Tiny Marine Microbes Exert Influence on Global Climate: Microorganisms Display a Behavior Characteristic of Larger Animals

New research indicates that the interactions of microscopic organisms around a particular organic material may alter the chemical properties of the ocean and ultimately influence global climate by affecting cloud formation in the atmosphere.

Justin Seymour, a research fellow at the University of Technology Sydney, is the lead author of a paper published in the July 16 issue of Science that describes how a relative of the smelly chemical that sea birds and seals use to locate prey, dimethylsulfide (DMS), may serve a similar purpose at the microbial scale, helping marine microorganisms find food and cycle chemicals that are important to climate.
"We found that ecological interactions and behavioral responses taking place within volumes of a fraction of a drop of seawater can ultimately influence important ocean chemical cycling processes," said Seymour.
Using microfluidic technology, the team of researchers led by Professor Roman Stocker of the Massachusetts Institute of Technology's Department of Civil and Environmental Engineering, recorded microbes swimming toward the chemical dimethylsulfoniopropionate (DMSP) as it was released into a tiny channel occupied by the microbes.
The fact that the microbes actively moved toward the DMSP indicates that the tiny organisms play a role in ocean sulphur and carbon cycles, which exert a powerful influence on Earth's climate. How fast the microorganisms consume DMSP -- rather than converting it into DMS -- is important because DMS is involved in the formation of clouds in the atmosphere. This in turn affects the heat balance of the atmosphere.
Seymour, Stocker, Professor Rafel Simó of the Institute for Marine Sciences in Barcelona, and MIT graduate student Tanvir Ahmed carried out the research in the MIT laboratory of Stocker, who pioneered the use of microfluidics and video microscopy in the study of ocean microbes. The new study is the first to make a visual record of microbial behaviour in the presence of DMSP.
"It's important to be able to directly look at an environment in order to understand its ecology," Stocker said. "We can now visualize the behavior of marine microorganisms much like ecologists have done with macro-organisms for a long time."
To do this, the team recreated a microcosm of the ocean environment using a microfluidic device about the size of a flash drive with minuscule channels engraved in a clear rubbery material. The scientists injected DMSP into the channel in a way that mimics the bursting of an algal cell after viral infection -- a common event in the ocean -- then, using a camera attached to a microscope, they recorded whether and how microbes swam towards the chemical.
The researchers found that some marine microbes, including bacteria, are attracted to DMSP because they feed on it, whereas others are drawn to the chemical because it signals the presence of prey. This challenges previous theories that this chemical might be a deterrent against predators.
"Our observations clearly show that, for some plankton, DMSP acts as an attractant towards prey rather than a deterrent," said Simó, an expert on the role of DMSP in the sulfur cycle, "By simulating the microscale patches of the chemical cue and directly monitoring the swimming responses of the predators towards these patches, we get a much more accurate perception of these important ecological interactions than can be obtained from traditional bulk approaches."
"These scientists have used impressive technology to study interactions between organisms and their chemical environment at the scales they actually take place," said David Garrison, director of the National Science Foundation (NSF)'s biological oceanography program. "The research will give us new insights on the workings of microbial assemblages in nature."
The research also indicates that marine microorganisms have at least one behavioral characteristic in common with larger sea and land animals: we're all drawn to food.
The team plans to extend the research from the laboratory to the ocean environment; the team is working on an experimental system that can be used on board oceanographic ships working with bacteria collected directly from the ocean.

Source: "Chemoattraction to Dimethylsulfoniopropionate Throughout the Marine Microbial Food Web," by Justin R. Seymour, Rafel Simó, Tanvir Ahmed and Roman Stocker. Science, 16 July 2010.

How Fast Can Microbes Break Down Oil Washed Onto Gulf Beaches?

A new Florida State University study is investigating how quickly the Deepwater Horizon oil carried into Gulf of Mexico beach sands is being degraded by the sands' natural microbial communities, and whether native oil-eating bacteria that wash ashore with the crude are helping or hindering that process.

What oceanography professors Markus Huettel and Joel E. Kostka learn will enable them to predict when most of the oil in the beaches will be gone. Their findings may also reveal ways to accelerate the oil degradation rate -- and speed matters, because toxic crude components that remain buried on Gulf Coast beaches may seep into the groundwater below.

"This enormous oil spill affects hundreds of miles of beaches in the Gulf of Mexico," Huettel said. "We can remove the oil from the beach surface, but oil is also carried deeper into the sand, and we need to understand what happens to that oil. Preventing groundwater contamination is crucial not only to Gulf Coast residents but also to coastal management and local economies like fisheries and tourism that depend on water quality."

"We will also study the effect of the dispersant known as Corexit on oil metabolism by natural microbial communities," Kostka said. "Through contacts in the field, my laboratory has acquired Corexit and source oil from the MC252 (Deepwater Horizon) well head for use in our experiments."

St. George Island, Fla., and Dauphin Island, Ala., have served as the primary research sites since early June, when the one-year study began. In addition, the researchers have obtained heavily oiled sand from Pensacola Beach, Fla., and from a barrier island off the Louisiana coast. If warranted by the oil's movement, they will also collect near-shore water and sediment samples from other Gulf beaches.

Funding for their collaborative research comes from a "RAPID" (Rapid Research Response) grant from the National Science Foundation.

Huettel and Kostka will analyze sediment cores collected from Gulf beaches to find out how much and to what depth oil washed onto the shore is carried into the sand; how rapidly microbes in the sand are breaking it down; and how the oil pollution may be impacting the structure and function of natural microbial communities that help to protect water quality on the coast.

"We'll also show how the oil itself alters the transport and filtration of oxygen-rich water into the beach by clogging the sand -- and how this clogging and resulting reduced oxygen availability in the sand affects the microbial community and degradation of buried oil," Huettel said.

Currents and winds carry the oil, and oil combined with dispersants -- chemicals that disperse the crude into very small oil droplets -- to the Gulf shores, where it washes up on sandy beaches.

Larger crude-oil accumulations such as pancake oil (round, flat accumulations of heavy crude oil) and tar balls (weathered crude oil accumulations that have been formed into ball-shaped structures) are deposited on the beach. Meanwhile, liquid oil (in the form of an oil sheen, or small dispersed droplets) can penetrate many feet deep into the permeable beach sand.

"Oil-filled water that washes up on the beach filters through the porous sediment and carries the oil with it into the sand," Huettel said. "In addition, the water-level drop between high and low tide causes a water-level drop within the beach sediment that can transport oil that has penetrated into the beach into even deeper sediment layers."

"Crude oil is a natural component that constantly seeps out of Gulf of Mexico sediments --obviously in much smaller quantities than those now caused by the drilling accident -- so native microbes have evolved that consume this oil and thereby degrade it," Kostka said. "These microorganisms include bacteria and also some microalgae that live in the water column and the sediments of the Gulf of Mexico."

Kostka said oil accumulations deposited on the beach surface are easily removed by, for example, scraping off the top layer of sand. However, the oil components that penetrate into the sand can only be removed by microbial degradation.

"If oxygen is present -- as it is in the water and in the upper layers of the beach sand -- the microbes decompose the oil aerobically (by using oxygen)," Kostka said. "This degradation process is much faster than the degradation under anaerobic conditions (when no oxygen is available), such as those found in deeper sediment layers of the beach. That's why at the site of the Exxon Valdez oil spill in Alaska, oil can still be found deeply buried in the gravel beach sediments, because anaerobic microbial degradation is slow and, in Alaska, slower still because of the cold climate."

"Unfortunately, said Huettel, "crude oil contains such harmful substances that even small amounts can kill fish larvae -- which means that oil stored in deep layers of beach sediment present a potential source of toxins to near-shore waters and groundwater."

Their NSF-funded study ("Rates and mechanisms controlling the degradation of crude oil from the MC252 spill in Gulf of Mexico beach sands") is the latest of several collaborations between Huettel and Kostka that have examined organic matter transport and degradation in Gulf sands. Florida State University (2010, July 8). How fast can microbes break down oil washed onto Gulf beaches?. ScienceDaily. Retrieved July 11, 2010, from http://www.sciencedaily.com/releases/2010/07/100707222312.htm

New Strain of Bacteria Discovered That Could Aid in Oil Spill, Other Environmental Cleanup

Researchers have discovered a new strain of bacteria that can produce non-toxic, comparatively inexpensive "rhamnolipids," and effectively help degrade polycyclic aromatic hydrocarbons, or PAHs -- environmental pollutants that are one of the most harmful aspects of oil spills.

Because of its unique characteristics, this new bacterial strain could be of considerable value in the long-term cleanup of the massive Gulf Coast oil spill, scientists say.

More research to further reduce costs and scale up production would be needed before its commercial use, they added.

The findings on this new bacterial strain that degrades the PAHs in oil and other hydrocarbons were just published in a professional journal,Biotechnology Advances, by researchers from Oregon State University and two collaborating universities in China. OSU is filing for a patent on the discovery.

"PAHs are a widespread group of toxic, carcinogenic and mutagenic compounds, but also one of the biggest concerns about oil spills," said Xihou Yin, a research assistant professor in the OSU College of Pharmacy.

"Some of the most toxic aspects of oil to fish, wildlife and humans are from PAHs," Yin said. "They can cause cancer, suppress immune system function, cause reproductive problems, nervous system effects and other health issues. This particular strain of bacteria appears to break up and degrade PAHs better than other approaches we have available."

The discovery is strain "NY3" of a common bacterium that has been known of for decades, called Pseudomonas aeruginosa. It was isolated from a site in Shaanxi Province in China, where soils had been contaminated by oil.

P. aeruginosa is widespread in the environment and can cause serious infections, but usually in people with health problems or compromised immune systems. However, some strains also have useful properties, including the ability to produce a group of "biosurfactants" called rhamnolipids.

A "surfactant," technically, is a type of wetting agent that lowers surface tension between liquids -- but we recognize surfactants more commonly in such products as dishwashing detergent or shampoo. Biosurfactants are produced by living cells such as bacteria, fungi and yeast, and are generally non-toxic, environmentally benign and biodegradable. By comparison, chemical surfactants, which are usually derived from petroleum, are commonly toxic to health and ecosystems, and resist complete degradation.

Biosurfactants of various types are already used in a wide range of applications, from food processing to productions of paints, cosmetics, household products and pharmaceuticals. But they also have uses in decontamination of water and soils, with abilities to degrade such toxic compounds as heavy metals, carcinogenic pesticides and hydrocarbons.

Although the type of biosurfactant called "rhamnolipids" have been used for many years, the newly discovered strain, NY3, stands out for some important reasons. Researchers said in the new study that it has an "extraordinary capacity" to produce rhamnolipids that could help break down oil, and then degrade some of its most serious toxic compounds, the PAHs.

Rhamnolipids are not toxic to microbial flora, human beings and animals, and they are completely biodegradable. These are compelling advantages over their synthetic chemical counterparts made from petroleum. Even at a very low concentration, rhamnolipids could remarkably increase the mobility, solubility and bioavailability of PAHs, and strain NY3 of P. aeruginosa has a strong capability of then degrading and decontaminating the PAHs.

"The real bottleneck to replacing synthetic chemicals with biosurfactants like rhamnolipid is the high cost of production," Yin said. "Most of the strains of P. aeruginosa now being used have a low yield of rhamnolipid. But strain NY3 has been optimized to produce a very high yield of 12 grams per liter, from initial production levels of 20 milligrams per liter."

By using low-cost sources of carbon or genetic engineering techniques, it may be possible to reduce costs even further and scale up production at very cost-effective levels, researchers said.

The rhamnolipids produced by NY3 strain appear to be stable in a wide range of temperature, pH and salinity conditions, and strain NY3 aggressively and efficiently degrades at least five PAH compounds of concern, the study showed. It's easy to grow and cultivate in many routine laboratory media, and might be available for commercial use in a fairly short time. Further support to develop the technology is going to be sought from the National Science Foundation.

"Compared to their chemically synthesized counterparts, microbial surfactants show great potential for useful activity with less environmental risk," the researchers wrote in their report. "The search for safe and efficient methods to remove environmental pollutants is a major impetus in the search for novel biosurfactant-producing and PAH-degrading microorganisms."

Collaborating on this research were scientists from Xi'an University of Architecture and Technology and Nanjing Agricultural University in China.

Marine Life Census Revealed Giant Undersea Microbial Mat

Ocean explorers are puzzling out Nature's purpose behind an astonishing variety of tiny ocean creatures like microbes and zooplankton animals -- each perhaps a ticket-holder in life's lottery, awaiting conditions that will allow it to prosper and dominate.

The inventory and study of the hardest-to-see sea species -- tiny microbes, zooplankton, larvae and burrowers in the sea bed, which together underpin almost all other life on Earth -- is the focus of four of 14 field projects of the Census of Marine Life.
Identifying species within these hard-to-see groups, where they are and in what numbers, and the environmental role of each, is critical for understanding the size, dynamics and stability of Earth's food chain, carbon cycle and other planetary fundamentals.
At the other end of the hard-to-see scale: microbes form mats on the sea floor off the west coast of South America that explorers recently found. The mats cover a surface comparable in size to Greece and rank among Earth's largest masses of life.
The research will be showcased October 4 at ceremonies in London to conclude the Census and its historic decade of exploration, research, recording and logging of marine life past and present, with predictions of what will live in the ocean in the future. The Census involves more than 2,000 scientists from 80+ nations -- one of the largest global scientific collaborations ever undertaken.
Microscopic microbes: huge in diversity, abundance, importance
Microbial cells in the oceans' water column number roughly 10 to the 30th (called a nonillion; expressed another way: 1,000 x 1 billion x 1 billion x 1 billion) and collectively weigh the equivalent of 240 billion African elephants. That's 35 elephants of marine microbes per person.
Constituting 50 to 90 percent of all ocean biomass, marine microbes are the tiniest cogs essential to planetary functioning. Yet until technological marvels of this millennium (especially high-throughput DNA sequencing) revealed the stunning extent of this microscopic world, it remained largely hidden from humankind.
"In no other realm of ocean life has the magnitude of Census discovery been as extensive as in the world of microbes," says Mitch Sogin of the Marine Biological Laboratory in Woods Hole, Massachusetts, leader of the International Census of Marine Microbes (ICoMM).
"Scientists are discovering and describing an astonishing new world of marine microbial diversity and abundance, distribution patterns and seasonal changes."
After drawing ocean samples from more than 1,200 sites worldwide, ICoMM researchers have amassed a database that includes 18 million DNA sequences of microbial life spanning more than 100 major phyla (one of the highest ranks of life in taxonomy, phyla are groupings of organisms based on their general body plan).
Revelations about the microbial world within a single decade have led researchers to dramatically revise their estimates of diversity -- there may be up to 100 times as many microbial genera as previously thought. Genus is the category of life ranked between family and species.
During an 11 month study in 2007, scientists sequenced the genes of more than 180,000 specimens from the Western English Channel. Although this level of sampling "far from exhausted the total diversity present," they wrote, one in every 25 readings yielded a new genus of bacteria (7,000 genera in all).
Also surprising scientists -- and considered one of the foremost discoveries of the decade-long global Census: "the rare biosphere" of microbes.
Many rare species in a sample stand opposite to a few species predominating. Wherever Census researchers looked they found many species in a sample represented by less than one in 10,000 of all individuals, including one-off singletons. Evidently many candidates, now rare, lie in wait to become dominant species if changes favor them.
The theory recently gained steam thanks to an ICoMM study of microbes adapted to conditions inside cone-like carbonate chimneys in "The Lost City Hydrothermal Field." The field lies 15 km (9.3 miles) west of the Mid-Atlantic Ridge near the latitude of Florida and Morocco. Hydrothermal vents have been active for at least 30,000 years in the field.
When methane and hydrogen-rich fluids just below the boiling point emerge from deep within Earth and collide with frigid seawater they build the chimneys. Through genetics, scientists determined that rare microbes in young chimneys "were commonly more abundant than in older chimneys, indicating that rare members can become dominant members when environmental conditions change."
John Baross of the University of Washington, who chairs ICoMM's scientific advisory council, notes that with traditional methods so far experts have isolated and characterized about 20,000 marine microbes.
Census research suggests that, within a particular size interval, more than 20 million types of bacteria live in sea water. However, Dr. Baross notes: "The total number of species of marine microbes, including both bacteria and archaea, based on molecular characterization, is likely closer to a billion."
"ICoMM has studied relatively few of the oceans' microbial environments. And there are bacteria associated with each of hundreds of thousands of larger marine animals, all of which have a microbial flora in their guts and attached to their outer surfaces that have likely co-evolved with the animals. Marine animals alone may account for hundreds of millions of microbial species. This is a huge frontier for the next decade."
Scientists approximate diversity by clustering microbes according to their genetic similarity and assign them to "operational taxonomic units."
A study of sponges from Australia's Great Barrier Reef discovered one that was host to almost 3,000 operational taxonomic units of bacteria.
"Tracking and visualizing such complex populations was impossible 10 years ago," says Dr. Baross. "Sequencing allows us to give the equivalent of an Internet URL to millions of microbes, to which we can attach all kinds of other information, like their favorite temperature and amount of salt and light."
And the variety of marine viruses may rival that of microbes. "The first census of marine viruses should be a goal of the next decade," he adds.
Sensitive microbes power Earth's respiratory system
Responsible for more than 95 percent of respiration in the oceans, members of the microbe family maintain the planet's habitability. Their importance is hard to overstate.
By turning atmospheric carbon dioxide absorbed by the ocean back into carbon to be sunk to the depths (and doing likewise with nitrogen, sulfur, iron, manganese and more), marine microbes regulate the composition of Earth's atmosphere, influence climate, recycle nutrients, and decompose pollutants.
Scientists are testing the sensitivity of marine microbes to such changes as the creeping acidification of the seas by rising atmospheric carbon dioxide levels, and which microbes thrive in different environments.
With respect to abundance, scientists in the 1950s estimated about 100,000 microbial cells inhabit 1 liter of seawater. That was off by orders of magnitude. More likely estimates are now more than 1 billion microorganisms in a liter of seawater or a gram of seabed mud.
The vastness of the oceans, covering 70 percent of Earth's surface at an average depth of 3,800 meters (2.4 mi), challenges the science. So too do the contrasts between populations at both surface and deep sea levels and between temperatures, from polar ice to water around undersea vent that would melt lead.
Says ICoMM program manager Linda Amaral Zettler: "There is enormous diversity on the sea floor we have only just begun to discover -- the deeper the depth, the less we know."
Last year, Casey Hubert of Germany's Max Planck Institute for Marine Microbiology and colleagues found that spores of bacteria typical in water warmer than 50°C (about 120°F) are also abundant in sediment under the Arctic Ocean. And they're replenished every year, leading scientists to speculate that warmth-loving "thermophile" bacteria originating in hot underwater crusts ride deep sea currents to the Arctic.
Marine explorers have yet to find any place on Earth cooler than 150°C (about 300°F) without life. Even the deepest mud ever recovered -- off the coast of Newfoundland 1,626 meters (about a mile) below the sea floor (and 4,560 meters, almost 3 miles below sea level) -- abounds in microbes. And spots hotter than 200°C (about 400°F) inside vents were found to have at least slimy biofilms -- a film of microorganisms sticking to each other.
Potential questions ahead for researchers into the distribution of marine microbes:
Are the rarest species the newest species?
Are all species everywhere in the oceans, albeit often in very low numbers?
Did a rare species found in one place come from a larger population where it is native?
"The extreme diversity and curious distribution of deep sea microbes are among the great mysteries of nature, and begs questions about the evolution of life on Earth," says Dr. Sogin.
Microbial mats: Among Earths largest living structures; recognized only recently
Led by Victor Gallardo, Vice-Chair of the Census Scientific Steering Committee, researchers based in Chile have discovered offshore a massive, diverse microbial ecosystem thriving mostly on hydrogen sulfide. It resembles an ecosystem of the Proterozoic period 2.5 billion to 650 million years ago.
At mid-depths of the ocean are oxygen minimum layers (or OML) -- where little oxygen mixes down from the surface or up from the cold, oxygenated water that sinks at the poles and oozes like poured cream along the sea floor to other world regions.
At the bottom of the OML: extreme hypoxia and even anoxia (total lack of oxygen). Hydrogen sulfide, one of the primordial substances, reigns.
With so little oxygen, most life cannot survive. But certain microbes can, and where the OML meets the continental shelf they have formed mats of multicellular filaments -- towering Goliaths by microbial standards at 2 cm (the width of a penny's face) up to 7 cm (2.75 inches -- the length of a side of a saltine cracker). The largest filaments are about half the width of a human hair, visible to the naked eye.
The microbial filaments form mats covering an underwater territory the size of Greece. Explorers found them off the central and northern parts of both Chile and Perú. The giant bacteria have been detected in sulfide seeps at the Galápagos Archipelago, Ecuador and off the Pacific coasts of Panamá and Costa Rica.
Investigators speculate that these microbial mats in low-oxygen layers may run from southern Chile to Colombia and may be present under all of the world's oxygen minimum layers.
"Some things are unknown because they are too small to see, and some things are unknown because they are too big to see," observes Dr. Gallardo.
Human activities may foster the mats too: Similar mats have been found in marine dead zones where wastes accumulate, such as under unregulated aquaculture systems.
Censusing the diverse, spectacular world of sea bugs called zooplankton
Led by Ann Bucklin, head of the University of Connecticut Marine Sciences Department, the Census of Marine Zooplankton (CMarZ) has united the world's specialists to paint an unprecedented global picture of the abundance, diversity and distribution of tiny, often transparent sea "bugs" that form a vital link in both the food chain and Earth's carbon cycle.
Like microbes, plankton species are typically found in very low abundance in any given place, though there are exceptions. Census scientists sampling the Black Sea, for example, found blooms of tiny comb jellies (ctenophores) vacuuming up all available nourishment, while minute copepods (crustaceans) dominated parts of the North Atlantic.
When CMarZ began in 2004, scientists had described about 7,000 marine species that remain planktonic throughout their lives (called holozooplankton; another 26,000 known species are classified as plankton in their larval stage but change lifestyle as they grow larger).
In decades to come, when all of the Census samples have been analyzed and described, Dr. Bucklin estimates the research will have roughly doubled to 14,000 the number of holozooplankton species known to science (of the estimated 15,000 to 20,000 thought to exist altogether).
"The Census has sampled more extensively, more intensively and more strategically than any previous project," she says. "The Census created an unprecedented opportunity for the fragmented international taxonomic community to look collectively for global patterns of diversity. Funding of such work by national or regional bodies typically limits the involvement of non-national investigators, which divides and partitions the research."
"The food web has a highly integrated structure; our research into it needs to be integrated too. The Census has helped develop a world view, and all of us who work in the field have treasured that."
Dr. Bucklin adds that functional biodiversity -- understanding the inter-relationships of species, and the unique (or replaceable) role of each species in an ecosystem -- is a frontier field of study. It will help determine the extent to which the food web is stable and resilient as species migrate if ocean temperatures change and if oceans acidify, impairing the formation of calcium carbonate shells grown by some planktonic species.
Like those studying microbes, zooplankton researchers use modern genetic identification techniques (DNA barcoding) to reveal "cryptic" species (which can be differentiated only through genetics), and to match larvae with adults.
Last year, CMarZ Steering Group member Tracey Sutton of the Virginia Institute of Marine Science and colleagues, led by the Smithsonian Institution's G. David Johnson, used genetics to correct a long-standing mistaken identity, an error in fish taxonomy.
Previously, the alien-like Mirapinnidae (tapetails), Megalomycteridae (bignose fishes) and Cetomimidae (whalefishes) constituted three different families in taxonomy based on their appearance, behaviour and other characteristics. Dr. Sutton and colleagues showed that they are, in fact, the larvae, males and females, respectively, of a single family, Cetomimidae.
Meanwhile, Colomban de Vargas, a CMarZ scientist from France, has called into question previous notions about climate conditions during the last ice age by revealing through DNA the hidden diversity of single-celled marine microorganisms called foraminifera (forams for short). The shells were associated with a particular temperature regime.
Thought at the time to be one species, fossil records of foram shells were advanced as evidence of ice age climate by the CLIMAP (Climate Investigation, Mapping, and Prediction) project of the 1970s and 1980s. Similar-looking shells may associated with different climates.
The new research shows there may be 20-50 times as many foram species as previously thought, potentially undermining CLIMAP conclusions.
"The discovery of this hidden diversity should encourage us to look back and re-examine previous studies," says Dr. Vargas.
Burrowers
The abyss -- the marine realm with least food -- may appear lifeless but is home to countless microscopic organisms smaller than 1 mm. Scientists with Census project CeDAMar use remotely-operated deep sea vehicles and other new technologies to study life in abyssal areas, many of them explored for the first time.
CeDAMar scientists say the most abundant multi-cellular organisms are roundworms (nematodes), which dominate the harsh abyssal conditions in numbers, biomass and diversity. In some places, more than 500,000 of them reside in a single square meter (1.2 square yards) of soft clay on the deep seafloor.
A tiny percentage of all roundworm species are now described and, with present techniques, the true extent of their diversity may never be known, experts say.
Another type of seaworms (polychaetes) may be just as species rich. Some 16,000 species are now known, with as many again thought to be awaiting discovery.
Questions about their role in the food chain, the significance of their high species diversity (perhaps related to living on diverse organic matter) and mysteries surrounding their reproduction and distribution likewise remain unsolved.
Loriciferans (affectionately dubbed "girdle wearers" due to characteristic hind shells resembling a corset) are among the smallest known multicellular marine animals, the average adult just 0.25 millimeters (1/100th of an inch) long.
They have a complex anatomy despite their minute size, with stiletto teeth and a head covered with delicate leaf or thorn-like appendages.
Soon after their first discovery in 1983 in shallow coastal waters, another loriciferan species was found at 8,260 meters (over 5 miles) depth. In the 1990's, still more species were found on seamounts.
Several hundred more loriciferans species found during the Census now await formal description. But the real surprise has been the astounding complexity of the animal's development, with nine stages distinguished, more than any similar creature in the deep sea.
Tiny copepod crustaceans form another group of deep sea inhabitants important because of both their species richness and sheer abundance.
Recent CeDAMar sampling astonished the specialists. On just two stops in the southeast Atlantic Angola Basin, they found almost 700 different copepod species (99 percent of them unfamiliar) in just 5.4 square meters (6.5 square yards), nearly twice the number of species described to date in the entire southern hemisphere.
"Such findings make us look at the deep sea from a new perspective," says CeDAMar leader Pedro Martinez Arbizu. "Far from being a lifeless desert, the deep sea rivals such highly diverse ecosystems as tropical rainforests and coral reefs. As tiny burrowers crawl around they help oxygenate sediments and interact with microbes to cycle nutrients and carbon on the ocean floor. Once again, the tiny play a mighty role."
"The inventory of life in the deep sea has only just begun, and much more remains to be done," he adds. "Sediment-covered seafloors cover more than 60 percent of Earth's surface. And, given these new insights, we cannot possibly use the deep-sea floor as a waste dump or subject it to unlimited resource extraction without massively impacting the marine communities living there."
The scientific chair of the entire Census, Ian Poiner, concluded: "The Census of Marine Life takes immense pride in recognizing the hidden majority."
Census of Marine Life: Final summaries and reports
Started in the year 2000, the Census of Marine Life has been a decade-long international research program uniting thousands of scientists worldwide with the goal of assessing and explaining the diversity, distribution and abundance of life in the seas. It has been supported by private sources and many government agencies.
The final reports of the Census of Marine Life will be presented and discussed in London in October. Three books will be launched. Many of the results described above will be documented in Life in the World's Oceans: Diversity, Distribution and Abundance, A.D. McIntyre, ed., Wiley-Blackwell, in press. Adapted from materials provided by Census of Marine Life.

Microbial Answer to Plastic Pollution

Fragments of plastic in the ocean are not just unsightly but potentially lethal to marine life. Coastal microbes may offer a smart solution to clean up plastic contamination, according to Jesse Harrison presenting his research at the Society for General Microbiology's spring meeting in Edinburgh.

The researchers from the University of Sheffield and the Centre for Environment, Fisheries and Aquaculture Science have shown that the combination of marine microbes that can grow on plastic waste varies significantly from microbial groups that colonise surfaces in the wider environment. This raises the possibility that the plastic-associated marine microbes have different activities that could contribute to the breakdown of these plastics or the toxic chemicals associated with them.
Plastic waste is a long-term problem as its breakdown in the environment may require thousands of years. "Plastics form a daily part of our lives and are treated as disposable by consumers. As such plastics comprise the most abundant and rapidly growing component of man-made litter entering the oceans," explained Jesse Harrison.
Over time the size of plastic fragments in the oceans decreases as a result of exposure to natural forces. Tiny fragments of 5 mm or less are called "microplastics" and are particularly dangerous as they can absorb toxic chemicals which are transported to marine animals when ingested.
While microbes are the most numerous organisms in the marine environment, this is the first DNA-based study to investigate how they interact with plastic fragments. The new study investigated the attachment of microbes to fragments of polyethylene -- a plastic commonly used for shopping bags. The scientists found that the plastic was rapidly colonised by multiple species of bacteria that congregated together to form a 'biofilm' on its surface. Interestingly, the biofilm was only formed by certain types of marine bacteria.
The group, led by Dr. Mark Osborn at Sheffield, plans to investigate how the microbial interaction with microplastics varies across different habitats within the coastal seabed -- research which they believe could have huge environmental benefits. "Microbes play a key role in the sustaining of all marine life and are the most likely of all organisms to break down toxic chemicals, or even the plastics themselves," suggested Mr Harrison. "This kind of rSociety for General Microbiology (2010, March 31). Microbial answer to plastic pollution?. ScienceDaily. Retrieved April 1, 2010, from http://www.sciencedaily.com­ /releases/2010/03/100329075919.htmesearch is also helping us unravel the global environmental impacts of plastic pollution," he said.

Dormant Microbes Promote Diversity, Serve Environment

The ability of microbes, tiny organisms that do big jobs in our environment, to go dormant not only can save them from death and possible extinction but may also play a key role in promoting biodiversity and ecosystem stability.

In a paper published this week in the Proceedings of National Academy of Sciences, Michigan State University's Jay Lennon and Stuart Jones described how they used a mathematical model and molecular tools to study how dormancy affects the biodiversity of natural microbial communities, especially in lakes.
Dormancy is a reversible state of low metabolic activity that an organism enters when it encounters stressful conditions, such as starvation or cold temperatures. The strategy is common among plants and animals, but is also used by some microbes, most notably bacteria that cause anthrax, tuberculosis and cholera. This new study shows that dormancy is not just important for disease-causing microbes, however.
"Microbes are the most abundant and diverse organisms on earth; they carry out essential ecosystem services" said Lennon, an assistant professor of microbiology and molecular genetics who is also affiliated with the W.K. Kellogg Biological Station. "Among these services are contaminant degradation, carbon sequestration and various processes that affect plant productivity."
Scientists have recently cataloged thousands of microbial species in soil and ocean samples. These extremely high levels of biodiversity may help ensure the stability of ecosystem processes in the face of environmental change. It is not clear, however, why microbial communities are so diverse. "We think," Lennon said. "that dormancy is a critical factor that maintains microbial diversity."
Gathering samples from Michigan lakes, Lennon and Stuart examined two very different groups of microbes -- bacteria and eukaryotes, which are primarily algae. With the molecular data and models they developed, the researchers found that microbial seed banks -- seeds that have been dormant in the lakes -- are important, but, in Lennon's words, "not all microbes are the same."
"Bacteria appear to rely on dormancy more so than eukaryotic microbes," he said. "When faced with unfavorable conditions bacteria may simply go to sleep. There are risks to this strategy -- but it pays off if a microbe wakes up before dying and conditions are favorable once it is resuscitated. Essentially, a dormant organism is able to escape the bad times."
On the other hand, the vast majority of algae and related species were metabolically active. "In lakes, dormancy was less important for eukaryotic microbes." Because they are larger than bacteria, algae sink faster and may not wake up before it is too late. These differences in dormancy may be important for predicting how populations respond to disturbance and environmental change.
One important discovery was that environmental conditions or "cues" seem to determine the microbes' degree of dormancy. Lennon said they found that dormancy was less common in high productivity lakes. Lake productivity tends to be controlled by nitrogen and phosphorus concentrations, which can be linked to climate change and land use activity.
Dormancy in microbes has been studied for more than a century, Lennon said, especially as it relates to disease. For example, tuberculosis can lay dormant in a human for years before becoming reactivated. Dormancy also appears to be important for microbes in the environment, and may help us understand what regulates the tremendous amount of microbial diversity that is found in virtually all natural ecosystems.

Genome Analysis of Marine Microbe Reveals a Metabolic Minimalist

Flightless birds, blind cave shrimp, and other oddities suggest a "use it or lose it" tendency in evolution. In the microbial world, an unusual marine microorganism appears to have ditched several major metabolic pathways, leaving it with a remarkably reduced set of genes.

This metabolic minimalist is a specialist uniquely suited to performing one very important function: taking nitrogen gas from the atmosphere and "fixing" it into a form that makes this essential nutrient available to other organisms. Nitrogen fixation fertilizes the oceans, controlling overall biological productivity and thereby affecting how much carbon dioxide the oceans absorb from the atmosphere.

Jonathan Zehr, the marine microbiologist who discovered the microbe, said it has stubbornly resisted efforts to grow it in the laboratory. But that hasn't stopped his team from determining the complete DNA sequence of its genome. Genome analysis enabled the researchers to reconstruct the organism's unusual metabolic lifestyle. They published their findings in Nature in a paper available online February 21.

Zehr, a professor of ocean sciences at the University of California, Santa Cruz, characterized the microbe as an atypical member of the cyanobacteria, a group of photosynthetic bacteria formerly known as blue-green algae. Still lacking a formal taxonomic classification, it is known only as UCYN-A. First detected in the open ocean near Hawaii in 1998, it is now known to be periodically abundant in tropical and subtropical waters throughout the world.

"Biogeochemists have never been able to balance the nitrogen budget of the oceans--there seems to be more nitrogen produced than we can account for from known organisms. So this organism may be an important part of the overall nitrogen budget," Zehr said.

In a 2008 paper in Science, Zehr's team reported that UCYN-A is completely lacking the genes for a key component of the photosynthetic apparatus. The missing parts, known as photosystem II, carry out the stage in photosynthesis that generates oxygen by splitting water molecules. This is significant because oxygen inhibits nitrogen fixation. Most nitrogen-fixing cyanobacteria carry out photosynthesis during the day and nitrogen fixation at night, but UCYN-A can fix nitrogen all day long.

The new paper extends the list of UCYN-A's missing metabolic pathways to include, among other things, a process central to aerobic metabolism known as the TCA cycle or Krebs cycle. It also lacks the Calvin cycle, which uses the carbon from carbon dioxide to build sugars, and it is unable to synthesize about half of the 20 essential amino acids.

"This thing is really stripped down," said James Tripp, a bioinformatics specialist at UCSC and lead author of the Naturepaper. "My analysis indicates it has to have an outside source to obtain sugars, amino acids, and two out of the four bases needed to make DNA."

Tripp performed the genome analysis reported in the paper. He worked closely with scientists at 454 Life Sciences, a Roche company based in Branford, Conn., that specializes in high-throughput DNA sequencing technology. The researchers applied new genome sequencing and assembly techniques to produce the complete genome sequence from natural samples of DNA. Because UCYN-A cannot be cultured, researchers used a cell-sorting technique called flow cytometry to obtain concentrated samples of the microbe from ocean water, and then extracted DNA from the cells for sequencing.

Although UCYN-A must depend on other organisms for key nutrients, the researchers have found no evidence that it lives in a close symbiotic association with another microorganism. Zehr said the failure to find another organism closely associated with it suggests two possibilities. "It might live in a cryptic association that's very hard to sample because it's fragile and just falls apart, or it may respond to blooms of other phytoplankton and live in the soup of nutrients excreted by other organisms," he said.

One of the striking things about UCYN-A's metabolism is that it lacks essential pathways other organisms use to generate energy for their cells. "Nitrogen fixation takes a lot of energy, but this thing has figured out how to fix nitrogen without the normal pathways used to fuel it in other organisms," Zehr said. "It presents a real evolutionary and ecological paradox."

In addition to Zehr and Tripp, the coauthors of the Nature paper include graduate student Shellie Bench, specialist Kendra Turk, and postdoctoral scholar Rachel Foster in Zehr's lab at UCSC, and Brian Desany, Faheem Niazi, and Jason Affourtit of 454 Life Sciences. This research was supported by the Gordon and Betty Moore Foundation, the National Science Foundation, and the NSF Center for Microbial Oceanography Research and Education.H. James Tripp, Shellie R. Bench, Kendra A. Turk, Rachel A. Foster, Brian A. Desany, Faheem Niazi, Jason P. Affourtit, Jonathan P. Zehr. Metabolic streamlining in an open-ocean nitrogen-fixing cyanobacterium. Nature, 2010; 464 (7285): 90 DOI: 10.1038/nature08786

Faster Method to Detect Bacterial Contamination in Coastal Waters Developed

Currently, beachgoers are informed about water-quality conditions based on results from the previous day's sample. Scientists must collect samples in the field, then return to a lab to culture them for analysis -- a process that takes a minimum of 24 hours.

Now, engineers from the UCLA Henry Samueli School of Engineering and Applied Science have sped up the process of analyzing bacterial concentrations to under one hour, through the development of a new in-field, rapid-detection method.
Since bacteria levels can change quickly in the water column, a one-day turnaround time simply isn't fast enough to adequately protect swimmers or prevent unnecessary beach closures, the engineers say.
This issue is especially pertinent in California, where gastrointestinal illness that can result from contact with contaminated beach waters has been estimated to cost Orange and Los Angeles county beach visitors between $21 million and $51 million per year in sick days and related issues.
Furthermore, California coastlines are subject to chronic water pollution problems due to sewage spills and urban runoff. Rainstorms in Southern California can further exacerbate this problem, as pollutants that have accumulated over time on street surfaces are suddenly flushed into our waterways and into the ocean.
Jenny Jay, UCLA associate professor of civil and environmental engineering, and Ph.D. student Christine Lee have advanced and tested a rapid method in marine and freshwater samples from beaches in Malibu and Santa Monica. To their knowledge, it is among the first viable in-field methods for rapid, portable fecal bacteria analysis. This research will be published in an upcoming issue of the Journal of Applied Microbiology and is currently available online.
Even for areas like the Southern California coast, which are close to state-of-the-art laboratories, transportation time, coupled with lab work, may mean that results often are not ready until the next day. With such a delay between sampling and results, the results may no longer be relevant due to the dynamic nature of water quality in beach environments.
The new rapid method represents a field-portable alternative to more expensive procedures, particularly where larger-scale, expensive equipment is not readily accessible. To decrease the time to determine results, the researchers have outfitted a portable kit to test samples for bacterial concentrations.
"We envision a tool that can be used by lifeguards to collect and analyze water samples throughout the day, providing beachgoers with up-to-date, near-real-time data on water conditions," Lee said. "This could also be useful in determining persistence of a bacterial contaminant after a pollution event, such as a sewage spill or a septic tank leaking."
"We are currently applying this method, in a new approach, to identifying contamination sources in which we can adaptively sample the environment in order to hone in on hotspots," Jay said.
The process uses magnetic beads conjugated to specific antibodies that identify and bind fecal bacteria that are used as standards for determining the safety of recreational waters, such as E. coli and Enterococcus.
After a few filtration and isolation steps, the sample organisms are lysed and treated with an enzyme that catalyzes a light-emitting reaction with target ATP, the energy currency of a cell. Cells break down ATP to obtain energy important for cellular processes.
Scientists can then determine bacterial concentrations based on how much light is released by using a luminometer, a device that detects light emissions.
The process is called covalently linked immunomagnetic separation/adenosine triphosphate quantification technique (Cov-IMS/ATP).
The paper's other co-authors are UCLA electrical engineering professor William Kaiser and John Griffith, Ph.D., a senior microbiologist with the Southern California Coastal Water Research Project.
For the Southern California coast, using this detection method could significantly inform source-tracking practices.
"UCLA's rapid-method work is very exciting," said Mark Gold, D.Env., president of the environmental group Heal the Bay. "It could result in faster notification of the public on the health risks of swimming at contaminated beaches and better protection of public health."

Long-Reigning Microbe Controlling Ocean Nitrogen Shares the Throne

Marine scientists long believed that a microbe called Trichodesmium, a member of a group called the cyanobacteria, reigned over the ocean's nitrogen budget.
New research results reported online February 25 in a paper in Science Express show that Trichodesmium may have to share its nitrogen-fixing throne: two others of its kind, small spherical species of nitrogen-fixing cyanobacteria called UCYN-A and Crocosphaera watsonii, are also abundant in the oceans.
One of them, UCYN-A, is more widely distributed than Trichodesmium, and can live in cooler waters.
Different nitrogen-fixing cyanobacteria, scientists have discovered, have varying preferences for water temperature and other environmental factors.
Pia Moisander and Jon Zehr of the University of California at Santa Cruz and their co-authors showed that actively nitrogen-fixing UCYN-A "can be found in great abundance at higher latitudes and deeper waters than Trichodesmium," says Moisander.
"Where Trichodesmium might be thought of as a warm-water microbe, UCYN-A likes it cooler," says Zehr. "This has far-reaching implications for the geographic distribution of the ocean's 'nitrogen fixers,' and for the process of nitrogen fixation itself."
According to co-author Joseph Montoya of the Georgia Institute of Technology, "we're now beginning to develop an appreciation for the biogeography of marine nitrogen fixation, and the broad range of oceanic habitats where nitrogen fixation makes a significant contribution to the overall nitrogen budget."
Most previous estimates of global nitrogen fixation were based on distributions of or factors that control the growth of Trichodesmium.
"The results of this study," says David Garrison, program director in the National Science Foundation (NSF)'s Directorate for Geosciences, "show that these novel microbes are found in the world's oceans in a distribution analogous to that of non-nitrogen-fixing cyanobacteria, which are widespread."
The research was also supported by NSF's Directorate for Biological Sciences and an NSF Science and Technology Center called C-MORE, the Center for Microbial Oceanography: Research and Education.
Trichodesmium, as well as UCYN-A and Crocosphaera watsonii, "fix" nitrogen in the seas, taking nitrogen gas from the air we breathe and converting it to chemical forms that other microorganisms can use to power their cellular machinery.
Nitrogen-fixing microorganisms are the key to the productivity of the oceans. Growth of microbes at the base of the food chain is dependent on nutrients like nitrogen, in the same way that agriculture on land depends on such nutrients.
Microorganisms that fix nitrogen play a central role, says Zehr, in the "vertical downward flux of organic matter to the deep ocean."
Life forms that are among our planet's smallest, he says, play a very large role. Through a series of steps in the nitrogen fixation process, they sequester carbon from the atmosphere, important in controlling Earth's climate.
Other authors of the paper are Roxanne Beinart and Ian Hewson of the University of California at Santa Cruz; Angelicque White of Oregon State University; Kenneth Johnson of the Monterey Bay Aquarium Research Institute; and Craig Carlson of the University of California at Santa Barbara.
The research received additional funding from the Gordon and Betty Moore Foundation.

Microbe Understudies Await Their Turn in the Limelight: Deep-Sea 'Lost City' Shows Rare Microbes Can Become Dominant

On the marine microbial stage, there appears to be a vast, varied group of understudies only too ready to step in when "star" microbes falter.

At least that's what happens at the Lost City hydrothermal vent field, according to work led by the University of Washington and published in the Proceedings of the National Academy of Sciences.

The Lost City hydrothermal vent field in the mid-Atlantic Ocean is the only one of its kind found thus far. It offers scientists access to microorganisms living in vents that range in age from newly formed to tens of thousands of years old. A bit player found in scant numbers in the younger, more active vents became the lead actor in a chimney more than 1,000 years old where venting has moderated and cooled, changing the ecosystem.

This is the first evidence that microorganisms can remain rare for such a long time before completely turning the tables to become dominant when ecosystems change, according to William Brazelton, a University of Washington postdoctoral researcher. It seems logical, but until recently, scientists weren't able to detect microorganisms at such low abundance, Brazelton says.

It was in 2006 that scientists, led by Mitchell Sogin of the Marine Biological Laboratory at Woods Hole, Mass., and a co-author of the PNAS paper, published the first paper saying microorganisms in the marine environment had been woefully undercounted. They used the latest DNA sequencing techniques and said marine microorganisms could be 10 to 100 times more diverse than previously thought. They coined the term "rare biosphere" to describe a vast but unrecognized group of microorganisms -- "rare" because each kind of microorganism, or taxa, appeared to be present in only very low numbers or abundance, so low that they were previously undetectable.

If the new way of determining microbial diversity was accurate, scientists were left to wonder why such a large collection of low-abundance organisms existed.

"A fundamental prediction of the 'rare biosphere' model is that when environmental conditions change, some of these rare, preadapted taxa can rapidly exploit the new conditions, increase in abundance and out-complete the once abundant organisms that were adapted to past conditions," Brazelton and his co-authors wrote. Yet, they continued, "No studies have tested this prediction by examining a shift in species composition involving extremely rare taxa occurring during a known time interval."

Until now.

Lost City was discovered during a National Science Foundation expedition in 2000 by UW oceanography professor and paper co-author Deborah Kelley and others. They were on board the research vessel Atlantis, which is one reason the field was called Lost City. The hot springs form in a very different way from the metal-rich, 700 degrees F black smoker vents scientists have known about since the 1970s. Water venting at Lost City is generally 200 F or less and the chimneys, vents and other structures at Lost City are nearly pure carbonate, the same material as limestone in caves. They are formed by a process called serpentinization, a chemical reaction between seawater and mantle rocks that underlie the field. The vent waters are highly alkaline and enriched in methane and hydrogen gases -- important energy sources for the microbes that inhabit Lost City.

Lost City also differs from the magma-driven hydrothermal systems in that it is very long-lived.

Whereas there have been numerous seasonal and short-term studies of microbial responses to environmental changes -- lasting years at the most -- the Lost City hydrothermal vent field provided a way to look at changes in vent ecosystems 1,000 years apart in age.

Analyses by Brazelton and colleagues revealed that DNA sequences that were rare in younger vents were abundant in older ones. Because it is likely that the older Lost City chimneys vented higher-temperature, more alkaline fluids when they were younger, scientists think that as the ecosystem changed some of the rare microorganisms came to the fore.

This round of near-disappearance and then dominance could have happened repeatedly during the 30,000 year lifetime of the Lost City vent field so the microorganisms present today are "pre-adapted" to certain conditions and are just waiting for the ecosystem to suit them best.

"The rare biosphere of the Lost City microbial community represents a large repository of genetic memory created during a long history of past environmental changes," the authors write. "The rare organisms were able to rapidly exploit the new niches as they arose because they had been previously selected for the same conditions in the past."

Co-author Sogin says: "The ecological shifts over time spans of thousands of years at Lost City show that some of these rare organisms that are very closely related to the dominant taxa are not artifacts of DNA sequencing. The organisms are real, they are capable of growing and very subtle shifts resulted in them becoming winning populations."

The work was funded by the National Science Foundation, NASA and the W.M. Keck Foundation. Other co-authors on the paper are John Baross, UW professor of oceanography; Chuan-Chou Shen, National Taiwan University, Taipei; Lawrence Edwards, University of Minnesota, Minneapolis; and Kristin Ludwig, recent UW graduate now at the Consortium for Ocean Leadership, Washington, D.C. Adapted from materials provided by University of Washington.

Chemical Imaging Of Deep-sea Microorganisms May Help Explain Lingering Nitrogen Mystery

Researchers at the California Institute of Technology (Caltech) have identified an unexpected metabolic ability within a symbiotic community of microorganisms that may help solve a lingering mystery about the world's nitrogen-cycling budget.

A paper about their work appears in the October 16 issue of the journal Science.
The element nitrogen is a critical part of amino acids, the building blocks of proteins, and therefore essential to all life. Although nitrogen is plentiful on Earth—it comprises 78 percent of the atmosphere, by volume—the element is usually found strongly bonded to itself, in the form of the diatomic gas N2. To be biologically useful, a nitrogen atom must be released from this coupling and converted to a reduced, or "fixed," state; reduced nitrogen atoms gain an electron, which makes them chemically reactive.
Although lightning, combustion, and other nonbiological processes can reduce nitrogen, far more is generated by nitrogen-fixing microorganisms such as bacteria—in particular, photosynthetic cyanobacteria. These organisms produce the bulk of the nitrogen available to living things in the ocean.
Still, when researchers add up all of the known sources of fixed nitrogen (biological and otherwise) in the global nitrogen cycle and compare it to the sinks—where nitrogen is taken up for growth and energy—they come up short. It appears that more nitrogen is being used than is being made. The apparent nitrogen budget, in effect, does not balance. This discrepancy had led scientists to question whether the nitrogen cycle is truly out of balance, or whether the known inventories of sources and sinks are misleadingly incomplete.
Victoria J. Orphan, an assistant professor of geobiology at Caltech, along with graduate student Anne E. Dekas and postdoctoral research scholar Rachel S. Poretsky, suggest the answer is, at least in part, an incomplete catalog of the sources of fixed nitrogen.
The team studied ocean sediment samples obtained in methane cold seeps located at a depth of about 1,800 feet. The area, known as the Eel River Basin, is located approximately 20 miles off the coast of the northern California town of Eureka, on a continental margin in a region supporting high levels of natural methane seepage at the seabed.
In the laboratory, the researchers examined the methane-rich sediment and the tiny microbial conglomerations that live within. These spherical cell conglomerates, averaging about 500 cells each, consist of two types of anaerobic microorganisms living in a unique symbiotic relationship fueled by methane. The first microorganism is a bacterium that reduces the chemical sulfate into sulfide (via a process that produces the rotten-egg odor of salt marshes and mud flats) to generate energy. The second is a methane-oxidizing archaeon (the archaea are a group of nonbacterial single-celled microorganisms). Working together, these two symbionts are responsible for consuming the majority of the naturally released methane in the deep sea.
Although these symbiotic associations themselves are not new—these conglomerations were discovered about a decade ago and are found on continental margins worldwide—the Caltech scientists discovered something unexpected: the methane-consuming archaea were actively fixing nitrogen, and sharing it with their bacterial neighbors.
"This is the first time that nitrogen fixation has been documented within methane-oxidizing archaea," Dekas says.
Interestingly, although these organisms have a nitrogen-poor diet of methane gas, they live in an environment that contains reduced nitrogen—in the form of ammonium and other chemicals—which means they shouldn't need to create their own. "It's possible that they do need to because they are living in a crowded community—a tightly packed ball—that prevents some organisms from having access to the nitrogen," she says. Another possibility is that these environments do not have as much biologically available reduced nitrogen as had been thought.
To determine that the archaea were indeed fixing nitrogen, the researchers first incubated the archaeal-bacterial assemblages with a dinitrogen gas, N2, that was composed of two atoms of nitrogen-15. Nitrogen-15 is a nonradioactive isotope of nitrogen that contains one more neutron than regular nitrogen (nitrogen-14) and can be used as a tracer for the incorporation of the element.
The researchers then used a technique called fluorescent in situ hybridization (FISH) to stain the two types of organisms in the sediment, and analyzed these cells for their nitrogen-15 content using a state-of-the-art instrument called a nanometer secondary ion mass spectrometer, or nanoSIMS. The nanoSIMS, which is housed at the Caltech Center for Microanalysis, is capable of collecting chemical and isotopic data at a spatial scale of 50 to 100 nanometers, or around five to 10 times smaller than the size of a single microbial cell.
Both the archaea and, to a lesser extent, their bacterial neighbors had incorporated the nitrogen-15, which could have happened only if the N2 had been fixed by the archaea—and then shared.
"The high spatial resolution of the nanoSIMS instrument—which produces a focused beam of ions that is smaller than a single cell—allowed us to directly pinpoint which of the symbiotic cells in the consortia had assimilated the nitrogen-15–labeled N2 into their biomass," Orphan notes.
The fixation process, say the scientists, is painfully slow; the organisms themselves have ultra-slow growth rates, doubling once every three to six months. "But they are passing on some nitrogen to their neighbors, which means they are producing more than they need," despite the energy cost of doing so, Dekas says. "We don't know what benefit the archaeal organisms get from sharing it, but we do know they need the bacterial symbiont to stay alive," she adds.
"Previously, assumptions about when and where nitrogen fixation takes place made it seem unlikely that nitrogen fixation would occur in this environment, or within such energetically starved organisms," Dekas says. "These results suggest that these assumptions may need to be reevaluated, and that there could be more nitrogen-fixing organisms in other unexpected environments. Together, these previously overlooked sources of nitrogen may be an important component in the marine nitrogen inventory."
The research in the paper, "Deep-Sea Archaea Fix and Share Nitrogen in Methane-Consuming Microbial Consortia," was supported by the National Science Foundation and the Gordon and Betty Moore Foundation.
Journal reference:
Anne E. Dekas, Rachel S. Poretsky, and Victoria J. Orphan. Deep-Sea Archaea Fix and Share Nitrogen in Methane-Consuming Microbial Consortia. Science, 2009; 326 (5951): 422 DOI: 10.1126/science.1178223
Adapted from materials provided by California Institute of Technology, via EurekAlert!, a service of AAAS.

Chemical Imaging Of Deep-sea Microorganisms May Help Explain Lingering Nitrogen Mystery

Researchers at the California Institute of Technology (Caltech) have identified an unexpected metabolic ability within a symbiotic community of microorganisms that may help solve a lingering mystery about the world's nitrogen-cycling budget.

A paper about their work appears in the October 16 issue of the journal Science.

The element nitrogen is a critical part of amino acids, the building blocks of proteins, and therefore essential to all life. Although nitrogen is plentiful on Earth—it comprises 78 percent of the atmosphere, by volume—the element is usually found strongly bonded to itself, in the form of the diatomic gas N₂. To be biologically useful, a nitrogen atom must be released from this coupling and converted to a reduced, or "fixed," state; reduced nitrogen atoms gain an electron, which makes them chemically reactive.

Although lightning, combustion, and other nonbiological processes can reduce nitrogen, far more is generated by nitrogen-fixing microorganisms such as bacteria—in particular, photosynthetic cyanobacteria. These organisms produce the bulk of the nitrogen available to living things in the ocean.

Still, when researchers add up all of the known sources of fixed nitrogen (biological and otherwise) in the global nitrogen cycle and compare it to the sinks—where nitrogen is taken up for growth and energy—they come up short. It appears that more nitrogen is being used than is being made. The apparent nitrogen budget, in effect, does not balance. This discrepancy had led scientists to question whether the nitrogen cycle is truly out of balance, or whether the known inventories of sources and sinks are misleadingly incomplete.

Victoria J. Orphan, an assistant professor of geobiology at Caltech, along with graduate student Anne E. Dekas and postdoctoral research scholar Rachel S. Poretsky, suggest the answer is, at least in part, an incomplete catalog of the sources of fixed nitrogen.

The team studied ocean sediment samples obtained in methane cold seeps located at a depth of about 1,800 feet. The area, known as the Eel River Basin, is located approximately 20 miles off the coast of the northern California town of Eureka, on a continental margin in a region supporting high levels of natural methane seepage at the seabed.

In the laboratory, the researchers examined the methane-rich sediment and the tiny microbial conglomerations that live within. These spherical cell conglomerates, averaging about 500 cells each, consist of two types of anaerobic microorganisms living in a unique symbiotic relationship fueled by methane. The first microorganism is a bacterium that reduces the chemical sulfate into sulfide (via a process that produces the rotten-egg odor of salt marshes and mud flats) to generate energy. The second is a methane-oxidizing archaeon (the archaea are a group of nonbacterial single-celled microorganisms). Working together, these two symbionts are responsible for consuming the majority of the naturally released methane in the deep sea.

Although these symbiotic associations themselves are not new—these conglomerations were discovered about a decade ago and are found on continental margins worldwide—the Caltech scientists discovered something unexpected: the methane-consuming archaea were actively fixing nitrogen, and sharing it with their bacterial neighbors.

"This is the first time that nitrogen fixation has been documented within methane-oxidizing archaea," Dekas says.

Interestingly, although these organisms have a nitrogen-poor diet of methane gas, they live in an environment that contains reduced nitrogen—in the form of ammonium and other chemicals—which means they shouldn't need to create their own. "It's possible that they do need to because they are living in a crowded community—a tightly packed ball—that prevents some organisms from having access to the nitrogen," she says. Another possibility is that these environments do not have as much biologically available reduced nitrogen as had been thought.

To determine that the archaea were indeed fixing nitrogen, the researchers first incubated the archaeal-bacterial assemblages with a dinitrogen gas, N₂, that was composed of two atoms of nitrogen-15. Nitrogen-15 is a nonradioactive isotope of nitrogen that contains one more neutron than regular nitrogen (nitrogen-14) and can be used as a tracer for the incorporation of the element.

The researchers then used a technique called fluorescent in situ hybridization (FISH) to stain the two types of organisms in the sediment, and analyzed these cells for their nitrogen-15 content using a state-of-the-art instrument called a nanometer secondary ion mass spectrometer, or nanoSIMS. The nanoSIMS, which is housed at the Caltech Center for Microanalysis, is capable of collecting chemical and isotopic data at a spatial scale of 50 to 100 nanometers, or around five to 10 times smaller than the size of a single microbial cell.

Both the archaea and, to a lesser extent, their bacterial neighbors had incorporated the nitrogen-15, which could have happened only if the N₂ had been fixed by the archaea—and then shared.

"The high spatial resolution of the nanoSIMS instrument—which produces a focused beam of ions that is smaller than a single cell—allowed us to directly pinpoint which of the symbiotic cells in the consortia had assimilated the nitrogen-15–labeled N₂ into their biomass," Orphan notes.

The fixation process, say the scientists, is painfully slow; the organisms themselves have ultra-slow growth rates, doubling once every three to six months. "But they are passing on some nitrogen to their neighbors, which means they are producing more than they need," despite the energy cost of doing so, Dekas says. "We don't know what benefit the archaeal organisms get from sharing it, but we do know they need the bacterial symbiont to stay alive," she adds.

"Previously, assumptions about when and where nitrogen fixation takes place made it seem unlikely that nitrogen fixation would occur in this environment, or within such energetically starved organisms," Dekas says. "These results suggest that these assumptions may need to be reevaluated, and that there could be more nitrogen-fixing organisms in other unexpected environments. Together, these previously overlooked sources of nitrogen may be an important component in the marine nitrogen inventory."

The research in the paper, "Deep-Sea Archaea Fix and Share Nitrogen in Methane-Consuming Microbial Consortia," was supported by the National Science Foundation and the Gordon and Betty Moore Foundation.

---

Journal reference:

1. Anne E. Dekas, Rachel S. Poretsky, and Victoria J. Orphan. Deep-Sea Archaea Fix and Share Nitrogen in Methane-Consuming Microbial Consortia. Science, 2009; 326 (5951): 422 DOI: 10.1126/science.1178223

Adapted from materials provided by California Institute of Technology, via EurekAlert!, a service of AAAS.

Planet's Nitrogen Cycle Overturned By 'Tiny Ammonia Eater Of The Seas'

It's not every day you find clues to the planet's inner workings in aquarium scum. But that's what happened a few years ago when University of Washington researchers cultured a tiny organism from the bottom of a Seattle Aquarium tank and found it can digest ammonia, a key environmental function. New results show this minute organism and its brethren play a more central role in the planet's ecology than previously suspected.

The findings, published online September 30 in the journal Nature, show that these microorganisms, members of ancient lineage called archaea, beat out all other marine life in the race for ammonia. Ecologists now assume that ammonia in the upper ocean will first be gobbled up by phytoplankton to make new cells, leaving very little ammonia for microbes to turn into nitrate.

"Our data suggests that it's the other way around," said co-author Willm Martens-Habbena, a UW postdoctoral researcher. "Archaea are capable of stealing the ammonia from other organisms and turning it into nitrate. Then it's the phytoplankton that take up that nitrate once again."

Ammonia is a waste product that can be toxic to animals. But plants, including phytoplankton, prize ammonia as the most energy-efficient way to build new cells.

The new paper also shows that archaea can scavenge nitrogen-containing ammonia in the most barren environments of the deep sea, solving a long-running mystery of how the microorganisms can survive in that environment. Archaea therefore not only play a role, but are central to the planetary nitrogen cycles on which all life depends.

"Bacterial nitrifiers were discovered in the late 19th century. One century later this other group of nitrifiers is discovered that is not a minor population, it turns out to be the major population," said co-author David Stahl, a UW professor with appointments in the departments of civil and environmental engineering and microbiology. "We have to revise our basic understanding of the nitrogen cycle."

In the tree of life, archaea occupy their own branch. Archaea were discovered only about 30 years ago and were first thought to exist only in extreme environments, such as hot springs or hydrothermal vents. They are now known to be more widespread.

In the early 1990s scientists collecting seawater found strands of genetic material that suggested at least 20 percent of the ocean's microbes are archaea, and circumstantial evidence suggested they might live off ammonia. Stahl's group in 2005 was the first to isolate the organism, which they got from a tropical tank in the Seattle Aquarium, and demonstrate that it can, in fact, grow by oxidizing ammonia. His lab and others have since found the organism in many marine environments, including Puget Sound and the North Sea. The microbe is likely ubiquitous on land and in the seas, they say.

The new experiments show that the organism can survive on a mere whiff of ammonia – 10 nanomolar concentration, equivalent to a teaspoon of ammonia salt in 10 million gallons of water. In the deep ocean there is no light and little carbon, so this trace amount of ammonia is the organism's only source of energy.

"What Willm's work has shown is that these archaea can grow at the vanishingly low concentrations of ammonia found in the ocean," Stahl said. "Until we made the measurements, no one thought it would be possible that an organism could live on these trace amounts of ammonia as a primary energy source."

That finding has two important implications for ocean ecosystems. Scientists knew that something was turning ammonia into nitrate in the deep ocean, but could not fathom what organism might be responsible. Now it appears archaea are those mysterious organisms.

And in the sun-dappled upper ocean waters, it appears that archaea can out-compete phytoplankton for ammonia. The same may be true in soil environments, the researchers say.

The archaea in question are small even by the standards of single-celled organisms. At 0.2 micrometers across, about 8 millionths of an inch, the only life forms smaller are viruses. Martens-Habbena speculates that archaea's size could explain how they are able to survive on such a scant energy supply. The strain used in these experiments is named Nitrosopumilus maritimus, which means "tiny ammonia-oxidizer of the sea."

A better understanding of archaea's lifestyle and role in nitrogen cycles not only would rewrite ecology textbooks. It could also have practical applications, such as devising natural ways to boost a soil's nitrogen content without needing to use chemical fertilizers, or designing sewage treatment plants that employ microbes to remove nitrogenous waste more efficiently, or understanding which microbes produce global-warming gases such as nitrous oxide.

The new findings will also affect the equations used in global climate models, researchers say. Computer models use global cycles of nitrogen and other chemicals to estimate how much carbon dioxide the oceans will absorb and ultimately sink to the bottom of the sea. The new findings suggest that most of the nitrate in the surface water comes from recycling of biomass, and not from the deep water as currently assumed.

"Our data suggest that the carbon pump is weaker than currently assumed, so current climate models may overestimate how much carbon can be absorbed by the oceans," Martens Habbena said.

Other co-authors are the UW's Paul Berube, Hidetoshi Urakawa and Jose de la Torre. The research was funded by the National Science Foundation.

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Adapted from materials provided by University of Washington.

New Genomic Model Defines Microbes By Diet; Provides Tool For Tracking Environmental Change

In line with the U.S. Department of Energy (DOE) interest in characterizing the biotic factors involved in global carbon cycling, the DOE Joint Genome Institute (JGI) characterizes a diverse array of plants, microorganisms, and the communities in which they reside to inform options for reducing and stabilizing atmospheric greenhouse gases.

Through a novel genomic approach detailed in the September 7 online edition and on the cover September 14 of the journal Proceedings of the National Academy of Sciences, an international team of scientists led by the University of New South Wales and the DOE JGI demonstrates how the microbial diversity of the oceans can be analyzed without necessarily cultivating samples in the laboratory.
"The model we describe is useful in studying whole marine microbial communities, or metagenomes, to better understand how communities in specific locations are evolving," said senior author Rick Cavicchioli of the University of New South Wales. "In essence, by analyzing and comparing the strategies of the dominant organisms we should have an idea of the carbon flux going through the environment which in turn will be affected by global warming.
The oceans, which make up 71 percent of our planet's surface, are home to microorganisms that are adapted to life strategies along a continuum of two extremes: those that thrive in nutrient-rich waters often associated with warmer regions and those that prefer nutrient-poor waters. Collected from waters off the Alaskan coast, the bacterium Sphingopyxis alaskensis was sequenced by the DOE JGI under the DOE's plan to study the biochemical pathways in microbial genomes and lay the groundwork for technologies based on that data which might be used to reduce greenhouse gas emissions. This bacterium, which has a nutrient-poor lifestyle, serves as a model microorganism that thrives in low-nutrient waters and is key to carbon sequestration in the oceans.
Cavicchioli and his lab compared the traits of S. alaskensis' genome against the genome of Photobacterium angustum, a bacterium collected and sequenced from the warmer, nutrient-rich waters off Sydney, Australia. They then tested the model developed based on these two genomes to successfully predict whether several dozen bacterial samples were those that grow in nutrient-rich environments like P. angustum or under nutrient-poor conditions, like S. alaskensis.
The researchers' findings also supported a long-held theory that though more microbial genome projects involve bacteria adapted to more nutrient-rich environments, in part because they are easier to cultivate, bacteria like S. alaskensis are more representative of microorganisms that are abundant and ecologically significant in the biosphere. DOE JGI Genome Biology Program head and study co-author Nikos Kyrpides said the finding supports the need to develop better techniques to isolate such microorganisms from nutrient-poor environments and sequence their genomes in order to better reflect the microbial biodiversity.
"The method used by Cavicchioli's group to predict bacterial habits lends credence to the idea that sequencing cultivated organisms is biased toward sequencing those that thrive in nutrient-rich conditions, even though those that get by in nutrient-poor conditions are more abundant in the environment," Kyrpides said. "Despite the number of microbial genome projects being done, these organisms represent just a fraction of the microbial diversity on the planet. To sequence microbial genomes that are representative of the environments in which they were collected and for a more systematic and comprehensive sampling of the Tree of Life, researchers need to increasingly develop and rely on other techniques such as single-cell sequencing to isolate DNA samples from harder-to-cultivate microbes residing in environments where nutrients are scarce."
Kyrpides' words were echoed by DOE JGI collaborator Ramunas Stepanauskas of the Bigelow Laboratory for Ocean Sciences, who said the model developed by Cavicchioli's team supports his own group's use of cultivation-independent, single-cell sequencing of marine microbes. "What the Australian group together with the DOE JGI has demonstrated is a more rigorous way of testing the long-standing notion that cultured microorganisms are biased toward the species that are adapted to nutrient-rich environments, which is, in effect an over-representation of their true abundance in the biosphere," he said. "Using their model, we can demonstrate that novel research tools, such as metagenomics and single-cell genomics, provide us with data of ecological relevance without biases due to microbial adaptations to incredibly diverse life strategies."
Cavicchioli said the researchers plan to apply the model to studying the microbial communities' relationships with climate change. As an example, he cites the end of phytoplankton bloom, which is believed to be relatively nutrient rich even in the absence of a chlorophyll spike. "A natural extension is to assess and monitor gene function," he said. "Now that we know 'who' is present, and what their 'lifestyle' is, we can ask, what exactly are they doing – assessing function."
Other authors on the study include DOE JGI's Alla Lapidus, Iain Anderson, A. Christine Munk, Chris Detter and Cliff Han. Other collaborating institutions are the J. Craig Venter Institute, the University of Maryland Biotechnology Institute and Istanbul University (Turkey).
Adapted from materials provided by DOE/Joint Genome Institute, via EurekAlert!, a service of AAAS.