Genome Analysis Suggests that the Soil Oligotrophic Bacterium Agromonas oligotrophica (Bradyrhizobium oligotrophicum) Is a Nitrogen-Fixing Symbiont of Aeschynomene indica
Genome Analysis Suggests that the Soil Oligotrophic Bacterium Agromonas oligotrophica (Bradyrhizobium oligotrophicum) Is a Nitrogen-Fixing Symbiont of Aeschynomene indica
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DOI：
10.1128/aem.00009-13
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发表时间：
2013-04-01
影响因子：
4.4
通讯作者：
Minamisawa, Kiwamu
中科院分区：
文献类型：
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作者：
Okubo, Takashi;Fukushima, Shohei;Minamisawa, Kiwamu
寡养农单胞菌S58（T）是从稻田土壤中分离到的一株能在极低营养环境中生长的固氮寡养细菌。在此，确定了S58的全基因组序列。结果表明，S58基因组由一条长8, 264, 165 bp的环状染色体组成，GC含量平均为65.1%，缺少一个完整的ABC基因，具有典型的共生岛结构。该基因组与Bradyrhizobium sp. ORS 278和Bradyrhizobium sp. BTAi 1的基因组具有很高的相似性，包括固氮和光合作用基因簇，这些基因簇以不依赖Nod因子的方式将水生豆科植物Aeschynomene indica同化。虽然非共生根瘤菌是土壤根瘤菌的重要组成部分，但我们发现，大多数与根瘤发育（ndv）和共生固氮（nif和fix）有关的基因与A. indica在ORS 278和S58基因组之间具有很好的保守性。因此，我们用5个A.寡营养型菌株（S58、S42、S55、S72和S80）。令人惊讶的是，所有五种A.寡养型根瘤菌在苜蓿根和/或茎上形成有效的固氮根瘤。indica，具有分化的拟杆菌。非共生（布雷迪）根瘤菌是土壤中不存在共生岛或共生质粒的根瘤菌种群的重要组成部分，但目前的研究结果表明，土壤中的A.寡养型通常具有与A.印度系统发育分析表明，Nod因子独立的共生与A。indica是光合慢生根瘤菌分支成员中缺乏共生ABC和共生岛的菌株的共同性状，包括A.寡营养的
Agromonas oligotrophica (Bradyrhizobium oligotrophicum) S58(T) is a nitrogen-fixing oligotrophic bacterium isolated from paddy field soil that is able to grow in extra-low-nutrient environments. Here, the complete genome sequence of S58 was determined. The S58 genome was found to comprise a circular chromosome of 8,264,165 bp with an average GC content of 65.1% lacking nodABC genes and the typical symbiosis island. The genome showed a high level of similarity to the genomes of Bradyrhizobium sp. ORS278 and Bradyrhizobium sp. BTAi1, including nitrogen fixation and photosynthesis gene clusters, which nodulate an aquatic legume plant, Aeschynomene indica, in a Nod factor-independent manner. Although nonsymbiotic (brady) rhizobia are significant components of rhizobial populations in soil, we found that most genes important for nodule development (ndv) and symbiotic nitrogen fixation (nif and fix) with A. indica were well conserved between the ORS278 and S58 genomes. Therefore, we performed inoculation experiments with five A. oligotrophica strains (S58, S42, S55, S72, and S80). Surprisingly, all five strains of A. oligotrophica formed effective nitrogen-fixing nodules on the roots and/or stems of A. indica, with differentiated bacteroids. Nonsymbiotic (brady) rhizobia are known to be significant components of rhizobial populations without a symbiosis island or symbiotic plasmids in soil, but the present results indicate that soil-dwelling A. oligotrophica generally possesses the ability to establish symbiosis with A. indica. Phylogenetic analyses suggest that Nod factor-independent symbiosis with A. indica is a common trait of nodABC- and symbiosis island-lacking strains within the members of the photosynthetic Bradyrhizobium clade, including A. oligotrophica.