Seasonal transition of active bacterial and archaeal communities in relation to water management in paddy soils

Hideomi Itoh, Satoshi Ishii, Yutaka Shiratori, Kenshiro Oshima, Shigeto Otsuka, Masahira Hattori, Keishi Senoo

Research output: Contribution to journalArticle

26 Citations (Scopus)

Abstract

Paddy soils have an environment in which waterlogging and drainage occur during the rice growing season. Fingerprinting analysis based on soil RNA indicated that active microbial populations changed in response to water management conditions, although the fundamental microbial community was stable as assessed by DNA-based fingerprinting analysis. Comparative clone library analysis based on bacterial and archaeal 16S rRNAs (5,277 and 5,436 clones, respectively) revealed stable and variable members under waterlogged or drained conditions. Clones related to the class Deltaproteobacteria and phylum Euryarchaeota were most frequently obtained from the samples collected under both waterlogged and drained conditions. Clones related to syntrophic hydrogen-producing bacteria, hydrogenotrophic methanogenic archaea, rice cluster III, V, and IV, and uncultured crenarchaeotal group 1.2 appeared in greater proportion in the samples collected under waterlogged conditions than in those collected under drained conditions, while clones belonging to rice cluster VI related to ammonia-oxidizing archaea (AOA) appeared at higher frequency in the samples collected under drained conditions than in those collected under waterlogged conditions. These results suggested that hydrogenotrophic methanogenesis may become active under waterlogged conditions, whereas ammonia oxidation may progress by rice cluster VI becoming active under drained conditions in the paddy field.

Original languageEnglish
Pages (from-to)370-380
Number of pages11
JournalMicrobes and Environments
Volume28
Issue number3
DOIs
Publication statusPublished - 2013
Externally publishedYes

Fingerprint

drained conditions
paddy soils
flooded conditions
water management
clone
rice
clones
soil
Archaea
ammonia
hydrogen-oxidizing bacteria
methanogenic bacterium
Euryarchaeota
waterlogging
delta-Proteobacteria
methanogenesis
paddy field
edaphic factors
RNA
microbial community

Keywords

  • Clone libraries
  • Paddy soil
  • Soil microbial diversity

ASJC Scopus subject areas

  • Plant Science
  • Soil Science
  • Ecology, Evolution, Behavior and Systematics

Cite this

Seasonal transition of active bacterial and archaeal communities in relation to water management in paddy soils. / Itoh, Hideomi; Ishii, Satoshi; Shiratori, Yutaka; Oshima, Kenshiro; Otsuka, Shigeto; Hattori, Masahira; Senoo, Keishi.

In: Microbes and Environments, Vol. 28, No. 3, 2013, p. 370-380.

Research output: Contribution to journalArticle

Itoh, Hideomi ; Ishii, Satoshi ; Shiratori, Yutaka ; Oshima, Kenshiro ; Otsuka, Shigeto ; Hattori, Masahira ; Senoo, Keishi. / Seasonal transition of active bacterial and archaeal communities in relation to water management in paddy soils. In: Microbes and Environments. 2013 ; Vol. 28, No. 3. pp. 370-380.
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