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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.
  • 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.”

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The U.S. Department of Energy's Ames Laboratory has discovered extreme "bounce," or super-elastic shape-memory properties in a material that could be applied for use as an actuator in the harshest of conditions, such as outer space, and might be the first in a whole new class of shape memory materials.

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Four Argonne Researchers Appointed Fellows of Scientific Societies

A select group of scientists at the U.S. Department of Energy's (DOE) Argonne National Laboratory has been honored as fellows of the American Physical Society and the Electrochemical Society. Physicists Kawtar Hafidi and Michael Carpenter have been appointed as American Physical Society fellows and Materials Scientist Khalil Amine and Chemist Chris Johnson have been elected as Electrochemical Society fellows.

Berkeley Lab and Hydro-Quebec Announce Partnership for Transportation Electrification and Energy Storage

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Two ORNL-Led Research Teams Receive $10.5 Million to Advance Quantum Computing for Scientific Applications

DOE's Office of Science has awarded two research teams, each headed by a member of ORNL's Quantum Information Science Group, more than $10 million over 5 years to both assess the feasibility of quantum architectures in addressing big science problems and to develop algorithms capable of harnessing the massive power predicted of quantum computing systems. The two projects are intended to work in concert to ensure synergy across DOE's quantum computing research spectrum and maximize mutual benefits.

Department of Energy Awards Flow Into Argonne

DOE Secretary Rick Perry awarded Argonne with nearly $4.7 million in projects as part of the DOE's Office of Technology Transition's Technology Commercialization Fund (TCF) in September.

NIH Awards $6.5 Million to Berkeley Lab for Augmenting Structural Biology Research Experience

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LIGO Announces Detection of Gravitational Waves From Colliding Neutron Stars

The U.S.-based Laser Interferometer Gravitational-Wave Observatory and the Virgo detector in Italy announced on Oct. 16 that all three of their detectors had picked up the ripples, or gravitational waves, from two neutron stars that collided 130 million years ago. Among other discoveries, the detection allowed scientists to use gravitational waves to directly calculate the rate at which the universe is expanding.

WVU Energy Conference to Address State's Economic Opportunities

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Exploring the Exotic World of Quarks and Gluons at the Dawn of the Exascale

As nuclear physicists delve ever deeper into the heart of matter, they require the tools to reveal the next layer of nature's secrets. Nowhere is that more true than in computational nuclear physics. A new research effort led by theorists at DOE's Thomas Jefferson National Accelerator Facility (Jefferson Lab) is now preparing for the next big leap forward in their studies thanks to funding under the 2017 SciDAC Awards for Computational Nuclear Physics.

Matthew Latimer Receives 2017 Lytle Award

A staff member at the Department of Energy's SLAC National Acceleratory Laboratory, Matthew Latimer is in charge of seven spectroscopy beamlines at SSRL. He was recently selected for the 2017 Farrel W. Lytle Award, established by the SSRL Users' Organization Executive Committee. The award promotes accomplishments in synchrotron science and supports collaboration among visiting scientists and staff who conduct research at SSRL.

Jefferson Lab Completes 12 GeV Upgrade

Nuclear physicists are now poised to embark on a new journey of discovery into the fundamental building blocks of the nucleus of the atom. The completion of the 12 GeV Upgrade Project of the Continuous Electron Beam Accelerator Facility (CEBAF) at the Department of Energy's Thomas Jefferson National Accelerator Facility (Jefferson Lab) heralds this new era to image nuclei at their deepest level.


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Hybrid Material Glows Like Jellyfish

Scientists combine biology, nanotechnology into composites that light up upon chemical stimulation.

Tiny Tornados at the Dawn of the Universe

Swirling soup of matter's fundamental building blocks spins ten billion trillion times faster than the most powerful tornado, setting new record for "vorticity."

On-Demand 3-D Printing of Tiny Magic Wands

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Discovering the Genetic Timekeepers in Bioenergy Crops

A new class of plant-specific genes required for flowering control in temperate grasses is found.

New Technology Illuminates Microbial Dark Matter

Demonstrating the microfluidic-based, mini-metagenomics approach on samples from hot springs shows how scientists can delve into microbes that can't be cultivated in a laboratory.

Tiny Green Algae Reveal Large Genomic Variation

First complete picture of genetic variations in a natural algal population could help explain how environmental changes affect global carbon cycles.

A Complex Little Alga that Lives by the Sea

The genetic material of Porphyra umbilicalis reveals the mechanisms by which it thrives in the stressful intertidal zone at the edge of the ocean.

Precise Radioactivity Measurements: A Controversy Settled

Simultaneous measurements of x-rays and gamma rays emitted in radioactive nuclear decays show that the vacancy left by an electron's departure, not the atomic structure, influences whether gamma rays are released.

OLYMPUS Experiment Sheds Light on Inner Workings of Protons

Seven-year study explains how packets of light are exchanged when protons meet electrons.


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