title: Metagenomic Analysis Revealed Methylamine and Ureide Utilization of Soybean-Associated Methylobacterium.
abstract: Methylobacterium inhabits the phyllosphere of a large number of plants. We herein report the results of comparative metagenome analyses on methylobacterial communities of soybean plants grown in an experimental field in Tohoku University (Kashimadai, Miyagi, Japan). Methylobacterium was identified as the most dominant genus (33%) among bacteria inhabiting soybean stems. We classified plant-derived Methylobacterium species into Groups I, II, and III based on 16S rRNA gene sequences, and found that Group I members (phylogenetically close to M. extorquens) were dominant in soybean-associated Methylobacterium. By comparing 29 genomes, we found that all Group I members possessed a complete set of genes for the N-methylglutamate pathway for methylamine utilization, and genes for urea degradation (urea carboxylase, urea amidolyase, and conventional urease). Only Group I members and soybean methylobacterial isolates grew in a culture supplemented with methylamine as the sole carbon source. They utilized urea or allantoin (a urea-related compound in legumes) as the sole nitrogen source; however, group III also utilized these compounds. The utilization of allantoin may be crucial in soybean-bacterial interactions because allantoin is a transported form of fixed nitrogen in legume plants. Soybean-derived Group I strain AMS5 colonized the model legume Lotus japonicus well. A comparison among the 29 genomes of plant-derived and other strains suggested that several candidate genes are involved in plant colonization such as csgG (curli fimbriae). Genes for the N-methylglutamate pathway and curli fimbriae were more abundant in soybean microbiomes than in rice microbiomes in the field. Based on these results, we discuss the lifestyle of Methylobacterium in the legume phyllosphere.
authors.affiliation: Graduate School of Life Sciences, Tohoku University.
authors.forename: Tomoyuki
authors.initials: T
authors.lastname: Minami
authors.forename: Misue
authors.initials: M
authors.lastname: Anda
authors.forename: Hisayuki
authors.initials: H
authors.lastname: Mitsui
authors.forename: Masayuki
authors.initials: M
authors.lastname: Sugawara
authors.forename: Takakazu
authors.initials: T
authors.lastname: Kaneko
authors.forename: Shusei
authors.initials: S
authors.lastname: Sato
authors.forename: Seishi
authors.initials: S
authors.lastname: Ikeda
authors.forename: Takashi
authors.initials: T
authors.lastname: Okubo
authors.forename: Hirohito
authors.initials: H
authors.lastname: Tsurumaru
authors.forename: Kiwamu
authors.initials: K
authors.lastname: Minamisawa
mesh_terms: D000481:Allantoin / Q000378:metabolism; D016000:Cluster Analysis; D004269:DNA, Bacterial / Q000737:chemistry / Q000235:genetics; D004275:DNA, Ribosomal / Q000737:chemistry / Q000235:genetics; D005838:Genotype; D007564:Japan; D054892:Metagenome; D056186:Metagenomics; D008744:Methylamines / Q000378:metabolism*; D020580:Methylobacterium / Q000145:classification / Q000235:genetics* / Q000378:metabolism*; D010802:Phylogeny; D018547:Plant Stems / Q000382:microbiology; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D017422:Sequence Analysis, DNA; D013025:Glycine max / Q000382:microbiology*; D014508:Urea / Q000378:metabolism*
chemical_list: D004269:DNA, Bacterial; D004275:DNA, Ribosomal; D008744:Methylamines; D012336:RNA, Ribosomal, 16S; D000481:Allantoin; D014508:Urea; C027451:methylamine