Comprehensive genomic analysis of Bacillus paralicheniformis strain BP9, pan-genomic and genetic basis of biocontrol mechanism.

Many Bacillus species are essential antibacterial agents, but their antibiosis potential still needs to be elucidated to its full extent. Here, we isolated a soil bacterium, BP9, which has significant antibiosis activity against fungal and bacterial pathogens. BP9 improved the growth of wheat seedlings via active colonization and demonstrated effective biofilm and swarming activity. BP9 sequenced genome contains 4282 genes with a mean G-C content of 45.94% of the whole genome. A single copy concatenated 802 core genes of 28 genomes, and their calculated average nucleotide identity (ANI) discriminated the strain BP9 from Bacillus licheniformis and classified it as Bacillus paralicheniformis. Furthermore, a comparative pan-genome analysis of 40 B. paralicheniformis strains suggested that the genetic repertoire of BP9 belongs to open-type genome species. A comparative analysis of a pan-genome dataset using the Kyoto Encyclopedia of Genes and Genomes (KEGG) and Cluster of Orthologous Gene groups (COG) revealed the diversity of secondary metabolic pathways, where BP9 distinguishes itself by exhibiting a greater prevalence of loci associated with the metabolism and transportation of organic and inorganic substances, carbohydrate and amino acid for effective inhabitation in diverse environments. The primary secondary metabolites and their genes involved in synthesizing bacillibactin, fencing, bacitracin, and lantibiotics were identified as acquired through a recent Horizontal gene transfer (HGT) event, which contributes to a significant part of the strain`s antimicrobial potential. Finally, we report some genes essential for plant-host interaction identified in BP9, which reduce spore germination and virulence of multiple fungal and bacterial species. The effective colonization, diverse predicted metabolic pathways and secondary metabolites (antibiotics) suggest testing the suitability of strain BP9 as a potential bio-preparation in agricultural fields.

Impact of dehydration on the physiochemical properties of Nostoc calcicola BOT1 and its untargeted metabolic profiling through UHPLC-HRMS.

The global population growth has led to a higher demand for food production, necessitating improvements in agricultural productivity. However, abiotic and biotic stresses pose significant challenges, reducing crop yields and impacting economic and social welfare. Drought, in particular, severely constrains agriculture, resulting in unproductive soil, reduced farmland, and jeopardized food security. Recently, the role of cyanobacteria from soil biocrusts in rehabilitating degraded land has gained attention due to their ability to enhance soil fertility and prevent erosion. The present study focused on Nostoc calcicola BOT1, an aquatic, diazotrophic cyanobacterial strain collected from an agricultural field at Banaras Hindu University, Varanasi, India. The aim was to investigate the effects of different dehydration treatments, specifically air drying (AD) and desiccator drying (DD) at various time intervals, on the physicochemical properties of N. calcicola BOT1. The impact of dehydration was assessed by analyzing the photosynthetic efficiency, pigments, biomolecules (carbohydrates, lipids, proteins, osmoprotectants), stress biomarkers, and non-enzymatic antioxidants. Furthermore, an analysis of the metabolic profiles of 96-hour DD and control mats was conducted using UHPLC-HRMS. Notably, there was a significant decrease in amino acid levels, while phenolic content, fatty acids, and lipids increased. These changes in metabolic activity during dehydration highlighted the presence of metabolite pools that contribute to the physiological and biochemical adjustments of N. calcicola BOT1, mitigating the impact of dehydration to some extent. Overall, present study demonstrated the accumulation of biochemical and non-enzymatic antioxidants in dehydrated mats, which could be utilized to stabilize unfavorable environmental conditions. Additionally, the strain N. calcicola BOT1 holds promise as a biofertilizer for semi-arid regions.

Platyphylloside, a potential inhibitor from epicarp of B. aegyptiaca against CYP450 protein in T. rubrum - In vitro and in silico approaches.

Trichophyton rubrum is one of the major disease causing pathogens in human; mainly it causes tinea pedis, tinea cruris and tinea corporis. Cytochrome P450 which considered to be an important protein that can impact ergosterol biosynthesis pathway. B. aegyptiaca is rich source of secondary metabolites with tremendous medicinal values and it has sweet pulp, leaves with spine, strong seed and oily kernel. The epicarp of the fruit was taken for this study to inhibit T. rubrum using in vitro and in silico techniques. The epicarp portion was extracted using various solvents and water. The anti-dermatophytic activity on T. rubrum of these extracts was assessed utilizing poison plate technique with 5 individual concentrations. The fractioned chloroform extract of epicarp had fully inhibited the growth of T. rubrum at 3 mg/ml. Further, the chloroform extract was subjected to LC-MS analysis, in total, 40 compounds were elucidated. Then, the derived compounds were included for predicting ADMETox properties using Qikprop module. From the analysis 40 compounds were identified to be eligible for docking process. Then the desirable compounds, drug Ketoconazole were subjected to docking analysis using Glide module of Schrödinger. It shows that Platyphylloside has better docking result than other compounds and drug Ketoconazole. Further, MD simulation was carried out for Ketoconazole-Cyp450 and Platyphylloside-CYP450 complexes using Desmond, Schrödinger. MD simulation study also confirmed that the Platyphylloside-CYP450 complex more stable. This study suggests that Platyphylloside may act as potential inhibitor and it could be further subjected to experimental analysis to inhibit the T. rubrum growth.

Biodegradation of naphthalene by biocatalysts isolated from the contaminated environment under optimal conditions.

Polycyclic aromatic hydrocarbons (PAHs) pollution occurs in freshwater and marine environment by anthropogenic activities. Moreover, analysis of the PAHs-degradation by the indigenous bacterial strains is limited, compared with other degraders. In this study, naphthalene (NAP) biodegrading bacteria were screened by enrichment culture method. Three bacterial strains were obtained for NAP degradation and identified as Bacillus cereus CK1, Pseudomonas aeruginosa KD4 and Enterobacter aerogenes SR6. The amount of hydrogen, carbon, sulphur and nitrogen of wastewater were analyzed. Total bacterial count increased at increasing incubation time (6-60 days) and moderately decreased at higher NAP concentrations. The bacterial population increased after 48 days at 250 ppm NAP (519 ± 15.3 MPM/mL) concentration and this level increased at 500 ppm NAP concentration (541 ± 12.5 MPM/mL). NAP was degraded by bacterial consortium within 36 h-99% at 30 °C. PAHs degrading bacteria were grown optimally at 4% inoculum concentrations. Bacterial consortium was able to degrade 98% NAP at pH 7.0 after 36 h incubation and degradation potential was improved (100%) after 34 h (pH 8.0). Also at pH 9.0, 100% biodegradation was registered after 36 h incubation. When the agitation speed enhanced from 50 ppm to 150 ppm, increased bacteria growth and increased NAP degradation within 42 h incubation. Among the nutrient sources, beef extract, peptone and glucose supplemented medium supported complete degradation of PAHs within 30 h, whereas peptone supported 94.3% degradation at this time. Glucose supplemented medium showed only 2.8% NAP degradation after 6 h incubation and reached maximum (100%) within 42 h incubation. Bacterial consortium can be used to reduce NAP under optimal process conditions and this method can be used for the removal of various hydrocarbon-compounds.

Immobilization of Halomonas halodurans and Bacillus halodurans in packed bed bioreactor for continuous removal of phenolic impurities in waste water.

Phenol is an organic contaminant widely distributed in wastewater. Biodegradation is one of the suitable methods used to remove phenol from the wastewater. In this study, the bacterial laccase and pectinase were analyzed and phenol degradation potential was studied. A total of six bacterial strains were selected and their phenol degrading potentials were studied. Laccase and pectinase producers were screened on substrate agar plates and several strains produced these enzymes in submerged fermentation. Among these enzyme producing strains, strain PD8 and PD22 exhibited potent phenol degrading ability than other strains. These two bacterial strains (Halomonas halodurans PD8 and Bacillus halodurans PD22) exhibited maximum growth in phenol-supplemented culture medium. These two organisms grown well at wide pH values (pH 3.0 and 10.0), survive well between 20 °C and 50 °C, and showed growth between 1 and 10% sodium chloride concentration. The lyophilized enzyme from PD8 and PD22 were immobilized with alginate beads cross liked with divalent cations. At 1% alginate, the binding efficiency was 40.2 ± 2.9% and it improved up to 2.0% concentration (67.5 ± 4.2%) and further increase on alginate concentration affected binding efficiency. Phenol degradation was maximum within 10 h of treatment in the immobilized packed bed column reactor (83.1 ± 3.2%) and colour removal efficiency was maximum at 12 h treatment (82.1 ± 3.9%). After four successive experimental trials more than 40% efficiency was achieved.

Prevalence of multidrug-resistant bacteria associated with polymicrobial infections.

BACKGROUND: Wounds remain the most important cause of postoperative mortality and morbidity and generate considerable additional social and healthcare costs. Most wounds are caused by various coliforms, Enterococcus fecalis, Proteus sp., and multidrug resistant Staphylococcus aureus. Wound is one of the leading cause of infections in the under developed and developing countries than developed nations. METHODS: A total of 43 samples associated with bacteremia and wound infection were collected. Biochemical characterization and culture characteristics of the drug resistant isolates were studied using MacConkey agar, blood agar and mannitol-salt agar. Antibiotic susceptibility analysis of the isolated strains was performed by disc diffusion method using various antibiotics. Prevalence of dug resistance among bacteria isolated from the wound was studied. The ability of Beta lactamase antibiotic producing bacterial strains were analyzed. RESULTS: A total of 168 bacterial strains were isolated showed high resistant towards ampicillin (89%), ciprofloxacin (90.8), cefepine (90.5), piperacillin (91.8), oxacillin (92.5), and imipenem (96.5). The isolated bacterial strains showed monobacterial as well as polybacterial growth on the surface of the wound. The isolated bacterial strains revealed 89% sensitivity against norfloxacin and 94.9 sensitivity against vancomycin. About 26% of bacterial strains degraded quinolones, whereas only 14% clinical isolates showed their ability to degrade aminoglycosides. A total of 27% bacteria degraded tetracycline and 51% of isolates degraded carbapenems compounds. Interestingly, E. faecalis was resistant against antibiotics such as, Oxacillin, Nalidic acid, Ofloxacin, Erythromycin, Norfloxacin, Ciprofloxacin, Ampicillin, Tetracycline, Cefepine, Amikacin, Cefurooxime, Vancomycin, Piperacillin, Imipenem and Gentamycin. Moreover, Proteus species was resistant against certain numbers of antibiotics namely, Ampicillin, Piperacillin, Oxacillin, Nalidic acid, Tetracycline, Erythromycin, Cefurooxime, Nitrofurantoin, Vancomycin and Imipenem. CONCLUSIONS: The isolated bacterial strains were resistant against various drugs including vancomycin. Staphylococci, and E. faecalisis strains showed resistance against various classes of antibiotics.