Comparative Genomics Analysis Provides New Strategies for Bacteriostatic Ability of Bacillus velezensis HAB-2

Abstract

Biocontrol formulations prepared from biocontrol bacteria are increasingly applied in sustainable agriculture. Notably, inoculants prepared from Bacillus strains have been proven efficient and environmentally friendly alternatives to chemical bactericides. The bacterium Bacillus velezensis HAB-2 (formerly classified as B. amyloliquefaciens HAB-2) is used as a biological control agent in agricultural fields. In this study, we reported a high-quality genome sequence of HAB-2 using third-generation sequencing technology (PacBio RS II). The 3.89 Mb genome encoded 3,820 predicted genes. Comparative analysis among the genome sequences of reference strains B. velezensis FZB42, B. amyloliquefaciens DSM7 and B. subtilis 168 with the HAB-2 genome revealed obvious differences in the variable part of the genomes, while the core genome shared by FZB42 and HAB-2 was similar (96.14%). However, there were differences in the prophage region among the four strains. The numbers of prophage regions and coding genes in HAB-2 and FZB42 were smaller than the other two strains. The HAB-2 genome showed superior ability to produce secondary metabolites and harbored 13 gene clusters involved in synthesis of antifungal and antibacterial acting secondary metabolites. Furthermore, there were two unique clusters: one cluster which encoded lanthipeptide was involved in mersacidin synthesis and another cluster which encoded ladderane was shown to direct an unknown compound. Multidomain enzymes, such as non-ribosomal peptide synthetase and polyketide synthase, control the biosynthesis of secondary metabolites and rely on 4′-phosphopantetheinyl transferases (PPTases). Key genes lpaH2 and a encoded PPTases in HAB-2 encoded 224 and 120 amino acids, respectively. The genomic features revealed that HAB-2 possesses immense potential to synthesize antimicrobial acting secondary metabolites by regulating and controlling gene clusters. The prophage regions and genes encoding PPTases may provide novel insight for the bacteriostatic mechanism of Bacillus in the biological control of plant diseases.

Genome mining reveals polysaccharide-degrading potential and new antimicrobial gene clusters of novel intestinal bacterium Paenibacillus jilinensis sp. nov.

“…Genomic screening for biosynthetic gene clusters (BGCs) of antibacterial substances has been increasingly utilized in natural product discovery due to the large amount of bacteria whole-genome sequencing data available [ 24 ]. The genome mining indicated the presence of BGCs coding for 6 antimicrobial substances in the genome of P. jilinensis YPG26 T : NRPS, PKS, lanthipeptide, proteusin, siderophore, and terpene (Fig.…”

Whole Genome Sequence of Bacillus velezensis Strain GUMT319: A Potential Biocontrol Agent Against Tobacco Black Shank Disease

“…B. velezensis strains have their own specific genomic characteristics, because these strains reside in different host plants and environments ( Wang et al, 2019 ). For instance, B. velezensis SQR9 isolated from the cucumber rhizosphere has been used as a BCA against fungal pathogens, mainly because of its ability to trigger ISR ( Borriss et al, 2018 ; Wu et al, 2018 ), while B. velezensis HAB-2 isolated from cotton has been used as a biological pesticide against bacterial pathogens ( Xu et al, 2020 ).…”

Antimicrobial Activity of Bacillus velezensis K-9 Against Potato Scab and Its Genome-wide Analysis

“…Six gene clusters were related to the antibacterial activity of Bacillus pumilus GLB197, and NRPS gene clusters were predicted to be used in the production of antibiotics. Xu et al 24 . sequenced the genome of Bacillus amylolitica HAB-2 and found that 13 gene clusters (NRPS and PKS, etc.)…”