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Background   Bacillus 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.    Results  Here, 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 C 52 H 91 N 7 O 13  and C 53 H 93 N 7 O 13 , which correspond to [Leu 7 ] surfactins C 14  and C 15  (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 ( is DDH), we confirm previous findings that many strains currently classified as  B. amyloliquefaciens  are actually  B. velezensis .    Conclusions  The 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 material  The online version of this article (10.1186/s12866-018-1380-8) contains supplementary material, which is available to authorized users.

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