Comparative Genome Analysis of Bacillus amyloliquefaciens Focusing on Phylogenomics, Functional Traits, and Prevalence of Antimicrobial and Virulence Genes

Hualin Liu; Vimalkumar Prajapati; Shobha Prajapati; Harsh Bais; Jianguo Lu

doi:10.3389/fgene.2021.724217

Comparative Genome Analysis of Bacillus amyloliquefaciens Focusing on Phylogenomics, Functional Traits, and Prevalence of Antimicrobial and Virulence Genes

Front Genet. 2021 Sep 30:12:724217. doi: 10.3389/fgene.2021.724217. eCollection 2021.

Authors

Hualin Liu¹, Vimalkumar Prajapati², Shobha Prajapati³, Harsh Bais⁴, Jianguo Lu^{1

5}

Affiliations

¹ School of Marine Sciences, Sun Yat-sen University, Zhuhai, China.
² Division of Microbiology and Environmental, Biotechnology, Aspee Shakilam Biotechnology Institute, Navsari Agricultural University, Surat, India.
³ SVP-A School of Sardar Vallabhbhai National Institute of Technology, Surat, India.
⁴ Delaware Biotechnology Institute, University of Delaware, Newark, DE, United States.
⁵ Southern Marine Science and Engineering Guangdong Laboratory, Zhuhai, China.

Abstract

Bacillus amyloliquefaciens is a gram-positive, nonpathogenic, endospore-forming, member of a group of free-living soil bacteria with a variety of traits including plant growth promotion, production of antifungal and antibacterial metabolites, and production of industrially important enzymes. We have attempted to reconstruct the biogeographical structure according to functional traits and the evolutionary lineage of B. amyloliquefaciens using comparative genomics analysis. All the available 96 genomes of B. amyloliquefaciens strains were curated from the NCBI genome database, having a variety of important functionalities in all sectors keeping a high focus on agricultural aspects. In-depth analysis was carried out to deduce the orthologous gene groups and whole-genome similarity. Pan genome analysis revealed that shell genes, soft core genes, core genes, and cloud genes comprise 17.09, 5.48, 8.96, and 68.47%, respectively, which demonstrates that genomes are very different in the gene content. It also indicates that the strains may have flexible environmental adaptability or versatile functions. Phylogenetic analysis showed that B. amyloliquefaciens is divided into two clades, and clade 2 is further dived into two different clusters. This reflects the difference in the sequence similarity and diversification that happened in the B. amyloliquefaciens genome. The majority of plant-associated strains of B. amyloliquefaciens were grouped in clade 2 (73 strains), while food-associated strains were in clade 1 (23 strains). Genome mining has been adopted to deduce antimicrobial resistance and virulence genes and their prevalence among all strains. The genes tmrB and yuaB codes for tunicamycin resistance protein and hydrophobic coat forming protein only exist in clade 2, while clpP, which codes for serine proteases, is only in clade 1. Genome plasticity of all strains of B. amyloliquefaciens reflects their adaption to different niches.

Keywords: B. amyloliquefaciens; antimicrobial resistance and virulence genes; comparative genomics; functional traits; genome evaluation; phylogenomics.