Characterization and complete genome analysis of the surfactin-producing, plant-protecting bacterium Bacillus velezensis 9D-6

Abstract

BackgroundBacillus velezensis is an endospore-forming, free-living soil bacterium with potential as a biopesticide against a broad spectrum of microbial pathogens of plants. Its potential for commercial development is enhanced by rapid replication and resistance to adverse environmental conditions, typical of Bacillus species. However, the use of beneficial microbes against phytopathogens has not gained dominance due to limitations that may be overcome with new biopesticidal strains and/or new biological knowledge.ResultsHere, we isolated B. velezensis strain 9D-6 and showed that it inhibits the in vitro growth of prokaryotic and eukaryotic pathogens, including the bacteria Bacillus cereus, Clavibacter michiganensis, Pantoea agglomerans, Ralstonia solanacearum, Xanthomonas campestris, and Xanthomonas euvesicatoria; and the fungi Alternaria solani, Cochliobolus carbonum, Fusarium oxysporum, Fusarium solani, Gibberella pulicaris, Gibberella zeae, Monilinia fructicola, Pyrenochaeta terrestris and Rhizoctonia solani. Antimicrobial compounds with activity against Clavibacter michiganensis were isolated from B. velezensis 9D-6 and characterized by high resolution LC-MS/MS, yielding formulae of C52H91N7O13 and C53H93N7O13, which correspond to [Leu7] surfactins C14 and C15 (also called surfactin B and surfactin C), respectively. We further sequenced the B. velezensis 9D-6 genome which consists of a single circular chromosome and revealed 13 gene clusters expected to participate in antimicrobial metabolite production, including surfactin and two metabolites that have not typically been found in this species - ladderane and lantipeptide. Despite being unable to inhibit the growth of Pseudomonas syringae DC3000 in an in vitro plate assay, B. velezensis 9D-6 significantly reduced root colonization by DC3000, suggesting that 9D-6 uses methods other than antimicrobials to control phytopathogens in the environment. Finally, using in silico DNA-DNA hybridization (isDDH), we confirm previous findings that many strains currently classified as B. amyloliquefaciens are actually B. velezensis.ConclusionsThe data presented here suggest B. velezensis 9D-6 as a candidate plant growth promoting bacterium (PGPB) and biopesticide, which uses a unique complement of antimicrobials, as well as other mechanisms, to protect plants against phytopathogens. Our results may contribute to future utilization of this strain, and will contribute to a knowledge base that will help to advance the field of microbial biocontrol.Electronic supplementary materialThe online version of this article (10.1186/s12866-018-1380-8) contains supplementary material, which is available to authorized users.

Reclassification of the biocontrol agents Bacillus subtilis BY-2 and Tu-100 as Bacillus velezensis and insights into the genomic and specialized metabolite diversity of the species

“…S1). The genome metrics of both strains fitted within the size range of 3.81–4.24 Mbp and 45.9–46.8 % GC reported for other completed genomes of B. velezensis [ 38 ]. The BY-2 and Tu-100 genomes were predicted to carry 3915 and 3893 genes, respectively, of which approximately 85 % (3328 and 3309 CDSs, respectively) were classified as protein coding sequences with COG function (Table S3).…”

Crop Protection against Botrytis cinerea by Rhizhosphere Biological Control Agent Bacillus velezensis XT1

“…With regard to fungal mycelium growth inhibition, several strains of B. velezensis have been reported to suppress the in vitro growth of fungal phytopathogens such as the biotrophic/saprotrophic Trichoderma , the hemibiotrophic Fusarium and the necrotrophics Alternaria and Monilinia [ 64 , 65 , 66 ]. In two previous studies, we demonstrated that strain XT1 inhibits the mycelium growth of Alternaria alternata , Fusarium oxysporum , Magnaporthe oryzae , Sclerotinia sclerotiorum and Thanatephorus cucumeris by over 40%.…”

A Review on the Biotechnological Applications of the Operational Group Bacillus amyloliquefaciens

“…The mode of action of non-ribosomal peptides involves the disruption to the cell membrane and inhibition on the transfer of peptidoglycan precursors to bactoprenol pyrophosphate [ 107 ]. In 2019, surfactins from B. velezensis 9D-6 were found to inhibit the in vitro growth of bacteria ( B. cereus , C. michiganensis , Pantoea agglomerans , Ralstonia solanacearum , Xanthomonas campestris and Xanthomonas euvesicatoria ) and fungi ( Alternaria solani , Cochliobolus carbonum , F. oxysporum , F. solani , Gibberella pulicaris , Gibberella zeae , Monilinia fructicola , Pyrenochaeta terrestris and R. solani ) pathogens [ 108 ]. In another related study , in silico genomic study of B. siamensis JFL15 had gene clusters involved in the biosynthesis of antimicrobial compounds.…”