Comparative Genomic Analysis of Bacillus amyloliquefaciens and Bacillus subtilis Reveals Evolutional Traits for Adaptation to Plant-Associated Habitats.
Comparative Genomic Analysis of Bacillus amyloliquefaciens and Bacillus subtilis Reveals Evolutional Traits for Adaptation to Plant-Associated Habitats.
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解淀粉芽孢杆菌和枯草芽孢杆菌的比较基因组分析揭示了适应植物相关生境的进化特征
DOI：
10.3389/fmicb.2016.02039
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发表时间：
2016
影响因子：
5.2
通讯作者：
Zhang R
中科院分区：
文献类型：
--
作者：
Zhang N;Yang D;Kendall JR;Borriss R;Druzhinina IS;Kubicek CP;Shen Q;Zhang R
枯草芽孢杆菌及其姊妹种B.amyloliquefaciens组成了一个进化紧凑但具有生理功能的细菌群，其中包括从不同栖息地分离的菌株。其中许多菌株被用作农业上的植物生长促进根际细菌(PGPR)和淀粉液化B.amyloliquefaciens-B.amyloliquefaciens亚种的植物专用亚种。Plantarum，最近被发现，在这里我们使用了31个全基因组[包括两个新测序的PGPR菌株：B.amyloliquefaciens NJN-6从Musa sp.(香蕉)和枯草芽孢杆菌HJ5。(棉花)]进行比较分析，并研究这两个物种在不同生态位中的基因组特征和进化特征。系统发生学分析表明，从植物相关(PA)生境分离的菌株与来自两个物种的非植物相关(NPA)生态位的菌株可以区分开来。与NPA菌株相比，PA菌株的核心基因组中与中间代谢和次生代谢物生物合成相关的基因更为丰富，并且还具有参与植物来源底物利用和抗生素合成的额外的特异性基因。进一步的基因得失分析表明，PA菌株在最初的分化事件中只获得了少数特异基因(解淀粉芽孢杆菌18/192，枯草杆菌53/688)，但大多数是在进化过程中由PA菌株的不同亚群相继获得的。本研究揭示了来自不同生态位的PA、NPA、B.amyloliquefaciens和B.subtilis的基因组差异及其所涉及的进化特性，对农业生产中PGPR菌株的筛选具有一定的指导意义。
Bacillus subtilis and its sister species B. amyloliquefaciens comprise an evolutionary compact but physiologically versatile group of bacteria that includes strains isolated from diverse habitats. Many of these strains are used as plant growth-promoting rhizobacteria (PGPR) in agriculture and a plant-specialized subspecies of B. amyloliquefaciens—B. amyloliquefaciens subsp. plantarum, has recently been recognized, here we used 31 whole genomes [including two newly sequenced PGPR strains: B. amyloliquefaciens NJN-6 isolated from Musa sp. (banana) and B. subtilis HJ5 from Gossypium sp. (cotton)] to perform comparative analysis and investigate the genomic characteristics and evolution traits of both species in different niches. Phylogenomic analysis indicated that strains isolated from plant-associated (PA) habitats could be distinguished from those from non-plant-associated (nPA) niches in both species. The core genomes of PA strains are more abundant in genes relevant to intermediary metabolism and secondary metabolites biosynthesis as compared with those of nPA strains, and they also possess additional specific genes involved in utilization of plant-derived substrates and synthesis of antibiotics. A further gene gain/loss analysis indicated that only a few of these specific genes (18/192 for B. amyloliquefaciens and 53/688 for B. subtilis) were acquired by PA strains at the initial divergence event, but most were obtained successively by different subgroups of PA stains during the evolutional process. This study demonstrated the genomic differences between PA and nPA B. amyloliquefaciens and B. subtilis from different niches and the involved evolutional traits, and has implications for screening of PGPR strains in agricultural production.