Constantine Alexander's blog

Operation Kimberley Miinimbi

The humpback whales of Antarctica face a new threat in their nursery of James Price Point in Western Australia. The oil and gas production operator Woodside and the West Australian Government want to drill and dredge in this whale nursery. The Sea Shepherd received an invitation from the Goolarabooloo native people to help them in their efforts to halt the construction. In honouring the Goolarabooloo, the Sea Shepherd Organization named this campaign Operation Kimberley Miinimbi, the Goolarabooloo name for the humpback whale.

 

 

 

Unexpected finding shows climate change complexities in soil

Nutrients bi-directionnal exchange between plant and fungi. Credit: Agriculture & Agrifood Canada

In a surprising finding, North Carolina State University researchers have shown that certain underground organisms thought to promote chemical interactions that make the soil a carbon sink actually play a more complex, dual role when atmospheric carbon levels rise.

In a paper published in the Aug. 31 edition of Science, North Carolina State University researchers show that important and common soil microscopic organisms, arbuscular mycorrhizal fungi (AMF), play a role in sequestering carbon below ground, trapping it from escaping into the atmosphere as a greenhouse gas.

Yet at the same time, the study shows, elevated levels of atmospheric carbon dioxide also increase a number of underground decomposing interactions that cause carbon to be released back into the atmosphere as a greenhouse gas. This greenhouse gas release essentially offsets any carbon sink benefits, the researchers found.

AMF have a win-win relationship with plants. The fungi take carbon from plants and provide nitrogen and other useful soil nutrients that plants need in order to grow and develop. Present in the roots of about 80 percent of plants that grow on land, AMF help hold this carbon in the ground by putting the brakes on the decomposition of soil organic matter, which prevents the carbon in the decomposing material from escaping into the atmosphere as a greenhouse gas.

But in four independent experiments described in the paper, the researchers show that plants increase their demand for soil nitrogen in the form of ammonia when atmospheric carbon levels rise. Sensing this need, AMF spur other soil micro-organisms to help fill the plant's need for ammonia. To do so, soil micro-organisms decompose soil organic matter, which allows the carbon to escape into the atmosphere.

"We showed that the fungi previously thought to control carbon in the soil can increase carbon decomposition when atmospheric carbon dioxide levels are elevated," says Dr. Shuijin Hu, associate professor of plant pathology at NC State and the corresponding author of the paper. "But if we effectively manage the nitrogen transformation process in the soil, we have a chance to manage carbon sequestration in the soil."

The study was funded by the U.S. Department of Agriculture (USDA). Drs. H. David Shew and Thomas Rufty co-authored the paper, as did Drs. Fitz Booker and Kent Burkey, who work at NC State and the USDA's Agriculture Research Service. The paper's first author is former NC State graduate student Lei Cheng; postdoctoral researchers Cong Tu and Lishi Zhou also co-authored the paper.

Reference: Arbuscular Mycorrhizal Fungi Increase Organic Carbon Decomposition Under Elevated CO2. Authors: Lei Cheng, Cong Tu, Lishi Zhou, H. David Shew, Thomas W. Rufty, Shuijin Hu, North Carolina State University; Fitz Booker and Kent Burkey, U.S. Dept. of Agriculture, Agriculture Research Service and North Carolina State University. Published: Online Aug. 30, 2012, in Science

Abstract: The extent to which terrestrial ecosystems can sequester carbon to mitigate climate change is a matter of debate. The stimulation of arbuscular mycorrhizal fungi (AMF) by elevated atmospheric carbon dioxide (CO2) has been assumed to be a major mechanism facilitating soil carbon sequestration by increasing carbon inputs to soil and by protecting organic carbon from decomposition via aggregation. We present evidence from four independent microcosm and field experiments demonstrating that CO2 enhancement of AMF results in significant soil carbon losses. Our findings challenge the assumption that AMF protect against degradation of organic carbon in soil and raise questions about the current prediction of terrestrial ecosystem carbon balance under future climate-change scenarios.

Contact: Mick Kulikowski
mick_kulikowski@ncsu.edu
919-515-8387
North Carolina State University

 

 

Study identifies prime source of ocean methane

		University of Illinois chemistry professor Wilfred van der Donk (left), microbiology professor William Metcalf and their colleagues discovered the origin of much of the methane in the oxygen-rich regions of the ocean. Credit: L. Brian Stauffer

Up to 4 percent of the methane on Earth comes from the ocean's oxygen-rich waters, but scientists have been unable to identify the source of this potent greenhouse gas. Now researchers report that they have found the culprit: a bit of "weird chemistry" practiced by the most abundant microbes on the planet.

The findings appear in the journal Science.

The researchers who made the discovery did not set out to explain ocean geochemistry. They were searching for new antibiotics. Their research, funded by the National Institutes of Health, explores an unusual class of potential antibiotic agents, called phosphonates, already in use in agriculture and medicine.

Many microbes produce phosphonates to thwart their competitors. Phosphonates mimic molecules the microbes use, but tend to be more resistant to enzymatic breakdown. The secret of their success is the durability of their carbon-phosphorus bond.

"We're looking at all kinds of antibiotics that have this carbon-phosphorus bond," said University of Illinois microbiology and Institute for Genomic Biology (IGB) professor William Metcalf, who led the study with chemistry and IGB professor Wilfred van der Donk. "So we found genes in a microbe that we thought would make an antibiotic. They didn't. They made something different altogether."

The microbe was Nitrosopumilus maritimus, one of the most abundant organisms on the planet and a resident of the oxygen-rich regions of the open ocean. When scanning microbial genomes for promising leads, Benjamin Griffin, a postdoctoral researcher in Metcalf's lab, noticed that N. maritimus had a gene for an enzyme that resembled other enzymes involved in phosphonate biosynthesis. He saw that the microbe also contained genes to make a molecule, called HEP, which is an intermediate in phosphonate biosynthesis.

To determine whether N. maritimus was actually producing a desirable phosphonate antibiotic, chemistry postdoctoral researcher Robert Cicchillo cloned the gene for the mysterious enzyme, expressed it in a bacterium (E. coli), and ramped up production of the enzyme. When the researchers added HEP to the enzyme, the chemical reaction that ensued produced a long sought-after compound, one that could explain the origin of methane in the aerobic ocean.

Scientists had been searching for this compound, methylphosphonic acid, since 2008, when David Karl at the University of Hawaii, Edward DeLong at MIT and their colleagues published an elegant – yet unproven – hypothesis to explain how methane was arising in the aerobic ocean. The only microbes known to produce methane are anaerobes, unable to tolerate oxygen. And yet the aerobic ocean is saturated with methane.

To explain this "methane paradox," Karl and DeLong noted that many aerobic marine microbes host an enzyme that can cleave the carbon-phosphorus bond. If that bond were embedded in a molecule with a single carbon atom, methylphosphonic acid, one of the byproducts of this cleavage would be methane. Karl and DeLong even showed that incubation of seawater microbes with methylphosphonic acid led to methane production.

"There was just one problem with this theory," van der Donk said. "Methylphosphonic acid has never been detected in marine ecosystems. And based on known chemical pathways, it was difficult to see how this compound could be made without invoking unusual biochemistry."

Van der Donk's lab conducted further experiments that demonstrated that the N. maritimus was actually synthesizing phosphonic acids.

"The chemical analysis was a Herculean effort," Metcalf said. The microbe is "one-tenth the size of the standard lab rat microbe, E. coli, and grows at much lower cell densities," he said. The team relied on N. maritimus discoverer David Stahl, of the University of Washington, to grow the microbe in culture for their analysis.

"So we grew 100 liters of culture to get a few, maybe 50 or 100 milligrams of cells, of which maybe 1 percent is phosphorus, of which maybe 5 percent is methylphosphonate," Metcalf said.

The experiments indicated that the methylphosphonate was bound to another molecule, likely a sugar attached to the microbe's surface, van der Donk said. When N. maritimus dies, other marine microbes break the carbon-phosphorus bond of the methylphosphonate to gobble up the phosphorus, an element that is rare in the oceans but essential to life. This encounter generates methane.

The biochemistry that allows N. maritimus to produce methylphosphonate is "unprecedented," Metcalf said.

"Organisms that make phosphonates tend to use weird chemistry for all kinds of things," van der Donk said. "But this is very unusual. One of the carbon atoms of the HEP is oxidized by four electrons and the other is turned into a methyl group. I'm not aware of any other cases where that happens."

The new findings will help those modeling the geochemistry of the ocean to understand climate change, Metcalf said.

"We know that about 20 percent of the greenhouse effect comes from methane and 4 percent of that comes from this previously unexplained source," he said. "You have to know where the methane comes from and where it goes to understand what will happen when the system changes."

Contact: Diana Yates
diya@illinois.edu
217-333-5802
University of Illinois at Urbana-Champaign

 

 

Viruses could be the key to healthy corals

Tel Aviv University develops treatment for deadly coral bacteria based on human medication

Corals are an invaluable part of the marine ecosystem, fostering biodiversity and protecting coastlines. But they're also increasingly endangered. Pathogenic bacteria, along with pollution and harmful fishing practices, are one of the biggest threats to the world's coral populations today.

One of the solutions to the crisis may lie in human medicine. Prof. Eugene Rosenberg of Tel Aviv University's Department of Molecular Microbiology and Biotechnology, working in collaboration with Dr. Ilil Atad of his own laboratory and Prof. Yossi Loya of TAU's Department of Zoology, has developed a treatment for coral infected by Thalassomonas loyana, otherwise known as White Plague disease. This deadly bacterium infects 9 percent of Favia favus corals on the Eilat coral reef in the Red Sea and readily transmits the disease to nearby healthy corals.

Their treatment uses viruses that infect bacteria by injecting genetic material into the bacteria, a therapy originally developed to treat bacterial infections in humans. In this case, the researchers isolated a virus called BA3, one of a category of viruses known as phages. After laboratory experiments showed that BA3 had the ability to kill off White Plague disease, field experiments in the Gulf of Eilat demonstrated that the treatment stopped the progression of the disease in infected corals and prevented the spread of the disease to surrounding healthy corals as well.

These findings were presented at the American Society for Microbiology's general meeting in June.

From human to marine medicine

Treating bacterial infections in corals is no easy task. Because corals don't produce antibodies like humans, they can't be immunized. And pharmaceutical antibiotics are not a viable option because the treatment releases the drugs into the sea, harming the marine environment.

The researchers applied their treatment to two groups of diseased coral, each surrounded by a circle of healthy corals. In the test group, the researchers injected the virus into the area at a concentration of 1000 per milliliter. The control group did not receive the virus.

After 24 hours, the difference in the outcome was highly significant, says Prof. Rosenberg. In the test group, the infection of the diseased coral ceased its progression, and the disease did not spread to the surrounding healthy corals. In the control group, however, the White Plague disease progressed rapidly in the original infected coral and spread to seven out of ten of the surrounding healthy corals.

Amplifying a natural process

One of the most surprising discoveries during the course of their research, says Prof. Rosenberg, was that some corals naturally posses the beneficial virus and are already resistant to infection by the pathogen. When the researchers tested the three corals in the control group that remained uninfected, they discovered that the virus was already present in their biological composition. "We found that this is a natural process that goes on all the time. What we are doing is only shifting the situation in favor of the virus," he explains.

This method of developing an antidote to specific pathogenic coral bacteria is a crucial breakthrough, Prof. Rosenberg says. Corals in different regions of the world are infected with different pathogens. For each location, it is necessary to isolate the appropriate virus. But microbiologists should be able to develop regionalized treatments based on the methods used by Prof. Rosenberg and his fellow researchers.

The next step is to develop an effective way to spread the viruses over large areas of an infected coral reef. Sufficient amounts of these viruses can be easily manufactured in the laboratory. After that, it's a question of technology and funding, Prof. Rosenberg adds.

American Friends of Tel Aviv University supports Israel's leading, most comprehensive and most sought-after center of higher learning. Independently ranked 94th among the world's top universities for the impact of its research, TAU's innovations and discoveries are cited more often by the global scientific community than all but 10 other universities. Internationally recognized for the scope and groundbreaking nature of its research and scholarship, Tel Aviv University consistently produces work with profound implications for the future.

Contact: George Hunka
ghunka@aftau.org
212-742-9070
American Friends of Tel Aviv University

 

 

Bees that go 'Cuckoo' in others' nests

5 new species of cuckoo bees from the Cape Verde Islands

		This shows a male (above) and female (below) of Thyreus denolii, one of the new species discovered and named for the Genoese navigator António de Noli who discovered the islands around 1456. Credit: Dr. Jakub Straka & Dr. Michael S. Engel.

The biota of island archipelagos is of considerable interest to biologists. These isolated areas often act as 'evolutionary laboratories', spawning biological diversity rapidly and permitting many mechanisms to be observed and studied over relatively short periods of time. Such islands are often the places of new discoveries, including the documentation of new species.

The Republic of Cape Verde comprises 10 inhabited islands about 570 kilometers off the coast of West Africa and have been known since at least 1456. Although the bee fauna of the islands was thought to be moderately well known, research by Dr. Jakub Straka of Charles University in Prague and Dr. Michael S. Engel of the University of Kansas have shown that this is not the case. A recent study published in the Open Access journal ZooKeys documents the cuckoo bee fauna of the islands, revealing that their entire fauna of cuckoo bee species is in fact new to science.

		This is the male of Chiasmognathus batelkai, a species from a group of minute cuckoo bees but at 3.2–4.2 mm in length it is the largest of its genus and represents a case of island ‘gigantism’. Credit: Dr. Jakub Straka & Dr. Michael S. Engel.

These bees, like the more widely known cuckoo birds, invade the nests of other host bee species. While the host is out collecting pollen for its brood, the cuckoo bee female enters the nest and deposits her eggs on the food resource. The cuckoo bee egg hatches and the immature promptly dispatches the host egg, leaving the pollen and nectar reserves for itself.

The Cape Verde cuckoos are mostly large, black-and-white species, almost zebra-like in their appearance. However, one species, Chiasmognathus batelkai, is quite small, merely 3.2 – 4.2 millimeters in length. Despite its small proportions, C. batelkai is still the largest species of its genus, a group which otherwise comprises even more diminutive species. It appears as though at slightly less than 5 mm, C. batelkai is a remarkable case of island 'gigantism', whereby founder effects or genetic drift lead to an increased body size in isolated populations during the initial stages of species origination and differentiation.

The researchers are now attempting to explore the diversity of the cuckoo bees' hosts and also to understand their evolutionary diversification across the archipelago.

Reference: Straka J, Engel MS (2012) The apid cuckoo bees of the Cape Verde Islands (Hymenoptera, Apidae). ZooKeys 218: 77. doi: 10.3897/zookeys.218.3683

Contact: Dr. Jakub Straka
straka.jakub.1@gmail.com
Pensoft Publishers

 

 

Coral scientists use new model to find where corals are most likely to survive climate change

		This image shows a WCS conservationist conducting research on coral reef systems in Indonesia's Karimunjawa Marine Park. Using a new coral assessment method for measuring resilience, a team of researchers have found that heat-tolerant coral species living in locations with wide temperature variations are most likely to survive in regions impacted by climate change. Credit: Fakhrizal Setiawan

Marine conservationists from the Wildlife Conservation Society working with other coral reef experts have identified heat-tolerant coral species living in locations with continuous background temperature variability as those having the best chance of surviving climate change, according to a new simplified method for measuring coral reef resilience.

Therefore, coral reefs with these characteristics should receive immediate attention for conserving this highly threatened ecosystem, according to the authors of a study appearing today in the online journal PLOS ONE.

The bewildering diversity of coral reef environments has made assessing and prioritizing them costly, and yet they require immediate action to respond to the threats of climate change. Combining expert opinion and scientific evidence, the scientists developed a simplified assessment that reduces this complexity to 11 key and easily measured factors. This finding greatly simplifies and reduces the time needed for assessments and, therefore, gives coral reef managers a cost-effective, evidence-based tool for gauging a reef's chances of survival.

"Coral reefs are astoundingly complex systems," said Dr. Tim McClanahan, lead author of the study and head of WCS's coral reef research and conservation program. "This reality sometimes leads to the assumption that evaluations and management strategies must also be complex. Our study reveals, however, that effective conservation decisions may hinge on a few easily measurable factors, and this can promote faster management actions."

The study streamlines a previous approach to measuring the resilience of coral reefs by squaring a currently used assessment models with expert opinions and existing data sets. Focusing on a comprehensive field study undertaken by WCS in Karimunjawa Marine Park, located on the coast of Java in Indonesia, McClanahan and his co-authors examined a previously employed complex and expensive assessment protocol that included over 60 factors—herbivorous fish diversity, bio-erosion rates, hard coral cover, and many others—in order to determine which factors were most important.

Using a filtering methodology using surveys and scientific literature, the research team winnowed the list to 11 easily measured factors. Among these, the most important factors favoring resilience are heat-resistant coral species and background temperature variability.

The researchers than used the data collected in the previous comprehensive survey of Karimunjawa Marine Park and reassessed it with the new model. The priorities reached were not the same as the first assessment, which suggested that largely unimportant factors biased the selection of sites in the first assessment while increasing the costs of the investigation.

While the new model offers a potentially valuable, cost-effective tool in ranking the resilience of coral reef systems, McClanahan said that further research is needed to evaluate the priority and types of heat-resistant corals and temperature variability needed for conservation planning. He added that one of the more exciting outputs was that the study prioritized future investigations by identifying factors that are least agreed on among scientists and that have the highest potential to promote the resilience of coral reefs.

"This method gives us a foundation for what could become an indispensible assessment tool for identifying conservation priorities," added McClanahan. "We suspect this protocol will drive investigations for the next decade."

The authors of the paper include: Tim McClanahan, Stuart Campbell, and Stacy Jupiter of the Wildlife Conservation Society, USA; S.D. Donner of the University of British Columbia, Canada; J.A. Maynard of the Australian Centre of Excellence for Risk Analysis, University of Melbourne, Australia; M.A. MacNeil of the Australian Institute of Marine Science; N.A.J. Graham of the ARC Centre of Excellence for Coral Reef Studies, James Cook University, Australia; J.M. Maina of Macquarie University, Australia; A.C. Baker of the Rosenstiel School of Marine and Atmospheric Science, University of Miami, USA; J.B. Alemu I of the Institute of Marine Affairs, Chaguaramus, Trinidad and Tobago, West Indies; M. Beger of the University of Queensland, Australia; E.S. Darling of Simon Fraser University, Canada; C.M. Eakin of Coral Reef Watch, National Oceanic and Atmospheric Administration; S.F. Heron of NOAA's Coral Reef Watch and the Marine Geophysical Laboratory, James Cook University, Australia; C.J. Lundquist of the National Institute of Water & Atmospheric Research, New Zealand; E. McLeod of The Nature Conservancy, USA; P.J. Mumby of the Marine Spatial Ecology Lab, University of Queensland, Australia; M.J. Paddack of Santa Barbara City College, USA; E.R. Selig of Conservation International, USA; and R. van Woesick of the Florida Institute of Technology, USA.

From Fiji to Kenya to Glover's Reef, Dr. McClanahan's research has been examining the ecology, fisheries, climate change effects, and management of coral reefs at key sites throughout the world. This work has been supported by the John D. and Catherine T. MacArthur Foundation and The Tiffany & Co. Foundation.

Contact: John Delaney
jdelaney@wcs.org
718-220-3275
Wildlife Conservation Society

 

 

New DNA-method tracks fish and whales in seawater

Danish researchers at University of Copenhagen lead the way for future monitoring of marine biodiversity and resources. By using DNA traces in seawater samples to keep track of fish and whales in the oceans. A half litre of seawater can contain evidence of local fish and whale faunas and combat traditional fishing methods. Their results are now published in the international scientific journal PLOS ONE.

"The new DNA-method means that we can keep better track of life beneath the surface of the oceans around the world, and better monitor and protect ocean biodiversity and resources," says PhD student Philip Francis Thomsen from the Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen.

Marine ecosystems worldwide are under threat with many fish species and populations suffering from human over-exploitation, which greatly impacts global biodiversity, economy and human health. Today, marine fish are largely surveyed using selective and invasive methods mostly limited to commercial species, and restricted to areas with favourable conditions.

However, researchers at Centre for GeoGenetics now lead the way for future monitoring of marine biodiversity. They have shown that seawater contains DNA from animals such as fish and whales. The species leave behind a trace of DNA that reveals their presence in the ocean based on water samples of just half a litre.

The groundbreaking results are now published as two papers in the open access international scientific journal PLOS ONE.

From freshwater to seawater

The development of the novel DNA monitoring approach was accomplished by PhD student Philip Francis Thomsen and Master's student Jos Kielgast from the Centre for GeoGenetics headed by Professor Eske Willerslev. In December last year, they showed that small freshwater samples contain DNA from several different threatened animals, and after having published these results they began to focus on seawater. Here it also proved possible to obtain DNA directly from the water, which originated from local species living in the area.

"We analysed seawater samples specifically for fish DNA and we were very surprised when the results started to show up on the screen. We ended up with DNA from 15 different fish species in water samples of just a half litre. We found DNA from both small and large fish, as well as both common species and rare guests. Cod, herring, eel, plaice, pilchard and many more have all left a DNA trace in the seawater," says Philip Francis Thomsen.

In the other study the researchers showed that it is also possible to obtain DNA from harbour porpoise in small water samples taken in the sea, so the approach is not only limited to fish, but can also track large marine mammals.

A new and efficient method

The study also compares the new DNA method with existing methods traditionally used for monitoring fish such as trawl and pots. Here, the DNA method proved as good as or mostly better than existing methods. Moreover, the DNA method has a big advantage that it can be performed virtually anywhere without impacting the local habitat – it just requires a sample of water. Associate Professor and fish expert Peter Rask Møller from the National History Museum of Denmark, who also participated in the study, is optimistic.

"The new DNA method has very interesting perspectives for monitoring marine fish. We always keep our eyes open for new methods to describe marine fish biodiversity in an efficient and standardised way. Here, I look very much forward to follow the DNA method in the future, and I think it could be very useful to employ in oceans around the world," says Peter Rask Møller.

The researchers also see great perspectives in the method for estimating fish stocks in the future.

References:

• Thomsen PF, Kielgast J, Iversen LL, Møller PR, Rasmussen M, et al. (2012) Detection of a Diverse Marine Fish Fauna Using Environmental DNA from Seawater Samples. PLoS ONE 7(8): e41732. doi:10.1371/journal.pone.0041732
• Foote AD, Thomsen PF, Sveegaard S, Wahlberg M, Kielgast J, et al. (2012) Investigating the Potential Use of Environmental DNA (eDNA) for Genetic Monitoring of Marine Mammals. PLoS ONE 7(8): e41781. doi:10.1371/journal.pone.0041781

Contact: Philip Francis Thomsen
pfthomsen@snm.ku.dk
45-27-14-20-46
University of Copenhagen