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  • richardmitnick 12:13 pm on November 9, 2015 Permalink | Reply
    Tags: , Microbes,   

    From NOVA: “Pushing the Limits of Life” 



    04 Nov 2015
    Carrie Arnold

    Everywhere scientists have looked on Earth, they have found signs of life. They’ve looked in the deepest oceans and the driest deserts, and in every case, life—in some form or another—was flourishing. But Kelly Wrighton and Mike Wilkins aren’t satisfied that the search is over, so they’re looking for life in a place more extreme than ever before.

    Which is why the married couple, both assistant professors of microbiology at Ohio State University, are at a new fracking well being drilled just outside Morgantown, West Virginia. Before Northeast Natural Energy can send down fluid to fracture the Marcellus Shales, buried more than 1.5 miles below the surface for 400 million years, Wrighton, Wilkins, and a team of scientists will be collecting rock samples hauled up from the deep.

    A closeup of the drill at the Morgantown site.

    Unlike previous samples, which were collected after the well had been fracked first and thus contaminated, these samples will be pristine. It will give the microbiologists their best shot to find signs of microbial life.

    Wrighton and Wilkins have spent their burgeoning careers studying the microbes dozens, even thousands of feet beneath the surface of the Earth. Such deep subsurface microbes have to contend with high temperatures, in some areas well above the boiling point of water. They also have to manage extremely high pressures and high concentrations of salt. Perhaps the most difficult task is finding energy. Cut off from solar energy, subsurface bacteria had to rely on chemical reactions or sinks of oil and natural gas to make their living.

    Signing on to the Morgantown project almost two years ago was a huge gamble, since no one knows whether life can survive in such an extreme environment. Wrighton and Wilkins used the expertise they had gathered in studying subsurface microbes as grad students and postdocs, and then spent more than a year working on the project full-time before the first samples could even be collected. Whatever they find, they hope to shed light on one of science’s big questions: Just how extreme can life get? Their answers could reveal the limits of life, the conditions beyond which living things just couldn’t hack it. It could also tell us more about how life might have first evolved and where else it could be found in the universe.

    “There’s an enormous reservoir of undiscovered life that’s really hard to get to,” Wilkins says.

    Earliest Extremes

    The study of microbes living in extreme environments—so-called extremophiles—is relatively new. In 1969, Indiana University bacteriologist Thomas Brock and his student Hudson Freeze traveled to Yellowstone National Park to search for bacteria living in the park’s hot springs. To many, the expedition seemed like little more than tilting at windmills. Any bacteria living in the hot springs would have to survive at temperatures greater than 158° Fahrenheit, a point at which most living things would be cooked. But when they sampled some pink muck from Mushroom Spring, just a few miles north of Old Faithful, Brock and Freeze found it teeming with life. Among scientists, their discovery of Thermus aquaticus is now more famous for its facilitation of the polymerase chain reaction, used in labs around the world for amplifying DNA. But in the 1960s and 1970s, Brock’s discovery showed the scientific community that bacteria could survive in environments far more extreme than anyone thought.

    Extremophiles give Grand Prismatic Spring in Yellowstone National Park its vivid colors.

    “Bacteria are able to grow…at any temperature at which there is liquid water, even in pools which are above the boiling point,” Brock wrote in a 1967 Science paper.

    The discovery that microbes could live in environments far more extreme than anyone suspected opened a wide range of habitats to microbial exploration. While some scientists explored the frigid, windswept deserts of Antarctica, others, like Bo Barker Jørgensen and Karsten Pedersen, geomicrobiologists at Aarhus University in Denmark and Chalmers University of Technology in Sweden, respectively, began taking advantage of burgeoning surveys of marine life. Part of these surveys included sampling sediments at the bottom of the ocean or deep underground, which Jørgensen, Pedersen, and others found teeming with life. “It took a decade to accept that life was actually that deep,” Pedersen says.

    These first studies, in the mid-1980s, showed that deep subsurface life can exist. Still, despite decades of work on the subject, there’s no formal definition of what “deep” really means, says Tori Hoehler, an astrobiologist at NASA’s Ames Science Center.

    “From the NASA perspective, the deep subsurface means that you’ve gone deep enough to escape the influence of the surface biosphere,” Hoehler says. “I’m not sure there’s a strict dividing line, but once you’re a few meters deep or so, it’s certainly a different world than on the surface.”

    Without the large-scale drilling projects used to study deep subsurface marine life, microbiologists like Tullis Onstott of Princeton University had to access the deep via existing digs. In 1996, Onstott began focusing on gold mines in South Africa, then as now some of the deepest mines in the world, with some nearly 2.5 miles below the surface. They are hot, dark, filthy places, and the working conditions are often deadly for miners. But for some microbes, this miners’ hell is pretty close to heaven.

    The first microbe Onstott found from his gold mine expeditions was related to Firmicutes, a type of microbe typically found in boiling hot springs, like those found in Yellowstone. This initial success enabled more trips back to the hellish environment found in the South African mines. In a 2006 Science paper, Onstott and colleagues published the discovery of a bacterial community living in a gold mind water reservoir 1.74 miles below the ground. The basalt surrounding the reservoir also contained large amounts of uranium, which made the rocks highly radioactive. The radioactivity split water molecules into oxygen and, more importantly, the hydrogen gas that the microbes used for food. “They gobble hydrogen up like potato chips,” Onstott says.

    Onstott has no idea how long the microbes have been down there, though he doubts they have been present since the rock was buried several billion years ago. The geological processes that molded and shaped the rock since their formation would have created temperatures and pressures high enough to kill any microbes that are native to those depths. Even so, Onstott believes that the microbes were able to survive on radioactivity for potentially millions of years.

    “It’s incredible how far down you can go and still detect life,” Wilkins says.

    Surviving for any length of time in such a stressful environment isn’t easy. The extreme heat of many of these locales can cause proteins to misfold, turning what are similar to beautiful pieces of origami into useless crumpled heaps of scrap paper. DNA also requires more maintenance down deep, as does the cellular membrane. “A bacterium has to be very metabolically active to keep its sh– together, or rather, keep its sh– inside the cell,” Onstott says. Keeping the cell in proper working order when under stress requires lots of energy, which can be hard to find even in the best of circumstances—and life in an underground vat of sizzling radioactive water most definitely is not.

    Mike Wilkins uses pressure chambers to encourage bacteria from deep underground to grow.

    In 2003, scientists discovered what remains the known upper temperature limit of life. A team from the University of Massachusetts, Amherst found strain 121, a microbe living in a deep sea vent off Puget Sound dividing, albeit slowly, at 121° Celsius, or 250˚ F.

    Lab experiments to define these limits have been difficult, as Thermus aquaticus routinely grows at temperatures above 90° Celsius in Yellowstone, but hasn’t been coaxed to grow in the lab above a temperature of around 80° Celsius. Still, to get life to grow at its hottest extreme, all other conditions have to be optimal. In life living deep below ground, those conditions are typically far from ideal, which means the upper temperature limit is likely much lower, although no one currently knows what that might be.

    One result of this high-stress, low-energy environment is that many of the microbes found far below ground divide much less frequently. The famous bacterium Escherichia coli can divide in less than 20 minutes in nutrient-rich growth media. Onstott believes that some of the microbes he has found in the South African gold mines might have doubling times in the decades, centuries, or even millennia. As a result, their numbers are likely going to be much lower than microbes found on the surface, simply because they can’t reproduce as quickly.

    Give them the right food, however, and all of that might change. Wrighton began her study of subsurface life by sampling the microbes found in a well that had already been fracked. In the process of fracking, energy companies typically flush the wells with hydrocarbon-rich liquids, both to get the natural gas out and to prevent microbes from corroding the pipes. But no fracking well can be sterilized completely. Microbes from the surface often make their way below ground, and frequently in very large numbers. For some bacteria, fracking fluids are an all-you-can-eat buffet.

    Wrighton wanted to know how these different communities of microbes lived together and how any deep subsurface life might affect microbial contaminants and vice versa. She was also curious about how the microbes made a living and what enzymes and genes were necessary to carry out basic functions. This, in turn, could provide a lot of information about how microbes interacted with each other to create rich, diverse communities.

    Microbiologists pulverized the shale samples to extract any chemicals that might suggest there’s life trapped inside.

    Her first glimpse at the microbial life in fracked wells led her to an even more fundamental question: Was anything down there in the first place? Wrighton’s instincts as a microbiologist told her yes, especially since scientists had found signs of life essentially everywhere else on Earth that they had looked. She began focusing her attention on the Marcellus Shale in Appalachia where an NSF-funded study would drill deep into the rock to obtain samples that Wrighton, Wilkins, and other researchers would have the opportunity to study. Since the shale was rich with seams of natural gas and other hydrocarbons, the microbes should have plenty to eat, she suspected. And the shale’s depth, at more than a mile, meant that it was deep enough to be completely isolated from the surface world but still accessible by drilling.

    Even more importantly, the site was pristine. It had never been previously drilled or fracked. This meant that if Wrighton could somehow account for any introduced contaminants, whatever other microbes she found were almost certainly native to the deep shales. To look for them, she teamed up with Wilkins and geologist Shikha Sharma from West Virginia University. The team would take a three-pronged approach: They would look for the chemical signs of life, seek out any microbial genetic material, and try to directly culture any microbes found.

    “We want to try and identify the chemical, physical, and biological factors that constrain life and try to formulate a recipe for what makes life possible,” Wrighton says.

    Together, they knew that if life could be found in the Marcellus shales, they would find it. The trio spent more than a year running mock experiments and honing their techniques to prepare for the arrival of their samples. After a series of delays, they finally got word that their samples would be drilled in early September.

    Drilling Deep

    You could hear the drill site long before you saw it. Nestled into a hillside outside of Morgantown and overlooking an old World War II munitions factory, a heavily rutted dirt road led up to a drill rig, a large blue metallic cylinder that rose for more than three stories from the rock below. The drill bit was more than a mile and a half below the surface, a distance long enough to hold nearly six Empire State Buildings placed end to end. Rebecca Daly, Wrighton’s lab manager, had gotten used to the din after spending several days at the site in preparation for the drilling that would yield her samples. Daly might have gotten used to the racket, but the oppressive late summer heat was something else entirely. Sweat streamed down her neck, soaking her long, blond ponytail.

    It didn’t dampen her enthusiasm, though. “This is such an incredible opportunity,” she says. “We’ve never been able to get pristine samples this deep before.”

    The drilling rig bores deep into the Earth to retrieve shale samples for microbiologists to study.

    Daly and Sharma had been up most of the night before, poring over geological data to identify the sites that would be most likely to hold signs of life. Formed more than 400 million years ago in the Devonian era, before dinosaurs roamed the Earth, the Marcellus shales are a tough place to survive. The shale is hot and salty, and it has relatively small amounts of two of the things microbes need the most to eke out a living: water and living space.

    But work by other geologists had shown that other shales had microfractures just big enough to provide a nice home to some bacteria. The team was also interested in the interface between the Marcellus shales and the rocks immediately above and below. “We think these will be the hot spots for life. There’s enough space for the microbes to grow, and they have the hydrocarbons that have diffused out of the shale that they can use for energy,” Wilkins says.

    Sharma’s analysis of the geology beneath Morgantown identified more than 50 different areas likely to yield good results, including places that contained water and organic carbon that the microbes could use for food. Before Northeast Natural Energy started drilling, the researchers dropped small fluorescent beads down the drill shaft that would allow them to identify areas on the samples potentially contaminated by surface material. Since these bacteria were apt to be more numerous and swamp any signals from native deep subsurface life, Wrighton and Wilkins needed to remove as much contamination as humanly possible.

    Drilling for their samples began on Friday morning and lasted for nearly 36 hours. As the sun climbed in the sky on Saturday morning, Daly’s heart began hammering. The last time these rocks had felt the warmth of the sun or the stirring air of a cool breeze, the first trees had just emerged, as had the first four-legged animals.

    After seemingly endless hours of waiting, Daly’s samples were ready. Handling the dark gray tiles that were roughly the size of a large palm and using a pair of latex gloves, Daly gently cleaned the tiles in a bath of salt water before placing them in a special storage container that removed all oxygen (although oxygen is necessary for us, it’s toxic to many subsurface microbes). Stacked in her car, it looked like Daly was transporting tiles to use in a kitchen or bathroom remodel, their slightly rough surface giving them a rustic feel. Then, she placed the boxes in the trunk of her car before racing back to Columbus along I-70.

    Wrighton, Wilkins, and Sharma had their samples, but it was anyone’s guess as to what they might find.

    Microbial Detritus

    When European explorers first set foot on new ground, they planted a flag to show that they had been there. Microbes do something similar, if you know what to look for, Sharma says. Microbes signal not with flags but with subtle chemical changes.

    Sharma began her career as a geologist while a university student in her native India. She was initially drawn not to rocks, but to the fact that the geologists “had the best field trips,” she says. Over the years, her scientific interests transitioned to include the chemical signatures of life that can be found in rocks. Just as humans leave signs of our presence by the strands of hair on the bathroom floor and the coat draped over the handrail, microbes, too, have their own way of saying “Kilroy was here.” These types of microbial graffiti are found in the chemical signatures on the rocks.

    “The kind of signatures that we see can tell us if the microbes have been doing their thing for a very, very long time,” Sharma says. “These things can’t happen in a day.”

    Shale samples in Shikha Sharma’s lab at West Virginia University

    Key to those signatures is carbon, the building block of life on this planet. All carbon has six protons in its nucleus, and most carbon is carbon-12, with six protons and six neutrons, but tiny amounts of carbon-13 and -14, with seven and eight neutrons, respectively, also exist. For reasons that aren’t entirely clear, living organisms prefer carbon-12 to carbon-13 and carbon-14. This preference means that rocks that ever contained life have relatively more carbon-13 and carbon-14 than rocks that didn’t, since microbes would have consumed more of the carbon-12.

    Although Sharma hasn’t ever looked for signatures of life in as extreme an environment as the current project, she has found signs in deep underground reservoirs, around 1.4 miles beneath the surface. DNA fingerprinting revealed a type of microbe known as a methanogen, which gives off methane as a by-product of metabolism much as humans exhale carbon dioxide. The reservoirs weren’t pristine, and there was no way to know whether these microbes were surface contaminants, but her results nonetheless revealed something important. “Even if they are contaminants, they are still active more than 7,800 feet below,” Sharma says.

    Sharma’s isotope fingerprinting can also determine whether these microbes are currently active or whether they’re merely a signature of life that was once there. Dead microbes, for example, leave traces of diglyceride fatty acids (DGFAs) as the fats in their cell wall decompose.

    These signatures can provide clues about which microbes are present, but not with the kind of detail that scientists need. This is where Wrighton comes in. Her expertise is in sequencing microbes that are present at very low levels. DNA degrades rapidly, which can make it harder to find than Sharma’s chemical signatures, but it also provides much more information about the microbial communities within. “We can create a metabolic blueprint about what these microbes are doing and how they’re living without having to touch a single Petri dish,” Wrighton says.

    To get at the DNA, Wrighton and her team of graduate students are grinding up the rock samples by hand, using a large, strong mortar and pestle. “It sounds like a giant construction zone. I’m pretty sure we’re the least popular lab in the building right now,” Wrighton says, laughing. They will then soak the rock in chemicals to extract any DNA. Her lab’s expertise combined with improved genetic sequencing technology should tease out the sequence of even a single bacterium.

    Wilkins, for his part, will be trying to coax these hard-to-grow microbes in the lab. Any microbes he finds will be fed a diet of ground up rock and be grown in the equivalent of a pressure cooker, to make the microbes feel right at home. Raising them in large numbers can tell Wilkins more about how they live and what they are like.

    Although they’ve had their samples for more than a month, even the most preliminary data answering the biggest question of all, is there any life down there, is still several months out. Wrighton remains optimistic that the shales or the layers immediately above and below will yield signs of life, “but we’re preparing for not finding anything,” she says.

    Whatever they find, the answers still matter. Knowing life’s potential limits also provides valuable information that could guide researchers looking for life not just here on Earth but also elsewhere in the universe. “So far, we’ve focused almost all our attention on the tiny skin of Earth that we live on,” Daly says. “But there’s just so much more out there.”

    See the full article here .

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    NOVA is the highest rated science series on television and the most watched documentary series on public television. It is also one of television’s most acclaimed series, having won every major television award, most of them many times over.

  • richardmitnick 3:01 pm on October 28, 2015 Permalink | Reply
    Tags: , , Microbes, Unified Microbiome Initiative   

    From LBL: “Scientists Call for National Effort to Understand and Harness Earth’s Microbes for Health, Energy, Agriculture, and Environment” 

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    Berkeley Lab

    October 28, 2015
    Dan Krotz 510-486-4019

    Berkeley Lab’s Microbes to Biomes initiative is designed to reveal, decode and harness microbes. Its goals are closely aligned with that of the Unified Microbiome Initiative, a national effort proposed by scientists.
    download mp4 video here.

    Microbes are essential to life on Earth. They’re found in soil and water and inside the human gut. In fact, nearly every habitat and organism hosts a community of microbes, called a microbiome. What’s more, microbes hold tremendous promise for innovations in medicine, energy, agriculture, and understanding climate change.

    Scientists have made great strides learning the functions of many microbes and microbiomes, but this research also highlights how much more there is to know about the connections between Earth’s microorganisms and a vast number of processes. Deciphering how microbes interact with each other, their hosts, and their environment could transform our understanding of the planet. It could also lead to new antibiotics, ways to fight obesity, drought-resistant crops, or next-gen biofuels, to name a few possibilities.

    To understand and harness the capabilities of Earth’s microbial ecosystems, nearly fifty scientists from Department of Energy national laboratories, universities, and research institutions have proposed a national effort called the Unified Microbiome Initiative. The scientists call for the initiative in a policy forum entitled “A unified initiative to harness Earth’s microbiomes” published Oct. 30, 2015, in the journal Science.

    The Unified Microbiome Initiative would involve many disciplines, including engineering, physical, life, and biomedical sciences; and collaborations between government institutions, private foundations, and industry. It would also entail the development of new tools that enable a mechanistic and predictive understanding of Earth’s microbial processes.

    Among the authors of the Science article are several scientists from the Department of Energy’s Lawrence Berkeley National Laboratory (Berkeley Lab). These are Berkeley Lab Director Paul Alivisatos; Eoin Brodie, Deputy Director of the Climate and Ecosystem Sciences Division; Mary Maxon, the Biosciences Area Principal Deputy; Eddy Rubin, Director of the Joint Genome Institute; and Peidong Yang, a Faculty Scientist in the Materials Sciences Division. Alivisatos is also the Director of the Kavli Energy Nanoscience Institute, and Yang is the Co-Director.

    This colorized microscopy image hints at the complexity of microbial life. It shows two bacterial cells in soil. The bacteria glue clay particles together and protect themselves from predators. This also stabilizes soil and stores carbon that could otherwise enter the atmosphere. (Credit: Manfred Auer, Berkeley Lab)

    Berkeley Lab has a long history of microbial research, from its pioneering work in metagenomics at the Joint Genome Institute, to the more recent Microbes to Biomes initiative, which is designed to harness microbes in ways that protect fuel and food supplies, environmental security, and health.

    The call for the Unified Microbiome Initiative comes at a critical time in microbial research. DNA sequencing has enabled scientists to detect microbes in every biological system, thriving deep underground and inside insects for example, and in mind-boggling numbers: Earth’s microbes outnumber the stars in the universe. But to benefit from this knowledge, this descriptive phase must transition to a new phase that explores how microbial communities function, how to predict their actions, and how to make use of them.

    “Technology has gotten us to the point where we realize that microbes are like dark matter in the universe. We know microbes are everywhere, and are far more complex than we previously thought, but we really need to understand how they communicate and relate to the environment,” says Brodie.

    “And just like physicists are trying to understand dark matter, we need to understand the functions of microbes and their genes. We need to study what life is like at the scale of microbes, and how they relate to the planet,” Brodie adds.

    This next phase of microbiome research will require strong ties between disciplines and institutions, and new technologies that accelerate discovery. The scientists map out several opportunities in the Science article. These include:

    Tools to understand the biochemical functions of gene products, a large portion of which are unknown.
    Technologies that quickly generate complete genomes from individual cells found in complex microbiomes.
    Imaging capabilities that visualize individual microbes, along with their interactions and chemical products, in complex microbial networks.
    Adaptive models that capture the complexity of interactions from molecules to microbes, and from microbial communities to ecosystems.

    Many of these new technologies would be flexible platforms, designed initially for microbial research, but likely to find uses in other fields.

    Ten years after the launch of the Unified Microbiome Initiative, the authors of the Science article envision an era in which a predictive understanding of microbial processes enables scientists to manage and design microbiomes in a responsible way—a key step toward harnessing their capabilities for beneficial applications.

    “This is an incredibly exciting time to be involved in microbial research,” says Brodie. “It has the potential to contribute to so many advances, such as in medicine, energy, agriculture, biomanufacturing, and the environment.”

    See the full article here .

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  • richardmitnick 7:13 pm on January 8, 2015 Permalink | Reply
    Tags: , Microbes,   

    From PNNL: “Decoding Microbial Interactions” 

    PNNL Lab

    December 2014
    Web Publishing Services

    Deep sequencing gives insights into mechanisms of microbial interactions

    Results: As scientists strive to gain a systems-level understanding of microbial communities, their task grows increasingly more complex. Yet the benefits of doing this work can lead to new ways to engineer these amazing biological systems with significant implications for bioenergy, carbon sequestration, and bioremediation.

    In ongoing work to integrate field investigations with well-controlled laboratory studies, scientists at Pacific Northwest National Laboratory grew two bacteria in a co-culture and applied deep transcriptome sequencing to study the physiological and genetic underpinnings driving interspecies interactions. They investigated the effect of co-cultivation and carbon flux directions on interactions between a salt-tolerant cyanobacterium, Synechococcus sp. PCC 7002 and a marine heterotroph, Shewanella putrefaciens W3-18-1. The results of this study, which appeared in The ISME Journal, provide novel and relevant insights into the physiological basis of microbial interactions.

    Representative micrograph of Synechococcus sp. PCC7002 (red) and Shewanella sp. W3-18-1 (green) cell aggregates formed in a co-culture grown under carbon-limited aerobic chemostat conditions using lactate as the sole source of carbon.

    Why It Matters: Phototrophs use energy from light to carry out various cellular metabolic processes, while heterotrophs use organic carbon for growth. In aquatic environments, an important class of interactions is based on cross-feeding and metabolite exchange, whereby photosynthetically fixed dissolved organic carbon (DOC) can elicit chemotactic responses that lead to spatial associations. This study provides initial insight into the complexity of photoautotrophic-heterotrophic interactions and brings new perspectives regarding their role in the robustness and stability of the association.

    “Our experiments suggest that material and energy flows in microbial communities strongly affect the nature and direction of interactions between primary producers and heterotrophic consumers,” said Dr. Alex Beliaev, a microbiologist at PNNL and lead author of the publication. “Knowing the fundamental rules that govern the functioning of complex biological systems will inform science and policy challenges associated with environmental stewardship and climate change. It will also guide development of technical programs, including biodesign of stable microbial communities for bioenergy and environmental applications.”

    See the full article here.

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    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.


  • richardmitnick 9:05 am on November 20, 2014 Permalink | Reply
    Tags: , , , Microbes   

    From AAAS: “Body’s bacteria may keep our brains healthy” 



    19 November 2014
    Elizabeth Pennisi

    The microbes that live in your body outnumber your cells 10 to one. Recent studies suggest these tiny organisms help us digest food and maintain our immune system. Now, researchers have discovered yet another way microbes keep us healthy: They are needed for closing the blood-brain barrier, a molecular fence that shuts out pathogens and molecules that could harm the brain.

    Lacking a strong blood-brain barrier, germ-free mice (left) can’t prevent a radioactive tracer (yellow) from entering the brain the way that mice with microbes (middle) can. But adding microbes to germ-free mice (right) restores the blood-brain barrier. (Miklós Tóth/Karolinkska Institutet)

    The findings suggest that a woman’s diet or exposure to antibiotics during pregnancy may influence the development of this barrier. The work could also lead to a better understanding of multiple sclerosis, in which a leaky blood-brain barrier may set the stage for a decline in brain function.

    The first evidence that bacteria may help fortify the body’s biological barriers came in 2001. Researchers discovered that microbes in the gut activate genes that code for gap junction proteins, which are critical to building the gut wall. Without these proteins, gut pathogens can enter the bloodstream and cause disease.

    In the new study, intestinal biologist Sven Pettersson and his postdoc Viorica Braniste of the Karolinska Institute in Stockholm decided to look at the blood-brain barrier, which also has gap junction proteins. They tested how leaky the blood-brain barrier was in developing and adult mice. Some of the rodents were brought up in a sterile environment and thus were germ-free, with no detectable microbes in their bodies. Braniste then injected antibodies—which are too big to get through the blood-brain barrier—into embryos developing within either germ-free moms or moms with the typical microbes, or microbiota.

    The studies showed that the blood-brain barrier typically forms a tight seal a little more than 17 days into development. Antibodies infiltrated the brains of all the embryos younger than 17 days, but they continued to enter the brains of embryos of germ-free mothers well beyond day 17, the team reports online today in Science Translational Medicine. Embryos from germ-free mothers also had fewer intact gap junction proteins, and gap junction protein genes in their brains were less active, which may explain the persistent leakiness. (The researchers didn’t look at the mice’s guts.)

    Germ-free mice even have leaky blood-brain barriers as adults. But those leaks closed after the researchers gave the animals the microbes from normal mice for 2 weeks, Pettersson says.

    The microbes have “a striking effect,” says Elaine Hsiao, a neurobiologist at the California Institute of Technology in Pasadena who was not involved in the study. The work suggests “a role for the [microbes] in regulating brain development and function.”

    But how? In the gut, bacteria may influence the gut wall’s integrity through one of their byproducts, energy-laden molecules called short-chain fatty acids. So Pettersson and his colleagues infected germ-free mice with either bacteria that made these fatty acids or ones that did not. The blood-brain barrier improved only when the bacteria made these fatty acids, Pettersson says. He thinks that these molecules may get into the blood and stimulate gene activity that leads to the closure of the barrier.

    The study is not perfect, Hsaio says. “Germ-free mice are useful tools for studying the microbiota, but the germ-free condition is artificial and involves widespread disruptions” in how the body functions, such as impaired immunity and loss of gut integrity. So these results in germ-free mice need to be confirmed in humans, she says.

    But at the very least, the findings point toward a new understanding of human health and disease, says Lora Hooper, an immunologist at the University of Texas Southwestern Medical Center in Dallas who was not involved in the work. With multiple sclerosis, neurobiologists are at a loss to explain why the disease progresses so erratically, so the idea that changes in the body’s microbes may alter the blood-brain barrier to make the brain more vulnerable to damage is appealing, Pettersson notes.

    Scientists, Hooper adds, should also investigate whether microbes help spur the development of the human fetus’s blood-brain barrier. It could be that taking antibiotics at the wrong time during pregnancy is creating abnormalities in the blood-brain barrier of the child, she says.

    See the full article here.

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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” 

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    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.


    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.

    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.

    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.”

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

    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.

    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.

    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.


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

    An INL Fact Sheet: “Microbial Metabolic Systems” 

    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.

    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.

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