Biology and Fertility of Soils

, Volume 46, Issue 4, pp 343–353

Diversity of methanogenic archaeal communities in Japanese paddy field ecosystem, estimated by denaturing gradient gel electrophoresis

Original Paper

DOI: 10.1007/s00374-009-0435-2

Cite this article as:
Watanabe, T., Kimura, M. & Asakawa, S. Biol Fertil Soils (2010) 46: 343. doi:10.1007/s00374-009-0435-2


Diversity of methanogenic archaeal communities in Japanese paddy field ecosystem was evaluated by the denaturing gradient gel electrophoresis (DGGE) after PCR amplification of the 16S rRNA genes (16S rDNAs), sequencing analysis and data evaluation by principal component analysis. Data were obtained from samples collected from the plowed soil layer, rice roots, rice straws incorporated in soil, plant residues (mixture of weeds, rice litters, rice roots, and rice stubbles) in soil, and composing rice straw. The number of bands of DGGE profiles ranged from 12 to 26 with the highest numbers in rice roots and rice straws incorporated in soil. However, the diversity indices based on both the numbers and intensity of bands indicated that the community of the plowed soil layer was the most diverse, even, and stable. Sequencing of the main DGGE bands showed the presence of Methanomicrobiales, Methanosarcinales, Methanobacteriaceae, and Methanocellales. The plowed soil layer included all phylogenetic groups of the methanogenic archaea of the other studied habitats, with prevalence of the members of Methanomicrobiales and Methanocellales. The phylogenetic diversity was compared with that of paddy soils collected in Italy, China, and the Philippines and that of 12 anaerobic environments (fen, waste, coast, permafrost, natural gas field, bovine rumen, riparian soil, termite, ciliate endosymboints, lake sediment, landfill, and seep rumen). The phylogenetic diversity was more similar among paddy soils than with the other anaerobic environments. Probably, the methanogenic archaeal communities of the paddy field soils were characterized by indigenous members and some of the members of the community of the plowed soil layer colonized rice roots, rice straws, and plant residues.


Methanogenic archaeaDenaturing gradient gel electrophoresisPaddy field ecosystem16S rRNA genePrincipal component analysis

Supplementary material

374_2009_435_MOESM1_ESM.pdf (55 kb)
Supplementary Table 1(PDF 55 kb)
374_2009_435_MOESM2_ESM.pdf (323 kb)
Supplementary Fig. 1(PDF 323 kb)
374_2009_435_MOESM3_ESM.pdf (92 kb)
Supplementary Fig. 2(PDF 92 kb)
374_2009_435_MOESM4_ESM.pdf (234 kb)
Supplementary Fig. 3(PDF 233 kb)

Copyright information

© Springer-Verlag 2010

Authors and Affiliations

  • Takeshi Watanabe
    • 1
  • Makoto Kimura
    • 1
  • Susumu Asakawa
    • 1
  1. 1.Laboratory of Soil Biology and Chemistry, Graduate School of Bioagricultural SciencesNagoya UniversityChikusaJapan