- 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.
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.
MORE NEWS FROM
Lawrence Berkeley National Laboratory
comments 
commenting policy
Finding Gene Neighbors Leads to New Protein Functions
As scientists have developed new technologies for gene sequencing, the availability of sequenced genes has grown exponentially, but scientists' ability to decipher the functions encoded in these sequences has not kept pace. In this study, researchers working with green algae discovered that physically clustered genes in eukaryotic genomes can be maintained over hundreds of millions of years. This phenomenon can help predict function.
Mapping Performance Variations to See How Lithium-Metal Batteries Fail
Scientists have identified the primary cause of failure in a state-of-the-art lithium-metal battery, of interest for long-range electric vehicles: electrolyte depletion.
Found: A fast and accurate way to optimize fusion energy devices
PPPL develops a model once thought to be impossible for delivering radio waves to heat tokamak plasmas.
To Cool Tomorrow's Buildings, Power Sector Must Grow
New study projects electricity demand tied to cooling U.S. buildings will grow as peak temperatures rise, alongside the need for an expanded power sector.
For Better Predictions, Researchers Evaluate Tropical Cyclone Simulation in the Energy Exascale Earth System Model
Infrastructure planning requires accurately predicting how tropical cyclones respond to environmental changes. To make those predictions, researchers use Earth system models. In this research, scientists analyzed tropical cyclones simulated by the Department of Energy's Energy Exascale Earth System Model (E3SM). They found that high resolution is critical to simulating tropical cyclones and their interactions with the ocean.
Experts' Predictions for Future Wind Energy Costs Drop Significantly
Technology and commercial advancements are expected to continue to drive down the cost of wind energy, according to a survey led by Berkeley Lab of the world's foremost wind power experts. Experts anticipate cost reductions of 17%-35% by 2035 and 37%-49% by 2050, driven by bigger and more efficient turbines, lower capital and operating costs, and other advancements.
Little swirling mysteries: New research uncovers dynamics of ultrasmall, ultrafast groups of atoms
Exploring and manipulating the behavior of polar vortices in material may lead to new technology for faster data transfer and storage. Researchers used the Advanced Photon Source at Argonne and the Linac Coherent Light Source at SLAC to learn more.
From Smoky Skies to a Green Horizon: Scientists Convert Fire-Risk Wood into Biofuel
Reliance on petroleum fuels and raging wildfires: Two separate, large-scale challenges that could be addressed by one scientific breakthrough. Researchers from two national laboratories have collaborated to develop a streamlined and efficient process for converting woody plant matter like forest overgrowth and agricultural waste - material that is currently burned either intentionally or unintentionally - into liquid biofuel.
Suppression of COVID-19 Waves Reflects Time-Dependent Social Activity, Not Herd Immunity
Scientists developed a new mathematical model for predicting how COVID-19 spreads, accounting for individuals' varying biological susceptibility and levels of social activity, which naturally change over time.
Plasma device designed for consumers can quickly disinfect surfaces
The COVID-19 pandemic has cast a harsh light on the urgent need for quick and easy techniques to sanitize and disinfect everyday high-touch objects such as doorknobs, pens, pencils, and personal protective gear worn to keep infections from spreading.
Department of Energy to Provide $2 Million for Traineeship in Isotope R&D and Production
Today, the U.S. Department of Energy (DOE) announced up to $2 million to establish a traineeship program to advance workforce development in the field of isotope production, processing, and associated research, with preference to minority serving institutions.
Department of Energy to Provide $10 Million for Research on Data Reduction for Science
Today, the U.S. Department of Energy (DOE) announced $10 million for foundational research to address the challenges of managing and processing the increasingly massive data sets produced by today's scientific instruments, facilities, and supercomputers in order to facilitate more efficient analysis.
ORNL's Honeycutt, Horvath Named SME 2021 Outstanding Young Manufacturing Engineers
Andrew Honeycutt and Nick Horvath, machine tool researchers at Oak Ridge National Laboratory, have been selected to receive the 2021 Geoffrey Boothroyd Outstanding Young Manufacturing Engineer Award from SME, the professional manufacturing engineering association.
Department of Energy to Provide $25 Million toward Development of a Quantum Internet
Today the U.S. Department of Energy (DOE) announced a plan to provide $25 million for basic research toward the development of a quantum internet.
Media Advisory - U.S. Secretary of Energy and Other Leading Experts Talk Preparation for the Effects of Climate Change
The escalating effects of climate change are evident across our country, from the damaging 2020 western wildfire season to February's southern deep freeze. The need has never been greater for a national strategy that combines the long-term goal of a 100% clean energy future with immediate, science-driven actions to help all communities overcome the effects of climate change.
Department of Energy to Provide $5 Million to Advance Workforce Development for High Energy Physics Instrumentation
Today, the U.S. Department of Energy (DOE) announced plans to provide $5 million to support a DOE traineeship program to address workforce needs in high energy physics instrumentation.
DOE Awards $110 Million to Small Businesses Pursuing Scientific, Clean Energy, and Climate Solutions
The U.S. Department of Energy (DOE) today announced awards totaling $110 million for diverse small businesses working on scientific, clean energy, and climate solutions for the American people.
Teachers Invited to Participate in Virtual Science Activities Night
Elementary and middle school teachers are invited to register now to participate in the annual Virginia Region II Teacher Night hosted by the U.S. Department of Energy's Thomas Jefferson National Accelerator Facility on April 14, 2021. The fully virtual event will allow educators to see demonstrations of new methods for teaching physical science concepts and safely meet and interact with their colleagues, all while they pick up one recertification point from the comfort of their own homes. Advance registration is required, and the event is open to all upper elementary and middle school teachers of physical science.
DOE Announces $29 Million for Ultramodern Data Analysis Tools
The U.S. Department of Energy (DOE) today announced $29 million to develop new tools to analyze massive amounts of scientific information, including artificial intelligence, machine learning, and advanced algorithms.
Argonne's 2021 Maria Goeppert Mayer Fellows bring new energy, promise to their fields
The Department of Energy's Argonne National Laboratory is proud to welcome five new FY21 Maria Goeppert Mayer Fellows to campus, each chosen for their incredible promise in their respective fields.
Harvesting Energy from Light using Bio-inspired Artificial Cells
Scientists designed and connected two different artificial cells to each other to produce molecules called ATP (adenosine triphosphate).
Engineering Living Scaffolds for Building Materials
Bone and mollusk shells are composite systems that combine living cells and inorganic components. This allows them to regenerate and change structure while also being very strong and durable. Borrowing from this amazing complexity, researchers have been exploring a new class of materials called engineered living materials (ELMs).
Excavating Quantum Information Buried in Noise
Researchers developed two new methods to assess and remove error in how scientists measure quantum systems. By reducing quantum "noise" - uncertainty inherent to quantum processes - these new methods improve accuracy and precision.
How Electrons Move in a Catastrophe
Lanthanum strontium manganite (LSMO) is a widely applicable material, from magnetic tunnel junctions to solid oxide fuel cells. However, when it gets thin, its behavior changes for the worse. The reason why was not known. Now, using two theoretical methods, a team determined what happens.
When Ions and Molecules Cluster
How an ion behaves when isolated within an analytical instrument can differ from how it behaves in the environment. Now, Xue-Bin Wang at Pacific Northwest National Laboratory devised a way to bring ions and molecules together in clusters to better discover their properties and predict their behavior.
Tune in to Tetrahedral Superstructures
Shape affects how the particles fit together and, in turn, the resulting material. For the first time, a team observed the self-assembly of nanoparticles with tetrahedral shapes.
Tracing Interstellar Dust Back to the Solar System's Formation
This study is the first to confirm dust particles pre-dating the formation of our solar system. Further study of these materials will enable a deeper understanding of the processes that formed and have since altered them.
Investigating Materials that Can Go the Distance in Fusion Reactors
Future fusion reactors will require materials that can withstand extreme operating conditions, including being bombarded by high-energy neutrons at high temperatures. Scientists recently irradiated titanium diboride (TiB2) in the High Flux Isotope Reactor (HFIR) to better understand the effects of fusion neutrons on performance.
Better 3-D Imaging of Tumors in the Breast with Less Radiation
In breast cancer screening, an imaging technique based on nuclear medicine is currently being used as a successful secondary screening tool alongside mammography to improve the accuracy of the diagnosis. Now, a team is hoping to improve this imaging technique.
Microbes are Metabolic Specialists
Scientists can use genetic information to measure if microbes in the environment can perform specific ecological roles. Researchers recently analyzed the genomes of over 6,000 microbial species.
Spotlight
Graduate students gather virtually for summer school at PPPL
Princeton Plasma Physics Laboratory
Virtual internships for physics students present challenges, build community
Princeton Plasma Physics Laboratory
Blocking the COVID-19 Virus's Exit Strategy
Brookhaven National Laboratory
From Nashville to New Hampshire, PPPL's student interns do research, attend classes and socialize from their home computers
Princeton Plasma Physics Laboratory
Graduate student at PPPL Ian Ochs wins top Princeton University fellowship
Princeton Plasma Physics Laboratory
Chicago Public School students go beyond coding and explore artificial intelligence with Argonne National Laboratory
Argonne National Laboratory
Barbara Garcia: A first-generation college student spends summer doing research at PPPL
Princeton Plasma Physics Laboratory
Argonne organization's scholarship fund blazes STEM pathway
Argonne National Laboratory
Brookhaven Lab, Suffolk Girl Scouts Launch Patch Program
Brookhaven National Laboratory
From an acoustic levitator to a "Neutron Bloodhound" robot, hands-on research inspires PPPL's summer interns
Princeton Plasma Physics Laboratory
Brookhaven Lab Celebrates the Bright Future of its 2019 Interns
Brookhaven National Laboratory
PPPL apprenticeship program offers young people chance to earn while they learn high-tech careers
Princeton Plasma Physics Laboratory
JSA Awards Graduate Fellowships for Research at Jefferson Lab
Thomas Jefferson National Accelerator Facility
ILSAMP Symposium showcases benefits for diverse students, STEM pipeline
Argonne National Laboratory
Integrating Scientific Computing into Science Curricula
Brookhaven National Laboratory
Students from Minnesota and Massachusetts Win DOE's 29th National Science Bowl(r)
Department of Energy, Office of Science
DOE's Science Graduate Student Research Program Selects 70 Students to Pursue Research at DOE Laboratories
Department of Energy, Office of Science
Young Women's Conference in STEM seeks to change the statistics one girl at a time
Princeton Plasma Physics Laboratory
Students team with Argonne scientists and engineers to learn about STEM careers
Argonne National Laboratory
Lynbrook High wins 2019 SLAC Regional Science Bowl competition
SLAC National Accelerator Laboratory
Equipping the next generation for a technological revolution
Argonne National Laboratory
Chemistry intern inspired by Argonne's real-world science
Argonne National Laboratory
Argonne intern streamlines the beamline
Argonne National Laboratory
Research on Light-Matter Interaction Could Lead to Improved Electronic and Optoelectronic Devices
Rensselaer Polytechnic Institute (RPI)
Innovating Our Energy Future
Oregon State University, College of Engineering
Physics graduate student takes her thesis research to a Department of Energy national lab
University of Alabama at Birmingham
"Model" students enjoy Argonne campus life
Argonne National Laboratory
Writing Code for a More Skilled and Diverse STEM Workforce
Brookhaven National Laboratory
New graduate student summer school launches at Princeton Plasma Physics Laboratory
Princeton Plasma Physics Laboratory
The Gridlock State
California State University (CSU) Chancellor's Office
Meet Jasmine Hatcher and Trishelle Copeland-Johnson
Brookhaven National Laboratory
Argonne hosts Modeling, Experimentation and Validation Summer School
Argonne National Laboratory
Undergraduate Students Extoll Benefits of National Laboratory Research Internships in Fusion and Plasma Science
Princeton Plasma Physics Laboratory
Students affected by Hurricane Maria bring their research to SLAC
SLAC National Accelerator Laboratory
Brookhaven Lab Pays Tribute to 2018 Summer Interns
Brookhaven National Laboratory
CSUMB Selected to Host Architecture at Zero Competition in 2019
California State University, Monterey Bay
From Hurricane Katrina Victim to Presidential Awardee: A SUNO Professor's Award-Winning Mentoring Efforts
Brookhaven National Laboratory
Department of Energy Invests $64 Million in Advanced Nuclear Technology
Rensselaer Polytechnic Institute (RPI)
Professor Miao Yu Named the Priti and Mukesh Chatter '82 Career Development Professor
Rensselaer Polytechnic Institute (RPI)
2018 RHIC & AGS Annual Users' Meeting: 'Illuminating the QCD Landscape'
Brookhaven National Laboratory
High-School Students Studying Carbon-Based Nanomaterials for Cancer Drug Delivery Visit Brookhaven Lab's Nanocenter
Brookhaven National Laboratory
Argonne welcomes The Martian author Andy Weir
Argonne National Laboratory
UW Professor and Clean Energy Institute Director Daniel Schwartz Wins Highest U.S. Award for STEM Mentors
University of Washington
Creating STEM Knowledge and Innovations to Solve Global Issues Like Water, Food, and Energy
Illinois Mathematics and Science Academy (IMSA)
Professor Emily Liu Receives $1.8 Million DoE Award for Solar Power Systems Research
Rensselaer Polytechnic Institute (RPI)
Celebrating 40 years of empowerment in science
Argonne National Laboratory
Showing results
0-6 Of 2215