloads and separate them from other possible causes of coral reef decline.

This research examined the effect of nutrient pollution on more than 1,200 corals in study plots near Key Largo, Fla., for signs of coral disease and bleaching, and removed other factors such as water depth, salinity or temperature that have complicated some previous surveys. Following regular injections of nutrients at the study sites, levels of coral disease and bleaching surged.

One disease that was particularly common was “dark spot syndrome,” found on about 50 percent of diseased individual corals. But researchers also noted that within one year after nutrient injections were stopped at the study site, the level of dark spot syndrome had receded to the same level as control study plots in which no nutrients had been injected.

The exact mechanism by which nutrient overload can affect corals is still unproven, researchers say, although there are theories. The nutrients may add pathogens, may provide the nutrients needed for existing pathogens to grow, may be directly toxic to corals and make them more vulnerable to pathogens – or some combination of these factors.

“A combination of increased stress and a higher level of pathogens is probably the mechanism that affects coral health,” Vega-Thurber said. “What’s exciting about this research is the clear experimental evidence that stopping the pollution can lead to coral recovery. A lot of people have been hoping for some news like this.

“Some of the corals left in the world are actually among the species that are most hardy,” she said. “The others are already dead. We’re desperately trying to save what’s left, and cleaning up the water may be one mechanism that has the most promise.”

VIDEO: This is an interview with Rebecca Vega-Thurber about new findings in a coral reef study off the Florida Keys.
Click here for more information.

Nutrient overloads can increase disease prevalence or severity on many organisms, including plants, amphibians and fish. They’ve also long been suspected in coral reef problems, along with other factors such as temperature stress, reduced fish abundance, increasing human population, and other concerns.

However, unlike factors such as global warming or human population growth, nutrient loading is something that might be more easily addressed on at least a local basis, Vega-Thurber said. Improved sewage treatment or best-management practices to minimize fertilizer runoff from agricultural or urban use might offer practical approaches to mitigate some coral reef declines, she said.


Collaborators on this research included Florida International University and the University of Florida. The work was supported by the National Science Foundation and Florida International University.

Editor’s Note: Digital images are available to illustrate this research:

Diver at study site: http://bit.ly/16bCW7w

Bleached coral: http://bit.ly/1bzLpjm

Nutrient dispenser: http://bit.ly/16gC8cp

A package of video interviews and associated B-roll, including underwater video, is also available for downloading in high resolution format:

Underwater b-roll:


Package interview with Dr. Rebecca Vega Thurber:


Dr. Rebecca Vega Thurber Interview:


Laboratory b-roll:


Rebecca Vega Thurber Interview (audio only):

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. cshl.edu/fastx_toolkit/).

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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[Coral-List] NMFS’ 90-day finding on petition to list 23 corals

Today the National Marine Fisheries Service published their 90-day finding
on a petition to list 23 coral species under the Endangered Species Act. The
23 corals are part of a wider set of 81 marine species the agency was
petitioned to list in July 2013. The finding determined that the available
information presents substantial scientific or commercial data or
information indicating that the petitioned action may be warranted for
three species (*Cantharellus noumeae, Siderastrea glynni*, and *Tubastraea
floreana*). We will initiate a status review of these species and we seek
information from interested parties and the public on the status, threats,
and conservation of these species. The public comment period opened today
and ends 24 December 2013. A 12-month finding on whether or not to propose
ESA listing for one or more of these three species is the next step in the

We also determined that the petition did not present substantial
information indicating the petitioned actions may be warranted for the
remaining 20 species. These 20 species are: *Acropora roseni, Acropora
suharsonoi, Alveopora excelsa, Alveopora minuta, Ctenella chagius,
Hydnophora bonsai, Isopora togianensis, Lithophyllon ranjithi, Lobophyllia
serratus, Millepora boschmai, Millepora striata, Montipora setosa,
Parasimplastrea sheppardi, Pectinia maxima, Pocillopora fungiformis,
Porites desilveri, Porites eridani, Porites ornata, Rhizopsammia
wellingtoni, *and *Stylophora madagascarensis*. This ends the review
process for these 20 species.

The 90-day finding, petition, link to the online public comment site, and
other information are all available at:

best regards


Dwayne Meadows, Ph.D.
Species of Concern National Program Coordinator
Endangered Species Division
Office of Protected Resources (F/PR3)
National Marine Fisheries Service
1315 East West Highway
Silver Spring, MD 20910
(301) 427-8467
FAX: (301) 713-4060

Marine Pollution Bulletin 44 (2002) 1206–1218: Characterizing stress gene expression in reef-building corals exposed to the mosquitoside dibrom q

Morgan and Snell 2002 Dibrom

Michael B. Morgan *, Terry W. Snell
Georgia Institute of Technology, School of Biology, Atlanta, GA 30332-0230, USA

We characterize two genes expressed in Acropora cervicornis upon exposure to 0.5 lg/l of dibrom, a pesticide used for mosquito control in the Florida Keys. Fragments of these genes were isolated, sequenced, and developed into chemiluminescent probes for Northern slot blots. Expression of target transcripts was detected in corals exposed to a variety of stressors including organophosphates, organochlorines, heavy metals, naphthalene, and temperature. Within the context of stressors examined, the D25 probe demonstrates toxicant and concentration specificity for organophosphates, whereas the D50 probe had broader specificity, detecting transcripts in corals exposed to dibrom, naphthalene, and temperature stress. After characterizing specificity in the lab, these probes were used on field samples taken from the Florida Keys. Both probes detected their targets in samples taken from the upper Florida Keys in August 2000. Preliminary search of sequence databases suggest similarity exists between D25 and a thioesterase.

MARINE ECOLOGY PROGRESS SERIES: Insecticides and a fungicide affect multiple coral life stages


Mar Ecol Prog Ser
Vol. 330: 127–137, 2007 Published January 25

Kathryn L. Markey1, 2, Andrew H. Baird3, Craig Humphrey2, Andrew P. Negri2,*
1 School of Marine Biology and Aquaculture, and 3ARC Centre of Excellence for Reef Studies, James Cook University,
Townsville, Queensland 4811, Australia
2 Australian Institute of Marine Science, PMB
3, Townsville, Queensland 4810, Australia

ABSTRACT: Coral reefs are under threat from land-based agricultural pollutants on a global scale.
The vulnerability of early life stages of corals is of particular concern. Here, we compared the sensitivity
of gametes, larvae and adult branches of the broadcast-spawning coral Acropora millepora
(Ehrenberg) to a number of common pollutants, including 4 classes of insecticides—2 organophosphates
(chlorpyrifos, profenofos), an organochlorine (endosulfan), a carbamate (carbaryl) and a
pyrethroid (permethrin)—and a fungicide (2-methoxyethylmercuric chloride, MEMC). Fertilisation
of gametes was not affected by any of the insecticides at concentrations up to 30 μg l–1. In contrast,
settlement and metamorphosis were reduced by between 50 and 100% following 18 h exposure to
very low concentrations (0.3 to 1.0 μg l–1) of each insecticide class. The insecticides had few visible
effects on adult branches following 96 h exposure to a concentration of 10 μg l–1, with the exception
of profenofos, which caused polyp retraction, bleaching (i.e. algal symbiont densities were reduced)
and a slight reduction in photosynthetic efficiency of the algal symbionts. The fungicide MEMC
affected all life-history stages: both fertilisation and metamorphosis were inhibited at 1.0 μg l–1, and
polyps became withdrawn and photosynthetic efficiency was slightly reduced at 1.0 μg l–1. At 10 μg
l–1 MEMC, branches bleached and some host tissue died. This high susceptibility of coral larvae to
pesticides at concentrations around their detection limit highlights the critical need to assess toxicity
against all life-history stages of keystone organisms: to focus on mature individuals may underestimate
species sensitivity.

Common Dreams: ‘Inhospitable Oceans’ Acidifying at Rate Unseen in 250 Million Years (or Ever)


Published on Monday, August 26, 2013
New study shows oceans in peril as acidification is happening at rate perhaps never seen in planet’s history
– Jon Queally, staff writer

(Photo: ‘Rough Ocean’/Flickr/Jacqueline Fasser)In both a new study published Monday and in a newspaper interview over the weekend, German marine biologist Hans Poertner warns the world that the crisis of ocean acidification—an intricately woven aspect of global warming and climate change—is now happening at a rate unparalleled in the life of the oceans for at least 250 million years and perhaps the fastest rate ever in the planet’s entire existence.

“The current rate of change is likely to be more than 10 times faster than it has been in any of the evolutionary crises in the earth’s history,” said Poertner in an interview with environmental journalist Fiona Harvey.

Ocean acidification—often called climate change’s “evil twin” by scientists and experts—happens as the pH level of seawater dwindles as it absorbs increasing amount of carbon dioxide (CO2) and though such fluctuations are a normally occurring phenomenon, when the balance tips too far, the acidification can imperil numerous types of marine life and is especially threatening to coral, shell fish, and other essential members of the ocean’s ecosystems.

Poertner—whose study, Inhospitable Oceans, was published Monday in the journal Nature Climate Change—says that if humanity’s industrial carbon emissions continue with a “business as usual” attitude, the problem of the oceans will be catastrophic.

To make comparisons, the study looked back at the ancient fossil record of the ocean to learn about what we can expect if the process continues unchecked. “The [effects observed] among invertebrates resembles those seen during the Permian Triassic extinctions 250m years ago, when carbon dioxide was also involved,” Poertner said. “The carbon dioxide range at which we see this sensitivity [to acidification] kicking in are the ones expected for the later part of this century and beyond.”

As Harvey explains:

Oceans are one of the biggest areas of focus for current climate change research. The gradual warming of the deep oceans, as warmer water from the surface circulates gradually to lower depths, is thought to be a significant factor in the earth’s climate. New science suggests that the absorption of heat by the oceans is probably one of the reasons that the observed warming in the last 15 years has been at a slightly slower pace than previously, and this is likely to form an important part of next month’s Intergovernmental Panel on Climate Change (IPCC) report.

The IPCC report, the first since 2007, will provide a comprehensive picture of our knowledge of climate change. It is expected to show that scientists are at least 95% certain that global warming is happening and caused by human activity, but that some uncertainties remain over the exact degree of the planet’s sensitivity to greenhouse gas increases.

And as Time points out in its review of the study:

Corals are likely to have the toughest time. The invertebrate species secretes calcium carbonate to make the rocky coastal reefs that form the basis of the most productive—and beautiful—ecosystems in the oceans. More acidic oceans will interfere with the ability of corals to form those reefs. Some coral have already shown the ability to adapt to lower pH levels, but combined with direct ocean warming—which can lead to coral bleaching, killing off whole reefs—many scientists believe that corals could become virtually extinct by the end of the century if we don’t reduce carbon emissions.

The Nature Climate Change study found that mollusks like oysters and squids will also struggle to adapt to acidification, though crustaceans like lobsters and crabs—which build lighter exoskeletons—seem likely to fare better. With fish it’s harder to know, though those species that live among coral reefs could be in trouble should the coral disappear. But ultimately, as the authors point out, “all considered groups are impacted negatively, albeit differently, even by moderate ocean acidification.” No one gets out untouched.


Why I am Still Opposed to Widening and Deepening Key West Harbor to Accommodate Larger Cruise Ships by DeeVon Quirolo

Points to consider in the discussion of whether to vote for a feasibility study to widen and deepen Key West harbor:

The science has been indisputable for a long long time on the negative impacts of siltation and dredging on or near coral reefs. Corals are living permanent structures on the ocean bottom comprised of colonies of living polyps that need clear, clean nutrient free waters to thrive. Dredging creates fine sediment and silt that covers corals, preventing photosynthesis and resulting in massive mortality, especially for Elkhorn and Staghorn corals–which cannot slough it off as can other corals. Such sedimentation also reduces the ability of all marinelife, including tarpon and other fish that utilize this area for habitat, to survive.

Episodic storm activity may stir up sediment but the wave action of those storms can also remove loose particulate matter from areas of the ocean bottom. While storm activities have historically affected visibility in the harbor and at the reefs, they do not compare in scale to the massive, chronic, intense effects of outright removal of habitat and the smothering of living formations by tons of dredge sediments that would occur immediately in the harbor and at nearby downstream coral reefs if additional widening and deepening of Key West Harbor were to occur.

It is incredulous to me that anyone associated with protecting coral reefs would dispute this elementary fact of coral ecology. In addition, the health of sea grasses and myriad other marinelife that depend upon this habitat would be severely impacted, including endangered sea turtles and dolphins.

The Key West Harbor Reconnaisance Report published November 2010 noted that the harbor is included in the “critical essential habitat” for both Elkhorn and Staghorn corals under the Endangered Species Listing for them. There has not been one case of allowing removal of critical essential habitat from the Jacksonville Corps of Engineers office in the last 15 years.

It states: “Under the Endangered Species Act (ESA) of 1973; the threatened coral Acropora cervicornis (staghorn coral) and Acropora palmata (elkhorn coral) could be located adjacent to the channel in the areas proposed for expansion as this area is designated as critical habitat for these species. While it is possible to relocate the actual colonies of coral, the critical habitat would be permanently removed. It is highly likely that the removal of several acres of occupied designated critical habitat (habitat where the species has been shown to be able to flourish under baseline conditions) could be considered an adverse modification of critical habitat under Section 7 of the ESA. This would be Jacksonville District’s first adverse modification of critical habitat determination in the last 15 years. It is also unknown what reasonable and prudent alternatives and measures National Marine Fisheries Service (NMFS) would include in a biological opinion to avoid the project adversely modifying designated critical habitat, as required under Section 7 of the Act.* It is expected that resource agencies would oppose any channel modifications outside the existing footprint.”

So this whole feasibility study could be a huge waste of money because there are good reasons why a permit would never be issued for the project thereafter. Surely we can find a more sustainable use of $5 million dollars—how about some stormwater treatment for the island of Key West to improve water quality?

The feasibility study is an effort to calculate the possibility of further widening and dredging in a harbor that was deepened just five years ago. Underneath Key West lies a fresh water aquifer. There are upwellings of fresh water in the harbor today. A massive deepening and widening may have severe unintended consequences on the aquifer, that at a minimum could result in salt water intrusion of that fresh water lens.

The last harbor dredging project just a few years ago included a mitigation plan by the Florida Keys National Marine Sanctuary to remove corals from the harbor with the purpose of restoring the damage. Despite their best efforts, there have been only a few of those corals planted in an offshore boat grounding site. For the most part, there has been no successful effort to restore the extent of coral colonies that existed in this area prior to the last dredging. It is therefore highly unlikely that another dredging project will succeed in restoring the habitat removed via mitigation this time either. It is just a false hope that the loss of biodiversity will be anything but an ecological disaster for this otherwise already stressed part of Key West’s coral reef ecosystem.

Often these dredge projects result in in-filling thereafter due to storm activity. Key West may be saddled with a harbor that produces chronic sedimentation without regular repeated environmentally destructive maintenance dredging. This will in turn affect the downstream coral reefs with additional chronic smothering contaminated sediment.

The greater question really is: How much more can the surrounding coral reef ecosystem of the Florida Keys handle in terms of human impacts? Isn’t it enough to have a thriving hotel, tourism and real estate industry? Can’t we draw a line in the sand and say “enough is enough”? Already the hoards of cruise ship visitors denigrates the downtown section to the exclusive benefit of a few businesses while high-end resorts and guesthouses hold their breath that this low-end massive impact to our quality of life will not repel their key markets. What about those who still hope that Key West can be a magic island home–don’t they deserve consideration?

Craig and I would encourage every voter in Key West to vote NO on the feasibility study to dredge Key West harbor….. again.

DeeVon Quirolo

[Coral-List] New Paper: Native Predators Do Not Control Lionfish by John Bruno

PLOS: goo.gl/rYfzx (http://t.co/GNmzGcCpNS)
July 12, 2013

We surveyed the abundance (density and biomass) of lionfish and native predatory fishes that could interact with lionfish (either through predation or competition) on 71 reefs in three biogeographic regions of the Caribbean. We found no relationship between the density or biomass of lionfish and that of native predators. Our results suggest that interactions with native predators do not influence the colonization or post-establishment population density of invasive lionfish on Caribbean reefs.

That does not mean native predators never eat lionfish. They probably do. But they don’t appear to measurably control lionfish populations. Furthermore, overfishing was not the cause (or a contributing factor) of the invasion. The “cause” was the introduction itself. Previous observations of reduced lionfish density within MPAs (e.g., Mumby et al 2011), which our results confirm, appear to be due to targeted culling by park managers rather than higher predator biomass.

John F Bruno, PhD
Department of Biology
UNC Chapel Hill
www.johnfbruno.com (http://www.johnfbruno.com)

WLOX: Scientists studying impact of oil spill on coral reefs


Posted: Jul 05, 2013 6:41 PM EST Updated: Jul 05, 2013 7:02 PM EST
By Steve Phillips – bio | email

GULFPORT, MS (WLOX) – Scientists studying the impact of the Deepwater Horizon oil spill invited the media aboard their research vessels Friday morning during a stop at the Port of Gulfport. Much of their research has focused on the oil spill’s impact on coral reefs in the Gulf.

The scientists gave a tour of their working laboratories aboard the Nautilus and the Endeavor. One researcher says the area around the Deepwater Horizon site is probably the best surveyed section of sea floor in the world. Still, three years after the oil spill, they are just beginning to discover the extent of its impact. The research vessel Nautilus uses a pair of remote operated vehicles or ROVs to explore coral reefs in deep water all around the oil spill site in the Gulf.

“We’ve been going back and taking pictures of the same corals, leaving physical markers on the floor, visiting the exact same coral colonies again and again, every three to four months since the spill occurred,” said Dr. Erik Cordes, the chief scientist aboard. Early images showed definite damage to the corals near the Deepwater Horizon site. The follow-up study on the health of the coral continues with varying results. “The story is really mixed. Some of them seem to be doing better than they were three years ago. And a lot of them seem to be doing much worse,” said Dr. Cordes.

While the Nautilus team focuses on coral, scientists aboard its sister research ship Endeavor are busy looking at what happens with oil and gas as it moves through the water column from sea floor to sea surface. “We’ve been doing experiments to see what happens to oil when it falls to the sea floor, when it rises up and what happens when the carbon from the oil enters organisms and move through the food web,” said Dr. Joseph Montoya, a professor of geology at Georgia Tech University. Large devices on deck allow the team to collect both sea floor sediment and water samples from around the oil spill site.

“We are interested in both what’s happening to the oil that was released during the Deepwater Horizon incident and in understanding what happens to oil in general terms so that we’ll be prepared if this were ever to happen again,” said Dr. Montoya.

“There are so many unanswered questions still to pursue. We’ve I think come up with some answers on this cruise, but I think we’ve come up with a lot more questions,” Dr. Cordes admitted.

The research consortium includes scientists from 17 different universities. The project headquarters is at the University of Mississippi.

Marine Pollution Bulletin Report: Lethal and sublethal effects of dredging on reef corals by Rolf P.M. Bak

Marine Pollution Bulletin, Volume 9, Issue 1, January 1978, Pages 14–16
Caribbean Marine Biological Institute (Carmabi), Piscaderabaai, Curaçao, Netherlands Antilles Netherlands


The full article is only available by paying $39.95, but the extract ends with one very strong statement for those who think that the sediment from storms compares to the avoidable impacts of dredging on corals. DV

Purchase $39.95


Effects of dredging on a coral reef are described. Under water light values at a depth of 12–13 m were reduced from about 30% to less than 1% surface illumination. Colonies of coral species which are inefficient sediment rejectors (Porites astreoides) lost their zooxanthellae and died. Calcification rates in Madracis mirabilis and Agaricia agaricites were observed to decrease by 33%. The period of suppressed calcification exceeds that of environmental disturbance.

Science Network: Offshore dredging severely impacts coral reefs

Thursday, 13 September 2012 06:00

Murky coral
The study found that sediment accumulation on coral tissue was a “strong and consistent cause of tissue mortality” and resulted in the death of whole coral fragments over prolonged periods.


Image: Dan Derret RESEARCH by the Australian Institute of Marine Science has discovered that proposed dredging works along the WA coast could severely impact certain coral species found in local waters.

Scientists from the Institute along with the Australian Research Centre of Excellence conducted laboratory tests to develop lethal and sub-lethal benchmarks for coral exposed to dredging-generated sediments related to offshore developments.

The researchers tested two species of coral found in offshore locations to six levels of total suspended solids for 16 weeks, including a four week recovery period.

They tested the horizontal foliaceous species Montipora Aequituberculata and the upright branching species Acropora Millepora, both of which are found along WA’s coast.

Montipora Aequituberculata proved to be more susceptible as after 12 weeks all coral tissue under the sediment had died, exposing white coral skeleton.

Australian Institute of Marine Science senior principal research scientist Ross Jones says the sediment can affect coral by impacting their ability to feed as well as settling on the coral’s surface, causing it to expend energy cleaning itself.

“It can also attenuate light—light attenuation is a key thing because a lot of these habitats are primary producer habitats so the corals and sea life need light to photosynthesise and light is attenuated by the sediments,” Dr Jones says.

“It is like having permanently cloudy weather all the time, so it has the potential to have an effect on the marine environment.”

The study found that sediment accumulation on coral tissue was a “strong and consistent cause of tissue mortality” and resulted in the death of whole coral fragments over prolonged periods.

“What the study showed was that one species which was generally a flat plate-like coral was affected more so that the branching Acropora species because the sediment began to pile up on the coral,” Dr Jones says.

“That happened to an extent and rate at which it couldn’t clear itself, so it gradually became buried because the sedimentation rate was faster than its ability to clear itself.”

Woodside Energy funded the study and was cited as the operator of the proposed $30 billion Browse liquefied natural gas development at James Price Point, north of Broome.

Dr Jones says Woodside commissioned the study because it was investigating the effects of dredging at Browse.

“This study was initially commissioned by Woodside to try and come up with some numbers to build an environmental assessment of the project,” Dr Jones says.

He says this report is only a small amount of the research that will be conducted in the next few years into what sediment does to corals and other marine life in response to the proposed dredging.

Key West Harbor Reconnaissance Report by US Army Corp of Engineers


Perhaps most importantly, this brief 7-page report ends with the following: DV

Under the Endangered Species Act (ESA) of 1973; the threatened coral Acropora cervicornis (staghorn coral) and Acropora palmata (elkhorn coral) could be located adjacent to the channel in the areas proposed for expansion (Figure 2) as this area is designated as critical habitat for these species. While it is possible to relocate the actual colonies of coral, the critical habitat would be permanently removed. It is highly likely that the removal of several acres of occupied designated critical habitat (habitat where the species has been shown to be able to flourish under baseline conditions) could be considered an adverse modification of critical habitat under Section 7 of the ESA. This would be Jacksonville District’s first adverse modification of critical habitat determination in the last 15 years. It is also unknown what reasonable and prudent alternatives and measures National Marine Fisheries Service (NMFS) would include in a biological opinion to avoid the project adversely modifying designated critical habitat, as required under Section 7 of the Act. It is expected that resource agencies would oppose any channel modifications outside the existing footprint.

Academia.Edu: Dredging and shipping impacts on southeast Florida coral reefs by Brian K. Walker, et. al.

Proceedings of the 12th International Coral Reef Symposium, Cairns, Australia, 9-13 July 201219A Human impacts on coral reefs: general session

Authors: Brian K. Walker 1, David S. Gilliam 1, Richard E. Dodge 1, Joanna Walczak²
1 National Coral Reef Institute, Nova Southeastern University, Dania Beach, FL, USA
² Florida Department of Environmental Protection, Miami, FL, USA
Corresponding author: walkerb@nova.edu

Many coastal regions have experienced extensive population growth during the last century. Commonly, this growth has led to port development and expansion as well as increased vessel activity which can have detrimental effects on coral reef ecosystems. In southeast Florida, three major ports built in the late 1920’s along 112 km of coastline occur in close proximity to a shallow coral reef ecosystem. Recent habitat mapping data were analyzed in GIS to quantify the type and area of coral reef habitats impacted by port and shipping activities. Impact areas were adjusted by impact severity: 100% of dredge and burial areas, 75% of grounding and anchoring areas, and 15% of areas in present anchorage. Estimates of recent local stony coral density and cover data were used to quantify affected corals and live cover. After adjusting for impact severity,312.5 hectares (ha) of impacted coral reef habitats were identified. Burial by dredge material accounted for 175.8 ha. Dredging of port inlet channels accounted for 84.5 ha of reef removal. And 47.6 ha were impacted from a large ship anchorage. Although the full extent of all ship groundings and anchor drags associated with the ports is unknown, the measured extents of these events totaled 6 ha. Based on the adjusted impact areas,over 8.1 million corals covering over 11.7 ha of live cover were impacted. Burial impacts were the greatest. The planned expansion of two of the ports would remove an additional approximate 9.95 ha of coral reef habitat.Ongoing marine spatial planning efforts are evaluating the placement of large ship anchorages in an effort reduce future impacts from ship anchoring. However, increasing populations and shipping needs will likely continue to be prioritized over protection of these valuable natural resources.

Full text and tables at:

NOAA: National Marine Sanctuaries Program: Florida Keys 2011 Condition Report


This report is best viewed by going to the link above. Below are a few key reports–I added the bold sections which I find the most disturbing.

Florida Keys National Marine Sanctuary
Condition Summary Table

1. Are specific or multiple stressors, including changing oceanographic and atmospheric conditions, affecting water quality and how are they changing?

Conditions appear to be declining
Large-scale changes in flushing dynamics over many decades have altered many aspects of water quality; nearshore problems related to runoff and other watershed stressors; localized problems related to infrastructure. Selected conditions may inhibit the development of assemblages and may cause measurable but not severe declines in living resources and habitats. In conjunction with the Environmental Protection Agency and Florida Department of Environmental Protection, the sanctuary will continue implementation of its Water Quality Protection Program and conduct long-term water quality monitoring and research to understand the effects of water transported from near-field and far-field sources, including Florida Bay on water quality in the sanctuary. New regulations prohibit discharge or deposit of sewage from marine sanitation devices (MSD) within the boundaries of the sanctuary and require MSDs be locked to prevent sewage discharge or deposit while inside sanctuary boundaries. The marine area surrounding the Florida Keys has been designated as a Particularly Sensitive Sea Area by the International Maritime Organization. Florida Department of Health Florida Healthy Beaches Program tests for the presence of fecal coliform and enterococci bacteria in beach water on a weekly basis, at 17 locations throughout the Keys. The MEERA Project, which is designed to provide early detection and assessment of biological events occurring in the Florida Keys and surrounding waters, continues to be supported by the sanctuary. A well-established law enforcement program is in place, including NOAA Fisheries Service, Florida Fish and Wildlife Conservation Commission, and U.S. Coast Guard.

2. What is the eutrophic condition of sanctuary waters and how is it changing?
Conditions do not appear to be changing
Long-term increase in inputs from land; large, persistent phytoplankton bloom events, many of which originate outside the sanctuary but enter and injure sanctuary resources. Selected conditions have caused or are likely to cause severe declines in some but not all living resources and habitats.

3. Do sanctuary waters pose risks to human health and how are they changing?
Conditions do not appear to be changing
Rating is a general assessment of “all waters” of the sanctuary, knowing that in very specific locations, the rating could be as low as “poor.” Increased frequency of HABs and periodic swim advisories. Selected conditions have resulted in isolated human impacts, but evidence does not justify widespread or persistent concern.

4. What are the levels of human activities that may influence water quality and how are they changing?
conditions appear to be improving
Historically, destructive activities have been widespread throughout the Florida Keys, but many recent management actions are intended to reduce threats to water quality. Selected activities have caused or are likely to cause severe impacts, and cases to date suggest a pervasive problem.

5. What are the abundance and distribution of major habitat types and how are they changing?
Conditions do not appear to be changing
In general, mangrove and benthic habitats are still present and their distribution is unchanged, with the exception of the mangrove community, which is about half of what it was historically. The addition of causeways has changed the distribution of nearshore benthic habitats in their vicinity. Selected habitat loss or alteration has taken place, precluding full development of living resource assemblages, but it is unlikely to cause substantial or persistent degradation in living resources or water quality. Marine zoning is used in the sanctuary to protect sensitive habitats like shallow coral reefs. Mooring buoys have been installed as a threat-reduction measure. Sanctuary staff and volunteers educate and inform boaters about the unique nature of the coral reef habitat, and organize shoreline clean-up and marine debris removal efforts. Sanctuary staff assess and restore vessel grounding injuries to seagrass and coral habitats, as well as perform coral rescue activities associated with coastal construction. Large vessel avoidance and Racon beacons in lighthouses have resulted in declines in large vessel groundings. An Area To Be Avoided was established to prevent ships larger than 50 meters in overall length from transiting through sensitive areas in the sanctuary. A well established permitting program is in place to issue a variety of permits for activities that are otherwise prohibited by sanctuary regulations. There is also a well-established law enforcement program in place, including NOAA Fisheries Service, the Florida Fish and Wildlife Conservation Commission, and the U.S. Coast Guard. State of Florida’s Mangrove Trimming and Preservation Act of 1996 (§403.9321-403.9333) regulates how mangroves can be trimmed and altered, and by whom.

6. What is the condition of biologically structured habitats and how is it changing?
conditions appear to be declining
Loss of shallow (<10 meters) Acropora and Montastraea corals has dramatically changed shallow habitats; regional declines in coral cover since the 1970s have led to changes in coral-algal abundance patterns in most habitats; destruction of seagrass by propeller scarring; vessel grounding impacts on benthic environment; alteration of hard-bottom habitat by illegal casitas. Selected habitat loss or alteration has caused or is likely to cause severe declines in some but not all living resources or water quality.

7. What are the contaminant concentrations in sanctuary habitats and how are they changing?
Few studies, but no synthesis of information.

8. What are the levels of human activities that may influence habitat quality and how are they changing?
conditions appear to be declining
Coastal development, highway construction, vessel groundings, over-fishing, shoreline hardening, marine debris (including derelict fishing gear), treasure salvaging, increasing number of private boats, and consequences of long-term changes in land cover on nearshore habitats. Selected activities have caused or are likely to cause severe impacts, and causes to date suggest a pervasive problem.

9. What is the status of biodiversity and how is it changing?
conditions appear to be declining
Relative abundance across a spectrum of species has been substantially altered, with the most significant being large reef-building corals, large-bodied fish, sea turtles, and many invertebrates, including, the long-spined sea urchin. Recovery is questionable. Selected biodiversity loss has caused or is likely to cause severe declines in some but not all ecosystem components and reduce ecosystem integrity. Marine zoning assists in the protection of the biological diversity of the marine environment in the Keys. Mooring buoys have been installed in these zones to reduce anchor damage to coral reef biota. The sanctuary’s education and outreach team established the “Blue Star” program to help reduce the impact of divers and snorkelers on the coral reef ecosystem. NOAA has also established the Dolphin SMART program encouraging responsible viewing of wild dolphins. Sanctuary staff assesses and restores vessel grounding injuries to seagrass and coral habitats, as well as performs coral rescue activities associated with coastal construction. NOAA Fisheries Service (American Recovery and Reinvestment Act) awarded $3.3 million to support Acropora coral recovery and restoration in Florida (including the Keys) and the U.S. Virgin Islands. Other coral nursery efforts are also underway that contribute to coral restoration. Private efforts examining potential of long-spined sea urchin recovery via nursery propagation and rearing are also underway. A well-established permitting program is in place to issue a variety of permits for activities that are otherwise prohibited by sanctuary regulations, including removal of the invasive lionfish from the small no-take zones. The Florida Keys “Bleach Watch” Program utilizes volunteers to provide reports from the reef on the actual condition of corals throughout the bleaching season. The sanctuary also participates in oil spill drills sponsored by the U.S. Coast Guard and is a partner in the Florida Reef Resilience Program. There is a well-established law enforcement program in place.

10. What is the status of environmentally sustainable fishing and how is it changing?
Historical effects of recreational and commercial fishing and collection of both targeted and non-targeted species; it is too early to determine ecosystem effects of new fishery regulations and new ecosystem approaches to fishery management. Extraction has caused or is likely to cause severe declines in some but not all ecosystem components and reduce ecosystem integrity.

11. What is the status of non-indigenous species and how is it changing?
conditions appear to be declining
Several species are known to exist; lionfish have already invaded and will likely cause ecosystem level impacts; impacts of other non-indigenous species have not been studied. Non-indigenous species may inhibit full community development and function, and may cause measurable but not severe degradation of ecosystem integrity.

12. What is the status of key species and how is it changing?
Conditions do not appear to be changing
Reduced abundance of selected key species including corals (many species), queen conch, long-spined sea urchin, groupers and sea turtles. The reduced abundance of selected keystone species has caused or is likely to cause severe declines in ecosystem integrity; or selected key species are at severely reduced levels, and recovery is unlikely.

13. What is the condition or health of key species and how is it changing?
conditions appear to be declining
Hard coral and gorgonian diseases and bleaching frequency and severity have caused substantial declines over the last two decades; long-term changes in seagrass condition; disease in sea turtles; sponge die- offs; low reproduction in queen conch; cyanobacterial blooms; lost fishing gear and other marine debris impacts on marine life. The comparatively poor condition of selected key resources makes prospects for recovery uncertain.

14. What are the levels of human activities that may influence living resource quality and how are they changing?
Conditions do not appear to be changing
Despite the human population decrease and overall reduction in fishing in the Florida Keys since the 1990s, heavy recreational and commercial fishing pressure continues to suppress biodiversity. Vessel groundings occur regularly within the sanctuary. Annual mean number of reported petroleum and chemical spills were around 150 during that time period, with diesel fuel, motor oil, and gasoline representing 49% of these incidents collectively. Over the long term, localized direct impacts may be overwhelmed by the adverse and wide-ranging indirect effects of anthropogenic climate change resulting in sea level rise, abnormal air and water temperatures, and changing ocean chemistry. Selected activities have caused or are likely to cause severe impacts, and cases to date suggest a pervasive problem.