nir gene‐based co‐occurrence patterns reveal assembly mechanisms of soil denitrifiers in response to fire
Summary Denitrification causes nitrogen losses from terrestrial ecosystems. The magnitude of nitrogen loss depends on the prevalence of denitrifiers, which show ecological differences if they harbour nirS or nirK genes encoding nitrite reductases with the same biological function. Thus, it is releva...
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Veröffentlicht in: | Environmental microbiology 2021-01, Vol.23 (1), p.239-251 |
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creator | Goberna, Marta Donat, Santiago Pérez‐Valera, Eduardo Hallin, Sara Verdú, Miguel |
description | Summary
Denitrification causes nitrogen losses from terrestrial ecosystems. The magnitude of nitrogen loss depends on the prevalence of denitrifiers, which show ecological differences if they harbour nirS or nirK genes encoding nitrite reductases with the same biological function. Thus, it is relevant to understand the mechanisms of co‐existence of denitrifiers, including their response to environmental filters and competition due to niche similarities. We propose a framework to analyse the co‐existence of denitrifiers across multiple assemblages by using nir gene‐based co‐occurrence networks. We applied it in Mediterranean soils before and during 1 year after an experimental fire. Burning did not modify nir community structure, but significantly impacted co‐occurrence patterns. Bacteria with the same nir co‐occurred in space, and those with different nir excluded each other, reflecting niche requirements: nirS abundance responded to nitrate and salinity, whereas nirK to iron content. Prior to fire, mutual exclusion between bacteria with the same nir suggested competition due to niche similarities. Burning provoked an immediate rise in mineral nitrogen and erased the signals of competition, which emerged again within days as nir abundances peaked. nir co‐occurrence patterns can help infer the assembly mechanisms of denitrifying communities, which control nitrogen losses in the face of ecological disturbance. |
doi_str_mv | 10.1111/1462-2920.15298 |
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Denitrification causes nitrogen losses from terrestrial ecosystems. The magnitude of nitrogen loss depends on the prevalence of denitrifiers, which show ecological differences if they harbour nirS or nirK genes encoding nitrite reductases with the same biological function. Thus, it is relevant to understand the mechanisms of co‐existence of denitrifiers, including their response to environmental filters and competition due to niche similarities. We propose a framework to analyse the co‐existence of denitrifiers across multiple assemblages by using nir gene‐based co‐occurrence networks. We applied it in Mediterranean soils before and during 1 year after an experimental fire. Burning did not modify nir community structure, but significantly impacted co‐occurrence patterns. Bacteria with the same nir co‐occurred in space, and those with different nir excluded each other, reflecting niche requirements: nirS abundance responded to nitrate and salinity, whereas nirK to iron content. Prior to fire, mutual exclusion between bacteria with the same nir suggested competition due to niche similarities. Burning provoked an immediate rise in mineral nitrogen and erased the signals of competition, which emerged again within days as nir abundances peaked. nir co‐occurrence patterns can help infer the assembly mechanisms of denitrifying communities, which control nitrogen losses in the face of ecological disturbance.</description><identifier>ISSN: 1462-2912</identifier><identifier>ISSN: 1462-2920</identifier><identifier>EISSN: 1462-2920</identifier><identifier>DOI: 10.1111/1462-2920.15298</identifier><identifier>PMID: 33118311</identifier><language>eng</language><publisher>Hoboken, USA: John Wiley & Sons, Inc</publisher><subject>Assembly ; Bacteria ; Bacteria - genetics ; Bacteria - metabolism ; Biological competition ; Burning ; Community structure ; Competition ; Denitrification ; Denitrification - genetics ; Denitrification - physiology ; Ecosystem ; Ecosystem disturbance ; Environmental Sciences ; Fires ; Microbiology ; Mikrobiologi ; Miljövetenskap ; Niches ; NiR gene ; Nitrates - metabolism ; Nitrite Reductases - genetics ; Nitrite Reductases - metabolism ; Nitrogen ; Nitrogen - metabolism ; Reductases ; Salinity ; Similarity ; Soil ; Soil - chemistry ; Soil Microbiology ; Terrestrial ecosystems ; Terrestrial environments</subject><ispartof>Environmental microbiology, 2021-01, Vol.23 (1), p.239-251</ispartof><rights>2020 Society for Applied Microbiology and John Wiley & Sons Ltd</rights><rights>2020 Society for Applied Microbiology and John Wiley & Sons Ltd.</rights><rights>2021 Society for Applied Microbiology and John Wiley & Sons Ltd</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c4108-456197d1216d5bf1d3690151f02c8962a7e41a5ccae9d3a894f72f930562f98e3</citedby><cites>FETCH-LOGICAL-c4108-456197d1216d5bf1d3690151f02c8962a7e41a5ccae9d3a894f72f930562f98e3</cites><orcidid>0000-0001-5303-3429</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://onlinelibrary.wiley.com/doi/pdf/10.1111%2F1462-2920.15298$$EPDF$$P50$$Gwiley$$H</linktopdf><linktohtml>$$Uhttps://onlinelibrary.wiley.com/doi/full/10.1111%2F1462-2920.15298$$EHTML$$P50$$Gwiley$$H</linktohtml><link.rule.ids>230,314,778,782,883,1414,4012,27910,27911,27912,45561,45562</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/33118311$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink><backlink>$$Uhttps://res.slu.se/id/publ/109250$$DView record from Swedish Publication Index$$Hfree_for_read</backlink></links><search><creatorcontrib>Goberna, Marta</creatorcontrib><creatorcontrib>Donat, Santiago</creatorcontrib><creatorcontrib>Pérez‐Valera, Eduardo</creatorcontrib><creatorcontrib>Hallin, Sara</creatorcontrib><creatorcontrib>Verdú, Miguel</creatorcontrib><creatorcontrib>Sveriges lantbruksuniversitet</creatorcontrib><title>nir gene‐based co‐occurrence patterns reveal assembly mechanisms of soil denitrifiers in response to fire</title><title>Environmental microbiology</title><addtitle>Environ Microbiol</addtitle><description>Summary
Denitrification causes nitrogen losses from terrestrial ecosystems. The magnitude of nitrogen loss depends on the prevalence of denitrifiers, which show ecological differences if they harbour nirS or nirK genes encoding nitrite reductases with the same biological function. Thus, it is relevant to understand the mechanisms of co‐existence of denitrifiers, including their response to environmental filters and competition due to niche similarities. We propose a framework to analyse the co‐existence of denitrifiers across multiple assemblages by using nir gene‐based co‐occurrence networks. We applied it in Mediterranean soils before and during 1 year after an experimental fire. Burning did not modify nir community structure, but significantly impacted co‐occurrence patterns. Bacteria with the same nir co‐occurred in space, and those with different nir excluded each other, reflecting niche requirements: nirS abundance responded to nitrate and salinity, whereas nirK to iron content. Prior to fire, mutual exclusion between bacteria with the same nir suggested competition due to niche similarities. Burning provoked an immediate rise in mineral nitrogen and erased the signals of competition, which emerged again within days as nir abundances peaked. nir co‐occurrence patterns can help infer the assembly mechanisms of denitrifying communities, which control nitrogen losses in the face of ecological disturbance.</description><subject>Assembly</subject><subject>Bacteria</subject><subject>Bacteria - genetics</subject><subject>Bacteria - metabolism</subject><subject>Biological competition</subject><subject>Burning</subject><subject>Community structure</subject><subject>Competition</subject><subject>Denitrification</subject><subject>Denitrification - genetics</subject><subject>Denitrification - physiology</subject><subject>Ecosystem</subject><subject>Ecosystem disturbance</subject><subject>Environmental Sciences</subject><subject>Fires</subject><subject>Microbiology</subject><subject>Mikrobiologi</subject><subject>Miljövetenskap</subject><subject>Niches</subject><subject>NiR gene</subject><subject>Nitrates - metabolism</subject><subject>Nitrite Reductases - genetics</subject><subject>Nitrite Reductases - metabolism</subject><subject>Nitrogen</subject><subject>Nitrogen - metabolism</subject><subject>Reductases</subject><subject>Salinity</subject><subject>Similarity</subject><subject>Soil</subject><subject>Soil - chemistry</subject><subject>Soil Microbiology</subject><subject>Terrestrial ecosystems</subject><subject>Terrestrial environments</subject><issn>1462-2912</issn><issn>1462-2920</issn><issn>1462-2920</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2021</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNqFkUFvFSEUhYnR2FpduzMkbty8FpiBgaVpWm1S40bXhGEuSjMDI3fG5u38Cf5Gf4k8p76FG0nIuZDvnEAOIS85O-d1XfBWiZ0woh6lMPoROT3ePD7OXJyQZ4h3jPGu6dhTctI0nOu6T8mUYqFfIMGvHz97hzBQn-uYvV9LgeSBzm5ZoCSkBb6DG6lDhKkf93QC_9WliBPSHCjmONIBUlxKDBEK0piqBeecEOiSaYgFnpMnwY0ILx70jHy-vvp0-X53-_HdzeXb251vOdO7VipuuoELrgbZBz40yjAueWDCa6OE66DlTnrvwAyN06YNnQimYVJV0dCckfMtF-9hXns7lzi5srfZRYvj2rtyEItgOTNCsmp4sxnmkr-tgIudInoYR5cgr2hFK6VuZMdVRV__g97ltaT6nUp12jCtVFupi43yJSMWCMc3cGYP1dlDOfZQlP1TXXW8eshd-wmGI_-3qwrIDbiPI-z_l2evPtxswb8BDTmlQw</recordid><startdate>202101</startdate><enddate>202101</enddate><creator>Goberna, Marta</creator><creator>Donat, Santiago</creator><creator>Pérez‐Valera, Eduardo</creator><creator>Hallin, Sara</creator><creator>Verdú, Miguel</creator><general>John Wiley & Sons, Inc</general><general>Wiley Subscription Services, Inc</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>7QH</scope><scope>7QL</scope><scope>7ST</scope><scope>7T7</scope><scope>7TN</scope><scope>7U9</scope><scope>7UA</scope><scope>8FD</scope><scope>C1K</scope><scope>F1W</scope><scope>FR3</scope><scope>H94</scope><scope>H95</scope><scope>H97</scope><scope>L.G</scope><scope>M7N</scope><scope>P64</scope><scope>SOI</scope><scope>7X8</scope><scope>ADTPV</scope><scope>AOWAS</scope><orcidid>https://orcid.org/0000-0001-5303-3429</orcidid></search><sort><creationdate>202101</creationdate><title>nir gene‐based co‐occurrence patterns reveal assembly mechanisms of soil denitrifiers in response to fire</title><author>Goberna, Marta ; Donat, Santiago ; Pérez‐Valera, Eduardo ; Hallin, Sara ; Verdú, Miguel</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c4108-456197d1216d5bf1d3690151f02c8962a7e41a5ccae9d3a894f72f930562f98e3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2021</creationdate><topic>Assembly</topic><topic>Bacteria</topic><topic>Bacteria - genetics</topic><topic>Bacteria - metabolism</topic><topic>Biological competition</topic><topic>Burning</topic><topic>Community structure</topic><topic>Competition</topic><topic>Denitrification</topic><topic>Denitrification - genetics</topic><topic>Denitrification - physiology</topic><topic>Ecosystem</topic><topic>Ecosystem disturbance</topic><topic>Environmental Sciences</topic><topic>Fires</topic><topic>Microbiology</topic><topic>Mikrobiologi</topic><topic>Miljövetenskap</topic><topic>Niches</topic><topic>NiR gene</topic><topic>Nitrates - metabolism</topic><topic>Nitrite Reductases - genetics</topic><topic>Nitrite Reductases - metabolism</topic><topic>Nitrogen</topic><topic>Nitrogen - metabolism</topic><topic>Reductases</topic><topic>Salinity</topic><topic>Similarity</topic><topic>Soil</topic><topic>Soil - chemistry</topic><topic>Soil Microbiology</topic><topic>Terrestrial ecosystems</topic><topic>Terrestrial environments</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Goberna, Marta</creatorcontrib><creatorcontrib>Donat, Santiago</creatorcontrib><creatorcontrib>Pérez‐Valera, Eduardo</creatorcontrib><creatorcontrib>Hallin, Sara</creatorcontrib><creatorcontrib>Verdú, Miguel</creatorcontrib><creatorcontrib>Sveriges lantbruksuniversitet</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Aqualine</collection><collection>Bacteriology Abstracts (Microbiology B)</collection><collection>Environment Abstracts</collection><collection>Industrial and Applied Microbiology Abstracts (Microbiology A)</collection><collection>Oceanic Abstracts</collection><collection>Virology and AIDS Abstracts</collection><collection>Water Resources Abstracts</collection><collection>Technology Research Database</collection><collection>Environmental Sciences and Pollution Management</collection><collection>ASFA: Aquatic Sciences and Fisheries Abstracts</collection><collection>Engineering Research Database</collection><collection>AIDS and Cancer Research Abstracts</collection><collection>Aquatic Science & Fisheries Abstracts (ASFA) 1: Biological Sciences & Living Resources</collection><collection>Aquatic Science & Fisheries Abstracts (ASFA) 3: Aquatic Pollution & Environmental Quality</collection><collection>Aquatic Science & Fisheries Abstracts (ASFA) Professional</collection><collection>Algology Mycology and Protozoology Abstracts (Microbiology C)</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Environment Abstracts</collection><collection>MEDLINE - Academic</collection><collection>SwePub</collection><collection>SwePub Articles</collection><jtitle>Environmental microbiology</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Goberna, Marta</au><au>Donat, Santiago</au><au>Pérez‐Valera, Eduardo</au><au>Hallin, Sara</au><au>Verdú, Miguel</au><aucorp>Sveriges lantbruksuniversitet</aucorp><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>nir gene‐based co‐occurrence patterns reveal assembly mechanisms of soil denitrifiers in response to fire</atitle><jtitle>Environmental microbiology</jtitle><addtitle>Environ Microbiol</addtitle><date>2021-01</date><risdate>2021</risdate><volume>23</volume><issue>1</issue><spage>239</spage><epage>251</epage><pages>239-251</pages><issn>1462-2912</issn><issn>1462-2920</issn><eissn>1462-2920</eissn><abstract>Summary
Denitrification causes nitrogen losses from terrestrial ecosystems. The magnitude of nitrogen loss depends on the prevalence of denitrifiers, which show ecological differences if they harbour nirS or nirK genes encoding nitrite reductases with the same biological function. Thus, it is relevant to understand the mechanisms of co‐existence of denitrifiers, including their response to environmental filters and competition due to niche similarities. We propose a framework to analyse the co‐existence of denitrifiers across multiple assemblages by using nir gene‐based co‐occurrence networks. We applied it in Mediterranean soils before and during 1 year after an experimental fire. Burning did not modify nir community structure, but significantly impacted co‐occurrence patterns. Bacteria with the same nir co‐occurred in space, and those with different nir excluded each other, reflecting niche requirements: nirS abundance responded to nitrate and salinity, whereas nirK to iron content. Prior to fire, mutual exclusion between bacteria with the same nir suggested competition due to niche similarities. Burning provoked an immediate rise in mineral nitrogen and erased the signals of competition, which emerged again within days as nir abundances peaked. nir co‐occurrence patterns can help infer the assembly mechanisms of denitrifying communities, which control nitrogen losses in the face of ecological disturbance.</abstract><cop>Hoboken, USA</cop><pub>John Wiley & Sons, Inc</pub><pmid>33118311</pmid><doi>10.1111/1462-2920.15298</doi><tpages>13</tpages><orcidid>https://orcid.org/0000-0001-5303-3429</orcidid></addata></record> |
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subjects | Assembly Bacteria Bacteria - genetics Bacteria - metabolism Biological competition Burning Community structure Competition Denitrification Denitrification - genetics Denitrification - physiology Ecosystem Ecosystem disturbance Environmental Sciences Fires Microbiology Mikrobiologi Miljövetenskap Niches NiR gene Nitrates - metabolism Nitrite Reductases - genetics Nitrite Reductases - metabolism Nitrogen Nitrogen - metabolism Reductases Salinity Similarity Soil Soil - chemistry Soil Microbiology Terrestrial ecosystems Terrestrial environments |
title | nir gene‐based co‐occurrence patterns reveal assembly mechanisms of soil denitrifiers in response to fire |
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