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  • richardmitnick 3:09 pm on August 20, 2014 Permalink | Reply
    Tags: , Microbes,   

    From SPACE.com: “Microbes Found Beneath Antarctic Ice: What It Means for Alien Life Hunt” 

    space-dot-com logo

    SPACE.com

    The discovery of a complex microbial ecosystem far beneath the Antarctic ice may be exciting, but it doesn’t necessarily mean that life teems on frigid worlds throughout the solar system, researchers caution.

    Scientists announced today (Aug. 20) in the journal Nature that many different types of microbes live in subglacial Lake Whillans, a body of fresh water entombed beneath 2,600 feet (800 meters) of Antarctic ice. Many of the micro-organisms in these dark depths apparently get their energy from rocks, the researchers report.

    The results could have implications for the search for life beyond Earth, notes Martyn Tranter of the University of Bristol in England, who did not participate in the study.

    “The team has opened a tantalizing window on microbial communities in the bed of the West Antarctic Ice Sheet, and on how they are maintained and self-organize,” Tranter wrote in an accompanying News and Views piece in the same issue of Nature. “The authors’ findings even beg the question of whether microbes could eat rock beneath ice sheets on extraterrestrial bodies such as Mars. This idea has more traction now.”

    But just how much traction is a matter of debate. For example, astrobiologist Chris McKay of NASA’s Ames Research Center in California doesn’t see much application to Mars or any other alien world.

    “First, it is clear that the water sampled is from a system that is flowing through ice and out to the ocean,” said McKay, who also was not part of the study team.

    “Second, and related to this, the results are not indicative of an ecosystem that is growing in a dark, nutrient-limited system,” McKay told Space.com via email. “They are consistent with debris from the overlying ice — known to contain micro-organisms — flowing through and out to the ocean. Interesting in its own right, but not a model for an isolated ice-covered ecosystem.”

    Isolated, ice-covered oceans exist on some moons of the outer solar system, such as Jupiter’s moon Europa and the Saturn satellite Enceladus — perhaps the two best bets to host life beyond Earth. McKay and other astrobiologists would love to know if these oceans do indeed host life.

    It may be possible to find out without even touching down on Europa or Enceladus. Plumes of water vapor spurt into space from the south polar regions of both moons, suggesting that flyby probes could sample their subsurface seas from afar.

    And Europa is on the minds of the higher-ups at both NASA and the European Space Agency (ESA). NASA is drawing up plans for a potential Europa mission that could blast off in the mid-2020s, while ESA aims to launch its JUpiter ICy moons Explorer (JUICE) mission —which would study the Jovian satellites Callisto and Ganymede in addition to Europa — in 2022.

    ESA JUICE

    See the full article here.

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  • richardmitnick 7:50 am on August 14, 2014 Permalink | Reply
    Tags: , , , Microbes,   

    From The New York Times: “Our Microbiome May Be Looking Out for Itself” 

    New York Times

    The New York Times

    AUG. 14, 2014
    Carl Zimmer

    Your body is home to about 100 trillion bacteria and other microbes, collectively known as your microbiome. Naturalists first became aware of our invisible lodgers in the 1600s, but it wasn’t until the past few years that we’ve become really familiar with them.

    This recent research has given the microbiome a cuddly kind of fame. We’ve come to appreciate how beneficial our microbes are — breaking down our food, fighting off infections and nurturing our immune system. It’s a lovely, invisible garden we should be tending for our own well-being.

    microbe
    A highly magnified view of Enterococcus faecalis, a bacterium that lives in the human gut. Microbes may affect our cravings, new research suggests. Credit Centers for Disease Control and Prevention

    But in the journal Bioessays, a team of scientists has raised a creepier possibility. Perhaps our menagerie of germs is also influencing our behavior in order to advance its own evolutionary success — giving us cravings for certain foods, for example.

    Maybe the microbiome is our puppet master.

    “One of the ways we started thinking about this was in a crime-novel perspective,” said Carlo C. Maley, an evolutionary biologist at the University of California, San Francisco, and a co-author of the new paper. What are the means, motives and opportunity for the microbes to manipulate us? They have all three.

    The idea that a simple organism could control a complex animal may sound like science fiction. In fact, there are many well-documented examples of parasites controlling their hosts.

    Some species of fungi, for example, infiltrate the brains of ants and coax them to climb plants and clamp onto the underside of leaves. The fungi then sprout out of the ants and send spores showering onto uninfected ants below.

    How parasites control their hosts remains mysterious. But it looks as if they release molecules that directly or indirectly can influence their brains.

    Our microbiome has the biochemical potential to do the same thing. In our guts, bacteria make some of the same chemicals that our neurons use to communicate with one another, such as dopamine and serotonin. And the microbes can deliver these neurological molecules to the dense web of nerve endings that line the gastrointestinal tract.

    A number of recent studies have shown that gut bacteria can use these signals to alter the biochemistry of the brain. Compared with ordinary mice, those raised free of germs behave differently in a number of ways. They are more anxious, for example, and have impaired memory.

    Adding certain species of bacteria to a normal mouse’s microbiome can reveal other ways in which they can influence behavior. Some bacteria lower stress levels in the mouse. When scientists sever the nerve relaying signals from the gut to the brain, this stress-reducing effect disappears.

    Some experiments suggest that bacteria also can influence the way their hosts eat. Germ-free mice develop more receptors for sweet flavors in their intestines, for example. They also prefer to drink sweeter drinks than normal mice do.

    Scientists have also found that bacteria can alter levels of hormones that govern appetite in mice.

    Dr. Maley and his colleagues argue that our eating habits create a strong motive for microbes to manipulate us. “From the microbe’s perspective, what we eat is a matter of life and death,” Dr. Maley said.

    Different species of microbes thrive on different kinds of food. If they can prompt us to eat more of the food they depend on, they can multiply.

    Microbial manipulations might fill in some of the puzzling holes in our understandings about food cravings, Dr. Maley said. Scientists have tried to explain food cravings as the body’s way to build up a supply of nutrients after deprivation, or as addictions, much like those for drugs like tobacco and cocaine.

    But both explanations fall short. Take chocolate: Many people crave it fiercely, but it isn’t an essential nutrient. And chocolate doesn’t drive people to increase their dose to get the same high. “You don’t need more chocolate at every sitting to enjoy it,” Dr. Maley said.

    Perhaps, he suggests, the certain kinds of bacteria that thrive on chocolate are coaxing us to feed them.

    John F. Cryan, a neuroscientist at University College Cork in Ireland who was not involved in the new study, suggested that microbes might also manipulate us in ways that benefited both them and us. “It’s probably not a simple parasitic scenario,” he said.

    Research by Dr. Cryan and others suggests that a healthy microbiome helps mammals develop socially. Germ-free mice, for example, tend to avoid contact with other mice.

    That social bonding is good for the mammals. But it may also be good for the bacteria.

    “When mammals are in social groups, they’re more likely to pass on microbes from one to the other,” Dr. Cryan said.

    “I think it’s a very interesting and compelling idea,” said Rob Knight, a microbiologist at the University of Colorado, who was also not involved in the new study.

    If microbes do in fact manipulate us, Dr. Knight said, we might be able to manipulate them for our own benefit — for example, by eating yogurt laced with bacteria that would make use crave healthy foods.

    “It would obviously be of tremendous practical importance,” Dr. Knight said. But he warned that research on the microbiome’s effects on behavior was “still in its early stages.”

    The most important thing to do now, Dr. Knight and other scientists said, was to run experiments to see if microbes really are manipulating us.

    Mark Lyte, a microbiologist at the Texas Tech University Health Sciences Center who pioneered this line of research in the 1990s, is now conducting some of those experiments. He’s investigating whether particular species of bacteria can change the preferences mice have for certain foods.

    “This is not a for-sure thing,” Dr. Lyte said. “It needs scientific, hard-core demonstration.”

    See the full article here.

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  • richardmitnick 10:08 am on February 16, 2014 Permalink | Reply
    Tags: , , Microbes   

    From UC Berkeley: “Geographic variation of human gut microbes tied to obesity” 

    UC Berkeley

    February 14, 2014
    Robert Sanders

    People living in cold, northern latitudes have bacteria in their guts that may predispose them to obesity, according to a new study by researchers at the University of California, Berkeley, and the University of Arizona, Tucson.

    gut
    The types of microbes that live in the human gut vary with latitude. People in northern climes have more obesity-related bacteria than do people living farther south. iStock photo.

    The researchers’ analysis of the gut microbes of more than a thousand people from around the world showed that those living in northern latitudes had more gut bacteria that have been linked to obesity than did people living farther south.

    The meta-analysis of six earlier studies was published this month in the online journal Biology Letters by UC Berkeley graduate student Taichi Suzuki and evolutionary biology professor Michael Worobey of the University of Arizona.

    “People think obesity is a bad thing, but maybe in the past getting more fat and more energy from the diet might have been important to survival in cold places. Our gut microbes today might be influenced by our ancestors,” said Suzuki, noting that one theory is that obesity-linked bacteria are better at extracting energy from food. “This suggests that what we call ‘healthy microbiota’ may differ in different geographic regions.”

    “This observation is pretty cool, but it is not clear why we are seeing the relationship we do with latitude,” Worobey said. “There is something amazing and weird going on with microbiomes.”

    To Worobey, the results are fascinating from an evolutionary biology perspective. “Maybe changes to your gut community of bacteria are important for allowing populations to adapt to different environmental conditions in lots of animals, including humans,” he said.

    Body size increases with latitude

    Suzuki proposed the study while rotating through Worobey’s lab during his first year as a graduate student at the University of Arizona. Studies of gut microbes have become a hot research area among scientists because the proportion of different types of bacteria and Archaea in the gut seems to be correlated with diseases ranging from diabetes and obesity to cancer. In particular, the group of bacteria called Firmicutes seems to dominate in the intestines of obese people – and obese mice – while a group called Bacteroidetes dominates in slimmer people and mice.

    Suzuki reasoned that, since animals and humans in the north tend to be larger in size – an observation called Bergmann’s rule – then perhaps their gut microbiota would contain a greater proportion of Firmicutes than Bacteriodetes. While at the University of Arizona, and since moving to UC Berkeley, Suzuki has been studying how rodents adapt to living at different latitudes.

    “It was almost as a lark,” Woroby said. “Taichi thought that if Firmicutes and Bacteroidetes are linked to obesity, why not look at large scale trends in humans. When he came back with results that really showed there was something to it, it was quite a surprise.”

    map
    The researchers looked at data from more than 1,000 people from around the world. The blue represents the proportion of obesity-related bacteria in the gut, while red is the proportion of bacteria associated with slimness.

    Suzuki used data published in six previous studies, totaling 1,020 people from 23 populations in Africa, Europe, North and South America and Asia. The data on gut microbiomes were essentially censuses of the types and numbers of bacteria and Archaea in people’s intestinal track.

    He found that the proportion of Firmicutes increased with latitude and the proportion of Bacteriodetes decreased with latitude, regardless of sex, age, or detection methods. African Americans showed the same patterns as Europeans and North Americans, not the pattern of Africans living in tropical areas.

    “Bergmann’s rule – that body size increases with latitude for many animals – is a good one and presumed to be an adaptation for dealing with cold environments,” said Suzuki’s advisor Michael Nachman, professor of integrative biology and director of UC Berkeley’s Museum of Vertebrate Zoology. “Whether gut microbes also help explain Bergmann’s rule will require experimental tests, but Taichi’s discovery adds an intriguing and completely overlooked piece of the puzzle to this otherwise well-studied evolutionary pattern.”

    See the full article here.

    Founded in the wake of the gold rush by leaders of the newly established 31st state, the University of California’s flagship campus at Berkeley has become one of the preeminent universities in the world. Its early guiding lights, charged with providing education (both “practical” and “classical”) for the state’s people, gradually established a distinguished faculty (with 22 Nobel laureates to date), a stellar research library, and more than 350 academic programs.

    UC Berkeley Seal


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  • richardmitnick 1:18 pm on August 19, 2013 Permalink | Reply
    Tags: , , , , , Microbes   

    From Caltech: “A Home for the Microbiome” 

    Caltech Logo
    Caltech

    Caltech biologists identify, for the first time, a mechanism by which beneficial bacteria reside and thrive in the gastrointestinal tract

    08/18/2013
    Katie Neith

    “The human body is full of tiny microorganisms—hundreds to thousands of species of bacteria collectively called the microbiome, which are believed to contribute to a healthy existence. The gastrointestinal (GI) tract—and the colon in particular—is home to the largest concentration and highest diversity of bacterial species. But how do these organisms persist and thrive in a system that is constantly in flux due to foods and fluids moving through it? A team led by California Institute of Technology (Caltech) biologist Sarkis Mazmanian believes it has found the answer, at least in one common group of bacteria: a set of genes that promotes stable microbial colonization of the gut.

    gut
    A section of mouse colon is shown with gut bacteria (outlined in yellow) residing within the crypt channel.Credit: Caltech / Mazmanian Lab

    A study describing the researchers’ findings was published as an advance online publication of the journal Nature on August 18.

    ‘By understanding how these microbes colonize, we may someday be able to devise ways to correct for abnormal changes in bacterial communities—changes that are thought to be connected to disorders like obesity, inflammatory bowel disease and autism,’ says Mazmanian, a professor of biology at Caltech whose work explores the link between human gut bacteria and health.”

    See the full article here.

    The California Institute of Technology (commonly referred to as Caltech) is a private research university located in Pasadena, California, United States. Caltech has six academic divisions with strong emphases on science and engineering. Its 124-acre (50 ha) primary campus is located approximately 11 mi (18 km) northeast of downtown Los Angeles. “The mission of the California Institute of Technology is to expand human knowledge and benefit society through research integrated with education. We investigate the most challenging, fundamental problems in science and technology in a singularly collegial, interdisciplinary atmosphere, while educating outstanding students to become creative members of society.”
    Caltech buildings


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  • richardmitnick 11:59 am on March 18, 2013 Permalink | Reply
    Tags: , , Microbes,   

    From PNNL: “Seeing the Messages Microbes Send” 

    Novel chemical imaging instrument shows how bacteria support diverse, nearby colonies

    March 2013
    Suraiya Farukhi
    Christine Sharp

    Results: With a novel technique that noninvasively analyzes microbes, scientists at Pacific Northwest National Laboratory profiled, for the first time, the chemicals that a cyanobacterium makes available to others. Over 4 days, Synechococcus sp. PCC 7002 steadily secretes two molecules that could be used as resources by other bacteria that are nearby. The technique that chemically profiles the microbial communities in both space and time is Nanospray Desorption Ionization Electrospray Mass Spectrometry, or nano-DESI. This instrument was built by Dr. Julia Laskin and her team at Pacific Northwest National Laboratory. This research graced the cover of Analyst.

    nano
    Scientists at Pacific Northwest National Laboratory used the nano-DESI to show how bacteria support other colonies. No image credit.

    ‘This is a tool that will help microbiologists identify molecules that promote or inhibit growth of microbial communities,’ said Lab Fellow Laskin. ‘It also gives us much better control for studying interactions between microbial communities.’

    Why It Matters: Understanding microbial ecology — how bacteria, algae and other microbes influence each other — could provide basic answers needed to advance sustainable energy. For example, Synechococcus sp. PCC 7002 uses carbon dioxide and sunlight to produce sugars that fuel the colony. Knowing how to best grow and modify these bacteria to mass-produce fuels could increase our nation’s energy independence. Here, nano-DESI provides key data for sustainable energy, but the opportunities stretch much farther.

    ‘Any place where there are microbes and you have a format where nano-DESI could be applied, you can study that ecology,’ said Dr. Allan Konopka, a biologist and Lab Fellow at PNNL who worked on the study. ‘This opens doors to a host of applications, such as understanding how bacteria associated with plant roots affect a plant.'”

    Pacific Northwest National Laboratory (PNNL) is one of the United States Department of Energy National Laboratories, managed by the Department of Energy’s Office of Science. The main campus of the laboratory is in Richland, Washington.

    PNNL scientists conduct basic and applied research and development to strengthen U.S. scientific foundations for fundamental research and innovation; prevent and counter acts of terrorism through applied research in information analysis, cyber security, and the nonproliferation of weapons of mass destruction; increase the U.S. energy capacity and reduce dependence on imported oil; and reduce the effects of human activity on the environment. PNNL has been operated by Battelle Memorial Institute since 1965.

    i1


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  • richardmitnick 1:46 pm on January 4, 2012 Permalink | Reply
    Tags: , , , Microbes   

    An INL Fact Sheet: “Microbial Metabolic Systems” 

    Description
    The Microbial Metabolic Systems focus at INL is a systems biology approach to more effectively understanding and controlling microbial processes. An enhanced understanding of key microbial processes is being gained by coupling existing genomics, transcriptomics, and proteomics efforts with new metabolomic techniques and data. We use hypothesis-driven research to investigate the impacts of environment, perturbations and manipulations on microbial systems for the purpose of controlling the products and applications of those systems.

    Our focus is on developing and using advanced metabolomic techniques to study C-1 prokaryotes. Our definition of “C-1” includes a variety of prokaryotic metabolic systems that involve the transformation of single-carbon compounds. We have targeted specific C-1 metabolic processes of interest to the Department of Energy (DOE):

    Methanogenesis – methane production by methanogenic bacteria
    Methanotrophy – methane/methanol utilization by methanotrophic bacteria
    Bioleaching – carbon fixation in chemoautolithotrophic bacteria and
archaea (e.g., Acidithiobacillus ferrooxidans, Acidianus spp., etc.)
    Calcite Precipitation – subsurface calcite precipitationt by urea hydrolyzing bacteria
    Bicarbonate Transport – photoautotrophic carbon fixation by cyanobacteria
    Hydrogenase Systems – hydrogen production by Carboxydothermus hydrogenoformans.

    i1
    Our focus is on developing and using advanced metabolomic techniques to study C-1 prokaryotes. Our definition of “C-1” includes a variety of prokaryotic metabolic systems that involve the transformation of single-carbon compounds. We have targeted specific C-1 metabolic processes of interest to the Department of Energy (DOE)

    INL is leveraging existing research programs and expertise in C-1 microbial metabolic systems to develop a recognized capability that will be more broadly applied to other microbial systems relevant to DOE missions.”

    See the full Fact Sheet here. There is a lot more information.

     
  • richardmitnick 4:11 pm on November 9, 2011 Permalink | Reply
    Tags: , , , , , Microbes   

    From Berkeley Lab: “Berkeley Lab Researchers Create First of Its Kind Gene Map of Sulfate-reducing Bacterium:” 


    Berkeley Lab

    Work Holds Implications for Future Bioremediation Efforts

    Lynn Yarris
    November 09, 2011

    Critical genetic secrets of a bacterium that holds potential for removing toxic and radioactive waste from the environment have been revealed in a study by researchers with the U.S. Department of Energy (DOE)’s Lawrence Berkeley National Laboratory (Berkeley Lab). The researchers have provided the first ever map of the genes that determine how these bacteria interact with their surrounding environment.

    ‘Knowing how bacteria respond to environmental changes is crucial to our understanding of how their physiology tracks with consequences that are both good, such as bioremediation, and bad, such as biofouling,’ says Aindrila Mukhopadhyay, a chemist with Berkeley Lab’s Physical Biosciences Division, who led this research. ‘We have reported the first systematic mapping of the genes in a sulfate-reducing bacterium – Desulfovibrio vulgaris – that regulate the mechanisms by which the bacteria perceive and respond to environmental signals.'”

    i1
    Desulfovibrio vulgaris is an anaerobic sulfate-eating microbe that can also consume toxic and radioactive waste, making it a prime candidate for bioremediation of contaminated environments. (Photo courtesy of Berkeley Lab)

    i3
    A first-of-its-kind gene map of the Desulfovibrio vulgaris bacterium could play an important role in future clean-ups of a wide range of contaminated environments. (Image courtesy of Berkeley Lab)

    See the full very important article here.

    A U.S. Department of Energy National Laboratory Operated by the University of California

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