Search Results (426)

The PGPR strain of Bacillus amyloliquefaciens MHR24 (MHR24) was recently reported as a strong biocontrol strain. In this study, MHR24 was used to investigate phyllosphere effects during inoculations of tomato leaves (Solanum lycopersicum L.). When MHR24 was inoculated on foliar tissue, it caused apical chlorosis symptoms at 3–6 days after infiltration or submersion, which suggests that the bacterium may adopt a potentially pathogenic lifestyle in the phyllosphere. In order to detect the MHR24 interaction with the plant, it was stained with the commercial fluorophore 8-hydroxypyrene-1,3,6-trisulfonic acid trisodium salt, selected from a pyrene series bearing diverse functional groups, based on several in vitro staining assays. Fluorescence used as a detection signal was observed by LSCM mainly in the vascular bundles, suggesting that rhizobacteria may preferentially colonize these tissue regions. Molecular docking, performed by analyzing the possible interactions between the outer membrane protein assembly factor BamB of the family protein B. amyloliquefaciens and the fluorophore, indicates that hydrogen bonds with serine 126 (SER126), serine 182 (SER182), isoleucine 180 (ILE180), and tryptophan 66 (TRP66), charges attraction and π-stacking with TRP66, and non-bonded attractions with leucine 224 (LEU224) can occur, which likely gives rise to a stable complex. These results are important in view of the application of MHR24 as part of a sustainable approach for increasing tomato crop production. Full article

Integrating biochar with plant growth-promoting rhizobacteria (PGPR) is a promising strategy for sustainable soil management; however, the synergistic mechanisms governing rhizosphere microbial assembly remain inadequately understood. In this study, we investigated the combined effects of maize biochar (YM) and Bacillus amyloliquefaciens (BA) on tomato performance, soil physicochemical properties, and bacterial community dynamics via a controlled pot experiment. The results demonstrated that the synergistic treatment (YMBA) significantly enhanced tomato yield by 18.3% compared to the control, outperforming individual applications. This promotion was coupled with a comprehensive improvement in soil fertility, characterized by significant increases in soil organic matter (SOM), available nutrients (N, P, and K), and the activities of urease and acid phosphatase. High-throughput sequencing revealed that YMBA treatment significantly restructured the rhizosphere bacterial community, significantly increasing microbial richness and diversity. Notably, the synergistic application promoted the recruitment of beneficial taxa, particularly within the phylum Pseudomonadota. Mantel test analysis further elucidated that SOM and available phosphorus (AP) were the primary environmental drivers shaping the bacterial community turnover. Our findings suggest that biochar acts as a functional niche that facilitates B. amyloliquefaciens colonization and modulates the indigenous microbiota, providing a theoretical framework for utilizing cross-trophic synergies to optimize crop productivity and soil health. Full article

Microbial communities associated with the rhizosphere and phyllosphere are recognized as fundamental components influencing essential plant processes, including nutrient acquisition, growth promotion, and tolerance to stress. Biological control agents (BCAs), such as Trichoderma spp. and Bacillus spp., are widely applied in citrus crops. However, while BCAs effectiveness against plant pathogens is widely established, their resulting impact on indigenous, non-target bacterial and fungal communities remains poorly understood. The aim of this study was to evaluate the non-target effects of two commercial microbial formulations—one containing Trichoderma asperellum ICC 012 and T. gamsii ICC 080, and the other Bacillus amyloliquefaciens QST 713—on the resident microbiomes of Citrus volkameriana seedlings by using the amplicon-based metagenomic analysis, targeting the 16S rRNA and ITS1 regions. The application of the Trichoderma formulation as a soil drench in the rhizosphere resulted in minimal changes to the overall composition and diversity (α- and β-diversity) of the bacterial communities. This stability is considered a desirable trait for overall soil health. However, specific taxonomic changes were observed, such as a notable decrease in the genus Rhodococcus (0.4% vs. 1.5% in controls) among bacteria. In the fungal communities, the treatment led to a significant shift in phylum relative abundance, characterized by an increase in Basidiomycota (38% vs. 28% in controls) and a corresponding decrease in Ascomycota (51% vs. 56% in controls). Successful colonization was confirmed by a substantially higher relative abundance of the inoculated Trichoderma genus compared to control plants (1.4% vs. 0.1% in controls). Conversely, the foliar application of the Bacillus product induced a substantial restructuring of the phyllosphere bacterial community. This treatment caused a statistically significant reduction in bacterial α-diversity and a clear differentiation in community composition (β-diversity) relative to untreated controls. The successful colonization by the BCA resulted in the dominance of the Bacillus genus in the treated samples (27% vs. 2% in controls). Importantly, this ecological shift was accompanied by the enrichment of other beneficial bacterial taxa, including Sphingomonas (15% vs. 4% in controls) and the Burkholderia-Caballeronia-Paraburkholderia group (4% vs. 2% in controls). While fungal phyla abundances remained generally stable in the phyllosphere, specific genera such as Cladosporium (15% vs. 23% in controls) and Symmetrospora (21% vs. 13% in controls) prevailed post-treatment. In conclusion, these findings highlight the importance of considering non-target microbiome shift when implementing microbial biocontrol strategies in citrus production systems, since in this study was demonstrated that commercial BCAs exert a markedly differential influence based on the compartment of application: Trichoderma promoted ecological stability in the rhizosphere, whereas Bacillus induced a directional community shift in the phyllosphere. Full article

Naturally abundant endophytes colonize plants internally without causing harm to their host plants. Endophytes are likely to occupy the same ecological niches as phytopathogens and thus have a high potential to be effective biological control agents. Their demonstrated ability to suppress more than one plant pathogen suggests that they can offer a viable alternative to chemical fungicides and a strategy for decreasing the inoculum potential of soil-borne pathogens. Some biocontrol endophytes are also known to improve soil health and the overall health of plants. However, the results in greenhouse studies do not always translate to consistent field efficacy. In this study, the efficacy of three endophytic bacterial isolates (PRT (Bacillus subtilis), PSL (Bacillus amyloliquefaciens), and IMC8 (Bacillus thuringiesis) were evaluated against Phytophthora capsici in a field environment and compared with two commercial biological fungicides, Serenade^® (Bayer Crop Science, St Louis MO, USA) and Double Nickel^® (Certis Biologicals, Columbia, MO, USA), and water control. Plants were inoculated with the bacteria strains using seed treatment for early plant colonization before transplanting to a field infested with P. capsici. Treatments with commercial bio-fungicides followed label recommendations. Data on plant growth vigor, disease severity, number of fruits, fruit size, total yield per plant, and percent of diseased fruits displayed significant differences between the bacteria treatments. While PRT was the best treatment for most traits, followed by PSL on pepper, PSL and Double Nickel were the best treatments on tomatoes. IMC8 was best for plant vigor and larger fruit size, but with fewer fruits per plant on both crops. This study suggests bacterial isolates PRT, PSL, and IMC8 can provide additional products for growth promotion and P. capsici disease management in pepper and tomatoes. Full article

Larix olgensis, a keystone timber species in Northeast China, is increasingly threatened by Neofusicoccum laricinum-induced shoot blight, a devastating disease that compromises forest health and necessitates sustainable management strategies. Here, we demonstrate that the endophytic bacterium Bacillus amyloliquefaciens JL54 elicits multifaceted defense responses in L. olgensis, enhancing resistance to pathogen infection. Greenhouse assays revealed that JL54 pretreatment reduced disease incidence by 12.5% and achieved 43.75% control efficacy while maintaining host vigor. Histochemical analyses identified JL54-induced rapid hydrogen peroxide (H₂O₂) accumulation, extensive lignin deposition, and localized programmed cell death (PCD), indicative of a primed immune response. Transcriptomic analyses uncovered distinct temporal defense patterns: early-stage responses (0 h post-inoculation) were characterized by upregulation of cutin, suberin, and wax biosynthesis pathways, reinforcing physical barriers, whereas late-stage responses (12 h post-inoculation) were dominated by ribosome- and proteostasis-related pathways (e.g., heat shock proteins [HSPs], glutathione S-transferases [GSTs]) to mitigate cellular damage. Biochemical assays corroborated these findings, with JL54 colonization reducing membrane lipid peroxidation (27.2% decrease in malondialdehyde content) and significantly elevating the activity of key defense enzymes, including peroxidase (POD), phenylalanine ammonia-lyase (PAL), and GST. Phytohormone profiling implicated jasmonic acid (JA) as the central mediator of induced systemic resistance (ISR), with JL54-potentiated JA signaling preceding pathogen containment. Collectively, these results demonstrate that JL54 contributes to a coordinated defense strategy in L. olgensis, integrating structural reinforcement (cuticle/lignin), oxidative stress management, and JA-mediated immune priming. These insights advance the understanding of endophyte-conferred resistance in conifers and highlight JL54’s potential as a biocontrol agent for sustainable forestry. Full article

Background: Salmonella enterica subsp. enterica serovar Gallinarum biovar Pullorum (Salmonella Pullorum) is a specific avian pathogen responsible for Pullorum disease, causing substantial economic losses to the global poultry industry. With the rising restrictions on antibiotic use, probiotics have emerged as promising therapeutic alternatives. The Bacillus subtilis group, including B. amyloliquefaciens and B. subtilis, is a collection of closely related species that has been widely used as a probiotic due to its broad-spectrum antimicrobial activity and other benefits. However, how the probiotics-derived antibacterial phenotype contributes to infection control is still unclear. Methods: In this study, we used two different antibacterial phenotype strains, B. amyloliquefaciens and B. subtilis, to treat S. Pullorum infections. The spores of two strains (10⁷ CFUs) were supplemented daily for 21 days. Results: The reduction in body weight gains and the severity of S. Pullorum-induced symptoms were ameliorated. Compared to B. subtilis, B. amyloliquefaciens exhibited a stronger host protection effect, manifested in a greater reduction in the bacterial load of S. Pullorum in organs throughout the infection. Furthermore, both strains enhanced cecal microbiota diversity, suppressed infection-associated taxa, and promoted beneficial genera. Conclusions: Our findings demonstrate that probiotic Bacillus can alleviate S. Pullorum infection and improve growth performance in poultry, especially the antimicrobial phenotype contributing to pathogen clearance. This work provides crucial insights for developing effective, probiotic-based strategies against Pullorum disease. Full article

Aflatoxin B1 (AFB1) poses a serious threat to global food and feed safety. Laccase-based enzymatic degradation represents a promising green strategy for AFB1 removal; however, its industrial application is severely limited by the rapid thermal inactivation of wild-type enzymes under high-temperature processing conditions (>70 °C). Here, we engineered the thermal stability of a laccase from Bacillus amyloliquefaciens B10 through an integrated strategy combining computational structural biology with semi-rational design. By coupling molecular dynamics (MD) simulations with folding free-energy (ΔΔG) calculations, we identified key flexible regions associated with thermal instability and subsequently implemented iterative saturation mutagenesis. The best single mutant, R196C, retained more than 96% relative activity after heat treatment at 80 °C for 10 min. Further iterative mutational stacking progressively enhanced thermostability: the R90E/R196C double mutant showed 1.25-fold higher activity at 80 °C than R196C, and the R90E/R196C/H54F triple mutant showed a further 1.16-fold increase over the double mutant. The final quadruple mutant, R90E/R196C/H54F/R253I, achieved 86.9% AFB1 degradation at 80 °C after 24 h. High-temperature MD simulations (100 ns at 353.15 K) indicated that the enhanced thermostability was associated with reduced conformational flexibility, lower radius of gyration (Rg) and solvent-accessible surface area (SASA), and a coil-to-β-sheet transition that contributed to stabilization of the protein core. In addition, efficient secretory expression of the engineered enzyme was achieved in Pichia pastoris, reaching 3.0 U/mL, while the crude enzyme maintained more than 70% activity at 80 °C. Collectively, these results provide a practical basis for the rational engineering and scalable production of thermostable biocatalysts for AFB1 detoxification-related applications of AFB1 control, and offer broader insights into the targeted enhancement of thermal stability in industrial enzymes. Full article

Botrytis cinerea, the causative agent of gray mold, is a major fungal pathogen affecting a wide range of economically important crops. To identify sustainable alternatives to chemical fungicides, this study characterized the biocontrol potential of two bacterial strains, Serratia quinivorans NFX21 and Pseudomonas thivervalensis NFX104, through genomic analysis and functional assays targeting key stages of fungal growth and plant infection. The NFX21 and NFX104 strains significantly inhibited B. cinerea mycelial growth (~35%) and strongly suppressed conidial germination with performances comparable to the reference biocontrol strain Bacillus amyloliquefaciens QST 713. In tomato detached-leaf and whole-plant pot assays, application of NFX21 and NFX104 significantly reduced gray mold incidence and lesion severity relative to nontreated infected plants (53–64%, detached leaves; 12–13%, whole-plant assays), achieving disease control levels similar to those obtained with the commercial biofungicide Serenade ASO^®. Whole-genome sequencing allowed the taxonomic assignment of the NFX strains and revealed a rich repertoire of biosynthetic gene clusters and antifungal determinants. The NFX21 genome contained genes associated with N-acyl-homoserine lactone-mediated quorum-sensing and production of lipopeptides, siderophores, and extracellular lytic enzymes. The NFX104 genome harbored clusters involved in the biosynthesis of multiple siderophores, 2,4-diacetylphloroglucinol and hydrogen cyanide. Moreover, both the NFX21 and NFX104 genomes contained additional low-homology clusters that potentially encode for novel unexplored metabolites. Collectively, these results support the translational potential of NFX21 and NFX104 as biocontrol candidates for sustainable, integrated management of gray mold caused by B. cinerea. Full article

Ochratoxin A (OTA), a secondary metabolite produced by Penicillium and Aspergillus species, contaminates food and feed globally, posing serious threats to both livestock and human health. Among current detoxification strategies, probiotic-based degradation of OTA has emerged as a key research focus. This study aimed to isolate safe probiotic strains with high OTA-detoxifying efficacy to support their potential application in feed and food industries. A total of 57 bacterial strains were isolated from environmental samples, including soil, moldy feed, and animal feces. Among these, a novel strain identified as Bacillus amyloliquefaciens MM28 demonstrated strong OTA-degrading activity, removing 86.31% of OTA (0.4 µg/mL) within 48 h. Whole-genome analysis indicated that B. amyloliquefaciens MM28 harbors functional genes related to glucose metabolism, membrane transport, and properties associated with antibacterial, antioxidant, and immunomodulatory activities, suggesting multiple beneficial traits. In a 28-day chronic exposure study, mice were administered B. amyloliquefaciens MM28 via gavage (1 × 10⁸ CFU/mL). Results showed that both female and male mice in the MM28 group exhibited higher body weight and improved growth performance compared to the PBS control group. Furthermore, intestinal morphology was enhanced in the MM28 group, as indicated by greater villus length and villus-length-to-crypt-depth ratio. The expression of proinflammatory cytokines was also reduced in the treated animals. Moreover, analysis of gut microbiota composition revealed that MM28 supplementation led to an increased abundance of Bacteroides and Desulfovibrio, alongside a reduction in Lachnospira and Oscillospira. In conclusion, this study demonstrates that Bacillus amyloliquefaciens MM28 is a safe and efficient strain capable of degrading OTA. These findings highlight its promising potential as a biological detoxifying agent in food and feed industries. Full article

Integrated fertilization using reduced chemical fertilizers and bio-organic fertilizers can maintain soil fertility with lower chemical inputs, yet its systemic effects on disease control, soil microbes, yield, and quality are not fully clear. This study aimed to: (1) evaluate the effects of Bacillus amyloliquefaciens Z2 and Trichoderma harzianum T22, alone or combined, on suppressing Fusarium wilt (Fusarium oxysporum f. sp. cucumerinum) and promoting cucumber growth in pot experiments; and (2) assess the field efficacy of reduced chemical fertilizer (75% N) plus microbial bio-organic fertilizer (25% N) for disease control, growth enhancement, and yield and quality improvement. To achieve these objectives, pot experiments were first conducted, followed by field experiments. Pot results indicated that individual and combined inoculants notably decreased the disease index (DI) by 40.48–68.75%, and significantly increased cucumber fresh shoot biomass by 16.86–26.75%, with the combined inoculants exhibiting the greatest effect. Field experiments indicated that the synthetic microbial bio-fertilizer has a greater advantage in promoting cucumber growth and disease suppression compared to a single bacterial bio-organic fertilizer. Specifically, the application of combined bio-fertilizers exhibited the best performance in decreasing cucumber DI by 51.54%, improving cucumber fresh shoot biomass by 12.19%, and enhancing cucumber yield by 21.02%, along with significantly improving fruit vitamin C content by 21.17% and increasing fruit total amino acids by 26.23% compared with the control. Rhizosphere soil analysis revealed that the application of combined bio-fertilizers enriched beneficial bacterial families (JG30-KF-AS9 and Sphingomonadaceae) and fungal genera (Chaetomiaceae and Condenascus) with known biocontrol functions and suppressed the proliferation of Fusarium. Overall, the integrated use of reduced chemical fertilizer combined with synthetic bio-organic fertilizer effectively suppresses cucumber wilt, optimizes microbial community structure, and improves cucumber yield and quality, furnishing a valuable foundation for microbial-assisted sustainable crop production. Full article

In this study, we evaluated the physiological effects of fermented metabolites derived from puffed grains (z), fermented using Bacillus amyloliquefaciens NPKE6, a strain isolated from Korean water kimchi. In vitro assays showed that NPKE6-FM significantly increased antioxidant enzyme activities (SOD, CAT, GPx) and digestive enzyme activities (α-amylase, protease), suggesting its strong biofunctional potential. To confirm its in vivo efficacy, we established two inflammatory disease models—ulcerative colitis and liver injury—in male C57BL/6 mice. Colitis was induced by oral administration of 1% dextran sodium sulfate (DSS, 1 mL), while liver injury was induced by intraperitoneal injection of acetaminophen (APAP, 300 mg/kg) three times per week for 4 weeks. In disease-induced control groups, elevated serum biomarkers (AST, ALT, ALP) and reduced antioxidant activity were observed. Experimental groups received 10 or 50 mg/kg/day of NPKE6-FM for 4 weeks. Treatment significantly restored antioxidant enzyme levels and reduced inflammatory markers such as TNF-α and IL-6. In the colitis model, NPKE6-FM alleviated DSS-induced tissue damage, evidenced by improved colon length, weight, and histological scores. Gene expression analysis showed downregulation of iNOS and COX-2 in colon tissues and Akt and MCP-1 in liver, indicating molecular anti-inflammatory effects. Although liver histopathology did not show marked improvement, biochemical and gene expression results supported its protective role. In summary, NPKE6-FM demonstrated potent antioxidant and anti-inflammatory activities in vitro and in vivo, indicating its potential as a functional food additive to prevent or alleviate inflammatory conditions such as colitis and liver injury. Full article

Gray mold disease severely impacts the yield and quality of Panax notoginseng (Burkill) F. H. Chen ex C. Chow & W.G. Huang. In this study, a strain of Botrytis fabiopsis J. Zhang, G.N. Wu & G.Q. Li labeled as 3-3 was isolated from the leaves affected by gray mould disease of P. notoginseng, identified as a novel pathogen for this plant. Targeting the strain 3-3, an antagonistic bacterial strain X30 was isolated from the leaves of P. notoginseng and was preliminarily identified as Bacillus amyloliquefaciens (Fukumoto) Priest et al. through morphological and molecular biological analyses. The in vitro antifungal test showed that strain X30, at a concentration of 1 × 10⁸ CFU mL⁻¹, had an inhibition rate of 84.63% against the B. fabiopsis strain 3-3, and it exhibited broad-spectrum antifungal activity against other major pathogenic fungi of P. notoginseng, including Alternaria alternata (Fr.) Keissl., Rhizoctonia solani J.G. Kühn and others. Additionally, strain X30 was found to produce ammonia, fix nitrogen, secrete plant growth hormones, and release multiple hydrolytic enzymes, thus possessing both plant-growth-promoting and antimicrobial traits. In pot experiments, an X30 suspension at 1 × 10⁸ CFU mL⁻¹ achieved 61.04% control rate against B. fabiopsis. Using non-targeted metabolomics, compounds in the culture filtrate of strain X30 were analyzed, and two organic acid compounds with antimicrobial activity were identified. Among them, phenylpyruvic acid had an EC₅₀ value of 312 µg mL⁻¹ against pathogen 3-3, while 2,6-dihydroxybenzoic acid had an EC₅₀ value of 660 µg mL⁻¹. B. amyloliquefaciens X30 provides a theoretical basis for developing green and efficient biocontrol agents against gray mould in P. notoginseng. Full article

Bacillus species are among the most widely used microbial agents in agricultural biocontrol, reflecting their ecological resilience, functional diversity, and long history of practical application. The antagonistic activity of Bacillus spp. against plant pathogens and their plant growth–promoting effects are well established. However, these biological functions are frequently considered in isolation from safety evaluations and regulatory decision-making, resulting in a fragmented evidence base. This review addresses this gap by providing an integrated synthesis of agriculturally relevant Bacillus taxa, explicitly linking biocontrol performance with strain-level safety considerations and regulatory assessment. This review focuses on the principal groups currently applied in agriculture, including the Bacillus subtilis lineage, notably B. amyloliquefaciens, B. velezensis, B. pumilus, and B. licheniformis, as well as B. thuringiensis and Cytobacillus firmus. Key mechanisms underlying biocontrol efficacy are examined alongside evidence from greenhouse and field applications. These mechanisms include the production of secondary metabolites and volatile compounds, biofilm formation, rhizosphere colonisation, and the induction of plant defence responses. Attention is given to environmental and operational factors that influence the consistency of performance. A central contribution of this review is the integration of functional evidence with safety-relevant considerations, such as realistic metabolite exposure, antimicrobial resistance potential, and ecological effects. Regulatory approaches in the European Union, the United States, and selected Organisation for Economic Co-operation and Development countries are compared to illustrate how such evidence informs risk assessment and supports the sustainable use of Bacillus-based biocontrol agents in modern agriculture. Full article

In Brazil, the olive tree (Olea europaea) is propagated by cuttings using indole-3-butyric acid (IBA) for rooting and sand as the substrate. Auxin-producing microorganisms may enhance this process when applied together with IBA. This study evaluated the rooting capacity of cuttings from four olive cultivars—Arbequina, Maria da Fé, Ascolano 315, and Koroneiki—treated with commercial products based on microorganisms, plus IBA. The biostimulants used were Bacillus amyloliquefaciens, Bacillus licheniformis, Bacillus subtilis, Trichoderma harzianum, and the commercial product Bioraiz^® (a mixed mineral fertilizer) in liquid formulation. Trichoderma harzianum and Bacillus spp. improved the quality of rooted cuttings, promoting the formation of more roots per cutting (about 10) and longer roots, on average of 8.1 cm in the cultivars Maria da Fé, Ascolano 315, and Arbequina. Cuttings treated with Trichoderma harzianum, Bacillus subtilis, and Bacillus licheniformis produced higher percentages of rooted cuttings, over 50%, and more developed root systems. Conversely, the control and Bioraiz^® showed weaker rooting performance, producing fewer than seven roots per cutting. Overall, the results highlight the potential of biostimulant applications, such as Trichoderma and Bacillus subtilis, as promising tools to optimize the rooting of olive tree cuttings, whereas the fertilizer showed limited effectiveness in promoting rooting. Full article

Bacillus amyloliquefaciens is an important agricultural microbial resource. This study focuses on the whole genome analysis and functional characterization of B. amyloliquefaciens SH-53, isolated from the Wuliang Mountain National Nature Reserve in Dali, Yunnan. The genomic feature analysis revealed that the genome of SH-53 contains 27 ribosomal RNA operons, 4078 protein-coding genes, and 250 prophage-related genes. Additionally, 12 biosynthetic gene clusters (BGCs) for secondary metabolites were predicted, of which 7 are novel gene clusters with unknown functions, showing significant differences compared to the known BGCs of conventional biocontrol strains. Functional potential analysis indicates that SH-53 possesses potential antagonistic activity against plant pathogenic bacteria and can colonize the plant rhizosphere through various mechanisms to exert growth-promoting effects. It is capable of synthesizing multiple antibacterial secondary metabolites, indole-3-acetic acid (IAA), iron carriers, secreting amylase, and efficiently utilizing sulfur sources. The genome also harbors a complete core gene network related to the induced systemic resistance (ISR) and supporting genes that maintain secondary metabolism homeostasis. In conclusion, B. amyloliquefaciens SH-53 exhibits rich biocontrol-related characteristics and unique secondary metabolic potential, indicating promising prospects for its development as an excellent biocontrol agent. Full article