Multifaceted biocontrol mechanisms of Bacillus amyloliquefaciens F028 against Botrytis cinerea in postharvest tomato fruit.

Investigation of flavor formation mechanism of broad bean paste fermented by Bacillus amyloliquefaciens SCPC-RY2021.

Seven commercially available seed-applied nematicides were evaluated in a greenhouse pot experiment and in two field experiments using Meloidogyne incognita-susceptible and partially resistant maturity group IV soybean cultivars. Nematicide treatments were abamectin, fluopyram, pydiflumetofen, Bacillus amyloliquefaciens (PTA4838), B. amyloliquefaciens + cis-jasmone, B. flavus (I-1582), and Burkholderia rinojensis (A396). Soybean plants were inoculated with approximately 3,000 M. incognita eggs/pot in the greenhouse experiment. Field experiments were conducted in sites with naturally high infestation levels, averaging 450 nematodes/100 cm3 soil after harvest. In the greenhouse, lower root galling and nematode reproduction were observed with seed-applied fluopyram compared to other nematicides and the non-treated control on a susceptible soybean cultivar. Whereas none of the seed-applied nematicides consistently suppressed root galling or protected grain yield in either the susceptible or partially resistant soybean cultivars in the field experiments. Nematicides provided an average of 0.3% yield protection for susceptible cultivars and had no measurable effect on partially resistant cultivars. In contrast, partially resistant cultivars produced, on average, 50% greater grain yield than the susceptible cultivar. These results demonstrate that seed-applied nematicides provide minimal yield protection under high M. incognita population densities, whereas host plant resistance remains the most effective and reliable management strategy in soybean production.

Given the rising global incidence of inflammatory bowel disease (IBD) and limited treatment options, probiotic efficacy is hindered by poor gastrointestinal survival. This study developed a self-coating biofilm technology to encapsulate the probiotic Bacillus amyloliquefaciens C-1 and yield cC-1. Biofilm-modified cC-1 exhibited a more negative zeta potential (-22.53 mV) compared to uncoated C-1 (-19.60 mV), representing a decrease of 2.93 mV decreased zeta potential, and it exhibited orders of magnitude higher survival than uncoated cells under simulated gastric acid (80.51% vs. 0.33%) and bile salt (84.32% vs. 1.64%). In DSS-induced colitis mice, oral administration of 10⁹ CFU cC-1 for 14 days significantly alleviated symptoms, reduced colon shortening and restored mucosal integrity. Mechanistically, cC-1 effectively downregulated pro-inflammatory cytokines (TNF-α, IL-1β, IL-6 and IFN-γ) in colon tissues; reshaped the diversity of gut microbiota by enriching beneficial Bacteroides; restored linoleic acid and glycerophospholipid metabolism, and suppressed expression of NF-κB signaling and cell adhesion molecule. Transcriptomic analysis confirmed that cC-1 reinstated host-microbe metabolic interactions with suppressed inflammatory pathways. This biofilm self-coating strategy substantially enhances probiotic gastrointestinal tolerance and exerts therapeutic effects through a multi-targeted mechanism (anti-inflammation, barrier repair, microbiota modulation, and metabolic reprogramming), offering a scalable and promising formulation for nutritional intervention in IBD.

Coral reef ecosystems face increasing threats from microbial diseases, especially those induced by bacterial infections. Conventional diagnostic techniques often require invasive sampling, extended processing time and are limited in their spatial applicability. Spectral reflectance analysis offers a non-invasive means for detecting subtle physiological alterations associated with coral disease; however, its application in characterizing microbiological changes remains largely unexplored. This research aimed to differentiate healthy from diseased coral colonies by analyzing the spectral fingerprints of the disease and their associated bacterial communities, using hyperspectral data, microbial profiling, and multivariate statistical analysis. The bacterial species identified in healthy coral samples included Bacillus subtilis, Cytobacillus firmus, Bacillus amyloliquefaciens, and Bacillus sporothermodurans. In contrast, the bacteria associated with diseased coral samples were Vibrio pelagius and Vibrio fortis. Healthy corals demonstrate consistently lower reflectance across all bands in comparison to diseased corals. The reflectance of diseased Favia lacuna showed a notable increase when compared to healthy specimens, especially at wavelengths of 594nm, 649nm, and 702nm. In contrast, Acropora humilis exhibited heightened peaks at wavelengths of 580nm, 693nm, and 702nm. The analysis of the second derivative revealed that coral colonies affected by disease exhibited distinct negative peaks at wavelengths of 450-460nm, 580-590nm, and 700-800nm. The identified peaks are likely associated with tissue thinning, skeletal exposure, or microbial biofilm accumulation rather than pigment absorption, given that this region is dominated by scattering effects. In contrast, healthy colonies exhibited stable characteristics at approximately 675nm, indicating the presence of intact symbiotic chlorophyll and preserved physiological structure. The present study demonstrates that hyperspectral reflectance profiling of bacterially infected corals shows promising potential as a non-invasive approach for differentiating healthy and diseased coral microbiomes. The integration of spectral indicators with microbial community data provides preliminary insights into coral health assessment and may contribute to the development of improved strategies for disease detection and understanding coral-microbe interactions under environmental stress.

Enhancement of glutaminase production through protein design and host strain modification in Bacillus amyloliquefaciens.

Bacillus amyloliquefaciens COFCAU_P1, an autochthonous probiotic from Labeo rohita, was genome sequenced (Illumina NovaSeq; GenBank JBHEQH000000000). Its 4.09 Mb genome encodes 4,351 genes linked to stress tolerance, nutrient utilization, antimicrobial defense, enzymes, and immunomodulation. Phylogenomics and functional evidence confirm its safety and probiotic potential for aquaculture applications in aquaculture systems.

Excessive ammonia accumulation in aquaculture effluents poses significant ecological and production challenges, necessitating sustainable remediation approaches. The present study reports the isolation and characterization of indigenous ammonia-utilizing bacteria from shrimp pond wastewater in Tuticorin, Southeast coast of India, and a comparative assessment of their utilization efficiencies as individual strains and synthetic consortia. Eleven isolates belonging to Bacillus, Pseudomonas, Burkholderia, Nitrosomonas, Rhizobacterium, and Agrobacterium spp. were identified through phenotypic characterization and 16S rRNA sequencing. Individual strains demonstrated 30-70% ammonia removal within 10days, with Nitrosomonas sp. exhibiting the highest efficiency (70%). Based on compatibility assays, five three-species consortia (C1-C5) were formulated. Among these, consortia C3 (Bacillus amyloliquefaciens, Burkholderia paludis, Nitrosomonas sp.) and C4 (Burkholderia cepacia, Nitrosomonas sp., Burkholderia seminalis) achieved superior performance, attaining approximately 85% ammonia utilization by day 10 under optimal conditions. The relatively balanced distribution within the consortia suggested potential cooperative or niche-partitioning effects. These results underscore the importance of species compatibility when designing microbial consortia and potential of synergistic indigenous microbial consortia as effective bioaugmentation agents for aquaculture wastewater treatment.

Endophytic bacteria serve as important resources for the development of novel biocontrol agents for sustainable agriculture. This study provides a detailed characterization of a newly isolated oat endophyte, Bacillus amyloliquefaciens Ba. YN.J3, using an integrated analysis of phenotypic, genomic, and comparative genomic data to explore its biocontrol and plant growth-promoting (PGP) potential. The current findings indicate that Ba. YN.J3 possessed efficient PGP and biocontrol potential both in vitro and in planta. Additionally, Ba. YN.J3 showed broad-spectrum antifungal activity against six major phytopathogens and was found to produce multiple cell wall-degrading enzymes (CWDEs) and siderophores, significantly increasing the growth of several crop species and regulating defense enzymes in oats. The complete 4.06Mb genome of Ba. YN.J3 contains numerous gene clusters encoding vital secondary metabolites (e.g., surfactin, fengycin), CWDEs, and proteins associated with PGP functions and chemotaxis. The genome also harbors a robust set of genes related to abiotic stress tolerance, suggesting its potential to survive and function effectively in challenging field environments. Furthermore, comparative genomic analysis revealed 830 strain-specific genes, including two unique gene families potentially associated with chemotaxis (flagellar rod protein FlgC) and nitrogen metabolism and assimilation (regulatory protein YutI). This integrated study provides genomic insights into the dual function of Ba. YN.J3 and its unique genetic determinants. The flgC and yutI gene families, in particular, offer potential genomics insights into its targeted antagonism and nutritional self-sufficiency. Hence, the current findings highlight Ba. YN.J3 as a promising candidate for the development of effective biopesticides and biofertilizers.

Biological control agents can offer an eco-friendly and more sustainable alternative to conventional chemical pesticides, providing protection against destructive pathogens, such as Phytophthora capsici, while reducing potential environmental harm associated with synthetic pesticide use in agricultural systems. This work evaluates the biocontrol effectiveness of Bacillus vallismortis, Bacillus amyloliquefaciens, Bacillus thuringiensis, and Bacillus subtilis, against the widespread plant pathogen Phytophthora capsici. Our studies showed that Bacillus thuringiensis and Bacillus subtilis promote plant growth and provide protection against Phytophthora capsici in both in vitro and in vivo greenhouse studies, while Bacillus vallismortis and Bacillus amyloliquefaciens were effective in vitro but not in vivo. Specifically, Bacillus thuringiensis was observed to both hinder the growth of Phytophthora capsici and enhance plant resilience to this pathogen, with B. thuringiensis-treated, pathogen-exposed plants displaying a 94.4% increase in root length and a 74.0% increase in shoot height compared to plants with only oomycete exposure. To probe the molecular interactions between the biocontrol agent and pathogen, a dual culture of Bacillus thuringiensis and Phytophthora capsici was analyzed in situ using a desorption electrospray ionization-mass spectrometry imaging (DESI-MSI) workflow. This approach interrogated the spatially oriented biochemical interactions that may serve as the molecular foundation for the effectiveness of these biological control agents in crop protection, identifying seven unique phenotypic regions within the dual culture. Herein, we demonstrate the benefits of biological control agent application in tomato cultivation and showcase the strengths of desorption electrospray ionization-mass spectrometry imaging when applied to the spatially resolved molecular characterization of agriculturally relevant microorganisms.

Enhancing the production and bioactivity of α-glucosidase-inhibitory exopolysaccharide from Bacillus amyloliquefaciens YP2 through genomics and metabolic pathway regulation.

Apple replant disease (ARD) is a major threat to the sustainable development of China's apple industry. It is primarily caused by the accumulation of phloridzin and the pathogen Fusarium proliferatum f.sp. malus domestica MR5 (Fpmd MR5). MdUGT88F1-mediated phloridzin biosynthesis is known to enhance disease resistance, but its role in shaping the rhizosphere microbiome and conferring resistance against Fpmd MR5 remains unclear. In this study, we used wild-type (WT) and MdUGT88F1 transgenic apple lines to systematically investigate the mechanism by which MdUGT88F1 regulates the rhizosphere microbiome to mitigate ARD. Compared with WT and MdUGT88F1-OE plants, MdUGT88F1-RNAi plants exhibited enhanced tolerance to ARD, as indicated by reduced disease severity, decreased abundance of Fpmd MR5 in the rhizosphere soil, and lower phloridzin content. Further greenhouse experiments demonstrated that the rhizosphere bacterial communities were triggered mainly by changes in community composition. Multi-omics joint analysis revealed that members of the family Bacillaceae with multiple plant growth-promoting traits were enriched in the MdUGT88F1-RNAi plant rhizosphere but only upon Fpmd MR5 invasion. MdUGT88F1-RNAi plants exhibited significantly higher exudation of D-tagatose, D-galactose, sucrose, 3-O-methyl-D-glucose, and maltitol. Interestingly, exogenous application of these compounds promoted the proliferation of Bacillus, enhancing plant resistance to Fpmd MR5. In vitro assays demonstrated that the recruited Bacillus significantly inhibited the hyphal growth and fumonisin B1 production of Fpmd MR5 and alleviated plant disease symptoms. We experimentally validated this observation by inoculating a synthetic microbial community (Bacillus velezensis, Bacillus mojavensis, Bacillus subtilis, Bacillus amyloliquefaciens, and Bacillus licheniformis) into replanted soil, which led to a significant reduction in pathogen Fusarium abundance and promoted plant growth. Overall, these findings highlight that plant disease resistance is a complex trait driven by dynamic interactions among the host genetic background, rhizospheric microbial communities, and pathogens. Targeted modulation of the rhizospheric microbiome represents a potent "prebiotic" strategy. This approach can indirectly enhance plant disease resistance by fostering beneficial microbial activity in the rhizosphere. This study also provides a theoretical basis and practical solutions for the green control of ARD through prebiotics and synthetic microbial communities. Video Abstract.

Rice blast, caused by the fungal pathogen Magnaporthe oryzae, poses a severe threat to global rice production. While biological control represents a promising sustainable strategy, the molecular mechanisms by which biocontrol agents suppress M. oryzae remain poorly understood. Our findings elucidate a novel mechanism of bacterial biocontrol, wherein a secreted bacterial protease modulates fungal signalling pathways to disrupt its environmental fitness and pathogenic structures, while enhancing host resistance to blast disease. We demonstrate that the Bacillus amyloliquefaciens SN16-1 exhibits antagonistic activity against M. oryzae Guy11. Integrated dual RNA sequencing and protein-protein interaction analysis revealed that the ergosterol biosynthesis pathway in M. oryzae is crucial for its pathogenicity and is markedly suppressed during co-culture with SN16-1. We identified MoERG1, a key enzyme in this pathway, as essential for fungal development and virulence. Further analysis showed that the serine protease AprE, secreted by SN16-1, is a critical mediator. AprE triggers the Hog1-MAPK signalling cascade in M. oryzae, leading to transcriptional repression of ergosterol biosynthesis genes, concomitant activation of plant disease resistance, and induction of ROS accumulation, hyperosmotic stress and apoptosis in fungal hyphae. This study provides new insights into host-microbe-pathogen interactions and offers an effective strategy for developing targeted biocontrol solutions against devastating plant diseases.

Genomic insights into endophytic Bacillus amyloliquefaciens BBE16 and Bacillus velezensis BBE18 reveal their biocontrol potential against Fusarium wilt in banana

Water scarcity, intensified by climate change, threatens tomato (Solanum lycopersicum) productivity, impacting growth, metabolism and secondary metabolite production. This study evaluated the effects of Azospirillum brasilense and Bacillus amyloliquefaciens inoculation in mitigating water stress in the Ibiza cultivar under 100%, 50% and 25% water replenishment. Severe water deficits significantly reduced morphological parameters, such as height, leaf number and dry mass. However, inoculation with B. amyloliquefaciens, particularly in combination with A. brasilense, enhanced dry mass accumulation, stem diameter and root development. Physiological analyses revealed higher electrolyte leakage and compromised membrane integrity due to water stress. Biochemical responses included increased antioxidant enzyme activity (SOD, CAT and APX) and proline accumulation, both modulated by bacterial inoculation. Interestingly, chlorophyll content increased at 25% water availability, suggesting an adaptive mechanism, while DNA content decreased. Secondary metabolites (flavonoids and phenolics) also responded to the interaction between irrigation levels and bacterial inoculation. The findings demonstrate that inoculation with A. brasilense and B. amyloliquefaciens is an effective approach to enhance tomato tolerance to water deficits by improving agronomic performance, strengthening antioxidant defences and regulating secondary metabolite production. This strategy supports the development of sustainable and adaptive agricultural practices in the face of increasing water scarcity.

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.

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.

Pectate lyases facilitate pathogen invasion by degrading pectic polysaccharides in the plant cell wall. Although xylanase inhibitor proteins (XIPs) are recognized as plant defense proteins against xylanases, their ability to inhibit pectate lyases remained unknown. Here, recombinant Bacillus amyloliquefaciens pectate lyase B (rePelB) displayed optimal activity at 60 °C and pH 5.0 and was enhanced more than 2-fold by 5 mM Ca2+. Recombinant Oryza sativa XIP (reOsXIP) competitively inhibited rePelB with a Ki of 98.68 nM. Fluorescence spectroscopy indicated static quenching upon rePelB-reOsXIP interaction. Molecular dynamics simulations revealed that the Lα4β5 loop of OsXIP inserts into the PelB catalytic groove, with a calculated binding free energy of -87.6 ± 7.4 kcal/mol. Alanine substitutions of PelB residues K99, S337, and V338 weakened binding and reduced inhibition by reOsXIP. These results provide the first evidence that XIP competitively inhibits a pectate lyase, highlighting a broader defensive role against plant cell wall-degrading enzymes.

Zearalenone (ZEN) is an estrogenic mycotoxin synthesized by specific fungal species that frequently colonize cereal crops such as maize, which is a fundamental component of animal feed. This mycotoxin induces significant reproductive disorders in swine and other livestock, resulting in considerable economic loss in the animal husbandry sector. ZEN contamination has emerged as a critical issue concerning global food and feed safety. The objective of this research was to isolate and characterize microorganisms from samples that can effectively detoxify ZEN. The samples were from six distinct sources: porcine feces, piggery soil, avian intestines, unpasteurized bovine milk, and feed that was left to mold. The spread plate technique was used to culture the samples and obtain pure cultures. The samples were identified by bacterial morphology and 16S rRNA gene sequencing. All the bacterial isolates identified in this study exhibited mycotoxin-degrading capabilities and included known ZEN-degrading species, Bacillus amyloliquefaciens and B. subtilis, with ZEN degradation ranging from 84.21% to 99.58%. A pure culture derived from piggery soil displayed particularly robust ZEN-degrading potential. Microscopic, biochemical, and molecular assessments substantiated the classification of this isolate as Priestia megaterium. This bacterium demonstrated ZEN-degrading ability (up to 0.5 mg/mL) and an elevated level of tolerance to various antibiotics (Multiple Antibiotic Resistance (MAR) index = 0.07). Additional research is necessary to investigate its potential application in the detoxification of ZEN.

XOD inhibition peptides obtained via fermentation of Salmon by Bacillus amyloliquefaciens and evaluation of their anti-hyperuricemia mechanism in HK-2 cells