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

ABSTRACT: 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.

SUBMITTER: Zhang N

PROVIDER: S-EPMC5169363 | biostudies-literature | 2016

REPOSITORIES: biostudies-literature

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

Zhang Nan N Yang Dongqing D Kendall Joshua R A JR Borriss Rainer R Druzhinina Irina S IS Kubicek Christian P CP Shen Qirong Q Zhang Ruifu R

Frontiers in microbiology 20161220

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 seq ...[more]

PMID: 28066362

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Project description:Bacillus subtilis produces a wide range of secondary metabolites providing diverse plant growth-promoting and biocontrol abilities. These secondary metabolites include nonribosomal peptides with strong antimicrobial properties, causing either cell lysis, pore formation in fungal membranes, inhibition of certain enzymes, or bacterial protein synthesis. However, the natural products of B. subtilis are mostly studied either in laboratory strains or in individual isolates, and therefore, a comparative overview of secondary metabolites from various environmental B. subtilis strains is missing. In this study, we isolated 23 B. subtilis strains from 11 sampling sites, compared the fungal inhibition profiles of wild types and their nonribosomal peptide mutants, followed the production of targeted lipopeptides, and determined the complete genomes of 13 soil isolates. We discovered that nonribosomal peptide production varied among B. subtilis strains coisolated from the same soil samples. In vitro antagonism assays revealed that biocontrol properties depend on the targeted plant pathogenic fungus and the tested B. subtilis isolate. While plipastatin alone is sufficient to inhibit Fusarium spp., a combination of plipastatin and surfactin is required to hinder growth of Botrytis cinerea Detailed genomic analysis revealed that altered nonribosomal peptide production profiles in specific isolates are due to missing core genes, nonsense mutation, or potentially altered gene regulation. Our study combines microbiological antagonism assays with chemical nonribosomal peptide detection and biosynthetic gene cluster predictions in diverse B. subtilis soil isolates to provide a broader overview of the secondary metabolite chemodiversity of B. subtilisIMPORTANCE Secondary or specialized metabolites with antimicrobial activities define the biocontrol properties of microorganisms. Members of the Bacillus genus produce a plethora of secondary metabolites, of which nonribosomally produced lipopeptides in particular display strong antifungal activity. To facilitate the prediction of the biocontrol potential of new Bacillus subtilis isolates, we have explored the in vitro antifungal inhibitory profiles of recent B. subtilis isolates, combined with analytical natural product chemistry, mutational analysis, and detailed genome analysis of biosynthetic gene clusters. Such a comparative analysis helped to explain why selected B. subtilis isolates lack the production of certain secondary metabolites.

Dataset Information

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

Publications

Comparative Genomic Analysis of <i>Bacillus amyloliquefaciens</i> and <i>Bacillus subtilis</i> Reveals Evolutional Traits for Adaptation to Plant-Associated Habitats.

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