pcaH, a molecular marker for estimating the diversity of the protocatechuate-degrading bacterial community in the soil environment
Microorganisms degrading phenolic compounds play an important role in soil carbon cycling as well as in pesticide degradation. The pcaH gene encoding a key ring-cleaving enzyme of the β-ketoadipate pathway was selected as a functional marker. Using a degenerate primer pair, pcaH fragments were clone...
Gespeichert in:
| Veröffentlicht in: | Pest management science 2007-05, Vol.63 (5), p.459-467 |
|---|---|
| Hauptverfasser: | , , , , |
| Format: | Artikel |
| Sprache: | eng |
| Schlagworte: | |
| Online-Zugang: | Volltext |
| Tags: |
Tag hinzufügen
Keine Tags, Fügen Sie den ersten Tag hinzu!
|
| container_end_page | 467 |
|---|---|
| container_issue | 5 |
| container_start_page | 459 |
| container_title | Pest management science |
| container_volume | 63 |
| creator | El Azhari, N Chabaud, S Percept, A Bru, D Martin-Laurent, F |
| description | Microorganisms degrading phenolic compounds play an important role in soil carbon cycling as well as in pesticide degradation. The pcaH gene encoding a key ring-cleaving enzyme of the β-ketoadipate pathway was selected as a functional marker. Using a degenerate primer pair, pcaH fragments were cloned from two agricultural soils. Restriction fragment length polymorphism (RFLP) screening of 150 pcaH clones yielded 68 RFLP families. Comparison of 86 deduced amino acid sequences displayed 70% identity to known PcaH sequences. Phylogenetic analysis results in two major groups mainly related to PcaH sequences from Actinobacteria and Proteobacteria phyla. This confirms that the developed primer pair targets a wide diversity of pcaH sequences, thereby constituting a suitable molecular marker to estimate the response of the pca community to agricultural practices. |
| doi_str_mv | 10.1002/ps.1357 |
| format | Article |
| fullrecord | <record><control><sourceid>proquest_hal_p</sourceid><recordid>TN_cdi_hal_primary_oai_HAL_hal_02666228v1</recordid><sourceformat>XML</sourceformat><sourcesystem>PC</sourcesystem><sourcerecordid>1254194221</sourcerecordid><originalsourceid>FETCH-LOGICAL-c4687-239d8e1535ceacb269016fd0975b953de83c0fb4006495d624a4949b71f935d03</originalsourceid><addsrcrecordid>eNp10dtu0zAYAOAIgdgYiDcACwkhBBk-x76cBqxIFacx6J3lOE7rkcTBTgq95clxlqq74sa2rO8_2H-WPUbwFEGI3_TxFBFW3MmOEcM8p1KKu4ezWB1lD2K8hhBKKfH97AgVFBeIw-Psb2_04jXQoPWNNWOjA2h1-GkDqH0ANg6u1YPr1mDYWFC5rQ3RDTvg65uLPvjBGz1YsxnTmld2HXQ18VKbwQanG2B8247dFOS6m6DoXQNst3XBd63thofZvVo30T7a7yfZ1ft3384X-fLTxYfzs2VuKBdFjomshEWMMGO1KTGXEPG6grJgpWSksoIYWJcUQk4lqzimmkoqywLVkrAKkpPs5Zx3oxvVh_SwsFNeO7U4W6rpDmLOOcZii5J9Ntv0wl9j-gZ17cfQpfYUxpgjQaFI6MWMTPAxBlsfsiKoprGoPqppLEk-2acby9ZWt24_hwSe74GORjd10J1x8dYJLgijOLlXs_vtGrv7Xz31-XJfNp-1i4P9c9BpvooXpGDqx8cLtXr7fQW_rr4omvzT2dfaK70OqYOrSwwRgbBIAamHfxDQuxo</addsrcrecordid><sourcetype>Open Access Repository</sourcetype><iscdi>true</iscdi><recordtype>article</recordtype><pqid>222618408</pqid></control><display><type>article</type><title>pcaH, a molecular marker for estimating the diversity of the protocatechuate-degrading bacterial community in the soil environment</title><source>MEDLINE</source><source>Access via Wiley Online Library</source><creator>El Azhari, N ; Chabaud, S ; Percept, A ; Bru, D ; Martin-Laurent, F</creator><creatorcontrib>El Azhari, N ; Chabaud, S ; Percept, A ; Bru, D ; Martin-Laurent, F</creatorcontrib><description>Microorganisms degrading phenolic compounds play an important role in soil carbon cycling as well as in pesticide degradation. The pcaH gene encoding a key ring-cleaving enzyme of the β-ketoadipate pathway was selected as a functional marker. Using a degenerate primer pair, pcaH fragments were cloned from two agricultural soils. Restriction fragment length polymorphism (RFLP) screening of 150 pcaH clones yielded 68 RFLP families. Comparison of 86 deduced amino acid sequences displayed 70% identity to known PcaH sequences. Phylogenetic analysis results in two major groups mainly related to PcaH sequences from Actinobacteria and Proteobacteria phyla. This confirms that the developed primer pair targets a wide diversity of pcaH sequences, thereby constituting a suitable molecular marker to estimate the response of the pca community to agricultural practices.</description><identifier>ISSN: 1526-498X</identifier><identifier>EISSN: 1526-4998</identifier><identifier>DOI: 10.1002/ps.1357</identifier><identifier>PMID: 17427160</identifier><identifier>CODEN: PMSCFC</identifier><language>eng</language><publisher>Chichester, UK: John Wiley & Sons, Ltd</publisher><subject>4-dioxygenase ; Actinobacteria ; Actinobacteria - classification ; Actinobacteria - genetics ; Actinobacteria - metabolism ; agricultural soils ; Amino Acid Sequence ; amino acid sequences ; Bacteria ; bacterial community ; Bacterial Proteins - genetics ; biodegradation ; Biodegradation, Environmental ; Biodiversity ; Biological and medical sciences ; Carbon - metabolism ; Cloning ; DNA fingerprinting ; DNA Primers ; Environmental Sciences ; Fundamental and applied biological sciences. Psychology ; genes ; Genetic diversity ; Genetic Markers ; Life Sciences ; microbial genetics ; Molecular Sequence Data ; nucleotide sequences ; Pesticides ; Pesticides - metabolism ; phenolic compounds ; Phylogeny ; Phytopathology. Animal pests. Plant and forest protection ; Polymorphism, Restriction Fragment Length ; Proteobacteria ; Proteobacteria - classification ; Proteobacteria - genetics ; Proteobacteria - metabolism ; protocatechuate 3 ; protocatechuate 3,4‐dioxygenase ; Protocatechuate-3,4-Dioxygenase - genetics ; Protocatechuate-3,4-Dioxygenase - metabolism ; protocatechuic acid ; quantitative analysis ; Sequence Alignment ; Sequence Analysis, Protein ; soil bacteria ; soil DNA ; Soil Microbiology ; Soils</subject><ispartof>Pest management science, 2007-05, Vol.63 (5), p.459-467</ispartof><rights>Copyright © 2007 Society of Chemical Industry</rights><rights>2007 INIST-CNRS</rights><rights>Copyright John Wiley and Sons, Limited May 2007</rights><rights>Distributed under a Creative Commons Attribution 4.0 International License</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c4687-239d8e1535ceacb269016fd0975b953de83c0fb4006495d624a4949b71f935d03</citedby><cites>FETCH-LOGICAL-c4687-239d8e1535ceacb269016fd0975b953de83c0fb4006495d624a4949b71f935d03</cites><orcidid>0000-0001-9410-8319</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://onlinelibrary.wiley.com/doi/pdf/10.1002%2Fps.1357$$EPDF$$P50$$Gwiley$$H</linktopdf><linktohtml>$$Uhttps://onlinelibrary.wiley.com/doi/full/10.1002%2Fps.1357$$EHTML$$P50$$Gwiley$$H</linktohtml><link.rule.ids>230,314,780,784,885,1417,27924,27925,45574,45575</link.rule.ids><backlink>$$Uhttp://pascal-francis.inist.fr/vibad/index.php?action=getRecordDetail&idt=18683542$$DView record in Pascal Francis$$Hfree_for_read</backlink><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/17427160$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink><backlink>$$Uhttps://hal.inrae.fr/hal-02666228$$DView record in HAL$$Hfree_for_read</backlink></links><search><creatorcontrib>El Azhari, N</creatorcontrib><creatorcontrib>Chabaud, S</creatorcontrib><creatorcontrib>Percept, A</creatorcontrib><creatorcontrib>Bru, D</creatorcontrib><creatorcontrib>Martin-Laurent, F</creatorcontrib><title>pcaH, a molecular marker for estimating the diversity of the protocatechuate-degrading bacterial community in the soil environment</title><title>Pest management science</title><addtitle>Pest. Manag. Sci</addtitle><description>Microorganisms degrading phenolic compounds play an important role in soil carbon cycling as well as in pesticide degradation. The pcaH gene encoding a key ring-cleaving enzyme of the β-ketoadipate pathway was selected as a functional marker. Using a degenerate primer pair, pcaH fragments were cloned from two agricultural soils. Restriction fragment length polymorphism (RFLP) screening of 150 pcaH clones yielded 68 RFLP families. Comparison of 86 deduced amino acid sequences displayed 70% identity to known PcaH sequences. Phylogenetic analysis results in two major groups mainly related to PcaH sequences from Actinobacteria and Proteobacteria phyla. This confirms that the developed primer pair targets a wide diversity of pcaH sequences, thereby constituting a suitable molecular marker to estimate the response of the pca community to agricultural practices.</description><subject>4-dioxygenase</subject><subject>Actinobacteria</subject><subject>Actinobacteria - classification</subject><subject>Actinobacteria - genetics</subject><subject>Actinobacteria - metabolism</subject><subject>agricultural soils</subject><subject>Amino Acid Sequence</subject><subject>amino acid sequences</subject><subject>Bacteria</subject><subject>bacterial community</subject><subject>Bacterial Proteins - genetics</subject><subject>biodegradation</subject><subject>Biodegradation, Environmental</subject><subject>Biodiversity</subject><subject>Biological and medical sciences</subject><subject>Carbon - metabolism</subject><subject>Cloning</subject><subject>DNA fingerprinting</subject><subject>DNA Primers</subject><subject>Environmental Sciences</subject><subject>Fundamental and applied biological sciences. Psychology</subject><subject>genes</subject><subject>Genetic diversity</subject><subject>Genetic Markers</subject><subject>Life Sciences</subject><subject>microbial genetics</subject><subject>Molecular Sequence Data</subject><subject>nucleotide sequences</subject><subject>Pesticides</subject><subject>Pesticides - metabolism</subject><subject>phenolic compounds</subject><subject>Phylogeny</subject><subject>Phytopathology. Animal pests. Plant and forest protection</subject><subject>Polymorphism, Restriction Fragment Length</subject><subject>Proteobacteria</subject><subject>Proteobacteria - classification</subject><subject>Proteobacteria - genetics</subject><subject>Proteobacteria - metabolism</subject><subject>protocatechuate 3</subject><subject>protocatechuate 3,4‐dioxygenase</subject><subject>Protocatechuate-3,4-Dioxygenase - genetics</subject><subject>Protocatechuate-3,4-Dioxygenase - metabolism</subject><subject>protocatechuic acid</subject><subject>quantitative analysis</subject><subject>Sequence Alignment</subject><subject>Sequence Analysis, Protein</subject><subject>soil bacteria</subject><subject>soil DNA</subject><subject>Soil Microbiology</subject><subject>Soils</subject><issn>1526-498X</issn><issn>1526-4998</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2007</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNp10dtu0zAYAOAIgdgYiDcACwkhBBk-x76cBqxIFacx6J3lOE7rkcTBTgq95clxlqq74sa2rO8_2H-WPUbwFEGI3_TxFBFW3MmOEcM8p1KKu4ezWB1lD2K8hhBKKfH97AgVFBeIw-Psb2_04jXQoPWNNWOjA2h1-GkDqH0ANg6u1YPr1mDYWFC5rQ3RDTvg65uLPvjBGz1YsxnTmld2HXQ18VKbwQanG2B8247dFOS6m6DoXQNst3XBd63thofZvVo30T7a7yfZ1ft3384X-fLTxYfzs2VuKBdFjomshEWMMGO1KTGXEPG6grJgpWSksoIYWJcUQk4lqzimmkoqywLVkrAKkpPs5Zx3oxvVh_SwsFNeO7U4W6rpDmLOOcZii5J9Ntv0wl9j-gZ17cfQpfYUxpgjQaFI6MWMTPAxBlsfsiKoprGoPqppLEk-2acby9ZWt24_hwSe74GORjd10J1x8dYJLgijOLlXs_vtGrv7Xz31-XJfNp-1i4P9c9BpvooXpGDqx8cLtXr7fQW_rr4omvzT2dfaK70OqYOrSwwRgbBIAamHfxDQuxo</recordid><startdate>200705</startdate><enddate>200705</enddate><creator>El Azhari, N</creator><creator>Chabaud, S</creator><creator>Percept, A</creator><creator>Bru, D</creator><creator>Martin-Laurent, F</creator><general>John Wiley & Sons, Ltd</general><general>Wiley</general><general>Wiley Subscription Services, Inc</general><scope>FBQ</scope><scope>BSCLL</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>7QR</scope><scope>7SS</scope><scope>7ST</scope><scope>7T7</scope><scope>7U7</scope><scope>8FD</scope><scope>C1K</scope><scope>FR3</scope><scope>P64</scope><scope>SOI</scope><scope>1XC</scope><orcidid>https://orcid.org/0000-0001-9410-8319</orcidid></search><sort><creationdate>200705</creationdate><title>pcaH, a molecular marker for estimating the diversity of the protocatechuate-degrading bacterial community in the soil environment</title><author>El Azhari, N ; Chabaud, S ; Percept, A ; Bru, D ; Martin-Laurent, F</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c4687-239d8e1535ceacb269016fd0975b953de83c0fb4006495d624a4949b71f935d03</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2007</creationdate><topic>4-dioxygenase</topic><topic>Actinobacteria</topic><topic>Actinobacteria - classification</topic><topic>Actinobacteria - genetics</topic><topic>Actinobacteria - metabolism</topic><topic>agricultural soils</topic><topic>Amino Acid Sequence</topic><topic>amino acid sequences</topic><topic>Bacteria</topic><topic>bacterial community</topic><topic>Bacterial Proteins - genetics</topic><topic>biodegradation</topic><topic>Biodegradation, Environmental</topic><topic>Biodiversity</topic><topic>Biological and medical sciences</topic><topic>Carbon - metabolism</topic><topic>Cloning</topic><topic>DNA fingerprinting</topic><topic>DNA Primers</topic><topic>Environmental Sciences</topic><topic>Fundamental and applied biological sciences. Psychology</topic><topic>genes</topic><topic>Genetic diversity</topic><topic>Genetic Markers</topic><topic>Life Sciences</topic><topic>microbial genetics</topic><topic>Molecular Sequence Data</topic><topic>nucleotide sequences</topic><topic>Pesticides</topic><topic>Pesticides - metabolism</topic><topic>phenolic compounds</topic><topic>Phylogeny</topic><topic>Phytopathology. Animal pests. Plant and forest protection</topic><topic>Polymorphism, Restriction Fragment Length</topic><topic>Proteobacteria</topic><topic>Proteobacteria - classification</topic><topic>Proteobacteria - genetics</topic><topic>Proteobacteria - metabolism</topic><topic>protocatechuate 3</topic><topic>protocatechuate 3,4‐dioxygenase</topic><topic>Protocatechuate-3,4-Dioxygenase - genetics</topic><topic>Protocatechuate-3,4-Dioxygenase - metabolism</topic><topic>protocatechuic acid</topic><topic>quantitative analysis</topic><topic>Sequence Alignment</topic><topic>Sequence Analysis, Protein</topic><topic>soil bacteria</topic><topic>soil DNA</topic><topic>Soil Microbiology</topic><topic>Soils</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>El Azhari, N</creatorcontrib><creatorcontrib>Chabaud, S</creatorcontrib><creatorcontrib>Percept, A</creatorcontrib><creatorcontrib>Bru, D</creatorcontrib><creatorcontrib>Martin-Laurent, F</creatorcontrib><collection>AGRIS</collection><collection>Istex</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>Chemoreception Abstracts</collection><collection>Entomology Abstracts (Full archive)</collection><collection>Environment Abstracts</collection><collection>Industrial and Applied Microbiology Abstracts (Microbiology A)</collection><collection>Toxicology 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>Environment Abstracts</collection><collection>Hyper Article en Ligne (HAL)</collection><jtitle>Pest management science</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>El Azhari, N</au><au>Chabaud, S</au><au>Percept, A</au><au>Bru, D</au><au>Martin-Laurent, F</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>pcaH, a molecular marker for estimating the diversity of the protocatechuate-degrading bacterial community in the soil environment</atitle><jtitle>Pest management science</jtitle><addtitle>Pest. Manag. Sci</addtitle><date>2007-05</date><risdate>2007</risdate><volume>63</volume><issue>5</issue><spage>459</spage><epage>467</epage><pages>459-467</pages><issn>1526-498X</issn><eissn>1526-4998</eissn><coden>PMSCFC</coden><abstract>Microorganisms degrading phenolic compounds play an important role in soil carbon cycling as well as in pesticide degradation. The pcaH gene encoding a key ring-cleaving enzyme of the β-ketoadipate pathway was selected as a functional marker. Using a degenerate primer pair, pcaH fragments were cloned from two agricultural soils. Restriction fragment length polymorphism (RFLP) screening of 150 pcaH clones yielded 68 RFLP families. Comparison of 86 deduced amino acid sequences displayed 70% identity to known PcaH sequences. Phylogenetic analysis results in two major groups mainly related to PcaH sequences from Actinobacteria and Proteobacteria phyla. This confirms that the developed primer pair targets a wide diversity of pcaH sequences, thereby constituting a suitable molecular marker to estimate the response of the pca community to agricultural practices.</abstract><cop>Chichester, UK</cop><pub>John Wiley & Sons, Ltd</pub><pmid>17427160</pmid><doi>10.1002/ps.1357</doi><tpages>9</tpages><orcidid>https://orcid.org/0000-0001-9410-8319</orcidid></addata></record> |
| fulltext | fulltext |
| identifier | ISSN: 1526-498X |
| ispartof | Pest management science, 2007-05, Vol.63 (5), p.459-467 |
| issn | 1526-498X 1526-4998 |
| language | eng |
| recordid | cdi_hal_primary_oai_HAL_hal_02666228v1 |
| source | MEDLINE; Access via Wiley Online Library |
| subjects | 4-dioxygenase Actinobacteria Actinobacteria - classification Actinobacteria - genetics Actinobacteria - metabolism agricultural soils Amino Acid Sequence amino acid sequences Bacteria bacterial community Bacterial Proteins - genetics biodegradation Biodegradation, Environmental Biodiversity Biological and medical sciences Carbon - metabolism Cloning DNA fingerprinting DNA Primers Environmental Sciences Fundamental and applied biological sciences. Psychology genes Genetic diversity Genetic Markers Life Sciences microbial genetics Molecular Sequence Data nucleotide sequences Pesticides Pesticides - metabolism phenolic compounds Phylogeny Phytopathology. Animal pests. Plant and forest protection Polymorphism, Restriction Fragment Length Proteobacteria Proteobacteria - classification Proteobacteria - genetics Proteobacteria - metabolism protocatechuate 3 protocatechuate 3,4‐dioxygenase Protocatechuate-3,4-Dioxygenase - genetics Protocatechuate-3,4-Dioxygenase - metabolism protocatechuic acid quantitative analysis Sequence Alignment Sequence Analysis, Protein soil bacteria soil DNA Soil Microbiology Soils |
| title | pcaH, a molecular marker for estimating the diversity of the protocatechuate-degrading bacterial community in the soil environment |
| url | https://sfx.bib-bvb.de/sfx_tum?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2024-12-25T12%3A16%3A12IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-proquest_hal_p&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=pcaH,%20a%20molecular%20marker%20for%20estimating%20the%20diversity%20of%20the%20protocatechuate-degrading%20bacterial%20community%20in%20the%20soil%20environment&rft.jtitle=Pest%20management%20science&rft.au=El%20Azhari,%20N&rft.date=2007-05&rft.volume=63&rft.issue=5&rft.spage=459&rft.epage=467&rft.pages=459-467&rft.issn=1526-498X&rft.eissn=1526-4998&rft.coden=PMSCFC&rft_id=info:doi/10.1002/ps.1357&rft_dat=%3Cproquest_hal_p%3E1254194221%3C/proquest_hal_p%3E%3Curl%3E%3C/url%3E&disable_directlink=true&sfx.directlink=off&sfx.report_link=0&rft_id=info:oai/&rft_pqid=222618408&rft_id=info:pmid/17427160&rfr_iscdi=true |