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

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.

Identification of Conserved Pathways in Bacillus Strains Known for Plant Growth-Promoting Behavior Using a Multifaceted Computational Approach

“…Other studies, such as Liu H et al [58], carried out comparative genomic analysis of 96 strains of Bacillus amyloliquefaciens to shed light and provide valuable insights into the phylogenetic relationship, ecological niches, and functional differences of B. amyloliquefaciens strains. Zhang N. et al [59] also performed a comparative genomic analysis of Bacillus amyloliquefaciens (BA) and Bacillus subtilis (BS) strains.…”

High pathogenicity island,aerandsitoperons: a “ménage à trois” inEscherichia coliextra-intestinal virulence

“…The arrival of rapid and inexpensive genome sequencing has shaken up these classical approaches by enabling largescale epidemiologic studies on bacterial virulence phenotypes 32 . These studies infer evolutionary scenarios leading to functional consequences, such as emergence of virulence, based solely on comparative phylogenomic data 18,[33][34][35][36][37] . Such sequence data can also be used in GWAS if they are linked to virulence phenotypes 15,38 .…”

Perspective on utilization of <i>Bacillus</i> species as plant probiotics for different crops in adverse conditions

“…Another growth-promoting effect is the biosynthesis of antimicrobial compounds by the biofilms that protect plants against infection by fungal, bacterial, and viral pathogens. Beyond direct nutrient contributions and pathogen defense, B. subtilis and B. amyloliquefaciens biofilms also induce systemic resistance in plants, priming their innate immunity to fight off diseases more effectively [13] , [14] . Therefore, Bacillus -based biofertilizers can be directly applied to the surface of the soil for the enhancement of the control of microbial growth of disease-causing pathogens.…”