Unveiled: Earth's Viral Diversity

DOE News

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.

MORE NEWS FROM

Lawrence Berkeley National Laboratory

MEDIA CONTACT

David Gilbert
Public Affairs Manager
U.S. Department of Energy Joint Genome Institute
degilbert@lbl.gov

CHANNELS

Chemistry, Environmental Science, Space and Astronomy, DOE Science News, DOE Science News, Local - California

KEYWORDS

virome, Virus, Genomics, Metagenomics, Microbes, Carbon Cycle, Biogeochemistry, Big Data, HPC, Environment, DOE Office of Science, CRISPR-Cas, Bacteria, Computational

Participating Labs

view all latest news

Breaking

Focus on Nuclear Waste Chemistry Could Help Hanford Cleanup Challenges

Participating Labs

In a first, researchers identify reddish coloring in an ancient fossil - a 3-million-year-old mouse

Researchers have for the first time detected chemical traces of red pigment in an ancient fossil - an exceptionally well-preserved mouse, not unlike today's field mice, that roamed the fields of what is now the German village of Willershausen around 3 million years ago.

Improving Isotope Supply for a Cancer-Fighting Drug

Production of actinium-227 ramps up for use in a drug to fight prostate cancer that has spread to bone.

Extracting Signs of the Elusive Neutrino

Scientists use software to "develop" images that trace neutrinos' interactions in a bath of cold liquid argon.

Machine learning speeds modeling of experiments aimed at capturing fusion energy on Earth to rapidly predict behavior of plasma that fuels fusion reactions

Release describes application of machine learning form of artificial intelligence to predict the behavior of fusion plasma.

Record-shattering underwater sound

A team of researchers has produced a record-shattering underwater sound with an intensity that eclipses that of a rocket launch. The intensity was equivalent to directing the electrical power of an entire city onto a single square meter, resulting in sound pressures above 270 decibels.

CosmoGAN: Training a Neural Network to Study Dark Matter

A Berkeley Lab-led research group is using a deep learning method known as generative adversarial networks to enhance the use of gravitational lensing in the study of dark matter.

Breakthrough Technique for Studying Gene Expression Takes Root in Plants

An open-source RNA analysis platform has been successfully used on plant cells for the first time - an advance that could herald a new era of fundamental research and bolster efforts to engineer more efficient food and biofuel crop plants. The technology, called Drop-seq, is a method for measuring the RNA present in individual cells, allowing scientists to see what genes are being expressed and how this relates to the specific functions of different cell types.

Bio-inspired material targets oceans' uranium stores for sustainable nuclear energy

Scientists have demonstrated a new bio-inspired material for an eco-friendly and cost-effective approach to recovering uranium from seawater. The low-cost polymer adsorbent could help push past bottlenecks in the cost and efficiency of extracting uranium resources from oceans for sustainable energy production.

Study Concludes Glassy Menagerie of Particles in Beach Sands Near Hiroshima is Fallout Debris from A-Bomb Blast

A years-long study that involved scientists and experiments at Berkeley Lab and UC Berkeley concluded that an odd assortment of particles found in beach sands in Japan are most likely fallout debris from the 1945 Hiroshima A-bomb blast.

New technique merging sound and math could help prevent plasma disruptions in fusion facilities

Scientists have created a novel method for measuring the stability of plasma in fusion facilities called "tokamaks." Involving an innovative use of a mathematical tool, the method might lead to a technique for stabilizing plasma and making fusion reactions more efficient.

Berkeley Lab Project to Pinpoint Methane 'Super Emitters'

Methane, a potent greenhouse gas that traps about 30 times more heat than carbon dioxide, is commonly released from rice fields, dairies, landfills, and oil and gas facilities - all of which are plentiful in California. Now Berkeley Lab has been awarded $6 million by the state to find "super emitters" of methane in an effort to quantify and potentially mitigate methane emissions.

Cryogenics equipment maker licenses ORNL auto-fill method for more efficient liquid helium use

Advanced Research Systems has licensed an ORNL technology designed to automatically refill liquid helium used in laboratory equipment for low-temperature scientific experiments, which will reduce downtime, recover more helium and increase overall efficiency.

New Argonne coating could have big implications for lithium batteries

In a new discovery, scientists at the U.S. Department of Energy's (DOE) Argonne National Laboratory have developed a new cathode coating by using an oxidative chemical vapor deposition technique. The new coating can keep the battery's cathode electrically and ionically conductive and ensures that the battery stays safe after many cycles.

Argonne's Chain Reaction Innovations appoints first advisory council

World-class energy leaders will offer their expertise to Chain Reaction Innovations (CRI), the entrepreneurship program at the U.S. Department of Energy's Argonne National Laboratory, as part of a new Advisory Council announced today. CRI has named 14 Advisory Council members, including investors, industry experts and business executives, to help guide its growth and strategy.

ORNL, Lincoln Electric to Advance Large-Scale Metal Additive Manufacturing Technology

The new agreement builds upon ORNL and Lincoln Electric's previous developments by extending additive technology to new materials, leveraging data analytics and enabling rapid manufacture of metal components in excess of 100 pounds per hour.

Students from Minnesota and Massachusetts Win DOE's 29th National Science Bowl(r)

Students from Wayzata High School in Plymouth, Minnesota, won the 2019 U.S. Department of Energy (DOE) National Science Bowl(r) (NSB) today in Washington, D.C. In the middle school competition, students from Jonas Clarke Middle School in Lexington, Massachusetts, took home first place.

Five new innovators join Chain Reaction Innovations in third cohort

Five new innovators will be joining Chain Reaction Innovations (CRI), the entrepreneurship program at the U.S. Department of Energy's (DOE's) Argonne National Laboratory, as part of the elite program's third cohort. Announced on Monday, April 22, these innovators were selected following an extensive national solicitation process and two-part pitch competition, with reviews from industry experts, investors, scientists and engineers.