DNA extraction method affects microbial community profiles from soils and sediment
To evaluate whether different deoxyribonucleic acid (DNA) extraction procedures can affect estimates of bacterial community composition, based on the 16S ribosomal ribonucleic acid gene denaturing gradient gel electrophoresis (DGGE) profiles, we compared four in situ lysis procedures using three soi...
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| Veröffentlicht in: | Applied microbiology and biotechnology 2007-12, Vol.77 (4), p.955-964 |
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| creator | Carrigg, Cora Rice, Olivia Kavanagh, Siobhán Collins, Gavin O'Flaherty, Vincent |
| description | To evaluate whether different deoxyribonucleic acid (DNA) extraction procedures can affect estimates of bacterial community composition, based on the 16S ribosomal ribonucleic acid gene denaturing gradient gel electrophoresis (DGGE) profiles, we compared four in situ lysis procedures using three soils and one marine sediment. Analysis of DGGE profiles, generated by polymerase chain reaction of purified DNA extracts, demonstrated that the choice of DNA extraction method significantly influenced the bacterial community profiles generated. This was reflected both in the number of bands or ribotypes detected from each sample and in subsequent principle coordinate analysis and unweighted-pair group method using arithmetic average analyses. The methods also differed significantly in their robustness, i.e. reproducibility across multiple analyses. Two methods, both based on bead beating, were demonstrated to be suitable for comparative studies of a range of soil and sediment types. |
| doi_str_mv | 10.1007/s00253-007-1219-y |
| format | Article |
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Analysis of DGGE profiles, generated by polymerase chain reaction of purified DNA extracts, demonstrated that the choice of DNA extraction method significantly influenced the bacterial community profiles generated. This was reflected both in the number of bands or ribotypes detected from each sample and in subsequent principle coordinate analysis and unweighted-pair group method using arithmetic average analyses. The methods also differed significantly in their robustness, i.e. reproducibility across multiple analyses. Two methods, both based on bead beating, were demonstrated to be suitable for comparative studies of a range of soil and sediment types.</description><identifier>ISSN: 0175-7598</identifier><identifier>EISSN: 1432-0614</identifier><identifier>DOI: 10.1007/s00253-007-1219-y</identifier><identifier>PMID: 17960375</identifier><identifier>CODEN: AMBIDG</identifier><language>eng</language><publisher>Berlin: Berlin/Heidelberg : Springer-Verlag</publisher><subject>Bacteria - genetics ; Biological and medical sciences ; Biotechnology ; Community composition ; Comparative studies ; Deoxyribonucleic acid ; DGGE ; DNA ; DNA extraction ; DNA, Bacterial - genetics ; DNA, Bacterial - isolation & purification ; DNA, Ribosomal - analysis ; Efficiency ; Electrophoresis, Polyacrylamide Gel - methods ; Environmental Microbiology ; Fundamental and applied biological sciences. Psychology ; Genes ; Geologic Sediments - microbiology ; Laboratories ; Lysis efficiency ; Marine sediments ; Methods ; Microbial diversity ; Microbiology ; Microorganisms ; Nucleic Acid Denaturation ; Polymerase chain reaction ; Reproducibility ; RNA, Ribosomal, 16S - genetics ; Sediments ; soil ; Soil Microbiology ; Soils ; Studies</subject><ispartof>Applied microbiology and biotechnology, 2007-12, Vol.77 (4), p.955-964</ispartof><rights>2008 INIST-CNRS</rights><rights>Springer-Verlag 2007</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c477t-6b345c2d39c85c8c34b62680e697ec03e767db3009e9bbc1952a3fd6151b93e03</citedby><cites>FETCH-LOGICAL-c477t-6b345c2d39c85c8c34b62680e697ec03e767db3009e9bbc1952a3fd6151b93e03</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><link.rule.ids>315,781,785,27929,27930</link.rule.ids><backlink>$$Uhttp://pascal-francis.inist.fr/vibad/index.php?action=getRecordDetail&idt=19959431$$DView record in Pascal Francis$$Hfree_for_read</backlink><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/17960375$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Carrigg, Cora</creatorcontrib><creatorcontrib>Rice, Olivia</creatorcontrib><creatorcontrib>Kavanagh, Siobhán</creatorcontrib><creatorcontrib>Collins, Gavin</creatorcontrib><creatorcontrib>O'Flaherty, Vincent</creatorcontrib><title>DNA extraction method affects microbial community profiles from soils and sediment</title><title>Applied microbiology and biotechnology</title><addtitle>Appl Microbiol Biotechnol</addtitle><description>To evaluate whether different deoxyribonucleic acid (DNA) extraction procedures can affect estimates of bacterial community composition, based on the 16S ribosomal ribonucleic acid gene denaturing gradient gel electrophoresis (DGGE) profiles, we compared four in situ lysis procedures using three soils and one marine sediment. Analysis of DGGE profiles, generated by polymerase chain reaction of purified DNA extracts, demonstrated that the choice of DNA extraction method significantly influenced the bacterial community profiles generated. This was reflected both in the number of bands or ribotypes detected from each sample and in subsequent principle coordinate analysis and unweighted-pair group method using arithmetic average analyses. The methods also differed significantly in their robustness, i.e. reproducibility across multiple analyses. Two methods, both based on bead beating, were demonstrated to be suitable for comparative studies of a range of soil and sediment types.</description><subject>Bacteria - genetics</subject><subject>Biological and medical sciences</subject><subject>Biotechnology</subject><subject>Community composition</subject><subject>Comparative studies</subject><subject>Deoxyribonucleic acid</subject><subject>DGGE</subject><subject>DNA</subject><subject>DNA extraction</subject><subject>DNA, Bacterial - genetics</subject><subject>DNA, Bacterial - isolation & purification</subject><subject>DNA, Ribosomal - analysis</subject><subject>Efficiency</subject><subject>Electrophoresis, Polyacrylamide Gel - methods</subject><subject>Environmental Microbiology</subject><subject>Fundamental and applied biological sciences. Psychology</subject><subject>Genes</subject><subject>Geologic Sediments - microbiology</subject><subject>Laboratories</subject><subject>Lysis efficiency</subject><subject>Marine sediments</subject><subject>Methods</subject><subject>Microbial diversity</subject><subject>Microbiology</subject><subject>Microorganisms</subject><subject>Nucleic Acid Denaturation</subject><subject>Polymerase chain reaction</subject><subject>Reproducibility</subject><subject>RNA, Ribosomal, 16S - genetics</subject><subject>Sediments</subject><subject>soil</subject><subject>Soil Microbiology</subject><subject>Soils</subject><subject>Studies</subject><issn>0175-7598</issn><issn>1432-0614</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2007</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>ABUWG</sourceid><sourceid>AFKRA</sourceid><sourceid>AZQEC</sourceid><sourceid>BENPR</sourceid><sourceid>CCPQU</sourceid><sourceid>DWQXO</sourceid><sourceid>GNUQQ</sourceid><recordid>eNqFkU9r3DAQxUVpaTbbfoBeWhFIb05mJEuyjiH9C6GFtjkLWZZaBdtKJRuy3z5adiHQS08zh98b5r1HyBuECwRQlwWACd7UtUGGutk9IxtsOWtAYvucbACVaJTQ3Qk5LeUOAFkn5UtygkpL4EpsyI8P366of1iydUtMM5388icN1Ibg3VLoFF1OfbQjdWma1jkuO3qfU4ijLzTkNNGS4lionQda_BAnPy-vyItgx-JfH-eW3H76-Ov6S3Pz_fPX66ubxrVKLY3seSscG7h2nXCd420vmezAS628A-6VVEPPAbTXfe9QC2Z5GCQK7DX3wLfk_eFufejv6stiplicH0c7-7QWIzvBZDX6X5ABQ4U1yS05-we8S2ueqwnDWE0MO80rhAeoJlNK9sHc5zjZvDMIZl-LOdRi9uu-FrOrmrfHw2s_-eFJceyhAudHwBZnx5Dt7GJ54rQWuuVYuXcHLthk7O9cmdufDLDG1DFd7fJHzp6dsg</recordid><startdate>20071201</startdate><enddate>20071201</enddate><creator>Carrigg, Cora</creator><creator>Rice, Olivia</creator><creator>Kavanagh, Siobhán</creator><creator>Collins, Gavin</creator><creator>O'Flaherty, Vincent</creator><general>Berlin/Heidelberg : Springer-Verlag</general><general>Springer</general><general>Springer Nature B.V</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>3V.</scope><scope>7QL</scope><scope>7T7</scope><scope>7WY</scope><scope>7WZ</scope><scope>7X7</scope><scope>7XB</scope><scope>87Z</scope><scope>88A</scope><scope>88E</scope><scope>88I</scope><scope>8AO</scope><scope>8FD</scope><scope>8FE</scope><scope>8FH</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>8FL</scope><scope>ABUWG</scope><scope>AFKRA</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BEZIV</scope><scope>BHPHI</scope><scope>C1K</scope><scope>CCPQU</scope><scope>DWQXO</scope><scope>FR3</scope><scope>FRNLG</scope><scope>FYUFA</scope><scope>F~G</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>HCIFZ</scope><scope>K60</scope><scope>K6~</scope><scope>K9.</scope><scope>L.-</scope><scope>LK8</scope><scope>M0C</scope><scope>M0S</scope><scope>M1P</scope><scope>M2P</scope><scope>M7N</scope><scope>M7P</scope><scope>P64</scope><scope>PQBIZ</scope><scope>PQBZA</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>Q9U</scope><scope>7TM</scope><scope>7TN</scope><scope>F1W</scope><scope>H95</scope><scope>H96</scope><scope>L.G</scope><scope>7X8</scope></search><sort><creationdate>20071201</creationdate><title>DNA extraction method affects microbial community profiles from soils and sediment</title><author>Carrigg, Cora ; Rice, Olivia ; Kavanagh, Siobhán ; Collins, Gavin ; O'Flaherty, Vincent</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c477t-6b345c2d39c85c8c34b62680e697ec03e767db3009e9bbc1952a3fd6151b93e03</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2007</creationdate><topic>Bacteria - genetics</topic><topic>Biological and medical sciences</topic><topic>Biotechnology</topic><topic>Community composition</topic><topic>Comparative studies</topic><topic>Deoxyribonucleic acid</topic><topic>DGGE</topic><topic>DNA</topic><topic>DNA extraction</topic><topic>DNA, Bacterial - genetics</topic><topic>DNA, Bacterial - isolation & purification</topic><topic>DNA, Ribosomal - analysis</topic><topic>Efficiency</topic><topic>Electrophoresis, Polyacrylamide Gel - methods</topic><topic>Environmental Microbiology</topic><topic>Fundamental and applied biological sciences. Psychology</topic><topic>Genes</topic><topic>Geologic Sediments - microbiology</topic><topic>Laboratories</topic><topic>Lysis efficiency</topic><topic>Marine sediments</topic><topic>Methods</topic><topic>Microbial diversity</topic><topic>Microbiology</topic><topic>Microorganisms</topic><topic>Nucleic Acid Denaturation</topic><topic>Polymerase chain reaction</topic><topic>Reproducibility</topic><topic>RNA, Ribosomal, 16S - genetics</topic><topic>Sediments</topic><topic>soil</topic><topic>Soil Microbiology</topic><topic>Soils</topic><topic>Studies</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Carrigg, Cora</creatorcontrib><creatorcontrib>Rice, Olivia</creatorcontrib><creatorcontrib>Kavanagh, Siobhán</creatorcontrib><creatorcontrib>Collins, Gavin</creatorcontrib><creatorcontrib>O'Flaherty, Vincent</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>ProQuest Central (Corporate)</collection><collection>Bacteriology Abstracts (Microbiology B)</collection><collection>Industrial and Applied Microbiology Abstracts (Microbiology A)</collection><collection>Access via ABI/INFORM (ProQuest)</collection><collection>ABI/INFORM Global (PDF only)</collection><collection>Health & Medical Collection</collection><collection>ProQuest Central (purchase pre-March 2016)</collection><collection>ABI/INFORM Global (Alumni Edition)</collection><collection>Biology Database (Alumni Edition)</collection><collection>Medical Database (Alumni Edition)</collection><collection>Science Database (Alumni Edition)</collection><collection>ProQuest Pharma Collection</collection><collection>Technology Research Database</collection><collection>ProQuest SciTech Collection</collection><collection>ProQuest Natural Science Collection</collection><collection>Hospital Premium Collection</collection><collection>Hospital Premium Collection (Alumni Edition)</collection><collection>ProQuest Central (Alumni) (purchase pre-March 2016)</collection><collection>ABI/INFORM Collection (Alumni Edition)</collection><collection>ProQuest Central (Alumni Edition)</collection><collection>ProQuest Central UK/Ireland</collection><collection>ProQuest Central Essentials</collection><collection>Biological Science Collection</collection><collection>ProQuest Central</collection><collection>Business Premium Collection</collection><collection>Natural Science Collection (ProQuest)</collection><collection>Environmental Sciences and Pollution Management</collection><collection>ProQuest One Community College</collection><collection>ProQuest Central Korea</collection><collection>Engineering Research Database</collection><collection>Business Premium Collection (Alumni)</collection><collection>Health Research Premium Collection</collection><collection>ABI/INFORM Global (Corporate)</collection><collection>Health Research Premium Collection (Alumni)</collection><collection>ProQuest Central Student</collection><collection>SciTech Premium Collection</collection><collection>ProQuest Business Collection (Alumni Edition)</collection><collection>ProQuest Business Collection</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>ABI/INFORM Professional Advanced</collection><collection>ProQuest Biological Science Collection</collection><collection>ABI/INFORM Global</collection><collection>Health & Medical Collection (Alumni Edition)</collection><collection>Medical Database</collection><collection>Science Database (ProQuest)</collection><collection>Algology Mycology and Protozoology Abstracts (Microbiology C)</collection><collection>Biological Science Database</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>ProQuest One Business</collection><collection>ProQuest One Business (Alumni)</collection><collection>ProQuest One Academic Eastern Edition (DO NOT USE)</collection><collection>ProQuest One Academic</collection><collection>ProQuest One Academic UKI Edition</collection><collection>ProQuest Central Basic</collection><collection>Nucleic Acids Abstracts</collection><collection>Oceanic Abstracts</collection><collection>ASFA: Aquatic Sciences and Fisheries Abstracts</collection><collection>Aquatic Science & Fisheries Abstracts (ASFA) 1: Biological Sciences & Living Resources</collection><collection>Aquatic Science & Fisheries Abstracts (ASFA) 2: Ocean Technology, Policy & Non-Living Resources</collection><collection>Aquatic Science & Fisheries Abstracts (ASFA) Professional</collection><collection>MEDLINE - 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Analysis of DGGE profiles, generated by polymerase chain reaction of purified DNA extracts, demonstrated that the choice of DNA extraction method significantly influenced the bacterial community profiles generated. This was reflected both in the number of bands or ribotypes detected from each sample and in subsequent principle coordinate analysis and unweighted-pair group method using arithmetic average analyses. The methods also differed significantly in their robustness, i.e. reproducibility across multiple analyses. Two methods, both based on bead beating, were demonstrated to be suitable for comparative studies of a range of soil and sediment types.</abstract><cop>Berlin</cop><pub>Berlin/Heidelberg : Springer-Verlag</pub><pmid>17960375</pmid><doi>10.1007/s00253-007-1219-y</doi><tpages>10</tpages></addata></record> |
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| subjects | Bacteria - genetics Biological and medical sciences Biotechnology Community composition Comparative studies Deoxyribonucleic acid DGGE DNA DNA extraction DNA, Bacterial - genetics DNA, Bacterial - isolation & purification DNA, Ribosomal - analysis Efficiency Electrophoresis, Polyacrylamide Gel - methods Environmental Microbiology Fundamental and applied biological sciences. Psychology Genes Geologic Sediments - microbiology Laboratories Lysis efficiency Marine sediments Methods Microbial diversity Microbiology Microorganisms Nucleic Acid Denaturation Polymerase chain reaction Reproducibility RNA, Ribosomal, 16S - genetics Sediments soil Soil Microbiology Soils Studies |
| title | DNA extraction method affects microbial community profiles from soils and sediment |
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