Metagenomic analysis of soil and freshwater from zoo agricultural area with organic fertilization
Microbial communities drive biogeochemical cycles in agricultural areas by decomposing organic materials and converting essential nutrients. Organic amendments improve soil quality by increasing the load of essential nutrients and enhancing the productivity. Additionally, fresh water used for irriga...
Gespeichert in:
| Veröffentlicht in: | PloS one 2017-12, Vol.12 (12), p.e0190178 |
|---|---|
| Hauptverfasser: | , , , , |
| Format: | Artikel |
| Sprache: | eng |
| Schlagworte: | |
| Online-Zugang: | Volltext |
| Tags: |
Tag hinzufügen
Keine Tags, Fügen Sie den ersten Tag hinzu!
|
| container_end_page | |
|---|---|
| container_issue | 12 |
| container_start_page | e0190178 |
| container_title | PloS one |
| container_volume | 12 |
| creator | Meneghine, Aylan K Nielsen, Shaun Varani, Alessandro M Thomas, Torsten Carareto Alves, Lucia Maria |
| description | Microbial communities drive biogeochemical cycles in agricultural areas by decomposing organic materials and converting essential nutrients. Organic amendments improve soil quality by increasing the load of essential nutrients and enhancing the productivity. Additionally, fresh water used for irrigation can affect soil quality of agricultural soils, mainly due to the presence of microbial contaminants and pathogens. In this study, we investigated how microbial communities in irrigation water might contribute to the microbial diversity and function of soil. Whole-metagenomic sequencing approaches were used to investigate the taxonomic and the functional profiles of microbial communities present in fresh water used for irrigation, and in soil from a vegetable crop, which received fertilization with organic compost made from animal carcasses. The taxonomic analysis revealed that the most abundant genera were Polynucleobacter (~8% relative abundance) and Bacillus (~10%) in fresh water and soil from the vegetable crop, respectively. Low abundance (0.38%) of cyanobacterial groups were identified. Based on functional gene prediction, denitrification appears to be an important process in the soil community analysed here. Conversely, genes for nitrogen fixation were abundant in freshwater, indicating that the N-fixation plays a crucial role in this particular ecosystem. Moreover, pathogenicity islands, antibiotic resistance and potential virulence related genes were identified in both samples, but no toxigenic genes were detected. This study provides a better understanding of the community structure of an area under strong agricultural activity with regular irrigation and fertilization with an organic compost made from animal carcasses. Additionally, the use of a metagenomic approach to investigate fresh water quality proved to be a relevant method to evaluate its use in an agricultural ecosystem. |
| doi_str_mv | 10.1371/journal.pone.0190178 |
| format | Article |
| fullrecord | <record><control><sourceid>gale_plos_</sourceid><recordid>TN_cdi_plos_journals_1980704172</recordid><sourceformat>XML</sourceformat><sourcesystem>PC</sourcesystem><galeid>A519847558</galeid><doaj_id>oai_doaj_org_article_2ee70d2d1ac74e7d823c06b7882e21bd</doaj_id><sourcerecordid>A519847558</sourcerecordid><originalsourceid>FETCH-LOGICAL-c692t-cbbbcc9c00587f9b4e5128add7745f52af91bd31c77dc3ab6f23c581362eefb13</originalsourceid><addsrcrecordid>eNqNktuL1DAYxYso7jr6H4gWBMGHGXNpm_RFWBYvAysL3l5DmkubodPMJqnr7l_vN053mYKC9KHh6-87OZyeLHuO0QpTht9u_BgG2a92fjArhGuEGX-QneKakmVFEH14dD7JnsS4QaikvKoeZyekJhWjNTvN5GeTZGsGv3Uql6B3E13Mvc2jdz0MdG6Did21TCbA0W_zW-9z2Qanxj6NQQIUjMyvXepyH1o5gI41Ibne3crk_PA0e2RlH82z6b3Ivn94_-380_Li8uP6_OxiqaqapKVqmkapWoFJzmzdFKbEhEutGStKWxJpa9xoihVjWlHZVJZQVXJMK2KMbTBdZC8PurveRzGlEwWuOWKowIwAsT4Q2suN2AW3leFGeOnEnwG4FxKMq94I0GRIE42lYoVhmsNlqGoY58SQvY9F9m66bWy2RiszJMhiJjr_MrhOtP6nKCH3giMQeDUJBH81mpj-YXmiWgmu3GA9iKmti0qclcAVrCw5UKu_UPBoA78V-mEdzGcLb2YLwCTzK7VyjFGsv375f_byx5x9fcR2Rvapi74f9z2Ic7A4gCr4GIOx98lhJPb1vktD7OstpnrD2ovj1O-X7vpMfwMX3vfQ</addsrcrecordid><sourcetype>Open Website</sourcetype><iscdi>true</iscdi><recordtype>article</recordtype><pqid>1980704172</pqid></control><display><type>article</type><title>Metagenomic analysis of soil and freshwater from zoo agricultural area with organic fertilization</title><source>MEDLINE</source><source>DOAJ Directory of Open Access Journals</source><source>Public Library of Science (PLoS)</source><source>EZB-FREE-00999 freely available EZB journals</source><source>PubMed Central</source><source>Free Full-Text Journals in Chemistry</source><creator>Meneghine, Aylan K ; Nielsen, Shaun ; Varani, Alessandro M ; Thomas, Torsten ; Carareto Alves, Lucia Maria</creator><contributor>Lin, Wen-Xiong</contributor><creatorcontrib>Meneghine, Aylan K ; Nielsen, Shaun ; Varani, Alessandro M ; Thomas, Torsten ; Carareto Alves, Lucia Maria ; Lin, Wen-Xiong</creatorcontrib><description>Microbial communities drive biogeochemical cycles in agricultural areas by decomposing organic materials and converting essential nutrients. Organic amendments improve soil quality by increasing the load of essential nutrients and enhancing the productivity. Additionally, fresh water used for irrigation can affect soil quality of agricultural soils, mainly due to the presence of microbial contaminants and pathogens. In this study, we investigated how microbial communities in irrigation water might contribute to the microbial diversity and function of soil. Whole-metagenomic sequencing approaches were used to investigate the taxonomic and the functional profiles of microbial communities present in fresh water used for irrigation, and in soil from a vegetable crop, which received fertilization with organic compost made from animal carcasses. The taxonomic analysis revealed that the most abundant genera were Polynucleobacter (~8% relative abundance) and Bacillus (~10%) in fresh water and soil from the vegetable crop, respectively. Low abundance (0.38%) of cyanobacterial groups were identified. Based on functional gene prediction, denitrification appears to be an important process in the soil community analysed here. Conversely, genes for nitrogen fixation were abundant in freshwater, indicating that the N-fixation plays a crucial role in this particular ecosystem. Moreover, pathogenicity islands, antibiotic resistance and potential virulence related genes were identified in both samples, but no toxigenic genes were detected. This study provides a better understanding of the community structure of an area under strong agricultural activity with regular irrigation and fertilization with an organic compost made from animal carcasses. Additionally, the use of a metagenomic approach to investigate fresh water quality proved to be a relevant method to evaluate its use in an agricultural ecosystem.</description><identifier>ISSN: 1932-6203</identifier><identifier>EISSN: 1932-6203</identifier><identifier>DOI: 10.1371/journal.pone.0190178</identifier><identifier>PMID: 29267397</identifier><language>eng</language><publisher>United States: Public Library of Science</publisher><subject>Abundance ; Agricultural ecosystems ; Agricultural land ; Agricultural practices ; Agricultural resources ; Analysis ; Animals ; Animals, Zoo ; Antibiotic resistance ; Antibiotics ; Australia ; Biogeochemical cycles ; Biogeochemistry ; Biology and Life Sciences ; Carcasses ; Communities ; Community structure ; Composting ; Composts ; Contaminants ; Crops ; Cyanobacteria ; Denitrification ; E coli ; Earth Sciences ; Ecology and Environmental Sciences ; Environmental aspects ; Escherichia coli ; Essential nutrients ; Fertilization ; Fertilizers ; Food ; Fresh water ; Fresh Water - microbiology ; Freshwater environments ; Genera ; Genes ; Influence ; Irrigation ; Irrigation water ; Manures ; Medicine and Health Sciences ; Meta-analysis ; Metagenomics ; Methods ; Microbial activity ; Microbial colonies ; Microbial contamination ; Microorganisms ; Nitrogen ; Nitrogen - metabolism ; Nitrogen fixation ; Nutrients ; Organic fertilizers ; Organic loading ; Organic materials ; Organic soils ; Pathogenicity ; Pathogenicity islands ; Pathogens ; Phosphorus ; Pollution load ; Relative abundance ; Sequences ; Soil analysis ; Soil contamination ; Soil improvement ; Soil investigations ; Soil Microbiology ; Soil nutrients ; Soil properties ; Soil quality ; Soil water ; Studies ; Taxonomy ; Vegetables ; Virulence ; Water Microbiology ; Water quality</subject><ispartof>PloS one, 2017-12, Vol.12 (12), p.e0190178</ispartof><rights>COPYRIGHT 2017 Public Library of Science</rights><rights>2017 Meneghine 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>2017 Meneghine et al 2017 Meneghine et al</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c692t-cbbbcc9c00587f9b4e5128add7745f52af91bd31c77dc3ab6f23c581362eefb13</citedby><cites>FETCH-LOGICAL-c692t-cbbbcc9c00587f9b4e5128add7745f52af91bd31c77dc3ab6f23c581362eefb13</cites><orcidid>0000-0002-8876-3269</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC5739480/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC5739480/$$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/29267397$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><contributor>Lin, Wen-Xiong</contributor><creatorcontrib>Meneghine, Aylan K</creatorcontrib><creatorcontrib>Nielsen, Shaun</creatorcontrib><creatorcontrib>Varani, Alessandro M</creatorcontrib><creatorcontrib>Thomas, Torsten</creatorcontrib><creatorcontrib>Carareto Alves, Lucia Maria</creatorcontrib><title>Metagenomic analysis of soil and freshwater from zoo agricultural area with organic fertilization</title><title>PloS one</title><addtitle>PLoS One</addtitle><description>Microbial communities drive biogeochemical cycles in agricultural areas by decomposing organic materials and converting essential nutrients. Organic amendments improve soil quality by increasing the load of essential nutrients and enhancing the productivity. Additionally, fresh water used for irrigation can affect soil quality of agricultural soils, mainly due to the presence of microbial contaminants and pathogens. In this study, we investigated how microbial communities in irrigation water might contribute to the microbial diversity and function of soil. Whole-metagenomic sequencing approaches were used to investigate the taxonomic and the functional profiles of microbial communities present in fresh water used for irrigation, and in soil from a vegetable crop, which received fertilization with organic compost made from animal carcasses. The taxonomic analysis revealed that the most abundant genera were Polynucleobacter (~8% relative abundance) and Bacillus (~10%) in fresh water and soil from the vegetable crop, respectively. Low abundance (0.38%) of cyanobacterial groups were identified. Based on functional gene prediction, denitrification appears to be an important process in the soil community analysed here. Conversely, genes for nitrogen fixation were abundant in freshwater, indicating that the N-fixation plays a crucial role in this particular ecosystem. Moreover, pathogenicity islands, antibiotic resistance and potential virulence related genes were identified in both samples, but no toxigenic genes were detected. This study provides a better understanding of the community structure of an area under strong agricultural activity with regular irrigation and fertilization with an organic compost made from animal carcasses. Additionally, the use of a metagenomic approach to investigate fresh water quality proved to be a relevant method to evaluate its use in an agricultural ecosystem.</description><subject>Abundance</subject><subject>Agricultural ecosystems</subject><subject>Agricultural land</subject><subject>Agricultural practices</subject><subject>Agricultural resources</subject><subject>Analysis</subject><subject>Animals</subject><subject>Animals, Zoo</subject><subject>Antibiotic resistance</subject><subject>Antibiotics</subject><subject>Australia</subject><subject>Biogeochemical cycles</subject><subject>Biogeochemistry</subject><subject>Biology and Life Sciences</subject><subject>Carcasses</subject><subject>Communities</subject><subject>Community structure</subject><subject>Composting</subject><subject>Composts</subject><subject>Contaminants</subject><subject>Crops</subject><subject>Cyanobacteria</subject><subject>Denitrification</subject><subject>E coli</subject><subject>Earth Sciences</subject><subject>Ecology and Environmental Sciences</subject><subject>Environmental aspects</subject><subject>Escherichia coli</subject><subject>Essential nutrients</subject><subject>Fertilization</subject><subject>Fertilizers</subject><subject>Food</subject><subject>Fresh water</subject><subject>Fresh Water - microbiology</subject><subject>Freshwater environments</subject><subject>Genera</subject><subject>Genes</subject><subject>Influence</subject><subject>Irrigation</subject><subject>Irrigation water</subject><subject>Manures</subject><subject>Medicine and Health Sciences</subject><subject>Meta-analysis</subject><subject>Metagenomics</subject><subject>Methods</subject><subject>Microbial activity</subject><subject>Microbial colonies</subject><subject>Microbial contamination</subject><subject>Microorganisms</subject><subject>Nitrogen</subject><subject>Nitrogen - metabolism</subject><subject>Nitrogen fixation</subject><subject>Nutrients</subject><subject>Organic fertilizers</subject><subject>Organic loading</subject><subject>Organic materials</subject><subject>Organic soils</subject><subject>Pathogenicity</subject><subject>Pathogenicity islands</subject><subject>Pathogens</subject><subject>Phosphorus</subject><subject>Pollution load</subject><subject>Relative abundance</subject><subject>Sequences</subject><subject>Soil analysis</subject><subject>Soil contamination</subject><subject>Soil improvement</subject><subject>Soil investigations</subject><subject>Soil Microbiology</subject><subject>Soil nutrients</subject><subject>Soil properties</subject><subject>Soil quality</subject><subject>Soil water</subject><subject>Studies</subject><subject>Taxonomy</subject><subject>Vegetables</subject><subject>Virulence</subject><subject>Water Microbiology</subject><subject>Water quality</subject><issn>1932-6203</issn><issn>1932-6203</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2017</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><sourceid>DOA</sourceid><recordid>eNqNktuL1DAYxYso7jr6H4gWBMGHGXNpm_RFWBYvAysL3l5DmkubodPMJqnr7l_vN053mYKC9KHh6-87OZyeLHuO0QpTht9u_BgG2a92fjArhGuEGX-QneKakmVFEH14dD7JnsS4QaikvKoeZyekJhWjNTvN5GeTZGsGv3Uql6B3E13Mvc2jdz0MdG6Did21TCbA0W_zW-9z2Qanxj6NQQIUjMyvXepyH1o5gI41Ibne3crk_PA0e2RlH82z6b3Ivn94_-380_Li8uP6_OxiqaqapKVqmkapWoFJzmzdFKbEhEutGStKWxJpa9xoihVjWlHZVJZQVXJMK2KMbTBdZC8PurveRzGlEwWuOWKowIwAsT4Q2suN2AW3leFGeOnEnwG4FxKMq94I0GRIE42lYoVhmsNlqGoY58SQvY9F9m66bWy2RiszJMhiJjr_MrhOtP6nKCH3giMQeDUJBH81mpj-YXmiWgmu3GA9iKmti0qclcAVrCw5UKu_UPBoA78V-mEdzGcLb2YLwCTzK7VyjFGsv375f_byx5x9fcR2Rvapi74f9z2Ic7A4gCr4GIOx98lhJPb1vktD7OstpnrD2ovj1O-X7vpMfwMX3vfQ</recordid><startdate>20171221</startdate><enddate>20171221</enddate><creator>Meneghine, Aylan K</creator><creator>Nielsen, Shaun</creator><creator>Varani, Alessandro M</creator><creator>Thomas, Torsten</creator><creator>Carareto Alves, Lucia Maria</creator><general>Public Library of Science</general><general>Public Library of Science (PLoS)</general><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>IOV</scope><scope>ISR</scope><scope>3V.</scope><scope>7QG</scope><scope>7QL</scope><scope>7QO</scope><scope>7RV</scope><scope>7SN</scope><scope>7SS</scope><scope>7T5</scope><scope>7TG</scope><scope>7TM</scope><scope>7U9</scope><scope>7X2</scope><scope>7X7</scope><scope>7XB</scope><scope>88E</scope><scope>8AO</scope><scope>8C1</scope><scope>8FD</scope><scope>8FE</scope><scope>8FG</scope><scope>8FH</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>ABJCF</scope><scope>ABUWG</scope><scope>AFKRA</scope><scope>ARAPS</scope><scope>ATCPS</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BGLVJ</scope><scope>BHPHI</scope><scope>C1K</scope><scope>CCPQU</scope><scope>D1I</scope><scope>DWQXO</scope><scope>FR3</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>H94</scope><scope>HCIFZ</scope><scope>K9.</scope><scope>KB.</scope><scope>KB0</scope><scope>KL.</scope><scope>L6V</scope><scope>LK8</scope><scope>M0K</scope><scope>M0S</scope><scope>M1P</scope><scope>M7N</scope><scope>M7P</scope><scope>M7S</scope><scope>NAPCQ</scope><scope>P5Z</scope><scope>P62</scope><scope>P64</scope><scope>PATMY</scope><scope>PDBOC</scope><scope>PIMPY</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PTHSS</scope><scope>PYCSY</scope><scope>RC3</scope><scope>5PM</scope><scope>DOA</scope><orcidid>https://orcid.org/0000-0002-8876-3269</orcidid></search><sort><creationdate>20171221</creationdate><title>Metagenomic analysis of soil and freshwater from zoo agricultural area with organic fertilization</title><author>Meneghine, Aylan K ; Nielsen, Shaun ; Varani, Alessandro M ; Thomas, Torsten ; Carareto Alves, Lucia Maria</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c692t-cbbbcc9c00587f9b4e5128add7745f52af91bd31c77dc3ab6f23c581362eefb13</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2017</creationdate><topic>Abundance</topic><topic>Agricultural ecosystems</topic><topic>Agricultural land</topic><topic>Agricultural practices</topic><topic>Agricultural resources</topic><topic>Analysis</topic><topic>Animals</topic><topic>Animals, Zoo</topic><topic>Antibiotic resistance</topic><topic>Antibiotics</topic><topic>Australia</topic><topic>Biogeochemical cycles</topic><topic>Biogeochemistry</topic><topic>Biology and Life Sciences</topic><topic>Carcasses</topic><topic>Communities</topic><topic>Community structure</topic><topic>Composting</topic><topic>Composts</topic><topic>Contaminants</topic><topic>Crops</topic><topic>Cyanobacteria</topic><topic>Denitrification</topic><topic>E coli</topic><topic>Earth Sciences</topic><topic>Ecology and Environmental Sciences</topic><topic>Environmental aspects</topic><topic>Escherichia coli</topic><topic>Essential nutrients</topic><topic>Fertilization</topic><topic>Fertilizers</topic><topic>Food</topic><topic>Fresh water</topic><topic>Fresh Water - microbiology</topic><topic>Freshwater environments</topic><topic>Genera</topic><topic>Genes</topic><topic>Influence</topic><topic>Irrigation</topic><topic>Irrigation water</topic><topic>Manures</topic><topic>Medicine and Health Sciences</topic><topic>Meta-analysis</topic><topic>Metagenomics</topic><topic>Methods</topic><topic>Microbial activity</topic><topic>Microbial colonies</topic><topic>Microbial contamination</topic><topic>Microorganisms</topic><topic>Nitrogen</topic><topic>Nitrogen - metabolism</topic><topic>Nitrogen fixation</topic><topic>Nutrients</topic><topic>Organic fertilizers</topic><topic>Organic loading</topic><topic>Organic materials</topic><topic>Organic soils</topic><topic>Pathogenicity</topic><topic>Pathogenicity islands</topic><topic>Pathogens</topic><topic>Phosphorus</topic><topic>Pollution load</topic><topic>Relative abundance</topic><topic>Sequences</topic><topic>Soil analysis</topic><topic>Soil contamination</topic><topic>Soil improvement</topic><topic>Soil investigations</topic><topic>Soil Microbiology</topic><topic>Soil nutrients</topic><topic>Soil properties</topic><topic>Soil quality</topic><topic>Soil water</topic><topic>Studies</topic><topic>Taxonomy</topic><topic>Vegetables</topic><topic>Virulence</topic><topic>Water Microbiology</topic><topic>Water quality</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Meneghine, Aylan K</creatorcontrib><creatorcontrib>Nielsen, Shaun</creatorcontrib><creatorcontrib>Varani, Alessandro M</creatorcontrib><creatorcontrib>Thomas, Torsten</creatorcontrib><creatorcontrib>Carareto Alves, Lucia Maria</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Gale In Context: Opposing Viewpoints</collection><collection>Gale In Context: Science</collection><collection>ProQuest Central (Corporate)</collection><collection>Animal Behavior Abstracts</collection><collection>Bacteriology Abstracts (Microbiology B)</collection><collection>Biotechnology Research Abstracts</collection><collection>Nursing & Allied Health Database</collection><collection>Ecology Abstracts</collection><collection>Entomology Abstracts (Full archive)</collection><collection>Immunology Abstracts</collection><collection>Meteorological & Geoastrophysical Abstracts</collection><collection>Nucleic Acids Abstracts</collection><collection>Virology and AIDS Abstracts</collection><collection>Agricultural Science Collection</collection><collection>Health & Medical Collection</collection><collection>ProQuest Central (purchase pre-March 2016)</collection><collection>Medical Database (Alumni Edition)</collection><collection>ProQuest Pharma Collection</collection><collection>Public Health Database</collection><collection>Technology Research Database</collection><collection>ProQuest SciTech Collection</collection><collection>ProQuest Technology 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>Materials Science & Engineering Collection</collection><collection>ProQuest Central (Alumni Edition)</collection><collection>ProQuest Central UK/Ireland</collection><collection>Advanced Technologies & Aerospace Collection</collection><collection>Agricultural & Environmental Science Collection</collection><collection>ProQuest Central Essentials</collection><collection>Biological Science Collection</collection><collection>ProQuest Central</collection><collection>Technology Collection</collection><collection>Natural Science Collection</collection><collection>Environmental Sciences and Pollution Management</collection><collection>ProQuest One Community College</collection><collection>ProQuest Materials Science Collection</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>AIDS and Cancer Research Abstracts</collection><collection>SciTech Premium Collection</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>Materials Science Database</collection><collection>Nursing & Allied Health Database (Alumni Edition)</collection><collection>Meteorological & Geoastrophysical Abstracts - Academic</collection><collection>ProQuest Engineering Collection</collection><collection>ProQuest Biological Science Collection</collection><collection>Agricultural Science Database</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>Engineering Database</collection><collection>Nursing & Allied Health Premium</collection><collection>Advanced Technologies & Aerospace Database</collection><collection>ProQuest Advanced Technologies & Aerospace Collection</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Environmental Science Database</collection><collection>Materials Science Collection</collection><collection>Publicly Available Content 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>Engineering Collection</collection><collection>Environmental Science Collection</collection><collection>Genetics Abstracts</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>Meneghine, Aylan K</au><au>Nielsen, Shaun</au><au>Varani, Alessandro M</au><au>Thomas, Torsten</au><au>Carareto Alves, Lucia Maria</au><au>Lin, Wen-Xiong</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Metagenomic analysis of soil and freshwater from zoo agricultural area with organic fertilization</atitle><jtitle>PloS one</jtitle><addtitle>PLoS One</addtitle><date>2017-12-21</date><risdate>2017</risdate><volume>12</volume><issue>12</issue><spage>e0190178</spage><pages>e0190178-</pages><issn>1932-6203</issn><eissn>1932-6203</eissn><abstract>Microbial communities drive biogeochemical cycles in agricultural areas by decomposing organic materials and converting essential nutrients. Organic amendments improve soil quality by increasing the load of essential nutrients and enhancing the productivity. Additionally, fresh water used for irrigation can affect soil quality of agricultural soils, mainly due to the presence of microbial contaminants and pathogens. In this study, we investigated how microbial communities in irrigation water might contribute to the microbial diversity and function of soil. Whole-metagenomic sequencing approaches were used to investigate the taxonomic and the functional profiles of microbial communities present in fresh water used for irrigation, and in soil from a vegetable crop, which received fertilization with organic compost made from animal carcasses. The taxonomic analysis revealed that the most abundant genera were Polynucleobacter (~8% relative abundance) and Bacillus (~10%) in fresh water and soil from the vegetable crop, respectively. Low abundance (0.38%) of cyanobacterial groups were identified. Based on functional gene prediction, denitrification appears to be an important process in the soil community analysed here. Conversely, genes for nitrogen fixation were abundant in freshwater, indicating that the N-fixation plays a crucial role in this particular ecosystem. Moreover, pathogenicity islands, antibiotic resistance and potential virulence related genes were identified in both samples, but no toxigenic genes were detected. This study provides a better understanding of the community structure of an area under strong agricultural activity with regular irrigation and fertilization with an organic compost made from animal carcasses. Additionally, the use of a metagenomic approach to investigate fresh water quality proved to be a relevant method to evaluate its use in an agricultural ecosystem.</abstract><cop>United States</cop><pub>Public Library of Science</pub><pmid>29267397</pmid><doi>10.1371/journal.pone.0190178</doi><tpages>e0190178</tpages><orcidid>https://orcid.org/0000-0002-8876-3269</orcidid><oa>free_for_read</oa></addata></record> |
| fulltext | fulltext |
| identifier | ISSN: 1932-6203 |
| ispartof | PloS one, 2017-12, Vol.12 (12), p.e0190178 |
| issn | 1932-6203 1932-6203 |
| language | eng |
| recordid | cdi_plos_journals_1980704172 |
| source | MEDLINE; DOAJ Directory of Open Access Journals; Public Library of Science (PLoS); EZB-FREE-00999 freely available EZB journals; PubMed Central; Free Full-Text Journals in Chemistry |
| subjects | Abundance Agricultural ecosystems Agricultural land Agricultural practices Agricultural resources Analysis Animals Animals, Zoo Antibiotic resistance Antibiotics Australia Biogeochemical cycles Biogeochemistry Biology and Life Sciences Carcasses Communities Community structure Composting Composts Contaminants Crops Cyanobacteria Denitrification E coli Earth Sciences Ecology and Environmental Sciences Environmental aspects Escherichia coli Essential nutrients Fertilization Fertilizers Food Fresh water Fresh Water - microbiology Freshwater environments Genera Genes Influence Irrigation Irrigation water Manures Medicine and Health Sciences Meta-analysis Metagenomics Methods Microbial activity Microbial colonies Microbial contamination Microorganisms Nitrogen Nitrogen - metabolism Nitrogen fixation Nutrients Organic fertilizers Organic loading Organic materials Organic soils Pathogenicity Pathogenicity islands Pathogens Phosphorus Pollution load Relative abundance Sequences Soil analysis Soil contamination Soil improvement Soil investigations Soil Microbiology Soil nutrients Soil properties Soil quality Soil water Studies Taxonomy Vegetables Virulence Water Microbiology Water quality |
| title | Metagenomic analysis of soil and freshwater from zoo agricultural area with organic fertilization |
| url | https://sfx.bib-bvb.de/sfx_tum?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2025-01-06T06%3A18%3A30IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-gale_plos_&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=Metagenomic%20analysis%20of%20soil%20and%20freshwater%20from%20zoo%20agricultural%20area%20with%20organic%20fertilization&rft.jtitle=PloS%20one&rft.au=Meneghine,%20Aylan%20K&rft.date=2017-12-21&rft.volume=12&rft.issue=12&rft.spage=e0190178&rft.pages=e0190178-&rft.issn=1932-6203&rft.eissn=1932-6203&rft_id=info:doi/10.1371/journal.pone.0190178&rft_dat=%3Cgale_plos_%3EA519847558%3C/gale_plos_%3E%3Curl%3E%3C/url%3E&disable_directlink=true&sfx.directlink=off&sfx.report_link=0&rft_id=info:oai/&rft_pqid=1980704172&rft_id=info:pmid/29267397&rft_galeid=A519847558&rft_doaj_id=oai_doaj_org_article_2ee70d2d1ac74e7d823c06b7882e21bd&rfr_iscdi=true |