Whole-genome sequencing of Bacillus subtilis XF-1 reveals mechanisms for biological control and multiple beneficial properties in plants

Abstract

Bacillus subtilis XF-1 is a gram-positive, plant-associated bacterium that stimulates plant growth and produces secondary metabolites that suppress soil-borne plant pathogens. In particular, it is especially highly efficient at controlling the clubroot disease of cruciferous crops. Its 4,061,186-bp genome contains an estimated 3853 protein-coding sequences and the 1155 genes of XF-1 are present in most genome-sequenced Bacillus strains: 3757 genes in B. subtilis 168, and 1164 in B. amyloliquefaciens FZB42. Analysis using the Cluster of Orthologous Groups database of proteins shows that 60 genes control bacterial mobility, 221 genes are related to cell wall and membrane biosynthesis, and more than 112 are genes associated with secondary metabolites. In addition, the genes contributed to the strain's plant colonization, bio-control and stimulation of plant growth. Sequencing of the genome is a fundamental step for developing a desired strain to serve as an efficient biological control agent and plant growth stimulator. Similar to other members of the taxon, XF-1 has a genome that contains giant gene clusters for the non-ribosomal synthesis of antifungal lipopeptides (surfactin and fengycin), the polyketides (macrolactin and bacillaene), the siderophore bacillibactin, and the dipeptide bacilysin. There are two synthesis pathways for volatile growth-promoting compounds. The expression of biosynthesized antibiotic peptides in XF-1 was revealed by matrix-assisted laser desorption/ionization-time of flight mass spectrometry.

A comprehensive understanding of the biocontrol potential of Bacillus velezensis LM2303 against Fusarium head blight

“…Efficient colonization on plant tissues, is a prerequisite for the biocontrol strains to survive, suppress plant disease or promote plant growth, while the process relies on the surface motility and efficient biofilm formation of bacteria cells [ 43 – 45 ].…”

“…So it is conceivable that strain LM2303 can actively reach the plant surface through passive movement or flagellum active swimming. The next important step of efficient colonization for biocontrol strains is to enable the formation of bacterial biofilm, which was formed by a variety of extracellular matrix including proteins, polysaccharides, charged polymers and amphiphilic molecules [ 43 ]. The yqxM - sipW - tasA operon encoding the TasA protein of biofilm, the regulator gene sinR and sinI , and the eps cluster encoding the exopolysaccharide of biofilm, were both found in the LM2303 genome ( Table 2 ).…”

“…Molybdenum cofactor, a relic of a nitrogen-fixing gene cluster or a cofactor for nitrogen assimilation, is encoded by the moa cluster containing 5 genes ( moaA - E ) in LM2303 [ 43 , 48 ]. Moreover, the genes for nitrate transporter ( narK ), anaerobic regulatory protein ( fnr 1672), probable transcription regulator ( arf M), nitrate reductase ( narG - J ), ammonium transporter ( nrgA ), nitrogen regulatory PII-like protein ( nrgB ), nitrate/nitrite response regulator ( narP ), were also found along with nitrite reductase large subunit ( nasD ), nitrite reductase small subunit ( nasE ), which all favor for nitrogen assimilation.…”

Purification and characterisation of a fungicidal peptide from Bacillus amyloliquefaciens NCPSJ7

“…For the antimicrobial substances secreted by B. amyloliquefaciens, most peptides were tested to be active against fungi. The most common class may be lipopeptides with small molecular mass, broadly including surfactin (~1.36 kDa), iturin (~1.1 kDa), and fengycin (~1.5 kDa), which have potent applications in food industry, therapeutics, plant protection, and insect control (Zhao et al 2014;Guo et al 2015;Meena & Kanwar 2015). Among the other fungicidal peptides from Bacillus amyloliquefaciens, a smaller peptide with the mass of 852.4 Da was purified and it showed activities against pathogenic fungi (Han et al 2015).…”

Draft Genome Sequence of Bacillus velezensis Lzh-a42, a Plant Growth-Promoting Rhizobacterium Isolated from Tomato Rhizosphere

“…For example, there were genes coding for the antibiotics bacilysin ( bacABCDE ; CXP43_RS19760 to CXP43_RS19740) ( 10 ), fengycin ( fenEDCBA ; CXP43_RS10610 to CXP43_RS10630) ( 11 ), bacillomycin ( bmyCBAD ; CXP43_RS10480 to CXP43_RS10495) ( 12 ), and surfactin ( srfAACD ; CXP43_RS01800 to CXP43_RS01810) ( 11 ). Genes coding for the antibacterial polyketides bacillaene (CXP43_RS08875 to CXP43_RS08920) ( 13 ) and difficidin (CXP43_RS12585 to CXP43_RS12655) ( 12 ) were also predicted.…”