Investigation of the potential of Brevibacillus spp. for the biosynthesis of nonribosomally produced bioactive compounds by combination of genome mining with MALDI-TOF mass spectrometry.

The biosynthetic potential of 11 Brevibacillus spp. strains was investigated by combination of genome mining with mass spectrometric analysis using MALDI-TOF mass spectrometry. These endophytic, plant associated Brevibacillus strains were isolated from crop plants, such as coffee and black pepper, in Vietnam. Draft genomes of these strains were available. They were classified (a) by comparison with type strains and a collection of genome-sequenced Brevibacillus spp. deposited in the NCBI data base as well as (b) by construction of a phylogenetic tree from the core sequences of publicly available genomes of Brevibacillus strains. They were identified as Brevibacillus brevis (1 strain); parabrevis (2 strains); porteri (3 strains); and 5 novel Brevibacillus genomospecies. Our work was specifically focused on the detection and characterization of nonribosomal peptides produced by these strains. Structural characterization of these compounds was performed by LIFT-MALDI-TOF/TOF mass spectrometric sequence analysis. The highlights of our work were the demonstration of the tyrocidines, a well-known family of cyclodecapeptides of great structural variability, as the main products of all investigated strains and the identification of a novel class of pentapeptides produced by B. brevis; B. schisleri; and B. porteri which we designate as brevipentins. Our biosynthetic studies demonstrate that knowledge of their biosynthetic capacity can efficiently assist classification of Brevibacillus species.

Plant-Associated Representatives of the Bacillus cereus Group Are a Rich Source of Antimicrobial Compounds.

Seventeen bacterial strains able to suppress plant pathogens have been isolated from healthy Vietnamese crop plants and taxonomically assigned as members of the Bacillus cereus group. In order to prove their potential as biocontrol agents, we perform a comprehensive analysis that included the whole-genome sequencing of selected strains and the mining for genes and gene clusters involved in the synthesis of endo- and exotoxins and secondary metabolites, such as antimicrobial peptides (AMPs). Kurstakin, thumolycin, and other AMPs were detected and characterized by different mass spectrometric methods, such as MALDI-TOF-MS and LIFT-MALDI-TOF/TOF fragment analysis. Based on their whole-genome sequences, the plant-associated isolates were assigned to the following species and subspecies: B. cereus subsp. cereus (6), B. cereus subsp. bombysepticus (5), Bacillus tropicus (2), and Bacillus pacificus. These three isolates represent novel genomospecies. Genes encoding entomopathogenic crystal and vegetative proteins were detected in B. cereus subsp. bombysepticus TK1. The in vitro assays revealed that many plant-associated isolates enhanced plant growth and suppressed plant pathogens. Our findings indicate that the plant-associated representatives of the B. cereus group are a rich source of putative antimicrobial compounds with potential in sustainable agriculture. However, the presence of virulence genes might restrict their application as biologicals in agriculture.

Draft Genome Sequences of 59 Endospore-Forming Gram-Positive Bacteria Associated with Crop Plants Grown in Vietnam.

We report the draft genome sequences of 59 Gram-positive bacterial strains that were isolated from Vietnamese crop plants. The strains were assigned to nine different Bacillus and Brevibacillus species. Ten strains classified as being a Bacillus sp. (3 strains), Brevibacillus sp. (6 strains), or Lysinibacillus sp. (1 strain) could not be identified to the species level.