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.

Whole genome sequencing provides evidence for Bacillus velezensis SH-1471 as a beneficial rhizosphere bacterium in plants

Bacillus is widely used in agriculture due to its diverse biological activities. We isolated a Bacillus velezensis SH-1471 from the rhizosphere soil of healthy tobacco, which has broad-spectrum antagonistic activity against a variety of plant pathogenic fungi such as Fusarium oxysporum, and can be colonized in the rhizosphere of a variety of plants. This study will further explore its mechanism by combining biological and molecular biology methods. SH-1471 contains a ring chromosome of 4,181,346 bp with a mean G + C content of 46.18%. We identified 14 homologous genes related to biosynthesis of resistant secondary metabolite, and three clusters encoded potential new antibacterial substances. It also contains a large number of genes from colonizing bacteria and genes related to plant bacterial interactions. It also contains genes related to environmental stress, as well as genes related to drug resistance. We also found that there are many metabolites in the strain that can inhibit the growth of pathogens. In addition, our indoor pot test found that SH-1471 has a good control effect on tomato wilt, and could significantly improve plant height, stem circumference, root length, root weight, and fresh weight and dry weight of the aboveground part of tomato seedlings. Therefore, SH-1471 is a potential biological control strain with important application value. The results of this study will help to further study the mechanism of SH-1471 in biological control of plant diseases and promote its application.

The sprT Gene of Bacillus velezensis FZB42 Is Involved in Biofilm Formation and Bacilysin Production

Bacillus velezensis FZB42, a representative strain of plant-growth-promoting rhizobacteria (PGPR), can form robust biofilm and produce multiple antibiotics against a wild range of phytopathogens. In this study, we observed different biofilm morphology of the mutant Y4, derived from a TnYLB-1 transposon insertion library of B. velezensis FZB42. We identified that the transposon was inserted into the sprT gene in Y4. Our bioinformatics analysis revealed that the SprT protein is an unstable hydrophilic protein located in the cytoplasm. It is highly conserved in Bacillus species and predicted to function as a metalloprotease by binding zinc ions. We also demonstrated that ΔsprT significantly reduced the swarming ability of FZB42 by ~5-fold and sporulation capacity by ~25-fold. In addition, the antagonistic experiments showed that, compared to the wild type, the ΔsprT strain exhibited significantly reduced inhibition against Staphylococcus aureus ATCC-9144 and Phytophthora sojae, indicating that the inactivation of sprT led to decreased production of the antibiotic bacilysin. The HPLC-MS analysis confirmed that bacilysin was indeed decreased in the ΔsprT strain, and qPCR analysis revealed that ΔsprT down-regulated the expression of the genes for bacilysin biosynthesis. Our results suggest that the sprT gene plays a regulatory role in multiple characteristics of B. velezensis FZB42, including biofilm formation, swarming, sporulation, and antibiotic production.

Mechanism of Cr(VI) removal by efficient Cr(VI)-resistant Bacillus mobilis CR3

Cr(VI) is a hazardous environmental pollutant that poses significant risks to ecosystems and human health. We successfully isolated a novel strain of Bacillus mobilis, strain CR3, from Cr(VI)-contaminated soil. Strain CR3 showed 86.70% removal capacity at 200 mg/L Cr(VI), and a good Cr(VI) removal capacity at different pH, temperature, coexisting ions, and electron donor conditions. Different concentrations of Cr(VI) affected the activity of CR3 cells and the removal rate of Cr(VI), and approximately 3.46% of total Cr was immobilized at the end of the reaction. The combination of SEM-EDS and TEM-EDS analysis showed that Cr accumulated both on the cell surface and inside the cells after treatment with Cr(VI). XPS analysis showed that both Cr(III) and Cr(VI) were present on the cell surface, and FTIR results indicated that the presence of Cr on the cell surface was mainly related to functional groups, such as O-H, phosphate, and -COOH. The removal of Cr(VI) was mainly achieved through bioreduction, which primarily occurred outside the cell. Metabolomics analysis revealed the upregulation of five metabolites, including phenol and L-carnosine, was closely associated with Cr(VI) reduction, heavy metal chelation, and detoxification mechanisms. In addition, numerous metabolites were linked to cellular homeostasis exhibited differential expression. Cr(VI) exerted inhibitory effects on the division rate and influenced critical pathways, including energy metabolism, nucleotide metabolism, and amino acid synthesis and catabolism. These findings reveal the molecular mechanism of Cr(VI) removal by strain CR3 and provide valuable insights to guide the remediation of Cr(VI)-contaminated sites.

Antifungal Effect of Bacillus velezensis ZN-S10 against Plant Pathogen Colletotrichum changpingense and Its Inhibition Mechanism

In order to optimize crop production and mitigate the adverse impacts associated with the utilization of chemical agents, it is necessary to explore new biocontrol agents. Bacillus velezensis has been widely studied as a biocontrol agent because of its efficient and ecofriendly plant disease control mechanisms. This study shows that the strain ZN-S10 effectively reduces the area of leaf spots caused by the pathogen Colletotrichum changpingense ZAFU0163-1, which affects conidia production and germination, inhibits mycelium growth, and induces mycelium deformation. In antifungal experiments with crude extracts, we observed a delay in the cell cycle of conidia, which may be responsible for the inhibition of conidial germination. Among the bioactive metabolites detected through integrated LC-MS- and GC-MS-based untargeted metabolomics, 7-O-Succinyl macrolactin A, telocinobufagin, and surfactin A may be the main antifungal metabolites of strain ZN-S10. The presence of 7-O-Succinyl macrolactin A could explain the cell damage in germ tubes. This is the first report of telocinobufagin detected in B. velezensis. These results are significant for understanding the inhibitory mechanisms employed by B. velezensis and should serve as a reference in the production of biocontrol agents.

Serine peptidase Vpr forms enzymatically active fibrils outside Bacillus bacteria revealed by cryo-EM

Bacteria develop a variety of extracellular fibrous structures crucial for their survival, such as flagella and pili. In this study, we use cryo-EM to identify protein fibrils surrounding lab-cultured Bacillus amyloiquefaciens and discover an unreported fibril species in addition to the flagellar fibrils. These previously unknown fibrils are composed of Vpr, an extracellular serine peptidase. We find that Vpr assembles into fibrils in an enzymatically active form, potentially representing a strategy of enriching Vpr activities around bacterial cells. Vpr fibrils are also observed under other culture conditions and around other Bacillus bacteria, such as Bacillus subtilis, which may suggest a general mechanism across all Bacillus bacterial groups. Taken together, our study reveals fibrils outside the bacterial cell and sheds light on the physiological role of these extracellular fibrils.

Food safety and biological control; genomic insights and antimicrobial potential of Bacillus velezensis FB2 against agricultural fungal pathogens

Development of natural, broad-spectrum, and eco-friendly bio-fungicides is of high interest in the agriculture and food industries. In this context, Bacillus genus has shown great potential for producing a wide range of antimicrobial metabolites against various pathogens. A Bacillus velezensis strain FB2 was isolated from an agricultural field of National Institute for Biotechnology and Genetic Engineering (NIBGE) Faisalabad, Pakistan, exhibiting good antifungal properties. The complete genome of this strain was sequenced, and its antifungal potential was assayed by dual culture method. Moreover, structural characterization of its antifungal metabolites, produced in vitro, were studied. Genome analysis and mining revealed the secondary metabolite gene clusters, encoding non-ribosomal peptides (NRPs) production (e.g., surfactin, iturin and fengycin) and polyketide (PK) synthesis (e.g., difficidin, bacillaene and macrolactin). Furthermore, the Bacillus velezensis FB2 strain was observed to possess in vitro antifungal activity; 41.64, 40.38 and 26% growth inhibition against major fungal pathogens i.e. Alternaria alternata, Fusarium oxysporum and Fusarium solani respectively. Its lipopeptide extract obtained by acid precipitation method was also found effective against the above-mentioned fungal pathogens. The ESI-MS/MS analysis indicated various homologs of surfactin and iturin-A, responsible for their antifungal activities. Overall, this study provides a better understanding of Bacillus velezensis FB2, as a promising candidate for biocontrol purposes, acting in a safe and sustainable way, to control plant pathogens.

Genome mining conformance to metabolite profile of Bacillus strains to control potato pathogens

Biocontrol agents are safe and effective methods for controlling plant disease pathogens, such as Fusarium solani, which causes dry wilt, and Pectobacterium spp., responsible for potato soft rot disease. Discovering agents that can effectively control both fungal and bacterial pathogens in potatoes has always presented a challenge. Biological controls were investigated using 500 bacterial strains isolated from rhizospheric microbial communities, along with two promising biocontrol strains: Pseudomonas (T17-4 and VUPf5). Bacillus velezensis (Q12 and US1) and Pseudomonas chlororaphis VUPf5 exhibited the highest inhibition of fungal growth and pathogenicity in both laboratory (48%, 48%, 38%) and greenhouse (100%, 85%, 90%) settings. Q12 demonstrated better control against bacterial pathogens in vivo (approximately 50%). Whole-genome sequencing of Q12 and US1 revealed a genome size of approximately 4.1 Mb. Q12 had 4413 gene IDs and 4300 coding sequences, while US1 had 4369 gene IDs and 4255 coding sequences. Q12 exhibited a higher number of genes classified under functional subcategories related to stress response, cell wall, capsule, levansucrase synthesis, and polysaccharide metabolism. Both Q12 and US1 contained eleven secondary metabolite gene clusters as identified by the antiSMASH and RAST servers. Notably, Q12 possessed the antibacterial locillomycin and iturin A gene clusters, which were absent in US1. This genetic information suggests that Q12 may have a more pronounced control over bacterial pathogens compared to US1. Metabolic profiling of the superior strains, as determined by LC/MS/MS, validated our genetic findings. The investigated strains produced compounds such as iturin A, bacillomycin D, surfactin, fengycin, phenazine derivatives, etc. These compounds reduced spore production and caused deformation of the hyphae in F. solani. In contrast, B. velezensis UR1, which lacked the production of surfactin, fengycin, and iturin, did not affect these structures and failed to inhibit the growth of any pathogens. Our findings suggest that locillomycin and iturin A may contribute to the enhanced control of bacterial pectolytic rot by Q12.

Remediation of fomesafen contaminated soil by Bacillus sp. Za: Degradation pathway, community structure and bioenhanced remediation

Fomesafen is a diphenyl ether herbicide used to control the growth of broadleaf weeds in bean fields. The persistence, phytotoxicity, and negative impact on crop rotation associated with this herbicide have led to an increasing concern about the buildup of fomesafen residues in agricultural soils. The exigent matter of treatment and remediation of soils contaminated with fomesafen has surfaced. Nevertheless, the degradation pathway of fomesafen in soil remains nebulous. In this study, Bacillus sp. Za was utilized to degrade fomesafen residues in black and yellow brown soils. Fomesafen's degradation rate by strain Za in black soil reached 74.4%, and in yellow brown soil was 69.2% within 30 days. Twelve intermediate metabolites of fomesafen were identified in different soils, with nine metabolites present in black soil and eight found in yellow brown soil. Subsequently, the degradation pathway of fomesafen within these two soils was inferred. The dynamic change process of soil bacterial community structure in the degradation of fomesafen by strain Za was analyzed. The results showed that strain Za potentially facilitate the restoration of bacterial community diversity and richness in soil samples treated with fomesafen, and there were significant differences in species composition at phylum and genus levels between these two soils. However, both soils shared a dominant phylum and genus, Actinobacteriota, Proteoobacteria, Firmicutes and Chloroflexi dominated in two soils, with a high relative abundance of Sphingomonas and Bacillus. Moreover, an intermediate metabolite acetaminophen degrading bacterium, designated as Pseudomonas sp. YXA-1, was isolated from yellow brown soil. When strain YXA-1 was employed in tandem with strain Za to remediate fomesafen contaminated soil, the degradation rate of fomesafen markedly increased. Overall, this study furnishes crucial insights into the degradation pathway of fomesafen in soil, and presents bacterial strain resources potentially beneficial for soil remediation in circumstances of fomesafen contamination.

Endophytic Bacillus sp. R1 and Its Roles in Assisting Phytoremediation and Alleviating the Toxicity of Aluminum Combined Phenanthrene Contaminations in Brassica napus

The release of organic and inorganic contaminants into soil from industry, agriculture, and urbanization has become a major issue of international concern, particularly the heavy metals such as aluminum (Al) and the chemical phenanthrene (PHE). Due to their potential toxicity and non-biodegrade in the environment, efficient remediation methods are urgently needed. Recently, research has comprehensively discussed using plants and their endophytes in bioremediation efforts. Endophytic Bacillus sp. R1, isolated from Brassica napus permanently contaminated with Al and PHE, has growth-promoting properties and can efficiently detoxify these contaminants. The pot experiment indicated that compared to the Al combined PHE contaminated soil alone treatment, the R1 treatment led to increased Al accumulation in canola roots across different levels of PHE, Al, and combined PHE and Al contamination. However, Al accumulation in canola shoots and seeds remained unchanged for all treatments. Moreover, PHE in canola roots and shoots was decreased by R1 inoculation and thereby reducing 26.12-60.61% PHE translocated into canola seeds. Additionally, R1 inoculation significantly increased the proportion of extractable Al and, decreased the proportion of acid-soluble inorganic Al and humic-acid Al, but did not affect the concentration of organically complexed Al. In summary, endophyte R1 can degrade PHE, improve canola roots' Al uptake by increasing soil available Al, and scavenge the reactive oxygen species through production of antioxidant enzymes to help alleviate the toxicity of canola co-contaminated with aluminum and phenanthrene.

Induced Resistance Mechanism of Bacillus velezensis S3-1 Against Pepper Wilt

In recent years, pepper wilt has emerged as a pivotal constraint on pepper yield augmentation. Bacillus velezensis S3-1, with a wide array of hosts, can be used as both a biocontrol agent and biofertilizer. Nonetheless, the precise mechanisms underpinning its employment in combating pepper wilt remain cloaked in ambiguity. In our study, we found that B. velezensis S3-1 could significantly inhibit Fusarium sp. F1T that caused pepper wilt. S3-1 could effectively inhibit both the growth and germination of F1T conidia, leading to a reduction in the spore germination percentage from 83.2 to 37.1% in vitro experiments. Additionally, leaf detachment experiments revealed that the volatile compounds produced by S3-1 could inhibit the spread of pepper leaf spot area. Moreover, we observed a significant decrease in the content of malondialdehyde (MDA) in pepper treated with S3-1, along with a significant increase in the content of soluble protein, polyphenol oxidase (PPO), peroxidase (POD), and phenylalanine ammonia-lyase (PAL) in pepper. Furthermore, RT-PCR analysis showed that the expression of the defense genes CaPR 1 and CaPIN II in pepper after treatment with S3-1 was significantly upregulated, suggesting that S3-1 had the potential to induce systemic resistance in pepper, thereby enhancing its disease resistance. Hence, our findings suggest that S3-1 can be a promising biocontrol agent for managing pepper wilt in modern agriculture.

Enhanced degradation of petroleum in saline soil by nitrogen stimulation and halophilic emulsifying bacteria Bacillus sp. Z-13

Remediation of petroleum-contaminated soil is a widely concerned challenge. As an ecofriendly method, the performance improvement of indigenous microbial degradation is facing the bottleneck. In this study, a strain with high efficiency of petroleum degradation was isolated from the petroleum-contaminated soil and identified and named as Bacillus sp. Z-13. The strain showed the ability to produce lipopeptide surfactant which could improve 66% more petroleum hydrocarbons eluted. Strain Z-13 and its biosurfactant exhibited broad environmental adaptability to salinity (0-8%), pH (6-9) and temperature (15-45 °C). With the addition of strain Z-13 and the stimulation of NH4Cl, up to 59% of the petroleum in the contaminated soil was removed at the carbon to nitrogen ratio of 10. Microbial community analysis showed that petroleum-degrading bacteria, represented by Bacillus, became the dominant species at genus level and played an important role in the remediation. Additionally, ammonium stimulation facilitated both pathways of ammonium assimilation and nitrification in native microorganisms to achieve efficient degradation of petroleum hydrocarbons. This study could provide a promising approach for stable, environmental-friendly and efficient remediation of petroleum-contaminated soil.