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Title: Molecular analyses of the methane-oxidizing microbial community in rice field soil by targeting the genes of the 16S rRNA, particulate methane monooxygenase, and methanol dehydrogenase

Abstract

Rice field soil with a nonsaturated water content induced CH{sub 4} consumption activity when it was supplemented with 5% CH{sub 4}. After a lag phase of 3 days, CH{sub 4} was consumed rapidly until the concentration was less than 1.8 parts per million by volume (ppmv). However, the soil was not able to maintain the oxidation activity at near-atmospheric CH{sub 4} mixing ratios. The soil microbial community was monitored by performing denaturing gradient gel electrophoresis (DGGE) during the oxidation process with different PCR primer sets based on the 16S rRNA gene and on functional genes. A universal small-subunit (SSU) ribosomal DNA (rDNA) primer set and 16S rDNA primer sets specifically targeting type 1 methylotrophs and type 2 methylotrophs were used. Functional PCR primers targeted the genes for particulate methane monooxygenase (pmoA) and methanol dehydrogenase (mxaF), which code for key enzymes in the catabolism of all methanotrophs. The yield of PCR products amplified from DNA in soil that oxidized CH{sub 4} was the same as the yield of PCR products amplified from control soil when the universal SSU rDNA primer set was used but was significantly greater when primer sets specific for methanotrophs were used. The DGGE patterns and the sequencesmore » of major DGGE bands obtained with the universal SSU rDNA primer set showed that the community structure was dominated by nonmethanotrophic populations related to the genera Flavobacterium and Bacillus and was not influenced by CH{sub 4}.« less

Authors:
; ;  [1]
  1. Max-Planck-Inst. fuer Terrestrische Mikrobiologie, Marburg (Germany)
Publication Date:
OSTI Identifier:
346829
Resource Type:
Journal Article
Journal Name:
Applied and Environmental Microbiology
Additional Journal Information:
Journal Volume: 65; Journal Issue: 5; Other Information: PBD: May 1999
Country of Publication:
United States
Language:
English
Subject:
54 ENVIRONMENTAL SCIENCES; METHANE; SOILS; METHANOTROPHIC BACTERIA; RIBOSOMAL RNA; DNA; GENES; OXIDOREDUCTASES; BIODEGRADATION

Citation Formats

Henckel, T, Friedrich, M, and Conrad, R. Molecular analyses of the methane-oxidizing microbial community in rice field soil by targeting the genes of the 16S rRNA, particulate methane monooxygenase, and methanol dehydrogenase. United States: N. p., 1999. Web.
Henckel, T, Friedrich, M, & Conrad, R. Molecular analyses of the methane-oxidizing microbial community in rice field soil by targeting the genes of the 16S rRNA, particulate methane monooxygenase, and methanol dehydrogenase. United States.
Henckel, T, Friedrich, M, and Conrad, R. 1999. "Molecular analyses of the methane-oxidizing microbial community in rice field soil by targeting the genes of the 16S rRNA, particulate methane monooxygenase, and methanol dehydrogenase". United States.
@article{osti_346829,
title = {Molecular analyses of the methane-oxidizing microbial community in rice field soil by targeting the genes of the 16S rRNA, particulate methane monooxygenase, and methanol dehydrogenase},
author = {Henckel, T and Friedrich, M and Conrad, R},
abstractNote = {Rice field soil with a nonsaturated water content induced CH{sub 4} consumption activity when it was supplemented with 5% CH{sub 4}. After a lag phase of 3 days, CH{sub 4} was consumed rapidly until the concentration was less than 1.8 parts per million by volume (ppmv). However, the soil was not able to maintain the oxidation activity at near-atmospheric CH{sub 4} mixing ratios. The soil microbial community was monitored by performing denaturing gradient gel electrophoresis (DGGE) during the oxidation process with different PCR primer sets based on the 16S rRNA gene and on functional genes. A universal small-subunit (SSU) ribosomal DNA (rDNA) primer set and 16S rDNA primer sets specifically targeting type 1 methylotrophs and type 2 methylotrophs were used. Functional PCR primers targeted the genes for particulate methane monooxygenase (pmoA) and methanol dehydrogenase (mxaF), which code for key enzymes in the catabolism of all methanotrophs. The yield of PCR products amplified from DNA in soil that oxidized CH{sub 4} was the same as the yield of PCR products amplified from control soil when the universal SSU rDNA primer set was used but was significantly greater when primer sets specific for methanotrophs were used. The DGGE patterns and the sequences of major DGGE bands obtained with the universal SSU rDNA primer set showed that the community structure was dominated by nonmethanotrophic populations related to the genera Flavobacterium and Bacillus and was not influenced by CH{sub 4}.},
doi = {},
url = {https://www.osti.gov/biblio/346829}, journal = {Applied and Environmental Microbiology},
number = 5,
volume = 65,
place = {United States},
year = {Sat May 01 00:00:00 EDT 1999},
month = {Sat May 01 00:00:00 EDT 1999}
}