title: Comparative Genomic Analysis ofBacillus amyloliquefaciensandBacillus subtilisReveals Evolutional Traits for Adaptation to Plant-Associated Habitats.
abstract: Bacillus subtilisand its sister speciesB. amyloliquefacienscomprise 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 ofB. amyloliquefaciens-B. amyloliquefacienssubsp.plantarum, has recently been recognized, here we used 31 whole genomes [including two newly sequenced PGPR strains:B. amyloliquefaciensNJN-6 isolated fromMusasp. (banana) andB. subtilisHJ5 fromGossypiumsp. (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 forB. amyloliquefaciensand 53/688 forB. 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 nPAB. amyloliquefaciensandB. subtilisfrom different niches and the involved evolutional traits, and has implications for screening of PGPR strains in agricultural production.
authors.affiliation: Jiangsu Key Lab and Engineering Center for Solid Organic Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University Nanjing, China.
authors.forename: Nan
authors.initials: N
authors.lastname: Zhang
authors.affiliation: Jiangsu Key Lab and Engineering Center for Solid Organic Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University Nanjing, China.
authors.forename: Dongqing
authors.initials: D
authors.lastname: Yang
authors.affiliation: Jiangsu Key Lab and Engineering Center for Solid Organic Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural UniversityNanjing, China; Department of Science and Technology, Evangel UniversitySpringfield, IL, USA.
authors.forename: Joshua R A
authors.initials: JR
authors.lastname: Kendall
authors.affiliation: Fachgebiet Phytomedizin, Institut für Agrar- und Gartenbauwissenschaften, Humboldt- Universität zu Berlin Germany.
authors.forename: Rainer
authors.initials: R
authors.lastname: Borriss
authors.affiliation: Research Area Biotechnology and Microbiology, Institute of Chemical Engineering, Vienna University of Technology Vienna, Austria.
authors.forename: Irina S
authors.initials: IS
authors.lastname: Druzhinina
authors.affiliation: Research Area Biotechnology and Microbiology, Institute of Chemical Engineering, Vienna University of Technology Vienna, Austria.
authors.forename: Christian P
authors.initials: CP
authors.lastname: Kubicek
authors.affiliation: Jiangsu Key Lab and Engineering Center for Solid Organic Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University Nanjing, China.
authors.forename: Qirong
authors.initials: Q
authors.lastname: Shen
authors.affiliation: Jiangsu Key Lab and Engineering Center for Solid Organic Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural UniversityNanjing, China; Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural SciencesBeijing, China.
authors.forename: Ruifu
authors.initials: R
authors.lastname: Zhang
keywords: Bacillus subtilis and Bacillus amyloliquefaciens; genome evolution; horizontal gene transfer; phylogenomics; plant-associated; rhizosphere adaptation