Molecular identification and safety assessment of the potential probiotic strain Bacillus paralicheniformis HMPM220325 isolated from artisanal fruit dairy products

Bacillus probiotics exhibit considerable economic potential owing to their heightened resilience to external stressors and relatively lower costs related to production and preservation. Although Bacillus paralicheniformis has been acknowledged as a plant-promoting bacterium for a long time, understanding its potential as a probiotic is still in its nascent stages. In this study, the safety and probiotic characteristics of a strain of HMPM220325, isolated from artisanal fruit dairy products, were examined through whole-genome sequencing and phenotypic analysis. The whole genome of HMPM220325 was analyzed for antimicrobial resistance genes, pathogenicity factors, and genes associated with probiotic traits including stress resistance, spore formation, gut adhesion, competitive exclusion of pathogens, bacteriocin expression, and carbohydrate metabolism related to prebiotic utilization. Also, wet lab experiments were conducted for the characterization of probiotics. The identification of the organism as B. paralicheniformis was verified. Its safety was assessed through in silico analysis, the haemolytic activity test, and the acute oral toxicity test. B. paralicheniformis HMPM220325 demonstrated its ability to survive in the pH range of 4-10 and bile salt concentrations of 0-0.9% (w/v), tolerate temperatures between 20 and 60 °C, and exhibit a robust antioxidant capacity. Moreover, B. paralicheniformis HMPM220325 demonstrated a moderate level of hydrophobicity, had the ability to form biofilms, achieved a self-aggregation rate of 51.77 ± 1.01% within 6 hours, and successfully colonized the mouse intestine for a duration of up to 17 days. Additionally, the genome of B. paralicheniformis HMPM220325 contains three gene clusters associated with the biosynthesis of bacteriocins and exhibits co-aggregation with Staphylococcus aureus, Pseudomonas aeruginosa, and Salmonella enterica serovar Typhimurium. The findings of the genomic analysis align with those obtained from the experimental investigation, thereby substantiating the potential of B. paralicheniformis HMPM220325 as a probiotic suitable for incorporation in dairy functional foods and feed applications.

Induction of antimicrobial, antioxidant metabolites production by co-cultivation of two red-sea-sponge-associated Aspergillus sp. CO2 and Bacillus sp. COBZ21

The growing spread of infectious diseases has become a potential global health threat to human beings. According to WHO reports, in this study, we investigated the impact of co-cultivating the isolated endophytic fungus Aspergillus sp. CO2 and Bacillus sp. COBZ21 as a method to stimulate the production of natural bioactive substances. (GC/MS)-based metabolomics profiling of two sponge-associated microbes, Aspergillus sp. CO2 and Bacillus sp. COBZ21, revealed that the co-culture of these two isolates induced the accumulation of metabolites that were not traced in their axenic cultures. By detection of different activities of extracts of Bacillus sp. COBZ21 and Aspergillus sp. CO2 and coculture between Bacillus sp. COBZ21 and Aspergillus sp. CO2. It was noted that the coculture strategy was the reason for a notable increase in some different activities, such as the antimicrobial activity, which showed potent activity against Escherichia coli ATCC 25,922, Staphylococcus aureus NRRLB-767, and Candida albicans ATCC 10,231. The antibiofilm activity showed significant biofilm inhibitory activity toward Bacillus subtilis ATCC 6633, Pseudomonas aeruginosa ATCC 10,145, and Staph aureus NRRLB-767, with activity up to 53.66, 71.17, and 47.89%, while it showed low activity against E. coli ATCC 25,922, while the antioxidant activity based on the DPPH assay showed maximum activity (75.25%). GC-MS investigations revealed the presence of variable chemical constituents belonging to different chemical categories, which reflected their chemical diversity. The main components are (+-) cis-Deethylburnamine (2.66%), Bis(3,6,9,12-tetraoxapentaethylene) crowno-N,N,N',N'-tetra methylpphanediamine (2.48%), and 11-phenyl-2,4,6,8-tetra(2-thienyl)-11-aza-5,13-dithiaeteracyclo[7.3.0.1(2,8)0.0(3,7)] trideca-3,6-diene-10,12,13-trione (3.13%), respectively, for Bacillus sp. axenic culture, Aspergillus sp. CO2, Aspergillus sp. CO2, and Bacillus sp. COBZ21 coculture. By studying the ADME-related physicochemical properties of coculture extract, the compound showed log Po/w values above 5 (8.82). The solubility of the substance was moderate. In order to provide a comprehensive definition of medicinal chemistry and leadlikness, it is important to note that the latter did not meet the criteria outlined in the rule of three (RO3). The toxicity prediction of the coculture extract was performed using the ProTox II web server, which showed that the selected compound has no pronounced toxicity.

Cellulase with Bacillus velezensis improves physicochemical characteristics, microbiota and metabolites of corn germ meal during two-stage co-fermentation

Corn germ meal (CGM) is one of the major byproducts of corn starch extraction. Although CGM has rich fiber content, it lacks good protein content and amino acid balance, and therefore cannot be fully utilized as animal feed. In this study, we investigated the processing effect of cellulase synergized with Bacillus velezensis on the nutritional value of pretreated CGM (PCGM) in two-stage solid-state fermentation (SSF). High-throughput sequencing technology was used to explore the dynamic changes in microbial diversity. The results showed that compared with four combinations of B. velezensis + Lactiplantibacillus plantarum (PCGM-BL), cellulase + L. plantarum (PCGM-CL),control group (PCGM-CK), and cellulase + B. velezensis + L. plantarum (PCGM-BCL), the fourth combination of PCGM-BCL significantly improved the nutritional characteristics of PCGM. After two-stage SSF (48 h), viable bacterial count and contents of crude protein (CP) and trichloroacetic acid-soluble protein (TCA-SP) all were increased in PCGM-BCL (p < 0.05), while the pH was reduced to 4.38 ± 0.02. In addition, compared with PCGM-BL, the cellulose degradation rate increased from 5.02 to 50.74%, increasing the amounts of short-chain fatty acids (216.61 ± 2.74 to 1727.55 ± 23.00 µg/g) and total amino acids (18.60 to 21.02%) in PCGM-BCL. Furthermore, high-throughput sequencing analysis revealed significant dynamic changes in microbial diversity. In the first stage of PCGM-BCL fermentation, Bacillus was the dominant genus (99.87%), which after 24 h of anaerobic fermentation changed to lactobacillus (37.45%). Kyoto Encylopaedia of Genes and Genomes (KEGG) metabolic pathway analysis revealed that the pathways related to the metabolism of carbohydrates, amino acids, cofactors, and vitamins accounted for more than 10% of the enriched pathways throughout the fermentation period. Concisely, we show that cellulase can effectively improve the nutritional value of PCGM when synergized with B. velezensis in two-stage SSF.

Immobilization of Cyclodextrin glycosyltransferase onto three dimensional- hydrophobic and two dimensional- hydrophilic supports: A comparative study

Cyclodextrin glycosyltransferase (CGTase) degrades starch into cyclodextrin via enzymatic activity. In this study, we immobilize CGTase from Thermoanaerobacter sp. on two supports, namely graphene nanoplatelets (GNP) consisting of short stacks of graphene nanoparticles and a calcium-based two-dimensional metal organic framework (Ca-TMA). The uptakes of CGTase on GNP and Ca-TMA reached 40 and 21 mg g-1 respectively, but immobilized CGTase on Ca-TMA showed a higher specific activity (38 U mg-1 ) than that on GNP (28 U mg-1 ). Analysis of secondary structures of CGTase, shows that immobilization reduces the proportion of β-sheets in CGTase from 56% in the free to 49% and 51.3% for GNP and Ca-TMA respectively, α-helix from 38.5% to 18.1 and 37.5%, but led to increased β-turns from 5.5 to 40% and 11.2% for GNP and Ca-TMA, respectively. Lower levels of conformational changes were observed over the more hydrophilic Ca-TMA compared to hydrophobic GNP, resulting in its better activity. Increased β-turns were found to correlate with lower β-CD production, while more β-sheets and α-helix favored more β-CD. Reusability studies revealed that GNP retains up to 74% of initial CGTase activity, while Ca-TMA dropped to 33% after eight consecutive uses. The results obtained in this work provide insight on the effect of support's surface properties on CGTase performance and can assist in developing robust CGTase-based biocatalysts for industrial application.

Lipoproteins are key immunostimulatory components of Bacillus species for dendritic cell maturation and activation

Dendritic cells (DCs) play an important role in immunity by sensing and responding to invasive microbes. Bacillus species are rod-shaped sporulating bacteria that include the pathogenic Bacillus cereus and commensal Bacillus subtilis. Although the interaction between DC and these two Bacillus species has been studied, their key structural component that prompts DC activation is poorly understood. Here, we investigated the two Bacillus species in DC activation by whole cells and their representative microbe-associated molecular patterns (MAMPs). MAMPs including lipoteichoic acid (LTA), lipoprotein (LPP), and peptidoglycan (PGN) were purified from the two Bacillus species. Among the MAMPs, LPP from both species most potently induced the maturation and activation of DCs while PGN, but not LTA, moderately stimulated DCs. LPPs from both Bacillus species enhanced the expression of DC maturation markers including CCR7, CD40, CD80, CD83, CD86, CD205, MHC-I, and MHC-II. Among the MAMPs from B. cereus, PGN most considerably lowered the endocytic capacity of DCs implying DC maturation whereas PGN from B. subtilis lowered it to a similar degree to its LPP. Furthermore, DCs sensitized with LPPs from both Bacillus species and PGN from B. subtilis moderately induced TNF-α and IL-6 production. Notably, a combination of MAMPs did not show any synergistic effect on DC activation. Taken together, our results demonstrate that LPP is the key structural component in B. cereus and B. subtilis that leads to DC activation.

[Genome Stability of Bacillus velezensis after Two-Year Exposure in Open Space]

Spore-forming bacteria have a unique resistance to negative environmental conditions, including aggressive space factors, and are an excellent model for studying adaptation mechanisms and survival strategies at the molecular level. The study analyzed the genome of Bacillus velezensis, which remained viable after a 2-year exposure in outer space on the outer surface of the ISS as part of the Test space experiment. A comparative analysis of the draft genomes of the exhibit strain and the ground control did not reveal significant changes; the average nucleotide identity was 99.98%, which indicates the ability of microorganisms to maintain genome stability in space conditions, due to both increased stress resistance of bacterial spores and efficient operation of the system of repair of accumulated changes. The study of a single nucleotide polymorphism in the genome of B. velezensis revealed nine point substitutions, three of which are in intergenic regions, six in protein-coding genes, three of them are missense mutations, two nucleotide deletions leading to a shift in the reading frame, and one synonymous substitution. The profiles of the housekeeping genes were determined during MLST typing and it was found that the allelic profiles obtained for B. velezensis T15.2 and 924 strains do not correspond to any of the previously described sequence types. The presented results indicate the ability of B. velezensis bacteria to maintain the viability of spores and the integrity of the genome for a long time under extreme conditions of outer space, which is important for the problem of planetary protection, as well as the potential possibility of performing biotechnological processes based on B. velezensis during space exploration.

Culex quinquefasciatus membrane-bound alkaline phosphatase is a putative receptor for Lysinibacillus sphaericus Tpp49Aa1 toxin

The binary toxin Cry48Aa1/Tpp49Aa1 produced by Lysinibacillus sphaericus exhibits potent toxicity against Culicidae larvae. Both Cry48Aa1 and Tpp49Aa1 toxins are crucial for binding to the toxin receptor in Culex quinquefasciatus larvae, albeit with different binding sites. Previous studies have identified Glu71, a membrane-bound α-glucosidase, as a putative binding protein for the Cry48Aa1 toxin, involved in the Cry48Aa1/Tpp49Aa1 toxicity. In this study, we employed pulldown assays to identify a group of Tpp49Aa1-binding proteins from C. quinquefasciatus solubilized midgut brush-border membrane proteins (BBMFs). RNA interference assays revealed that the silencing of an alkaline phosphatase gene (referred to as ALP1263) in C. quinquefasciatus resulted in a significant reduction in larval mortality upon exposure to Cry48Aa1/Tpp49Aa1 toxin in vivo. Furthermore, the ALP1263 protein exhibited specific and high-affinity binding to the Tpp49Aa1 toxin, with a dissociation constant (Kd) of approximately 57.3 nM. The dot blot analysis demonstrated that Tpp49Aa1 C-terminal region was essential for its interaction with the ALP1263 protein. In summary, our findings establish ALP1263 as a functional receptor for Tpp49Aa1 and emphasize its role in the toxicity of Cry48Aa1/Tpp49Aa1.

Green synthesis of biogenic selenium nanoparticles functionalized with ginger dietary extract targeting virulence factor and biofilm formation in Candida albicans

To treat the systemic infections caused by Candida albicans (C. albicans), various drugs have been used, however, infections still persisted due to virulence factors and increasing antifungal resistance. As a solution to this problem, we synthesized selenium nanoparticles (SeNPs) by using Bacillus cereus bacteria. This is the first study to report a higher (70 %) reduction of selenite ions into SeNPs in under 6 h. The as-synthesized, biogenic SeNPs were used to deliver bioactive constituents of aqueous extract of ginger for inhibiting the growth and biofilm (virulence factors) in C. albicans. UV-visible spectroscopy revealed a characteristic absorption at 280 nm, and Raman spectroscopy showed a characteristic peak shift at 253 cm-1 for the biogenic SeNPs. The synthesized SeNPs are spherical with 240-250 nm in size as determined by electron microscopy. Fourier transform infrared spectroscopy confirmed the functionalization of antifungal constituents of ginger over the SeNPs (formation of Ginger@SeNPs nanoconjugates). In contrast to biogenic SeNPs, nanoconjugates were active against C. albicans for inhibiting growth and biofilm formation. In order to reveal antifungal mechanism of nanoconjugates', real-time polymerase chain reaction (RT-PCR) analysis was performed, according to RT-PCR analysis, the nanoconjugates target virulence genes involved in C. albicans hyphae and biofilm formation. Nanoconjugates inhibited 25 % growth of human embryonic kidney (HEK) 293 cell line, indicating moderate cytotoxicity of active nanoconjugates in an in-vitro cytotoxicity study. Therefore, biogenic SeNPs conjugated with ginger dietary extract may be a potential antifungal agent and drug carrier for inhibiting C. albicans growth and biofilm formation.

Biodegradation of naphthalene - Ecofriendly approach for soil pollution mitigation

Naphthalene (NPT), a widely used household pest repellent and insecticide obtained from crude oil, serves as a toxic pollutant to non-target living matter. The stable and resistant nature of NPT makes it difficult to degrade through the physiochemical processes. The present study investigated the bacterial degradation of NPT isolated from crude oil-contaminated soil. Initially, the potent bacteria, Bacillus sp. GN 3.4, were isolated by enrichment culture method and subsequently assessed for NPT biodegradation. The optimum conditions for NPT biodegradation were pH 7.0 at 37 °C, 80 mg/L (initial NPT), 3% v/v (inoculum dose), and 7 days of treatment which showed 100% biodegradation. Furthermore, GC-MS analysis revealed the presence of degradation metabolites, namely, salicylate and hydroquinone indicating potential metabolic pathways. Considering the water-solubility and non-toxic nature of these metabolites, the results imply that Bacillus sp. GN 3.4. could potentially play a role in bioremediation by aiding in eliminating NPT from the soil.

Characterization of lignin and hemicellulose degrading bacteria isolated from cow rumen and forest soil: Unveiling a novel enzymatic model for rice straw deconstruction

Application of greener pretreatment technology using robust ligninolytic bacteria for short duration to deconstruct rice straw and enhance bioethanol production is currently lacking. The objective of this study is to characterize three bacterial strains isolated from the milieux of cow rumen and forest soil and explore their capabilities of breaking down lignocellulose - an essential process in bioethanol production. Using biochemical and genomic analyses these strains were identified as Bacillus sp. HSTU-bmb18, Bacillus sp. HSTU-bmb19, and Citrobacter sp. HSTU-bmb20. Genomic analysis of the strains unveiled validated model hemicellulases, multicopper oxidases, and pectate lyases. These enzymes exhibited interactions with distinct lignocellulose substrates, further affirmed by their stability in molecular dynamic simulations. A comprehensive expression of ligninolytic pathways, including β-ketoadipate, phenyl acetate, and benzoate, was observed within the HSTU-bmb20 genome. The strains secreted approximately 75-82 U/mL of cellulase, xylase, pectinase, and lignin peroxidase. FT-IR analysis of the bacterial treated rice straw fibers revealed that the intensity of lignin-related peaks decreased, while cellulose-related peaks sharpened. The values of crystallinity index for the untreated control and the treated rice straw with either HSTU-bmb18, or HSTU-bmb19, or HSTU-bmb20 were recorded to be 34.48, 28.49, 29.36, 31.75, respectively, which are much higher than that of 13.53 noted for those treated with the bacterial consortium. The ratio of fermentable cellulose in rice straw increased by 1.25-, 1.79-, 1.93- and 2.17-fold following treatments with HSTU-bmb18, HSTU-bmb20, HSTU-bmb19, and a mixed consortium of these three strains, respectively. These aggregative results suggested a novel model for rice straw deconstruction utilizing hydrolytic enzymes of the consortium, revealing superior efficacy compared to individual strains, and advancing cost-effective, affordable, and sustainable green technology.

Let There Be Light: Genome Reduction Enables Bacillus subtilis to Produce Disulfide-Bonded Gaussia Luciferase

Bacillus subtilis is a major workhorse for enzyme production in industrially relevant quantities. Compared to mammalian-based expression systems, B. subtilis presents intrinsic advantages, such as high growth rates, high space-time yield, unique protein secretion capabilities, and low maintenance costs. However, B. subtilis shows clear limitations in the production of biopharmaceuticals, especially proteins from eukaryotic origin that contain multiple disulfide bonds. In the present study, we deployed genome minimization, signal peptide screening, and coexpression of recombinant thiol oxidases as strategies to improve the ability of B. subtilis to secrete proteins with multiple disulfide bonds. Different genome-reduced strains served as the chassis for expressing the model protein Gaussia Luciferase (GLuc), which contains five disulfide bonds. These chassis lack extracellular proteases, prophages, and key sporulation genes. Importantly, compared to the reference strain with a full-size genome, the best-performing genome-minimized strain achieved over 3000-fold increased secretion of active GLuc while growing to lower cell densities. Our results show that high-level GLuc secretion relates, at least in part, to the absence of major extracellular proteases. In addition, we show that the thiol-disulfide oxidoreductase requirements for disulfide bonding have changed upon genome reduction. Altogether, our results highlight genome-engineered Bacillus strains as promising expression platforms for proteins with multiple disulfide bonds.

Bacillus G7 improves adaptation to salt stress in Olea europaea L. plantlets, enhancing water use efficiency and preventing oxidative stress

In addition to genetic adaptative mechanisms, plants retrieve additional help from the surrounding microbiome, especially beneficial bacterial strains (PGPB) that contribute to plant fitness by modulating plant physiology to fine-tune adaptation to environmental changes. The aim of this study was to determine the mechanisms by which the PGPB Bacillus G7 stimulates the adaptive mechanisms of Olea europaea plantlets to high-salinity conditions, exploring changes at the physiological, metabolic and gene expression levels. On the one hand, G7 prevented photosynthetic imbalance under saline stress, increasing the maximum photosynthetic efficiency of photosystem II (Fv/Fm) and energy dissipation (NPQ) and protecting against photooxidative stress. On the other hand, despite the decrease in effective PSII quantum yield (ΦPSII), net carbon fixation was significantly improved, resulting in significant increases in osmolytes and antioxidants, suggesting an improvement in the use of absorbed energy. Water use efficiency (WUE) was significantly improved. Strong genetic reprogramming was evidenced by the transcriptome that revealed involvement of the ABA-mediated pathway based on upregulation of ABA synthesis- and ABA-sensing-related genes together with a strong downregulation of the PLC2 phosphatase family, repressors of ABA-response elements and upregulation of ion homeostasis-related genes. The ion homeostasis response was activated faster in G7-treated plants, as suggested by qPCR data. All these results reveal the multitargeted improvement of plant metabolism under salt stress by Bacillus G7, which allows growth under water limitation conditions, an excellent trait to develop biofertilizers for agriculture under harsh conditions supporting the use of biofertilizers among the new farming practices to meet the increasing demand for food.

Unraveling the genome of Bacillus velezensis MEP218, a strain producing fengycin homologs with broad antibacterial activity: comprehensive comparative genome analysis

Bacillus sp. MEP218, a soil bacterium with high potential as a source of bioactive molecules, produces mostly C16-C17 fengycin and other cyclic lipopeptides (CLP) when growing under previously optimized culture conditions. This work addressed the elucidation of the genome sequence of MEP218 and its taxonomic classification. The genome comprises 3,944,892 bp, with a total of 3474 coding sequences and a G + C content of 46.59%. Our phylogenetic analysis to determine the taxonomic position demonstrated that the assignment of the MEP218 strain to Bacillus velezensis species provides insights into its evolutionary context and potential functional attributes. The in silico genome analysis revealed eleven gene clusters involved in the synthesis of secondary metabolites, including non-ribosomal CLP (fengycins and surfactin), polyketides, terpenes, and bacteriocins. Furthermore, genes encoding phytase, involved in the release of phytic phosphate for plant and animal nutrition, or other enzymes such as cellulase, xylanase, and alpha 1-4 glucanase were detected. In vitro antagonistic assays against Salmonella typhimurium, Acinetobacter baumanii, Escherichia coli, among others, demonstrated a broad spectrum of C16-C17 fengycin produced by MEP218. MEP218 genome sequence analysis expanded our understanding of the diversity and genetic relationships within the Bacillus genus and updated the Bacillus databases with its unique trait to produce antibacterial fengycins and its potential as a resource of biotechnologically useful enzymes.

Diamide-based screening method for the isolation of improved oxidative stress tolerance phenotypes in Bacillus mutant libraries

IMPORTANCE

During their life cycle, bacteria are exposed to a range of different stresses that need to be managed appropriately in order to ensure their growth and viability. This applies not only to bacteria in their natural habitats but also to bacteria employed in biotechnological production processes. Oxidative stress is one of these stresses that may originate either from bacterial metabolism or external factors. In biotechnological settings, it is of critical importance that production strains are resistant to oxidative stresses. Accordingly, this also applies to the major industrial cell factory Bacillus subtilis. In the present study, we, therefore, developed a screen for B. subtilis strains with enhanced oxidative stress tolerance. The results show that our approach is feasible and time-, space-, and resource-efficient. We, therefore, anticipate that it will enhance the development of more robust industrial production strains with improved robustness under conditions of oxidative stress.

Identification of bioactive compounds of Bacillus velezensis HNA3 that contribute to its dual effects as plant growth promoter and biocontrol against post-harvested fungi

IMPORTANCE

The current study is an extension to our previous work on the plant growth-promoting rhizobacteria (PGPR) Bacillus velezensis HNA3 strain, which comes to confirm and reveals the huge stock of active secondary metabolites produced by HNA3. HNA3-emitted volatile organic compounds (VOCs) have demonstrated the capacity to impede the growth of phytopathogens affecting some fruits and vegetables, even in the absence of direct contact. Additionally, these volatiles enhanced soybean seed germination by breaking seed dormancy and inducing root system development. Furthermore, they promoted seedling growth, giving it prominence in soybean cultivation. The relevance of active volatiles derives from the fact that they can be developed as natural-safe biocontrol agents and plant promoters. This research validates the remarkable bioactivities exhibited by the Bacillus velezensis HNA3 and their potential applications in agriculture as an inoculant, encompassing biocontrol, plant growth promotion, and seed germination activities, thereby offering a safer alternative to hazardous chemicals.

Biodegradation of furfuryl alcohol by indigenous Bacillus species of industrial effluent-contaminated sites: estimation, biokinetics and toxicity assessment of bio-transformed metabolites

Furfuryl alcohol (FA) and other furanic compounds have garnered considerable attention in the quest for sustainable alternatives. FA-based resins have been used in various sectors that entail the release of FA into the environment. Hence, to ensure sustainability in this scenario, devising a dependable approach to its degradation is imperative. Given the crucial role of bacterial strains in the biodegradation of various organic pollutants, this study investigates the microbial degradation of FA, using bacterial strains isolated from sites that are constantly exposed to industrial waste. Three potential isolates were identified as B. paramycoides, B. cereus, and B. tequilensis by 16S rRNA gene sequencing. At a concentration of 300 µg/ml, these isolates demonstrated efficient FA degradation; 60-70% (at 300 µg/ml FA) and 50-60%, (at 500 µg/ml FA). Fourier-transform infrared (FTIR) spectroscopy and High-Performance Liquid Chromatography (HPLC) analysis further supported the result that the bacterial isolates consumed FA as the carbon source. Liquid chromatography-mass spectrometry (LC-MS) facilitates the detection of the major metabolic intermediate product in which FA gets transformed. The prominent peaks at 113 and 119 m/z obtained in the MS spectra of the degraded FA samples indicated the possibility of the conversion of FA into furoic acid or levulinic acid. The phytotoxicity bioassay findings revealed the non-toxic nature of the bio-transformed products as compared to pure FA. This investigation presents the initial documentation of the FA degradative potential of Bacillus strains, thereby augmenting the understanding of the prospective implementation of Bacillus species in industrial waste treatment projects.

Monitoring Phenotype Heterogeneity at the Single-Cell Level within Bacillus Populations Producing Poly-3-hydroxybutyrate by Label-Free Super-resolution Infrared Imaging

Phenotypic heterogeneity is commonly found among bacterial cells within microbial populations due to intrinsic factors as well as equipping the organisms to respond to external perturbations. The emergence of phenotypic heterogeneity in bacterial populations, particularly in the context of using these bacteria as microbial cell factories, is a major concern for industrial bioprocessing applications. This is due to the potential impact on overall productivity by allowing the growth of subpopulations consisting of inefficient producer cells. Monitoring the spread of phenotypes across bacterial cells within the same population at the single-cell level is key to the development of robust, high-yield bioprocesses. Here, we discuss the novel development of optical photothermal infrared (O-PTIR) spectroscopy to probe phenotypic heterogeneity within Bacillus strains by monitoring the production of the bioplastic poly-3-hydroxybutyrate (PHB) at the single-cell level. Measurements obtained on single-point and in imaging mode show significant variability in the PHB content within bacterial cells, ranging from whether or not a cell produces PHB to variations in the intragranular biochemistry of PHB within bacterial cells. Our results show the ability of O-PTIR spectroscopy to probe PHB production at the single-cell level in a rapid, label-free, and semiquantitative manner. These findings highlight the potential of O-PTIR spectroscopy in single-cell microbial metabolomics as a whole-organism fingerprinting tool that can be used to monitor the dynamic of bacterial populations as well as for understanding their mechanisms for dealing with environmental stress, which is crucial for metabolic engineering research.

Effect of weak electrical stimulation on m-dichlorobenzene biodegradation in biotrickling filters: Insights from performance and microbial community analysis

The microbial electrolysis cell coupled with the biotrickling filters (MEC-BTF) was developed for enhancing the biodegradation of gaseous m-dichlorobenzene (m-DCB) through weak electrical stimulation. The maximum removal efficiency and elimination capacity in MEC-BTF were 1.48 and 1.65 times higher than those in open-circuit BTF (OC-BTF), respectively. Weak electrical stimulation had a positive impact on the characteristics of the biofilm. Additionally, microbial community analysis revealed that weak electrical stimulation increased the abundance of key functional genera (e.g., Rhodanobacter and Bacillus) and genes (e.g., catA/E and E1.3.1.32), thereby accelerating reductive dechlorination and ring-opening of m-DCB. Macrogenomic sequencing further revealed that electron transfer pathway in MEC-BTF might be mediated through extracellular electroactive mediators and cytochromes.

degQ associated with the degS/degU two-component system regulates biofilm formation, antimicrobial metabolite production, and biocontrol activity in Bacillus velezensis DMW1

The gram-positive bacterium Bacillus velezensis strain DMW1 produces a high level of antimicrobial metabolites that can suppress the growth of phytopathogens. We investigated the mechanism used by degQ and the degS/degU two-component system to regulate the biocontrol characteristics of DMW1. When degQ and degU were deleted, the biofilm formation, cell motility, colonization activities, and antifungal abilities of ΔdegQ and ΔdegU were significantly reduced compared to wild-type DMW1. The expression levels of biofilm-related genes (epsA, epsB, epsC, and tasA) and swarming-related genes (swrA and swrB) were all down-regulated. We also evaluated the impact on secondary metabolites of these two genes. The degQ and degU genes reduced surfactin and macrolactin production and up-regulated the production of fengycin, iturin, bacillaene, and difficidin metabolites. The reverse transcription-quantitative PCR results were consistent with these observations. Electrophoretic mobility shift assay and microscale thermophoresis revealed that DegU can bind to the promoter regions of these six antimicrobial metabolite genes and regulate their synthesis. In conclusion, we provided systematic evidence to demonstrate that the degQ and degU genes are important regulators of multicellular behaviour and antimicrobial metabolic processes in B. velezensis DMW1 and suggested novel amenable strains to be used for the industrial production of antimicrobial metabolites.

Enhanced biodegradation of phenol by microbial collaboration: Resistance, metabolite utilization, and pH stabilization

Mixed culture of microorganisms is an effective method to remove high concentration of phenol from wastewater. Currently, the mechanism of how microorganisms collaborate to enhance the biodegradation of phenol is still a challenge. In this study, the isolated Bacillus subtilis ZWB1 and Bacillus velezensis ZWB2 were co-cultured to enhance phenol biodegradation, and the mechanism of microbial collaboration was further explored. The co-culture of strains could significantly increase the rate (16.7 mg/L·h, 1000 mg/L) and concentration of phenol degradation (1500 mg/L), comparing with mono-culture of ZWB1 (4.2 mg/L·h, 150 mg/L) and ZWB2 (6.9 mg/L·h, 1000 mg/L), among which the highest degraded concentration of phenol for ZWB1 and ZWB2 was 150 and 1000 mg/L. Further, the mechanism of microbial collaboration to enhance phenol biodegradation was raised: the decrease of antioxidant enzymes, and increase of degrading enzymes and surfactants on content after co-culture, assisted the microorganisms in withstanding phenol; Bacillus subtilis ZWB1 used the metabolites of Bacillus velezensis ZWB2 to promote its growth, and further to degrade phenol rapidly; Bacillus subtilis ZWB1 alleviated the damage, which resulted from the pH drop (5.8) of the fermentation broth during phenol degradation that inhibited the growth and degraded ability of Bacillus velezensis ZWB2, making the pH of fermentation broth stable at 7. Metabolic analysis showed that co-culture of strains could produce more alkaline and buffering compounds and pairs, to stabilize pH and reduce the toxicity of acidity on ZWB2, thus increasing the degradation rate. This study explains the mechanism of microbial collaboration on phenol biodegradation from multiple perspectives, especially pH stabilization, which provides a theoretical basis for the degradation of pollutants by co-culture microorganisms.

Unraveling the molecular mechanisms of selenite reduction: transcriptomic analysis of Bacillus reveals the key role of sulfur assimilation

Selenite biotransformation by microorganisms is an effective detoxification and assimilation process. However, current knowledge of the molecular mechanisms of selenite reduction remains circumscribed. Here, the reduction of Se(IV) by a highly selenite-resistant Bacillus sp. SL (up to 50 mM) was systematically analyzed, and the molecular mechanisms of selenite reduction were investigated. Remarkably, 10 mM selenite was entirely transformed by the strain SL within 20 h, demonstrating a faster conversion rate compared to other microorganisms. Furthermore, glutathione (GSH) and exopolysaccharides (EPS) changes were also monitored during the process. Transcriptomic analysis revealed that the genes of ferredoxin-sulfite oxidoreductase (6.82) and sulfate adenylyltransferase (6.32) were significantly upregulated, indicating that the sulfur assimilation pathway is the primary reducing pathway involved in selenite reduction by strain SL. Moreover, key genes associated with NAD(P)/FAD-dependent oxidoreductases and thioredoxin were significantly upregulated. The reduction of Se(IV) was mediated by multiple pathways in strain SL. To our knowledge, this is the initial report to identify the involvement of sulfur assimilation pathway in selenite reduction for bacillus, which is rare in aerobic bacteria.

Co-application of copper nanoparticles and metal tolerant Bacillus sp. for improving growth of spinach plants in chromium contaminated soil

Chromium (Cr) is classified as a toxic metal as it exerts harmful effects on plants and human life. Bacterial-assisted nano-phytoremediation is an emerging and environment friendly technique that can be used for the detoxification of such pollutants. In current study, pot experiment was conducted in which spinach plants were grown in soil containing chromium (0, 5, 10, 20 mgkg-1) and treated with selected strain of Bacillus sp. and Cu-O nanoparticle (CuONPs). Data related to plant's growth, physiological parameters, and biochemical tests was collected and analyzed using an appropriate statistical test. It was observed that under chromium stress, all plant's growth parameters were significantly enhanced in response to co-application of CuONPs and Bacillus sp. Similarly, higher levels of catalase, superoxide dismutase, malondialdehyde, and hydrogen peroxide were also observed. However, contents of anthocyanin, carotenoid, total chlorophyll, chlorophyll a & b, were lowered under chromium stress, which were raised in response to the combined application of CuONPs and Bacillus sp. Moreover, this co-application has significant positive effect on total soluble protein, free amino acid, and total phenolics. From this study, it was evident that combined application of Bacillus sp. and CuONP alleviated metal-induced toxicity in spinach plants. The findings from current study may provide new insights for agronomic research for the utilization of bacterial-assisted nano-phytoremediation of contaminated sites.

Impact of biosurfactant produced by Bacillus spp. on biodegradation efficiency of crude oil and anthracene

Biosurfactants are surface active molecules generated by various microorganisms, including bacteria, actinobacteria, algae, and fungi. In this study, bacterial strains are isolated from soil contaminated with used motor oil and examined for potential biosurfactant production. A minimum salt medium (MSM), with crude oil as the only carbon source, is used to isolate potential biosurfactant-producing bacterial strains. About 23 strains are isolated, and all are subjected to the primary screening methods for biosurfactant production. Based on the emulsification index, oil displacement, and drop collapse screening methods, two isolates with potential biosurfactant-producing ability are selected for further studies. The synthesis of biosurfactants, crude oil and anthracene biodegradation is carried out with strains DTS1 and DTS2. Both strains show significant outcomes in crude oil degradation. In addition, both strains can utilize anthracene as the sole carbon source. During the degradation course, changes in the growth conditions are continuously monitored by measuring turbidity and pH. In this degradation study, the biosurfactant production aptitude of the isolated strains plays an essential role in increasing the bioavailability of hydrophobic hydrocarbons. These strains are identified down to the molecular level by employing 16S rRNA gene sequencing, and the acquired sequences are submitted to get the accession numbers. These prospective strains can be utilized to remediate hydrocarbon-contaminated environments.

Characterization of the Novel Leaderless Bacteriocin, Bawcin, from Bacillus wiedmannii

The rise of drug-resistant bacteria is a major threat to public health, highlighting the urgent need for new antimicrobial compounds and treatments. Bacteriocins, which are ribosomally synthesized antimicrobial peptides produced by bacteria, hold promise as alternatives to conventional antibiotics. In this study, we identified and characterized a novel leaderless bacteriocin, bawcin, the first bacteriocin to be characterized from a Bacillus wiedmannii species. Chemically synthesized and purified bawcin was shown to be active against a broad range of Gram-positive bacteria, including foodborne pathogens Staphylococcus aureus, Bacillus cereus, and Listeria monocytogenes. Stability screening revealed that bawcin is stable over a wide range of pH (2.0-10.0), temperature conditions (25-100 °C), and against the proteases, papain and pepsin. Lastly, three-dimensional structure homology modeling suggests that bawcin contains a saposin-fold with amphipathic helices and a highly cationic surface that may be critical for membrane interaction and the subsequent cell death of its targets. This study provides the foundational understanding of the activity and properties of bawcin, offering valuable insights into its applications across different antimicrobial uses, including as a natural preservative in food and livestock industries.

Characterization and applications of glutaminase free L-asparaginase from indigenous Bacillus halotolerans ASN9

L-asparaginase (L-ASNase) is a versatile anticancer and acrylamide reduction enzyme predominantly used in medical and food industries. However, the high specificity of L-asparaginase formulations for glutamine, low thermostability, and blood clearance are the major disadvantages. Present study describes production, characterization, and applications of glutaminase free extracellular L-asparaginase from indigenous Bacillus halotolerans ASN9 isolated from soil sample. L-asparaginase production was optimized in M9 medium (containing 0.2% sucrose and 1% L-asparagine) that yielded maximum L-ASNase with a specific activity of 256 U mg-1 at pH 6 and 37°C. L-asparaginase was purified through acetone precipitation and Sephadex G-100 column, yielding 48.9 and 24% recovery, respectively. Enzyme kinetics revealed a Vmax of 466 mM min-1 and Km of 0.097 mM. Purified L-ASNase showed no activity against glutamine. The purified glutaminase free L-ASNase has a molecular mass of 60 kDa and an optimum specific activity of 3083 U mg-1 at pH 7 and 37°C. The enzyme retains its activity and stability over a wide range of pH and temperature, in the presence of selected protein inhibitors (SDS, β-mercaptoethanol), CoCl2, KCl, and NaCl. The enzyme also exhibited antioxidant activity against DPPH radical (IC50 value 70.7 μg mL-1) and anticancer activity against U87 human malignant glioma (IC50 55 μg mL-1) and Huh7 human hepatocellular carcinoma (IC50 37 μg mL-1) cell lines. Normal human embryonic kidney cells (HEK293) had greater than 80% cell viability with purified L-ASNase indicating its least cytotoxicity against normal cells. The present work identified potent glutaminase free L-ASNase from B. halotolerans ASN9 that performs well in a wide range of environmental conditions indicating its suitability for various commercial applications.