Temporal shifts in diversity and quantity of nirS and nirK in a rice paddy field soil

Megumi Yoshida, Satoshi Ishii, Shigeto Otsuka, Keishi Senoo

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160 Scopus citations


Denitrification is an important part of the nitrogen cycle in the environment, and diverse bacteria, archaea, and fungi are known to have denitrifying ability. Rice paddy field soils have been known to have strong denitrifying activity, but the microbes responsible for denitrification in rice paddy field soils are not well known. Present study analyzed the diversity and quantity of the nitrite reductase genes (nirS and nirK) in a rice paddy field soil, sampled four times in one rice-growing season. Clone library analyses suggested that the denitrifier community composition varied over sampling time. Although many clones were distantly related to the known NirS or NirK, some clones were related to the NirS from Burkholderiales and Rhodocyclales bacteria, and some were related to the NirK from Rhizobiales bacteria. These denitrifiers may play an important role in denitrification in the rice paddy field soil. The quantitative PCR results showed that nirK was more abundant than nirS in all soil samples, but the nirK/nirS ratio decreased after water logging. These results suggest that both diversity and quantity changed over time in the rice paddy field soil, in response to the soil condition.

Original languageEnglish (US)
Pages (from-to)2044-2051
Number of pages8
JournalSoil Biology and Biochemistry
Issue number10
StatePublished - Oct 2009

Bibliographical note

Funding Information:
This work was supported by the Program for Promotion of Basic Research Activities for Innovative Biosciences (PROBRAIN) from Bio-oriented Technology Research Advancement Institution, Tokyo, Japan. Additional financial support was provided by a Grant-in-Aid for Scientific Research from Japan Society for the Promotion of Science (JSPS), and a Grant-in-Aid (Soil eDNA) from Ministry of Agricultural, Forestry, and Fisheries of Japan. M.Y. was supported by Grant-in-Aid for JSPS Fellows.


  • Clone library analysis
  • Denitrification
  • Functional gene diversity
  • Nitrite reductase
  • Real-time PCR
  • Rice paddy field
  • Temporal dynamics
  • nirK
  • nirS


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