Doe Science news source
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.
  • 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.

X
X
X
  • Filters

  • × Clear Filters

Self-Assembling 3D Battery Would Charge in Seconds

A cross-campus collaboration led by Ulrich Wiesner, professor of engineering at Cornell University, has resulted in a novel energy storage device architecture that has the potential for lightning-quick charges for electronic devices.

Understanding the Generation of Light-Induced Electrical Current in Atomically Thin Nanomaterials

Scientists added an imaging capability to Brookhaven Lab's Center for Functional Nanomaterials that could provide the optoelectronic information needed to improve the performance of devices for power generation, communications, data storage, and lighting.

Diamond 'Spin-Off' Tech Could Lead to Low-Cost Medical Imaging and Drug Discovery Tools

An international team led by scientists at Berkeley Lab and UC Berkeley discovered how to exploit defects in nanoscale and microscale diamonds and potentially enhance the sensitivity of magnetic resonance imaging and nuclear magnetic resonance systems while eliminating the need for their costly and bulky superconducting magnets.

PROSPECTing For Antineutrinos

The Precision Reactor Oscillation and Spectrum Experiment (PROSPECT) has completed installation of a novel antineutrino detector that will probe the possible existence of a new form of matter - sterile neutrinos.

How to Cope with Cases of Mistaken Identity: MINERvA's Tale of Pions and Neutrinos

Neutral pion production is a major character in a story of mistaken identity worthy of an Agatha Christie novel.

Perfecting the Noise-Canceling Neutrino Detector

MicroBooNE neutrino experiment cuts through the noise, clearing the way for signals made by the hard-to-detect particle.

Supersonic Waves May Help Electronics Beat the Heat

Researchers at the Department of Energy's Oak Ridge National Laboratory made the first observations of waves of atomic rearrangements, known as phasons, propagating supersonically through a vibrating crystal lattice--a discovery that may dramatically improve heat transport in insulators and enable new strategies for heat management in future electronics devices.

Riding Bacterium to the Bank

Jet fuel, pantyhose and plastic soda bottles are all products currently derived from petroleum. Sandia National Laboratories scientists have demonstrated a new technology based on bioengineered bacteria that makes it feasible to produce all three from renewable plant sources.

Flexible, Highly Efficient Multimodal Energy Harvesting

A piezoelectric ceramic foam supported by a flexible polymer support provides a 10-fold increase in the ability to harvest mechanical and thermal energy over standard piezo composites, according to Penn State researchers.

PNNL Successfully Vitrifies Three Gallons of Radioactive Tank Waste

News Release RICHLAND, Wash. -- In a first-of-its-kind demonstration, researchers at the Department of Energy's Pacific Northwest National Laboratory have vitrified low-activity waste from underground storage tanks at Hanford, immobilizing the radioactive and chemical materials within a durable glass waste form.Approximately three gallons of low-activity Hanford tank waste were vitrified at PNNL's Radiochemical Processing Laboratory in April.


  • Filters

  • × Clear Filters

Power to the People

The University of Utah College of Engineering has received a $2 million grant to create a laboratory and develop new technology for communities with backup power sources, known as microgrids, so they can quickly and more securely operate in the event of a massive power outage due to a natural disaster or cyberattack.

The U. S. Department of Energy Announces $34 Million for Small Business Research and Development Grants

U.S. Energy Secretary Rick Perry announced that the Department of Energy will award 219 grants totaling $34 million to 183 small businesses in 41 states. Funded through DOE's Small Business Innovation Research (SBIR) and Small Business Technology Transfer (STTR) programs, today's selections are for Phase I research and development.

Raising the Heat to Lower the Cost of Solar Energy

Sandia National Laboratories will receive $10.5 million from the Department of Energy to research and design a cheaper and more efficient solar energy system.The work focuses on refining a specific type of utility-scale solar energy technology that uses mirrors to reflect and concentrate sunlight onto a receiver on a tower.

Solar Turbines, Inc. Selects Penn State to Establish Center of Excellence in Gas Turbines

After completing an extensive evaluation of institutions of higher learning in the United States and Europe, Solar Turbines Incorporated has chosen Penn State as a university partner to establish a center of excellence in gas turbines. The center involves numerous faculty across Penn State's College of Engineering.

ORNL Facility Receives American Nuclear Society's Historic Landmark Designation

The American Nuclear Society has designated the Radiochemical Engineering Development Center at the Department of Energy's Oak Ridge National Laboratory an ANS Nuclear Historic Landmark, recognizing more than 50 years of isotope production and nuclear fuel cycle research.

Steven Cowley named director of DOE's Princeton Plasma Physics Laboratory

Steven Cowley, a theoretical physicist and international authority on fusion energy, has been named director of the U.S. Department of Energy's (DOE) Princeton Plasma Physics Laboratory (PPPL), effective July 1.

Scientists Turn X-ray Laser Into World's Fastest Water Heater

Scientists have used a powerful X-ray laser at the Department of Energy's SLAC National Accelerator Laboratory to heat water from room temperature to 100,000 degrees Celsius in less than a tenth of a picosecond, or millionth of a millionth of a second.

PNNL Part of a New National Center for Near-Atomic Resolution of Biological Molecules

A collaboration between the Pacific Northwest National Laboratory and Oregon Health & Science University has been chosen as a national center for a Nobel Prize-winning method of imaging, cryo-electron microscopy, that is revolutionizing structural biology.

SLAC Will Open One of Three NIH National Service Centers for Cryo-Electron Microscopy

The National Institutes of Health announced today that it will establish a national service and training center for cryogenic electron microscopy research at the Department of Energy's SLAC National Accelerator Laboratory.

Planck Collaboration Wins 2018 Gruber Cosmology Prize

The Planck Team--including researchers in Lawrence Berkeley National Laboratory's (Berkeley Lab's) Computational Research and Physics divisions--have been awarded the 2018 Gruber Cosmology Prize.


  • Filters

  • × Clear Filters

The Secret to Measuring an Antineutrino's Energy

Scientists are developing better models that describe both neutrino and antineutrino data, which can offer insights into the nature of the universe.

How to Cope with Cases of Mistaken Identity: MINERvA's Tale of Pions and Neutrinos

Neutral pion production is a major character in a story of mistaken identity worthy of an Agatha Christie novel.

Perfecting the Noise-Canceling Neutrino Detector

MicroBooNE neutrino experiment cuts through the noise, clearing the way for signals made by the hard-to-detect particle.

Keeping Tabs on Polysulfides in Batteries

Optimizing lithium-sulfur battery electrolytes for long life.

Huge "Thermometer" Takes Temperatures of Tiny Samples

New spectroscopic technique measures heat in itty-bitty volumes that could reveal insights for electronics and energy technology.

Water, Water, Everywhere, but How Does It Flow?

Scientists use new X-ray technique to see how water moves at the molecular level.

Magnetized Plasmas That "Twist Light" Can Produce Powerful Microscopes and More

A non-twisting laser beam moving through magnetized plasma turns into an optical vortex that traps, rotates, and controls microscopic particles, opening new frontiers in imaging.

Whistling While You Work: Fusion Scientists Find Inspiration in Atmospheric Whistles

Just like lightning, fusion plasmas contain odd electromagnetic whistler waves that could control destructive electrons in fusion reactors.

Zero Tolerance in Tokamaks: Eliminating Small Instabilities Before They Become Disruptions

Energetic ions and beam heating cause or calm instabilities, depending on the tokamak's magnetic field.

MURR Becomes First Reactor Facility to Join DOE's Isotope Program

DOE and MURR partner to ensure scientists have access to essential research isotopes.


Spotlight

Monday May 07, 2018, 10:30 AM

Introducing Graduate Students Across the Globe to Photon Science

Brookhaven National Laboratory

Wednesday May 02, 2018, 04:05 PM

Students from Massachusetts and Washington Win DOE's 28th National Science Bowl(r)

Department of Energy, Office of Science

Thursday April 12, 2018, 07:05 PM

The Race for Young Scientific Minds

Argonne National Laboratory

Wednesday March 14, 2018, 02:05 PM

Q&A: Al Ashley Reflects on His Efforts to Diversify SLAC and Beyond

SLAC National Accelerator Laboratory

Thursday February 15, 2018, 12:05 PM

Insights on Innovation in Energy, Humanitarian Aid Highlight UVA Darden's Net Impact Week

University of Virginia Darden School of Business

Friday February 09, 2018, 11:05 AM

Ivy League Graduate, Writer and Activist with Dyslexia Visits CSUCI to Reframe the Concept of Learning Disabilities

California State University, Channel Islands

Wednesday January 17, 2018, 12:05 PM

Photographer Adam Nadel Selected as Fermilab's New Artist-in-Residence for 2018

Fermi National Accelerator Laboratory (Fermilab)

Wednesday January 17, 2018, 12:05 PM

Fermilab Computing Partners with Argonne, Local Schools for Hour of Code

Fermi National Accelerator Laboratory (Fermilab)

Wednesday December 20, 2017, 01:05 PM

Q&A: Sam Webb Teaches X-Ray Science from a Remote Classroom

SLAC National Accelerator Laboratory

Monday December 18, 2017, 01:05 PM

The Future of Today's Electric Power Systems

Rensselaer Polytechnic Institute (RPI)

Monday December 18, 2017, 12:05 PM

Supporting the Development of Offshore Wind Power Plants

Rensselaer Polytechnic Institute (RPI)

Tuesday October 03, 2017, 01:05 PM

Stairway to Science

Argonne National Laboratory

Thursday September 28, 2017, 12:05 PM

After-School Energy Rush

Argonne National Laboratory

Thursday September 28, 2017, 10:05 AM

Bringing Diversity Into Computational Science Through Student Outreach

Brookhaven National Laboratory

Thursday September 21, 2017, 03:05 PM

From Science to Finance: SLAC Summer Interns Forge New Paths in STEM

SLAC National Accelerator Laboratory

Thursday September 07, 2017, 02:05 PM

Students Discuss 'Cosmic Opportunities' at 45th Annual SLAC Summer Institute

SLAC National Accelerator Laboratory

Thursday August 31, 2017, 05:05 PM

Binghamton University Opens $70 Million Smart Energy Building

Binghamton University, State University of New York

Wednesday August 23, 2017, 05:05 PM

Widening Horizons for High Schoolers with Code

Argonne National Laboratory

Saturday May 20, 2017, 12:05 PM

Rensselaer Polytechnic Institute Graduates Urged to Embrace Change at 211th Commencement

Rensselaer Polytechnic Institute (RPI)

Monday May 15, 2017, 01:05 PM

ORNL, University of Tennessee Launch New Doctoral Program in Data Science

Oak Ridge National Laboratory

Friday April 07, 2017, 11:05 AM

Champions in Science: Profile of Jonathan Kirzner

Department of Energy, Office of Science

Wednesday April 05, 2017, 12:05 PM

High-Schooler Solves College-Level Security Puzzle From Argonne, Sparks Interest in Career

Argonne National Laboratory

Tuesday March 28, 2017, 12:05 PM

Champions in Science: Profile of Jenica Jacobi

Department of Energy, Office of Science

Friday March 24, 2017, 10:40 AM

Great Neck South High School Wins Regional Science Bowl at Brookhaven Lab

Brookhaven National Laboratory

Wednesday February 15, 2017, 04:05 PM

Middle Schoolers Test Their Knowledge at Science Bowl Competition

Argonne National Laboratory

Friday January 27, 2017, 04:00 PM

Haslam Visits ORNL to Highlight State's Role in Discovering Tennessine

Oak Ridge National Laboratory

Tuesday November 08, 2016, 12:05 PM

Internship Program Helps Foster Development of Future Nuclear Scientists

Oak Ridge National Laboratory

Friday May 13, 2016, 04:05 PM

More Than 12,000 Explore Jefferson Lab During April 30 Open House

Thomas Jefferson National Accelerator Facility

Monday April 25, 2016, 05:05 PM

Giving Back to National Science Bowl

Ames Laboratory

Friday March 25, 2016, 12:05 PM

NMSU Undergrad Tackles 3D Particle Scattering Animations After Receiving JSA Research Assistantship

Thomas Jefferson National Accelerator Facility

Tuesday February 02, 2016, 10:05 AM

Shannon Greco: A Self-Described "STEM Education Zealot"

Princeton Plasma Physics Laboratory

Monday November 16, 2015, 04:05 PM

Rare Earths for Life: An 85th Birthday Visit with Mr. Rare Earth

Ames Laboratory

Tuesday October 20, 2015, 01:05 PM

Meet Robert Palomino: 'Give Everything a Shot!'

Brookhaven National Laboratory

Tuesday April 22, 2014, 11:30 AM

University of Utah Makes Solar Accessible

University of Utah

Wednesday March 06, 2013, 03:40 PM

Student Innovator at Rensselaer Polytechnic Institute Seeks Brighter, Smarter, and More Efficient LEDs

Rensselaer Polytechnic Institute (RPI)

Friday November 16, 2012, 10:00 AM

Texas Tech Energy Commerce Students, Community Light up Tent City

Texas Tech University

Wednesday November 23, 2011, 10:45 AM

Don't Get 'Frosted' Over Heating Your Home This Winter

Temple University

Wednesday July 06, 2011, 06:00 PM

New Research Center To Tackle Critical Challenges Related to Aircraft Design, Wind Energy, Smart Buildings

Rensselaer Polytechnic Institute (RPI)

Friday April 22, 2011, 09:00 AM

First Polymer Solar-Thermal Device Heats Home, Saves Money

Wake Forest University

Friday April 15, 2011, 12:25 PM

Like Superman, American University Will Get Its Energy from the Sun

American University

Thursday February 10, 2011, 05:00 PM

ARRA Grant to Help Fund Seminary Building Green Roof

University of Chicago

Tuesday December 07, 2010, 05:00 PM

UC San Diego Installing 2.8 Megawatt Fuel Cell to Anchor Energy Innovation Park

University of California San Diego

Monday November 01, 2010, 12:50 PM

Rensselaer Smart Lighting Engineering Research Center Announces First Deployment of New Technology on Campus

Rensselaer Polytechnic Institute (RPI)

Friday September 10, 2010, 12:40 PM

Ithaca College Will Host Regional Clean Energy Summit

Ithaca College

Tuesday July 27, 2010, 10:30 AM

Texas Governor Announces $8.4 Million Award to Create Renewable Energy Institute

Texas Tech University

Friday May 07, 2010, 04:20 PM

Creighton University to Offer New Alternative Energy Program

Creighton University

Wednesday May 05, 2010, 09:30 AM

National Engineering Program Seeks Subject Matter Experts in Energy

JETS Junior Engineering Technical Society

Wednesday April 21, 2010, 12:30 PM

Students Using Solar Power To Create Sustainable Solutions for Haiti, Peru

Rensselaer Polytechnic Institute (RPI)





Showing results

0-4 Of 2215