The genome of Bacillus tequilensis EA-CB0015 sheds light into its epiphytic lifestyle and potential as a biocontrol agent

Abstract

Different Bacillus species have successfully been used as biopesticides against a broad range of plant pathogens. Among these, Bacillus tequilensis EA-CB0015 has shown to efficiently control Black sigatoka disease in banana plants, presumably by mechanisms of adaptation that involve modifying the phyllosphere environment. Here, we report the complete genome of strain EA-CB0015, its precise taxonomic identity, and determined key genetic features that may contribute to its effective biocontrol of plant pathogens. We found that B. tequilensis EA-CB0015 harbors a singular 4 Mb circular chromosome, with 3,951 protein-coding sequences. Multi-locus sequence analysis (MLSA) and average nucleotide identity (ANI) analysis classified strain EA-CB0015 as B. tequilensis. Encoded within its genome are biosynthetic gene clusters (BGCs) for surfactin, iturin, plipastatin, bacillibactin, bacilysin, subtilosin A, sporulation killing factor, and other natural products that may facilitate inter-microbial warfare. Genes for indole-acetic acid (IAA) synthesis, the use of diverse carbon sources, and a multicellular lifestyle involving motility, biofilm formation, quorum sensing, competence, and sporulation suggest EA-CB0015 is adept at colonizing plant surfaces. Defensive mechanisms to survive invading viral infections and preserve genome integrity include putative type I and type II restriction modification (RM) and toxin/antitoxin (TA) systems. The presence of bacteriophage sequences, genomic islands, transposable elements, virulence factors, and antibiotic resistance genes indicate prior occurrences of genetic exchange. Altogether, the genome of EA-CB0015 supports its function as a biocontrol agent against phytopathogens and suggest it has adapted to thrive within phyllosphere environments.

Enhanced Iturin A Production of Engineered Bacillus amyloliquefaciens by Knockout of Endogenous Plasmid and Rap Phosphatase Genes

“…amyloliquefaciens proved unsuccessful. The obstacle lies in the fact that many untamed Bacillus species harbor restriction-modification (RM) systems, encompassing restriction enzymes that degrade DNA and modifying enzymes that alter the DNA’s base structure . This modification shields the DNA from degradation by restriction enzymes, effectively thwarting the infiltration of foreign DNA and impeding the breakdown of its enzymes.…”

“…The obstacle lies in the fact that many untamed Bacillus species harbor restrictionmodification (RM) systems, encompassing restriction enzymes that degrade DNA and modifying enzymes that alter the DNA's base structure. 23 This modification shields the DNA from degradation by restriction enzymes, effectively thwarting the infiltration of foreign DNA and impeding the breakdown of its enzymes. B. amyloliquefaciens is the source of the BamH I restriction enzyme, and the existence of its own BamH I RM system poses obstacles to several genetic modification procedures.…”

Brevibacillus brevis HNCS-1: a biocontrol bacterium against tea plant diseases

“…The metabolic pathway database of AMPs, which can annotate the protein gene clusters of biocontrol bacteria at the gene level and predict the results of secondary metabolites, has been perpetually improved, making the rapid identification of AMPs feasible. In addition, with the continuous publication of multiple microbial genomes and the comparison of microbial genomes between different individuals of the same species, it is gradually recognized that a single reference genome cannot represent diversity within a species (Cuellar-Gaviria et al, 2023 ; Wan et al, 2023 ).…”