Comparative Genomics of Bacillus amyloliquefaciens Strains Reveals a Core Genome with Traits for Habitat Adaptation and a Secondary Metabolites Rich Accessory Genome

Abstract

The Gram positive, non-pathogenic endospore-forming soil inhabiting prokaryote Bacillus amyloliquefaciens is a plant growth-promoting rhizobacterium. Bacillus amyloliquefaciens processes wide biocontrol abilities and numerous strains have been reported to suppress diverse bacterial, fungal and fungal-like pathogens. Knowledge about strain level biocontrol abilities is warranted to translate this knowledge into developing more efficient biocontrol agents and bio-fertilizers. Ever-expanding genome studies of B. amyloliquefaciens are showing tremendous increase in strain-specific new secondary metabolite clusters which play key roles in the suppression of pathogens and plant growth promotion. In this report, we have used genome mining of all sequenced B. amyloliquefaciens genomes to highlight species boundaries, the diverse strategies used by different strains to promote plant growth and the diversity of their secondary metabolites. Genome composition of the targeted strains suggest regions of genomic plasticity that shape the structure and function of these genomes and govern strain adaptation to different niches. Our results indicated that B. amyloliquefaciens: (i) suffer taxonomic imprecision that blurs the debate over inter-strain genome diversity and dynamics, (ii) have diverse strategies to promote plant growth and development, (iii) have an unlocked, yet to be delimited impressive arsenal of secondary metabolites and products, (iv) have large number of so-called orphan gene clusters, i.e., biosynthetic clusters for which the corresponding metabolites are yet unknown, and (v) have a dynamic pan genome with a secondary metabolite rich accessory genome.

Biocontrol Potential of a Novel Endophytic Bacterium From Mulberry (Morus) Tree

“…Strain ZJU1 is a cultured representative that was initially identified by 16S rRNA analysis as Bacillus amyloliquefaciens. It is well-established that the species B. amyloliquefaciens is associated with many plants (Belbahri et al, 2017), whereas to the best of our knowledge, this is the first report of the presence of B. amyloliquefaciens inside woody tree leaves. Phylogenetic reconstruction based on 16S rRNA sequences also showed that ZJU1 forms a phylogenetic lineage distinct from other B. amyloliquefaciens strains (Figure 2A).…”

Comparative genomic and secretomic characterisation of endophytic Bacillus velezensis LC1 producing bioethanol from bamboo lignocellulose

“…Mugsy was used to align the genomic data, and the bx-python tool kit (https://bitbucket.org/james_taylor/bx-python) was used to concatenate homologous blocks. RAxML version 7.2.8 (24) and FigTree version 1.3.1 (http://tree.bio.ed.ac.uk /software/fifigtree/) was used to construct and visualise phylogenetic trees from concatenated blocks using 1000 bootstrap replicates and the maximum-likelihood method. The CAZyome phylogenomic analysis was performed on homologous CAZy genes.…”

The “Three Cs” of Novel Antibiotic Discovery and Production through Synthetic Biology: Biosynthetic Gene Clusters, Heterologous Chassis, and Synthetic Microbial Consortia

“…Improving upon its previous iterations, BAGEL3 introduces the ability to input raw DNA sequences instead of annotated genomes, and broadens the detection of gene clusters to include RiPPs (examples described include cyanobactins, sactipeptides, and linaridins). A range of antimicrobial peptide‐encoding gene clusters has been identified using BAGEL3, from Staphylococcus capitis TE8, Bacillus pumilus , and Bacillus amyloliquefaciens . For example, while genome‐mining work of Belbahri et al on plant‐associated bacteria Bacillus amyloliquefaciens describes known BGCs for fengycin, bacilysin, and mersacidin (among others), it also discusses hundreds of unknown secondary metabolites of multiple subclasses (e.g., microcins, bacteriocins, and NRPSs) requiring further characterization from numerous genome‐sequenced B. amyloliquefaciens strains.…”

“…For example, while genome‐mining work of Belbahri et al on plant‐associated bacteria Bacillus amyloliquefaciens describes known BGCs for fengycin, bacilysin, and mersacidin (among others), it also discusses hundreds of unknown secondary metabolites of multiple subclasses (e.g., microcins, bacteriocins, and NRPSs) requiring further characterization from numerous genome‐sequenced B. amyloliquefaciens strains. This is a potential “gold‐mine” of peptide antibiotics . Another tool for the genome annotation of prokaryotes is PRISM3 (Prediction Informatics for Secondary Metabolomes: https://magarveylab.ca/prism/), which, alongside genome mining, focuses upon chemical structure prediction of nonribosomal peptides and type I and II polyketides .…”