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    The DOE Science News Source is a Newswise initiative to promote research news from the Office of Science of the DOE to the public and news media.
    • 2015-05-12 12:05:00
    • Article ID: 634189

    Using Microbial Communities to Assess Environmental Contamination

    ENIGMA Study Shows Natural Bacterial Communities as Effective Geochemical Biosensors

    • Credit: Courtesy of Oak Ridge National Laboratory

      The Bear Creek watershed in Oak Ridge, TN, was a a crucial site for the early development of nuclear weapons under the Manhattan Project and harbors spectacular geochemical gradients.

    • Credit: Courtesy of ENIGMA

      An ENIGMA research project showed that environmental site contamination with (a) uranium and (b) nitrate can be effectively identified using bacterial DNA.

    First there were canaries in coal mines, now there are microbes at nuclear waste sites, oil spills and other contaminated environments. A multi-institutional team of more than 30 scientists has found that statistical analysis of DNA from natural microbial communities can be used to accurately identify environmental contaminants and serve as quantitative geochemical biosensors. This study was sponsored by ENIGMA, a U.S. Department of Energy (DOE) Office of Science “Scientific Focus Area Program” based at the Lawrence Berkeley National Laboratory (Berkeley Lab).

    “Changes induced in the natural microbial community structure by contaminants lasts long after the contaminants themselves have become undetectable,” says Terry Hazen, an internationally recognized authority on microbial ecology who led the research.

    “This means the DNA of these microbial communities can be used as a forensic tool for measuring anthropogenic effects on the environment.”

    Hazen, who holds joint appointments with DOE’s Oak Ridge National Laboratory (ORNL) and the University of Tennessee at Knoxville, is the corresponding author of a paper detailing the results of this ENIGMA study in mBio, the online open-access journal of the American Society for Microbiology. The paper is titled “Natural Bacterial Communities Serve as Quantitative Geochemical Biosensors.” For a complete list of authors go here.

    For this study, the ENIGMA collaborators identified the most independent and interesting groundwater well clusters from 25 years of monitoring data collected at the Bear Creek watershed in Oak Ridge. This watershed was a crucial site for the early development of nuclear weapons under the Manhattan Project and harbors spectacular geochemical gradients. The collaborators

    then collected a large number of microbial DNA samples from the identified wells in combination with 28 other physical/chemical characteristics.

    “The wells we sampled typically contain a high number of particulates in the groundwater, thus causing the filters we collected DNA on to clog easily,” says Andrea Rocha, a post-doctoral associate in Hazen’s research group, who spent three months collecting samples from the watershed. “We had to change our filters each time they clogged until we obtained our required four liters of groundwater. Sometimes this meant changing filters five to six times for one well.”

    Analysis of the DNA data from the collected groundwater samples was carried out via a technique called “supervised machine-learning,” which the ENIGMA team applied to high-throughput DNA sequencing data.

    “Because microbial communities continuously sense and respond to their environments, they form a ubiquitous environmental surveillance network that can be inexpensively digitized through DNA sequencing,” Hazen says. “Our idea was to determine whether and how information encoded in bacterial communities might be tapped to quantitatively characterize the environment.”

    While previous research demonstrated that specific proteins or

    whole bacterial cells could be used as biosensors to translate environmental signals into machine-readable data, the focus of the ENIGMA study was on the integration of information gathered from native bacterial communities containing billions of cells and encompassing thousands of taxonomic groups.

    With just the sequencing data from the 16S rRNA gene alone, the ENIGMA team was able to quantitatively produce “a rich catalogue of 26 geochemical features” from 93 groundwater wells with highly differing geochemistry characteristics. These features were then used to predict contamination. The accuracy for predicting uranium contamination of the groundwater was about 88-percent, and the accuracy for predicting nitrate contamination was about 73-percent.

    “Our work shows that knowing what bacteria are present allows us to infer something about the current or past chemistry of a site,” says Eric Alm, an MIT microbiologist and one of the principal investigators on this project. “The next big challenge will be to understand why different bacteria are associated with different environmental conditions.”

    As human populations continue to grow and the industrialization of developing nations continues to expand, the impact of human activity on the environment is only going to intensify. Measuring the causes and consequences of these impacts is a challenge that science must meet. The ENIGMA project demonstrates one path towards meeting this objective.

    “It takes an integrated team to tackle a large problem like this,” says Paul Adams, the SFA Laboratory Research Manager for ENIGMA. “The work with these natural microbial communities highlights what can be achieved through interdisciplinary research that harnesses ENIGMA’s scientific expertise in field sampling, high throughput sequencing, and computational analysis.”

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    Bright Skies for Plant-Based Jet Fuels

    Bright Skies for Plant-Based Jet Fuels

    With an estimated daily fuel demand of more than 5 million barrels per day, the global aviation sector is incredibly energy-intensive and almost entirely reliant on petroleum-based fuels. However, a new analysis by scientists at Berkeley Lab shows that sustainable plant-based bio-jet fuels could provide a competitive alternative to conventional fuels if current development and scale-up initiatives continue to push ahead successfully.

    Sampling Guts of Live Moose to Understand How They Break Down Biomass

    Sampling Guts of Live Moose to Understand How They Break Down Biomass

    First-of-a-kind study advances understanding of microbial and viral communities involved in biomass breakdown.

    Cause of Cathode Degradation Identified for Nickel-rich Materials

    Cause of Cathode Degradation Identified for Nickel-rich Materials

    A team of scientists including researchers at the U.S. Department of Energy's (DOE) Brookhaven National Laboratory and SLAC National Accelerator Laboratory have identified the causes of degradation in a cathode material for lithium-ion batteries, as well as possible remedies. Their findings, published on Mar. 7 in Advanced Functional Materials, could lead to the development of more affordable and better performing batteries for electric vehicles.

    Uncovering Uncultivated Microbes in the Human Gut

    Uncovering Uncultivated Microbes in the Human Gut

    A human's health is shaped both by environmental factors and the body's interactions with the microbiome, particularly in the gut. Genome sequences are critical for characterizing individual microbes and understanding their functional roles. However, previous studies have estimated that only 50 percent of species in the gut microbiome have a sequenced genome, in part because many species have not yet been cultivated for study.

    Scientists Track Patterns of Island Growth in Crystals

    Scientists Track Patterns of Island Growth in Crystals

    In a new study from the U.S. Department of Energy's (DOE) Argonne National Laboratory, scientists have found that the seemingly random arrangement of islands that form to begin new layers during crystal growth can actually be very similar from layer to layer. The discovery may help scientists better understand of some of the mechanisms behind defect formation, as well as develop techniques to synthesize new types of crystals.

    Sea Quark Surprise Reveals Deeper Complexity in Proton Spin Puzzle

    Sea Quark Surprise Reveals Deeper Complexity in Proton Spin Puzzle

    New data from the STAR experiment at the Relativistic Heavy Ion Collider (RHIC) add detail and complexity to an intriguing puzzle that scientists have been seeking to solve: how the building blocks that make up a proton contribute to its spin. The results reveal that different flavors of antiquarks contribute differently to spin--and in a way that's opposite to those flavors' relative abundance.

    Fitting a Square Peg in a Round Hole: The Surprising Structure of Uranium Bound in Hematite

    Fitting a Square Peg in a Round Hole: The Surprising Structure of Uranium Bound in Hematite

    An atomic view of how toxic uranium binds to iron minerals in the environment enables better predictions of its behavior.

    How Injected Microbes Persist in Hydraulically Fractured Shale

    How Injected Microbes Persist in Hydraulically Fractured Shale

    Scientists reveal the importance of an amino acid that supplies energy and protection for microbial communities deep underground.

    Engineering Living 'Scaffolds' for Building Materials

    Engineering Living 'Scaffolds' for Building Materials

    Researchers at DOE's Lawrence Berkeley National Laboratory have developed a platform that uses living cells as "scaffolds" for self-assembled composite materials. The technology could enable self-healing materials and other advanced applications in bioelectronics, biosensing, and smart materials.

    Researchers reverse the flow of time on IBM's quantum computer

    Researchers reverse the flow of time on IBM's quantum computer

    An international team of scientists led by the U.S. Department of Energy's (DOE) Argonne National Laboratory explored the concept of reversing time in a first-of-its-kind experiment, managing to return a computer briefly to the past. The results, published March 13 in the journal Scientific Reports, suggest new paths for exploring the backward flow of time in quantum systems and present new possibilities for quantum computer program testing and error correction.


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    DOE extends University PPPL contract

    DOE extends University PPPL contract

    The DOE has extended until 2022 its contract with Princeton University to manage the Princeton Plasma Physics Laboratory, which is dedicated to enabling the scientific breakthroughs required to develop fusion as a safe, clean and abundant energy source.

    Fermilab, international partners break ground on new state-of-the-art particle accelerator

    Fermilab, international partners break ground on new state-of-the-art particle accelerator

    With a ceremony held on March 15, the U.S. Department of Energy's Fermi National Accelerator Laboratory officially broke ground on a major new particle accelerator project that will power cutting-edge physics experiments for many decades to come.

    Argonne's Ali Erdemir elected to National Academy of Engineering for pivotal discoveries in tribology

    Argonne's Ali Erdemir elected to National Academy of Engineering for pivotal discoveries in tribology

    Distinguished Fellow Ali Erdemir from the U.S. Department of Energy's (DOE) Argonne National Laboratory has been elected a member of the National Academy of Engineering (NAE), one of the highest professional distinctions accorded to engineers.

    Department of Energy to Provide $30 Million for Fusion Research on International Facilities

    The U.S. Department of Energy (DOE) announced a plan to provide $30 million for experimental research on magnetic fusion energy science at international fusion facilities known as tokamaks.

    HPC4Manufacturing Program names four awardees for latest round of DOE funding

    HPC4Manufacturing Program names four awardees for latest round of DOE funding

    The High Performance Computing for Manufacturing Program (HPC4Mfg) today announced the recipients of $1.2 million in federal funding for four public/private projects aimed at solving key manufacturing challenges in steelmaking and aluminum production through supercomputing.

    DOE Announces $100 Million in Small Business Innovation and Technology Funding

    The U.S. Department of Energy (DOE) Small Business Innovation Research (SBIR) and Small Business Technology Transfer (STTR) programs issued its FY 2019 Phase II Release 2 Funding Opportunity Announcement (FOA) with approximately $100 million in available funding.

    SURA Releases Jefferson Lab Economic Impact Study

    SURA Releases Jefferson Lab Economic Impact Study

    A new study commissioned by the Southeastern Universities Research Association on the local, state and nationwide impacts of the U.S. Department of Energy's Thomas Jefferson National Accelerator Facility has found that the laboratory generated $556.9 million in output and provided labor income for 3,448 workers nationwide last year.

    ReactWell licenses ORNL catalyst for energy conversion applications

    ReactWell licenses ORNL catalyst for energy conversion applications

    ReactWell has licensed a novel waste-to-fuel technology from Oak Ridge National Laboratory to improve energy conversion methods for cleaner, more efficient oil and gas, chemical and bioenergy production.

    Kwok named Outstanding Referee by American Physical Society

    Kwok named Outstanding Referee by American Physical Society

    Argonne distinguished fellow Wai-Kwong Kwok has been named a 2019 Outstanding Referee by the American Physical Society.

    Babinec to coordinate Argonne's grid energy storage program

    Babinec to coordinate Argonne's grid energy storage program

    The U.S. Department of Energy's (DOE) Argonne National Laboratory has appointed Susan Babinec to drive a comprehensive strategy that expands Argonne's future grid vision to include a range of optimized energy storage capabilities. By integrating its deep resources in grid design and energy storage with national and industry needs, Argonne will provide innovative solutions for the future grid.


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    Sampling Guts of Live Moose to Understand How They Break Down Biomass

    Sampling Guts of Live Moose to Understand How They Break Down Biomass

    First-of-a-kind study advances understanding of microbial and viral communities involved in biomass breakdown.

    Fitting a Square Peg in a Round Hole: The Surprising Structure of Uranium Bound in Hematite

    Fitting a Square Peg in a Round Hole: The Surprising Structure of Uranium Bound in Hematite

    An atomic view of how toxic uranium binds to iron minerals in the environment enables better predictions of its behavior.

    How Injected Microbes Persist in Hydraulically Fractured Shale

    How Injected Microbes Persist in Hydraulically Fractured Shale

    Scientists reveal the importance of an amino acid that supplies energy and protection for microbial communities deep underground.

    Unique Interface and Unexpected Behavior Help Explain How Heavy Metals Act

    Unique Interface and Unexpected Behavior Help Explain How Heavy Metals Act

    Three types of water molecules form around a platinum-based ion, offering insights for waste processing and metal refining.

    To Grow or Not to Grow? That Is the Question for Plants

    To Grow or Not to Grow? That Is the Question for Plants

    Scientists show metabolic tradeoffs result from a specific change to the grow-defend balance.

    Forming the Ion that Made the Universe

    Forming the Ion that Made the Universe

    Research offers details on the chemistry of trihydrogen ion.

    Water: Lead, Follow, or Get Out of the Way

    Water: Lead, Follow, or Get Out of the Way

    Elegant theory shows how water helps separate ions involved in material synthesis and manufacturing.

    Seeing Coherent Patterns at the Microscopic Scale

    Seeing Coherent Patterns at the Microscopic Scale

    Review highlights insights into coherence, which could help overcome roadblocks in next-generation energy systems.

    A Simplified Way to Predict the Function of Microbial Communities

    A Simplified Way to Predict the Function of Microbial Communities

    A pioneering study offers an easier approach to study how microbes work and could help scientists advance models of the cycling of elements and nutrients in frequently flooded soils.

    Squeezed Quantum Dots Produce More Stable Light

    Squeezed Quantum Dots Produce More Stable Light

    Exploiting a strain-engineering approach could provide nanoscale light sources with a nonfluctuating emission wavelength for use in sensors, quantum communication, and imaging.


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