与田间种植的水稻嫩枝相关的细菌群落的系统发育和功能
Phylogeny and functions of bacterial communities associated with field-grown rice shoots.
作者信息
Okubo Takashi, Ikeda Seishi, Sasaki Kazuhiro, Ohshima Kenshiro, Hattori Masahira, Sato Tadashi, Minamisawa Kiwamu
机构信息
Graduate School of Life Sciences, Tohoku University.
出版信息
Microbes Environ. 2014 Sep 17;29(3):329-32. doi: 10.1264/jsme2.me14077. Epub 2014 Aug 12.
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.
摘要
宏基因组分析应用于两个田间种植水稻品种日本晴和卡萨拉斯的地上部相关细菌群落。在这两个品种中，地上部微生物群落主要由α-变形菌纲（51 - 52%）、放线菌门（11 - 15%）、γ-变形菌纲（9 - 10%）和β-变形菌纲（4 - 10%）组成。与公共数据库中的其他水稻微生物群落（根、根际和叶际）相比，地上部微生物群落含有丰富的C1化合物代谢和1-氨基环丙烷-1-羧酸分解代谢基因，但吲哚-3-乙酸产生和固氮基因较少。除根际外，在所有微生物群落中均检测到水杨酸羟化酶。这些基因组特征有助于理解水稻地上部的植物-微生物相互作用和生物地球化学代谢。
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2
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6
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7
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8
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9
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10
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