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  • richardmitnick 10:17 am on January 9, 2017 Permalink | Reply
    Tags: 16S rRNA sequencing, Archaea, , Microbes, , Polymerase chain reaction, Prokaryotes, The Never-Ending Quest to Rewrite the Tree of Life   

    From NOVA: “The Never-Ending Quest to Rewrite the Tree of Life” 



    04 Jan 2017
    Carrie Arnold

    The bottom of the ocean is one of the most mysterious places on the planet, but microbiologist Karen Lloyd of the University of Tennessee, Knoxville, wanted to go deeper than that. In 2010, she was a postdoc at Aarhus University in Denmark, and Lloyd wanted to see what microbes were living more than 400 feet beneath the sea floor.

    Like nearly all microbiologists doing this type of census, she relied on 16S rRNA sequencing to determine who was there. Developed by microbiologist Carl Woese in the late 1970s, the technique looks for variation in the 16S rRNA gene, one that’s common to all organisms (it’s key to turning DNA into protein, one of life’s of the most fundamental processes). When Lloyd compared what she had seen under the microscope to what her sequencing data said, however, she knew her DNA results were missing a huge portion of the life hidden underneath the ocean.

    “I had two problems with just 16S sequencing. One, I knew it would miss organisms, and two, it’s not good for understanding small differences between microbes,” Lloyd says.

    Scientists use heat maps like these to visualize the diversity of bacteria in various environments. Credits below.

    Technology had made gene sequencing much quicker and easier compared to when Woese first started his work back in the 1970s, but the principle remained the same. The 16S rRNA gene codes for a portion of the machinery used by prokaryotes to make protein, which is a central activity in the cell. All microbes have a copy of this gene, but different species have slightly different copies. If two species are closely related, their 16S rRNA sequences will be nearly identical; more distantly related organisms will have a greater number of differences. It not only gave researchers a way to quantify evolutionary relationships between species, Woese’s work also revealed an entirely new branch on the tree of life—the archaea, a group of microscopic organisms distinct from bacteria.

    Woese’s success in using 16S rRNA to rewrite the tree of life no doubt encouraged its widespread use. But as Lloyd and other scientists began to realize, some microbes carry a version that is significantly different from that seen in other bacteria or archaea. Since biologists depended on this similarity to identify an organism, they began to realize that they were leaving out potentially significant portions of life from their investigations.

    These concerns culminated approximately ten years ago during a period when sequencing technologies were rapidly accelerating. During this time, researchers figured out how to prepare DNA for sequencing without needing to know anything about the organism you were studying. At the same time, scientists invented a strategy to isolate single cells. At her lab at the Joint Genome Institute outside San Francisco, microbiologist Tanja Woyke put these two strategies together to sequence the genomes of individual microbial cells. Meanwhile, Jill Banfield, across the bay at the University of California, Berkeley, used a different approach called metagenomics that sequenced genes from multiple species at once, and used computer algorithms to reconstruct each organism’s genome. Over the past several years, their work has helped illuminate the massive amount of microbial dark matter that comprises life on Earth.

    “These two strategies really complement each other. They have opened up our ability to see the true diversity of microbial life,” says Roger Lasken, a microbial geneticist at the J. Craig Venter Institute.

    Microbial Dark Matter

    When Woese sequenced the 16S genes of the microbes that would come to be known as archaea, they were completely different from most of the other bacterial sequences he had accumulated. They lacked a true nucleus, like other bacteria, but their metabolisms were completely different. These microbes also tended to favor extreme environments, such as those at high temperatures (hot springs and hydrothermal vents), high salt concentrations, or high acidity. Sensing their ancient origins, Woese named these microbes the archaea, and gave them their own branch on the tree of life.

    Woese did all of his original sequencing by hand, a laborious process that took years. Later, DNA sequencing machines greatly simplified the work, although it still required amplifying the small amount of DNA present using a technique known as polymerase chain reaction, or PCR, before sequencing. The utility of 16S sequencing soon made the technique one of the mainstays of the microbiology lab, along with the Petri dish and the microscope.

    The method uses a set of what’s known as universal primers—short strands of RNA or DNA that help jump start the duplication of DNA—to make lots of copies of the 16S gene so it can be sequenced. The primers bound to a set of DNA sequences flanking the 16S gene that were thought to be common to all organisms. This acted like a set of bookends to identify the region to be copied by PCR. As DNA sequencing technology improved, researchers began amplifying and sequencing 16S genes in environmental samples as a way of identifying the microbes present without the need to grow them in the lab. Since scientists have only been able to culture about one in 100 microbial species, this method opened broad swaths of biodiversity that would otherwise have remained invisible.

    “We didn’t know that these deep branches existed. Trying to study life from just 16S rRNA sequences is like trying to understand all animals by visiting a zoo,” says Lionel Guy, a microbiologist from Uppsala University in Sweden.

    Access mp4 video here .
    Discover how to interpret and create evolutionary trees, then explore the tree of life in NOVA’s Evolution Lab.

    It didn’t take long, however, for scientists to realize the universal primers weren’t nearly as universal as researchers had hoped. The use of the primers rested on the assumption that all organisms, even unknown ones, would have similar DNA sequences surrounding the 16S rRNA gene. But that meant that any true oddballs probably wouldn’t have 16S rRNA sequences that matched the universal primers—they would remain invisible. These uncultured, unsequenced species were nicknamed “microbial dark matter” by Stanford University bioengineer and physicist Stephen Quake in a 2007 PNAS paper.

    The name, he says, is analogous to dark matter in physics, which is invisible but thought to make up the bulk of the universe. “It took DNA technology to realize the depth of the problem. I mean, holy crap, there’s a lot more out there than we can discover,” Quake says.

    Quake’s snappy portmanteau translated into the Microbial Dark Matter project—an ongoing quest in microbiology, led by Woyke, to understand the branches on the tree of life that remain shrouded in mystery by isolating DNA from single bacterial and archaeal cells. These microbial misfits intrigued Lloyd as well, and she believed the subsurface had many more of them than anyone thought. Her task was to find them.

    “We had no idea what was really there, but we knew it was something,” Lloyd says.

    To solve her Rumsfeldian dilemma of identifying both her known and unknown unknowns, Lloyd needed a DNA sequencing method that would allow her to sequence the genomes of the microbes in her sample without any preconceived notions of what they looked like. As it turns out, a scientist in New Haven, Connecticut was doing just that.

    Search for Primers

    In the 1990s, Roger Lasken had recognized the problems with traditional 16S rRNA and other forms of sequencing. Not only did you need to know something about the DNA sequence ahead of time in order to make enough genetic material to be sequenced, you also needed a fairly large sample. The result was a significant limitation in the types of material that could be sequenced. Lasken wanted to be able to sequence the genome of a single cell without needing to know anything about it.

    Then employed at the biotech firm Molecular Staging, Lasken began work on what he called multiple displacement amplification (MDA). He built on a recently discovered DNA polymerase (the enzyme that adds nucleotides, one by one, to a growing piece of DNA) called φ29 DNA polymerase. Compared to the more commonly used Taq polymerase, the φ29 polymerase created much longer strands of DNA and could operate at much cooler temperatures. Scientists had also developed random primers, small pieces of randomly generated DNA. Unlike the universal primers, which were designed to match specific DNA sequences 20–30 nucleotides in length, random primers were only six nucleotides long. This meant they were small enough to match pieces of DNA on any genome. With enough random primers to act as starting points for the MDA process, scientists could confidently amplify and sequence all the genetic material in a sample. The bonus inherent in the random primers was that scientists didn’t need to know anything about the sample they were sequencing in order to begin work.

    “For the first time, you didn’t need to culture an organism or amplify its DNA to sequence it,” he says.

    The method had only been tested on relatively small pieces of DNA. Lasken’s major breakthrough was making the system work for larger chromosomes, including those in humans, which was published in 2002 in PNAS. Lasken was halfway to his goal—his next step was figuring out how to do this in a single bacterium, which would enable researchers to sequence any microbial cell they found. In 2005, Lasken and colleagues managed to isolate a single E. coli cell and sequence its 16S rRNA gene using MDA. It was a good proof of principle that the system worked, but to understand the range and depth of microbial biodiversity, researchers like Tanja Woyke, the microbiologist at the Joint Genome Institute, needed to look at the entire genome of a single cell. In theory, the system should work neatly: grab a single cell, amplify its DNA, and then sequence it. But putting all of the steps together and working on the kinks in the system would require years of work.

    Woyke had spent her postdoc at the Joint Genome Institute sequencing DNA from samples not grown in the lab, but drawn directly from the environment, like a scoop of soil. At the time, she was using metagenomics, which amplified and sequenced DNA directly from environmental samples, yielding millions of As, Ts, Gs, and Cs from even a thimble of dirt. Woyke’s problem was determining which genes belonged to which microbe, a key step in assembling a complete genome. Nor was she able to study different strains of the same microbe that were present in a sample because their genomes were just too similar to tell apart using the available sequencing technology. What’s more, the sequences from common species often completely drowned out the data from more rare ones.

    “I kept thinking to myself, wouldn’t it be nice to get the entire genome from just a single cell,” Woyke says. Single-cell genomics would enable her to match a genome and a microbe with near 100% certainty, and it would also allow her to identify species with only a few individuals in any sample. Woyke saw a chance to make her mark with these rare but environmentally important species.

    Soon after that, she read Lasken’s paper and decided to try his technique on microbes she had isolated from the grass sharpshooter Draeculacephala minerva, an important plant pest. One of her biggest challenges was contamination. Pieces of DNA are everywhere—on our hands, on tables and lab benches, and in the water. The short, random primers upon which single-cell sequencing was built could help amplify these fragments of DNA just as easily as they could the microbial genomes Woyke was studying. “If someone in the lab had a cat, it could pick up cat DNA,” Woyke says of the technique.

    In 2010, after more than a year of work, Woyke had her first genome, that of Sulcia bacteria, which had a small genome and could only live inside the grass sharpshooter. Each cell also carried two copies of the genome, which helped make Woyke’s work easier. It was a test case that proved the method, but to shine a spotlight on the world’s hidden microbial biodiversity, Woyke would need to figure out how to sequence the genomes from multiple individual microbes.

    Work with Jonathan Eisen, a microbiologist at UC Davis, on the Genomic Encyclopedia of Bacteria and Archaea Project, known as GEBA, enabled her lab to set up a pipeline to perform single cell sequencing on multiple organisms at once. GEBA, which seeks to sequence thousands of bacterial and archaeal genomes, provided a perfect entry to her Microbial Dark Matter sequencing project. More than half of all known bacterial phyla—the taxonomic rank just below kingdom—were only represented by a single 16S rRNA sequence.

    “We knew that there were far more microbes and a far greater diversity of life than just those organisms being studied in the lab,” says Matthew Kane, a program director at the National Science Foundation and a former microbiologist. Studying the select few organisms that scientists could grow in pure culture was “useful for picking apart how cells work, but not for understanding life on Earth.”

    GEBA was a start, but even the best encyclopedia is no match for even the smallest public library. Woyke’s Microbial Dark Matter project would lay the foundation for the first of those libraries. She didn’t want to fill it with just any sequences, however. Common bacteria like E. coli, Salmonella, and Clostridium were the Dr. Seuss books and Shakespeare plays of the microbial world—every library had copies, though they represented only a tiny slice of all published works. Woyke was after the bacterial and archaeal equivalents of rare, single-edition books. So she began searching in extreme environments including boiling hot springs of caustic acid, volcanic vents at the bottom of the ocean, and deep inside abandoned mines.

    Using the single-celled sequencing techniques that she had perfected at the Joint Genome Institute, Woyke and her colleagues ended up with exactly 201 genomes from these candidate phyla, representing 29 branches on the tree of life that scientists knew nothing about. “For many phyla, this was the first genomic data anyone had seen,” she says.

    The results, published in Nature in 2013, identified some unusual species for which even Woyke wasn’t prepared. Up until that study, all organisms used the same sequence of three DNA nucleotides to signal the stop of a protein, one of the most fundamental components of any organism’s genome. Several of the species of archaea identified by Woyke and her colleagues, however, used a completely different stop signal. The discovery was not unlike traveling to a different country and having the familiar red stop sign replaced by a purple square, she says. Their work also identified other rare and bizarre features of the organisms’ metabolisms that make them unique among Earth’s biodiversity. Other microbial dark matter sequencing projects, both under Woyke’s Microbial Dark Matter project umbrella and other independent ventures, identified microbes from unusual phyla living in our mouths.

    Some of the extremeophile archaea that Woyke and her colleagues identified were so unlike other forms of life that they grouped them into their own superset of phyla, known as DPANN (Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanohaloarchaeota, and Nanoarchaeota). The only thing that scientists knew about these organisms were the genomes that Woyke had sequenced, isolated from individual organisms. These single-cell sequencing projects are key not just for filling in the foliage on the tree of life, but also for demonstrating just how much remains unknown, and Woyke and her team have been at the forefront of these discoveries, Kane says.

    Sequencing microbes cell by cell, however, isn’t the only method for uncovering Earth’s hidden biodiversity. Just a few miles from Woyke’s lab, microbiologist Jill Banfield at UC Berkeley is taking a different approach that also has also produced promising results.

    Studying the Uncultured

    Typically, to study microbes, scientists have grown them in a pure culture from a single individual. Though useful for studying these organisms in the laboratory, most microbes live in complex communities of many individuals from different species. Starting in the early 2000s, genetic sequencing technologies had advanced to the point where researchers could study the complex array of microbial genomes without necessarily needing to culture each individual organism. Known as metagenomics, the field began with scientists focused on which genes were found in the wild, which would hint at how each species or strain of microbe could survive in different environments.

    Just as Woyke was doubling down on single-cell sequencing, Banfield began using metagenomics to obtain a more nuanced and detailed picture of microbial ecology. The problems she faced, though very different from Woyke’s, were no less vexing. Like Woyke, Banfield focused on extreme environments: acrid hydrothermal vents at the bottom of the ocean that belched a vile mixture of sulfuric acid and smoke; an aquifer flowing through toxic mine tailings in Rifle, Colorado; a salt flat in Chile’s perpetually parched Atacama Desert; and water found in the Iron Mountain Mine in Northern California that is some of the most acidic found anywhere on Earth. Also like Woyke, Banfield knew that identifying the full range of microbes living in these hellish environments would mean moving away from using the standard set of 16S rRNA primers. The main issue Banfield and colleagues faced was figuring out how to assemble the mixture of genetic material they isolated from their samples into discrete genomes.

    A web of connectivity calculated by Banfield and her collaborators shows how different proteins illustrate relationships between different microbes.
    Credit below.

    The solution wasn’t a new laboratory technique, but a different way of processing the data. Researchers obtain their metagenomic information by drawing a sample from a particular environment, isolating the DNA, and sequencing it. The process of sequencing breaks each genome down into smaller chunks of DNA that computers then reassemble. Reassembling a single genome isn’t unlike assembling a jigsaw puzzle, says Laura Hug, a microbiologist at the University of Waterloo in Ontario, Canada, and a former postdoc in Banfield’s lab.

    When faced with just one puzzle, people generally work out a strategy, like assembling all the corners and edges, grouping the remaining pieces into different colors, and slowly putting it all together. It’s a challenging task with a single genome, but it’s even more difficult in metagenomics. “In metagenomics, you can have hundreds or even thousands of puzzles, many of them might be all blue, and you have no idea what the final picture looks like. The computers have to figure out which blue pieces go together and try to extract a full, accurate puzzle from this jumble,” Hug says. Not surprisingly, the early days of metagenomics were filled with incomplete and misassembled genomes.

    Banfield’s breakthrough helped tame the task. She and her team developed a better method for binning, the formal name for the computer process that sorts through the pile of DNA jigsaw pieces and arranges them into a final product. As her lab made improvements, they were able to survey an increasing range of environments looking for rare and bizarre microbes. Progress was rapid. In the 1980s, most of the bacteria and archaea that scientists knew about fit into 12 major phyla. By 2014, scientists had increased that number to more than 50. But in a single 2015 Nature paper, Banfield and her colleagues added an additional 35 phyla of bacteria to the tree of life.

    The latest tree of life was produced when Banfield and her colleagues added another 35 major groups, known as phyla. Credit below.

    Because researchers knew essentially nothing about these bacteria, they dubbed them the “candidate phyla radiation”—or CPR—the bacterial equivalent of Woyke’s DPANN. Like the archaea, these bacteria were grouped together because of their similarities to each other and their stark differences to other bacteria. Banfield and colleagues estimated that the CPR organisms may encompass more than 15% of all bacterial species.

    “This wasn’t like discovering a new species of mammal,” Hug says. “It was like discovering that mammals existed at all, and that they’re all around us and we didn’t know it.”

    Nine months later, in April 2016, Hug, Banfield, and their colleagues used past studies to construct a new tree of life. Their result reaffirmed Woese’s original 1978 tree, showing humans and, indeed, most plants and animals, as mere twigs. This new tree, however, was much fuller, with far more branches and twigs and a richer array of foliage. Thanks in no small part to the efforts of Banfield and Woyke, our understanding of life is, perhaps, no longer a newborn sapling, but a rapidly maturing young tree on its way to becoming a fully rooted adult.

    Photo credits: Miller et al. 2013/PLOS, Podell et al. 2013/PLOS, Hug et al. 2016/UC Berkeley

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  • richardmitnick 7:26 am on March 17, 2016 Permalink | Reply
    Tags: , Microbes,   

    From PNNL: “Consorting with the Right Microbes” 

    PNNL Lab

    March 2016
    No writer credit found

    Microbes in soil

    Using microbial consortia may boost success of biotechnologies

    Results: Around the world, researchers are studying microbes to see if these tiny organisms can be used to solve a host of problems, from cleaning up toxic waste to providing renewable energy. Unfortunately, attempts to develop biotechnologies often fall short because they focus on a limited set of single, highly engineered organisms. Such organisms frequently do not perform as efficiently or stably in an application as they do in the laboratory.

    Now, an internationally recognized group of scientists, organized by Pacific Northwest National Laboratory microbiologists Dr. Stephen Lindemann and Dr. Alexander Beliaev, has reviewed the state of the science to determine how biotechnological use of communities of multiple microbes, or microbial consortia, might transcend the limitations of single organisms.

    They posit that the time is ripe for design and control of microbial communities, and that achieving the ability to engineer microbial ecosystems will require a level of understanding of the mechanisms driving microbial community function only possible from combining recent advances in systems biology, computational modeling, and synthetic biology.

    These new perspectives stemmed from a panel at the 15th International Symposium on Microbial Ecology in Seoul and appear in the International Society for Microbial Ecology’s (ISME) official publication, The ISME Journal.

    Why It Matters: Agriculture has long known that monocultures, or growing only one type of crop, can be susceptible to changes in the environment. For example, relatively small or poorly timed changes in rainfall can cause major losses in production for some crops. In contrast, growing several crops with different tolerances to drought might more stably provide food, no matter the weather for a given year. The same principle applies to microbes, which are drivers of global geochemical cycles and catalysts for renewable fuels and chemicals. Microbial communities can prove to be more reliable than engineered “superbugs” and more robust against unpredictable environment than individual microbes. This reliability is the key to using them for industrial purposes.

    “The promise that this field has to offer is great,” said Beliaev. “Transformative biotechnologies will help overcome the energy, health, and environmental problems of the future, and the process of learning to design and control ecological phenomena has and will undoubtedly continue to yield new insights on the fundamentals of life.”

    Methods: Seven scientists from PNNL, Montana State University, Fred Hutchinson Cancer Research Center, and the Swiss Federal Institute of Technology brought perspectives from different scientific approaches, research programs, and countries to analyze the state of the science. They used questions posed by experts who attended the ISME symposium to outline key issues.

    Drawing on their years of experience and amassed knowledge, the group determined that successful biosystems design is contingent both on the understanding of microbial physiology and accuracy of computational models that describe how organisms interact. An iterative design-build-test approach that can predict interspecies dynamics and analyze energy and material flows in a community will help scientists better understand how these consortia can be used for biotechnologies.

    What’s Next? PNNL’s microbial research program continues to expand the foundation of biological systems design. Ideally, advances in this field will allow scientists to control safety, productivity, and stability of natural and designed microbial ecosystems.

    Sponsors: The U.S. Department of Energy’s Office of Science, Office of Biological and Environmental Research, supported this work via the Genomic Science Program under the PNNL Foundational Scientific Focus Area. MWF is supported by the Scientific Focus Area Program at Lawrence Berkeley National Laboratory. HCB participated with support from the Linus Pauling Distinguished Postdoctoral Fellowship, a Laboratory Directed Research and Development Program at PNNL.

    Research Team: Alexander S. Beliaev, Hans C. Bernstein, Jim K. Fredrickson, Stephen R. Lindemann, and Hyun-Seob Song, Pacific Northwest National Laboratory; Matthew W. Fields, Montana State University; Wenying Shou, Fred Hutchinson Cancer Research Center; and David R. Johnson, Swiss Federal Institute of Technology.

    Reference: Lindemann SR, HC Bernstein, H-S Song, JK Fredrickson, MW Fields, W Shou, DR Johnson, and AS Beliaev. 2016. “Engineering Microbial Consortia for Controllable Outputs.” The ISME Journal: Multidisciplinary Journal of Microbial Ecology. Advance online publication 11 March 2016. DOI: 10.1038/ismej.2016.26.

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    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.


  • richardmitnick 10:59 am on March 15, 2016 Permalink | Reply
    Tags: , Microbes,   

    From PNNL: “Microbes may not be so adaptable to climate change” 

    PNNL Lab

    March 15, 2016
    Tom Rickey, PNNL, (509) 375-3732

    Microbes in soil
    Microbes in the soil are central players converting carbon into greenhouse gases.
    Courtesy of Alice Dohnalkova/PNNL

    Microbes in soil — organisms that exert enormous influence over our planet’s carbon cycle — may not be as adaptable to climate change as most scientists have presumed, according to a paper published March 2 in PLOS One.

    The finding means that a big piece of the puzzle regarding the future climate of our warming planet just got a little tougher to fit into current computer models.

    Soil holds an enormous pool of carbon — in a forest, for instance, usually there is more carbon beneath the surface than in the trees above — and what happens to that carbon is an important factor in the future of our planet. Bacteria, fungi and other microbes are central players, converting carbon and other elements in the soil into carbon dioxide and other gases that are expelled into the atmosphere.

    “Soil is the major buffer system for environmental changes, and the microbial community is the basis for that resilience. If the microbial community is not as resilient as we had assumed, then it calls into question the resilience of the overall environment to climate change,” said author Vanessa Bailey of the Department of Energy’s Pacific Northwest National Laboratory.

    The findings are based on a unique 17-year study of transplanted soils on a mountain in eastern Washington state. The team moved some samples of soil down the mountainside 500 meters to a warmer, drier climate, and other samples up 500 meters to a cooler, moister climate. After 17 years, they analyzed both sets of soil in the laboratory, as well as “control” samples from both sites that had never been moved.

    The scientists analyzed the make-up of the microbial communities, their enzyme activity, and their rates of respiration — how quickly microbes convert carbon in the soil into carbon dioxide which is released to the atmosphere.

    The scientists found less adaptability than they expected, even after 17 years. While the microbial make-up of the samples did not change much at all, the microbes in both sets of transplanted soils retained many of the traits they had in their “native” climate, including to a large degree their original rate of respiration.

    The message, the authors say, is that scientists can’t simply assume that microbes will nimbly respond to climate change.

    “The fact that the soils’ native environment continued to exert profound influence on microbial activity 17 years later is quite surprising,” said co-author Ben Bond-Lamberty, a scientist with the Joint Global Change Research Institute, a partnership between PNNL and the University of Maryland in College Park, Md.

    “We can’t assume that soils will respond to climate changes in the ways that many scientific models have assumed,” Bond-Lamberty added.

    In their study, the PNNL scientists took advantage of a mountain location where the climate changes quickly as one moves higher. Just 500 meters up the mountain, temperatures cooled about 5 degrees Celsius on average and rainfall increased about 5 centimeters annually. That translates to more vegetation at the higher location and thus more carbon available to microbial communities.

    The microbes native to the higher site respired at a higher rate naturally, due to the moister climate and a more plentiful supply of carbon in their environment; when they were moved to the lower, warmer site, they continued to respire at a faster rate than the surrounding “native” soils and microbes. And the microbes transplanted from lower ground to higher ground had an unusually small response to the temperature change, though biological theory and climate models predict a larger change.

    “With our changing climate, all microbes will be experiencing new conditions and more extremes,” said Bailey, a soil microbiologist. “Climate change won’t translate simply to steady warming everywhere. There will be storm surges, longer droughts; some places may end up experiencing more mild climates. This study gives us a glimpse of how microbes could weather such changes under one set of conditions. They may be constrained in surprising ways.”

    The study was funded by the Department of Energy Office of Science. Measurements of various forms of carbon were done at EMSL, the Environmental Molecular Sciences Laboratory, a DOE Office of Science user facility at PNNL.

    Reference: Ben Bond-Lamberty, Harvey Bolton, Sarah Fansler, Alejandro Heredia-Langner, Chongxuan Liu, Lee Ann McCue, Jeffrey Smith, Vanessa Bailey, Soil respiration and bacterial structure and function after 17 years of a reciprocal soil transplant experiment, PLOS One, March 2, 2016, DOI: 10.1371/journal.pone.0150599.

    See the full article here .

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    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.


  • richardmitnick 8:36 am on December 13, 2015 Permalink | Reply
    Tags: AGAR shortage, , Microbes,   

    From Nature: “Lab staple agar hit by seaweed shortage” 

    Nature Mag

    08 December 2015
    Ewen Callaway

    Restrictions on harvests and exports of Gelidium seaweed in Morocco have affected the global supply of the lab reagent agar.Abdelhak Senna/AFP/Getty

    Microbiology’s most important reagent is in short supply, with potential consequences for research, public health and clinical labs around the world.

    Agar — the seaweed-derived, gelatinous substance that biologists use to culture microbes — is experiencing a global downturn, marine biologists, agar producers and industry analysts told Nature. “There’s not enough seaweed for everyone, so basically we are now reducing our production,” says Pedro Sanchez, deputy managing director of Industrias Roko in Polígono de Silvota, Spain, which processes seaweed to make some 40% of the world’s agar.

    The shortage can be traced to newly enforced trade restrictions on the seaweed, arising from environmental concerns that the algae are being overharvested. It is unclear how deeply the dearth will hit researchers, but it has already pushed wholesale prices of agar to an all-time high of around US$35–45 per kilogram — nearly triple the price before scarcities began. Individual researchers, who buy packaged agar from lab-supply companies, can pay many times this amount.

    Contamination hits cell work. Mycoplasma (orange) can surround and infect cells and invalidate results of gene-expression studies.Linda Stannard, UCT/SPL

    One major supplier, Thermo Fisher Scientific of Waltham, Massachusetts, says that it has stopped selling two ‘raw’ agar products — agar that has not been mixed with other ingredients — until 2016, so that it can prioritize more-popular products that contain a mixture of agar and growth nutrients. The company reports that about 200 of its customers have been affected. Another major lab-supply company, Millipore Sigma in Billerica, Massachusetts, has also halted sales of raw agar, and it says that it will re-evaluate its supplies early next year.

    Millipore Sigma blames the shortage on competition from food companies for purified agar. The global demand from food-makers, at several thousand tonnes annually, dwarfs the 900 tonnes that go to lab-supply companies.

    Prized material

    Formed of long chains of sugar molecules, agar is prized by microbiologists for its ability to form hard gels when mixed with water and growth nutrients. When a solution of bacteria is spread onto an agar-lined plate, individual cells grow into distinct colonies, allowing researchers to isolate each different strain in the mixture.

    Adam Roberts, a microbiologist at University College London, drew attention to the agar-supply problem last month, when he tweeted a letter from Thermo Fisher announcing its suspension of some agar sales. His lab depends on the product to identify new antimicrobial compounds in soil bacteria.

    Roberts managed to source raw agar from another supplier, but he says that his lab may have to begin rationing it and prioritizing some experiments over others. “It would be a bloody nightmare,” he says. When a colleague at another institution heard about Roberts’s agar-supply problem, she started to hoard her own stash. “If it gets more serious and hard to come by, I don’t know what we’ll do,” says Roberts.

    Since the introduction of agar plates in the 1880s — which enabled researchers to isolate tuberculosis, cholera and other disease-causing bacteria for the first time — bacteriological agar has been derived from a clutch of red seaweed species belonging to the genus Gelidium.

    Promising antibiotic found in microbial ‘dark matter’. IChip device allows ‘unculturable’ bacteria to be studied for their ability to produce antibiotics. Slava Epstein

    Algae of this type grow atop rocky sea beds, forming vast underwater lawns of bushy, red fronds, and they favour cool, turbulent waters that provide a steady supply of oxygen and other nutrients — a preference that makes industrial-scale farming impossible. “It’s not cultivated, and it’s not possible to cultivate — although we’ve wasted a lot of money trying to do it in the past,” says Sanchez. In some places, Gelidium is harvested by underwater divers or when the tides roll in, but the seaweed is most commonly collected when storms wash it ashore.

    The geographical sources of Gelidium have shifted over the decades. Before the Second World War, Japan was king; Portugal was also once a leading supplier. Now, most of the world’s agar derives from Gelidium grown in Morocco, with Spain in second place and Portugal, France, Mexico, Chile, South Africa, Japan and South Korea all contributing smaller quantities (see ‘Seaweed shortage’).

    Current agar deficiencies are due mostly to an unsteady supply of Moroccan Gelidium, say industry insiders. Throughout the 2000s, the nation regularly harvested as much as 14,000 tonnes per year, which was sold on to foreign and domestic agar producers. But citing concerns over dwindling Gelidium populations, the Moroccan government cut the legal annual harvest to around 6,000 tonnes, and has limited foreign exports of the algae to around 1,200 tonnes. Although the changes were imposed in 2010, the country only began to enforce these trade limits last year, says Sanchez.

    Gold rush

    There is evidence, says marine ecologist Ricardo Melo at the University of Lisbon, that Moroccan Gelidium stocks were being overharvested by throngs of beach-combers in search of ‘red gold’, as the seaweed is known. But Melo says that the trade restrictions make little sense from a conservation point of view.

    The domestic Moroccan market is now flooded with Gelidium, while the rest of the world struggles with a massive shortage. This has benefited Morocco’s lone agar producer, which can now buy the seaweed at rock-bottom prices, but the move has vastly increased the cost for producers elsewhere.

    Mining the microbial dark matter. Illustration by Thomas Porostocky

    And that means that companies such as Thermo Fisher and Millipore Sigma, which buy purified agar from producers and sell it on to researchers as packaged products, have little choice but to pay the skyrocketing prices that agar now commands, says Dennis Seisun, who runs an industry-analysis firm called IMR International in San Diego, California. “The ones that had contracts with the suppliers are getting preferential treatment, but I’m pretty sure they’re not getting all they want.”

    The European Commission has complained to the Moroccan government that the country’s export restrictions violate its free-trade agreements with European Union countries, but to little avail. And prospects for new sources of Gelidium are bleak. Unexploited populations of the seaweed exist off the shores of North Korea, but “it’s not easy to work in a country like North Korea”, says Sanchez.

    Agar substitutes, such as a seaweed product called carrageenan, have proved unsuitable for culturing microbes. Before a technician introduced agar to his lab, pioneering German microbiologist Robert Koch isolated bacteria on potato slices. “Unless we go back to what Koch used to do — use a potato,” Roberts says, “there’s no real alternative.”

    Nature 528, 171–17 (10 December 2015) doi:10.1038/528171a

    See the full article here .

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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” 

    Berkeley Logo

    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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    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.


  • 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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