Response of total and nitrate-dissimilating bacteria to reduced N deposition in a spruce forest soil profile
A field-scale manipulation experiment conducted for 16 years in a Norway spruce forest at Solling, Central Germany, was used to follow the long-term response of total soil bacteria, nitrate reducers and denitrifiers under conditions of reduced N deposition. N was experimentally removed from throughf...
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creator | Kandeler, Ellen Brune, Thomas Enowashu, Esther Dörr, Nicole Guggenberger, Georg Lamersdorf, Norbert Philippot, Laurent |
description | A field-scale manipulation experiment conducted for 16 years in a Norway spruce forest at Solling, Central Germany, was used to follow the long-term response of total soil bacteria, nitrate reducers and denitrifiers under conditions of reduced N deposition. N was experimentally removed from throughfall by a roof construction ('clean rain plot'). We used substrate-induced respiration (SIR) to characterize the active fraction of soil microbial biomass and potential nitrate reduction to quantify the activity of nitrate reducers. The abundance of total bacteria, nitrate reducers and denitrifiers in different soil layers was analysed by quantitative PCR of 16S rRNA gene, nitrate reduction and denitrification genes. Reduced N deposition temporarily affected the active fraction of the total microbial community (SIR) as well as nitrate reductase activity. However, the size of the total, nitrate reducer and denitrifier communities did not respond to reduced N deposition. Soil depth and sampling date had a greater influence on the density and activity of soil microorganisms than reduced deposition. An increase in the nosZ/16S rRNA gene and nosZ/nirK ratios with soil depth suggests that the proportion of denitrifiers capable of reducing N₂O into N₂ is larger in the mineral soil layer than in the organic layer. |
doi_str_mv | 10.1111/j.1574-6941.2008.00632.x |
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N was experimentally removed from throughfall by a roof construction ('clean rain plot'). We used substrate-induced respiration (SIR) to characterize the active fraction of soil microbial biomass and potential nitrate reduction to quantify the activity of nitrate reducers. The abundance of total bacteria, nitrate reducers and denitrifiers in different soil layers was analysed by quantitative PCR of 16S rRNA gene, nitrate reduction and denitrification genes. Reduced N deposition temporarily affected the active fraction of the total microbial community (SIR) as well as nitrate reductase activity. However, the size of the total, nitrate reducer and denitrifier communities did not respond to reduced N deposition. Soil depth and sampling date had a greater influence on the density and activity of soil microorganisms than reduced deposition. An increase in the nosZ/16S rRNA gene and nosZ/nirK ratios with soil depth suggests that the proportion of denitrifiers capable of reducing N₂O into N₂ is larger in the mineral soil layer than in the organic layer.</description><identifier>ISSN: 0168-6496</identifier><identifier>EISSN: 1574-6941</identifier><identifier>DOI: 10.1111/j.1574-6941.2008.00632.x</identifier><identifier>PMID: 19220860</identifier><language>eng</language><publisher>Oxford, UK: Oxford, UK : Blackwell Publishing Ltd</publisher><subject>16S rRNA gene ; Animal, plant and microbial ecology ; Bacteria ; Bacteria - genetics ; Bacteria - metabolism ; Biological and medical sciences ; Biomarkers ; Biomass ; clean rain ; Coniferous forests ; Denitrification ; denitrifiers ; Deposition ; DNA, Bacterial - genetics ; Ecology ; Ecosystem ; forest soil ; Forest soils ; Forests ; Fundamental and applied biological sciences. Psychology ; Genes, Bacterial ; Genes, rRNA ; Life Sciences ; Microbial ecology ; Microbiology ; Microbiology and Parasitology ; Microorganisms ; N deposition ; NirK protein ; nitrate reducers ; Nitrate reductase ; Nitrate Reductase - metabolism ; Nitrate reduction ; Nitrates ; Nitrates - metabolism ; Nitrous oxide ; Norway ; Picea - microbiology ; Picea abies ; Pine trees ; Reductases ; Reduction ; RNA, Ribosomal, 16S - genetics ; rRNA 16S ; Soil - analysis ; Soil bacteria ; Soil depth ; Soil layers ; Soil Microbiology ; Soil microorganisms ; Soil profiles ; Soil properties ; Soils ; Substrates ; Throughfall ; Trees - microbiology</subject><ispartof>FEMS microbiology ecology, 2009-03, Vol.67 (3), p.444-454</ispartof><rights>2009 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved 2009</rights><rights>2008 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved</rights><rights>2009 INIST-CNRS</rights><rights>2009 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. 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-c6552-28d00728d4fbc07e2e0b9af7d3b33106d99587b51e1b197587bf01436b2967283</citedby></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://onlinelibrary.wiley.com/doi/pdf/10.1111%2Fj.1574-6941.2008.00632.x$$EPDF$$P50$$Gwiley$$H</linktopdf><linktohtml>$$Uhttps://onlinelibrary.wiley.com/doi/full/10.1111%2Fj.1574-6941.2008.00632.x$$EHTML$$P50$$Gwiley$$H</linktohtml><link.rule.ids>230,314,777,781,882,1412,27905,27906,45555,45556</link.rule.ids><backlink>$$Uhttp://pascal-francis.inist.fr/vibad/index.php?action=getRecordDetail&idt=21120135$$DView record in Pascal Francis$$Hfree_for_read</backlink><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/19220860$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink><backlink>$$Uhttps://hal.inrae.fr/hal-02663716$$DView record in HAL$$Hfree_for_read</backlink></links><search><creatorcontrib>Kandeler, Ellen</creatorcontrib><creatorcontrib>Brune, Thomas</creatorcontrib><creatorcontrib>Enowashu, Esther</creatorcontrib><creatorcontrib>Dörr, Nicole</creatorcontrib><creatorcontrib>Guggenberger, Georg</creatorcontrib><creatorcontrib>Lamersdorf, Norbert</creatorcontrib><creatorcontrib>Philippot, Laurent</creatorcontrib><title>Response of total and nitrate-dissimilating bacteria to reduced N deposition in a spruce forest soil profile</title><title>FEMS microbiology ecology</title><addtitle>FEMS Microbiol Ecol</addtitle><description>A field-scale manipulation experiment conducted for 16 years in a Norway spruce forest at Solling, Central Germany, was used to follow the long-term response of total soil bacteria, nitrate reducers and denitrifiers under conditions of reduced N deposition. N was experimentally removed from throughfall by a roof construction ('clean rain plot'). We used substrate-induced respiration (SIR) to characterize the active fraction of soil microbial biomass and potential nitrate reduction to quantify the activity of nitrate reducers. The abundance of total bacteria, nitrate reducers and denitrifiers in different soil layers was analysed by quantitative PCR of 16S rRNA gene, nitrate reduction and denitrification genes. Reduced N deposition temporarily affected the active fraction of the total microbial community (SIR) as well as nitrate reductase activity. However, the size of the total, nitrate reducer and denitrifier communities did not respond to reduced N deposition. Soil depth and sampling date had a greater influence on the density and activity of soil microorganisms than reduced deposition. An increase in the nosZ/16S rRNA gene and nosZ/nirK ratios with soil depth suggests that the proportion of denitrifiers capable of reducing N₂O into N₂ is larger in the mineral soil layer than in the organic layer.</description><subject>16S rRNA gene</subject><subject>Animal, plant and microbial ecology</subject><subject>Bacteria</subject><subject>Bacteria - genetics</subject><subject>Bacteria - metabolism</subject><subject>Biological and medical sciences</subject><subject>Biomarkers</subject><subject>Biomass</subject><subject>clean rain</subject><subject>Coniferous forests</subject><subject>Denitrification</subject><subject>denitrifiers</subject><subject>Deposition</subject><subject>DNA, Bacterial - genetics</subject><subject>Ecology</subject><subject>Ecosystem</subject><subject>forest soil</subject><subject>Forest soils</subject><subject>Forests</subject><subject>Fundamental and applied biological sciences. Psychology</subject><subject>Genes, Bacterial</subject><subject>Genes, rRNA</subject><subject>Life Sciences</subject><subject>Microbial ecology</subject><subject>Microbiology</subject><subject>Microbiology and Parasitology</subject><subject>Microorganisms</subject><subject>N deposition</subject><subject>NirK protein</subject><subject>nitrate reducers</subject><subject>Nitrate reductase</subject><subject>Nitrate Reductase - metabolism</subject><subject>Nitrate reduction</subject><subject>Nitrates</subject><subject>Nitrates - metabolism</subject><subject>Nitrous oxide</subject><subject>Norway</subject><subject>Picea - microbiology</subject><subject>Picea abies</subject><subject>Pine trees</subject><subject>Reductases</subject><subject>Reduction</subject><subject>RNA, Ribosomal, 16S - genetics</subject><subject>rRNA 16S</subject><subject>Soil - analysis</subject><subject>Soil bacteria</subject><subject>Soil depth</subject><subject>Soil layers</subject><subject>Soil Microbiology</subject><subject>Soil microorganisms</subject><subject>Soil profiles</subject><subject>Soil properties</subject><subject>Soils</subject><subject>Substrates</subject><subject>Throughfall</subject><subject>Trees - microbiology</subject><issn>0168-6496</issn><issn>1574-6941</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2009</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>eNqFktFr1TAUxoMo7jr9FzQgCj70epK0pw34MsbmhKuCuueQtunMJbfpkla3_950vV5BkeUhCTm_L3zJ-QihDNYsjbfbNSvKPEOZszUHqNYAKPj65gFZHQoPyQoYVhnmEo_Ikxi3AKwQOTwmR0xyDhXCirgvJg6-j4b6jo5-1I7qvqW9HYMeTdbaGO3OOj3a_orWuhlNsDqBNJh2akxLP9HWDD7a0fqe2p5qGoeQKrTzwcSRRm8dHYLvrDNPyaNOu2ie7ddjcnl-9u30Itt8fv_h9GSTNVgUPONVC1CmOe_qBkrDDdRSd2UraiEYYCtlUZV1wQyrmSznfQcsF1hziUknjsmb5d7v2qkh2J0Ot8prqy5ONmo-A44oSoY_WGJfL2zyeD0lx2pnY2Oc073xU1SIUnApyntBDiJhab4fBIRczODLv8Ctn0KffkZxAVgILAVP1PM9NdU70x7e87uHCXi1B3RstOuC7hsbDxxnjAMTReLeLdzP1IrbP_eAmjOltmqOjpqjM1us1F2m1I06P_uIdz7EIvfT8B9x9o84qV4sqk57pa9CMnb5dfaTslhJVuTiF6UU0_M</recordid><startdate>200903</startdate><enddate>200903</enddate><creator>Kandeler, Ellen</creator><creator>Brune, Thomas</creator><creator>Enowashu, Esther</creator><creator>Dörr, Nicole</creator><creator>Guggenberger, Georg</creator><creator>Lamersdorf, Norbert</creator><creator>Philippot, Laurent</creator><general>Oxford, UK : Blackwell Publishing Ltd</general><general>Blackwell Publishing Ltd</general><general>Blackwell</general><general>Oxford University Press</general><general>Wiley-Blackwell</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>3V.</scope><scope>7QL</scope><scope>7QP</scope><scope>7QR</scope><scope>7SN</scope><scope>7T7</scope><scope>7TK</scope><scope>7TM</scope><scope>7X7</scope><scope>7XB</scope><scope>88E</scope><scope>8FD</scope><scope>8FE</scope><scope>8FH</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>ABUWG</scope><scope>AEUYN</scope><scope>AFKRA</scope><scope>ATCPS</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BHPHI</scope><scope>C1K</scope><scope>CCPQU</scope><scope>DWQXO</scope><scope>FR3</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>HCIFZ</scope><scope>K9.</scope><scope>LK8</scope><scope>M0S</scope><scope>M1P</scope><scope>M7N</scope><scope>M7P</scope><scope>P64</scope><scope>PATMY</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PYCSY</scope><scope>RC3</scope><scope>7X8</scope><scope>1XC</scope></search><sort><creationdate>200903</creationdate><title>Response of total and nitrate-dissimilating bacteria to reduced N deposition in a spruce forest soil profile</title><author>Kandeler, Ellen ; Brune, Thomas ; Enowashu, Esther ; Dörr, Nicole ; Guggenberger, Georg ; Lamersdorf, Norbert ; Philippot, Laurent</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c6552-28d00728d4fbc07e2e0b9af7d3b33106d99587b51e1b197587bf01436b2967283</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2009</creationdate><topic>16S rRNA gene</topic><topic>Animal, plant and microbial ecology</topic><topic>Bacteria</topic><topic>Bacteria - genetics</topic><topic>Bacteria - metabolism</topic><topic>Biological and medical sciences</topic><topic>Biomarkers</topic><topic>Biomass</topic><topic>clean rain</topic><topic>Coniferous forests</topic><topic>Denitrification</topic><topic>denitrifiers</topic><topic>Deposition</topic><topic>DNA, Bacterial - genetics</topic><topic>Ecology</topic><topic>Ecosystem</topic><topic>forest soil</topic><topic>Forest soils</topic><topic>Forests</topic><topic>Fundamental and applied biological sciences. Psychology</topic><topic>Genes, Bacterial</topic><topic>Genes, rRNA</topic><topic>Life Sciences</topic><topic>Microbial ecology</topic><topic>Microbiology</topic><topic>Microbiology and Parasitology</topic><topic>Microorganisms</topic><topic>N deposition</topic><topic>NirK protein</topic><topic>nitrate reducers</topic><topic>Nitrate reductase</topic><topic>Nitrate Reductase - metabolism</topic><topic>Nitrate reduction</topic><topic>Nitrates</topic><topic>Nitrates - metabolism</topic><topic>Nitrous oxide</topic><topic>Norway</topic><topic>Picea - microbiology</topic><topic>Picea abies</topic><topic>Pine trees</topic><topic>Reductases</topic><topic>Reduction</topic><topic>RNA, Ribosomal, 16S - genetics</topic><topic>rRNA 16S</topic><topic>Soil - analysis</topic><topic>Soil bacteria</topic><topic>Soil depth</topic><topic>Soil layers</topic><topic>Soil Microbiology</topic><topic>Soil microorganisms</topic><topic>Soil profiles</topic><topic>Soil properties</topic><topic>Soils</topic><topic>Substrates</topic><topic>Throughfall</topic><topic>Trees - microbiology</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Kandeler, Ellen</creatorcontrib><creatorcontrib>Brune, Thomas</creatorcontrib><creatorcontrib>Enowashu, Esther</creatorcontrib><creatorcontrib>Dörr, Nicole</creatorcontrib><creatorcontrib>Guggenberger, Georg</creatorcontrib><creatorcontrib>Lamersdorf, Norbert</creatorcontrib><creatorcontrib>Philippot, Laurent</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>ProQuest Central (Corporate)</collection><collection>Bacteriology Abstracts (Microbiology B)</collection><collection>Calcium & Calcified Tissue Abstracts</collection><collection>Chemoreception Abstracts</collection><collection>Ecology Abstracts</collection><collection>Industrial and Applied Microbiology Abstracts (Microbiology A)</collection><collection>Neurosciences Abstracts</collection><collection>Nucleic Acids Abstracts</collection><collection>Health & Medical Collection</collection><collection>ProQuest Central (purchase pre-March 2016)</collection><collection>Medical Database (Alumni Edition)</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>ProQuest Central (Alumni Edition)</collection><collection>ProQuest One Sustainability</collection><collection>ProQuest Central UK/Ireland</collection><collection>Agricultural & Environmental Science Collection</collection><collection>ProQuest Central Essentials</collection><collection>Biological Science Collection</collection><collection>ProQuest Central</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>Health Research Premium Collection</collection><collection>Health Research Premium Collection (Alumni)</collection><collection>ProQuest Central Student</collection><collection>SciTech Premium Collection</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>ProQuest Biological Science Collection</collection><collection>Health & Medical Collection (Alumni Edition)</collection><collection>Medical Database</collection><collection>Algology Mycology and Protozoology Abstracts (Microbiology C)</collection><collection>Biological Science Database</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Environmental Science Database</collection><collection>ProQuest One Academic Eastern Edition (DO NOT USE)</collection><collection>ProQuest One Academic</collection><collection>ProQuest One Academic UKI Edition</collection><collection>Environmental Science Collection</collection><collection>Genetics Abstracts</collection><collection>MEDLINE - Academic</collection><collection>Hyper Article en Ligne (HAL)</collection><jtitle>FEMS microbiology ecology</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Kandeler, Ellen</au><au>Brune, Thomas</au><au>Enowashu, Esther</au><au>Dörr, Nicole</au><au>Guggenberger, Georg</au><au>Lamersdorf, Norbert</au><au>Philippot, Laurent</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Response of total and nitrate-dissimilating bacteria to reduced N deposition in a spruce forest soil profile</atitle><jtitle>FEMS microbiology ecology</jtitle><addtitle>FEMS Microbiol Ecol</addtitle><date>2009-03</date><risdate>2009</risdate><volume>67</volume><issue>3</issue><spage>444</spage><epage>454</epage><pages>444-454</pages><issn>0168-6496</issn><eissn>1574-6941</eissn><abstract>A field-scale manipulation experiment conducted for 16 years in a Norway spruce forest at Solling, Central Germany, was used to follow the long-term response of total soil bacteria, nitrate reducers and denitrifiers under conditions of reduced N deposition. N was experimentally removed from throughfall by a roof construction ('clean rain plot'). We used substrate-induced respiration (SIR) to characterize the active fraction of soil microbial biomass and potential nitrate reduction to quantify the activity of nitrate reducers. The abundance of total bacteria, nitrate reducers and denitrifiers in different soil layers was analysed by quantitative PCR of 16S rRNA gene, nitrate reduction and denitrification genes. Reduced N deposition temporarily affected the active fraction of the total microbial community (SIR) as well as nitrate reductase activity. However, the size of the total, nitrate reducer and denitrifier communities did not respond to reduced N deposition. Soil depth and sampling date had a greater influence on the density and activity of soil microorganisms than reduced deposition. An increase in the nosZ/16S rRNA gene and nosZ/nirK ratios with soil depth suggests that the proportion of denitrifiers capable of reducing N₂O into N₂ is larger in the mineral soil layer than in the organic layer.</abstract><cop>Oxford, UK</cop><pub>Oxford, UK : Blackwell Publishing Ltd</pub><pmid>19220860</pmid><doi>10.1111/j.1574-6941.2008.00632.x</doi><tpages>11</tpages><oa>free_for_read</oa></addata></record> |
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subjects | 16S rRNA gene Animal, plant and microbial ecology Bacteria Bacteria - genetics Bacteria - metabolism Biological and medical sciences Biomarkers Biomass clean rain Coniferous forests Denitrification denitrifiers Deposition DNA, Bacterial - genetics Ecology Ecosystem forest soil Forest soils Forests Fundamental and applied biological sciences. Psychology Genes, Bacterial Genes, rRNA Life Sciences Microbial ecology Microbiology Microbiology and Parasitology Microorganisms N deposition NirK protein nitrate reducers Nitrate reductase Nitrate Reductase - metabolism Nitrate reduction Nitrates Nitrates - metabolism Nitrous oxide Norway Picea - microbiology Picea abies Pine trees Reductases Reduction RNA, Ribosomal, 16S - genetics rRNA 16S Soil - analysis Soil bacteria Soil depth Soil layers Soil Microbiology Soil microorganisms Soil profiles Soil properties Soils Substrates Throughfall Trees - microbiology |
title | Response of total and nitrate-dissimilating bacteria to reduced N deposition in a spruce forest soil profile |
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