{"334871":{"#nid":"334871","#data":{"type":"news","title":"Dyeing to Learn More About Marine Viruses","body":[{"value":"\u003Cp\u003EThe sheer volume of cyanobacteria in the oceans makes them major players in the global carbon cycle and responsible for as much as a third of the carbon fixed. These photosynthetic microbes, which include Prochlorococcus and Synechococcus, are tiny \u2013 as many as 100 million cells can be found in a single liter of water \u2013 and yet they are not the most abundant entities on Earth. That distinction goes to viruses, up to 100 million of which can be found per 1 mL of seawater. However, researchers know very little about the viruses in the water, other than that there are three kinds of viruses, and that they are capable of drastically decreasing cyanobacterial populations, affecting the global regulation of biogeochemical cycles.\u003C\/p\u003E\u003Cp\u003ETo help resolve this conspicuous lack of knowledge and learn more about viral diversity, a team led by Matt Sullivan, a professor at the University of Arizona and a collaborator with the U.S. Department of Energy Joint Genome Institute (DOE JGI), a DOE Office of Science User Facility, conducted a population-scale survey using a game-changing new technique. Their results, he said, suggest that there is an ecology of viruses and it can be studied by harnessing more traditional approaches that have been applied to larger organisms. The work was published online July 13, 2014 in Nature.\u003C\/p\u003E\u003Cp\u003E\u201cI often joke that viruses are only as interesting as their microbial hosts,\u201d Sullivan said, \u201cwhich makes cyanophages pretty important. Not only do they affect marine photosynthesis through mortality of cyanobacteria, but these viruses also encode photosynthesis genes \u2013 decade-old finding made in collaboration with JGI \u2013 that means cyanophages help drive global biogeochemical cycles that are crucial for running all kinds of energy conversions on the planet. The challenge for us, if we wanted to develop predictive capacity, was to develop a method that allowed us to simultaneously examine thousands (or more) of wild cyanobacterial viruses from the millions of non-cyanobacterial viruses in seawater \u2013 this would get us beyond learning about them one at a time.\u201d\u003C\/p\u003E\u003Cp\u003ESullivan\u2019s team focused on the cyanophages isolated from a single sample of water collected in Monterey Bay, Calif. To resolve the challenge of figuring out \u201cwho infects whom\u201d among marine viruses and cyanobacteria, they used a technique known as viral tagging, in which viruses and so-called \u201chost bait\u201d are stained with a fluorescent dye in order to find out with which hosts the phages associate. Sullivan credits the original idea for the project to study co-author Phil Hugenholtz, formerly a DOE JGI researcher and now Director of the Australian Centre for Ecogenomics at the University of Queensland.\u003C\/p\u003E\u003Cp\u003E\u201cWe subsequently found out that the basic idea of \u201clabeling\u201d bacteria with fluorescent viruses wasn\u2019t novel, it had been proposed back in 1985, but the novelty of viral tagging lies in combining this with flow sorting and sequencing,\u201d said Hugenholtz. \u201cViral tagging combined with flow sorting and sequencing provides an unbiased view of host-phage range.\u201d\u003C\/p\u003E\u003Cp\u003EAfter screening for cyanophages that were tagged as being associated with a single Synechococcus strain (SynWH803), samples of the viral community metagenomes were sent to the DOE JGI for sequencing as part of a Community Science Program project proposed by Sullivan. The results indicated that there were \u201cat least\u201d 26 viral populations associated with the cyanobacterial strain, and many of them had been found and identified in culture. Additionally, the researchers wrote, \u201cviral tagging also provided evidence\u2026 for 42 new uncultured viruses specific to SynWH7803\u2026. [A]n unprecedented diversity of specific viruses were recovered for this single host despite two decades of isolation studies.\u201d\u003C\/p\u003E\u003Cp\u003EThe study also benefited from collaboration with Joshua Weitz, an Associate Professor and theoretical ecologist from the Georgia Institute of Technology, who was on sabbatical in the Sullivan Lab at UA. \u201cThis new method provides incredibly novel sequence data on viruses linked to a particular host,\u201d Weitz explained. \u201cThe work is foundational for developing a means to count genome-based populations that serve as starting material for more rigorous predictive models of how viruses interact with their host microbes. Instead of counting \u2018dots\u2019 we can now map viral populations with their genomes, providing information about who they are and what they do.\u201d\u003C\/p\u003E\u003Cp\u003EThe team made several key findings, perhaps chief among them was that the fluorescently-tagged cyanophages sequenced existed in discrete populations when plotted in \u2018genome sequence space\u2019 (an abstract method the researchers used to visualize the relatedness of many viruses at once). This means that the conventional knowledge of viral genomes evolving by \u201crampant mosaicism\u201d \u2013 i.e., recombining segments or modules from different cyanophages \u2013 might be wrong. Instead, these cyanophage genome \u201cclusters\u201d suggested that there was discrete population structure in the wild.\u003C\/p\u003E\u003Cp\u003E\u201cThe novel finding here isn\u2019t the number of viruses, but rather the structured nature of the populations,\u201d Sullivan said. \u201cWith these discrete populations in a complex natural community and the genome sequence information linked to each population, we are generating hypotheses on what might be driving particular population-host interactions and the abundances of particular populations \u2013 that\u2019s viral ecology. And you can track how one population changes over time at a genetic level \u2013 that\u2019s viral evolution,\u201d he said. \u201cThe thinking before was that the viral genome sequence space would be one big blur, but this suggests there are units that we can count and study. That represents a whole new ballgame and opens up viral ecology to utilize decades of theory and practice from the study of more traditional study of larger organisms. Additionally, our method of viral tagging should be generalizable to many other virus-host studies so it should transform the way viruses in nature are studied moving forward.\u201d\u003C\/p\u003E\u003Cp\u003EMatt Sullivan spoke about marine viruses at the 2012 DOE JGI Genomics of Energy \u0026amp; Environment Meeting. Watch the video at \u003Ca title=\u0022http:\/\/bit.ly\/JGI7Sullivan\u0022 href=\u0022http:\/\/bit.ly\/JGI7Sullivan\u0022\u003Ehttp:\/\/bit.ly\/JGI7Sullivan\u003C\/a\u003E. The Sullivan lab maintains publicly available protocols and informatics tools at \u003Ca title=\u0022http:\/\/eebweb.arizona.edu\/Faculty\/mbsulli\/\u0022 href=\u0022http:\/\/eebweb.arizona.edu\/Faculty\/mbsulli\/\u0022\u003Ehttp:\/\/eebweb.arizona.edu\/Faculty\/mbsulli\/\u003C\/a\u003E.\u003C\/p\u003E","summary":null,"format":"limited_html"}],"field_subtitle":"","field_summary":[{"value":"\u003Cp\u003EThe sheer volume of cyanobacteria in the oceans makes them major players in the global carbon cycle and responsible for as much as a third of the carbon fixed. These photosynthetic microbes, which include Prochlorococcus and Synechococcus, are tiny \u2013 as many as 100 million cells can be found in a single liter of water \u2013 and yet they are not the most abundant entities on Earth. That distinction goes to viruses, up to 100 million of which can be found per 1 mL of seawater. However, researchers know very little about the viruses in the water, other than that there are three kinds of viruses, and that they are capable of drastically decreasing cyanobacterial populations, affecting the global regulation of biogeochemical cycles.\u003C\/p\u003E","format":"limited_html"}],"field_summary_sentence":[{"value":"The sheer volume of cyanobacteria in the oceans makes them major players in the global carbon cycle and responsible for as much as a third of the carbon fixed."}],"uid":"27245","created_gmt":"2014-10-17 07:06:20","changed_gmt":"2016-10-08 03:17:19","author":"Troy Hilley","boilerplate_text":"","field_publication":"","field_article_url":"","dateline":{"date":"2014-10-17T00:00:00-04:00","iso_date":"2014-10-17T00:00:00-04:00","tz":"America\/New_York"},"extras":[],"groups":[{"id":"1275","name":"School of Biological Sciences"}],"categories":[{"id":"146","name":"Life Sciences and Biology"}],"keywords":[{"id":"11599","name":"Joshua Weitz"},{"id":"11384","name":"viruses"}],"core_research_areas":[],"news_room_topics":[],"event_categories":[],"invited_audience":[],"affiliations":[],"classification":[],"areas_of_expertise":[],"news_and_recent_appearances":[],"phone":[],"contact":[],"email":[],"slides":[],"orientation":[],"userdata":""}}}