Microbial populations responsive to denitrification-inducing conditions in rice paddy soil, as revealed by comparative 16S rRNA gene analysis

Satoshi Ishii, Michihiro Yamamoto, Mami Kikuchi, Kenshiro Oshima, Masahira Hattori, Shigeto Otsuka, Keishi Senoo

Research output: Contribution to journalArticle

63 Citations (Scopus)

Abstract

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.

Original languageEnglish
Pages (from-to)7070-7078
Number of pages9
JournalApplied and Environmental Microbiology
Volume75
Issue number22
DOIs
Publication statusPublished - 2009 Nov
Externally publishedYes

Fingerprint

Denitrification
rice soils
paddy soils
rRNA Genes
denitrification
paddies
Soil
rice
Herbaspirillum
ribosomal RNA
clones
gene
clone
nitrates
Clone Cells
Symbiobacterium
Nitrates
Population
Rhodocyclales
soil

ASJC Scopus subject areas

  • Applied Microbiology and Biotechnology
  • Food Science
  • Biotechnology
  • Ecology

Cite this

Microbial populations responsive to denitrification-inducing conditions in rice paddy soil, as revealed by comparative 16S rRNA gene analysis. / Ishii, Satoshi; Yamamoto, Michihiro; Kikuchi, Mami; Oshima, Kenshiro; Hattori, Masahira; Otsuka, Shigeto; Senoo, Keishi.

In: Applied and Environmental Microbiology, Vol. 75, No. 22, 11.2009, p. 7070-7078.

Research output: Contribution to journalArticle

Ishii, Satoshi ; Yamamoto, Michihiro ; Kikuchi, Mami ; Oshima, Kenshiro ; Hattori, Masahira ; Otsuka, Shigeto ; Senoo, Keishi. / Microbial populations responsive to denitrification-inducing conditions in rice paddy soil, as revealed by comparative 16S rRNA gene analysis. In: Applied and Environmental Microbiology. 2009 ; Vol. 75, No. 22. pp. 7070-7078.
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