Genetic, Epigenetic and Phenotypic Diversity of Four Bacillus velezensis Strains Used for Plant Protection or as Probiotics

Abstract

Bacillus velezensis strains are applied as ecologically safe biopesticides, plant growth promoting rhizobacteria (PGPR), and in veterinary probiotics. They are abundant in various environments including soil, plants, marine habitats, the intestinal micro-flora, etc. The mechanisms underlying this adaptive plasticity and bioactivity are not well understood, nor is it clear why several strains outperform other same species isolates by their bioactivities. The main objective of this work was to demonstrate versatility of bioactivities and lifestyle strategies of the selected B. velezensis strains suitable to serve as model organisms in future studies. Here, we performed a comparative study of newly sequenced genomes of four B. velezensis isolates with distinct phenotypes and isolation origin, which were assessed by RNA sequencing under the effect of root exudate stimuli and profiled by epigenetic modifications of chromosomal DNA. Among the selected strains, UCMB5044 is an oligotrophic PGPR strain adapted to nutrient poor desert soils. UCMB5113 and At1 are endophytes that colonize plants and require nutrient rich media. In contrast, the probiotic strain, UCMB5007, is a copiotroph, which shows no propensity to colonize plants. PacBio and Illumina sequencing approaches were used to generate complete genome assemblies, tracing epigenetic modifications, and determine gene expression profiles. All sequence data was deposited at NCBI. The strains, UCMB5113 and At1, show 99% sequence identity and similar phenotypes despite being isolated from geographically distant regions. UCMB5007 and UCMB5044 represent another group of organisms with almost identical genomes but dissimilar phenotypes and plant colonization propensity. The two plant associated strains, UCMB5044 and UCMB5113, share 398 genes putatively associated with root colonization, which are activated by exposure to maize root exudates. In contrast, UCMB5007 did not respond to root exudate stimuli. It was hypothesized that alterations in the global methylation pattern and some other epigenetic modifications enable adaptation of strains to different habitats and therefore may be of importance in terms of the biotechnological applicability of these bacteria. Contrary, the ability to grow on root exudates as a sole source of nutrients or a strong antagonism against phytopathogens showed by the strains in vitro cannot be considered as good predictors of PGPR activities.

Bacillus velezensis 83 a bacterial strain from mango phyllosphere, useful for biological control and plant growth promotion

“…These methyltransferases can interfere in the sequences of the promoters in the genes (i.e. in the transcriptional regulator SigA which in turn regulates other sigma factors) which affects their expression and causes phenotypic differences between the strains when faced with environmental stimuli (Reva et al 2019 ). In terms of gene expression, the B. amyloliquefaciens LL3 strain is a model because it is a glutamate-independent producer of γ-PGA and several mutants have been constructed.…”

“…For example, the strains B. velezensis UCMB5044 (a oligotrophic PGPR isolated from desert soils), B. velezensis UCMB5113 and B. velezensis At1 (both strain plant endophytes) and B. velezensis UCMB55007 (a copiotroph isolated from calf gut) share 99% of genetic homology. However, their gene expression in response to root maize exudates were significantly different because they possess different DNA methylation patterns (Reva et al 2019 ).…”

Exploration of endo-xylanase from novel strain ofBacillus velezensisAG20 isolated from the cave of Meghalaya

“…This is the first ever report of Bacillus velezensis from the caves of Meghalaya, India and rest of the world ever. Earlier, this novel group of bacteria was reported from plant root isolate and nutrient poor desert soil secretes beneficial metabolites for plant growth promotion and protection as probiotics (43, 44). Positive correlation of high GC content and basic melting temperature were owing to thermotolerent property of Bacillus velezensis AG20.…”

Effect of Bacillus velezensis to substitute in-feed antibiotics on the production, blood biochemistry and egg quality indices of laying hens

“…Bacillus velezensis has been widely used as a biological control agent in agricultural elds due to its excellent ability to suppress plant diseases [24,25]. It is considered as a potential rhizobacterial organism with extraordinary biosynthetic machinery, which can trigger innate immunity in plants [26].…”