A simple and efficient method for concentration of ocean viruses by chemical flocculation
Summary Ocean viruses alter ecosystems through host mortality, horizontal gene transfer and by facilitating remineralization of limiting nutrients. However, the study of wild viral populations is limited by inefficient and unreliable concentration techniques. Here, we develop a new technique to reco...
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| Veröffentlicht in: | Environmental microbiology reports 2011-04, Vol.3 (2), p.195-202 |
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| creator | John, Seth G. Mendez, Carolina B. Deng, Li Poulos, Bonnie Kauffman, Anne Kathryn M. Kern, Suzanne Brum, Jennifer Polz, Martin F. Boyle, Edward A. Sullivan, Matthew B. |
| description | Summary
Ocean viruses alter ecosystems through host mortality, horizontal gene transfer and by facilitating remineralization of limiting nutrients. However, the study of wild viral populations is limited by inefficient and unreliable concentration techniques. Here, we develop a new technique to recover viruses from natural waters using iron‐based flocculation and large‐pore‐size filtration, followed by resuspension of virus‐containing precipitates in a pH 6 buffer. Recovered viruses are amenable to gene sequencing, and a variable proportion of phages, depending upon the phage, retain their infectivity when recovered. This Fe‐based virus flocculation, filtration and resuspension method (FFR) is efficient (> 90% recovery), reliable, inexpensive and adaptable to many aspects of marine viral ecology and genomics research. |
| doi_str_mv | 10.1111/j.1758-2229.2010.00208.x |
| format | Article |
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Ocean viruses alter ecosystems through host mortality, horizontal gene transfer and by facilitating remineralization of limiting nutrients. However, the study of wild viral populations is limited by inefficient and unreliable concentration techniques. Here, we develop a new technique to recover viruses from natural waters using iron‐based flocculation and large‐pore‐size filtration, followed by resuspension of virus‐containing precipitates in a pH 6 buffer. Recovered viruses are amenable to gene sequencing, and a variable proportion of phages, depending upon the phage, retain their infectivity when recovered. This Fe‐based virus flocculation, filtration and resuspension method (FFR) is efficient (> 90% recovery), reliable, inexpensive and adaptable to many aspects of marine viral ecology and genomics research.</description><identifier>ISSN: 1758-2229</identifier><identifier>EISSN: 1758-2229</identifier><identifier>DOI: 10.1111/j.1758-2229.2010.00208.x</identifier><identifier>PMID: 21572525</identifier><language>eng</language><publisher>Oxford, UK: Blackwell Publishing Ltd</publisher><subject>Brief Reports ; Filtration ; Flocculation ; Gene sequencing ; Gene transfer ; Horizontal transfer ; Infectivity ; Iron ; Limiting nutrients ; Marine ecology ; Marine ecosystems ; Methods ; Natural waters ; Nutrients ; Phages ; Population studies ; Precipitates ; Remineralization ; Seawater ; Viruses</subject><ispartof>Environmental microbiology reports, 2011-04, Vol.3 (2), p.195-202</ispartof><rights>2010 Society for Applied Microbiology and Blackwell Publishing Ltd</rights><rights>Copyright John Wiley & Sons, Inc. 2011</rights><rights>Journal compilation © 2011 Society for Applied Microbiology and Blackwell Publishing Ltd</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c6068-7fa4ed611f0762b75525cea9708b81171d4cb01e54491d2c7ec3f833cd3d2ae33</citedby><cites>FETCH-LOGICAL-c6068-7fa4ed611f0762b75525cea9708b81171d4cb01e54491d2c7ec3f833cd3d2ae33</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://onlinelibrary.wiley.com/doi/pdf/10.1111%2Fj.1758-2229.2010.00208.x$$EPDF$$P50$$Gwiley$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://onlinelibrary.wiley.com/doi/full/10.1111%2Fj.1758-2229.2010.00208.x$$EHTML$$P50$$Gwiley$$Hfree_for_read</linktohtml><link.rule.ids>230,314,780,784,885,1416,27923,27924,45573,45574</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/21572525$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>John, Seth G.</creatorcontrib><creatorcontrib>Mendez, Carolina B.</creatorcontrib><creatorcontrib>Deng, Li</creatorcontrib><creatorcontrib>Poulos, Bonnie</creatorcontrib><creatorcontrib>Kauffman, Anne Kathryn M.</creatorcontrib><creatorcontrib>Kern, Suzanne</creatorcontrib><creatorcontrib>Brum, Jennifer</creatorcontrib><creatorcontrib>Polz, Martin F.</creatorcontrib><creatorcontrib>Boyle, Edward A.</creatorcontrib><creatorcontrib>Sullivan, Matthew B.</creatorcontrib><title>A simple and efficient method for concentration of ocean viruses by chemical flocculation</title><title>Environmental microbiology reports</title><addtitle>Environ Microbiol Rep</addtitle><description>Summary
Ocean viruses alter ecosystems through host mortality, horizontal gene transfer and by facilitating remineralization of limiting nutrients. However, the study of wild viral populations is limited by inefficient and unreliable concentration techniques. Here, we develop a new technique to recover viruses from natural waters using iron‐based flocculation and large‐pore‐size filtration, followed by resuspension of virus‐containing precipitates in a pH 6 buffer. Recovered viruses are amenable to gene sequencing, and a variable proportion of phages, depending upon the phage, retain their infectivity when recovered. This Fe‐based virus flocculation, filtration and resuspension method (FFR) is efficient (> 90% recovery), reliable, inexpensive and adaptable to many aspects of marine viral ecology and genomics research.</description><subject>Brief Reports</subject><subject>Filtration</subject><subject>Flocculation</subject><subject>Gene sequencing</subject><subject>Gene transfer</subject><subject>Horizontal transfer</subject><subject>Infectivity</subject><subject>Iron</subject><subject>Limiting nutrients</subject><subject>Marine ecology</subject><subject>Marine ecosystems</subject><subject>Methods</subject><subject>Natural waters</subject><subject>Nutrients</subject><subject>Phages</subject><subject>Population studies</subject><subject>Precipitates</subject><subject>Remineralization</subject><subject>Seawater</subject><subject>Viruses</subject><issn>1758-2229</issn><issn>1758-2229</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2011</creationdate><recordtype>article</recordtype><sourceid>24P</sourceid><sourceid>WIN</sourceid><recordid>eNqNkU1v1DAQhiMEoqXwF5AlLlyy-COxsweQqlW7VFo-DkDFaeQ4Y9ZLEm_tpOz-e7xNWRVO-GJr5nlfz-jNMsLojKXzZjNjqqxyzvl8xmmqUsppNds9yk6PjccP3ifZsxg3lMpiTvnT7ISzUvGSl6fZ93MSXbdtkei-IWitMw77gXQ4rH1DrA_E-N6kUtCD8z3xlniDuie3LowRI6n3xKyxc0a3xLbemLG9I59nT6xuI764v8-yr5cXXxbv89Wn5dXifJUbSWWVK6sLbCRjlirJa1WmsZL_XNGqrhhTrClMTRmWRTFnDTcKjbCVEKYRDdcoxFn2bvLdjnWHzTRqC9vgOh324LWDvzu9W8MPfwuCVip9kAxe3xsEfzNiHKBz0WDb6h79GIFVXDKplJAJffUPuvFj6NN6yW3OuVSsYImqJsoEH2NAexyGUTjkBxs4RAOHaOCQH9zlB7skfflwmaPwT2AJeDsBv1yL-_82hosPV0V6JX0-6V0ccHfU6_ATpBKqhOuPS7hciG9Lfr2Cz-I3hue5EQ</recordid><startdate>201104</startdate><enddate>201104</enddate><creator>John, Seth G.</creator><creator>Mendez, Carolina B.</creator><creator>Deng, Li</creator><creator>Poulos, Bonnie</creator><creator>Kauffman, Anne Kathryn M.</creator><creator>Kern, Suzanne</creator><creator>Brum, Jennifer</creator><creator>Polz, Martin F.</creator><creator>Boyle, Edward A.</creator><creator>Sullivan, Matthew B.</creator><general>Blackwell Publishing Ltd</general><general>John Wiley & Sons, Inc</general><scope>BSCLL</scope><scope>24P</scope><scope>WIN</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7X8</scope><scope>5PM</scope></search><sort><creationdate>201104</creationdate><title>A simple and efficient method for concentration of ocean viruses by chemical flocculation</title><author>John, Seth G. ; Mendez, Carolina B. ; Deng, Li ; Poulos, Bonnie ; Kauffman, Anne Kathryn M. ; Kern, Suzanne ; Brum, Jennifer ; Polz, Martin F. ; Boyle, Edward A. ; Sullivan, Matthew B.</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c6068-7fa4ed611f0762b75525cea9708b81171d4cb01e54491d2c7ec3f833cd3d2ae33</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2011</creationdate><topic>Brief Reports</topic><topic>Filtration</topic><topic>Flocculation</topic><topic>Gene sequencing</topic><topic>Gene transfer</topic><topic>Horizontal transfer</topic><topic>Infectivity</topic><topic>Iron</topic><topic>Limiting nutrients</topic><topic>Marine ecology</topic><topic>Marine ecosystems</topic><topic>Methods</topic><topic>Natural waters</topic><topic>Nutrients</topic><topic>Phages</topic><topic>Population studies</topic><topic>Precipitates</topic><topic>Remineralization</topic><topic>Seawater</topic><topic>Viruses</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>John, Seth G.</creatorcontrib><creatorcontrib>Mendez, Carolina B.</creatorcontrib><creatorcontrib>Deng, Li</creatorcontrib><creatorcontrib>Poulos, Bonnie</creatorcontrib><creatorcontrib>Kauffman, Anne Kathryn M.</creatorcontrib><creatorcontrib>Kern, Suzanne</creatorcontrib><creatorcontrib>Brum, Jennifer</creatorcontrib><creatorcontrib>Polz, Martin F.</creatorcontrib><creatorcontrib>Boyle, Edward A.</creatorcontrib><creatorcontrib>Sullivan, Matthew B.</creatorcontrib><collection>Istex</collection><collection>Wiley-Blackwell Open Access Titles</collection><collection>Wiley Free Content</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>Environmental microbiology reports</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>John, Seth G.</au><au>Mendez, Carolina B.</au><au>Deng, Li</au><au>Poulos, Bonnie</au><au>Kauffman, Anne Kathryn M.</au><au>Kern, Suzanne</au><au>Brum, Jennifer</au><au>Polz, Martin F.</au><au>Boyle, Edward A.</au><au>Sullivan, Matthew B.</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>A simple and efficient method for concentration of ocean viruses by chemical flocculation</atitle><jtitle>Environmental microbiology reports</jtitle><addtitle>Environ Microbiol Rep</addtitle><date>2011-04</date><risdate>2011</risdate><volume>3</volume><issue>2</issue><spage>195</spage><epage>202</epage><pages>195-202</pages><issn>1758-2229</issn><eissn>1758-2229</eissn><abstract>Summary
Ocean viruses alter ecosystems through host mortality, horizontal gene transfer and by facilitating remineralization of limiting nutrients. However, the study of wild viral populations is limited by inefficient and unreliable concentration techniques. Here, we develop a new technique to recover viruses from natural waters using iron‐based flocculation and large‐pore‐size filtration, followed by resuspension of virus‐containing precipitates in a pH 6 buffer. Recovered viruses are amenable to gene sequencing, and a variable proportion of phages, depending upon the phage, retain their infectivity when recovered. This Fe‐based virus flocculation, filtration and resuspension method (FFR) is efficient (> 90% recovery), reliable, inexpensive and adaptable to many aspects of marine viral ecology and genomics research.</abstract><cop>Oxford, UK</cop><pub>Blackwell Publishing Ltd</pub><pmid>21572525</pmid><doi>10.1111/j.1758-2229.2010.00208.x</doi><tpages>8</tpages><oa>free_for_read</oa></addata></record> |
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| source | Wiley Online Library All Journals |
| subjects | Brief Reports Filtration Flocculation Gene sequencing Gene transfer Horizontal transfer Infectivity Iron Limiting nutrients Marine ecology Marine ecosystems Methods Natural waters Nutrients Phages Population studies Precipitates Remineralization Seawater Viruses |
| title | A simple and efficient method for concentration of ocean viruses by chemical flocculation |
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