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Identification of Active Denitrifiers in Rice Paddy Soil by DNA- and RNA-based Analyses

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Date 2012 Sep 14
PMID 22972387
Citations 21
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Abstract

Denitrification occurs markedly in rice paddy fields; however, few microbes that are actively involved in denitrification in these environments have been identified. In this study, we used a laboratory soil microcosm system in which denitrification activity was enhanced. DNA and RNA were extracted from soil at six time points after enhancing denitrification activity, and quantitative PCR and clone library analyses were performed targeting the 16S rRNA gene and denitrification functional genes (nirS, nirK and nosZ) to clarify which microbes are actively involved in denitrification in rice paddy soil. Based on the quantitative PCR results, transcription levels of the functional genes agreed with the denitrification activity, although gene abundance did not change at the DNA level. Diverse denitrifiers were detected in clone library analysis, but comparative analysis suggested that only some of the putative denitrifiers, especially those belonging to the orders Neisseriales, Rhodocyclales and Burkholderiales, were actively involved in denitrification in rice paddy soil.

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References
1.
Throback I, Enwall K, Jarvis A, Hallin S . Reassessing PCR primers targeting nirS, nirK and nosZ genes for community surveys of denitrifying bacteria with DGGE. FEMS Microbiol Ecol. 2009; 49(3):401-17. DOI: 10.1016/j.femsec.2004.04.011. View

2.
Yoshida M, Ishii S, Otsuka S, Senoo K . nirK-harboring denitrifiers are more responsive to denitrification- inducing conditions in rice paddy soil than nirS-harboring bacteria. Microbes Environ. 2011; 25(1):45-8. DOI: 10.1264/jsme2.me09160. View

3.
Sharma S, Aneja M, Mayer J, Munch J, Schloter M . Diversity of transcripts of nitrite reductase genes (nirK and nirS) in rhizospheres of grain legumes. Appl Environ Microbiol. 2005; 71(4):2001-7. PMC: 1082563. DOI: 10.1128/AEM.71.4.2001-2007.2005. View

4.
Prieme A, Braker G, Tiedje J . Diversity of nitrite reductase (nirK and nirS) gene fragments in forested upland and wetland soils. Appl Environ Microbiol. 2002; 68(4):1893-900. PMC: 123828. DOI: 10.1128/AEM.68.4.1893-1900.2002. View

5.
Zumft W . Cell biology and molecular basis of denitrification. Microbiol Mol Biol Rev. 1997; 61(4):533-616. PMC: 232623. DOI: 10.1128/mmbr.61.4.533-616.1997. View