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Applied and Environmental Microbiology, November 2009, p. 7070-7078, Vol. 75, No. 22
0099-2240/09/$08.00+0     doi:10.1128/AEM.01481-09
Copyright © 2009, American Society for Microbiology. All Rights Reserved.

Microbial Populations Responsive to Denitrification-Inducing Conditions in Rice Paddy Soil, as Revealed by Comparative 16S rRNA Gene Analysis{triangledown} ,{dagger}

Satoshi Ishii,1* Michihiro Yamamoto,1 Mami Kikuchi,2 Kenshiro Oshima,2 Masahira Hattori,2 Shigeto Otsuka,1 and Keishi Senoo1

Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan,1 Department of Computational Biology, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan2

Received 24 June 2009/ Accepted 15 September 2009

Rice paddy soil has been shown to have strong denitrifying activity. However, the microbial populations responsible for nitrate respiration and denitrification have not been well characterized. In this study, we performed a clone library analysis of >1,000 clones of the nearly full-length 16S rRNA gene to characterize bacterial community structure in rice paddy soil. We also identified potential key players in nitrate respiration and denitrification by comparing the community structures of soils with strong denitrifying activity to those of soils without denitrifying activity. Clone library analysis showed that bacteria belonging to the phylum Firmicutes, including a unique Symbiobacterium clade, dominated the clones obtained in this study. Using the template match method, several operational taxonomic units (OTUs), most belonging to the orders Burkholderiales and Rhodocyclales, were identified as OTUs that were specifically enriched in the sample with strong denitrifying activity. Almost one-half of these OTUs were classified in the genus Herbaspirillum and appeared >10-fold more frequently in the soils with strong denitrifying activity than in the soils without denitrifying activity. Therefore, OTUs related to Herbaspirillum are potential key players in nitrate respiration and denitrification under the conditions used.

* Corresponding author. Mailing address: Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan. Phone: 81-1-5841-5140. Fax: 81-1-5841-8042. E-mail: anaerobe{at}mail.ecc.u-tokyo.ac.jp

{triangledown} Published ahead of print on 18 September 2009.

{dagger} Supplemental material for this article may be found at http://aem.asm.org/.

Applied and Environmental Microbiology, November 2009, p. 7070-7078, Vol. 75, No. 22
0099-2240/09/$08.00+0     doi:10.1128/AEM.01481-09
Copyright © 2009, American Society for Microbiology. All Rights Reserved.





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