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    • 2016-08-15 20:30:15
    • Article ID: 659162

    Unveiled: Earth's Viral Diversity

    Environmental datasets help researchers double the number of microbial phyla known to be infected by viruses

    • Credit: Graphic by Zosia Rostomian, Berkeley Lab

      DOE JGI researchers utilized the largest collection of assembled metagenomic datasets from around the world to uncover over 125,000 partial and complete viral genomes, the majority of them infecting microbes.

    The number of microbes in, on, and around the planet – on the order of a nonillion, or 1030 – is estimated to outnumber the stars in the Milky Way. Microbes are known to play crucial roles in regulating carbon fixation, as well as maintaining global cycles involving nitrogen, sulfur, and phosphorus and other nutrients, but the majority of them remain uncultured and unknown. The U.S. Department of Energy (DOE) is targeting this “microbial dark matter” to better understand the planet’s microbial diversity and glean from nature lessons that can be applied toward energy and environmental challenges.

    Plumbing the Earth’s microbial diversity, though, requires learning more about the poorly-studied relationships between microbes and the viruses that infect them, viruses that impact the microbes’ abilities to regulate global cycles. Although the number of viruses is estimated to be at least two orders of magnitude more than the microbial cells on the planet, there are currently less than 2,200 sequenced DNA virus genomes, compared to the approximately 50,000 bacterial genomes, in sequence databases. In a study published online August 17, 2016 in Nature, researchers at the U.S. Department of Energy Joint Genome Institute (DOE JGI), a DOE Office of Science User Facility at Lawrence Berkeley National Laboratory, utilized the largest collection of assembled metagenomic datasets from around the world to uncover over 125,000 partial and complete viral genomes, the majority of them infecting microbes. This single effort increases the number of known viral genes by a factor of 16, and provides researchers with a unique resource of viral sequence information.

    “It is the first time that someone has looked systematically across all habitats and across such a large compendium of data,” said study senior author and DOE JGI Prokaryote Super Program head Nikos Kyrpides. “A key to uncover all these novel viruses was the sensitive computational approach we have developed along this work.”

    "A key to uncover novel viruses"

    That approach, explained first author and postdoctoral fellow David Paez-Espino, involved using a non-targeted metagenomic approach, referencing both isolate viruses and manually curated viral protein models, and what he described as “the largest and most diverse dataset to date.” The team analyzed over 5 trillion bases (Terabases or Tb) of sequence available in the DOE JGI’s Integrated Microbial Genomes with Microbiome Samples (IMG/M) system collected from 3,042 samples around the world from 10 different habitat types. Their efforts to sift through the veritable haystack of datasets yielded over 125,000 viral sequences containing 2.79 million proteins.

    The team matched viral sequences against multiple samples in multiple habitats. For example, one viral group they identified was found in 95 percent of all samples in the ocean’s twilight zone – a region located between 200 and 1,000 meters below the ocean surface where insufficient sunlight penetrates for microorganisms to perform photosynthesis.

    By analyzing a CRISPR-Cas system – an immune mechanism in bacteria that confers resistance to foreign genetic elements by incorporating short sequences from infecting viruses and phages – the team was able to generate a database of 3.5 million spacer sequences in IMG. These spacers, fragments of phage genetic sequences retained by the host, can then be used to explore viral and phage metagenomes for where the fragments may have originally come from. Also, using mainly this approach, the team computationally identified the host for nearly 10,000 viruses. “The majority of these connections were previously unknown, and include the identification of organisms serving as viral hosts from 16 prokaryotic phyla for which no viruses have previously been identified,” they reported.

    Beacons for CRISPR-Cas proteins

    Jan-Fang Cheng, head of the DOE JGI’s Functional Genomics group, said the work being done by Kyrpides’ group in identifying new viral sequences will help the Synthetic Biology group develop novel promoters that can work in many bacterial hosts. “We are constantly searching for regulatory DNA parts that will work across many different phyla, and that would allow us to build genes and pathways that can express in many different hosts.”

    Cheng also anticipated that the expanded viral sequence space generated by Kyrpides’ team will allow researchers to look for other genetic sequences known as proto-spacer adjacent motifs (PAMs). These sequences lie next to spacer sequencers in phages and are used as beacons by CRISPR-Cas proteins, triggering actions such as editing or regulating a gene. “People are looking for new PAM sequences and new Cas9s, and with this new information, if you can map the spacer sequence back to the same phage and align them and see what’s in common in neighboring sequences, then you could ID new PAM sequences.”

    “We believe that the finding of many large phages including the longest phage genome reported thus far points to the limitations of conventional virome enrichment and sequencing strategies which may bias the studies against the highly novel viruses with unusual properties”, said Natalia Ivanova, group lead in the Super Program and co-author of this study.

    “One of the most important aspects of this study is that we did not focus on a single habitat type. Instead, we explored the global virome and examined the flow of viruses across all ecosystems," said Kyrpides. "We have increased the number of viral sequences by 50x, and 99 percent of the virus families identified are not closely related to any previously sequenced virus. This provides an enormous amount of new data that would be studied in more detail in the years to come. We have more than doubled the number of microbial phyla that serve as hosts to viruses, and have created the first global viral distribution map. The amount of analysis and discoveries that we anticipate will follow this dataset cannot be overstated.”

    The work used resources at the National Energy Research Scientific Computing Center, a DOE Office of Science User Facility at Lawrence Berkeley National Laboratory.

    ***

    The U.S. Department of Energy Joint Genome Institute, a DOE Office of Science User Facility at Lawrence Berkeley National Laboratory, is committed to advancing genomics in support of DOE missions related to clean energy generation and environmental characterization and cleanup. DOE JGI, headquartered in Walnut Creek, Calif., provides integrated high-throughput sequencing and computational analysis that enable systems-based scientific approaches to these challenges. Follow @doe_jgi on Twitter.

    DOE’s Office of Science is the largest supporter of basic research in the physical sciences in the United States, and is working to address some of the most pressing challenges of our time. For more information, please visit science.energy.gov.

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    Hidden Giants in Forest Soils

    Viruses can infect the microbes residing in, on and around soils, impacting their ability to regulate these global cycles. In Nature Communications, giant virus genomes have been discovered for the first time in a forest soil ecosystem by researchers from the DOE Joint Genome Institute and the University of Massachusetts-Amherst.

    Scientists Produce 3-D Chemical Maps of Single Bacteria

    Scientists at the National Synchrotron Light Source II (NSLS-II)--a U.S. Department of Energy (DOE) Office of Science User Facility at DOE's Brookhaven National Laboratory--have used ultrabright x-rays to image single bacteria with higher spatial resolution than ever before. Their work, published in Scientific Reports, demonstrates an x-ray imaging technique, called x-ray fluorescence microscopy (XRF), as an effective approach to produce 3-D images of small biological samples.

    Making X-ray Microscopy 10 Times Faster

    Microscopes make the invisible visible. And compared to conventional light microscopes, transmission x-ray microscopes (TXM) can see into samples with much higher resolution, revealing extraordinary details. Researchers across a wide range of scientific fields use TXM to see the structural and chemical makeup of their samples--everything from biological cells to energy storage materials.

    Microbes Eat the Same in Labs and the Desert

    Analyses of natural communities forming soil crusts agree with laboratory studies of isolated microbe-metabolite relationships.

    Self-Sensing Materials Are Here

    Oak Ridge National Laboratory researchers invented a way to make a nanomaterial-embedded composite that is stronger than other fiber-reinforced composites and imbued with a new capability--the ability to monitor its own structural health.

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    Opening Access to Explore the Synthetic Chemistry of Neptunium

    New, easily prepared starting material opens access to learning more about a difficult-to-control element in nuclear waste.

    Symbiosis a Driver of Truffle Diversity

    Truffles are thought of as dining delicacies but they play an important role in soil ecosystem services as the fruiting bodies of the ectomycorrhizal (ECM) fungal symbionts residing on host plant roots. An international team sought insights into the ECM lifestyle of truffle-forming species through a comparative analysis of eight fungal genomes.

    Climate Simulations Project Wetter, Windier Hurricanes

    New supercomputer simulations by climate scientists at the Department of Energy's Lawrence Berkeley National Laboratory (Berkeley Lab) have shown that climate change intensified the amount of rainfall in recent hurricanes such as Katrina, Irma, and Maria by 5 to 10 percent. They further found that if those hurricanes were to occur in a future world that is warmer than present, those storms would have even more rainfall and stronger winds.

    Tiny Titanium Barrier Halts Big Problem in Fuel-Producing Solar Cells

    New design coats molecular components and dramatically improves stability under tough, oxidizing conditions.


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    Seven ORNL researchers named 2019 INCITE award winners

    Seven researchers from the Department of Energy's Oak Ridge National Laboratory have been chosen by the Innovative and Novel Computational Impact on Theory and Experiment, also known as INCITE, program to lead scientific investigations that require the nation's most powerful computers. The ORNL-based projects span a broad range of the scientific spectrum and represent the potential of high-performance computing in ensuring America's scientific competitiveness and energy security.

    DOE Laboratories Win Gordon Bell Prize

    Two U.S. Department of Energy (DOE) National Laboratories were recently awarded the 2018 Association for Computing Machinery's (ACM's) Gordon Bell Prize.

    Department of Energy Announces 32 R&D 100 Award Winners

    DOE researchers have won 32 of the R&D 100 awards given out this year by R&D Magazine. The annual awards are given in recognition of exceptional new products or processes that were developed and introduced into the marketplace during the previous year.

    Jefferson Lab Shares 2018 R&D 100 Award for Cancer Treatment Monitoring System

    The OARtrac(r) system, built by RadiaDyne and including technologies developed by scientists at the U.S. Department of Energy's Thomas Jefferson National Accelerator Facility, has been awarded a 2018 R&D 100 Award by R&D Magazine.

    Four Argonne Technologies Receive 2018 R&D 100 Awards

    Four Argonne research projects have earned R&D 100 Awards, long considered the "Oscars" of scientific innovation.

    Argonne's Min Si receives early career award from IEEE Computer Society

    Argonne's Min Si wins Award for Excellence for Early Career Researchers in High Performance Computing through the Institute of Electrical and Electronics Engineers.

    Jefferson Lab Director Appointed to Distinguished Professorship

    Stuart Henderson, director of the Department of Energy's Thomas Jefferson National Accelerator Facility, has been appointed the Governor's Distinguished CEBAF professor at Old Dominion University. The position is supported by the Commonwealth of Virginia and is named for the Continuous Electron Beam Accelerator Facility, which is the main research facility located at Jefferson Lab.

    DOE issues call for HPC for Energy Innovation proposals

    The U.S. Department of Energy's (DOE) High Performance Computing for Energy Innovation (HPC4EI) Initiative today issued its first joint solicitation for the High Performance Computing for Manufacturing Program (HPC4Mfg) and the High Performance Computing for Materials Program (HPC4Mtls).

    DOE funding advances project to turn captured CO2 into key chemicals

    The U.S. Department of Energy has selected Southern Research for an award of up to $1.5 million to advance technology for carbon dioxide utilization.

    Sierra Reaches Higher Altitudes, Takes Number Two Spot on List of Fastest Supercomputers

    Sierra, Lawrence Livermore National Laboratory's newest supercomputer, rose to second place on the list of the world's fastest computing systems, TOP500 List representatives announced Monday at the International Conference for High Performance Computing, Networking, Storage and Analysis conference (SC18) in Dallas.


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    Microbes Eat the Same in Labs and the Desert

    Analyses of natural communities forming soil crusts agree with laboratory studies of isolated microbe-metabolite relationships.

    Diverse Biofeedstocks Have High Ethanol Yields and Offer Biorefineries Flexibility

    Evidence suggests that biorefineries can accept various feedstocks without negatively impacting the amount of ethanol produced per acre.

    Opening Access to Explore the Synthetic Chemistry of Neptunium

    New, easily prepared starting material opens access to learning more about a difficult-to-control element in nuclear waste.

    Tiny Titanium Barrier Halts Big Problem in Fuel-Producing Solar Cells

    New design coats molecular components and dramatically improves stability under tough, oxidizing conditions.

    Turning Wood Scraps into Tape

    A new chemical process converts a component of wasted wood pulp and other biomass into high-value pressure-sensitive adhesives.

    Very Heavy Elements Deliver More Electrons

    Scientists revise understanding of the limits of bonding for very electron-rich heavy elements.

    Probing Water's "No-Man's Land" Temperature Region

    Measuring the physical properties of water at previously unexplored temperatures offers insights into one of the world's essential liquids.

    Novel Soil Bacteria with Unusual Genes Synthesize Unique Antibiotic Precursors

    A large-scale soil project uncovered genetic information from bacteria with the capacity to make specialized molecules that could lead to new pharmaceuticals.

    Warmer Temperatures Lengthen Growing Season, Increase Plants' Vulnerability to Frost

    Experimental warming treatments show how peatland forests may respond to future environmental change.

    Rising Stars Seek to Learn from the Master: Mother Nature

    A trio of scientists was recognized for their early career successes in uncovering how microbes produce fuel, insights that could change our energy portfolio


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