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.
  • 2017-10-11 11:00:23
  • Article ID: 682705

Tracking the Viral Parasites of Giant Viruses over Time

Virophage database doubles with discovery in freshwater lakes datasets

  • Credit: Image courtesy of Trina McMahon

    Using metagenome data sets collected over several years in northern freshwater lakes, a team led by researchers at The Ohio State University and the U.S. Department of Energy Joint Genome Institute (DOE JGI) uncovered 25 novel sequences of virophages. Reported October 11, 2017 in Nature Communications, the identification of these novel sequences effectively doubles the number of virophages known since their discovery a decade ago. The team used data from a 3-year metagenomic time series collected from Trout Bog Lake, a small acidic bog in Wisconsin by collaborators at the University of Wisconsin-Madison.

In freshwater lakes, microbes regulate the flow of carbon and determine if the bodies of water serve as carbon sinks or carbon sources. Algae and cyanobacteria in particular can trap and use carbon, but their capacity to do so may be impacted by viruses. Viruses exist amidst all bacteria, usually in a 10-fold excess, and are made up of various sizes ranging from giant viruses, to  much smaller viruses known as virophages (which live in giant viruses and use their machinery to replicate and spread.) Virophages can change the way a giant virus interacts with its host eukaryotic cell. For example, if algae are co-infected by a virophage and giant virus, the virophage limits the giant virus’ ability to replicate efficiently. This reduces the impact a giant virus has on the diversion of nutrients, allowing the host algae to multiply, which could lead to more frequent algal blooms.

Using metagenome data sets collected over several years in northern freshwater lakes, a team led by researchers at The Ohio State University and the U.S. Department of Energy Joint Genome Institute (DOE JGI), a DOE Office of Science User Facility, uncovered 25 novel sequences of virophages. Reported October 11, 2017 in Nature Communications, the identification of these novel sequences effectively doubles the number of virophages known since their discovery a decade ago.

“Usually metagenome data sets are one-offs,” said DOE JGI scientist and first author Simon Roux. “People had started to see virophages in metagenomes, but no one had a long time-series until now. Was it here once? Always? We never really knew this, but it’s a critical piece of information to understand their importance.”

The work stemmed from a Community Science Program (CSP) proposal involving northern freshwater lakes by KT (Trina) McMahon of the University of Wisconsin-Madison. Samples of microbial communities in Lake Mendota and Trout Bog Lake were regularly collected over several years as part of the NSF-funded North Temperate Lakes Long Term Ecological Research (NTL-LTER) project of the National Science Foundation. Sequencing and analyzing these metagenomes from the 3-year and the 5-year time-series is allowing researchers to identify the community members, determine their metabolic pathways, and follow changes in communities over several years.

Beyond looking at the microbial communities, McMahon and Rex Malmstrom, head of the DOE JGI Micro-Scale Applications group, asked collaborator Matt Sullivan at The Ohio State University if he’d be interested in using the same metagenomic data sets to look at the lakes’ viral ecology. Roux started mining the data sets while still a postdoctoral fellow with the Sullivan lab. “I knew there were lots of viruses in the sequence data, but not that some the viruses were themselves hosts to other viruses,” said Malmstrom. “With time series data we could do more than assemble genome and build phylogenetic trees, the data allowed us to examine genetic variation within populations and look for co-occurrence and abundance patterns between virophages and their giant virus hosts. With so many time points in the data set, you can find strong connections.”

Trina McMahon, whose CSP datasets were the basis of this work, says having the viral ecology information helps form a more complete picture of the ecosystem. “We are thrilled to have one more piece of the puzzle. Viruses are clearly playing a major role in shaping community composition and therefore function, of the whole lake ecosystem. My own lab lacks the expertise to tackle viruses alone, hence the collaboration with Simon and Matt Sullivan is so important. Our long term goal is to learn enough about the forces controlling community assembly and dynamics, as well as the ecological traits of each lineage, in order to create more predictive models about how freshwater lakes will respond to climate and land-use change, at an ecosystem scale.”

Aside from doubling the number of virophages in public databases, the time series allowed Roux and his colleagues to see the viruses’ ecological profiles – if factors such as the seasons or abundance of particular microbes influenced their own presence. Through co-occurrence analysis, the researchers associated the virophages with sequences of known lineages of giant viruses, and proposed the existence of 3 new groups of candidate giant viruses infected by virophages. These co-occurrence analyses also allowed them to find putative associations between the giant virus sequences and specific eukaryotic hosts.

“These findings are correlation-based,” noted Roux, “but it’s a good example of a metagenomics use case. Metagenomes helped us not only discover new viral diversity and determine what it should do in the ecosystem, but it helps us design hypothesis and follow-up experiments about virus-host interactions so we’re not just throwing out a wide net blindly.”

X
X
X
  • Filters

  • × Clear Filters

Opening Windows for New Spintronic Studies

A surprising discovery could potentially offer major advantages in speed, heat dissipation and power consumption in electronic devices.

Sunlight Stimulates Microbial Respiration of Carbon in Surface Waters

This research offers new information to understand the role of microorganisms in elemental cycling in the Arctic.

Pulling Needles Out of Haystacks: With Computation, Researchers Identify Promising Solid Oxide Fuel Cell Materials

Using advanced computational methods, University of Wisconsin-Madison materials scientists have discovered new materials that could bring widespread commercial use of solid oxide fuel cells closer to reality.

Imaging Individual Flexible DNA 'Building Blocks' in 3-D

A team of researchers from Lawrence Berkeley National Lab (Berkeley Lab) and Ohio State University have generated 3-D images from 129 individual molecules of flexible DNA origami particles. Their work provides the first experimental verification of the theoretical model of DNA origami. https://newscenter.lbl.gov/2018/02/22/imaging-individual-flexible-dna-building-blocks-3-d

Remembering Really Fast

Colossal magnetoresistance at terahertz frequencies in thin composites boosts novel memory devices operated at extremely high speed.

In a First, Tiny Diamond Anvils Trigger Chemical Reactions by Squeezing

Menlo Park, Calif. --Scientists have turned the smallest possible bits of diamond and other super-hard specks into "molecular anvils" that squeeze and twist molecules until chemical bonds break and atoms exchange electrons. These are the first such chemical reactions triggered by mechanical pressure alone, and researchers say the method offers a new way to do chemistry at the molecular level that is greener, more efficient and much more precise.

Berkeley Lab "Minimalist Machine Learning" Algorithms Analyze Images From Very Little Data

Berkeley Lab mathematicians have developed a new approach to machine learning aimed at experimental imaging data. Rather than relying on the tens or hundreds of thousands of images used by typical machine learning methods, this new approach "learns" much more quickly and requires far fewer images.

Tuning Quantum Light Sources

First known material capable of emitting single photons at room temperature and telecom wavelengths.

Working Night and Day

Day-night changes in light and temperature power a low-cost material assembly that mimics biological self-copying.

Squeezing Into the Best Shape

Gel uses nanoparticles for on-demand control of droplet shapes, of interest for energy storage and catalysis.


  • Filters

  • × Clear Filters

ORNL Wins Four FLC Technology Transfer Awards

Four technologies developed at the Department of Energy's Oak Ridge National Laboratory have earned 2018 Excellence in Technology Transfer Awards from the Federal Laboratory Consortium for Technology Transfer (FLC).

Pacific Northwest National Laboratory, OHSU Create Joint Research Co-Laboratory to Advance Precision Medicine

News Release PORTLAND, Ore. -- Pacific Northwest National Laboratory and OHSU today announced a joint collaboration to improve patient care by focusing research on highly complex sets of biomedical data, and the tools to interpret them.The OHSU-PNNL Precision Medicine Innovation Co-Laboratory, called PMedIC, will provide a comprehensive ecosystem for scientists to utilize integrated 'omics, data science and imaging technologies in their research in order to advance precision medicine -- an approach to disease treatment that takes into account individual variability in genes, environment and lifestyle for each person.

The Mysteries of Plasma and Solar Eruptions Earn PPPL Graduate an Astrophysics Prize

Article describes dissertation award for graduate of Princeton University Department of Astrophysical Sciences.

45-Year-Old Telescope Gets a Makeover to Demystify Dark Energy

Forty-five years ago this month, a telescope tucked inside a 14-story, 500-ton dome atop a mile-high peak in Arizona took in the night sky for the first time and recorded its observations on glass photographic plates. Today, the dome closes on the previous science chapters of the 4-meter Nicholas U. Mayall Telescope and starts preparing for its new role in creating the largest 3-D map of the universe. This map could help determine why the universe is expanding at faster and faster rates, driven by an unknown force called dark energy.

MSU Uses $3 Million NASA Grant to Find Better Ways to Regulate Dams

Michigan State University researchers, equipped with $3 million from NASA, will investigate innovative methods to improve dams so that they are less harmful to people and the environment.

Harker School Wins Second Consecutive SLAC Regional DOE Science Bowl

Twenty-four teams from 16 Bay Area high schools faced off Feb. 3 in the SLAC Regional DOE Science Bowl, a series of fast-paced question-and-answer matches that test knowledge in biology, chemistry, physics, earth and space sciences, energy and math. The competition is hosted annually by the Department of Energy's SLAC National Accelerator Laboratory.

David Asner Named Deputy Associate Laboratory Director and Head of the Instrumentation Division in Brookhaven Lab's Nuclear and Particle Physics Directorate

A particle physicist with extensive leadership and management experience, Asner will help expand a portfolio of physics programs and oversee instrumentation research and development.

UIC to Provide Energy-Saving 'Kits' with $3.1m in Funding From ComEd

The University of Illinois at Chicago's Energy Resources Center has received funding from ComEd to provide energy-efficient LED light bulbs, advanced power strips, and educational material to income-qualified participants in northern Illinois.As part of a $3.1 million year-long investment, the utility company will fund the Low Income Kit Energy (LIKE) program, allowing engineers at UIC's Energy Resources Center to provide energy-saving kits to 35,000 eligible individuals and/or families.

DOE's HPC4Manufacturing Program Seeks Industry Proposals

The Department of Energy (DOE) on Feb. 1 announced up to $3 million will be made available to U.S. manufacturers for public/private projects aimed at applying high performance computing to industry challenges for the advancement of energy innovation.

Elke-Caroline Aschenauer Awarded Prestigious Humboldt Research Award

UPTON, NY -- Elke-Caroline Aschenauer, a senior physicist at the U.S. Department of Energy's Brookhaven National Laboratory, has been awarded a Humboldt Research Award for her contributions to the field of experimental nuclear physics. This prestigious international award--issued by the Alexander von Humboldt Foundation in Bonn, Germany--comes with a prize of EUR60,000 (more than $70,000 U.


  • Filters

  • × Clear Filters

Sunlight Stimulates Microbial Respiration of Carbon in Surface Waters

This research offers new information to understand the role of microorganisms in elemental cycling in the Arctic.

Defects and Surface Reactions Boost Batteries

Defect-enhanced transport and complex phase growth are changing design rules for lithium-ion batteries.

Remembering Really Fast

Colossal magnetoresistance at terahertz frequencies in thin composites boosts novel memory devices operated at extremely high speed.

Tuning Quantum Light Sources

First known material capable of emitting single photons at room temperature and telecom wavelengths.

Working Night and Day

Day-night changes in light and temperature power a low-cost material assembly that mimics biological self-copying.

A Nanowire Array to Screen Drugs for Neurodegenerative Diseases

Engineers develop wires that penetrate neurons and measure their activity

Squeezing Into the Best Shape

Gel uses nanoparticles for on-demand control of droplet shapes, of interest for energy storage and catalysis.

Forcing the Hand of Elusive Electrons

Current generated when light hits a material reveals electrons behaving like an elusive particle.

Single Atoms in Nano-Cages

Tiny cages can trap and release inert argon gas atoms, allowing their further study and providing a new way to capture rare gases.

Unwavering Juggler with Three Extra Electrons

Simulations discovered the first molecule with three extra electrons and extraordinary stability.


Spotlight

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)

Wednesday March 03, 2010, 07:00 PM

Helping Hydrogen: Student Inventor Tackles Challenge of Hydrogen Storage

Rensselaer Polytechnic Institute (RPI)

Thursday February 04, 2010, 02:00 PM

Turning Exercise into Electricity

Furman University

Thursday November 12, 2009, 12:45 PM

Campus Leaders Showing the Way to a Sustainable, Clean Energy Future

National Wildlife Federation (NWF)

Tuesday November 03, 2009, 04:20 PM

Furman University Receives $2.5 Million DOE Grant for Geothermal Project

Furman University





Showing results

0-4 Of 2215