Search Results (79)

Background: Here, we report the isolation and identification of a Paenibacillus polymyxa strain from the citizen science project, Swab and Send. P. polymyxa is well known for its production of polymyxin E (colistin), and polymyxin B. Polymyxins are ranked in the highest-priority critically important antimicrobial classification by the WHO and are of particular importance for treating Gram-negative multi-drug-resistant pathogens. Due to their clinical use, most of the literature focusses on these polymyxin variants, and there is sparse genetic research on other polymyxin variants. Methods: The Paenibacillus polymyxa 1G strain was isolated and tested for antimicrobial activity using a combination of on-agar and liquid-based inhibition assays to detect antimicrobial activity against Escherichia coli. The isolate was also tested for activity in liquid media against a panel of isolates showing various resistances to test if our strain could overcome current clinically important resistance mechanisms. Our isolate was whole-genome-sequenced, and bioinformatics was carried out on the resulting sequence to analyse the relevant biosynthetic gene cluster. The cell-free supernatant from the P. polymyxa 1G isolate was also analysed using mass spectrometry to confirm the production of the polymyxin. Results: P. polymyxa 1G was active on agar and resulted in antimicrobial activity, with a 99% reduction in area under the curve when tested in liquid media against E. coli. P. polymyxa 1G did not inhibit the growth of E. coli containing mcr-1 or mcr-4 colistin-resistance genes. Using whole genome sequencing, we are able to describe the biosynthetic gene cluster of the putative polymyxin A, compare the pmxA, pmxB, and pmxE genes to five other polymyxin genes that encode known polymyxin variants, and provide mass spectrometry data that supports the production of polymyxin A₁ (1157 m/z) and A₂ (1143 m/z). Conclusions: Here, we report the isolation and identification of a P. polymyxa strain producing a polymyxin A-like compound that was discovered through the citizen science project, Swab and Send. We add to the genetic and mass spectrometry data for polymyxin A, and demonstrate that this putative polymyxin A, produced naturally by our strain, is unable to overcome the current clinically relevant resistance mechanisms to colistin. Full article

Fusarium head blight (FHB) caused by Fusarium graminearum leads to huge yield losses and mycotoxin contamination in wheat globally. Paenibacillus polymyxa with strong antagonistic activity was preliminarily identified. To clarify the key antifungal component, an extracellular protein was purified via ammonium sulfate precipitation, DEAE-52 anion-exchange and Sephadex G-75 gel filtration chromatography. SDS-PAGE showed a single band at 76 kDa. liquid chromatography–tandem mass spectrometry (LC-MS/MS) analysis confirmed this protein belongs to glycosyl hydrolase family with 86% sequence coverage. Biochemical characterization showed that the crude protein was stable at 40–90 °C and pH 3.0–9.0, sensitive to proteinase K, trypsin and neutral protease. The purified 76 kDa protein exhibited antifungal activity against F. graminearum. The gene encoding this protein was cloned and expressed in Escherichia coli. The renatured recombinant protein p76kd showed comparable antifungal activity to the native protein. This study purified and characterized a 76 kDa protein annotated as a glycosyl hydrolase via LC-MS/MS peptide matching; its antifungal function is presumed to originate from the conserved glycosyl hydrolase domain according to existing homologous research, which is distinct from previously reported lipopeptides or uncharacterized complexes. This protein provides a promising candidate for the biocontrol of FHB and related fungal diseases in cereal crops. Full article

The influence of Bacillus subtilis (Solution A) and Paenibacillus polymyxa (Solution B) bacteria on the properties of conventional concrete with a design compressive strength of f′c = 210 kg/cm² and on the repair of microcracks and fissures was evaluated. Yura Type IP and Frontera Type IP cements were used, together with aggregates from the Chiguata and La Poderosa quarries (Arequipa, Peru). Two mix design methods were applied: ACI 211 and the fineness modulus of the combined aggregates. For microcrack repair, injections of Solutions A and B were applied, followed by either water curing or curing in the corresponding bacterial solution. For water replacement, both solutions were used at concentrations of 10%, 15%, and 20%. Compressive strengths were measured at 7, 14, 21, and 28 days. The results indicate that bacterial incorporation, together with reductions in the effective water-to-cement ratio associated with bacterial solution replacement, was associated with improvements in compressive strength and microcrack repair through mechanisms consistent with calcium carbonate (CaCO₃) precipitation. For the injection group, a maximum strength of 196.09 kg/cm² was obtained. For the water replacement group, a maximum strength of 335.71 kg/cm² was reached, representing a 59.9% increase over the standard design. The P. polymyxa solution consistently outperformed B. subtilis across all groups and concentrations evaluated. These findings suggest that bacterial solutions—particularly P. polymyxa—may represent a promising complementary strategy to improve concrete performance and durability under the evaluated experimental conditions. Full article

Wheat common bunt, caused by Tilletia foetida Liro, is a devastating disease in wheat production. In this study, the antagonistic endophytic bacteria 29-Y2 were screened based on the germination rate of teliospore and the control effect of wheat common bunt. During primary screening, 29-Y2 had the best performance, with a 96.73% inhibition on TFL spore germination. In the deep screening, the control effect of 29-Y2 on wheat common bunt was 66.12% in pots. Based on morphological, physiological, and biochemical characteristics and molecular biological identification, the antagonist 29-Y2 was identified as Paenibacillus polymyxa. The antagonist 29-Y2 promoted the germination rate of wheat seeds and the growth of wheat seedlings at a solution dilution of 10⁻⁵ cfu/mL. In different field trials, the antagonists 29-Y2 both had better control efficiencies of 62.31% and 67.62% for wheat common bunt. In order to further promote the inhibition activities of 29-Y2, the optimal culture condition was 11.1 g/L of glucose, 20 g/L of yeast extract powder, 3.8 g/L of soybean pepyone and 10 g/L of NaCl based on the response surface methodology; the liquid loading volume was 15 mL, of which the inoculant amount accounted for 2%, the pH was 6.8, the temperature was 30 °C and the rotation speed was 186 r/min for 26 h. When the fermentation broth obtained under these cultivation conditions was diluted 10,000 times, the inhibition rate of TFL teliospore germination could reach 80.32%. The fermentation broth control effect in pots improved from 57.77% to 84.17%. It was a promising endophytic bacterium for the prevention and control of wheat common bunt. Full article

Concrete infrastructure in coastal regions is prone to premature degradation due to crack formation under aggressive environmental exposure. Conventional repair methods remain costly and often ineffective. This study evaluates a biomineral self-healing system incorporating Paenibacillus polymyxa spores and calcium carbonate (CaCO₃) to improve the durability and mechanical performance of medium-strength concrete with a design compressive strength of 21 MPa, intended for vulnerable coastal housing. A full factorial experimental program was conducted using three bacterial concentrations (1.0%, 1.5%, 2.0% of mixing water volume) and three CaCO₃ dosages (3%, 5%, 7% as cement replacement). Specimens were pre-cracked under compressive loading, exposed to a simulated coastal environment, and monitored for 28 days. The optimal formulation (2% bacteria + 5% CaCO₃) yielded an 8.8% increase in compressive strength and a 24% increase in flexural strength compared with the control. Crack width reduction reached up to 0.23 mm (65.7%) under wet curing, with effective sealing observed for cracks ≤ 0.5 mm. Recovered compressive strength after healing reached 17.3 MPa, equivalent to 71% of the design strength. These findings demonstrate the potential of P. polymyxa as a viable non-ureolytic agent for self-healing concrete, offering a simple and scalable strategy to extend service life in resource-limited coastal regions while supporting Sustainable Development Goals 9 and 11. Full article

Paenibacillus polymyxa is a promising biocontrol agent based on many applications in agriculture. In this study, characterization of a novel strain JX-1 was performed by various comparative phenotypic assays including cell wall-degrading enzyme activity assay, antagonism in vitro and in planta and multi-omics analysis consisting of whole-genome sequencing and metabolomic analysis. The results showed that JX-1 produced protease, cellulase, and pectinase, with protease activity exceeding other P. polymyxa strains. The supernatant and VOCs produced by JX-1 both contain components that effectively antagonize both bacteria and fungi. JX-1 inhibited Fusarium verticillioides, Sclerotinia sclerotiorum, Botrytis cinerea and Sclerotium rolfsii. Furthermore, it significantly reduced the severity of clubroot in Arabidopsis thaliana and Brassica rapa in planta, resulting in an improvement in the total shoot fresh weight. The closely related P. polymyxa strain JX-2 (ANI = 99.96% compared to strain JX-1) was used for comparative phenotyping and multi-omics analysis that implicated extracellular proteases and some small peptides could be essential for clubroot biocontrol. Genomic analysis of strain JX-1 confirmed that it is indeed P. polymyxa (ANI > 95% compared to reference strains). Moreover, JX-1 harbors predicted carbohydrate-active enzymes (CAZymes), 16 extracellular protease genes, and 17 gene clusters with biosynthetic potential (NRPS/PKS hybrids). Metabolomic profiling of the culture supernatant further identified differential accumulation of hydrophobic-amino-acid-containing small peptides, providing a metabolic basis for the observed antagonism and offering leads for future mechanistic studies. These findings establish JX-1 as a broad-spectrum biocontrol agent against clubroot disease. Full article

Traditional pixian douban is characterized by elevated salt concentrations, often exceeding 12%. Given the established correlation between high-salt diets and various health disorders, the necessity for effective salinity reduction becomes evident. However, the reduction in salt content may result in quality deterioration. To address the adverse effects associated with decreased salt concentration, the strain Paenibacillus polymyxa M17 27-6, which possesses the capability to produce antimicrobial compounds, was used in the fermentation of low-salt pixian douban. Additionally, we employed low-salt uninoculated and high-salt uninoculated groups as fermentation controls, with the entire fermentation cycle lasting 35 d. In terms of safety, microbial diversity sequencing and the content of biogenic amines and aflatoxin B1 were conducted. Microbial diversity sequencing analyses indicated the presence of potentially pathogenic Escherichia and Shigella, as well as the spoilage-causing Trichosporon and Issatchenkia, in the uninoculated low-salt group, whereas no contaminating bacteria were detected in the inoculated group. Relative to the uninoculated low-salt group, levels of aflatoxin B1 and biogenic amines were significantly reduced. In terms of quality and volatiles, compared to the uninoculated high-salt group, concentrations of amino acid nitrogen and total acids increased to 0.93 g/100 g and 1.21 g/100 g, respectively, alongside significantly enhanced levels of organic acids and antioxidant activity. At the same time, volatile compound content and abundance increased. In conclusion, the incorporation of P. polymyxa M17 27-6 in the production of low-salt broad-bean paste effectively enhances quality and safety and provides a theoretical basis for developing low-salt pixian douban products. Full article

Polymyxins, including polymyxin B (PMB), are last-resort antibiotics against multidrug-resistant Gram-negative infections in humans and livestock. Residual polymyxins from wastewater and manure can accumulate in soil, facilitating the emergence and spread of polymyxin resistance. Paenibacillus polymyxa, a natural polymyxin producer used in crop cultivation, may increase soil polymyxin burden. Since PMB strongly adsorbs to soil, its reliable quantification has been challenging. To address this, the extraction solvent and solid-phase extraction procedure were optimized to improve recovery and reduce matrix effects. We developed and validated a UPLC-MS/MS method to quantify PMB in soil. The method showed linearity (10–1000 ng/g), with a limit of detection of 0.86 ng/g and a limit of quantification of 2.12 ng/g. Method validation confirmed acceptable analytical performance. A 28-day monitoring of PMB in soil inoculated with varying P. polymyxa doses revealed a dose-dependent increase over the first 14 days, followed by a decline; PMB remained detectable on day 28. Ecological risk assessment using the risk quotient (RQ) indicated that PMB levels in the high-dose group (2 × 10⁸ CFU/100 g) approached the high-risk threshold (RQ ≥ 1) on day 14, while lower doses posed low to medium risk. This work provides a soil PMB quantification method and insight into the ecological risk of P. polymyxa application. Full article

The undefined microbial ecology of Aconitum carmichaelii root rot in western Yunnan constrains the advancement of eco-friendly control strategies. The identification of potential pathogenic determinants affecting A. carmichaelii growth is imperative for sustainable cultivation and ecosystem integrity. High-throughput sequencing was employed to profile microbial communities across four critical niches, namely rhizosphere soil, tuberous root epidermis, root endosphere, and fibrous roots of healthy and diseased A. carmichaelii. The physicochemical properties of corresponding rhizosphere soils were concurrently analyzed. Putative pathogens were isolated from diseased rhizospheres and tubers through culturing with Koch’s postulates validation, while beneficial microorganisms exhibiting antagonism against pathogens and plant growth-promoting (PGP) traits were isolated from healthy rhizospheres. Highly virulent strains (2F14, FZ1, L23) and their consortia were targeted for suppression. Strain DX3, demonstrating optimal PGP and antagonistic capacity in vitro, was selected for pot trials evaluating growth enhancement and disease control efficacy. Significant disparities in rhizosphere soil properties and bacterial/fungal community structures were evident between healthy and diseased cohorts. Fifteen putative pathogens spanning eight species across four genera were isolated: Fusarium solani, F. avenaceum, Clonostachys rosea, Mucor racemosus, M. irregularis, M. hiemalis, Serratia liquefaciens, and S. marcescens. Concurrently, eight PGP biocontrol strains were identified: Bacillus amyloliquefaciens, B. velezensis, B. subtilis, B. pumilus, and Paenibacillus polymyxa. Pot trials revealed that Bacillus spp. enhanced soil physiochemical properties through nitrogen fixation, phosphate solubilization, potassium mobilization, siderophore production, and cellulose degradation, significantly promoting plant growth. Critically, DX3 inoculation elevated defense-related enzyme activities in A. carmichaelii, enhanced host resistance to root rot, and achieved >50% disease suppression efficacy. This work delineates key pathogenic determinants of Yunnan A. carmichaelii root rot and identifies promising multifunctional microbial resources with dual PGP and biocontrol attributes. Our findings provide novel insights into rhizosphere microbiome-mediated plant health and establish a paradigm for sustainable disease management. Full article

Microbially mediated biological nitrogen fixation is pivotal to sustainable agricultural development. However, optimizing nitrogenase activity in native biological nitrogen-fixing bacteria has been hindered by the complexities of genetic manipulation. Heterologous expression has served as a foundational strategy for engineering next-generation nitrogen-fixing microbial agents. In this study, genomic analysis of Paenibacillus polymyxa CR1 revealed an 11 kb nitrogen-fixing (nif) gene cluster. The nif cluster was first synthesized and then assembled using ExoCET technology and finally integrated into the genome of Bacillus subtilis 168 via double-exchange recombination. RT-PCR confirmed the transcription of the nif cluster; however, no nitrogenase activity was detected in the acetylene reduction assay. A promoter replacement strategy (replacing the native promoter with P_veg) enabled B. subtilis to produce active nitrogenase. However, stronger promoters—namely, P₄₃ and P_tp2—did not further enhance nitrogenase activity. This demonstrates that promoter selection requires balancing transcriptional strength with systemic compatibility, particularly for metalloenzymes demanding precise cofactor assembly. This is the first report describing the heterologous expression of the nif gene cluster in B. subtilis, establishing a foundation for engineering high-efficiency nitrogen-fixing biofertilizers. Full article

Rhizosphere microorganisms play pivotal roles in mitigating the challenges associated with continuous cropping in melon cultivation. While grafting and plant growth-promoting rhizobacteria (PGPR) independently influence rhizosphere microbial communities, their combined effects remain largely unexplored. This study investigates the synergistic regulation of Paenibacillus polymyxa NBmelon-1 inoculation and grafting on rhizosphere microbiome assembly, plant performance, and disease resistance in melon self-rootstocks. Field experiments demonstrated that NBmelon-1 inoculation significantly enhanced rootstock stem diameter (95.3% increase in spring) and root development, achieving a graft survival rate exceeding 95%. The combined treatment (NB+GJ) increased scion fruit yield by 29.8% in autumn and 36.5% in spring, as well as the single-fruit weight by 22.5% in autumn and 37.3% in spring, while maintaining fruit morphology. Integrated 16S rRNA and ITS sequencing revealed that the NB+GJ treatment selectively enriched antagonistic bacterial phyla (e.g., Firmicutes and Actinobacteriota) and suppressed pathogenic fungi (e.g., Fusarium and Melanconiella). Seasonal shifts in microbial diversity and functional gene profiles underscored the dynamic interplay between treatments and environmental factors. These findings establish a novel strategy for optimizing melon self-rootstock grafting systems and sustainably managing soil-borne diseases. Full article

Fusarium root rot, a destructive soil-borne fungal disease, necessitates eco-friendly biocontrol strategies. This study developed a microbial seed-coating approach using the antagonistic strain Paenibacillus polymyxa ZF129, formulated into a microencapsulated powder (10⁸ CFU/g) and a suspension (CS-ZF129). CS-ZF129 application enhanced cucumber resistance, achieving 46.30 ± 0.02% disease suppression while promoting root growth. The maximum increase in the fresh weight of the root in the promotion of rectangular growth was 47.16%. The colonization dynamics of ZF129 in the rhizosphere were systematically tracked, revealing its antagonistic correlation with Fusarium proliferation. An enzymatic activity analysis further uncovered the underlying regulatory mechanisms, demonstrating induced defense responses through pathogenesis-related protein activation. These findings highlight ZF129’s dual functionality as a biocontrol agent and a plant growth promoter, offering a sustainable strategy against soil-borne pathogens. Full article

Fusarium oxysporum is a fungal plant pathogen for over 100 agricultural crop species. There are strategies for managing Fusarium wilt, including antagonistic bacteria that offer a promising and sustainable effect. In this work, among the various endophytic bacterial strains, Paenibacillus polymyxa EB.KN35 was selected as the best antifungal strain against F. oxysporum. For eco-friendly biomass production of this bacterium, some agricultural byproducts were tested for cultivation, and a soybean processing byproduct (SPBP) was found to be a suitable C/N source for P. polymyxa EB.KN35 fermentation. The utilization of a 14 L bioreactor system for P. polymyxa EB.KN35 fermentation achieved a high biomass productivity (3.46 × 10¹¹ CFU/mL) in a short time (8 h). In bioactive compound analysis, EB.KN35 was found to be secreting several plant growth-promoting compounds such as GA3, IAA, kinetin, and zeatin (via HPLC) and eleven volatile compounds (via GC–MS). The docking study indicated that some volatile compounds (1, 2, 4, and 9) may play a significant role in inhibiting F. oxysporum. The study results highlight the potential for reusing a soybean processing byproduct as a C/N source for the bioproduction of P. polymyxa EB.KN35 with potential use as a biocontrol agent and biofertilizer. Full article

A field trial was conducted on eight-year-old ‘Anna’ apple (Malus domestica) trees from 2021 to 2023 in northern Egypt. The objective of this study was to determine the effects of replacing mineral fertilizer with compost and microorganism applications. Treatments were prepared using combinations of three mineral fertilizer NPK (nitrogen (N), phosphorus (P) and potassium (K)) levels (75% recommended NPK rate, 50% and 25% recommended rate), with two compost levels (with/without) and two bacteria/fungi biological blend (PGPM) levels (with/without). This design resulted in 12 treatments in addition to a control treatment consisting of the full NPK recommended rate (100% NPK). Leaf nutrient concentrations, vegetative growth, fruit set percentage, fruit drop percentage, yield and fruit quality were measured in 2022 and 2023. Our results indicated that vegetative growth parameters were significantly influenced by the fertilizer treatments in both seasons. The application of 75% NPK + compost + PGPM or 50% NPK + compost + PGPM significantly increased shoot length, shoot diameter, leaf area and leaf-specific weight compared with the control (100% NPK). The greatest values of leaf nutrients and production and quality parameters were obtained with treatments 75% NPK + compost + PGPM or 50% NPK + compost + PGPM. Applying 75% NPK + compost + PGPM or 50%NPK + compost + PGPM increased total soluble solids and anthocyanin concentrations but reduced fruit nitrate and nitrite levels compared with the control (100% NPK). This study shows that it is possible to reduce mineral fertilizer application by 25–50% while improving the yield if compost and microbial inoculants are applied. Full article

Microalgal biotechnology is gaining attention due to its potential to produce pigments, lipids, biofuels, and value-added products. However, challenges persist in terms of the economic viability of microalgal lipid production in photobioreactors due to slow growth rates, expensive media, complex downstream processing, limited product yields, and contamination risks. Recent studies suggest that co-cultivating microalgae with bacteria can enhance the profitability of microalgal bioprocesses. Immobilizing bacteria offers advantages such as protection against shear forces, the prevention of overgrowth, and continuous product secretion. Previous work has shown that biopolymeric immobilization of Paenibacillus polymyxa enhances 2,3-butanediol production. In this study, a novel co-fermentation process was developed by exploiting the chemical crosstalk between a freshwater microalga Scenedesmus obliquus, also known as Tetradesmus obliquus, and an immobilized plant-growth-promoting bacterium, Paenibacillus polymyxa. This co-cultivation resulted in increased metabolite production, with a 1.5-fold increase in the bacterial 2,3-butanediol concentration and a 3-fold increase in the microalgal growth rates compared to these values in free-cell co-cultivation. Moreover, the co-culture with the immobilized bacterium exhibited a 5-fold increase in the photosynthetic pigments and a 3-fold increase in the microalgal lipid concentration compared to these values in free-cell co-cultivation. A fixed bed photobioreactor was further constructed, and the co-cultivation bioprocess was implemented to improve the bacterial 2,3-butanediol and microalgal lipid production. In conclusion, this study provides conclusive evidence for the potential of co-cultivation and biopolymeric immobilization techniques to enhance 2,3-butanediol and lipid production. Full article