Archive for the ‘Bacteria’ Category

plants

Plants that were frozen during the “Little Ice Age” centuries ago have been observed sprouting new growth, scientists say. Samples of 400-year-old plants known as bryophytes have flourished under laboratory conditions. Researchers say this back-from-the-dead trick has implications for how ecosystems recover from the planet’s cyclic long periods of ice coverage. The findings appear in Proceedings of the National Academy of Sciences.

They come from a group from the University of Alberta, who were exploring an area around the Teardrop Glacier, high in the Canadian Arctic. The glaciers in the region have been receding at rates that have sharply accelerated since 2004, at about 3-4m per year. That is exposing land that has not seen light of day since the so-called Little Ice Age, a widespread climatic cooling that ran roughly from AD 1550 to AD 1850.

“We ended up walking along the edge of the glacier margin and we saw these huge populations coming out from underneath the glacier that seemed to have a greenish tint,” said Catherine La Farge, lead author of the study.

Bryophytes are different from the land plants that we know best, in that they do not have vascular tissue that helps pump fluids around different parts of the organism. They can survive being completely desiccated in long Arctic winters, returning to growth in warmer times, but Dr La Farge was surprised by an emergence of bryophytes that had been buried under ice for so long.

“When we looked at them in detail and brought them to the lab, I could see some of the stems actually had new growth of green lateral branches, and that said to me that these guys are regenerating in the field, and that blew my mind,” she told BBC News. “If you think of ice sheets covering the landscape, we’ve always thought that plants have to come in from refugia around the margins of an ice system, never considering land plants as coming out from underneath a glacier.”

But the retreating ice at Sverdrup Pass, where the Teardrop Glacier is located, is uncovering an array of life, including cyanobacteria and green terrestrial algae. Many of the species spotted there are entirely new to science.

“It’s a whole world of what’s coming out from underneath the glaciers that really needs to be studied,” Dr La Farge said.

“The glaciers are disappearing pretty fast – they’re going to expose all this terrestrial vegetation, and that’s going to have a big impact.”

http://www.bbc.co.uk/news/science-environment-22656239

Clostridium%20difficile%20C

Two studies have found that depression and the use of certain antidepressants are both associated with increased risk for Clostridium difficile infection, an increasingly common cause of diarrhea that in the worst cases can be fatal.

Researchers studied 16,781 men and women, average age 68, using hospital records and interviews to record cases of the infection, often called C. diff, and diagnoses of depression. The interviews were conducted biennially from 1991 to 2007 to gather self-reports of feelings of sadness and other emotional problems. There were 404 cases of C. difficile infection. After adjusting for other variables, the researchers found that the risk of C. diff infection among people with a history of depression or depressive symptoms was 36 to 47 percent greater than among people without depression.

A second study, involving 4,047 hospitalized patients, average age 58, found a similar association of infection with depression. In addition, it found an association of some antidepressants — Remeron, Prozac and trazodone — with C. diff infection. There was no association with other antidepressants. “We have known for a long time that depression is associated with changes in the gastrointestinal system,” said the lead author, Mary A.M. Rogers, a research assistant professor at the University of Michigan, “and this interaction between the brain and the gut deserves more study.”

Both reports appeared in the journal BMC Medicine.

http://well.blogs.nytimes.com/2013/05/08/depression-may-raise-risk-of-gut-infection/

1_12797_Cass-A-NASA
Radioactive iron may be first fossil imprint of a nearby cosmic explosion.

by Alexandra Witze

Sediment in a deep-sea core may hold radioactive iron spewed by a distant supernova 2.2 million years ago and preserved in the fossilized remains of iron-loving bacteria. If confirmed, the iron traces would be the first biological signature of a specific exploding star.

Shawn Bishop, a physicist at the Technical University of Munich in Germany, reported preliminary findings on 14 April at a meeting of the American Physical Society in Denver, Colorado.

In 2004, scientists reported finding the isotope iron-60, which does not form on Earth, in a piece of sea floor from the Pacific Ocean. They calculated how long ago this radioactive isotope had arrived by using the rate at which it decays over time. The culprit, they concluded, was a supernova in the cosmic neighbourhood.

Bishop wondered if he could find signs of that explosion in the fossil record on Earth. Some natural candidates are certain species of bacteria that gather iron from their environment to create 100-nanometre-wide magnetic crystals, which the microbes use to orient themselves within Earth’s magnetic field so that they can navigate to their preferred conditions. These ‘magnetotactic’ bacteria live in sea-floor sediments.

So Bishop and his colleagues acquired parts of a sediment core from the eastern equatorial Pacific Ocean, dating to between about 1.7 million and 3.3 million years ago. They took sediment samples from strata corresponding to periods roughly 100,000 years apart, and treated them with a chemical technique that extracts iron-60 but not iron from nonbiological sources, such as soil washing off the continents. The scientists then ran the samples through a mass spectrometer to see if any iron-60 was present.

And it was. “It looks like there’s something there,” Bishop told reporters at the Denver meeting. The levels of iron-60 are minuscule, but the only place they seem to appear is in layers dated to around 2.2 million years ago. This apparent signal of iron-60, Bishop said, could be the remains of magnetite (Fe3O4) chains formed by bacteria on the sea floor as radioactive supernova debris showered on them from the atmosphere, after crossing inter-stellar space at nearly the speed of light.

No one is sure what particular star might have exploded at this time, although one paper points to suspects in the Scorpius–Centaurus stellar association, at a distance of about 130 parsecs (424 light years) from the Sun3.

“I’m really excited about this,” says Brian Thomas, an astrophysicist at Washburn University in Topeka, Kansas, who was not involved in the work. “The nice thing is that it’s directly tied to a specific event.”

“For me, philosophically, the charm is that this is sitting in the fossil record of our planet,” Bishop says. He and his team are now working on a second core, also from the Pacific, to see if it too holds the iron-60 signal.

http://www.nature.com/news/supernova-left-its-mark-in-ancient-bacteria-1.12797

dn23277-1_300

Hollywood director James Cameron found little evidence of life when he descended nearly 11,000 metres to the deepest point in the world’s oceans last year. If only he had taken a microscope and looked just a few centimetres deeper.

Ronnie Glud at the University of Southern Denmark in Odense, and his colleagues, have discovered unusually high levels of microbial activity in the sediments at the site of Cameron’s dive – Challenger Deep at the bottom of the western Pacific’s Mariana Trench.

Glud’s team dispatched autonomous sensors and sample collectors into the trench to measure microbial activity in the top 20 centimetres of sediment on the sea bed. The pressure there is almost 1100 times greater than at the surface. Finding food, however, is an even greater challenge than surviving high pressures for anything calling the trench home.

Any nourishment must come in the form of detritus falling from the surface ocean, most of which is consumed by other organisms on the way down. Only 1 per cent of the organic matter generated at the surface reaches the sea floor’s abyssal plains, 3000 to 6000 metres below sea level. So what are the chances of organic matter making it even deeper, into the trenches that form when one tectonic plate ploughs beneath another?

Surprisingly, the odds seem high. Glud’s team compared sediment samples taken from Challenger Deep and a reference site on the nearby abyssal plain. The bacteria at Challenger Deep were around 10 times as abundant as those on the abyssal plain, with every cubic centimetre of sediment containing 10 million microbes. The deep microbes were also twice as active as their shallower kin.

These figures make sense, says Glud, because ocean trenches are particularly good at capturing sediment. They are broad as well as deep, with a steep slope down to the deepest point, so any sediment falling on their flanks quickly cascades down to the bottom in muddy avalanches. Although the sediment may contain no more than 1 per cent organic matter, so much of it ends up at Challenger Deep that the level of microbial activity shoots up.

“There is much more than meets the eye at the bottom of the sea,” says Hans Røy, at Aarhus University in Denmark. Last year, he studied seafloor sediments below the north Pacific gyre – an area that, unlike Challenger Deep, is almost devoid of nutrients. Remarkably, though, even here Røy found living microbes.

“With the exception of temperatures much above boiling, bacteria seem to cope with everything this planet can throw at them,” he says.

Journal reference: Nature Geoscience, DOI: 10.1038/ngeo1773

http://www.newscientist.com/article/dn23277-deepest-point-in-the-ocean-is-teeming-with-life.html?cmpid=RSS|NSNS|2012-GLOBAL|online-news

sn-atmosphere

Each year, hundreds of millions of metric tons of dust, water, and humanmade pollutants make their way into the atmosphere, often traveling between continents on jet streams. Now a new study confirms that some microbes make the trip with them, seeding the skies with billions of bacteria and other organisms—and potentially affecting the weather. What’s more, some of these high-flying organisms may actually be able to feed while traveling through the clouds, forming an active ecosystem high above the surface of the Earth.

The discovery came about when a team of scientists based at the Georgia Institute of Technology in Atlanta hitched a ride on nine NASA airplane flights aimed at studying hurricanes. Previous studies carried out at the tops of mountains hinted that researchers were likely to find microorganisms at high altitudes, but no one had ever attempted to catalog the microscopic life floating above the oceans—let alone during raging tropical storms. After all, it isn’t easy to take air samples while your plane is flying through a hurricane.

Despite the technical challenges, the researchers managed to collect thousands upon thousands of airborne microorganisms floating in the troposphere about 10 kilometers over the Caribbean, as well as the continental United States and the coast of California. Studying their genes back on Earth, the scientists counted an average of 5100 bacterial cells per cubic meter of air, they report in the Proceedings of the National Academy of Sciences. Although the researchers also captured various types of fungal cells, the bacteria were over two orders of magnitude more abundant in their samples. Well over 60% of all the microbes collected were still alive.

The researchers cataloged a total of 314 different families of bacteria in their samples. Because the type of genetic analysis they used didn’t allow them to identify precise species, it’s not clear if any of the bugs they found are pathogens. Still, the scientists offer the somewhat reassuring news that bacteria associated with human and animal feces only showed up in the air samples taken after Hurricanes Karl and Earl. In fact, these storms seemed to kick up a wide variety of microbes, especially from populated areas, that don’t normally make it to the troposphere.

This uptick in aerial microbial diversity after hurricanes supports the idea that the storms “serve as an atmospheric escalator,” plucking dirt, dust, seawater, and, now, microbes off Earth’s surface and carrying them high into the sky, says Dale Griffin, an environmental and public health microbiologist with the U.S. Geological Survey in St. Petersburg, Florida, who was not involved in the study.

Although many of the organisms borne aloft are likely occasional visitors to the upper troposphere, 17 types of bacteria turned up in every sample. Researchers like environmental microbiologist and co-author Kostas Konstantinidis suspect that these microbes may have evolved to survive for weeks in the sky, perhaps as a way to travel from place to place and spread their genes across the globe. “Not everybody makes it up there,” he says. “It’s only a few that have something unique about their cells” that allows them survive the trip.

The scientists point out that two of the 17 most common families of bacteria in the upper troposphere feed on oxalic acid, one of the most abundant chemical compounds in the sky. This observation raises the question of whether the traveling bacteria might be eating, growing, and perhaps even reproducing 10 kilometers above the surface of Earth. “That’s a big question in the field right now,” Griffin says. “Can you view [the atmosphere] as an ecosystem?”

David Smith, a microbiologist at NASA’s Kennedy Space Center in Florida, warns against jumping to such dramatic conclusions. He also observed a wide variety of microbes in the air above Oregon’s Mount Bachelor in a separate study, but he believes they must hibernate for the duration of their long, cold trips between far-flung terrestrial ecosystems. “While it’s really exciting to think about microorganisms in the atmosphere that are potentially making a living, there’s no evidence of that so far.”

Even if microbes spend their atmospheric travels in dormancy, that doesn’t mean they don’t have a job to do up there. Many microbial cells are the perfect size and texture to cause water vapor to condense or even form ice around them, meaning that they may be able to seed clouds. If these microorganisms are causing clouds to form, they could be having a substantial impact on the weather. By continuing to study the sky’s microbiome, Konstantinidis and his team hope to soon be able to incorporate its effects into atmospheric models.

http://news.sciencemag.org/sciencenow/2013/01/microbes-survive-and-maybe-thriv.html

gold

Mythical King Midas was ultimately doomed because everything he touched turned to gold. Now, the reverse has been found in bacteria that owe their survival to a natural Midas touch.

Delftia acidovorans lives in sticky biofilms that form on top of gold deposits, but exposure to dissolved gold ions can kill it. That’s because although metallic gold is unreactive, the ions are toxic.

To protect itself, the bacterium has evolved a chemical that detoxifies gold ions by turning them into harmless gold nanoparticles. These accumulate safely outside the bacterial cells.

“This could have potential for gold extraction,” says Nathan Magarvey of McMaster University in Hamilton, Ontario, who led the team that uncovered the bugs’ protective trick. “You could use the bug, or the molecules they secrete.”

He says the discovery could be used to dissolve gold out of water carrying it, or to design sensors that would identify gold-rich streams and rivers.

The protective chemical is a protein dubbed delftibactin A. The bugs secrete it into the surroundings when they sense gold ions, and it chemically changes the ions into particles of gold 25 to 50 nanometres across. The particles accumulate wherever the bugs grow, creating patches of gold.

But don’t go scanning streams for golden shimmers: the nanoparticle patches do not reflect light in the same way as bigger chunks of the metal – giving them a deep purple colour.

When Magarvey deliberately snipped out the gene that makes delftibactin A, the bacteria died or struggled to survive exposure to gold chloride. Adding the protein to the petri dish rescued them.

The bacterium Magarvey investigated is one of two species that thrive on gold, both identified a decade or so ago by Frank Reith of the University of Adelaide in Australia. In 2009 Reith discovered that the other species, Cupriavidus metallidurans, survives using the slightly riskier strategy of changing gold ions into gold inside its cells.

“If delftibactin is selective for gold, it might be useful for gold recovery or as a biosensor,” says Reith. “But how much dissolved gold is out there is difficult to say.”

Journal reference: Nature Chemical Biology, DOI: 10.1038/NCHEMBIO.1179

http://www.newscientist.com/article/dn23129-bug-protects-itself-by-turning-its-environment-to-gold.html?cmpid=RSS|NSNS|2012-GLOBAL|online-news

subglacial lake 4
subglacial lake 3
subglacial lake 2
subglacial lake 1

The search continues for life in subglacial Lake Whillans, 2,600 feet below the surface of the West Antarctic Ice Sheet—but a thrilling preliminary result has detected signs of life.

At 6:20am on January 28, four people in sterile white Tyvek suits tended to a wench winding cable onto the drill platform. One person knocked frost off the cable as it emerged from the ice borehole a few feet below. The object of their attention finally rose into sight: a gray plastic vessel, as long as a baseball bat, filled with water from Lake Whillans, half a mile below.

The bottle was hurried into a 40-foot cargo container outfitted as a laboratory on skis. Some of the lake water was squirted into bottles of media in order to grow whatever microbes might inhabit the lake. Those cultures could require weeks to produce results. But one test has already produced an interesting preliminary finding. When lake water was viewed under a microscope, cells were seen: their tiny bodies glowed green in response to DNA-sensitive dye. It was the first evidence of life in an Antarctic subglacial lake.

(A Russian team has reported that two types of bacteria were found in water from subglacial Lake Vostok, but DNA sequences matched those of bacteria that are known to live inside kerosene—causing the scientists to conclude that those bacteria came from kerosene drilling fluid used to bore the hole, and not from Lake Vostok itself.)

In order to conclusively demonstrate that Lake Whillans harbors life, the researchers will need to complete more time-consuming experiments showing that the cells actually grow—since dead cells can sometimes show up under a microscope with DNA-sensitive staining. And weeks or months will pass before it is known whether these cells represent known types of microbes, or something never seen before. But a couple of things seem likely. Most of those microbes probably subsist by chewing on rocks. And despite being sealed beneath 2,600 feet of ice, they probably have a steady supply of oxygen.

The oxygen comes from water melting off the base of the ice sheet—maybe a few penny thicknesses of ice per year. “When you melt ice, you’re liberating the air bubbles [trapped in that ice],” says Mark Skidmore, a geomicrobiologist at Montana State University who is part of the Whillans drilling, or WISSARD, project. “That’s 20 percent oxygen,” he says. “It’s being supplied to the bed of the glacier.”

In one possible scenario, lake bacteria could live on commonly occurring pyrite minerals that contain iron and sulfur. The bacteria would obtain energy by using oxygen to essentially “burn” that iron and sulfur (analogous to the way that animals use oxygen to slowly burn sugars and fats). Small amounts of sulfuric acid would seep out as a byproduct; that acid would attack other minerals in the sands and sediments of the lake—leaching out sodium, potassium, calcium, and other materials that would accumulate in the water.

This process, called weathering, breaks down billions of tons of minerals across the Earth’s surface each year. Researchers working on the National Science Foundation-funded WISSARD project hope to learn whether something like this also happens under the massive ice sheets covering Antarctica and Greenland. They’ve already seen one tantalizing sign.

The half mile of glacial ice sitting atop Lake Whillans is quite pure—derived from snow that fell onto Antarctica thousands of years ago. It contains only one-hundredth the level of dissolved minerals that are seen in a clear mountain creek, or in tap water from a typical city. But a sensor lowered down the borehole this week showed that dissolved minerals were far more abundant in the lake itself. “The fact that we see high concentrations is suggestive that there’s some interesting water-rock-microbe interaction that’s going on,” says Andrew Mitchell, a microbial geochemist from Aberystwyth University in the UK who is working this month at Lake Whillans.

Microbes, in other words, might well be munching on minerals under the ice sheet. The Whillans team will take months or years to unravel this picture. They will perform experiments to see whether microbes taken from the lake metabolize iron, sulfur, or other components of minerals. And they will analyze the DNA of those microbes to see whether they’re related to rock-chewing bacteria that are already known to science.

Antarctica isn’t the only place in the solar system where water sits concealed in the dark beneath thick ice. Europa and Enceladus (moons of Jupiter and Saturn, respectively) are also thought to harbor oceans of liquid water. What is learned at Lake Whillans could shed light on how best to look for life in these other places.

http://blogs.discovermagazine.com/crux/2013/01/29/first-evidence-of-life-in-antarctic-subglacial-lake/

Thanks to Kebmodee for bringing this to the attention of the It’s Interesting community.