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DNA isolation from soil samples for cloning in different hosts
Many protocols to extract DNA directly from soil samples have been developed in recent years. We employed two extraction methods which differed in the method of lysis and compared these methods with respect to yield, purity and degree of shearing. The main focus was on the specific isolation of DNA...
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Published in: | Applied microbiology and biotechnology 2004-06, Vol.64 (5), p.665-670 |
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description | Many protocols to extract DNA directly from soil samples have been developed in recent years. We employed two extraction methods which differed in the method of lysis and compared these methods with respect to yield, purity and degree of shearing. The main focus was on the specific isolation of DNA from different microorganisms, especially DNA from actinomycetes, as these cells are very difficult to lyse, in contrast to non-actinomycetes. Thus, we used both methods to isolate DNA from Pseudomonas, Arthrobacter and Rhodococcus and from soil spiked with the respective microorganisms. Both methods rendered high DNA yields with a low degree of shearing, but differed in the type of cells that were lysed. By one protocol (utilizing enzymatic lysis) only DNA from the Gram-negative Pseudomonas strain could be obtained whereas, by the other protocol (utilizing mechanical lysis), all microorganisms that were used could be lysed and DNA extracted from them. Using a combination of both protocols, DNA from those organisms could be obtained selectively. Furthermore, one of the protocols was modified, resulting in higher DNA yield and purity. |
doi_str_mv | 10.1007/s00253-003-1528-8 |
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We employed two extraction methods which differed in the method of lysis and compared these methods with respect to yield, purity and degree of shearing. The main focus was on the specific isolation of DNA from different microorganisms, especially DNA from actinomycetes, as these cells are very difficult to lyse, in contrast to non-actinomycetes. Thus, we used both methods to isolate DNA from Pseudomonas, Arthrobacter and Rhodococcus and from soil spiked with the respective microorganisms. Both methods rendered high DNA yields with a low degree of shearing, but differed in the type of cells that were lysed. By one protocol (utilizing enzymatic lysis) only DNA from the Gram-negative Pseudomonas strain could be obtained whereas, by the other protocol (utilizing mechanical lysis), all microorganisms that were used could be lysed and DNA extracted from them. Using a combination of both protocols, DNA from those organisms could be obtained selectively. Furthermore, one of the protocols was modified, resulting in higher DNA yield and purity.</description><identifier>ISSN: 0175-7598</identifier><identifier>EISSN: 1432-0614</identifier><identifier>DOI: 10.1007/s00253-003-1528-8</identifier><identifier>PMID: 14758515</identifier><identifier>CODEN: AMBIDG</identifier><language>eng</language><publisher>Berlin: Springer</publisher><subject>Actinobacteria - genetics ; Actinomycetes ; Arthrobacter ; Biological and medical sciences ; Biotechnology ; Cloning ; Cloning, Molecular ; Deoxyribonucleic acid ; DNA ; DNA, Bacterial - chemistry ; DNA, Bacterial - genetics ; DNA, Bacterial - isolation & purification ; extraction ; Fundamental and applied biological sciences. Psychology ; Gram-negative bacteria ; Gram-positive bacteria ; Methods ; Microorganisms ; Polymerase Chain Reaction ; Pseudomonas ; Rhodococcus ; RNA, Ribosomal, 23S - chemistry ; RNA, Ribosomal, 23S - genetics ; soil bacteria ; soil biology ; Soil Microbiology ; Specimen Handling - methods</subject><ispartof>Applied microbiology and biotechnology, 2004-06, Vol.64 (5), p.665-670</ispartof><rights>2004 INIST-CNRS</rights><rights>Springer-Verlag 2004</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c555t-c49d97f312b47071d5843ab1d034de12b54249fb60e84e40fe0cd41e2a3b904e3</citedby></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.proquest.com/docview/621073662/fulltextPDF?pq-origsite=primo$$EPDF$$P50$$Gproquest$$H</linktopdf><linktohtml>$$Uhttps://www.proquest.com/docview/621073662?pq-origsite=primo$$EHTML$$P50$$Gproquest$$H</linktohtml><link.rule.ids>314,780,784,11688,27924,27925,36060,36061,44363,74895</link.rule.ids><backlink>$$Uhttp://pascal-francis.inist.fr/vibad/index.php?action=getRecordDetail&idt=15849134$$DView record in Pascal Francis$$Hfree_for_read</backlink><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/14758515$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Kauffmann, I.M</creatorcontrib><creatorcontrib>Schmitt, J</creatorcontrib><creatorcontrib>Schmid, R.D</creatorcontrib><title>DNA isolation from soil samples for cloning in different hosts</title><title>Applied microbiology and biotechnology</title><addtitle>Appl Microbiol Biotechnol</addtitle><description>Many protocols to extract DNA directly from soil samples have been developed in recent years. We employed two extraction methods which differed in the method of lysis and compared these methods with respect to yield, purity and degree of shearing. The main focus was on the specific isolation of DNA from different microorganisms, especially DNA from actinomycetes, as these cells are very difficult to lyse, in contrast to non-actinomycetes. Thus, we used both methods to isolate DNA from Pseudomonas, Arthrobacter and Rhodococcus and from soil spiked with the respective microorganisms. Both methods rendered high DNA yields with a low degree of shearing, but differed in the type of cells that were lysed. By one protocol (utilizing enzymatic lysis) only DNA from the Gram-negative Pseudomonas strain could be obtained whereas, by the other protocol (utilizing mechanical lysis), all microorganisms that were used could be lysed and DNA extracted from them. Using a combination of both protocols, DNA from those organisms could be obtained selectively. Furthermore, one of the protocols was modified, resulting in higher DNA yield and purity.</description><subject>Actinobacteria - genetics</subject><subject>Actinomycetes</subject><subject>Arthrobacter</subject><subject>Biological and medical sciences</subject><subject>Biotechnology</subject><subject>Cloning</subject><subject>Cloning, Molecular</subject><subject>Deoxyribonucleic acid</subject><subject>DNA</subject><subject>DNA, Bacterial - chemistry</subject><subject>DNA, Bacterial - genetics</subject><subject>DNA, Bacterial - isolation & purification</subject><subject>extraction</subject><subject>Fundamental and applied biological sciences. Psychology</subject><subject>Gram-negative bacteria</subject><subject>Gram-positive bacteria</subject><subject>Methods</subject><subject>Microorganisms</subject><subject>Polymerase Chain Reaction</subject><subject>Pseudomonas</subject><subject>Rhodococcus</subject><subject>RNA, Ribosomal, 23S - chemistry</subject><subject>RNA, Ribosomal, 23S - genetics</subject><subject>soil bacteria</subject><subject>soil biology</subject><subject>Soil Microbiology</subject><subject>Specimen Handling - methods</subject><issn>0175-7598</issn><issn>1432-0614</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2004</creationdate><recordtype>article</recordtype><sourceid>M0C</sourceid><recordid>eNqF0U1rFTEUBuBQKvZa_QHd2CDobvScfGcjlPoJpV1o1yEzk9SUmcltMnfhvzflXih04ypweM4LOS8hZwgfEUB_qgBM8g6AdyiZ6cwR2aDgrAOF4phsALXstLTmhLyq9R4AmVHqJTlBoaWRKDfk85frC5pqnvya8kJjyTOtOU20-nk7hUpjLnSY8pKWO5oWOqYYQwnLSv_kutbX5EX0Uw1vDu8puf329fflj-7q5vvPy4urbpBSrt0g7Gh15Mh6oUHjKI3gvscRuBhDm0rBhI29gmBEEBADDKPAwDzvLYjAT8mHfe625IddqKubUx3CNPkl5F11Gi1DkPq_EA0osFI1-O4ZvM-7srRPONWiNFeKNYR7NJRcawnRbUuaffnrENxjBW5fgWsVuMcKnGk7bw_Bu34O49PG4eYNvD8AXwc_xeKXIdUn125jkYvmzvcu-uz8XWnm9hcD5ACWm3YW_g_R_JUX</recordid><startdate>20040601</startdate><enddate>20040601</enddate><creator>Kauffmann, I.M</creator><creator>Schmitt, J</creator><creator>Schmid, R.D</creator><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>7X8</scope></search><sort><creationdate>20040601</creationdate><title>DNA isolation from soil samples for cloning in different hosts</title><author>Kauffmann, I.M ; Schmitt, J ; Schmid, R.D</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c555t-c49d97f312b47071d5843ab1d034de12b54249fb60e84e40fe0cd41e2a3b904e3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2004</creationdate><topic>Actinobacteria - genetics</topic><topic>Actinomycetes</topic><topic>Arthrobacter</topic><topic>Biological and medical sciences</topic><topic>Biotechnology</topic><topic>Cloning</topic><topic>Cloning, Molecular</topic><topic>Deoxyribonucleic acid</topic><topic>DNA</topic><topic>DNA, Bacterial - chemistry</topic><topic>DNA, Bacterial - genetics</topic><topic>DNA, Bacterial - isolation & purification</topic><topic>extraction</topic><topic>Fundamental and applied biological sciences. Psychology</topic><topic>Gram-negative bacteria</topic><topic>Gram-positive bacteria</topic><topic>Methods</topic><topic>Microorganisms</topic><topic>Polymerase Chain Reaction</topic><topic>Pseudomonas</topic><topic>Rhodococcus</topic><topic>RNA, Ribosomal, 23S - chemistry</topic><topic>RNA, Ribosomal, 23S - genetics</topic><topic>soil bacteria</topic><topic>soil biology</topic><topic>Soil Microbiology</topic><topic>Specimen Handling - methods</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Kauffmann, I.M</creatorcontrib><creatorcontrib>Schmitt, J</creatorcontrib><creatorcontrib>Schmid, R.D</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>ABI/INFORM Collection</collection><collection>ABI/INFORM Global (PDF only)</collection><collection>Health & Medical Collection (Proquest)</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)</collection><collection>ProQuest Central</collection><collection>ProQuest Central Essentials</collection><collection>Biological Science Collection</collection><collection>AUTh Library subscriptions: ProQuest Central</collection><collection>Business Premium Collection</collection><collection>Natural Science Collection</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>One Business (ProQuest)</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>MEDLINE - Academic</collection><jtitle>Applied microbiology and biotechnology</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Kauffmann, I.M</au><au>Schmitt, J</au><au>Schmid, R.D</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>DNA isolation from soil samples for cloning in different hosts</atitle><jtitle>Applied microbiology and biotechnology</jtitle><addtitle>Appl Microbiol Biotechnol</addtitle><date>2004-06-01</date><risdate>2004</risdate><volume>64</volume><issue>5</issue><spage>665</spage><epage>670</epage><pages>665-670</pages><issn>0175-7598</issn><eissn>1432-0614</eissn><coden>AMBIDG</coden><abstract>Many protocols to extract DNA directly from soil samples have been developed in recent years. We employed two extraction methods which differed in the method of lysis and compared these methods with respect to yield, purity and degree of shearing. The main focus was on the specific isolation of DNA from different microorganisms, especially DNA from actinomycetes, as these cells are very difficult to lyse, in contrast to non-actinomycetes. Thus, we used both methods to isolate DNA from Pseudomonas, Arthrobacter and Rhodococcus and from soil spiked with the respective microorganisms. Both methods rendered high DNA yields with a low degree of shearing, but differed in the type of cells that were lysed. By one protocol (utilizing enzymatic lysis) only DNA from the Gram-negative Pseudomonas strain could be obtained whereas, by the other protocol (utilizing mechanical lysis), all microorganisms that were used could be lysed and DNA extracted from them. Using a combination of both protocols, DNA from those organisms could be obtained selectively. Furthermore, one of the protocols was modified, resulting in higher DNA yield and purity.</abstract><cop>Berlin</cop><pub>Springer</pub><pmid>14758515</pmid><doi>10.1007/s00253-003-1528-8</doi><tpages>6</tpages><oa>free_for_read</oa></addata></record> |
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subjects | Actinobacteria - genetics Actinomycetes Arthrobacter Biological and medical sciences Biotechnology Cloning Cloning, Molecular Deoxyribonucleic acid DNA DNA, Bacterial - chemistry DNA, Bacterial - genetics DNA, Bacterial - isolation & purification extraction Fundamental and applied biological sciences. Psychology Gram-negative bacteria Gram-positive bacteria Methods Microorganisms Polymerase Chain Reaction Pseudomonas Rhodococcus RNA, Ribosomal, 23S - chemistry RNA, Ribosomal, 23S - genetics soil bacteria soil biology Soil Microbiology Specimen Handling - methods |
title | DNA isolation from soil samples for cloning in different hosts |
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