Microbial functional genes involved in nitrogen fixation, nitrification and denitrification in forest ecosystems

The understanding of nitrogen (N) cycling in forest ecosystems has undergone a major shift in the past decade as molecular methods are being used to link microorganisms to key processes in soil. The analysis of the abundance and community structure of functional genes involved in the biogeochemical...

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Published inSoil biology & biochemistry Vol. 75; pp. 11 - 25
Main Authors Levy-Booth, David J., Prescott, Cindy E., Grayston, Susan J.
Format Journal Article
LanguageEnglish
Published Amsterdam Elsevier Ltd 01.08.2014
Elsevier
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Abstract The understanding of nitrogen (N) cycling in forest ecosystems has undergone a major shift in the past decade as molecular methods are being used to link microorganisms to key processes in soil. The analysis of the abundance and community structure of functional genes involved in the biogeochemical cycling of N in forest soils offers an approach to directly link microbial groups to soil characteristics and ecosystem processes. The majority of N entering ecosystems is biologically-derived from fixation of atmospheric N2. Molecular studies of N-fixation use the nitrogenase reductase (nifH) marker gene, and can be used to link N-fixation to other N- and C-cycling processes. Inorganic N entering soil via N-fixation, fertilization and deposition can have several fates, depending on the soil environment and the microbial community. The loss of N from forests stands subject to fertilization and atmospheric deposition is of increasing interest as the outputs of nitrate (NO3−) and nitrous oxide (N2O) are implicated in ground water pollution and climate change, respectively. Ammonia-oxidizing bacteria (AOB) and archaea (AOA) oxidize ammonia (NH3) to NO3− as the first step of nitrification and are studied using the ammonium monooxygenase (amoA) marker. The abundance and community structure of ammonia-oxidizers is largely dependent on pH and availability of reactive N forms, and can change rapidly following N addition or after fire. These organisms can also release N2O during nitrifier denitrification or through linked nitrification–denitrification. In some forest soils, N2O emissions are correlated with genes in the denitrification pathway (napA, narG, nirK, nirS, nosZ) making these genes useful indicators of greenhouse gas (GHG) flux potential. A review of this topic is timely as there is currently much concern regarding the effect of N fertilization and deposition on North American and European forests due to the potential alteration of dissimilative N-cycling processes and the potential for increased N2O emissions in forest stands. •Functional gene studies improve models of soil function, e.g., greenhouse gas rates.•Nitrification genes (amoA) are influenced by pH and influence N2O emission.•N2O production/reduction gene abundance linked to N2O emissions in forests.
AbstractList The understanding of nitrogen (N) cycling in forest ecosystems has undergone a major shift in the past decade as molecular methods are being used to link microorganisms to key processes in soil. The analysis of the abundance and community structure of functional genes involved in the biogeochemical cycling of N in forest soils offers an approach to directly link microbial groups to soil characteristics and ecosystem processes. The majority of N entering ecosystems is biologically-derived from fixation of atmospheric N sub(2). Molecular studies of N-fixation use the nitrogenase reductase (nifH) marker gene, and can be used to link N-fixation to other N- and C-cycling processes. Inorganic N entering soil via N-fixation, fertilization and deposition can have several fates, depending on the soil environment and the microbial community. The loss of N from forests stands subject to fertilization and atmospheric deposition is of increasing interest as the outputs of nitrate (NO sub(3) super(-)) and nitrous oxide (N sub(2)O) are implicated in ground water pollution and climate change, respectively. Ammonia-oxidizing bacteria (AOB) and archaea (AOA) oxidize ammonia (NH sub(3)) to NO sub(3) super(-) as the first step of nitrification and are studied using the ammonium monooxygenase (amoA) marker. The abundance and community structure of ammonia-oxidizers is largely dependent on pH and availability of reactive N forms, and can change rapidly following N addition or after fire. These organisms can also release N sub(2)O during nitrifier denitrification or through linked nitrification-denitrification. In some forest soils, N sub(2)O emissions are correlated with genes in the denitrification pathway (napA, narG, nirK, nirS, nosZ) making these genes useful indicators of greenhouse gas (GHG) flux potential. A review of this topic is timely as there is currently much concern regarding the effect of N fertilization and deposition on North American and European forests due to the potential alteration of dissimilative N-cycling processes and the potential for increased N sub(2)O emissions in forest stands.
The understanding of nitrogen (N) cycling in forest ecosystems has undergone a major shift in the past decade as molecular methods are being used to link microorganisms to key processes in soil. The analysis of the abundance and community structure of functional genes involved in the biogeochemical cycling of N in forest soils offers an approach to directly link microbial groups to soil characteristics and ecosystem processes. The majority of N entering ecosystems is biologically-derived from fixation of atmospheric N2. Molecular studies of N-fixation use the nitrogenase reductase (nifH) marker gene, and can be used to link N-fixation to other N- and C-cycling processes. Inorganic N entering soil via N-fixation, fertilization and deposition can have several fates, depending on the soil environment and the microbial community. The loss of N from forests stands subject to fertilization and atmospheric deposition is of increasing interest as the outputs of nitrate (NO3−) and nitrous oxide (N2O) are implicated in ground water pollution and climate change, respectively. Ammonia-oxidizing bacteria (AOB) and archaea (AOA) oxidize ammonia (NH3) to NO3− as the first step of nitrification and are studied using the ammonium monooxygenase (amoA) marker. The abundance and community structure of ammonia-oxidizers is largely dependent on pH and availability of reactive N forms, and can change rapidly following N addition or after fire. These organisms can also release N2O during nitrifier denitrification or through linked nitrification–denitrification. In some forest soils, N2O emissions are correlated with genes in the denitrification pathway (napA, narG, nirK, nirS, nosZ) making these genes useful indicators of greenhouse gas (GHG) flux potential. A review of this topic is timely as there is currently much concern regarding the effect of N fertilization and deposition on North American and European forests due to the potential alteration of dissimilative N-cycling processes and the potential for increased N2O emissions in forest stands. •Functional gene studies improve models of soil function, e.g., greenhouse gas rates.•Nitrification genes (amoA) are influenced by pH and influence N2O emission.•N2O production/reduction gene abundance linked to N2O emissions in forests.
Author Prescott, Cindy E.
Grayston, Susan J.
Levy-Booth, David J.
Author_xml – sequence: 1
  givenname: David J.
  surname: Levy-Booth
  fullname: Levy-Booth, David J.
  email: dlevybooth@gmail.com
– sequence: 2
  givenname: Cindy E.
  orcidid: 0000-0003-1482-4580
  surname: Prescott
  fullname: Prescott, Cindy E.
– sequence: 3
  givenname: Susan J.
  surname: Grayston
  fullname: Grayston, Susan J.
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ID FETCH-LOGICAL-c438t-5b396f01632a5ba86c9eb9753b152a879f014037278873999cb20830965711553
IEDL.DBID AIKHN
ISSN 0038-0717
IngestDate Fri Oct 25 09:35:55 EDT 2024
Fri Dec 06 04:13:27 EST 2024
Fri Nov 25 01:12:21 EST 2022
Fri Feb 23 02:23:27 EST 2024
IsPeerReviewed true
IsScholarly true
Keywords Denitrification
Forest
Nitrous oxide
Functional genes
Nitrogen cycling
Nitrification
Forests
Forest zone
Nitrogen cycle
Gene
Ecosystem
Nitrogen fixation
Soil science
Microorganism
Nitrogen protoxide
Language English
License CC BY 4.0
LinkModel DirectLink
MergedId FETCHMERGED-LOGICAL-c438t-5b396f01632a5ba86c9eb9753b152a879f014037278873999cb20830965711553
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content type line 23
ORCID 0000-0003-1482-4580
PQID 1544005302
PQPubID 23462
PageCount 15
ParticipantIDs proquest_miscellaneous_1544005302
crossref_primary_10_1016_j_soilbio_2014_03_021
pascalfrancis_primary_28547093
elsevier_sciencedirect_doi_10_1016_j_soilbio_2014_03_021
PublicationCentury 2000
PublicationDate 2014-08-01
PublicationDateYYYYMMDD 2014-08-01
PublicationDate_xml – month: 08
  year: 2014
  text: 2014-08-01
  day: 01
PublicationDecade 2010
PublicationPlace Amsterdam
PublicationPlace_xml – name: Amsterdam
PublicationTitle Soil biology & biochemistry
PublicationYear 2014
Publisher Elsevier Ltd
Elsevier
Publisher_xml – name: Elsevier Ltd
– name: Elsevier
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Snippet The understanding of nitrogen (N) cycling in forest ecosystems has undergone a major shift in the past decade as molecular methods are being used to link...
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SubjectTerms Agronomy. Soil science and plant productions
Archaea
Biochemistry and biology
Biological and medical sciences
Chemical, physicochemical, biochemical and biological properties
Denitrification
Forest
Functional genes
Fundamental and applied biological sciences. Psychology
Nitrification
Nitrogen cycling
Nitrous oxide
Physics, chemistry, biochemistry and biology of agricultural and forest soils
Soil science
Title Microbial functional genes involved in nitrogen fixation, nitrification and denitrification in forest ecosystems
URI https://dx.doi.org/10.1016/j.soilbio.2014.03.021
https://search.proquest.com/docview/1544005302
Volume 75
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