Abstract
The Bacillus velezensis strain PG12, belonging to the Bacillus amyloliquefaciens group, is an endophytic bacterium known for its antimicrobial activities against crop pathogens. However, our knowledge of the molecular basis underlying its biocontrol activity and the relatedness of different strains in the Bacillus amyloliquefaciens group is limited. Here, we sequenced and analyzed the genome of PG12 to test its taxonomic affiliation and identified genes involved in the biocontrol activity. The phylogenomic analysis results indicate that PG12 belongs to B. velezensis, a subgroup of the B. amyloliquefaciens group. By comparing the genomes of 22 strains in this group, we confirmed that it comprises three different phylogenetic lineages: B. amyloliquefaciens, B. velezensis and B. siamensis. Three secondary metabolism gene clusters related to the production of lipopeptides, namely fengycin, iturin and surfactin, were identified in the genomes of the B. amyloliquefaciens group. The core genome of B. velezensis is enriched in secondary metabolism genes compared with B. siamensis and B. amyloliquefaciens. Three of the five genes pertaining to the gene cluster responsible for fengycin biosynthesis (fenBCD) were found in B. velezensis and B. siamensis, but not in B. amyloliquefaciens. Phenotypic analysis showed that the ∆fenA mutant of PG12 displayed significantly decreased biofilm formation and swarming motility, which indicates that fengycin contributes to the colonization and pathogen control abilities of PG12. Our results also suggest that B. siamensis and B. velezensis have acquired the fenBCD genes from Paenibacillus spp. by horizontal gene transfer (HGT). Taken together, the results provide insights into the evolutionary pattern of the B. amyloliquefaciens group strains and will promote further researches on their taxonomy and functional genomics.
Highlights
Pathogenic microorganisms affecting plant health are a major and chronic threat to food production worldwide (Compant et al 2005)
Genome features of B. velezensis PG12 To identify genetic factors involved in the biocontrol activity of B. velezensis PG12, the genome of this strain was sequenced and analyzed
Phylogenomic analysis of B. velezensis PG12 Preliminary molecular identification based on 16S rDNA and gyrA sequences assigned PG12 strains to B. amyloliquefaciens (Chen et al 2016)
Summary
Pathogenic microorganisms affecting plant health are a major and chronic threat to food production worldwide (Compant et al 2005). The genus Bacillus represents a large group of Grampositive bacteria belonging to the Firmicutes phylum They are capable of forming stable dormant structures called endospores in nutrient-poor and stressful environmental conditions (Hamdache et al 2013). The bacteria from this group can inhabit a large variety of ecological niches, including soil, water, plant surfaces and rhizosphere (Siefert et al 2000; Feng et al 2014; Kim et al 2015; Gao et al 2019). The antibiotic activity of Bacillus species is partly driven by the secretion of active lipopeptides These cyclic lipopeptides belong to three main families: surfactin (surfactin, lychenisin, pumilacidin and halobacilin), iturin (iturin, bacillomycin and mycosubtilin) and fengycin (fengycin, plipastatin and maltacin) (Zhao et al 2017; Fira et al 2018). Studies have revealed that lipopeptides play an important role in maintaining colonization behaviors such as biofilm formation and swarming motility (Luo et al 2014; Fan et al 2017b)
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