title: Phylogeny and functions of bacterial communities associated with field-grown rice shoots.
abstract: Metagenomic analysis was applied to bacterial communities associated with the shoots of two field-grown rice cultivars, Nipponbare and Kasalath. In both cultivars, shoot microbiomes were dominated by Alphaproteobacteria (51-52%), Actinobacteria (11-15%), Gammaproteobacteria (9-10%), and Betaproteobacteria (4-10%). Compared with other rice microbiomes (root, rhizosphere, and phyllosphere) in public databases, the shoot microbiomes harbored abundant genes for C1 compound metabolism and 1-aminocyclopropane-1-carboxylate catabolism, but fewer genes for indole-3-acetic acid production and nitrogen fixation. Salicylate hydroxylase was detected in all microbiomes, except the rhizosphere. These genomic features facilitate understanding of plant-microbe interactions and biogeochemical metabolism in rice shoots.
authors.affiliation: Graduate School of Life Sciences, Tohoku University.
authors.forename: Takashi
authors.initials: T
authors.lastname: Okubo
authors.forename: Seishi
authors.initials: S
authors.lastname: Ikeda
authors.forename: Kazuhiro
authors.initials: K
authors.lastname: Sasaki
authors.forename: Kenshiro
authors.initials: K
authors.lastname: Ohshima
authors.forename: Masahira
authors.initials: M
authors.lastname: Hattori
authors.forename: Tadashi
authors.initials: T
authors.lastname: Sato
authors.forename: Kiwamu
authors.initials: K
authors.lastname: Minamisawa
mesh_terms: D001419:Bacteria / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification*; D001426:Bacterial Proteins / Q000235:genetics / Q000378:metabolism; D044822:Biodiversity; D008969:Molecular Sequence Data; D012275:Oryza / Q000145:classification / Q000254:growth & development / Q000382:microbiology*; D010802:Phylogeny; D018517:Plant Roots / Q000254:growth & development / Q000382:microbiology; D018520:Plant Shoots / Q000254:growth & development / Q000382:microbiology*; D058441:Rhizosphere; D012988:Soil Microbiology
chemical_list: D001426:Bacterial Proteins