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.
Highlights
Pathogenic microorganisms are a major and chronic threat to food production and ecosystem stability all over the world by infecting plant tissue and affecting plant health (Compant et al, 2005)
The numbers of genes representing the core genome of strains HAB-2, FZB42, DSM7 and 168 were 3820, 3855, 4102, and 4536, respectively (Table 1)
We compared genome sequences of reference strains B. velezensis FZB42, B. amyloliquefaciens DSM7, and B. subtilis 168, and conducted phylogenomic analysis; the result showed that HAB-2 was B. velezensis, which was previously classified as B. amyloliquefaciens
Summary
Pathogenic microorganisms are a major and chronic threat to food production and ecosystem stability all over the world by infecting plant tissue and affecting plant health (Compant et al, 2005). As the human population has increased and agricultural production has intensified over the past few decades, producers have been increasingly dependent on agrochemicals to control plant diseases (Schäfer and Adams, 2015). Researchers and producers realize the need for alternatives to chemical pesticides to avoid damaging the environment. Use of beneficial bacteria as alternatives to chemical pesticides in plant protection is steadily increasing and is beginning to replace some chemical pesticides (Qiao et al, 2014). There were 434 actual microbial pesticides, and registered biological pesticides only accounted for 2.9% of the total pesticide products. Prevention and control of plant diseases are still dominated by chemical pesticides in China, and the road to replace them with biological pesticides is long, but the development potential is huge. Researchers are focusing on the antibacterial mechanisms of biocontrol bacteria
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