Archive for January, 2012

L’acidification menace les écosystèmes marins (in French)

Une part importante du dioxyde de carbone libéré dans l’atmosphère par la combustion des énergies fossiles se retrouve dans l’océan, où il augmente l’acidité de l’eau. Les organismes marins en souffriront.

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Primordial soup or vinaigrette: did the RNA world evolve at acidic pH?

Background
The RNA world concept has wide, though certainly not unanimous, support within the origin-of-life scientific community. One view is that life may have emerged as early as the Hadean Eon 4.3-3.8 billion years ago with an atmosphere of high CO2 producing an acidic ocean of the order of pH 3.5-6. Compatible with this scenario is the intriguing proposal that life arose near alkaline (pH 9-11) deep-sea hydrothermal vents like those of the ‘Lost City’, with the interface with the acidic ocean creating a proton gradient sufficient to drive the first metabolism. However, RNA is most stable at pH 4-5 and is unstable at alkaline pH, raising the possibility that RNA may have first arisen in the acidic ocean itself (possibly near an acidic hydrothermal vent), acidic volcanic lake or comet pond. As the Hadean Eon progressed, the ocean pH is inferred to have gradually risen to near neutral as atmospheric CO2 levels decreased.

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).

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Sea cucumbers may save Great Barrier Reef

Tropical sea cucumbers and their faeces could save coral reefs from the harmful impacts of climate change, scientists have found.
Scientists at One Tree Island, the University of Sydney’s research station on the Great Barrier Reef, say sea cucumbers reduce the impact of ocean acidification on coral growth.
“When they ingest sand, the natural digestive processes in the sea cucumber’s gut increases the pH levels of the water on the reef where they defecate,” Tree Island director professor Maria Byrne said.
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This works to counter the negative effects of ocean acidification.
One of the by-products when sea cucumbers digest sand is also calcium carbonate (CaCO3), which is a key component of coral.
“To survive, coral reefs must accumulate CaCO3 at a rate greater than or equal to the CaCO3 that is eroded from the reef,” Professor Byrne said.
“The research at One Tree Island showed that, in a healthy reef, dissolution of calcium carbonate sediment by sea cucumbers and other bioeroders appears to be an important component of the natural calcium carbonate turnover.”
The ammonia waste produced when sea cucumbers digest sand also serves to fertilise the surrounding area, providing nutrients for coral growth.
Sea cucumbers are among the largest invertebrates found on tropical reefs.
About 30 species are commercially harvested by the fishery industry along the Great Barrier Reef and throughout the tropics.
“We urgently need to understand the impact of removing sea cucumbers and other invertebrates on reef health and resilience at a time when reefs face an uncertain future,” Professor Byrne said.

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Oyster shell dissolution rates in estuarine waters: effects of pH and shell legacy

Oyster shell is a crucial component of healthy oyster reefs. Shell planting has been a main component of oyster restoration efforts in many habitats and has been carried out on scales from individual and grassroots efforts to multiagency efforts across entire estuaries. However, the cycling and lifetime of the shell that makes up the bulk of an oyster reef has only recently received attention, and most of the work to date has focused on the role of epi- and endobionts on shell degradation. Here we report findings from a laboratory study in which we manipulated pH in a flow-through control system using water from the mesohaline mouth of the Patuxent River to measure dissolution rates of intact oyster shell. Shells from the Eastern oyster (Crassostrea virginica Gmelin 1791) with three different legacies were exposed to 4 levels of pH that encompass a range typical of the mesohaline waters of the Chesapeake Bay (7.2–7.9 on the NBS scale). Mass loss over a 2-wk period was used to measure dissolution rate on 3 shell legacies: fresh, weathered, and dredged. We found that pH and shell legacy had significant effects on shell dissolution rate, with lower pH increasing dissolution rate. Fresh shell had the highest dissolution rate, followed by weathered then dredged shell. Dissolution rates were significantly different among all 4 pH treatments, except between the lowest (7.2) and the next lowest (7.4); however, shells lost mass even under noncorrosive conditions (7.9). We discuss the implications of our findings to ongoing efforts to understand shell budgets and cycling in oyster reef habitat, the interaction of biological and geochemical agents of shell degradation, and the complexity associated with shell carbonate cycling in the unique milieu of the oyster reef.

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Organic matter exudation by Emiliania huxleyi under simulated future ocean conditions

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.

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Global decline in ocean ventilation, oxygenation, and productivity during the Paleocene-Eocene Thermal Maximum: Implications for the benthic extinction

The prominent global warming event at the Paleocene-Eocene boundary (55 Ma), referred to as the Paleocene-Eocene Thermal Maximum (PETM), was characterized by rapid temperature increase and changes in the global carbon cycle in <10,000 yr, and a major extinction of benthic foraminifera. We explore potential causes of this extinction in response to environmental changes linked to a massive carbon injection by comparing sedimentary records with results from a comprehensive climate–carbon cycle model, and infer that an increase in oceanic vertical temperature gradients and stratification led to decreased productivity and oxygen depletion in the deep sea. Globally, productivity diminished particularly in the equatorial zone by weakening of the trades and hence upwelling, leading to a decline in food supply for benthic organisms. In contrast, near the Ross Sea, export of organic matter into the deep sea was enhanced due to increased near-surface mixing related to a positive salinity anomaly caused by a rise in wind-driven vertical mixing, contributing to the depletion of the deep-sea oxygen concentration, combined with a sluggish deep-sea circulation. The extinction of deep-sea benthic foraminifera at the PETM thus was probably caused by multiple environmental changes, including decreased carbonate saturation and ocean acidification, lowered oxygen levels, and a globally reduced food supply, all related to a massive carbon injection.

Continue reading ‘Global decline in ocean ventilation, oxygenation, and productivity during the Paleocene-Eocene Thermal Maximum: Implications for the benthic extinction’

Chemical oceanography PhD position

The Ocean Acidification Research Center (OARC) at the University of Alaska Fairbanks (UAF) is seeking a graduate student to conduct a fully funded project in the western Arctic Ocean to better understand the controls on carbonate mineral saturation states and ocean acidification in the region. Funding includes full stipend, tuition, health insurance and travel support for one annual meeting. The ideal applicant will have a background (either undergraduate or preferably M.S.) in marine chemistry or a closely related field. The project will require extensive fieldwork in the Arctic Ocean and the applicant must be able to start by June 1, 2012.

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Ocean acidification and coral reefs: Eat, think, and be merry science cafe

Date/Time: On January 31, 2012 from 7:00 pm to 9:00 pm
Location: Luna Star Cafe

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.

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Coral and mollusc responses to acidified ocean

Coral and mollusc species with an outer layer of protective tissue are more able to withstand acidic seawater than some other species, according to a recent study. However, higher temperatures projected under climate change are likely to worsen the impact of ocean acidification on coral and molluscs, even affecting those that are otherwise resistant to higher levels of acidity.

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.

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Ocean acidification study clarifies effects of CO2

Might a penguin’s next meal be affected by the exhaust from your tailpipe? The answer may be yes, when you add your exhaust fumes to the total amount of carbon dioxide lofted into the atmosphere by humans since the Industrial Revolution. One-third of that carbon dioxide is absorbed by the world’s oceans, making them more acidic and affecting marine life.

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.

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