Exploring the Nature of the Antimicrobial Metabolites Produced by Paenibacillus ehimensis Soil Isolate MZ921932 Using a Metagenomic Nanopore Sequencing Coupled with LC-Mass Analysis

The continuous emergence of multidrug-resistant (MDR) pathogens poses a global threat to public health. Accordingly, global efforts are continuously conducted to find new approaches to infection control by rapidly discovering antibiotics, particularly those that retain activities against MDR pathogens. In this study, metagenomic nanopore sequence analysis coupled with spectroscopic methods has been conducted for rapid exploring of the various active metabolites produced by Paenibacillus ehimensis soil isolate. Preliminary soil screening resulted in selection of a Gram-positive isolate identified via 16S ribosomal RNA gene sequencing as Paenibacillus ehimensis MZ921932. The isolate showed a broad range of activity against MDR Gram-positive, Gram-negative, and Candida spp. A metagenomics sequence analysis of the soil sample harboring Paenibacillus ehimensis isolate MZ921932 (NCBI GenBank accession PRJNA785410) revealed the presence of conserved biosynthetic gene clusters of petrobactin, tridecaptin, locillomycin (β-lactone), polymyxin, and macrobrevin (polyketides). The liquid chromatography/mass (LC/MS) analysis of the Paenibacillus ehimensis metabolites confirmed the presence of petrobactin, locillomycin, and macrobrevin. In conclusion, Paenibacillus ehimensis isolate MZ921932 is a promising rich source for broad spectrum antimicrobial metabolites. The metagenomic nanopore sequence analysis was a rapid, easy, and efficient method for the preliminary detection of the nature of the expected active metabolites. LC/MS spectral analysis was employed for further confirmation of the nature of the respective active metabolites.

Molecular Characterization and Heterologous Production of the Bacteriocin Peocin, a DNA Starvation/Stationary Phase Protection Protein, from Paenibacillus ehimensis NPUST1

The production of a bacteriocin-like substance with antimicrobial activity, named peocin, by the probiotic Paenibacillus ehimensis NPUST1 was previously reported by our laboratory. The present study aimed to identify peocin and increase the peocin yield by heterologous expression in Escherichia coli BL21(DE3). Peocin was identified as a DNA starvation/stationary phase protection protein, also called DNA-binding protein from starved cells (Dps), by gel overlay and LC-MS/MS analysis. For mass production of peocin, fed-batch cultivation of E. coli was performed using a pH-stat control system. Purification by simple nickel affinity chromatography and dialysis yielded 45.3 mg of purified peocin from a 20-mL fed-batch culture (49.3% recovery). The biological activity of the purified peocin was confirmed by determination of the MIC and MBC against diverse pathogens. Purified peocin exhibited antimicrobial activity against aquatic, food spoilage, clinical and antibiotic-resistant pathogens. In an in vivo challenge test, zebrafish treated with purified peocin exhibited significantly increased survival rates after A. hydrophila challenge. The present study is the first to show the antimicrobial activity of Dps and provides an efficient strategy for production of bioactive peocin, which will aid the development of peocin as a novel antimicrobial agent with potential applications in diverse industries.

Antifungal activity of various chitinolytic bacteria against Colletotrichum in pepper

Colletotrichum gleosporioides causes the anthracnose disease in plants including vegetables and fruits. The pathogenicity of the strains was confirmed by using pepper fruit inoculation assays. The chitinolytic bacterial strains Paenibacillus elgii HOA73, Lysobacter capsici HS124, Streptomyces griseus, Pseudomonas fluorescens, and Paenibacillus ehimensis MA2012 were evaluated against the phytopathogenic fungal strains. The bacteria significantly inhibited C. gleosporioides strain 40003, the inhibition ranging from 17% to 37%. Similarly, 5–41% inhibition of C. gleosporioides 40896 was noticed. Moreover, C. gleosporioides 40965 and 42113 were also inhibited. The n-butanol extracted crude compound of P. ehimensis MA2012 completely inhibited the spore germination of the phytopathogen. Hence the chitinolysis may be considered as an important trait for screening the biocontrol bacteria against anthracnose.

Polyfunctional Biopreparations-Crude Oil Destructors: The Effect on Plants and the Content of Oil in the Soil

The results of an experiment on cleaning oil-contaminated soil and accelerating the restoration of its fertility with the aid of combined biopreparations containing bacteria that degrade oil and microorganisms that can stimulate the growth and development of plants. It is shown that the introduction of bacterial mixtures reduced the oil content by 3.1–3.6 times and increased by 2-3 orders the number of basic physiological groups of soil microorganisms participating in its transformation, and also accelerated the germination of seeds (for 2 days) and the beginning (for 6–7 days) of all stages of oat development, used as a phytomeliorant. The most effective was a biopreparation consisting of a consortium of microorganisms Acinetobacter calcoaceticus IB DT-5.1/ 1 and Ochrobactrum intermedium IB DT-5.3/2 and strains of Pseudomonas koreensis IB-4 and Paenibacillus ehimensis IB 739, which, among other things, increased the mass of oat shoots in 2.3–2.6 times and their length is 54.0–77.8% compared to plants in the soil untreated with bacteria with oil.