By Tia Ghose
LiveScience

The genome of mysterious bacteria that lurk in hospital drains has been sequenced.

Low levels of the bacteria, known only as candidate phylum TM6, have been found in water systems around the world, yet because they could not be cultured in the lab, almost nothing was known about them.

The new research, detailed Monday in the journal Proceedings of the National Academy of Sciences, could be the first step in understanding exactly what these bacteria do, said study co-author Jeffrey McLean, a microbial geneticist at the J. Craig Venter Institute in La Jolla, Calif.

"They're this dark matter of life," McLean said. "We keep seeing them, but we don't have any other information about them. We don't know what they're doing in the environment. It could range from being beneficial to being harmful."

Dark matter
Though known bacteria get all the headlines, all around us are a host of other microbes about which little is known. Scientists occasionally detect traces of DNA from these elusive bacteria, but know almost nothing about what they do and whether they are harmful.

In 1996, researchers first identified one such bug, which they dubbed Candidate Phylum TM6. The bacteria seemed to pervade the world's water systems.

To identify the mysterious bacteria, McLean and his colleagues scraped gunk from a hospital sink drain. The goo contained the genes from a host of different bacteria, so the team used fluorescent tags to identify the DNA inside single cells.

Once they found single cells, they separated them and then broke the DNA from those individual cells into snippets. They then compared that DNA with known genomes for other bacteria, both to eliminate known bacteria and to reconstruct a genome for unknown species. [Unraveling the Genome: 6 Molecular Milestones]

Symbiotic bacteria
They were able to reconstruct about 90 percent of the genome for Candidate Phylum TM6. Based on the fact that the bacteria can't make its own amino acids, the building blocks that make up proteins, the team thinks the bacteria need a host to survive. TM6, they say, may live either on a single-celled microorganism called an amoeba, or on top of another bacterium that forms a biofilm, a slimy mix of bacteria that sticks to surfaces, McLean said.

Right now, they don't know if the TM6 bacteria are harmful or not, but other bugs that live inside amoebas are.

"Pathogens like Legionella and Francisellahave been able to colonize humans because they first colonized an amoeba," McLean told LiveScience.

Now that they have the genome, and know, for instance, that TM6 needs a host to survive, the researchers hope to finally culture the bacterium and learn how it behaves.

The research is "a technical tour-de-force," said Moselio Schaechter, a bacteriologist at San Diego State University, who was not involved in the study.

Still, without culturing the bacteria, the researchers can't say much about its biology. For instance, a DNA sequence of a bacterium found in a sink drain is just a snapshot of the bacterium's life and doesn't say how long it was there or how common it is in that location.

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Anni Glud

The central part of the autonomous instrument that was deployed to measure the oxygen dynamics of the sea-bed in the Mariana Trench at a depth of 11 km. Data documented intensified microbial life in the bottom of the trench as compared to conditions at the surrounding abyssal plains at 6 km water depth.

By Charles Q. Choi, OurAmazingPlanet 

The deepest oceanic trench on Earth is home to a surprisingly active community of bacteria, suggesting other trenches may be hotspots of microbial life, researchers say.

Life in the deep ocean often relies on organic matter snowing down from above. As these particles waft down, their nutrients get degraded by microbes attached to them, so only 1 to 2 percent of the organic matter produced in surface waters is expected to make it to the average ocean depth of about 12,150 feet (3,700 meters). Just how much makes it to the very deepest parts is unknown.

To learn more about life in the dirt at the ocean's depths, scientists used a submersible lander to analyze mud from the surface of Challenger Deep, the deepest spot of the Mariana Trench at the bottom of the central west Pacific Ocean. This 36,000-foot-deep (11,000 m) trench is the deepest known point on Earth's surface.

Natural trap
The researchers analyzed the levels of oxygen consumption within the sediments, which revealed how active the deep-sea microbes were. They discovered unexpectedly high rates of oxygen consumption from the Mariana seafloor, indicating a microbial community twice as active as that of a nearby 19,700-foot (6,000 m) site about 35 miles to the south. [Strangest Places Where Life Is Found on Earth]

"In the most remote, inhospitable places, you can actually have higher activity than their surroundings," researcher Ronnie Glud, a biogeochemist at the Southern Danish University in Odense, Denmark, told OurAmazingPlanet.

Sediments from Challenger Deep also had significantly higher levels of microbes and organic compounds than the nearby, more elevated site. The investigators suggest the Mariana Trench acts as a natural trap for sediments from up high. Similar effects are seen in other submarine canyons.

"It acts as a trap just because it's a big hole. If you have a hole in a garden, it just fills up because things blowing over it tend to fall in, and the same is true with the seafloor," Glud said. The trench is also located in a subduction zone where one of the tectonic plates making up the surface of the Earth is diving under another, "and these areas are very unstable, and frequently see earthquakes that can trigger mudslides that transport material into the trench," he added.

Microbes, microbes everywhere
Another team of scientists recently discovered communities of microbes thriving in the oceanic crust. That research looked at rocks up to about 1,150 to 1,900 feet (350 to 580 m) below the seafloor under about 8,500 feet (2,600 m)  of water off the coast of the northwestern United States. These microbes apparently live off energy from chemical reactions between water and rock instead of nutrients snowing from above.

"You can find microbes everywhere — they're extremely adaptable to conditions, and survive wherever they are," Glud said.

The researchers are now analyzing other trenches to see what bacterial activity is also relatively high there. They also want to learn more about the genetics of bacteria in the Mariana Trench and other trenches "to see how special these bacteria are compared to other bacteria," Glud said.

The scientists detailed their findings online March 17 in the journal Nature Geoscience.

Follow OurAmazingPlanet @OAPlanet, Facebook and Google+.Original article at LiveScience's OurAmazingPlanet.

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Josh Landis, National Science Foundation

Russia's Vostok Station, in a photograph taken during the 2000 to 2001 field season.

By Elizabeth Howell
LiveScience

Late last week, a Russian news outlet reported that scientists at Antarctica's Lake Vostok, buried under miles of ice, said they had found bacteria that appeared to be new to science. Now, the head of that lab has said the signature is actually just contamination, leading outside researchers to say that the Russian team rushed too quickly to announce the possibility of new bacterial life.

Russian news media reported last week that the team had found DNA from a microbe that did not appear in databases and is only 86 percent similar to others on Earth — considered a reliable threshold of new life.

On Monday, the lab analyzing the finding said it was not new bacteria that generated the signal, but contamination.

"We found certain specimens, although not many. All of them were contaminants," laboratory head Vladimir Korolyov said in a quote attributed in media reports to the Interfax news agency.

The quick backtrack illustrates the danger of bypassing peer review when announcing new results, Peter Doran, an Arctic and Antarctic researcher at the University of Illinois at Chicago, told OurAmazingPlanet.

'You can say anything you want in a press release'
Peer review is the scientific process that all findings must undergo before work is published, generally in the form of a paper in a scientific journal. The research comes under the scrutiny of other scientists in the field and is validated and questioned before anything goes to print. That's not the case in a news report.

For that reason, the scientists who OurAmazingPlanet spoke with said that it was hard for them to discuss why the Russians failed since they do not even know, for example, what contaminates were found in the lab. That information could take weeks or months to surface.

"You can say anything you want in a press release," Doran said. "The peer review literature (by contrast) is very controlled. It needs to be substantiated, and written in clear language."

"I tell my students," he continued, "don't trust anything you read in the popular press. Even if there is a paper, there's often a disconnect between what is in the paper and in the popular press."

Peer review, however, can take years, acknowledged David Pearce, a researcher with the British Antarctic Survey who worked on a similar British effort to drill into buried Lake Ellsworth. (That effort failed and is being subject to a review board. The results should be published around May, at which point the British will decide whether to try again.) [Extreme Antarctica: Amazing Photos of Lake Ellsworth]

Taxpayers are often impatient to find out what is going on, Pearce said, and the press works to fill that need. A balance must be struck between these needs, he added.

"It's important (the public) is kept informed of what's going on, and the interesting things that are coming out," Pearce said. Science, by contrast, requires time and careful thought.

"You do want to find out what's happened to the research money," he added, "but you don't want to say too much too soon."

Sterilization part of best practice
The Russian researchers not only faced challenges concerning announcing their findings, but also scientific challenges in their quest to discover life.

It's still not known what kind of life, if any, lies below the 2 miles (3 kilometers) of ice that sits on top of Lake Vostok. As far as researchers know, the underground freshwater has been lying there untouched for more than a million years.

Confirming that any possible signature of life is not a contaminant is complicated, to say the least.

There's a strict protocol the Americans strive to follow in Antarctica, said Doran, who is familiar with the practices of the U.S. Whillans Ice Stream Subglacial Access Research Drilling project (WISSARD) team that worked this year at Antarctica's Lake Whillans.

Doran could not speak specifically to the Russians, but said the American work demonstrates a good methodology.

In WISSARD's case, it involves sterilizing all the equipment with hydrogen peroxide gel or a similar product, then hermetically sealing it in bags for shipment. Scientists on-site sterilize the water in the drill system through several steps that include filters and life-killing ultraviolet radiation.

As the drill progresses through the ice, the scientists monitor cell counts to make sure there are no unexplained jumps.

WISSARD recently announced life findings of its own, but Doran was equally skeptical of that until a paper comes out confirming the work. [Gallery: Finding Life in a Buried Antarctic Lake]

To the WISSARD announcement, Doran said, "I understand how it happened. There are embedded reporters in the field with them. They are sitting around the dinner table together, and drinking Scotch together, and the reporters are right there (when scientists say) 'Our cell counts are way up when we've gone into the lake water.'"

"Of course that gets reported, but without the peer review literature, it's still a violation of how the standard things are done," Doran said.

Follow Elizabeth Howell @howellspace. Follow OurAmazingPlanet @OAPlanet, Facebook and Google+.

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Josh Landis, National Science Foundation

Russia's Vostok Station, in a photograph taken during the 2000 to 2001 field season.

By Elizabeth Howell, OurAmazingPlanet

A new type of microbe has been found at a lake buried under Antarctica's thick ice, according to news reports. The find may unveil clues of the surrounding environment in the lake, according to scientists.

The bacteria, said to be only 86 percent similar to other types known to exist on Earth, was discovered in a water sample taken from Lake Vostok, which sits under more than 2 miles (3 kilometers) of Antarctic ice. The freshwater lake has likely been buried, unaltered, under the ice for the past million years.

Russian scientists reportedly obtained the water samples in 2012 when they drilled all the way down to the lake's surface. They ran the bacteria's composition through a global database and were not able to find anything similar to its type. Scientists couldn't even figure out the bacteria's descendents.

"After putting aside all possible elements of contamination, DNA was found that did not coincide with any of the well-known types in the global database," said Sergey Bulat, a geneticist at the Saint Petersburg Institute of Nuclear Physics, in a quote attributed in media reports to RIA Novosti news service.

"We are calling this life form unclassified and unidentified," he added.

Understanding the environment
While the bacteria still needs to be confirmed, its potential is already drawing attention from other Antarctic scientists.

Life forms are shaped by the environment they live in, and often shape that environment in return. Finding out more about bacteria in Lake Vostok, therefore, will help researchers picture what living in the lake is like for these tiny microorganisms.

"The study of looking at the organisms and their environment is really the study of ecology," said Alison Murray, an associate research professor at the Desert Research Institute (an environmental research group based in Nevada) who also does Antarctic research herself.

"By learning more about the life forms that live in Vostok, that will probably teach us a bit about the lake itself," Murray told OurAmazingPlanet.

Murray, who is familiar with the Russian researchers' work, said the group is a "very careful team of scientists" who would have put the bacteria through several validity tests before releasing the news.

Understanding bacterial life on Earth is also considered a possible research direction for finding life on other planets, including Mars.

'If this is real, it is very exciting'
The 86 percent similarity figure, to Murray, is a plausible indicator that this could be a new type of bacteria. Since all Earthly life is related to each other in some way, anything below about 80 percent would draw concern, Murray added.

At least one other scientist, however, expressed caution about the finding, saying that more information is needed before drawing conclusions.
"If this is real, it is very exciting," Peter Doran, a microbiologist at the University of Illinois at Chicago, wrote in an e-mail to OurAmazingPlanet. He is a frequent visitor to the Arctic and Antarctica for his research.

"I would caution, though, that this type of 'press release' science is a little dangerous. It really needs to go through the rigor of peer review by other experts in the field before I'll jump on board," he said. "Having others looking at their methods and data will provide support for their conclusions."

Russian scientists successfully dug through to the buried lake again in January this year, retrieving more samples for later analysis.

Meanwhile, a British team had to call off their quest in December to dig to Lake Ellsworth, another Antarctic subglacial lake, after they encountered technical difficulties.

Follow Elizabeth Howell @howellspace. Follow OurAmazingPlanet @OAPlanet,Facebookand Google+.

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MODIS Land Rapid Response Team at NASA GSF

Researchers used samples from the Sargasso Sea and coastal Oregon waters, finding four new viruses that killed the most abundant bacteria in the oceans (SAR11) in lab experiments. Here, a phytoplankton bloom in the South Atlantic Ocean.

By Wynne Parry
LiveScience

The discovery of new viruses that appear to be spread around the world's oceans hints at a war waging between such viruses and their prey: an abundant group of bacteria.

The bacteria, collectively known as SAR11, are the most abundant organisms known to inhabit seawater.

"They are everywhere, from the surface down to the bottom, from pole to pole," said study researcher Stephen Giovannoni, a professor of microbiology at Oregon State University, adding that SAR11 microbes are most abundant in the warm waters of ocean gyres, or rotating currents, where they can account for as much as 40 percent of plankton cells.

Bacteria killers
In 1990, Giovannoni's lab first identified these microbes using DNA (the genetic code deoxyribonucleic acid) found in water collected near Bermuda in the Sargasso Sea. Microbes in this group were later identified in waters around the world. [Image Gallery: Lost in the Bermuda Triangle]

Michael Rappe, SOEST / UHM

An electron micrograph of SAR11 bacteria strain HIMB4 cultured from Kaneohe Bay, Oahu, Hawaii.

More recently, using samples collected from the Sargasso Sea as well as from coastal Oregon waters, Giovannoni's team identified the four new viruses, which, the team found, killed SAR11 cells in laboratory experiments. They dubbed the viruses "pelagiphages," because they infect bacteria in the open ocean.

The team sequenced the genomes of these pelagiphages and compared these with DNA from other viruses. They found similarities between the pelagiphages and viruses that attack other ocean-dwelling bacteria. One of the new viruses, however, was so new that it created a new group, called a subfamily, of so-called podoviruses.

To get an idea of the geographic spread of these pelagiphages and their close relatives, the researchers compared their sequences with viral genetic material contained in samples from the Pacific Ocean and elsewhere.

Their results indicate these are the most abundant marine viruses seen so far, Giovannoni told LiveScience.

Explaining SAR11's success
The discovery offers clues to SAR11's success. While some had speculated that the abundance of SAR11 microbes resulted from the bacteria's ability to evade predators such as viruses, Giovannoni and colleagues have suggested the microbes' key talent was their ability to grow by converting organic carbon molecules —dissolved, brothlike, in seawater — into carbon dioxide. (SAR11 microbes are thought to play an important role in the planet's carbon cycle.)

The discovery of abundant viruses that prey upon SAR11 supports the latter theory about the bacteria's success, Giovannoni said.

"They can be killed by the viruses, but they are still successful, because they are always growing," he said.

Viruses and their hosts often engage in an evolutionary arms race. In a paper to be published online on Thursday by the journal Nature, Giovannoni and colleagues suggest the abundance of SAR11 cells may give them an advantage by making it easier for them to share helpful DNA with each other, a common bacterial strategy. This genetic exchange enables the bacteria to adapt to the viruses, which must then adapt their counterattack.

The value of old-school technique
Giovannoni noted that the team had used a combination of genomic analysis and traditional lab techniques for this research.

As the cost of generating genetic sequence data drops, researchers are turning to this technology more and more. However, old-fashioned lab work, testing viruses isolated from seawater in cultures of SAR11 cells, was a crucial part of this research, he said.

While genomic analysis — which looks at an organism's genetic blueprint or genome — is a powerful tool, it has limitations, Giovannoni pointed out. One of the viruses was so new to science that its DNA sequence could not be identified by the most widely used methods of DNA analysis; only a new and particularly powerful analysis tool allowed researchers to recognize genes it contained that were distantly related to those from other viruses, he told LiveScience.

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NCAR

Bacteria living in storm clouds could seed the ice crystals that form rain, new research suggests.

By Tia Ghose, LiveScience

The storm clouds in Earth's atmosphere are filled with microbial life, according to a new study.

The research, published Jan. 23 in the journal PLoS One, revealed that hailstones drawn from storm clouds harbor several species of bacteria that tend to reside on plants, as well as thousands of organic compounds normally found in soil. Some of the bacterial species can seed the tiny ice crystals that lead to rain, suggesting they play a role in causing rain.

"Those storm clouds are quite violent phenomena," said study co-author Tina Santl Temkiv, an environmental chemist at Aarhus University in Denmark. "They are sucking huge amounts of air from under the clouds, and that's how the bacteria probably got into the cloud."

Living on a cloud
In the past, researchers have found bacterial life in clouds that drift over mountaintops. Bacteria have been found as far up as 24.8 miles and may even survive as spores into space, Temkiv said. [ Holey Clouds: Gallery of Formations Cut By Airplanes ]

Temkiv and her colleagues wanted to see if bacteria lived in the violent storm clouds that hover above the Earth's surface. To find out, they studied 42 hailstones that had formed in a thunderstorm over Ljubljana, Slovenia, in May 2009.

After carefully removing the outer layer and sterilizing the hailstone, they analyzed its chemical composition.

The team found thousands of organic, or carbon-containing, compounds — nearly as many as found in a typical river, Temkiv said. In addition, they found several species of bacteria that normally live on plants. Some of the bacteria make a pinkish pigment that allows them to withstand the punishing ultraviolet rays in the atmosphere.

Some of bacteria found are ice-nucleators, meaning they can act as seeds for ice crystals to attach to in the clouds above Earth. When these same ice crystals get large enough, they fall as rain or snow, depending on the air temperature.

The findings suggest that bacteria could influence weather patterns, possibly making rain, Temkiv said.

"They may be growing in clouds, increasing in number and then modifying the chemistry in the cloud but also in the atmosphere indirectly," she told LiveScience.

The researchers think the bacteria come from the air hovering just above Earth that gets swept into the storm clouds through updrafts. That would suggest the atmosphere is a thread that can connect distant ecosystems, and that certain bacteria may be better at colonizing faraway environments, Pierre Amato, a researcher at France's Blaise Pascal University who was not involved in the study, wrote in an email.

"Clouds can be thought of as transient ecosystems selecting for certain [types of bacteria] that are better fitted than others, and that can thus quickly disperse over the globe," Amato said. "Understanding how microbes disperse is relevant, of course, for epidemiology, and also for microbial ecology."

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