Doney SC, 2011. L’acidification menace les écosystèmes marins. Dossier Pour la Science 73. Article (subscription required).

Presentation of the hypothesis
We propose that RNA is well suited for a world evolving at acidic pH. This is supported by the enhanced stability at acidic pH of not only the RNA phosphodiester bond but also of the aminoacyl-(t)RNA and peptide bonds. Examples of in vitro-selected ribozymes with activities at acid pH have recently been documented. The subsequent transition to a DNA genome could have been partly driven by the gradual rise in ocean pH, since DNA has greater stability than RNA at alkaline pH, but not at acidic pH.

Testing the hypothesis
We have proposed mechanisms for two key RNA world activities that are compatible with an acidic milieu: (i) non-enzymatic RNA replication of a hemi-protonated cytosine-rich oligonucleotide, and (ii) specific aminoacylation of tRNA/hairpins through triple helix interactions between the helical aminoacyl stem and a single-stranded aminoacylating ribozyme.

Implications of the hypothesis
Our hypothesis casts doubt on the hypothesis that RNA evolved in the vicinity of alkaline hydrothermal vents. The ability of RNA to form protonated base pairs and triples at acidic pH suggests that standard base pairing may not have been a dominant requirement of the early RNA world.

Reviewers: This article was reviewed by Eugene Koonin, Anthony Poole and Charles Carter (nominated by David Ardell).

Bernhardt, HS & Tate WP, 2012. Primordial soup or vinaigrette: did the RNA world evolve at acidic pH? Biology Direct 7:4, doi:10.1186/1745-6150-7-4. Article.

The Sydney Morning Herald, 30 January 2012. Article.

Waldbusser GG, Steenson RA & Green MA, 2011. oyster shell dissolution rates in estuarine waters: effects of ph and shell legacy. Journal of Shellfish Research 30(3), 659-669. Article (subscription required).

Emiliania huxleyi (strain B 92/11) was exposed to different growth, CO₂ and temperature conditions in phosphorous controlled chemostats, to investigate effects on organic carbon exudation, and partitioning between the pools of particulate organic carbon (POC) and dissolved organic carbon (DOC). ¹⁴C incubation measurements for primary production (PP) and for extracellular release (ER) were performed. Chemical analysis included amount and composition of high molecular weight dissolved combined carbohydrates (>1 kDa, HMW-dCCHO), particulate combined carbohydrates (pCCHO) and the carbon content of transparent exopolymer particles (TEP-C). Applied CO₂ and temperature conditions were 300, 550 and 900 μatm pCO₂ at 14 °C, and additionally 900 μatm pCO₂ at 18 °C simulating a greenhouse ocean scenario. A reduction in growth rate from μ =0.3 d⁻¹ to μ =0.1 d⁻¹ induced the most profound effect on the performance of E. huxleyi, relative to the effect of elevated CO₂ and temperature. At μ =0.3 d⁻¹, PP was significantly higher at elevated CO₂ and temperature. DO¹⁴C production correlated to PO¹⁴C production in all cultures, resulting in similar percentages of extracellular release (DO¹⁴C/PP × 100; PER) of averaged 3.74 ± 0.94%. At μ =0.1 d⁻¹, PO¹⁴C decreased significantly, while exudation of DO¹⁴C increased, thus leading to a stronger partitioning from the particulate to the dissolved pool. Maximum PER of 16.3 ± 2.3% were observed at μ =0.1 d⁻¹ at greenhouse conditions. Concentrations of HMW-dCCHO and pCCHO were generally higher at μ =0.1 d⁻¹ compared to μ =0.3 d⁻¹. At μ =0.3 d⁻¹, pCCHO concentration increased significantly along with elevated CO₂ and temperature. Despite of high PER, the percentage of HMW-dCCHO was smallest at greenhouse conditions. However, highest TEP-formation was observed under greenhouse conditions, together with a pronounced increase in pCCHO concentration, suggesting a stronger partitioning of PP from DOC to POC by coagulation of exudates. Our results imply that greenhouse condition will enhance exudation processes in E. huxleyi and may affect organic carbon partitioning in the ocean due to an enhanced transfer of HMW-dCCHO to TEP by aggregation processes.

Borchard C., & Engel A., 2012. Organic matter exudation by Emiliania huxleyi under simulated future ocean conditions. Biogeosciences Discussions 9(1):1199-1236. Article.

Winguth A. M. E., Thomas E., & Winguth C., in press. Global decline in ocean ventilation, oxygenation, and productivity during the Paleocene-Eocene Thermal Maximum: Implications for the benthic extinction. Geology doi:10.1130/G32529.1. Article (subscription required).

For more information please visit www.sfos.uaf.edu/oarc or contact Professor Jeremy Mathis jmathis@sfos.uaf.edu.
Applications can be submitted at http://www.sfos.uaf.edu/.

University of Alaska Fairbanks, Ocean Acidification Research Center, Web site.

Remy Okazaki is a doctoral candidate in the University of Miami Rosentiel School of Marine and Atmospheric Science (RSMS) studying how corals from various environments respond to ocean acidification. As the first guest lecturer of the spring 2012 Eat, Think, and Be Merry Science Cafe, Okazaki will present his research entitled, “Ocean Acidification and Coral Reefs”.

The Eat, Think, and Be Merry Science Cafe, held at the Luna Star Cafe in North Miami, gives students and the community the opportunity to discuss timely scientific issues with researchers in a relaxed conversational setting. The event will begin at 7:00 p.m. on Tuesday, Jan. 31 at the Luna Star Cafe in North Miami. For more information, please follow the link below.

Contact: Elaine Pritzker
Email: epritzke@fiu.edu
Phone: (305) 919-5861
Url: http://casgroup.fiu.edu/SEAS/events.php?id=2045

Florida International University, Web site.

The increasing atmospheric concentrations of CO2 are making the oceans more acidic. Seawater absorbs some of the CO2 from the atmosphere, and it is thought that by 2100, this will increase the acidity of surface ocean waters by 0.3-0.5 pH units. Acidity reduces the amount of available carbonate used by some marine organisms, such as corals and  molluscs, to form shells and skeletons out of calcium carbonate.  Previous studies suggest different species of marine organisms that form shells and skeletons vary in their sensitivity to ocean acidification. It
is thought that an outer layer of living tissue on these organisms protects the skeleton or shell from dissolving in more acidic seawater.

Partly funded under the EU MedSeA project, the researchers compared the rates at which they form shells and skeletons (a process known as  calcification) and lost (a process known as  dissolution) in samples of the corals Balanophyllia europaea (which has a protective outer layer of tissue) and Cladocora caespitose (which does not have a protective layer);  and in samples of the molluscs Mytilus galloprovincialis (a mussel with an outer layer protecting the shell) and Patella caerulea, (a limpet with no protective layer).

Samples of the corals and molluscs were transplanted into water off the Island of Ischia in Italy. Volcanic activity from nearby Mount Vesuvius causes CO2 to bubble up from the ocean floor, creating naturally occurring acidified seawater with a range of different pH conditions. Currently, normal seawater is pH 8.1, but by 2100, it is projected to be  7.8 (lower pH denotes more acidity). In waters of pH 7.8 at the test site, corals and molluscs were able to continue calcifying, in some cases at faster than normal rates.  However, as the water became more acidic, the rate at which shells and skeletons dissolved increased. How much dissolved depended on the amount of protective tissue covering the shells or skeletons.
Living molluscs and limpets transplanted to the acidic waters continued to calcify at pH 8.1 (normal seawater) and pH 7.4. Mussels were able to increase the rate of calcification even at pH 7.2. Limpets living in highly acidic areas of the  sea (pH 6.5) were able to increase their rate of calcification, possibly in response to the higher rates of dissolution of the shells.

Both species of coral in the test area were able to continue calcifying, although this rate decreased by 30% at pH 7.4 for C. caespitose, in contrast to B. europaea, which exhibited an increased rate of calcification at higher levels of acidity. The corrosive action of the seawater was evident on C. caespitose, whereas B. europaea was unaffected and protected by an outer layer of tissue.

However, coral and molluscs were more susceptible to the effects of ocean acidification under higher temperatures. Under unusually high temperatures in September 2009, for example,  B. europaea  samples in water of pH 8.0 continued to calcify normally, but almost stopped at pH 7.4. A warming Mediterranean Sea is likely to worsen the impact of ocean acidification, affecting even those organisms that were resistant to higher levels of acidity.

Source: Rodolfo-Metalpa, R., Houlbrèque, F., Tambutté É. et al. (2011) Coral and mollusc resistance to ocean acidification adversely affected by warming. Nature Climate Change. 1:308-312.
Contact: riccardo@rodolfo-metalpa.com
Theme(s): Climate change and energy, Marine ecosystems

Science for Environment Policy, DG Environment News Alert Service, 19 January 2012. Article.

A UC Santa Barbara marine scientist and a team of 18 other researchers have reported results of the broadest worldwide study of ocean acidification to date. Acidification is known to be a direct result of the increasing amount of greenhouse gas emissions. The scientists used sensors developed at Scripps Institution of Oceanography at UC San Diego to measure the acidity of 15 ocean locations, including seawater in the Antarctic, and in temperate and tropical waters.

As oceans become more acidic, with a lower pH, marine organisms are stressed and entire ecosystems are affected, according to the scientists. Gretchen E. Hofmann, an eco-physiologist and professor in UC Santa Barbara’s Department of Ecology, Evolution & Marine Biology, is lead author of the recent article in PLoS ONE that describes the research.

“We were able to illustrate how parts of the world’s oceans currently have different pH, and thus how they might respond to climate changes in the future,” said Hofmann. “The sensors allowed us to capture that.” The sensors recorded at least 30 days of continuous pH values in each area of the study.

Since the beginning of the industrial revolution, human activities have accelerated the release of carbon dioxide into the atmosphere as carbon dioxide mixes with water. The two molecules combine to become carbonic acid, making seawater more acidic. As billions of molecules combine and go through this process, the overall pH of the oceans decreases, causing ocean acidification.

Acidification limits the amount of carbonate forms that are needed by marine invertebrates, such as coral, urchins, snails, and shellfish, to make their skeletons. As the concentration of carbonates decreases in acidified water, it is harder to make a shell. And, the structures of some organisms may dissolve when water chemistry becomes too unfavorable.

“The emerging pH data from sensors allows us to design lab experiments that have a present-day environmental context,” said Hofmann. “The experiments will allow us to see how organisms are adapted now, and how they might respond to climate change in the future.”

Hofmann researched the Antarctic, where she has worked extensively, as well as an area of coral reefs around the South Pacific island of Moorea, where UC Santa Barbara has a Long-Term Ecological Research (LTER) project. She also studied the coastal waters of Santa Barbara, in conjunction with the university’s Santa Barbara Coastal LTER. The research team provided 30 days of pH data from other ocean areas around the world.

The researchers found that, in some places such as Antarctica and the Line Islands of the South Pacific, the range of pH variance is much more limited than in areas of the California coast that are subject to large vertical movements of water, known as upwellings. In some of the study areas, the researchers found that the decrease in seawater pH being caused by greenhouse gas emissions is still within the bounds of natural pH fluctuation. Other areas already experience daily acidity levels that scientists had expected would only be reached at the end of this century.

“This study is important for identifying the complexity of the ocean acidification problem around the globe,” said co-author Jennifer Smith, a marine biologist with Scripps. “Our data show such huge variability in seawater pH, both within and across marine ecosystems, making global predictions of the impacts of ocean acidification a big challenge.”

Todd Martz, a marine chemistry researcher at Scripps, developed the sensor. “When I arrived at Scripps, we re-engineered my prototype design, and since then I have not been able to keep up with all of the requests for sensors,” said Martz. “Because every sensor used in this study was built at Scripps, I was in a unique position to assimilate a number of datasets, collected independently by researchers who otherwise would not have been in communication with each other. Each time someone deployed a sensor, they would send me the data, and eventually it became clear that a synthesis should be done to cross-compare this diverse collection of measurements.” Hoffman worked with Martz to put together the research team to create that synthesis.

The team noted that the Scripps sensors, called “SeaFET” and “SeapHOx,” allow researchers to continuously and autonomously monitor pH from remote parts of the world, providing important baselines from which scientists can monitor future changes caused by ocean acidification.

Despite surveying 15 different ocean regions, the authors noted that they only made observations on coastal surface oceans, and that more study is needed in deeper ocean regions farther away from land.

Hofmann is the director of the Center for the Study of Ocean Acidification and Ocean Change, a UC multicampus initiative. Hofmann participated in writing a report on ocean acidification while on the National Research Council’s Ocean Acidification Committee, and she is currently participating as a lead author on the National Climate Assessment. Hofmann is a member of the National Science Foundation’s Office of Polar Programs Advisory Panel, and she is an Aldo Leopold Fellow.

In addition to Hofmann, Martz, and Smith, co-authors include Emily B. Rivest and Pauline Yu of UC Santa Barbara; Uwe Send, Lisa Levin, Yuichiro Takeshita, Nichole N. Price, Brittany Peterson and Christina A. Frieder of Scripps; Paul Matson and Kenneth Johnson of the Monterey Bay Aquarium Research Institute; Fiorenza Micheli and Kristy Kroeker of Stanford University; Adina Paytan and Elizabeth Derse Crook of UC Santa Cruz; and Maria Cristina Gambi of Stazione Zoologica Anton Dohrn in Naples, Italy.

Funding for instrument development and related field work came from several sources, including the National Science Foundation, the David and Lucile Packard Foundation, the University of California, the Gordon and Betty Moore Foundation, the Nature Conservancy, the WWW Foundation, Scott and Karin Wilson, the Rhodes family and NOAA.

Gail Gallessich, University of California News, 23 January 2012. Article.