Microbes and Environments
Online ISSN : 1347-4405
Print ISSN : 1342-6311
ISSN-L : 1342-6311
Regular Papers
Complete Genome Sequence of Bradyrhizobium sp. S23321: Insights into Symbiosis Evolution in Soil Oligotrophs
Takashi OkuboTakahiro TsukuiHiroko MaitaShinobu OkamotoKenshiro OshimaTakatomo FujisawaAkihiro SaitoHiroyuki FutamataReiko HattoriYumi ShimomuraShin HarutaSho MorimotoYong WangYoriko SakaiMasahira HattoriShin-ichi AizawaKenji V. P. NagashimaSachiko MasudaTsutomu HattoriAkifumi YamashitaZhihua BaoMasahito HayatsuHiromi Kajiya-KanegaeIkuo YoshinagaKazunori SakamotoKoki ToyotaMitsuteru NakaoMitsuyo KoharaMizue AndaRieko NiwaPark Jung-HwanReiko Sameshima-SaitoShin-ichi TokudaSumiko YamamotoSyuji YamamotoTadashi YokoyamaTomoko AkutsuYasukazu NakamuraYuka Nakahira-YanakaYuko Takada HoshinoHideki HirakawaHisayuki MitsuiKimihiro TerasawaManabu ItakuraShusei SatoWakako Ikeda-OhtsuboNatsuko SakakuraEli KaminumaKiwamu Minamisawa
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2012 Volume 27 Issue 3 Pages 306-315

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Abstract

Bradyrhizobium sp. S23321 is an oligotrophic bacterium isolated from paddy field soil. Although S23321 is phylogenetically close to Bradyrhizobium japonicum USDA110, a legume symbiont, it is unable to induce root nodules in siratro, a legume often used for testing Nod factor-dependent nodulation. The genome of S23321 is a single circular chromosome, 7,231,841 bp in length, with an average GC content of 64.3%. The genome contains 6,898 potential protein-encoding genes, one set of rRNA genes, and 45 tRNA genes. Comparison of the genome structure between S23321 and USDA110 showed strong colinearity; however, the symbiosis islands present in USDA110 were absent in S23321, whose genome lacked a chaperonin gene cluster (groELS3) for symbiosis regulation found in USDA110. A comparison of sequences around the tRNA-Val gene strongly suggested that S23321 contains an ancestral-type genome that precedes the acquisition of a symbiosis island by horizontal gene transfer. Although S23321 contains a nif (nitrogen fixation) gene cluster, the organization, homology, and phylogeny of the genes in this cluster were more similar to those of photosynthetic bradyrhizobia ORS278 and BTAi1 than to those on the symbiosis island of USDA110. In addition, we found genes encoding a complete photosynthetic system, many ABC transporters for amino acids and oligopeptides, two types (polar and lateral) of flagella, multiple respiratory chains, and a system for lignin monomer catabolism in the S23321 genome. These features suggest that S23321 is able to adapt to a wide range of environments, probably including low-nutrient conditions, with multiple survival strategies in soil and rhizosphere.

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© 2012 Japanese Society of Microbial Ecology / Japanese Society of Soil Microbiology / Taiwan Society of Microbial Ecology
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