Stable isotope probing in the metagenomics era: A bridge towards improved bioremediation
Microbial biodegradation and biotransformation reactions are essential to most bioremediation processes, yet the specific organisms, genes, and mechanisms involved are often not well understood. Stable isotope probing (SIP) enables researchers to directly link microbial metabolic capability to phylo...
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| Veröffentlicht in: | Biotechnology advances 2013-03, Vol.31 (2), p.154-165 |
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| creator | Uhlik, Ondrej Leewis, Mary-Cathrine Strejcek, Michal Musilova, Lucie Mackova, Martina Leigh, Mary Beth Macek, Tomas |
| description | Microbial biodegradation and biotransformation reactions are essential to most bioremediation processes, yet the specific organisms, genes, and mechanisms involved are often not well understood. Stable isotope probing (SIP) enables researchers to directly link microbial metabolic capability to phylogenetic and metagenomic information within a community context by tracking isotopically labeled substances into phylogenetically and functionally informative biomarkers. SIP is thus applicable as a tool for the identification of active members of the microbial community and associated genes integral to the community functional potential, such as biodegradative processes. The rapid evolution of SIP over the last decade and integration with metagenomics provide researchers with a much deeper insight into potential biodegradative genes, processes, and applications, thereby enabling an improved mechanistic understanding that can facilitate advances in the field of bioremediation. |
| doi_str_mv | 10.1016/j.biotechadv.2012.09.003 |
| format | Article |
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Stable isotope probing (SIP) enables researchers to directly link microbial metabolic capability to phylogenetic and metagenomic information within a community context by tracking isotopically labeled substances into phylogenetically and functionally informative biomarkers. SIP is thus applicable as a tool for the identification of active members of the microbial community and associated genes integral to the community functional potential, such as biodegradative processes. 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Psychology ; Gene-targeted metagenomics ; genes ; High-throughput microarrays ; High-throughput sequencing ; isotope labeling ; Isotope Labeling - methods ; Metagenomics ; Metagenomics - methods ; Metagenomics - trends ; microbial communities ; Phylogeny ; Sequence-based screening ; Stable isotope probing ; stable isotopes</subject><ispartof>Biotechnology advances, 2013-03, Vol.31 (2), p.154-165</ispartof><rights>2012 Elsevier Inc.</rights><rights>2014 INIST-CNRS</rights><rights>Copyright © 2012 Elsevier Inc. All rights reserved.</rights><rights>2012 Elsevier Inc. All rights reserved. 2012</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c533t-69d53da9f7984f341c7a7e0f8c25b2c8e24c628aa6b40a67a61b3291e40fad9c3</citedby><cites>FETCH-LOGICAL-c533t-69d53da9f7984f341c7a7e0f8c25b2c8e24c628aa6b40a67a61b3291e40fad9c3</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktohtml>$$Uhttps://dx.doi.org/10.1016/j.biotechadv.2012.09.003$$EHTML$$P50$$Gelsevier$$H</linktohtml><link.rule.ids>230,314,780,784,885,3550,27924,27925,45995</link.rule.ids><backlink>$$Uhttp://pascal-francis.inist.fr/vibad/index.php?action=getRecordDetail&idt=27081143$$DView record in Pascal Francis$$Hfree_for_read</backlink><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/23022353$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Uhlik, Ondrej</creatorcontrib><creatorcontrib>Leewis, Mary-Cathrine</creatorcontrib><creatorcontrib>Strejcek, Michal</creatorcontrib><creatorcontrib>Musilova, Lucie</creatorcontrib><creatorcontrib>Mackova, Martina</creatorcontrib><creatorcontrib>Leigh, Mary Beth</creatorcontrib><creatorcontrib>Macek, Tomas</creatorcontrib><title>Stable isotope probing in the metagenomics era: A bridge towards improved bioremediation</title><title>Biotechnology advances</title><addtitle>Biotechnol Adv</addtitle><description>Microbial biodegradation and biotransformation reactions are essential to most bioremediation processes, yet the specific organisms, genes, and mechanisms involved are often not well understood. Stable isotope probing (SIP) enables researchers to directly link microbial metabolic capability to phylogenetic and metagenomic information within a community context by tracking isotopically labeled substances into phylogenetically and functionally informative biomarkers. SIP is thus applicable as a tool for the identification of active members of the microbial community and associated genes integral to the community functional potential, such as biodegradative processes. The rapid evolution of SIP over the last decade and integration with metagenomics provide researchers with a much deeper insight into potential biodegradative genes, processes, and applications, thereby enabling an improved mechanistic understanding that can facilitate advances in the field of bioremediation.</description><subject>Biodegradation</subject><subject>Biodegradation, Environmental</subject><subject>Biological and medical sciences</subject><subject>biomarkers</subject><subject>Bioremediation</subject><subject>Biotechnology</subject><subject>biotransformation</subject><subject>Carbon - metabolism</subject><subject>Carbon flow</subject><subject>Environmental Pollutants - metabolism</subject><subject>Function-based screening</subject><subject>Fundamental and applied biological sciences. Psychology</subject><subject>Gene-targeted metagenomics</subject><subject>genes</subject><subject>High-throughput microarrays</subject><subject>High-throughput sequencing</subject><subject>isotope labeling</subject><subject>Isotope Labeling - methods</subject><subject>Metagenomics</subject><subject>Metagenomics - methods</subject><subject>Metagenomics - trends</subject><subject>microbial communities</subject><subject>Phylogeny</subject><subject>Sequence-based screening</subject><subject>Stable isotope probing</subject><subject>stable isotopes</subject><issn>0734-9750</issn><issn>1873-1899</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2013</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNqFkMFu1DAURS0EotPCL4A3LBOe7TiJWSCVigJSJRalEjvrxXnJeDQTj2wziL_HoyktrFh54XPvfTqMcQG1ANG-3dSDD5ncGsdDLUHIGkwNoJ6wleg7VYnemKdsBZ1qKtNpOGPnKW0AhAatnrMzqUBKpdWKfb_NOGyJ-xRy2BPfxzD4ZeZ-4XlNfEcZZ1rCzrvEKeI7fsmH6MeZeA4_MY6J-13JHGjk5aRIOxo9Zh-WF-zZhNtEL-_fC3Z3_fHb1efq5uunL1eXN5XTSuWqNaNWI5qpM30zqUa4DjuCqXdSD9L1JBvXyh6xHRrAtsNWDEoaQQ1MOBqnLtj7U-_-x1DGHS054tbuo99h_GUDevvvz-LXdg4Hq3TXQ2NKQX8qcDGkFGl6yAqwR9t2Yx9t26NtC8YW2yX66u_th-AfvQV4cw9gcridIi7Op0eug16I5si9PnETBotzLMzdbVlqAUDrVupCfDgRVFwePEWbnKfFFd2RXLZj8P-_9zdrLK6f</recordid><startdate>20130301</startdate><enddate>20130301</enddate><creator>Uhlik, Ondrej</creator><creator>Leewis, Mary-Cathrine</creator><creator>Strejcek, Michal</creator><creator>Musilova, Lucie</creator><creator>Mackova, Martina</creator><creator>Leigh, Mary Beth</creator><creator>Macek, Tomas</creator><general>Elsevier Inc</general><general>Elsevier</general><scope>FBQ</scope><scope>IQODW</scope><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>5PM</scope></search><sort><creationdate>20130301</creationdate><title>Stable isotope probing in the metagenomics era: A bridge towards improved bioremediation</title><author>Uhlik, Ondrej ; Leewis, Mary-Cathrine ; Strejcek, Michal ; Musilova, Lucie ; Mackova, Martina ; Leigh, Mary Beth ; Macek, Tomas</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c533t-69d53da9f7984f341c7a7e0f8c25b2c8e24c628aa6b40a67a61b3291e40fad9c3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2013</creationdate><topic>Biodegradation</topic><topic>Biodegradation, Environmental</topic><topic>Biological and medical sciences</topic><topic>biomarkers</topic><topic>Bioremediation</topic><topic>Biotechnology</topic><topic>biotransformation</topic><topic>Carbon - metabolism</topic><topic>Carbon flow</topic><topic>Environmental Pollutants - metabolism</topic><topic>Function-based screening</topic><topic>Fundamental and applied biological sciences. Psychology</topic><topic>Gene-targeted metagenomics</topic><topic>genes</topic><topic>High-throughput microarrays</topic><topic>High-throughput sequencing</topic><topic>isotope labeling</topic><topic>Isotope Labeling - methods</topic><topic>Metagenomics</topic><topic>Metagenomics - methods</topic><topic>Metagenomics - trends</topic><topic>microbial communities</topic><topic>Phylogeny</topic><topic>Sequence-based screening</topic><topic>Stable isotope probing</topic><topic>stable isotopes</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Uhlik, Ondrej</creatorcontrib><creatorcontrib>Leewis, Mary-Cathrine</creatorcontrib><creatorcontrib>Strejcek, Michal</creatorcontrib><creatorcontrib>Musilova, Lucie</creatorcontrib><creatorcontrib>Mackova, Martina</creatorcontrib><creatorcontrib>Leigh, Mary Beth</creatorcontrib><creatorcontrib>Macek, Tomas</creatorcontrib><collection>AGRIS</collection><collection>Pascal-Francis</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>Biotechnology advances</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Uhlik, Ondrej</au><au>Leewis, Mary-Cathrine</au><au>Strejcek, Michal</au><au>Musilova, Lucie</au><au>Mackova, Martina</au><au>Leigh, Mary Beth</au><au>Macek, Tomas</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Stable isotope probing in the metagenomics era: A bridge towards improved bioremediation</atitle><jtitle>Biotechnology advances</jtitle><addtitle>Biotechnol Adv</addtitle><date>2013-03-01</date><risdate>2013</risdate><volume>31</volume><issue>2</issue><spage>154</spage><epage>165</epage><pages>154-165</pages><issn>0734-9750</issn><eissn>1873-1899</eissn><coden>BIADDD</coden><abstract>Microbial biodegradation and biotransformation reactions are essential to most bioremediation processes, yet the specific organisms, genes, and mechanisms involved are often not well understood. Stable isotope probing (SIP) enables researchers to directly link microbial metabolic capability to phylogenetic and metagenomic information within a community context by tracking isotopically labeled substances into phylogenetically and functionally informative biomarkers. SIP is thus applicable as a tool for the identification of active members of the microbial community and associated genes integral to the community functional potential, such as biodegradative processes. The rapid evolution of SIP over the last decade and integration with metagenomics provide researchers with a much deeper insight into potential biodegradative genes, processes, and applications, thereby enabling an improved mechanistic understanding that can facilitate advances in the field of bioremediation.</abstract><cop>Kidlington</cop><pub>Elsevier Inc</pub><pmid>23022353</pmid><doi>10.1016/j.biotechadv.2012.09.003</doi><tpages>12</tpages><oa>free_for_read</oa></addata></record> |
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| language | eng |
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| source | MEDLINE; Access via ScienceDirect (Elsevier) |
| subjects | Biodegradation Biodegradation, Environmental Biological and medical sciences biomarkers Bioremediation Biotechnology biotransformation Carbon - metabolism Carbon flow Environmental Pollutants - metabolism Function-based screening Fundamental and applied biological sciences. Psychology Gene-targeted metagenomics genes High-throughput microarrays High-throughput sequencing isotope labeling Isotope Labeling - methods Metagenomics Metagenomics - methods Metagenomics - trends microbial communities Phylogeny Sequence-based screening Stable isotope probing stable isotopes |
| title | Stable isotope probing in the metagenomics era: A bridge towards improved bioremediation |
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