Effects of Fertilization and Sampling Time on Composition and Diversity of Entire and Active Bacterial Communities in German Grassland Soils
Soil bacteria are major players in driving and regulating ecosystem processes. Thus, the identification of factors shaping the diversity and structure of these communities is crucial for understanding bacterial-mediated processes such as nutrient transformation and cycling. As most studies only targ...
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| description | Soil bacteria are major players in driving and regulating ecosystem processes. Thus, the identification of factors shaping the diversity and structure of these communities is crucial for understanding bacterial-mediated processes such as nutrient transformation and cycling. As most studies only target the entire soil bacterial community, the response of active community members to environmental changes is still poorly understood. The objective of this study was to investigate the effect of fertilizer application and sampling time on structure and diversity of potentially active (RNA-based) and the entire (DNA-based) bacterial communities in German grassland soils. Analysis of more than 2.3 million 16S rRNA transcripts and gene sequences derived from amplicon-based sequencing of 16S rRNA genes revealed that fertilizer application and sampling time significantly altered the diversity and composition of entire and active bacterial communities. Although the composition of both the entire and the active bacterial community was correlated with environmental factors such as pH or C/N ratio, the active community showed a higher sensitivity to environmental changes than the entire community. In addition, functional analyses were performed based on predictions derived from 16S rRNA data. Genes encoding the uptake of nitrate/nitrite, nitrification, and denitrification were significantly more abundant in fertilized plots compared to non-fertilized plots. Hence, this study provided novel insights into changes in dynamics and functions of soil bacterial communities as response to season and fertilizer application. |
| doi_str_mv | 10.1371/journal.pone.0145575 |
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Thus, the identification of factors shaping the diversity and structure of these communities is crucial for understanding bacterial-mediated processes such as nutrient transformation and cycling. As most studies only target the entire soil bacterial community, the response of active community members to environmental changes is still poorly understood. The objective of this study was to investigate the effect of fertilizer application and sampling time on structure and diversity of potentially active (RNA-based) and the entire (DNA-based) bacterial communities in German grassland soils. Analysis of more than 2.3 million 16S rRNA transcripts and gene sequences derived from amplicon-based sequencing of 16S rRNA genes revealed that fertilizer application and sampling time significantly altered the diversity and composition of entire and active bacterial communities. Although the composition of both the entire and the active bacterial community was correlated with environmental factors such as pH or C/N ratio, the active community showed a higher sensitivity to environmental changes than the entire community. In addition, functional analyses were performed based on predictions derived from 16S rRNA data. Genes encoding the uptake of nitrate/nitrite, nitrification, and denitrification were significantly more abundant in fertilized plots compared to non-fertilized plots. Hence, this study provided novel insights into changes in dynamics and functions of soil bacterial communities as response to season and fertilizer application.</description><identifier>ISSN: 1932-6203</identifier><identifier>EISSN: 1932-6203</identifier><identifier>DOI: 10.1371/journal.pone.0145575</identifier><identifier>PMID: 26694644</identifier><language>eng</language><publisher>United States: Public Library of Science</publisher><subject>Analysis ; Bacteria ; Bacteria - classification ; Bacteria - genetics ; Bacteria - growth & development ; Carbon/nitrogen ratio ; Communities ; Data processing ; Denitrification ; Deoxyribonucleic acid ; DNA ; Ecosystems ; Environmental aspects ; Environmental changes ; Environmental factors ; Fertilization ; Fertilizer application ; Fertilizers ; Gene sequencing ; Genes ; Genomics ; Germany ; Grassland ; Grasslands ; Hypotheses ; Laboratories ; Metabolism ; Microbial Consortia - physiology ; Nitrification ; Nitrogen ; Nutrient cycles ; pH effects ; Ribonucleic acid ; RNA ; RNA, Bacterial - genetics ; RNA, Ribosomal, 16S - genetics ; rRNA 16S ; Sampling ; Seasons ; Sensitivity analysis ; Soil analysis ; Soil bacteria ; Soil dynamics ; Soil fertility ; Soil Microbiology ; Soil microorganisms ; Soils ; Studies ; Transformation</subject><ispartof>PloS one, 2015-12, Vol.10 (12), p.e0145575-e0145575</ispartof><rights>COPYRIGHT 2015 Public Library of Science</rights><rights>2015 Herzog et al. This is an open access article distributed under the terms of the Creative Commons Attribution License: http://creativecommons.org/licenses/by/4.0/ (the “License”), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><rights>2015 Herzog et al 2015 Herzog et al</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c692t-9342bb058a90b88dabd1f229cf75d2427d57e10646b9fc98ca07250bd0960aee3</citedby><cites>FETCH-LOGICAL-c692t-9342bb058a90b88dabd1f229cf75d2427d57e10646b9fc98ca07250bd0960aee3</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC4687936/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC4687936/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,727,780,784,864,885,2102,2928,23866,27924,27925,53791,53793,79600,79601</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/26694644$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><contributor>Moora, Mari</contributor><creatorcontrib>Herzog, Sarah</creatorcontrib><creatorcontrib>Wemheuer, Franziska</creatorcontrib><creatorcontrib>Wemheuer, Bernd</creatorcontrib><creatorcontrib>Daniel, Rolf</creatorcontrib><title>Effects of Fertilization and Sampling Time on Composition and Diversity of Entire and Active Bacterial Communities in German Grassland Soils</title><title>PloS one</title><addtitle>PLoS One</addtitle><description>Soil bacteria are major players in driving and regulating ecosystem processes. Thus, the identification of factors shaping the diversity and structure of these communities is crucial for understanding bacterial-mediated processes such as nutrient transformation and cycling. As most studies only target the entire soil bacterial community, the response of active community members to environmental changes is still poorly understood. The objective of this study was to investigate the effect of fertilizer application and sampling time on structure and diversity of potentially active (RNA-based) and the entire (DNA-based) bacterial communities in German grassland soils. Analysis of more than 2.3 million 16S rRNA transcripts and gene sequences derived from amplicon-based sequencing of 16S rRNA genes revealed that fertilizer application and sampling time significantly altered the diversity and composition of entire and active bacterial communities. 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Hence, this study provided novel insights into changes in dynamics and functions of soil bacterial communities as response to season and fertilizer application.</description><subject>Analysis</subject><subject>Bacteria</subject><subject>Bacteria - classification</subject><subject>Bacteria - genetics</subject><subject>Bacteria - growth & development</subject><subject>Carbon/nitrogen ratio</subject><subject>Communities</subject><subject>Data processing</subject><subject>Denitrification</subject><subject>Deoxyribonucleic acid</subject><subject>DNA</subject><subject>Ecosystems</subject><subject>Environmental aspects</subject><subject>Environmental changes</subject><subject>Environmental factors</subject><subject>Fertilization</subject><subject>Fertilizer application</subject><subject>Fertilizers</subject><subject>Gene sequencing</subject><subject>Genes</subject><subject>Genomics</subject><subject>Germany</subject><subject>Grassland</subject><subject>Grasslands</subject><subject>Hypotheses</subject><subject>Laboratories</subject><subject>Metabolism</subject><subject>Microbial Consortia - 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Academic</collection><collection>PubMed Central (Full Participant titles)</collection><collection>DOAJ Directory of Open Access Journals</collection><jtitle>PloS one</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Herzog, Sarah</au><au>Wemheuer, Franziska</au><au>Wemheuer, Bernd</au><au>Daniel, Rolf</au><au>Moora, Mari</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Effects of Fertilization and Sampling Time on Composition and Diversity of Entire and Active Bacterial Communities in German Grassland Soils</atitle><jtitle>PloS one</jtitle><addtitle>PLoS One</addtitle><date>2015-12-22</date><risdate>2015</risdate><volume>10</volume><issue>12</issue><spage>e0145575</spage><epage>e0145575</epage><pages>e0145575-e0145575</pages><issn>1932-6203</issn><eissn>1932-6203</eissn><abstract>Soil bacteria are major players in driving and regulating ecosystem processes. Thus, the identification of factors shaping the diversity and structure of these communities is crucial for understanding bacterial-mediated processes such as nutrient transformation and cycling. As most studies only target the entire soil bacterial community, the response of active community members to environmental changes is still poorly understood. The objective of this study was to investigate the effect of fertilizer application and sampling time on structure and diversity of potentially active (RNA-based) and the entire (DNA-based) bacterial communities in German grassland soils. Analysis of more than 2.3 million 16S rRNA transcripts and gene sequences derived from amplicon-based sequencing of 16S rRNA genes revealed that fertilizer application and sampling time significantly altered the diversity and composition of entire and active bacterial communities. Although the composition of both the entire and the active bacterial community was correlated with environmental factors such as pH or C/N ratio, the active community showed a higher sensitivity to environmental changes than the entire community. In addition, functional analyses were performed based on predictions derived from 16S rRNA data. Genes encoding the uptake of nitrate/nitrite, nitrification, and denitrification were significantly more abundant in fertilized plots compared to non-fertilized plots. Hence, this study provided novel insights into changes in dynamics and functions of soil bacterial communities as response to season and fertilizer application.</abstract><cop>United States</cop><pub>Public Library of Science</pub><pmid>26694644</pmid><doi>10.1371/journal.pone.0145575</doi><oa>free_for_read</oa></addata></record> |
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| subjects | Analysis Bacteria Bacteria - classification Bacteria - genetics Bacteria - growth & development Carbon/nitrogen ratio Communities Data processing Denitrification Deoxyribonucleic acid DNA Ecosystems Environmental aspects Environmental changes Environmental factors Fertilization Fertilizer application Fertilizers Gene sequencing Genes Genomics Germany Grassland Grasslands Hypotheses Laboratories Metabolism Microbial Consortia - physiology Nitrification Nitrogen Nutrient cycles pH effects Ribonucleic acid RNA RNA, Bacterial - genetics RNA, Ribosomal, 16S - genetics rRNA 16S Sampling Seasons Sensitivity analysis Soil analysis Soil bacteria Soil dynamics Soil fertility Soil Microbiology Soil microorganisms Soils Studies Transformation |
| title | Effects of Fertilization and Sampling Time on Composition and Diversity of Entire and Active Bacterial Communities in German Grassland Soils |
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