Abstract
The present study reports the isolation of antibacterial exhibiting Bacillus pumilus (B. pumilus) SF-4 from soil field. The genome of this strain SF-4 was sequenced and analyzed to acquire in-depth genomic level insight related to functional diversity, evolutionary history, and biosynthetic potential. The genome of the strain SF-4 harbor 12 Biosynthetic Gene Clusters (BGCs) including four Non-ribosomal peptide synthetases (NRPSs), two terpenes, and one each of Type III polyketide synthases (PKSs), hybrid (NRPS/PKS), lipopeptide, β-lactone, and bacteriocin clusters. Plant growth-promoting genes associated with de-nitrification, iron acquisition, phosphate solubilization, and nitrogen metabolism were also observed in the genome. Furthermore, all the available complete genomes of B. pumilus strains were used to highlight species boundaries and diverse niche adaptation strategies. Phylogenetic analyses revealed local diversification and indicate that strain SF-4 is a sister group to SAFR-032 and 150a. Pan-genome analyses of 12 targeted strains showed regions of genome plasticity which regulate function of these strains and proposed direct strain adaptations to specific habitats. The unique genome pool carries genes mostly associated with “biosynthesis of secondary metabolites, transport, and catabolism” (Q), “replication, recombination and repair” (L), and “unknown function” (S) clusters of orthologous groups (COG) categories. Moreover, a total of 952 unique genes and 168 exclusively absent genes were prioritized across the 12 genomes. While newly sequenced B. pumilus SF-4 genome consists of 520 accessory, 59 unique, and seven exclusively absent genes. The current study demonstrates genomic differences among 12 B. pumilus strains and offers comprehensive knowledge of the respective genome architecture which may assist in the agronomic application of this strain in future.
Highlights
Soil salinity, iron/phosphorus deficiency, and drought stress are the major problems that can limit plant growth and its associated products [1]
The antibacterial activity of strain SF-4 was evaluated against a set of Gram-positive and Gram-negative American Type Culture Collection (ATCC) bacterial strains (Streptococcus pneumoniae 6305, Shigella flexneri 12022, Klebsiella pneumoniae 13889, Staphylococcus aureus 6538, Escherichia coli 8739, Salmonella typhimurium 14028, Listeria monocytogenes 13932, and Pseudomonas aeruginosa 9027) on Muller-Hinton agar (MHA) plates
The strain SF-4 exhibited higher activity against P. aeruginosa and S. flexneri while it showed the lowest activity against S. typhimurium (Supplementary File 1, Figure S1)
Summary
Iron/phosphorus deficiency, and drought stress are the major problems that can limit plant growth and its associated products [1]. Certain beneficial soil bacteria could play a significant role in iron/phosphorus deposition, drought, and salinity stress and can promote plant growth and crop yields [2,3]. Plant growth-promoting bacteria establish specific symbiotic interactions with plants and colonize intracellularly or intercellularly without causing any infection. These bacterial strains could be used in biocontrol, bio-fertilization, and biostimulation to improve plant growth under various harsh conditions [4]. In iron-deficient soil, plants like red clover recruit certain types of rhizosphere bacteria with greater capacity for siderophore synthesis. The focus of recent research is switched towards alternative strategies that employ potential bacteria for biocontrol
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