Forum for Science, Industry and Business

Sponsored by:     3M 
Search our Site:


Tiniest catch: University of Arizona scientists' fishing expedition reveals viral diversity in the sea


A fishing expedition of microscopic proportions led by University of Arizona ecologists revealed that the lines between virus types in nature are less blurred than previously thought.

Using lab-cultured bacteria as "bait," a team of scientists led by Matthew Sullivan has sequenced complete and partial genomes of about 10 million viruses from an ocean water sample in a single experiment.

This is an electron microscopy image of a virus sample collected during a research cruise with the 'Western Flyer' off the coast of Monterey Bay, California.

Credit: Sullivan lab

The study, published online on July 14 by the journal Nature, revealed that the genomes of viruses in natural ecosystems fall into more distinct categories than previously thought. This enables scientists to recognize actual populations of viruses in nature for the first time.

"You could count the number of viruses from a soil or water sample in a microscope, but you would have no idea what hosts they infect or what their genomes were like," said Sullivan, an associate professor in the UA's Department of Ecology and Evolutionary Biology and member of the UA's BIO5 Institute.

"Our new approach for the first time links those same viruses to their host cells. In doing so, we gain access to viral genomes in a way that opens up a window into the roles these viruses play in nature."

Sullivan's team developed a new approach called viral tagging, which uses cultivated bacterial hosts as "bait" to fish for viruses that infect that host. The scientists then isolate the DNA of those viruses and decipher their sequence.

"Instead of a continuum, we found at least 17 distinct types of viruses in a single sample of Pacific Ocean seawater, including several that are new to science – all associated with the single 'bait' host used in the experiment," Sullivan said.

The research lays the groundwork for a genome-based system of identifying virus populations, which is fundamental for studying the ecology and evolution of viruses in nature.

"Before our study, the prevailing view was that the genome sequences of viruses in a given environment or ecosystem formed a continuum," Sullivan said. "In other words, the lines between different types of viruses appeared blurred, which prevented scientists who wanted to assess the diversity of viruses in the wild from recognizing and counting distinct types of viruses when they sampled for them."

"Microbes are now recognized as drivers of the biogeochemical engines that fuel Earth, and the viruses that infect them control these processes by transferring genes between microbes, killing them in great numbers and reprogramming their metabolisms," explained the first author of the study, Li Deng, a former postdoctoral researcher in Sullivan's lab who now is a research scientist at the Helmholtz Research Center for Environmental Health in Neuherberg, Germany. "Our study for the first time provides the methodology needed to match viruses to their host microbes at scales relevant to nature."

Getting a grip on the diversity of viruses infecting a particular host is critical beyond environmental sciences, Deng said, and has implications for understanding how viruses affect pathogens that cause human disease, which in turn is relevant for vaccine design and antiviral drug therapy.

Sullivan estimates that up to 99 percent of microbes that populate the oceans and drive global processes such as nutrient cycles and climate have not yet been cultivated in the lab, which makes their viruses similarly inaccessible.

"For the first time we can count virus types," he explained, "and we can ask questions like, 'Which virus is more abundant in one environment than another?' Further, the genomic data gives us a way to infer what a virus might do to its bacterial host."

The study benefited from collaboration with Joshua Weitz, an associate professor and theoretical ecologist from the Georgia Institute of Technology who spent time as a visiting researcher in the Sullivan lab.

The new data help scientists like Weitz develop new concepts and theories about how viruses and bacteria interact in nature.

"This new method provides incredibly novel sequence data on viruses linked to a particular host," Weitz explained. "The work is foundational for developing a means to count genome-based populations that serve as starting material for predictive models of how viruses interact with their host microbes. We can now map viral populations with their genomes, providing information about who they are and what they do."


The study, "Viral tagging reveals discrete populations in Synechococcus viral genome sequence space," was co-first authored by Cesar Ignacio-Espinoza, a doctoral candidate in molecular and cellular biology; Ann Gregory, a doctoral candidate in soil, water and environmental sciences; and Bonnie Poulos, assistant research scientist in cecology and evolutionary biology. In addition to Weitz, co-authors not at the UA include Georgia and Philip Hugenholtz of the Australian Centre for Ecogenomics at the University of Queensland in Brisbane, Australia.

The research paper is online at

Daniel Stolte | Eurek Alert!

Further reports about: Arizona bacteria bacterial fishing genomes infect interact microbes populations sequence types viruses

More articles from Ecology, The Environment and Conservation:

nachricht Invasive Insects Cost the World Billions Per Year
04.10.2016 | University of Adelaide

nachricht Malaysia's unique freshwater mussels in danger
27.09.2016 | The University of Nottingham Malaysia Campus

All articles from Ecology, The Environment and Conservation >>>

The most recent press releases about innovation >>>

Die letzten 5 Focus-News des innovations-reports im Überblick:

Im Focus: New 3-D wiring technique brings scalable quantum computers closer to reality

Researchers from the Institute for Quantum Computing (IQC) at the University of Waterloo led the development of a new extensible wiring technique capable of controlling superconducting quantum bits, representing a significant step towards to the realization of a scalable quantum computer.

"The quantum socket is a wiring method that uses three-dimensional wires based on spring-loaded pins to address individual qubits," said Jeremy Béjanin, a PhD...

Im Focus: Scientists develop a semiconductor nanocomposite material that moves in response to light

In a paper in Scientific Reports, a research team at Worcester Polytechnic Institute describes a novel light-activated phenomenon that could become the basis for applications as diverse as microscopic robotic grippers and more efficient solar cells.

A research team at Worcester Polytechnic Institute (WPI) has developed a revolutionary, light-activated semiconductor nanocomposite material that can be used...

Im Focus: Diamonds aren't forever: Sandia, Harvard team create first quantum computer bridge

By forcefully embedding two silicon atoms in a diamond matrix, Sandia researchers have demonstrated for the first time on a single chip all the components needed to create a quantum bridge to link quantum computers together.

"People have already built small quantum computers," says Sandia researcher Ryan Camacho. "Maybe the first useful one won't be a single giant quantum computer...

Im Focus: New Products - Highlights of COMPAMED 2016

COMPAMED has become the leading international marketplace for suppliers of medical manufacturing. The trade fair, which takes place every November and is co-located to MEDICA in Dusseldorf, has been steadily growing over the past years and shows that medical technology remains a rapidly growing market.

In 2016, the joint pavilion by the IVAM Microtechnology Network, the Product Market “High-tech for Medical Devices”, will be located in Hall 8a again and will...

Im Focus: Ultra-thin ferroelectric material for next-generation electronics

'Ferroelectric' materials can switch between different states of electrical polarization in response to an external electric field. This flexibility means they show promise for many applications, for example in electronic devices and computer memory. Current ferroelectric materials are highly valued for their thermal and chemical stability and rapid electro-mechanical responses, but creating a material that is scalable down to the tiny sizes needed for technologies like silicon-based semiconductors (Si-based CMOS) has proven challenging.

Now, Hiroshi Funakubo and co-workers at the Tokyo Institute of Technology, in collaboration with researchers across Japan, have conducted experiments to...

All Focus news of the innovation-report >>>



Event News

#IC2S2: When Social Science meets Computer Science - GESIS will host the IC2S2 conference 2017

14.10.2016 | Event News

Agricultural Trade Developments and Potentials in Central Asia and the South Caucasus

14.10.2016 | Event News

World Health Summit – Day Three: A Call to Action

12.10.2016 | Event News

Latest News

Resolving the mystery of preeclampsia

21.10.2016 | Health and Medicine

Stanford researchers create new special-purpose computer that may someday save us billions

21.10.2016 | Information Technology

From ancient fossils to future cars

21.10.2016 | Materials Sciences

More VideoLinks >>>