Featured Research

from universities, journals, and other organizations

Tiniest catch: Scientists' fishing expedition reveals viral diversity in sea

Date:
July 17, 2014
Source:
University of Arizona
Summary:
Using bacteria as bait, scientists caught wild ocean viruses and then deciphered their genomes. They learned that the genetic lines between virus types in nature are less blurred than previously thought. This enables scientists to recognize actual populations of viruses in nature for the first time.

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

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.

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."


Story Source:

The above story is based on materials provided by University of Arizona. The original article was written by Daniel Stolte. Note: Materials may be edited for content and length.


Journal Reference:

  1. Li Deng, J. Cesar Ignacio-Espinoza, Ann C. Gregory, Bonnie T. Poulos, Joshua S. Weitz, Philip Hugenholtz, Matthew B. Sullivan. Viral tagging reveals discrete populations in Synechococcus viral genome sequence space. Nature, 2014; DOI: 10.1038/nature13459

Cite This Page:

University of Arizona. "Tiniest catch: Scientists' fishing expedition reveals viral diversity in sea." ScienceDaily. ScienceDaily, 17 July 2014. <www.sciencedaily.com/releases/2014/07/140717180450.htm>.
University of Arizona. (2014, July 17). Tiniest catch: Scientists' fishing expedition reveals viral diversity in sea. ScienceDaily. Retrieved October 21, 2014 from www.sciencedaily.com/releases/2014/07/140717180450.htm
University of Arizona. "Tiniest catch: Scientists' fishing expedition reveals viral diversity in sea." ScienceDaily. www.sciencedaily.com/releases/2014/07/140717180450.htm (accessed October 21, 2014).

Share This



More Plants & Animals News

Tuesday, October 21, 2014

Featured Research

from universities, journals, and other organizations


Featured Videos

from AP, Reuters, AFP, and other news services

White Lion Cubs Born in Belgrade Zoo

White Lion Cubs Born in Belgrade Zoo

AFP (Oct. 20, 2014) Two white lion cubs, an extremely rare subspecies of the African lion, were recently born at Belgrade Zoo. They are being bottle fed by zoo keepers after they were rejected by their mother after birth. Duration: 00:42 Video provided by AFP
Powered by NewsLook.com
Traditional Farming Methods Gaining Ground in Mali

Traditional Farming Methods Gaining Ground in Mali

AFP (Oct. 20, 2014) He is leading a one man agricultural revolution in Mali - Oumar Diatabe uses traditional farming methods to get the most out of his land and is teaching others across the country how to do the same. Duration: 01:44 Video provided by AFP
Powered by NewsLook.com
Goliath Spider Will Give You Nightmares

Goliath Spider Will Give You Nightmares

Buzz60 (Oct. 20, 2014) An entomologist stumbled upon a South American Goliath Birdeater. With a name like that, you know it's a terrifying creepy crawler. Sean Dowling (@SeanDowlingTV) has the details. Video provided by Buzz60
Powered by NewsLook.com
Adorable Video of Baby Rhino and Lamb Friend Playing

Adorable Video of Baby Rhino and Lamb Friend Playing

Buzz60 (Oct. 20, 2014) Gertjie the Rhino and Lammie the Lamb are teaching the world about animal conservation and friendship. TC Newman (@PurpleTCNewman) has the adorable video! Video provided by Buzz60
Powered by NewsLook.com

Search ScienceDaily

Number of stories in archives: 140,361

Find with keyword(s):
Enter a keyword or phrase to search ScienceDaily for related topics and research stories.

Save/Print:
Share:

Breaking News:

Strange & Offbeat Stories


Plants & Animals

Earth & Climate

Fossils & Ruins

In Other News

... from NewsDaily.com

Science News

Health News

Environment News

Technology News



Save/Print:
Share:

Free Subscriptions


Get the latest science news with ScienceDaily's free email newsletters, updated daily and weekly. Or view hourly updated newsfeeds in your RSS reader:

Get Social & Mobile


Keep up to date with the latest news from ScienceDaily via social networks and mobile apps:

Have Feedback?


Tell us what you think of ScienceDaily -- we welcome both positive and negative comments. Have any problems using the site? Questions?
Mobile: iPhone Android Web
Follow: Facebook Twitter Google+
Subscribe: RSS Feeds Email Newsletters
Latest Headlines Health & Medicine Mind & Brain Space & Time Matter & Energy Computers & Math Plants & Animals Earth & Climate Fossils & Ruins