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Biodegradation of the herbicide mecoprop-p with soil depth and its relationship with class III tfdA genes
Mecoprop-p [(R)-2-(4-chloro-2-methylphenoxy) propanoic acid) is widely used in agriculture and poses an environmental concern because of its susceptibility to leach from soil to water. We investigated the effect of soil depth on mecoprop-p biodegradation and its relationship with the number and dive...
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| Published in: | Soil biology & biochemistry 2010, Vol.42 (1), p.32-39 |
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| Main Authors: | , , , , , , , |
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| cites | cdi_FETCH-LOGICAL-c411t-f2f6e366400f9a5be68d39ad3406d5bbc0cff9ef0f785eaab26fa0dabcb5385b3 |
| container_end_page | 39 |
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| container_title | Soil biology & biochemistry |
| container_volume | 42 |
| creator | Rodríguez-Cruz, M a Sonia Bælum, Jacob Shaw, Liz J. Sørensen, Sebastian R. Shi, Shengjing Aspray, Thomas Jacobsen, Carsten S. Bending, Gary D. |
| description | Mecoprop-p [(R)-2-(4-chloro-2-methylphenoxy) propanoic acid) is widely used in agriculture and poses an environmental concern because of its susceptibility to leach from soil to water. We investigated the effect of soil depth on mecoprop-p biodegradation and its relationship with the number and diversity of
tfdA related genes, which are the most widely known genes involved in degradation of the phenoxyalkanoic acid group of herbicides by bacteria. Mecoprop-p half-life (DT
50) was approximately 12 days in soil sampled from |
| doi_str_mv | 10.1016/j.soilbio.2009.09.018 |
| format | article |
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tfdA related genes, which are the most widely known genes involved in degradation of the phenoxyalkanoic acid group of herbicides by bacteria. Mecoprop-p half-life (DT
50) was approximately 12 days in soil sampled from <30 cm depth, and increased progressively with soil depth, reaching over 84 days at 70–80 cm. In sub-soil there was a lag period of between 23 and 34 days prior to a phase of rapid degradation. No lag phase occurred in top-soil samples prior to the onset of degradation. The maximum degradation rate was the same in top-soil and sub-soil samples. Although diverse
tfdAα and
tfdA genes were present prior to mecoprop-p degradation, real time PCR revealed that degradation was associated with proliferation of
tfdA genes. The number of
tfdA genes and the most probable number of mecoprop-p degrading organisms in soil prior to mecoprop-p addition were below the limit of quantification and detection respectively. Melting curves from the real time PCR analysis showed that prior to mecoprop-p degradation both class I and class III
tfdA genes were present in top- and sub-soil samples. However at all soil depths only
tfdA class III genes proliferated during degradation. Denaturing gradient gel electrophoresis confirmed that class III
tfdA genes were associated with mecoprop-p degradation. Degradation was not associated with the induction of novel
tfdA genes in top- or sub-soil samples, and there were no apparent differences in
tfdA gene diversity with soil depth prior to or following degradation.</description><identifier>ISSN: 0038-0717</identifier><identifier>EISSN: 1879-3428</identifier><identifier>DOI: 10.1016/j.soilbio.2009.09.018</identifier><language>eng</language><publisher>Elsevier Ltd</publisher><subject>Biodegradation ; Diversity ; gene expression ; half life ; herbicides ; leaching ; mecoprop ; Mecoprop-p ; microbial genetics ; polymerase chain reaction ; Quantitative PCR ; soil bacteria ; Soil depth ; soil microorganisms ; subsoil ; tfdA ; topsoil</subject><ispartof>Soil biology & biochemistry, 2010, Vol.42 (1), p.32-39</ispartof><rights>2009 Elsevier Ltd</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c411t-f2f6e366400f9a5be68d39ad3406d5bbc0cff9ef0f785eaab26fa0dabcb5385b3</citedby><cites>FETCH-LOGICAL-c411t-f2f6e366400f9a5be68d39ad3406d5bbc0cff9ef0f785eaab26fa0dabcb5385b3</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><link.rule.ids>314,777,781,4010,27904,27905,27906</link.rule.ids></links><search><creatorcontrib>Rodríguez-Cruz, M a Sonia</creatorcontrib><creatorcontrib>Bælum, Jacob</creatorcontrib><creatorcontrib>Shaw, Liz J.</creatorcontrib><creatorcontrib>Sørensen, Sebastian R.</creatorcontrib><creatorcontrib>Shi, Shengjing</creatorcontrib><creatorcontrib>Aspray, Thomas</creatorcontrib><creatorcontrib>Jacobsen, Carsten S.</creatorcontrib><creatorcontrib>Bending, Gary D.</creatorcontrib><title>Biodegradation of the herbicide mecoprop-p with soil depth and its relationship with class III tfdA genes</title><title>Soil biology & biochemistry</title><description>Mecoprop-p [(R)-2-(4-chloro-2-methylphenoxy) propanoic acid) is widely used in agriculture and poses an environmental concern because of its susceptibility to leach from soil to water. We investigated the effect of soil depth on mecoprop-p biodegradation and its relationship with the number and diversity of
tfdA related genes, which are the most widely known genes involved in degradation of the phenoxyalkanoic acid group of herbicides by bacteria. Mecoprop-p half-life (DT
50) was approximately 12 days in soil sampled from <30 cm depth, and increased progressively with soil depth, reaching over 84 days at 70–80 cm. In sub-soil there was a lag period of between 23 and 34 days prior to a phase of rapid degradation. No lag phase occurred in top-soil samples prior to the onset of degradation. The maximum degradation rate was the same in top-soil and sub-soil samples. Although diverse
tfdAα and
tfdA genes were present prior to mecoprop-p degradation, real time PCR revealed that degradation was associated with proliferation of
tfdA genes. The number of
tfdA genes and the most probable number of mecoprop-p degrading organisms in soil prior to mecoprop-p addition were below the limit of quantification and detection respectively. Melting curves from the real time PCR analysis showed that prior to mecoprop-p degradation both class I and class III
tfdA genes were present in top- and sub-soil samples. However at all soil depths only
tfdA class III genes proliferated during degradation. Denaturing gradient gel electrophoresis confirmed that class III
tfdA genes were associated with mecoprop-p degradation. Degradation was not associated with the induction of novel
tfdA genes in top- or sub-soil samples, and there were no apparent differences in
tfdA gene diversity with soil depth prior to or following degradation.</description><subject>Biodegradation</subject><subject>Diversity</subject><subject>gene expression</subject><subject>half life</subject><subject>herbicides</subject><subject>leaching</subject><subject>mecoprop</subject><subject>Mecoprop-p</subject><subject>microbial genetics</subject><subject>polymerase chain reaction</subject><subject>Quantitative PCR</subject><subject>soil bacteria</subject><subject>Soil depth</subject><subject>soil microorganisms</subject><subject>subsoil</subject><subject>tfdA</subject><subject>topsoil</subject><issn>0038-0717</issn><issn>1879-3428</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2010</creationdate><recordtype>article</recordtype><recordid>eNqFkE1P3DAQhq2qlboFfkJVn7hlGceJk5wqiqBdCYkDcLb8Md6dVTYOdijqvyfp7h3plWYOzzsfL2PfBawFCHW1X-dIvaW4LgG69SLRfmIr0TZdIauy_cxWALItoBHNV_Yt5z0AlLWQK0a_KHrcJuPNRHHgMfBph3yHyZIjj_yALo4pjsXI32ja8WUV9zjOrRk8pynzhP1_c97RCXK9yZlvNhs-BX_NtzhgPmdfgukzXpzqGXu-u326-VPcP_ze3FzfF64SYipCGRRKpSqA0Jnaomq97IyXFShfW-vAhdBhgNC0NRpjSxUMeGOdrWVbW3nGLo9z56tfXjFP-kDZYd-bAeNr1qUQTaegncH6CLoUc04Y9JjoYNI_LUAvweq9PgWrl2D1IrH4fhx9wURttomyfn4sQUgQjahUp2bi55HA-c-_hElnRzg49JTQTdpH-mDHO49sj-Y</recordid><startdate>2010</startdate><enddate>2010</enddate><creator>Rodríguez-Cruz, M a Sonia</creator><creator>Bælum, Jacob</creator><creator>Shaw, Liz J.</creator><creator>Sørensen, Sebastian R.</creator><creator>Shi, Shengjing</creator><creator>Aspray, Thomas</creator><creator>Jacobsen, Carsten S.</creator><creator>Bending, Gary D.</creator><general>Elsevier Ltd</general><scope>FBQ</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7QL</scope><scope>7QO</scope><scope>7SN</scope><scope>7T7</scope><scope>7TV</scope><scope>7UA</scope><scope>8FD</scope><scope>C1K</scope><scope>FR3</scope><scope>P64</scope><scope>RC3</scope></search><sort><creationdate>2010</creationdate><title>Biodegradation of the herbicide mecoprop-p with soil depth and its relationship with class III tfdA genes</title><author>Rodríguez-Cruz, M a Sonia ; Bælum, Jacob ; Shaw, Liz J. ; Sørensen, Sebastian R. ; Shi, Shengjing ; Aspray, Thomas ; Jacobsen, Carsten S. ; Bending, Gary D.</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c411t-f2f6e366400f9a5be68d39ad3406d5bbc0cff9ef0f785eaab26fa0dabcb5385b3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2010</creationdate><topic>Biodegradation</topic><topic>Diversity</topic><topic>gene expression</topic><topic>half life</topic><topic>herbicides</topic><topic>leaching</topic><topic>mecoprop</topic><topic>Mecoprop-p</topic><topic>microbial genetics</topic><topic>polymerase chain reaction</topic><topic>Quantitative PCR</topic><topic>soil bacteria</topic><topic>Soil depth</topic><topic>soil microorganisms</topic><topic>subsoil</topic><topic>tfdA</topic><topic>topsoil</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Rodríguez-Cruz, M a Sonia</creatorcontrib><creatorcontrib>Bælum, Jacob</creatorcontrib><creatorcontrib>Shaw, Liz J.</creatorcontrib><creatorcontrib>Sørensen, Sebastian R.</creatorcontrib><creatorcontrib>Shi, Shengjing</creatorcontrib><creatorcontrib>Aspray, Thomas</creatorcontrib><creatorcontrib>Jacobsen, Carsten S.</creatorcontrib><creatorcontrib>Bending, Gary D.</creatorcontrib><collection>AGRIS</collection><collection>CrossRef</collection><collection>Bacteriology Abstracts (Microbiology B)</collection><collection>Biotechnology Research Abstracts</collection><collection>Ecology Abstracts</collection><collection>Industrial and Applied Microbiology Abstracts (Microbiology A)</collection><collection>Pollution Abstracts</collection><collection>Water Resources 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>Genetics Abstracts</collection><jtitle>Soil biology & biochemistry</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Rodríguez-Cruz, M a Sonia</au><au>Bælum, Jacob</au><au>Shaw, Liz J.</au><au>Sørensen, Sebastian R.</au><au>Shi, Shengjing</au><au>Aspray, Thomas</au><au>Jacobsen, Carsten S.</au><au>Bending, Gary D.</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Biodegradation of the herbicide mecoprop-p with soil depth and its relationship with class III tfdA genes</atitle><jtitle>Soil biology & biochemistry</jtitle><date>2010</date><risdate>2010</risdate><volume>42</volume><issue>1</issue><spage>32</spage><epage>39</epage><pages>32-39</pages><issn>0038-0717</issn><eissn>1879-3428</eissn><abstract>Mecoprop-p [(R)-2-(4-chloro-2-methylphenoxy) propanoic acid) is widely used in agriculture and poses an environmental concern because of its susceptibility to leach from soil to water. We investigated the effect of soil depth on mecoprop-p biodegradation and its relationship with the number and diversity of
tfdA related genes, which are the most widely known genes involved in degradation of the phenoxyalkanoic acid group of herbicides by bacteria. Mecoprop-p half-life (DT
50) was approximately 12 days in soil sampled from <30 cm depth, and increased progressively with soil depth, reaching over 84 days at 70–80 cm. In sub-soil there was a lag period of between 23 and 34 days prior to a phase of rapid degradation. No lag phase occurred in top-soil samples prior to the onset of degradation. The maximum degradation rate was the same in top-soil and sub-soil samples. Although diverse
tfdAα and
tfdA genes were present prior to mecoprop-p degradation, real time PCR revealed that degradation was associated with proliferation of
tfdA genes. The number of
tfdA genes and the most probable number of mecoprop-p degrading organisms in soil prior to mecoprop-p addition were below the limit of quantification and detection respectively. Melting curves from the real time PCR analysis showed that prior to mecoprop-p degradation both class I and class III
tfdA genes were present in top- and sub-soil samples. However at all soil depths only
tfdA class III genes proliferated during degradation. Denaturing gradient gel electrophoresis confirmed that class III
tfdA genes were associated with mecoprop-p degradation. Degradation was not associated with the induction of novel
tfdA genes in top- or sub-soil samples, and there were no apparent differences in
tfdA gene diversity with soil depth prior to or following degradation.</abstract><pub>Elsevier Ltd</pub><doi>10.1016/j.soilbio.2009.09.018</doi><tpages>8</tpages><oa>free_for_read</oa></addata></record> |
| fulltext | fulltext |
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| issn | 0038-0717 1879-3428 |
| language | eng |
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| source | Elsevier |
| subjects | Biodegradation Diversity gene expression half life herbicides leaching mecoprop Mecoprop-p microbial genetics polymerase chain reaction Quantitative PCR soil bacteria Soil depth soil microorganisms subsoil tfdA topsoil |
| title | Biodegradation of the herbicide mecoprop-p with soil depth and its relationship with class III tfdA genes |
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