OCEAN PHOSPHORUS CYCLE AND THE ROLE OF MICROBES

FROM:  NATIONAL SCIENCE FOUNDATION
Revealing the ocean's hidden fertilizer
Tiny marine plants play major role in phosphorus cycle
Phosphorus is one of the most common substances on Earth.

An essential nutrient for every living organism--humans require approximately 700 milligrams per day--we're rarely concerned about consuming enough because it is in most of the foods we eat.

Despite its ubiquity and living organisms' dependence on it, we know surprisingly little about how it moves, or cycles, through the ocean environment.

Scientists studying the marine phosphorous cycle have known that phosphorus was absorbed by plants and animals and released back to seawater in the form of phosphate as these plants and animals decay and die.

But a growing body of research hints that microbes in the ocean transform phosphorus in ways that remain a mystery.

Hidden role of ocean's microbes

A new study by a research team from the Woods Hole Oceanographic Institution (WHOI) and Columbia University reveals for the first time a marine phosphorus cycle that is much more complex than previously thought.

The work also highlights the important but previously hidden role that some microbial communities play in using and breaking down forms of this essential element.

A paper reporting the findings is published this week in the journal Science.

"A reason to be excited about this elegant study is in the paper's last sentence: 'the environmental, ecological and evolutionary controls ...remain completely unknown,'" says Don Rice, program director in the National Science Foundation's (NSF) Division of Ocean Sciences, which funded the research through its Chemical Oceanography Program. "There's still a lot we don't know about the sea."

The work is also supported by an NSF Dimensions of Biodiversity grant.

"This is an exciting new discovery that closes a fundamental knowledge gap in our understanding of the marine phosphorus cycle," says the paper's lead author Ben Van Mooy, a biochemist at WHOI.

Much like phosphorus-based fertilizers boost the growth of plants on land, phosphorus in the ocean promotes the production of microbes and tiny marine plants called phytoplankton, which compose the base of the marine food chain.

Phosphonate mystery

It's been unclear exactly how phytoplankton are using the most abundant forms of phosphorus found in the ocean--phosphates and a strange form of phosphorus called phosphonates.

"Phosphonates have always been a huge mystery," Van Mooy says.

"No one's been able to figure out exactly what they are, and more importantly, if they're made and consumed quickly by microbes, or if they're just lying around in the ocean."

To find out more about phosphonates and how microbes metabolize them, the researchers took samples of seawater at a series of stations during a research cruise from Bermuda to Barbados.

They added phosphate to the samples so they could see the microbes in action.

The research team used ion chromatography onboard ship for water chemistry analyses, which allowed the scientists to observe how quickly microbes reacted to the added phosphate in the seawater.

"The ion chromatograph [IC] separates out the different families of molecules," explains Van Mooy.

"We added radioactive phosphate, then isolated the phosphonate to see if the samples became radioactive, too. It's the radioactive technique that let us see how fast phosphate was transformed to phosphonate."

Enter the microbes

The researchers found that about 5 percent of the phosphate in the shallow water samples was taken up by the microbes and changed to phosphonates.

In deeper water samples, which were taken at depths of 40 and 150 meters (131 feet and 492 feet), about 15 to 20 percent of the phosphates became phosphonates.

"Although evidence of the cycling of phosphonates has been mounting for nearly a decade, these results show for the first time that microbes are producing phosphonates in the ocean, and that it is happening very quickly," says paper co-author Sonya Dyhrman of Columbia University.

"An exciting aspect of this study was the application of the IC method at sea. In near-real-time, we could tell that the phosphate we added was being transformed to phosphonate."

Better understanding of phosphorus cycle

A better understanding of phosphorus cycling in the oceans is important, as it affects the marine food web and, therefore, the ability of the oceans to absorb atmospheric carbon dioxide.

The researchers say that solving the mystery of phosphonates also reinforces the need to identify the full suite of phosphorus biochemicals being produced and metabolized by marine microbes, and what physiological roles they serve for these cells.

"Such work will help us further resolve the complexities of how this critical element is cycled in the ocean," Dyhrman adds.

Grants from the Simons Foundation also supported the work.

-NSF-
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Cheryl Dybas, NSF

VIRUSES IN THE DEEP

FROM:  NATIONAL SCIENCE FOUNDATION
The 'intraterrestrials': New viruses discovered in ocean depths

Viruses infect methane-eating archaea beneath the seafloor
The intraterrestrials, they might be called.

Strange creatures live in the deep sea, but few are odder than the viruses that inhabit deep ocean methane seeps and prey on single-celled microorganisms called archaea.

The least understood of life's three primary domains, archaea thrive in the most extreme environments on the planet: near hot ocean rift vents, in acid mine drainage, in the saltiest of evaporation ponds and in petroleum deposits deep underground.

Virus in the deep blue sea

While searching the ocean's depths for evidence of viruses, scientists have found a remarkable new one, a virus that seemingly infects archaea that live beneath the ocean floor.

The researchers were surprised to discover that the virus selectively targets one of its own genes for mutation, and that this capacity is also shared by archaea themselves.

The findings appear today in a paper in the journal Nature Communications.

The project was supported by a National Science Foundation (NSF) Dimensions of Biodiversity grant to characterize microbial diversity in methane seep ecosystems. Dimensions of Biodiversity is supported by NSF's Directorates for Biological Sciences and Geosciences.

New information about life in ocean depths

"Life far beneath the Earth's subsurface is an enigma," said Matt Kane, program director in NSF's Division of Environmental Biology. "By probing deep into our planet, these scientists have discovered new information about Earth's microbes and how they evolve."

"Our study uncovers mechanisms by which viruses and archaea can adapt in this hostile environment," said David Valentine, a geoscientist at the University of California Santa Barbara (UCSB) and co-author of the paper.

The results, he said, raise new questions about the evolution and interaction of the microbes that call the planet's interior home.

"It's now thought that there's more biomass inside the Earth than anywhere else, just living very slowly in this dark, energy-limited environment," said paper co-author Sarah Bagby of UCSB.

Using the submersible Alvin, Valentine and colleagues collected samples from a deep-ocean methane seep by pushing tubes into the ocean floor and retrieving sediments.

The contents were brought back to the lab and fed methane gas, helping the methane-eating archaea in the samples to grow.

When the team assayed the samples for viral infection, they discovered a new virus with a distinctive genetic fingerprint that suggested its likely host was methane-eating archaea.

Genetic sequence of new virus holds the key

The researchers used the genetic sequence of the new virus to chart other occurrences in global databases.

"We found a partial genetic match from methane seeps off Norway and California," said lead author Blair Paul of UCSB. "The evidence suggests that this viral type is distributed around the globe in deep ocean methane seeps."

Further investigation revealed another unexpected finding: a small genetic element, known as a diversity-generating retroelement, that accelerates mutation of a specific section of the virus's genome.

Such elements had been previously identified in bacteria and their viruses, but never among archaea or the viruses that infect them.

"These researchers have shown that cutting-edge genomic approaches can help us understand how microbes function in remote and poorly known environments such as ocean depths," said David Garrison, program director in NSF's Division of Ocean Sciences.

While the self-guided mutation element in the archaea virus resembles known bacterial elements, the researchers found that it has a divergent evolutionary history.

"The target of guided mutation--the tips of the virus that make first contact when infecting a cell--is similar," said Paul.

"But the ability to mutate those tips is an offensive countermeasure against the cell's defenses, a move that resembles a molecular arms race."

Unusual genetic adaptations

Having found guided mutation in a virus-infecting archaea, the scientists reasoned that archaea themselves might use the same mechanism for genetic adaptation.

In an exhaustive search, they identified parallel features in the genomes of a subterranean group of archaea known as nanoarchaea.

Unlike the deep-ocean virus that uses guided mutation to alter a single gene, the nanoarchaea target at least four distinct genes.

"It's a new record," said Bagby.

"Bacteria had been observed to target two genes with this mechanism. That may not seem like a huge difference, but targeting four is extraordinary."

According to Valentine, the genetic mutation that fosters these potential variations may be key to the survival of archaea beneath the Earth's surface.

"The cell is choosing to modify certain proteins," he said. "It's doing its own protein engineering. While we don't yet know what those proteins are being used for, learning about the process can tell us something about the environment in which these organisms thrive."

Viral DNA sequencing was provided through a Gordon and Betty Moore Foundation grant. The research team also included scientists from the University of California, Los Angeles; the University of California, San Diego; and the U.S. Department of Energy's Joint Genome Institute.

-NSF-
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Cheryl Dybas, NSF

SCIENTISTS STUDY CHANGES IN MERCURY LEVELS IN OCEANS

FROM:  NATIONAL SCIENCE FOUNDATION 

Mercury in the world's oceans: On the rise

New results show three times as much in upper oceans since Industrial Revolution times

Little was known about how much mercury in the environment was the result of human activities, or how much "bioavailable" mercury was in the world's oceans. Until now.

The first direct calculation of mercury pollution in the world's oceans, based on data from 12 oceanographic sampling cruises during the last eight years, is reported in this week's issue of the journal Nature.

The scientists involved are affiliated with the Woods Hole Oceanographic Institution (WHOI) in Massachusetts, Wright State University in Ohio, the Observatoire Midi-Pyréneés in France and the Royal Netherlands Institute for Sea Research in the Netherlands.

The research was funded by the National Science Foundation (NSF) and the European Research Council. It was led by WHOI marine chemist Carl Lamborg. The results offer a look at the global distribution of mercury in the marine environment.

"Mercury is an environmental poison that's detectable wherever we look for it, including the ocean abyss," says Don Rice, director of the NSF's Chemical Oceanography Program.

"These scientists have reminded us that the problem is far from abatement, especially in regions of the world's oceans where the human fingerprint is most distinct."

Mercury is a naturally occurring element as well as a by-product of such human activities as burning coal and making cement.

"If we want to regulate mercury emissions into the environment and in the food we eat, we should first know how much is there and how much human activity is adding every year," says Lamborg.

"At the moment, however, there is no way to look at a water sample and tell the difference between mercury that came from pollution and mercury that came from natural sources. Now we at least have a way to separate the bulk contributions of natural and human sources over time."

The group started by looking at data that reveal details about ocean levels of phosphate, a substance that is better studied in the oceans than mercury and that behaves in much the same way as mercury.

Phosphate is a nutrient that, like mercury, is taken up into the marine food web by binding with organic material.

By determining the ratio of phosphate-to-mercury in water deeper than 1,000 meters (3,300 feet) that has not been in contact with Earth's atmosphere since the Industrial Revolution, the researchers were able to estimate mercury in the oceans that originated from natural sources such as the breakdown, or weathering, of rocks on land.

Their findings agreed with what they would expect to see given the pattern of global ocean circulation.

North Atlantic waters, for example, showed the most obvious signs of mercury pollution because that's where surface waters sink to form deep and intermediate water flows.

The tropical and Northeast Pacific, on the other hand, were relatively unaffected; it takes centuries for deep ocean water to circulate to these regions.

Determining the contribution of mercury from human activity required another step.

To obtain estimates for shallower waters and to provide numbers for the amount of mercury in the oceans, the scientists needed a tracer--a substance that could be linked with major human activities that release mercury into the environment.

They found it in one of the most well-studied gases of the past 40 years: carbon dioxide. Databases containing information on carbon dioxide in ocean waters are extensive and readily available for every ocean at all depths.

Because much of the mercury and carbon dioxide from human sources comes from the same activities, the team was able to derive with an index relating the two.

The results show that the oceans contain about 60,000 to 80,000 tons of mercury pollution.

Ocean waters shallower than about 100 meters (300 feet) have tripled in mercury concentration since the Industrial Revolution. Mercury in the oceans as a whole has increased roughly 10 percent over pre-industrial times.

"The next 50 years could very well add the same amount we've seen in the past 150," says Lamborg.

"We don't know what that means for fish and marine mammals, but likely that some fish contain at least three times more mercury than 150 years ago. It could be more.

"The key is that now we have some solid numbers on which to base continued work."

-NSF-

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Cheryl Dybas, NSF

NSF REPORTS OCEAN MICROBES HAVE DAILY CYCLES OF ACTIVITY

FROM:  NATIONAL SCIENCE FOUNDATION 

Ocean's microbial megacity: Like humans, the sea's most abundant organisms have clear daily cycles

Coordinated timing may have implications for ocean food web

Imagine the open ocean as a microbial megacity, teeming with life too small to be seen.

In every drop of water, hundreds of types of bacteria can be found.

Now scientists have discovered that communities of these ocean microbes have their own daily cycles--not unlike the residents of a bustling city who tend to wake up, commute, work and eat at the same times.

Light-loving photoautotrophs--bacteria that need solar energy to help them photosynthesize food from inorganic substances--have been known to sun themselves on a regular schedule.

But in new research results published in this week's issue of the journal Science, researchers working at Station ALOHA, a deep ocean study site 100 kilometers north of Oahu, Hawaii, observed species of bacteria turning on cycling genes at slightly different times.

The switches suggest a wave of activity that passes through the microbial community.

"I like to say that they are singing in harmony," said Edward DeLong, a biological oceanographer at the University of Hawaii at Manoa and an author of this week's paper.

"For any given species, the gene transcripts for specific metabolic pathways turn on at the same time each day."

The observations were made possible by advanced microbial community RNA sequencing techniques, which allow for whole-genome profiling of multiple species at once.

DeLong and colleagues deployed a free-drifting robotic Environmental Sample Processor (ESP) as part of a National Science Foundation (NSF) Center for Microbial Oceanography: Research and Education (C-MORE) research expedition to Station ALOHA.

Riding the same ocean currents as the microbes it follows, the ESP is equipped to harvest the samples needed for this high-frequency, time-resolved analysis of microbial community dynamics.

What the scientists saw was intriguing: different species of bacteria expressing different types of genes in varying, but consistent, cycles--turning on, for example, restorative genes needed to rebuild solar-collecting powers at night, then ramping up with different gene activity to build new proteins during the day.

"It was almost like a shift of hourly workers punching in and out on a clock," DeLong said.

"This research is a major advance in understanding microbial communities through studies of gene expression in a dynamic environment," said Matt Kane, a program director in NSF's Directorate for Biological Sciences, which co-funds C-MORE with NSF's Directorate for Geosciences.

"It was accomplished by combining new instrumentation for remote sampling with state-of-the-art molecular biological techniques."

The coordinated timing of gene firing across different species of ocean microbes could have important implications for energy transformation in the sea.

"For decades, microbiologists have suspected that marine bacteria were actively responding to day-night cycles," said Mike Sieracki, a program director in NSF's Directorate for Geosciences.

"These researchers have shown that ocean bacteria are indeed very active and likely are synchronized with the sun."

The mechanisms that regulate this periodicity remain to be determined.

Can you set your watch by them?

DeLong said that you can, but it matters whether you're tracking the bacteria in the lab or at sea.

For example, maximum light levels at Station ALOHA are different than light conditions in experimental settings in the laboratory, which may have an effect on microbes' activity and daily cycles.

"That's part of why it's so important to conduct this research in the open ocean environment," said DeLong.

"There are some fundamental laws to be learned about how organisms interact to make the system work better as a whole and to be more efficient."

Co-authors of the paper are Elizabeth Ottesen, Curtis Young, Scott Gifford, John Eppley, Roman Marin III, Stephan Schuster and Christopher Scholin.

The research also was funded by the Gordon and Betty Moore Foundation.

-NSF-


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