Are Symbiotic Methanotrophs Key Microbes for N Acquisition in Paddy Rice Root?

  • Minamisawa Kiwamu
    Graduate School of Life Sciences, Tohoku University
  • Imaizumi-Anraku Haruko
    Department of Plant Sciences, National Institute of Agrobiological Sciences
  • Bao Zhihua
    Graduate School of Life Sciences, Tohoku University College of Environmental and Resource Science, Inner Mongolia University
  • Shinoda Ryo
    Graduate School of Life Sciences, Tohoku University
  • Okubo Takashi
    Graduate School of Life Sciences, Tohoku University
  • Ikeda Seishi
    Memuro Research Station, National Agricultural Research Center for Hokkaido Region

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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 also indicate 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).

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