Are symbiotic methanotrophs key microbes for N acquisition in paddy rice root?

Kiwamu Minamisawa, Haruko Imaizumi-Anraku, Zhihua Bao, Ryo Shinoda, Takashi Okubo, Seishi Ikeda

Research output: Contribution to journalArticlepeer-review

29 Citations (Scopus)


The relationships between biogeochemical processes and microbial functions in rice (Oryza sativa) paddies have been the focus of a large number of studies. A mechanistic understanding of methane–nitrogen (CH4–N) cycle interactions is a key unresolved issue in research on rice paddies. This minireview is an opinion paper for highlighting the mechanisms underlying the interactions between biogeochemical processes and plant-associated microbes based on recent metagenomic, metaproteomic, and isotope analyses. A rice symbiotic gene, relevant to rhizobial nodulation and mycorrhization in plants, likely accommodates diazotrophic methanotrophs or the associated bacterial community in root tissues under low-N fertilizer management, which may permit rice plants to acquire N via N2 fixation. The amount of N fixed in rice roots was previously estimated to be approximately 12% of plant N based on measurements of 15N natural abundance in a paddy field experiment. Community analyses alsoindicate that methanotroph populations in rice roots are susceptible to environmental conditions such as the microclimate of rice paddies. Therefore, CH4 oxidation by methanotrophs is a driving force in shaping bacterial communities in rice roots grown in CH4-rich environments. Based on these findings, we propose a hypothesis with unanswered questions to describe the interplay between rice plants, root microbiomes, and their biogeochemical functions (CH4 oxidation and N2 fixation).

Original languageEnglish
Pages (from-to)4-10
Number of pages7
JournalMicrobes and Environments
Issue number1
Publication statusPublished - 2016 Mar 26


  • Methane oxidation
  • Nitrogen fertilizer
  • Nitrogen fixation
  • Paddy rice
  • Symbiosis


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