Identification and characterization of the endophytic bacterium Bacillus atrophaeus XW2, antagonistic towards Colletotrichum gloeosporioides

Optimization of Fermentation and Biocontrol Efficacy of Bacillus atrophaeus XHG-1-3m2

Biological control plays an increasingly important role in various aspects of modern agriculture and forestry. Identifying biocontrol strains with commercial potential for effective disease management is currently a focal point in biological control research. In this study, Bacillus atrophaeus XHG-1-3m2, a strain with significant biocontrol potential against Wilsonomyces carpophilus causing shot hole disease in wild apricots, was developed. The study determined the antibacterial activity of the fermentation broth, the optimal fermentation medium composition and conditions, and explored its effectiveness in controlling Wilsonomyces carpophilus. The optimal fermentation medium for strain XHG-1-3m2 comprises 12.5 g/L yeast extract, 12.5 g/L soy peptone, 10.0 g/L sodium chloride, 1 g/L ammonium chloride, 1 g/L potassium dihydrogen phosphate, 1 g/L disodium hydrogen phosphate, and 0.5 g/L magnesium sulfate heptahydrate. With an initial pH of 7.0, a liquid volume of 40%, an inoculum volume of 3%, and shaking incubation at 28 °C for 24 h, the viable cell count reached 14 × 109 CFU/mL. In vitro and in vivo tests on leaves revealed that the fermentation broth and the biocontrol biofertilizer derived from this strain inhibited the leaf lesions caused by Wilsonomyces carpophilus on wild apricots, achieving inhibition rates of 94.62% and 82.46%, respectively.

Chemical and genetic characterization of lipopeptides from Bacillus velezensis and Paenibacillus ottowii with activity against Fusarium verticillioides

Introduction

The fungus Fusarium verticillioides significantly threatens maize crops in tropical soils. In light of this, biological control has emerged as a promising strategy to reduce fungicide costs and environmental risks. In this study, we aimed to test the antifungal activity of cell-free supernatant (CFS) from three Bacillus velezensis (CT02, IM14, and LIS05) and one Paenibacillus ottowii (LIS04) against F. verticillioides, thereby contributing to the development of effective biocontrol measures.

Methods

The research employed a comprehensive approach. The antifungal activity of the bacterial strains was tested using cell-free supernatant (CFS) from three Bacillus velezensis (CT02, IM14, and LIS05) and one Paenibacillus ottowii (LIS04). The UPLC-MS evaluated the CFS to identify the main bioactive molecules involved in the inhibitory effect on F. verticillioides. Scanning electron microscopy (SEM) was used to assess the impact of CFS on spores and hyphae, and genome sequencing was conducted to identify the genes involved in biological control. These robust methodologies ensure the reliability and validate our findings.

Results

The CFS of the four strains demonstrated significant inhibition of fungal growth. The UPLC-MS analysis revealed the presence of lipopeptides with antifungal activity, including surfactin and fengycins A and B expressed by the three strains of Bacillus velezensis and iturin A expressed by strains LIS05 and IM14. For Paenibacillus ottowii, fusaricidins, ABCDE, and five previously unreported lipopeptides were detected. Scanning electron microscopy (SEM) showed that treatments with CFS led to significant distortion and breakage of the F. verticillioides hyphae, in addition to the formation of cavities in the membrane. Genome mining confirmed the presence of genes coding for the lipopeptides identified by UPLC-MS, including the gene for iturin in CTO2. Genomic sequencing revealed that CT02, IM14, and LIS05 belong to different strains of Bacillus velezensis, and LIS04 belongs to Paenibacillus ottowii, a species recently described.

Discussion

The four bacterial strains, including three novel strains identified as Bacillus velezensis and one as the recently described species Paenibacillus ottowii, demonstrate significant potential as biocontrol agents for managing fungal disease. This finding underscores the novelty and potential impact of our research.

Comparative genomic analysis of Bacillus atrophaeus HAB-5 reveals genes associated with antimicrobial and plant growth-promoting activities

Bacillus atrophaeus HAB-5 is a plant growth-promoting rhizobacterium (PGPR) that exhibits several biotechnological traits, such as enhancing plant growth, colonizing the rhizosphere, and engaging in biocontrol activities. In this study, we conducted whole-genome sequencing of B. atrophaeus HAB-5 using the single-molecule real-time (SMRT) sequencing platform by Pacific Biosciences (PacBio; United States), which has a circular chromosome with a total length of 4,083,597 bp and a G + C content of 44.21%. The comparative genomic analysis of B. atrophaeus HAB-5 with other strains, Bacillus amyloliquefaciens DSM7, B. atrophaeus SRCM101359, Bacillus velezensis FZB42, B. velezensis HAB-2, and Bacillus subtilis 168, revealed that these strains share 2,465 CDSs, while 599 CDSs are exclusive to the B. atrophaeus HAB-5 strain. Many gene clusters in the B. atrophaeus HAB-5 genome are associated with the production of antimicrobial lipopeptides and polypeptides. These gene clusters comprise distinct enzymes that encode three NRPs, two Transat-Pks, one terpene, one lanthipeptide, one T3PKS, one Ripp, and one thiopeptide. In addition to the likely IAA-producing genes (trpA, trpB, trpC, trpD, trpE, trpS, ywkB, miaA, and nadE), there are probable genes that produce volatile chemicals (acoA, acoB, acoR, acuB, and acuC). Moreover, HAB-5 contained genes linked to iron transportation (fbpA, fetB, feuC, feuB, feuA, and fecD), sulfur metabolism (cysC, sat, cysK, cysS, and sulP), phosphorus solubilization (ispH, pstA, pstC, pstS, pstB, gltP, and phoH), and nitrogen fixation (nif3-like, gltP, gltX, glnR, glnA, nadR, nirB, nirD, nasD, narl, narH, narJ, and nark). In conclusion, this study provides a comprehensive genomic analysis of B. atrophaeus HAB-5, pinpointing the genes and genomic regions linked to the antimicrobial properties of the strain. These findings advance our knowledge of the genetic basis of the antimicrobial properties of B. atrophaeus and imply that HAB-5 may employ a variety of commercial biopesticides and biofertilizers as a substitute strategy to increase agricultural output and manage a variety of plant diseases.

Uncovering the antifungal activities of wild apple-associated bacteria against two canker-causing fungi, Cytospora mali and C. parasitica

Cytospora canker has become a devastating disease of apple species worldwide, and in severe cases, it may cause dieback of entire trees. The aim of this study was to characterize the diversity of cultivable bacteria from the wild apple microbiota and to determine their antifungal ability against the canker-causing pathogenic fungi Cytospora mali and C. parasitica. Five bacterial strains belonging to the species Bacillus amyloliquefaciens, B. atrophaeus, B. methylotrophicus, B. mojavensis, and Pseudomonas synxantha showed strong antagonistic effects against pathogenic fungi. Therefore, since the abovementioned Bacillus species produce known antifungal compounds, we characterized the antifungal compounds produced by Ps. synxantha. Bacteria grown on nutritional liquid medium were dehydrated, and the active compound from the crude extract was isolated and analysed via a range of chromatographic processes. High-performance liquid chromatography, mass spectrometry, and nuclear magnetic resonance analyses revealed a bioactive antifungal compound, phenazine-1-carboxylic acid (PCA). The minimum inhibitory concentration (MIC) demonstrated that PCA inhibited mycelial growth, with a MIC of 10 mg mL-1. The results suggested that PCA could be used as a potential compound to control C. mali and C. malicola, and it is a potential alternative for postharvest control of canker disease.

Exploration of the Biocontrol Activity of Bacillus atrophaeus Strain HF1 against Pear Valsa Canker Caused by Valsa pyri

Valsa pyri-induced pear Valsa canker is among the most prevalent diseases to impact pear quality and yields. Biocontrol strategies to control plant disease represent an attractive alternative to the application of fungicides. In this study, the potential utility of Bacillus atrophaeus strain HF1 was assessed as a biocontrol agent against pear Valsa canker. Strain HF1 suppressed V. pyri mycelium growth by 61.20% and induced the development of malformed hyphae. Both culture filtrate and volatile organic compounds (VOCs) derived from strain HF1 were able to antagonize V. pyri growth. Treatment with strain HF1-derived culture filtrate or VOCs also induced the destruction of hyphal cell membranes. Headspace mixtures prepared from strain HF1 were analyzed, leading to the identification of 27 potential VOCs. Of the thirteen pure chemicals tested, iberverin, hexanoic acid, and 2-methylvaleraldehyde exhibited the strongest antifungal effects on V. pyri, with respective EC50 values of 0.30, 6.65, and 74.07 μL L-1. Fumigation treatment of pear twigs with each of these three compounds was also sufficient to prevent the development of pear Valsa canker. As such, these results demonstrate that B. atrophaeus strain HF1 and the volatile compounds iberverin, hexanoic acid, and 2-methylvaleraldehyde exhibit promise as novel candidate biocontrol agents against pear Valsa canker.

Strong Opponent of Walnut Anthracnose-Bacillus velezensis and Its Transcriptome Analysis

Walnut is a significant economic tree species worldwide. Walnut anthracnose, caused by the pathogen Colletotrichum gloeosporioides, greatly reduces walnut production and economic benefits. Our study showed that Bacillus velezensis effectively halted the growth of C. gloeosporioides, inducing noticeable abnormalities such as hyphal breakage and distortion, thereby curtailing the pathogen's virulence. A 50-100 times dilution of B. velezensis fermentation broth, applied every two to three days, served as an efficient protective layer for walnut leaves and fruits against C. gloeosporioides infection. Transcriptomic analysis of B. velezensis unveiled its dynamic response against C. gloeosporioides. On the second day, B. velezensis upregulated a significant number of differentially expressed genes related to the synthesis of metabolic products, amino acid biosynthesis, and motility. On the fourth day, continuous synthesis of metabolic products and amino acids, along with differential expression of spore-related genes, was observed. By the sixth day, the focus shifted towards environmental adaptation and carbon source utilization. Throughout the process, B. velezensis likely employed strategies such as the release of metabolic products, increased chemotaxis, and nutrient competition to exert its antagonistic effect on C. gloeosporioides. Fluorescence quantitative results showed that 15 primer pairs were up-regulated and 15 were down-regulated, with a 100% similarity rate to transcriptome sequencing results, confirming their authenticity. These findings provided a foundation for the widespread application of B. velezensis as a biocontrol agent in agriculture and forestry.

Characterization of the Mechanism of Action of Serratia rubidaea Mar61-01 against Botrytis cinerea in Strawberries

Several bacterial strains belonging to Serratia spp. possess biocontrol capability, both against phytopathogens and human pathogenic species, thanks to the production of secondary metabolites, including as a red-pink, non-diffusible pigment, 2-methyl-3-pentyl-6-methoxyprodiginine (prodigiosin). Botrytis cinerea is the causal agent of gray mold, which is an economically relevant disease of many crops worldwide. Gray mold is normally controlled by chemical fungicides, but the environmental and health concerns about the overuse of pesticides call for environmentally friendly approaches, such as the use of biocontrol agents. In this study, the efficacy of a specific strain of Serratia rubidaea (Mar61-01) and its metabolite prodigiosin were assessed against B. cinerea under in vitro and in vivo conditions. This strain was effective against B. cinerea, and the effect of prodigiosin was confirmed under in vitro and in vivo conditions. The strain suppressed mycelial growth of B. cinerea (71.72%) in the dual-culture method. The volatile compounds produced by the strain inhibited mycelial growth and conidia germination of B. cinerea by 65.01% and 71.63%, respectively. Efficacy of prodigiosin produced by S. rubidaea Mar61-01 on mycelial biomass of B. cinerea was 94.15% at the highest concentration tested (420 µg/mL). The effect of prodigiosin on plant enzymes associated with induction of resistance was also studied, indicating that the activity of polyphenol oxidase (PPO), superoxide dismutase (SOD) and phenylalanine ammonia lyase (PAL) were increased when prodigiosin was added to the B. cinerea inoculum on strawberry fruits, while catalase (CAT) and peroxidase (POD) did not change. In addition, the volatile organic compounds (VOCs) produced by S. rubidaea Mar61-01 reduced mycelial growth and inhibited conidial germination of B. cinerea in vitro. The findings confirmed the relevant role of prodigiosin produced by S. rubidaea Mar61-01 in the biocontrol of B. cinerea of strawberries, but also indicate that there are multiple mechanisms of action, where the VOCs produced by the bacterium and the plant-defense reaction may contribute to the control of the phytopathogen. Serratia rubidaea Mar61-01 could be a suitable strain, both to enlarge our knowledge about the potential of Serratia as a biocontrol agent of B. cinerea and to develop new biofungicides to protect strawberries in post-harvest biocontrol.

Deciphering the Biomolecules from Bacillus atrophaeus NMB01 Untangles the Anti-Oomycetes Action of Trioxsalen and Corynan-17-ol, Against Phytophthora infestans Inciting Late Blight of Potato

The antagonistic Bacillus spp. is known well for the production of versatile antimicrobial biomolecules with broad spectrum of action against different types of plant pathogens. Considering the significance of metabolically active biomolecules, attempts were made to decipher the anti-oomycete nature of biomolecules produced by Bacillus atrophaeus NMB01 during di-trophic interaction with Phytophthora infestans. Ten biomolecules produced by B. atrophaeus NMB01 during di-trophic interaction with P. infestans were docked against the twelve target proteins of P. infestans. Molecular docking of biomolecules reported trioxsalen and corynan-17-ol,18,19-didehydro-10-methoxy-acetate(ester) as best hits with highest binding energy in the range of - 7.5 to - 5 kcal/mol against target proteins of P. infestans. Comparatively less binding energy was observed for commercially available fungicides mandipropamid and metalaxyl on docking against the target proteins of P. infestans. We also confirmed the direct impact of trioxsalen andcorynan-17-ol, on P. infestans under in vitro with 66% and 50% inhibition of mycelial growth of P. infestans, respectively. This is the first study attempted to untangle the role of bioactive anti-oomycete compounds produced by B. atrophaeus strain NMB01 during di-trophic interaction with P. infestans against late blight pathogen P. infestans infecting potato. From the present study, we conclude that the biomolecules, trioxsalen and corynan-17-ol, can be explored for the management of P. infestans, the incitant of late blight of potato.

Graphical Abstract

Supplementary Information

The online version contains supplementary material available at 10.1007/s12088-022-01044-7.

Volatile organic compounds of Bacillus atrophaeus HAB-5 inhibit the growth of Colletotrichum gloeosporioides

The use of fungicides to control plant diseases creates a potential health risk. One alternative to this problem is the biological control, which has been succesfully applied to control plant diseases. Bacillus atrophaeus HAB-5 exhibits a high inhibitory acitivities against different fungal pathogens and suppresses them. The aim of current studies is to produce and identify the antifungal compounds produced by the strain HAB-5. We found that the submerge fermentation harvested from Luria-Bertani (LB) medium had the highest activity against Colletotrichum gloeosporioides. The petroleum ether crude extract was strongly bioactive and its activity was stable after heat treatment, pH treatment, illuminated light as well as ultra violet exposition. The antifungal compounds were purified using gel chromatography column. Based on Gas Chromatography-Mass Spectrometry (GC-MS) analysis, nineteen different volatile organic compounds (VOCs) were identified included the range of alkanes, alkenes, alcohols, and organics acid. Among these identified compounds, Chloroacetic acid, tetradecyl esters followed by Octadecane and Hexadecanoic acid, methyl ester showed antifungal activity against C. gloeosporioides. Our results clearly showed Chloroacetic acid, tetradecyl esters; Octadecane and Hexadecanoic acid, methyl ester are key inhibitory compounds produced by Bacillus atrophaeus HAB-5 against C. gloeosporioides.

Genomewide Transcriptome Profiles Reveal How Bacillus subtilis Lipopeptides Inhibit Microsclerotia Formation in Verticillium dahliae

Verticillium dahliae is a soilborne fungus and the primary causal agent of vascular wilt diseases worldwide. The fungus produces melanized microsclerotia that are crucially important for the survival and spread of V. dahliae. There are no fungicides available that are both effective and environmentally friendly to suppress the fungus. Previously, Bacillus subtilis C232 was isolated from soil and was demonstrated to suppress microsclerotia formation in V. dahliae. In this study, liquid chromatography coupled with mass spectrometry revealed that the antifungal substance is actually a mixture of lipopeptides. Exposure of V. dahliae to these lipopeptides resulted in hyphal swelling, cell lysis, and downregulation of melanin-related genes. RNA sequencing analyses of the lipopeptide-suppressed transcriptome during microsclerotial development revealed that 5,974 genes (2,131 upregulated and 3,843 downregulated) were differentially expressed versus nonsuppressive conditions. Furthermore, gene ontology enrichment analyses revealed that genes involved in response to stress, cellular metabolic processes, and translation were significantly enriched. Additionally, the lipopeptides inhibited expression of genes associated with secondary metabolism, protein catabolism, and the high-osmolarity glycerol response signaling pathway. Together, these findings provide evidence for the mechanism by which B. subtilis lipopeptides suppress microsclerotia formation. The transcriptomic insight garnered here may facilitate the development of biological agents to combat Verticillium wilt.

Analysis of the Complete Genome Sequence of Bacillus atrophaeus GQJK17 Reveals Its Biocontrol Characteristics as a Plant Growth-Promoting Rhizobacterium

Bacillus atrophaeus GQJK17 was isolated from the rhizosphere of Lycium barbarum L. in China, which was shown to be a plant growth-promoting rhizobacterium as a new biological agent against pathogenic fungi and gram-positive bacteria. We present its biological characteristics and complete genome sequence, which contains a 4,325,818 bp circular chromosome with 4,181 coding DNA sequences and a G+C content of 43.3%. A genome analysis revealed a total of 8 candidate gene clusters for producing antimicrobial secondary metabolites, including surfactin, bacillaene, fengycin, and bacillibactin. Some other antimicrobial and plant growth-promoting genes were also discovered. Our results provide insights into the genetic and biological basis of B. atrophaeus strains as a biocontrol agent for application in agriculture.

Identification and characterization of a new Bacillus atrophaeus strain B5 as biocontrol agent of postharvest anthracnose disease in soursop (Annona muricata) and avocado (Persea americana)

Anthracnose is a fungal disease caused by Colletotrichum species that is detrimental to numerous fruit, including soursop and avocado. The use of fungicides to maintain the high quality of fruit creates a potential health risk. One alternative to this problem is the biological control, which has been applied successfully during postharvest. The Bacillus species are one of the most studied biological agents against postharvest pathogens because accomplish their biocontrol performance by producing a variety of metabolites. In this study, we evaluated the activity of metabolites contained in the cell free supernatant, obtained from Bacillus strain B5 culture, against micelial growth and spore germination of two virulent strains of C. gloeosporioides isolated from soursop and avocado. On the basis of 16S rDNA gene sequence analysis, this strain was identified as Bacillus atrophaeus. A preventive treatment using cell free supernatant, reduced severity and incidence of anthracnose disease on harvested soursop and avocado fruit. B. atrophaeus strain B5 harbors genes involved in the production of antibiotics such as surfactin, bacillomycin and iturin, which could be contributing to the efficiency of the preventive treatment during postharvest. The antagonistic role of metabolites contained in the cell free supernatant against anthracnose disease, provide a new approach by which to attack this problem and can help reduce the use of chemical pesticides, environmental pollution, leading to the safer fruit preservation.