Xie Jianbo, Shi Haowen, Du Zhenglin, Wang Tianshu, Liu Xiaomeng, Chen Sanfeng
Key Laboratory for Agrobiotechnology, China Agricultural University, Beijing 100193, P. R. China.
Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, P. R. China.
Sci Rep. 2016 Feb 9;6:21329. doi: 10.1038/srep21329.
Paenibacillus polymyxa has widely been studied as a model of plant-growth promoting rhizobacteria (PGPR). Here, the genome sequences of 9 P. polymyxa strains, together with 26 other sequenced Paenibacillus spp., were comparatively studied. Phylogenetic analysis of the concatenated 244 single-copy core genes suggests that the 9 P. polymyxa strains and 5 other Paenibacillus spp., isolated from diverse geographic regions and ecological niches, formed a closely related clade (here it is called Poly-clade). Analysis of single nucleotide polymorphisms (SNPs) reveals local diversification of the 14 Poly-clade genomes. SNPs were not evenly distributed throughout the 14 genomes and the regions with high SNP density contain the genes related to secondary metabolism, including genes coding for polyketide. Recombination played an important role in the genetic diversity of this clade, although the rate of recombination was clearly lower than mutation. Some genes relevant to plant-growth promoting traits, i.e. phosphate solubilization and IAA production, are well conserved, while some genes relevant to nitrogen fixation and antibiotics synthesis are evolved with diversity in this Poly-clade. This study reveals that both P. polymyxa and its closely related species have plant growth promoting traits and they have great potential uses in agriculture and horticulture as PGPR.
多粘芽孢杆菌作为植物促生根际细菌（PGPR）的模型已得到广泛研究。在此，对9株多粘芽孢杆菌菌株的基因组序列以及另外26株已测序的芽孢杆菌属物种进行了比较研究。对串联的244个单拷贝核心基因的系统发育分析表明，从不同地理区域和生态位分离出的9株多粘芽孢杆菌菌株和另外5株芽孢杆菌属物种形成了一个密切相关的进化枝（在此称为多进化枝）。单核苷酸多态性（SNP）分析揭示了14个多进化枝基因组的局部多样化。SNP在14个基因组中分布不均，SNP密度高的区域包含与次级代谢相关的基因，包括编码聚酮化合物的基因。重组在该进化枝的遗传多样性中发挥了重要作用，尽管重组率明显低于突变率。一些与促进植物生长特性相关的基因，即磷溶解和吲哚乙酸产生相关基因，高度保守，而一些与固氮和抗生素合成相关的基因在这个多进化枝中呈现出多样性进化。这项研究表明，多粘芽孢杆菌及其近缘物种都具有促进植物生长的特性，它们作为PGPR在农业和园艺领域具有巨大的潜在应用价值。
