Low Nitrogen Fertilization Adapts Rice Root Microbiome to Low Nutrient Environment by Changing Biogeochemical Functions

  • Ikeda Seishi
    Graduate School of Life Sciences, Tohoku University Memuro Research Station, National Agricultural Research Center for Hokkaido Region
  • Sasaki Kazuhiro
    Graduate School of Life Sciences, Tohoku University
  • Okubo Takashi
    Graduate School of Life Sciences, Tohoku University
  • Yamashita Akifumu
    Graduate School of Life Sciences, Tohoku University
  • Terasawa Kimihiro
    Graduate School of Life Sciences, Tohoku University
  • Bao Zhihua
    Graduate School of Life Sciences, Tohoku University
  • Liu Dongyan
    Soil Biology and Chemistry, Graduate School of Bioagricultural Sciences, Nagoya University
  • Watanabe Takeshi
    Soil Biology and Chemistry, Graduate School of Bioagricultural Sciences, Nagoya University
  • Murase Jun
    Soil Biology and Chemistry, Graduate School of Bioagricultural Sciences, Nagoya University
  • Asakawa Susumu
    Soil Biology and Chemistry, Graduate School of Bioagricultural Sciences, Nagoya University
  • Eda Shima
    Graduate School of Life Sciences, Tohoku University
  • Mitsui Hisayuki
    Graduate School of Life Sciences, Tohoku University
  • Sato Tadashi
    Graduate School of Life Sciences, Tohoku University
  • Minamisawa Kiwamu
    Graduate School of Life Sciences, Tohoku University

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Reduced fertilizer usage is one of the objectives of field management in the pursuit of sustainable agriculture. Here, we report on shifts of bacterial communities in paddy rice ecosystems with low (LN), standard (SN), and high (HN) levels of N fertilizer application (0, 30, and 300 kg N ha−1, respectively). The LN field had received no N fertilizer for 5 years prior to the experiment. The LN and HN plants showed a 50% decrease and a 60% increase in biomass compared with the SN plant biomass, respectively. Analyses of 16S rRNA genes suggested shifts of bacterial communities between the LN and SN root microbiomes, which were statistically confirmed by metagenome analyses. The relative abundances of Burkholderia, Bradyrhizobium and Methylosinus were significantly increased in root microbiome of the LN field relative to the SN field. Conversely, the abundance of methanogenic archaea was reduced in the LN field relative to the SN field. The functional genes for methane oxidation (pmo and mmo) and plant association (acdS and iaaMH) were significantly abundant in the LN root microbiome. Quantitative PCR of pmoA/mcrA genes and a 13C methane experiment provided evidence of more active methane oxidation in the rice roots of the LN field. In addition, functional genes for the metabolism of N, S, Fe, and aromatic compounds were more abundant in the LN root microbiome. These results suggest that low-N-fertilizer management is an important factor in shaping the microbial community structure containing key microbes for plant associations and biogeochemical processes in paddy rice ecosystems.

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