Novel Plant-Associated Brevibacillus and Lysinibacillus Genomospecies Harbor a Rich Biosynthetic Potential of Antimicrobial Compounds

Abstract

We have previously reported the draft genome sequences of 59 endospore-forming Gram-positive bacterial strains isolated from Vietnamese crop plants due to their ability to suppress plant pathogens. Based on their draft genome sequence, eleven of them were assigned to the Brevibacillus and one to the Lysinibacillus genus. Further analysis including full genome sequencing revealed that several of these strains represent novel genomospecies. In vitro and in vivo assays demonstrated their ability to promote plant growth, as well as the strong biocontrol potential of Brevibacilli directed against phytopathogenic bacteria, fungi, and nematodes. Genome mining identified 157 natural product biosynthesis gene clusters (BGCs), including 36 novel BGCs not present in the MIBiG data bank. Our findings indicate that plant-associated Brevibacilli are a rich source of putative antimicrobial compounds and might serve as a valuable starting point for the development of novel biocontrol agents.

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

“…Short-read sequencing has been previously described [14]. Long-read sequencing was conducted in house with the Oxford Nanopore MinION with the flowcell (R9.4.1), as described previously [3]. The quality of assemblies was assessed by determining the ratio of falsely trimmed proteins by using Ideel (https://github.com/phiweger/ideel, accessed on 1 November 2021).…”

“…The genome coverage of the obtained contigs was 50× in average. Genome annotation and visualization was performed as described previously [3].…”

“…Similar rates were previously detected in representatives of B. velezensis [4] and Brevibacillus spp. [3]. In order to examine the inhibiting effects against phytopathogenic nematodes more directly, we isolated a representative strain of Meloidogyne sp.…”

“…Similar rates were previously detected in representatives of B. velezensis [4] and Brevibacillus spp. [3].…”

“…Based on their draft genome sequences, the isolates were taxonomically assigned as being members of the Bacillaceae family, representing four main taxonomic groups: Lysinibacillus spp., Brevibacillus spp., the Bacillus subtilis species complex, and the Bacillus cereus group [2]. Our further studies revealed that, in contrast to Lysinibacillus sp., the plant-associated Brevibacilli harbored a multitude of interesting antimicrobial peptides with a strong potential to suppress phytopathogenic bacteria, fungi, and nematodes [3]. The Bacillus velezensis isolates TL7 and S1, members of the B. subtilis species complex, were identified in large-scale trials as the most promising candidates for developing efficient biocontrol agents [4].…”