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DNA extractions from deep subseafloor sediments: Novel cryogenic-mill-based procedure and comparison to existing protocols
Extracting DNA from deep subsurface sediments is challenging given the complexity of sediments types, low biomasses, resting structures (spores, cysts) frequently encountered in deep sediments, and the potential presence of enzymatic inhibitors. Promising results for cell lysis efficiency were recen...
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Published in: | Journal of microbiological methods 2011-12, Vol.87 (3), p.355-362 |
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description | Extracting DNA from deep subsurface sediments is challenging given the complexity of sediments types, low biomasses, resting structures (spores, cysts) frequently encountered in deep sediments, and the potential presence of enzymatic inhibitors. Promising results for cell lysis efficiency were recently obtained by use of a cryogenic mill (Lipp et al., 2008). These findings encouraged us to devise a DNA extraction protocol using this tool. Thirteen procedures involving a combination of grinding in liquid nitrogen (for various durations and beating rates) with different chemical solutions (phenol, chloroform, SDS, sarkosyl, proteinase, GTC), or with use of DNA recovery kits (MagExtractor®) were compared. Effective DNA extraction was evaluated in terms of cell lysis efficiency, DNA extraction efficiency, DNA yield and determination of prokaryotic diversity. Results were compared to those obtained by standard protocols: the FastDNA®SPIN kit for soil and the Zhou protocol. For most sediment types grinding in a cryogenic mill at a low beating rate in combination with direct phenol-chloroform extraction resulted in much higher DNA yields than those obtained using classical procedures. In general (except for clay-rich sediments), this procedure provided high-quality crude extracts for direct downstream nested-PCR, from cell numbers as low as 1.1×106 cells/cm3. This procedure is simple, rapid, low-cost, and could be used with minor modifications for large-scale DNA extractions for a variety of experimental goals.
► Cryogenic-mill was tested as a tool for the first step of DNA extraction from subsurface sediments. ► High cell lysis efficiencies using cryogenic-mill were obtained on different sediment types. ► Thirteen procedures were compared to recover DNA: chemical extractions or kits. ► Grinding at low beating rate followed by phenol-chloroform extraction results in high DNA yields. ► It provides high-quality crude extracts for direct downstream nested-PCR, from low cell numbers. |
doi_str_mv | 10.1016/j.mimet.2011.09.015 |
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► Cryogenic-mill was tested as a tool for the first step of DNA extraction from subsurface sediments. ► High cell lysis efficiencies using cryogenic-mill were obtained on different sediment types. ► Thirteen procedures were compared to recover DNA: chemical extractions or kits. ► Grinding at low beating rate followed by phenol-chloroform extraction results in high DNA yields. ► It provides high-quality crude extracts for direct downstream nested-PCR, from low cell numbers.</description><identifier>ISSN: 0167-7012</identifier><identifier>EISSN: 1872-8359</identifier><identifier>DOI: 10.1016/j.mimet.2011.09.015</identifier><identifier>PMID: 22005039</identifier><identifier>CODEN: JMIMDQ</identifier><language>eng</language><publisher>Amsterdam: Elsevier B.V</publisher><subject>Biodiversity ; Biological and medical sciences ; chloroform ; Cold Temperature ; Deep subsurface biosphere ; DNA ; DNA extraction ; DNA, Archaeal - genetics ; DNA, Archaeal - isolation & purification ; DNA, Bacterial - genetics ; DNA, Bacterial - isolation & purification ; Fundamental and applied biological sciences. Psychology ; Geologic Sediments - microbiology ; grinding ; Life Sciences ; Liquid-Liquid Extraction - methods ; Metagenomics - methods ; Microbiology ; nitrogen ; phenol ; polymerase chain reaction ; proteinases ; Sediment ; sediments ; soil ; Specimen Handling - methods ; spores</subject><ispartof>Journal of microbiological methods, 2011-12, Vol.87 (3), p.355-362</ispartof><rights>2011 Elsevier B.V.</rights><rights>2015 INIST-CNRS</rights><rights>Copyright © 2011 Elsevier B.V. All rights reserved.</rights><rights>Distributed under a Creative Commons Attribution 4.0 International License</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c589t-c9a9f05cd1b5def911b405c4dd6b5b9128670118ce806520e459f5c95cedc76d3</citedby><cites>FETCH-LOGICAL-c589t-c9a9f05cd1b5def911b405c4dd6b5b9128670118ce806520e459f5c95cedc76d3</cites><orcidid>0000-0002-7578-3455 ; 0000-0003-3879-4400 ; 0000-0002-1966-7249</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><link.rule.ids>230,314,780,784,885,27924,27925</link.rule.ids><backlink>$$Uhttp://pascal-francis.inist.fr/vibad/index.php?action=getRecordDetail&idt=24785591$$DView record in Pascal Francis$$Hfree_for_read</backlink><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/22005039$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink><backlink>$$Uhttps://hal.science/hal-04499073$$DView record in HAL$$Hfree_for_read</backlink></links><search><creatorcontrib>Alain, Karine</creatorcontrib><creatorcontrib>Callac, Nolwenn</creatorcontrib><creatorcontrib>Ciobanu, Maria-Cristina</creatorcontrib><creatorcontrib>Reynaud, Yann</creatorcontrib><creatorcontrib>Duthoit, Frédérique</creatorcontrib><creatorcontrib>Jebbar, Mohamed</creatorcontrib><title>DNA extractions from deep subseafloor sediments: Novel cryogenic-mill-based procedure and comparison to existing protocols</title><title>Journal of microbiological methods</title><addtitle>J Microbiol Methods</addtitle><description>Extracting DNA from deep subsurface sediments is challenging given the complexity of sediments types, low biomasses, resting structures (spores, cysts) frequently encountered in deep sediments, and the potential presence of enzymatic inhibitors. Promising results for cell lysis efficiency were recently obtained by use of a cryogenic mill (Lipp et al., 2008). These findings encouraged us to devise a DNA extraction protocol using this tool. Thirteen procedures involving a combination of grinding in liquid nitrogen (for various durations and beating rates) with different chemical solutions (phenol, chloroform, SDS, sarkosyl, proteinase, GTC), or with use of DNA recovery kits (MagExtractor®) were compared. Effective DNA extraction was evaluated in terms of cell lysis efficiency, DNA extraction efficiency, DNA yield and determination of prokaryotic diversity. Results were compared to those obtained by standard protocols: the FastDNA®SPIN kit for soil and the Zhou protocol. For most sediment types grinding in a cryogenic mill at a low beating rate in combination with direct phenol-chloroform extraction resulted in much higher DNA yields than those obtained using classical procedures. In general (except for clay-rich sediments), this procedure provided high-quality crude extracts for direct downstream nested-PCR, from cell numbers as low as 1.1×106 cells/cm3. This procedure is simple, rapid, low-cost, and could be used with minor modifications for large-scale DNA extractions for a variety of experimental goals.
► Cryogenic-mill was tested as a tool for the first step of DNA extraction from subsurface sediments. ► High cell lysis efficiencies using cryogenic-mill were obtained on different sediment types. ► Thirteen procedures were compared to recover DNA: chemical extractions or kits. ► Grinding at low beating rate followed by phenol-chloroform extraction results in high DNA yields. ► It provides high-quality crude extracts for direct downstream nested-PCR, from low cell numbers.</description><subject>Biodiversity</subject><subject>Biological and medical sciences</subject><subject>chloroform</subject><subject>Cold Temperature</subject><subject>Deep subsurface biosphere</subject><subject>DNA</subject><subject>DNA extraction</subject><subject>DNA, Archaeal - genetics</subject><subject>DNA, Archaeal - isolation & purification</subject><subject>DNA, Bacterial - genetics</subject><subject>DNA, Bacterial - isolation & purification</subject><subject>Fundamental and applied biological sciences. Psychology</subject><subject>Geologic Sediments - microbiology</subject><subject>grinding</subject><subject>Life Sciences</subject><subject>Liquid-Liquid Extraction - methods</subject><subject>Metagenomics - methods</subject><subject>Microbiology</subject><subject>nitrogen</subject><subject>phenol</subject><subject>polymerase chain reaction</subject><subject>proteinases</subject><subject>Sediment</subject><subject>sediments</subject><subject>soil</subject><subject>Specimen Handling - methods</subject><subject>spores</subject><issn>0167-7012</issn><issn>1872-8359</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2011</creationdate><recordtype>article</recordtype><recordid>eNqF0c-P1CAUB3BiNO44-heYKBdjPHR8tKUFEw-T9ceaTNaD7plQeB2ZtGWEduL610vtuN70RCAfeO_xJeQpgw0DVr0-bHrX47jJgbENyA0wfo-smKjzTBRc3ierpOqsBpZfkEcxHiCJohQPyUWeA3Ao5Ir8fHe9pfhjDNqMzg-RtsH31CIeaZyaiLrtvA80ok21hjG-odf-hB014dbvcXAm613XZY1Ogh6DN2ingFQPlhrfH3Vw0Q909KmGi6Mb9jMavfFdfEwetLqL-OS8rsnNh_dfL6-y3eePny63u8xwIcfMSC1b4MayhltsJWNNmbaltVXDG8lyUaURmTAooOI5YMlly43kqRVTV7ZYk1fLu990p47B9TrcKq-dutru1HwGZSkl1MWJJftysanL7xPGUfUuGuw6PaCfokrVWcVBiP9LKCG5HJIsFmmCjzFge9cEAzUnqQ7qd5JqTlKBVHNOa_Ls_P7U9Gjv7vyJLoEXZ6Cj0V0b9GBc_OvKWnAu55GeL67VXul9CkTdfEmVKgAoClHWSbxdBKYUTg6DisbhkP7PBTSjst79s9Vfdh3Hcw</recordid><startdate>20111201</startdate><enddate>20111201</enddate><creator>Alain, Karine</creator><creator>Callac, Nolwenn</creator><creator>Ciobanu, Maria-Cristina</creator><creator>Reynaud, Yann</creator><creator>Duthoit, Frédérique</creator><creator>Jebbar, Mohamed</creator><general>Elsevier B.V</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>7X8</scope><scope>7T7</scope><scope>7TM</scope><scope>8FD</scope><scope>C1K</scope><scope>FR3</scope><scope>P64</scope><scope>1XC</scope><orcidid>https://orcid.org/0000-0002-7578-3455</orcidid><orcidid>https://orcid.org/0000-0003-3879-4400</orcidid><orcidid>https://orcid.org/0000-0002-1966-7249</orcidid></search><sort><creationdate>20111201</creationdate><title>DNA extractions from deep subseafloor sediments: Novel cryogenic-mill-based procedure and comparison to existing protocols</title><author>Alain, Karine ; Callac, Nolwenn ; Ciobanu, Maria-Cristina ; Reynaud, Yann ; Duthoit, Frédérique ; Jebbar, Mohamed</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c589t-c9a9f05cd1b5def911b405c4dd6b5b9128670118ce806520e459f5c95cedc76d3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2011</creationdate><topic>Biodiversity</topic><topic>Biological and medical sciences</topic><topic>chloroform</topic><topic>Cold Temperature</topic><topic>Deep subsurface biosphere</topic><topic>DNA</topic><topic>DNA extraction</topic><topic>DNA, Archaeal - genetics</topic><topic>DNA, Archaeal - isolation & purification</topic><topic>DNA, Bacterial - genetics</topic><topic>DNA, Bacterial - isolation & purification</topic><topic>Fundamental and applied biological sciences. Psychology</topic><topic>Geologic Sediments - microbiology</topic><topic>grinding</topic><topic>Life Sciences</topic><topic>Liquid-Liquid Extraction - methods</topic><topic>Metagenomics - methods</topic><topic>Microbiology</topic><topic>nitrogen</topic><topic>phenol</topic><topic>polymerase chain reaction</topic><topic>proteinases</topic><topic>Sediment</topic><topic>sediments</topic><topic>soil</topic><topic>Specimen Handling - methods</topic><topic>spores</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Alain, Karine</creatorcontrib><creatorcontrib>Callac, Nolwenn</creatorcontrib><creatorcontrib>Ciobanu, Maria-Cristina</creatorcontrib><creatorcontrib>Reynaud, Yann</creatorcontrib><creatorcontrib>Duthoit, Frédérique</creatorcontrib><creatorcontrib>Jebbar, Mohamed</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>MEDLINE - Academic</collection><collection>Industrial and Applied Microbiology Abstracts (Microbiology A)</collection><collection>Nucleic Acids Abstracts</collection><collection>Technology Research Database</collection><collection>Environmental Sciences and Pollution Management</collection><collection>Engineering Research Database</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Hyper Article en Ligne (HAL)</collection><jtitle>Journal of microbiological methods</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Alain, Karine</au><au>Callac, Nolwenn</au><au>Ciobanu, Maria-Cristina</au><au>Reynaud, Yann</au><au>Duthoit, Frédérique</au><au>Jebbar, Mohamed</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>DNA extractions from deep subseafloor sediments: Novel cryogenic-mill-based procedure and comparison to existing protocols</atitle><jtitle>Journal of microbiological methods</jtitle><addtitle>J Microbiol Methods</addtitle><date>2011-12-01</date><risdate>2011</risdate><volume>87</volume><issue>3</issue><spage>355</spage><epage>362</epage><pages>355-362</pages><issn>0167-7012</issn><eissn>1872-8359</eissn><coden>JMIMDQ</coden><abstract>Extracting DNA from deep subsurface sediments is challenging given the complexity of sediments types, low biomasses, resting structures (spores, cysts) frequently encountered in deep sediments, and the potential presence of enzymatic inhibitors. Promising results for cell lysis efficiency were recently obtained by use of a cryogenic mill (Lipp et al., 2008). These findings encouraged us to devise a DNA extraction protocol using this tool. Thirteen procedures involving a combination of grinding in liquid nitrogen (for various durations and beating rates) with different chemical solutions (phenol, chloroform, SDS, sarkosyl, proteinase, GTC), or with use of DNA recovery kits (MagExtractor®) were compared. Effective DNA extraction was evaluated in terms of cell lysis efficiency, DNA extraction efficiency, DNA yield and determination of prokaryotic diversity. Results were compared to those obtained by standard protocols: the FastDNA®SPIN kit for soil and the Zhou protocol. For most sediment types grinding in a cryogenic mill at a low beating rate in combination with direct phenol-chloroform extraction resulted in much higher DNA yields than those obtained using classical procedures. In general (except for clay-rich sediments), this procedure provided high-quality crude extracts for direct downstream nested-PCR, from cell numbers as low as 1.1×106 cells/cm3. This procedure is simple, rapid, low-cost, and could be used with minor modifications for large-scale DNA extractions for a variety of experimental goals.
► Cryogenic-mill was tested as a tool for the first step of DNA extraction from subsurface sediments. ► High cell lysis efficiencies using cryogenic-mill were obtained on different sediment types. ► Thirteen procedures were compared to recover DNA: chemical extractions or kits. ► Grinding at low beating rate followed by phenol-chloroform extraction results in high DNA yields. ► It provides high-quality crude extracts for direct downstream nested-PCR, from low cell numbers.</abstract><cop>Amsterdam</cop><pub>Elsevier B.V</pub><pmid>22005039</pmid><doi>10.1016/j.mimet.2011.09.015</doi><tpages>8</tpages><orcidid>https://orcid.org/0000-0002-7578-3455</orcidid><orcidid>https://orcid.org/0000-0003-3879-4400</orcidid><orcidid>https://orcid.org/0000-0002-1966-7249</orcidid><oa>free_for_read</oa></addata></record> |
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subjects | Biodiversity Biological and medical sciences chloroform Cold Temperature Deep subsurface biosphere DNA DNA extraction DNA, Archaeal - genetics DNA, Archaeal - isolation & purification DNA, Bacterial - genetics DNA, Bacterial - isolation & purification Fundamental and applied biological sciences. Psychology Geologic Sediments - microbiology grinding Life Sciences Liquid-Liquid Extraction - methods Metagenomics - methods Microbiology nitrogen phenol polymerase chain reaction proteinases Sediment sediments soil Specimen Handling - methods spores |
title | DNA extractions from deep subseafloor sediments: Novel cryogenic-mill-based procedure and comparison to existing protocols |
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