Influence of oxic/anoxic fluctuations on ammonia oxidizers and nitrification potential in a wet tropical soil
Abstract Ammonia oxidation is a key process in the global nitrogen cycle. However, in tropical soils, little is known about ammonia-oxidizing microorganisms and how characteristically variable oxygen regimes affect their activity. We investigated the influence of brief anaerobic periods on ammonia o...
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| Veröffentlicht in: | FEMS microbiology ecology 2013-07, Vol.85 (1), p.179-194 |
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| creator | Pett-Ridge, Jennifer Petersen, Dorthe G. Nuccio, Erin Firestone, Mary K. |
| description | Abstract
Ammonia oxidation is a key process in the global nitrogen cycle. However, in tropical soils, little is known about ammonia-oxidizing microorganisms and how characteristically variable oxygen regimes affect their activity. We investigated the influence of brief anaerobic periods on ammonia oxidation along an elevation, moisture, and oxygen availability gradient in wet tropical soils. Soils from three forest types were incubated for up to 36 weeks in lab microcosms under three regimes: (1) static aerobic; (2) static anaerobic; and (3) fluctuating (aerobic/anaerobic). Nitrification potential was measured in field-fresh soils and incubated soils. The native ammonia-oxidizing community was also characterized, based on diversity assessments (clone libraries) and quantification of the ammonia monooxygenase α–subunit (amoA) gene. These relatively low pH soils appear to be dominated by ammonia-oxidizing archaea (AOA), and AOA communities in the three soil types differed significantly in their ability to oxidize ammonia. Soils from an intermediate elevation, and those incubated with fluctuating redox conditions, tended to have the highest nitrification potential following an influx of oxygen, although all soils retained the capacity to nitrify even after long anoxic periods. Together, these results suggest that wet tropical soil AOA are tolerant of extended periods of anoxia. |
| doi_str_mv | 10.1111/1574-6941.12111 |
| format | Article |
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Ammonia oxidation is a key process in the global nitrogen cycle. However, in tropical soils, little is known about ammonia-oxidizing microorganisms and how characteristically variable oxygen regimes affect their activity. We investigated the influence of brief anaerobic periods on ammonia oxidation along an elevation, moisture, and oxygen availability gradient in wet tropical soils. Soils from three forest types were incubated for up to 36 weeks in lab microcosms under three regimes: (1) static aerobic; (2) static anaerobic; and (3) fluctuating (aerobic/anaerobic). Nitrification potential was measured in field-fresh soils and incubated soils. The native ammonia-oxidizing community was also characterized, based on diversity assessments (clone libraries) and quantification of the ammonia monooxygenase α–subunit (amoA) gene. These relatively low pH soils appear to be dominated by ammonia-oxidizing archaea (AOA), and AOA communities in the three soil types differed significantly in their ability to oxidize ammonia. Soils from an intermediate elevation, and those incubated with fluctuating redox conditions, tended to have the highest nitrification potential following an influx of oxygen, although all soils retained the capacity to nitrify even after long anoxic periods. Together, these results suggest that wet tropical soil AOA are tolerant of extended periods of anoxia.</description><identifier>ISSN: 0168-6496</identifier><identifier>EISSN: 1574-6941</identifier><identifier>DOI: 10.1111/1574-6941.12111</identifier><identifier>PMID: 23556538</identifier><identifier>CODEN: FMECEZ</identifier><language>eng</language><publisher>Oxford, UK: Blackwell Publishing Ltd</publisher><subject>Aerobiosis ; Ammonia ; Ammonia - metabolism ; amoA ; Anaerobiosis ; Animal, plant and microbial ecology ; Anoxia ; Archaea ; Archaea - classification ; Archaea - isolation & purification ; Archaea - metabolism ; Bacteria - genetics ; Bacteria - isolation & purification ; Bacteria - metabolism ; Bacteriology ; Biological and medical sciences ; Ecology ; Fundamental and applied biological sciences. Psychology ; Microbial ecology ; Microbiology ; Microorganisms ; Miscellaneous ; Nitrification ; nitrifiers ; Nitrogen cycle ; Oxidation ; Oxidation-Reduction ; Oxidoreductases - genetics ; Oxygen ; oxygen depletion ; Puerto Rico ; redox oscillation ; Soil ; Soil Microbiology ; Soil pH ; Soil types ; Trees ; Tropical Climate ; Tropical environments ; Various environments (extraatmospheric space, air, water)</subject><ispartof>FEMS microbiology ecology, 2013-07, Vol.85 (1), p.179-194</ispartof><rights>2013 Federation of European Microbiological Societies 2013</rights><rights>2013 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved</rights><rights>2014 INIST-CNRS</rights><rights>2013 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.</rights><rights>Copyright © 2013 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c5761-11fa3285830e0b2049d2a42f4f977868f044f2d1fed7584a692d31e1f44011d3</citedby><cites>FETCH-LOGICAL-c5761-11fa3285830e0b2049d2a42f4f977868f044f2d1fed7584a692d31e1f44011d3</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://onlinelibrary.wiley.com/doi/pdf/10.1111%2F1574-6941.12111$$EPDF$$P50$$Gwiley$$H</linktopdf><linktohtml>$$Uhttps://onlinelibrary.wiley.com/doi/full/10.1111%2F1574-6941.12111$$EHTML$$P50$$Gwiley$$H</linktohtml><link.rule.ids>314,780,784,1417,27924,27925,45574,45575</link.rule.ids><backlink>$$Uhttp://pascal-francis.inist.fr/vibad/index.php?action=getRecordDetail&idt=27439410$$DView record in Pascal Francis$$Hfree_for_read</backlink><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/23556538$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Pett-Ridge, Jennifer</creatorcontrib><creatorcontrib>Petersen, Dorthe G.</creatorcontrib><creatorcontrib>Nuccio, Erin</creatorcontrib><creatorcontrib>Firestone, Mary K.</creatorcontrib><title>Influence of oxic/anoxic fluctuations on ammonia oxidizers and nitrification potential in a wet tropical soil</title><title>FEMS microbiology ecology</title><addtitle>FEMS Microbiol Ecol</addtitle><description>Abstract
Ammonia oxidation is a key process in the global nitrogen cycle. However, in tropical soils, little is known about ammonia-oxidizing microorganisms and how characteristically variable oxygen regimes affect their activity. We investigated the influence of brief anaerobic periods on ammonia oxidation along an elevation, moisture, and oxygen availability gradient in wet tropical soils. Soils from three forest types were incubated for up to 36 weeks in lab microcosms under three regimes: (1) static aerobic; (2) static anaerobic; and (3) fluctuating (aerobic/anaerobic). Nitrification potential was measured in field-fresh soils and incubated soils. The native ammonia-oxidizing community was also characterized, based on diversity assessments (clone libraries) and quantification of the ammonia monooxygenase α–subunit (amoA) gene. These relatively low pH soils appear to be dominated by ammonia-oxidizing archaea (AOA), and AOA communities in the three soil types differed significantly in their ability to oxidize ammonia. Soils from an intermediate elevation, and those incubated with fluctuating redox conditions, tended to have the highest nitrification potential following an influx of oxygen, although all soils retained the capacity to nitrify even after long anoxic periods. Together, these results suggest that wet tropical soil AOA are tolerant of extended periods of anoxia.</description><subject>Aerobiosis</subject><subject>Ammonia</subject><subject>Ammonia - metabolism</subject><subject>amoA</subject><subject>Anaerobiosis</subject><subject>Animal, plant and microbial ecology</subject><subject>Anoxia</subject><subject>Archaea</subject><subject>Archaea - classification</subject><subject>Archaea - isolation & purification</subject><subject>Archaea - metabolism</subject><subject>Bacteria - genetics</subject><subject>Bacteria - isolation & purification</subject><subject>Bacteria - metabolism</subject><subject>Bacteriology</subject><subject>Biological and medical sciences</subject><subject>Ecology</subject><subject>Fundamental and applied biological sciences. Psychology</subject><subject>Microbial ecology</subject><subject>Microbiology</subject><subject>Microorganisms</subject><subject>Miscellaneous</subject><subject>Nitrification</subject><subject>nitrifiers</subject><subject>Nitrogen cycle</subject><subject>Oxidation</subject><subject>Oxidation-Reduction</subject><subject>Oxidoreductases - genetics</subject><subject>Oxygen</subject><subject>oxygen depletion</subject><subject>Puerto Rico</subject><subject>redox oscillation</subject><subject>Soil</subject><subject>Soil Microbiology</subject><subject>Soil pH</subject><subject>Soil types</subject><subject>Trees</subject><subject>Tropical Climate</subject><subject>Tropical environments</subject><subject>Various environments (extraatmospheric space, air, water)</subject><issn>0168-6496</issn><issn>1574-6941</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2013</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNqNkc1rFTEUxYMo7bN27U4CIogwfbn5nCyltFqouOk-pDMJpMwkYzJDrX-9mb7XD0TQbC65-Z2TmxyE3gI5gbq2IBRvpOZwArTuX6DNY-cl2hCQbSO5lofodSk3hIBgnBygQ8qEkIK1GzReRD8sLnYOJ4_Tz9BtbVwLru1uXuwcUiw4RWzHMcVgV6YPv1wu2MYexzDn4EN3z-EpzS7OwQ44VAG-dTOec5rq8YBLCsMb9MrbobjjfT1CV-dnV6dfm8vvXy5OP182nVASGgBvGW1Fy4gj15Rw3VPLqedeK9XK1hPOPe3Bu16Jllupac_AgeecAPTsCH3c2U45_Vhcmc0YSueGwUaXlmKAaa1BK8b_A5VagQYhKvr-D_QmLTnWd6xUKyShSlVqu6O6nErJzpsph9HmOwPErJmZNSGzJmTuM6uKd3vf5Xp0_SP_EFIFPuwBW-pP-mxjF8oTpzirbqRyYsfdhsHd_etec3727WGATztdWqa_qppn0_4G2tW4lw</recordid><startdate>201307</startdate><enddate>201307</enddate><creator>Pett-Ridge, Jennifer</creator><creator>Petersen, Dorthe G.</creator><creator>Nuccio, Erin</creator><creator>Firestone, Mary K.</creator><general>Blackwell Publishing Ltd</general><general>Blackwell</general><general>Oxford University Press</general><scope>IQODW</scope><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>7QL</scope><scope>7QP</scope><scope>7QR</scope><scope>7SN</scope><scope>7T7</scope><scope>7TK</scope><scope>7TM</scope><scope>8FD</scope><scope>C1K</scope><scope>FR3</scope><scope>K9.</scope><scope>M7N</scope><scope>P64</scope><scope>RC3</scope><scope>7X8</scope></search><sort><creationdate>201307</creationdate><title>Influence of oxic/anoxic fluctuations on ammonia oxidizers and nitrification potential in a wet tropical soil</title><author>Pett-Ridge, Jennifer ; Petersen, Dorthe G. ; Nuccio, Erin ; Firestone, Mary K.</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c5761-11fa3285830e0b2049d2a42f4f977868f044f2d1fed7584a692d31e1f44011d3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2013</creationdate><topic>Aerobiosis</topic><topic>Ammonia</topic><topic>Ammonia - metabolism</topic><topic>amoA</topic><topic>Anaerobiosis</topic><topic>Animal, plant and microbial ecology</topic><topic>Anoxia</topic><topic>Archaea</topic><topic>Archaea - classification</topic><topic>Archaea - isolation & purification</topic><topic>Archaea - metabolism</topic><topic>Bacteria - genetics</topic><topic>Bacteria - isolation & purification</topic><topic>Bacteria - metabolism</topic><topic>Bacteriology</topic><topic>Biological and medical sciences</topic><topic>Ecology</topic><topic>Fundamental and applied biological sciences. Psychology</topic><topic>Microbial ecology</topic><topic>Microbiology</topic><topic>Microorganisms</topic><topic>Miscellaneous</topic><topic>Nitrification</topic><topic>nitrifiers</topic><topic>Nitrogen cycle</topic><topic>Oxidation</topic><topic>Oxidation-Reduction</topic><topic>Oxidoreductases - genetics</topic><topic>Oxygen</topic><topic>oxygen depletion</topic><topic>Puerto Rico</topic><topic>redox oscillation</topic><topic>Soil</topic><topic>Soil Microbiology</topic><topic>Soil pH</topic><topic>Soil types</topic><topic>Trees</topic><topic>Tropical Climate</topic><topic>Tropical environments</topic><topic>Various environments (extraatmospheric space, air, water)</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Pett-Ridge, Jennifer</creatorcontrib><creatorcontrib>Petersen, Dorthe G.</creatorcontrib><creatorcontrib>Nuccio, Erin</creatorcontrib><creatorcontrib>Firestone, Mary K.</creatorcontrib><collection>Pascal-Francis</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</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>Technology Research Database</collection><collection>Environmental Sciences and Pollution Management</collection><collection>Engineering Research Database</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>Algology Mycology and Protozoology Abstracts (Microbiology C)</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Genetics Abstracts</collection><collection>MEDLINE - Academic</collection><jtitle>FEMS microbiology ecology</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Pett-Ridge, Jennifer</au><au>Petersen, Dorthe G.</au><au>Nuccio, Erin</au><au>Firestone, Mary K.</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Influence of oxic/anoxic fluctuations on ammonia oxidizers and nitrification potential in a wet tropical soil</atitle><jtitle>FEMS microbiology ecology</jtitle><addtitle>FEMS Microbiol Ecol</addtitle><date>2013-07</date><risdate>2013</risdate><volume>85</volume><issue>1</issue><spage>179</spage><epage>194</epage><pages>179-194</pages><issn>0168-6496</issn><eissn>1574-6941</eissn><coden>FMECEZ</coden><abstract>Abstract
Ammonia oxidation is a key process in the global nitrogen cycle. However, in tropical soils, little is known about ammonia-oxidizing microorganisms and how characteristically variable oxygen regimes affect their activity. We investigated the influence of brief anaerobic periods on ammonia oxidation along an elevation, moisture, and oxygen availability gradient in wet tropical soils. Soils from three forest types were incubated for up to 36 weeks in lab microcosms under three regimes: (1) static aerobic; (2) static anaerobic; and (3) fluctuating (aerobic/anaerobic). Nitrification potential was measured in field-fresh soils and incubated soils. The native ammonia-oxidizing community was also characterized, based on diversity assessments (clone libraries) and quantification of the ammonia monooxygenase α–subunit (amoA) gene. These relatively low pH soils appear to be dominated by ammonia-oxidizing archaea (AOA), and AOA communities in the three soil types differed significantly in their ability to oxidize ammonia. Soils from an intermediate elevation, and those incubated with fluctuating redox conditions, tended to have the highest nitrification potential following an influx of oxygen, although all soils retained the capacity to nitrify even after long anoxic periods. Together, these results suggest that wet tropical soil AOA are tolerant of extended periods of anoxia.</abstract><cop>Oxford, UK</cop><pub>Blackwell Publishing Ltd</pub><pmid>23556538</pmid><doi>10.1111/1574-6941.12111</doi><tpages>16</tpages><oa>free_for_read</oa></addata></record> |
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| source | MEDLINE; Elektronische Zeitschriftenbibliothek - Frei zugängliche E-Journals; Oxford Journals Open Access Collection; Wiley Online Library All Journals |
| subjects | Aerobiosis Ammonia Ammonia - metabolism amoA Anaerobiosis Animal, plant and microbial ecology Anoxia Archaea Archaea - classification Archaea - isolation & purification Archaea - metabolism Bacteria - genetics Bacteria - isolation & purification Bacteria - metabolism Bacteriology Biological and medical sciences Ecology Fundamental and applied biological sciences. Psychology Microbial ecology Microbiology Microorganisms Miscellaneous Nitrification nitrifiers Nitrogen cycle Oxidation Oxidation-Reduction Oxidoreductases - genetics Oxygen oxygen depletion Puerto Rico redox oscillation Soil Soil Microbiology Soil pH Soil types Trees Tropical Climate Tropical environments Various environments (extraatmospheric space, air, water) |
| title | Influence of oxic/anoxic fluctuations on ammonia oxidizers and nitrification potential in a wet tropical soil |
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