Low nitrogen fertilization adapts rice root Microbiome to low nutrient environment by changing biogeochemical functions

Seishi Ikeda, Kazuhiro Sasaki, Takashi Okubo, Akifumu Yamashita, Kimihiro Terasawa, Zhihua Bao, Dongyan Liu, Takeshi Watanabe, Jun Murase, Susumu Asakawa, Shima Eda, Hisayuki Mitsui, Tadashi Sato, Kiwamu Minamisawa

    Research output: Contribution to journalArticlepeer-review

    46 Citations (Scopus)

    Abstract

    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 confrmed by metagenome analyses. The relative abundances of Burkholderia, Bradyrhizobium and Methylosinus were signifcantly 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 signifcantly 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.

    Original languageEnglish
    Pages (from-to)50-59
    Number of pages10
    JournalMicrobes and environments
    Volume29
    Issue number1
    DOIs
    Publication statusPublished - 2014

    Keywords

    • Metagenome analysis
    • Methane cycle
    • Nitrogen fertilizer
    • Rice paddy field
    • Root microbiome

    ASJC Scopus subject areas

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

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