Metagenomic analysis of the bacterial community associated with the taproot of sugar beet

Hirohito Tsurumaru, Takashi Okubo, Kazuyuki Okazaki, Megumi Hashimoto, Kaori Kakizaki, Eiko Hanzawa, Hiroyuki Takahashi, Noriyuki Asanome, Fukuyo Tanaka, Yasuyo Sekiyama, Seishi Ikeda, Kiwamu Minamisawa

    Research output: Contribution to journalArticlepeer-review

    29 Citations (Scopus)

    Abstract

    We analyzed a metagenome of the bacterial community associated with the taproot of sugar beet (Beta vulgaris L.) in order to investigate the genes involved in plant growth-promoting traits (PGPTs), namely 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase, indole acetic acid (IAA), N2 fixation, phosphate solubilization, pyrroloquinoline quinone, siderophores, and plant disease suppression as well as methanol, sucrose, and betaine utilization. The most frequently detected gene among the PGPT categories encoded β-1,3-glucanase (18 per 105 reads), which plays a role in the suppression of plant diseases. Genes involved in phosphate solubilization (e.g., for quinoprotein glucose dehydrogenase), methanol utilization (e.g., for methanol dehydrogenase), siderophore production (e.g. isochorismate pyruvate lyase), and ACC deaminase were also abundant. These results suggested that such PGPTs are crucially involved in supporting the growth of sugar beet. In contrast, genes for IAA production (iaaM and ipdC) were less abundant (~1 per 105 reads). N 2 fixation genes (nifHDK) were not detected; bacterial N2-fixing activity was not observed in the 15N2-feeding experiment. An analysis of nitrogen metabolism suggested that the sugar beet microbiome mainly utilized ammonium and nitroalkane as nitrogen sources. Thus, N 2 fixation and IAA production did not appear to contribute to sugar beet growth. Taxonomic assignment of this metagenome revealed the high abundance of Mesorhizobium, Bradyrhizobium, and Streptomyces, suggesting that these genera have ecologically important roles in the taproot of sugar beet. Bradyrhizobium-assigned reads in particular were found in almost all categories of dominant PGPTs with high abundance. The present study revealed the characteristic functional genes in the taproot-associated microbiome of sugar beet, and suggest the opportunity to select sugar beet growth-promoting bacteria.

    Original languageEnglish
    Pages (from-to)63-69
    Number of pages7
    JournalMicrobes and environments
    Volume30
    Issue number1
    DOIs
    Publication statusPublished - 2015

    Keywords

    • Key words: bradyrhizobium
    • Metagenome
    • Plant growth-promoting bacteria
    • Quinoprotein glucose dehydrogenase
    • Sugar beet

    ASJC Scopus subject areas

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

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