AUTHOR=Zhang Nan , Yang Dongqing , Kendall Joshua R. A. , Borriss Rainer , Druzhinina Irina S. , Kubicek Christian P. , Shen Qirong , Zhang Ruifu 

TITLE=Comparative Genomic Analysis of Bacillus amyloliquefaciens and Bacillus subtilis Reveals Evolutional Traits for Adaptation to Plant-Associated Habitats

JOURNAL=Frontiers in Microbiology

VOLUME=7

YEAR=2016

URL=https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2016.02039

DOI=10.3389/fmicb.2016.02039

ISSN=1664-302X

ABSTRACT=<p><italic>Bacillus subtilis</italic> and its sister species <italic>B. amyloliquefaciens</italic> 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 <italic>B. amyloliquefaciens—B. amyloliquefaciens</italic> subsp. <italic>plantarum</italic>, has recently been recognized, here we used 31 whole genomes [including two newly sequenced PGPR strains: <italic>B. amyloliquefaciens</italic> NJN-6 isolated from <italic>Musa</italic> sp. (banana) and <italic>B. subtilis</italic> HJ5 from <italic>Gossypium</italic> 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 <italic>B. amyloliquefaciens</italic> and 53/688 for <italic>B. subtilis</italic>) 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 <italic>B. amyloliquefaciens</italic> and <italic>B. subtilis</italic> from different niches and the involved evolutional traits, and has implications for screening of PGPR strains in agricultural production.</p>