Antifungal potential against Sclerotinia sclerotiorum (Lib.) de Bary and plant growth promoting abilities of Bacillus isolates from canola (Brassica napus L.) roots

Unraveling Whole-Genome Sequence and Functional Characterization of P. megaterium PH3

Priestia megaterium (P. megaterium PH3) is an endophytic bacterium isolated from peanuts. It has natural resveratrol production ability and shows potential application value. This study analyzed its genetic function and metabolic mechanism through whole-genome sequencing and found that the genome size is 5,960,365 bp, the GC content is 37.62%, and 6132 genes are annotated. Functional analysis showed that this strain contained 149 carbohydrate active enzyme genes, 7 secondary metabolite synthesis gene clusters, 509 virulence genes, and 273 drug-resistance genes. At the same time, this strain has the ability to regulate salt stress, low temperature, and hypoxia. Genomic analysis reveals a stilbene-synthase-containing type III polyketide synthase gene cluster that contributes to resveratrol synthesis. A safety assessment showed that the strain is non-hemolytic, does not produce amino acid decarboxylase, and is not resistant to multiple antibiotics. In the mouse model, P. megaterium PH3 did not have significant effects on body weight, behavior, or physiological indicators. These results provide important basic data and theoretical support for its industrial application and the research and development of plant protection agents.

Evaluation of the Antifungal and Biochemical Activities of Fungicides and Biological Agents against Ginseng Sclerotinia Root Rot Caused by Sclerotinia nivalis

The objective of this study was to identify effective agents for the prevention and control of ginseng Sclerotinia root rot disease caused by Sclerotinia nivalis. The inhibitory effects of 16 chemical fungicides and 10 biocontrol agents (strains) on mycelial growth and sclerotium formation in S. nivalis were determined using a plate confrontation essay. The results showed that the best chemical agents for inhibiting the mycelial growth and sclerotium formation of S. nivalis were fluconazole and fludioxonil, while Bacillus amyloliquefaciens FS6 and B. subtilis (Kono) were the best biocontrol agents (strains). The results of field trials in 2022 and 2023 showed that the control effects of fluconazole and fludioxonil on ginseng Sclerotinia root rot disease were 90.60-98.16%, and those of the biocontrol agents B. amyloliquefaciens FS6 and B. subtilis (Kono) were 94.80-97.24%, respectively. Chemical agents produced abnormal and twisted mycelia, while the biocontrol agents increased mycelial branching, dilated the mycelium tip, and revealed an abnormal balloon. All of the fungicides decreased the ergosterol content, changed the cell membrane permeability, and increased the protein and nucleic acid permeability. These results suggest that these are potential agents for controlling ginseng Sclerotinia root rot disease, and their biochemical mechanisms of chemical and biocontrol of this disease were demonstrated.

Exploring plant growth promoting traits and biocontrol potential of new isolated Bacillus subtilis BS-2301 strain in suppressing Sclerotinia sclerotiorum through various mechanisms

Sclerotinia sclerotiorum (Lib.) de Bary is the causative agent of stem white mold disease which severely reduces major crop productivity including soybean and rapeseed worldwide. The current study aimed to explore plant growth-promoting traits and biocontrol of new isolated Bacillus subtilis BS-2301 to suppress S. sclerotiorum through various mechanisms. The results indicated that the BS-2301 exhibited strong biocontrol potential against S. sclerotiorum up to 74% both in dual culture and partition plate experiments. The BS-2301 and its crude extract significantly suppressed S. sclerotiorum growth involving excessive reactive oxygen species (ROS) production in mycelia for rapid death. Furthermore, the treated hyphae produced low oxalic acid (OA), a crucial pathogenicity factor of S. sclerotiorum. The SEM and TEM microscopy of S. sclerotiorum showed severe damage in terms of cell wall, cell membrane breakage, cytoplasm displacement, and organelles disintegration compared to control. The pathogenicity of S. sclerotiorum exposed to BS-2301 had less disease progression potential on soybean leaves in the detached leaf assay experiment. Remarkably, the strain also demonstrated broad-range antagonistic activity with 70%, and 68% inhibition rates against Phytophthora sojae and Fusarium oxysporum, respectively. Furthermore, the strain exhibits multiple plant growth-promoting and disease-prevention traits, including the production of indole-3-acetic acid (IAA), siderophores, amylases, cellulases and proteases as well as harboring calcium phosphate decomposition activity. In comparison to the control, the BS-2301 also showed great potential for enhancing soybean seedlings growth for different parameters, including shoot length 31.23%, root length 29.87%, total fresh weight 33.45%, and total dry weight 27.56%. The antioxidant enzymes like CAT, POD, SOD and APX under BS-2301 treatment were up-regulated in S. sclerotiorum infected plants along with the positive regulation of defense-related genes (PR1-2, PR10, PAL1, AOS, CHS, and PDF1.2). These findings demonstrate that the BS-2301 strain possesses a notable broad-spectrum biocontrol potential against different phytopathogens and provides new insight in suppressing S. sclerotiorum through various mechanisms. Therefore, BS-2301 will be helpful in the development of biofertilizers for sustainable agricultural practices.

Biocontrol and growth promotion potential of Bacillus velezensis NT35 on Panax ginseng based on the multifunctional effect

The Bacillus velezensis strain NT35, which has strong biocontrol ability, was isolated from the rhizosphere soil of Panax ginseng. The antifungal effects of the NT35 strain against the mycelium and spore growth of Ilyonectria robusta, which causes ginseng rusty root rot, were determined. The inhibitory rate of I. robusta mycelial growth was 94.12% when the concentration of the NT35 strain was 107 CFU·mL-1, and the inhibitory rates of I. robusta sporulation and spore germination reached 100 and 90.31%, respectively, when the concentration of the NT35 strain was 104 and 108 CFU·mL-1, respectively. Strain NT35 had good prevention effects against ginseng rust rot indoors and in the field with the control effect 51.99%, which was similar to that of commercial chemical and biocontrol agents. The labeled strain NT35-Rif160-Stre400 was obtained and colonized ginseng roots, leaves, stems and rhizosphere soil after 90 days. Bacillus velezensis NT35 can induce a significant increase in the expression of five defensive enzyme-encoding genes and ginsenoside biosynthesis-related genes in ginseng. In the rhizosphere soil, the four soil enzymes and the microbial community improved during different periods of ginseng growth in response to the biocontrol strain NT35. The NT35 strain can recruit several beneficial bacteria, such as Luteimonas, Nocardioides, Sphingomonas, and Gemmatimonas, from the rhizosphere soil and reduce the relative abundance of Ilyonectria, Fusarium, Neonectria and Dactylonectria, which cause root rot and rusty root rot in ginseng plants. The disease indices were significantly negatively correlated with the abundances of Sphingomonas and Trichoderma. Additionally, Sphingomonadales, Sphingomonadaceae and actinomycetes were significantly enriched under the NT35 treatment according to LEfSe analysis. These results lay the foundation for the development of a biological agent based on strain NT35.

Bacillus velezensis LT1: a potential biocontrol agent for southern blight on Coptis chinensis

Introduction

Southern blight, caused by Sclerotium rolfsii, poses a serious threat to the cultivation of Coptis chinensis, a plant with significant medicinal value. The overreliance on fungicides for controlling this pathogen has led to environmental concerns and resistance issues. There is an urgent need for alternative, sustainable disease management strategies.

Methods

In this study, Bacillus velezensis LT1 was isolated from the rhizosphere soil of diseased C. chinensis plants. Its biocontrol efficacy against S. rolfsii LC1 was evaluated through a confrontation assay. The antimicrobial lipopeptides in the fermentation liquid of B. velezensis LT1 were identified using Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF-MS). The effects of B. velezensis LT1 on the mycelial morphology of S. rolfsii LC1 were examined using scanning electron microscopy (SEM) and transmission electron microscopy (TEM).

Results

The confrontation assay indicated that B. velezensis LT1 significantly inhibited the growth of S. rolfsii LC1, with an inhibition efficiency of 78.41%. MALDI-TOF-MS analysis detected the presence of bacillomycin, surfactin, iturin, and fengycin in the fermentation liquid, all known for their antifungal properties. SEM and TEM observations revealed that the mycelial and cellular structures of S. rolfsii LC1 were markedly distorted when exposed to B. velezensis LT1.

Discussion

The findings demonstrate that B. velezensis LT1 has considerable potential as a biocontrol agent against S. rolfsii LC1. The identified lipopeptides likely contribute to the antifungal activity, and the morphological damage to S. rolfsii LC1 suggests a mechanism of action. This study underscores the importance of exploring microbial biocontrol agents as a sustainable alternative to chemical fungicides in the management of plant diseases. Further research into the genetic and functional aspects of B. velezensis LT1 could provide deeper insights into its biocontrol mechanisms and facilitate its application in agriculture.

Genome-guided purification of high amounts of the siderophore ornibactin and detection of potentially novel burkholdine derivatives produced by Burkholderia catarinensis 89T

AIM

The increased availability of genome sequences has enabled the development of valuable tools for the prediction and identification of bacterial natural products. Burkholderia catarinensis 89T produces siderophores and an unknown potent antifungal metabolite. The aim of this work was to identify and purify natural products of B. catarinensis 89T through a genome-guided approach.

MATERIALS AND METHODS

The analysis of B. catarinensis 89T genome revealed 16 clusters putatively related to secondary metabolism and antibiotics production. Of particular note was the identification of a nonribosomal peptide synthetase (NRPS) cluster related to the production of the siderophore ornibactin, a hybrid NRPS-polyketide synthase Type 1 cluster for the production of the antifungal glycolipopeptide burkholdine, and a gene cluster encoding homoserine lactones (HSL), probably involved in the regulation of both metabolites. We were able to purify high amounts of the ornibactin derivatives D/C6 and F/C8, while also detecting the derivative B/C4 in mass spectrometry investigations. A group of metabolites with molecular masses ranging from 1188 to 1272 Da could be detected in MS experiments, which we postulate to be new burkholdine analogs produced by B. catarinensis. The comparison of B. catarinensis BGCs with other Bcc members corroborates the hypothesis that this bacterium could produce new derivatives of these metabolites. Moreover, the quorum sensing metabolites C6-HSL, C8-HSL, and 3OH-C8-HSL were observed in LC-MS/MS analysis.

CONCLUSION

The new species B. catarinensis is a potential source of new bioactive secondary metabolites. Our results highlight the importance of genome-guided purification and identification of metabolites of biotechnological importance.

Siderophore of plant growth promoting rhizobacterium origin reduces reactive oxygen species mediated injury in Solanum spp. caused by fungal pathogens

AIMS

The study aims to explore antifungal properties of bacillibactin siderophore produced by the plant growth-promoting rhizobacterium (PGPR) Bacillus subtilis against fungal phytopathogens Alternaria porri and Fusarium equiseti isolated from Solanum lycopersicum and Solanum melongena plants.

METHODS AND RESULTS

Alternaria porri and F. equiseti were isolated from infected plants of eggplant and tomato, respectively. A plate assay was employed to assess the effect of bacillibactin against the phytopathogens. The antifungal potential of the PGPR was evaluated by estimation of dry fungal biomass, visualization of cellular deformity using compound and scanning electron microscopy, antioxidative enzyme assay and analysis of membrane damage via using lipid peroxidation. Inductively coupled plasma atomic emission spectroscopy (ICP-AES) analysis was employed to investigate changes in intracellular iron content. The impact of bacillibactin on pathogenesis was evaluated by infecting detached leaves of S. lycopersicum and S. melongena plants with both the pathogens and treating the infected leaves with bacillibactin. Leaves were further investigated for ROS accumulation, extent of necrosis and cell death. Our findings revealed significant damage to the hyphal structure of A. porri and F. equiseti following treatment with bacillibactin. Biomass reduction, elevated antioxidative enzyme levels, and membrane damage further substantiated the inhibitory effects of the siderophore on fungal growth. ICP-AES analysis indicates an increase in intracellular iron content suggesting enhanced iron uptake facilitated by bacillibactin. Moreover, application of 1500 µg ml-1 bacillibactin on infected leaves demonstrated a substantial inhibition of ROS accumulation, necrosis, and cell death upon bacillibactin treatment.

CONCLUSIONS

This study confirms the potent antagonistic activity of bacillibactin against both the phytopathogens A. porri and F. equiseti growth, supporting its potential as a promising biological control agent for fungal plant diseases. Bacillibactin-induced morphological, physiological, and biochemical alterations in the isolated fungi and pathogen-infected leaves highlight the prospects of bacillibactin as an effective and sustainable solution to mitigate economic losses associated with fungal infections in vegetable crops.

Mechanism of Salt Tolerance and Plant Growth Promotion in Priestia megaterium ZS-3 Revealed by Cellular Metabolism and Whole-Genome Studies

Approximately one-third of agricultural land worldwide is affected by salinity, which limits the productivity and sustainability of crop ecosystems. Plant-growth-promoting rhizobacteria (PGPR) are a potential solution to this problem, as PGPR increases crop yield through improving soil fertility and stress resistance. Previous studies have shown that Priestia megaterium ZS-3(ZS-3) can effectively help plants tolerate salinity stress. However, how ZS-3 regulates its metabolic adaptations in saline environments remains unclear. In this study, we monitored the metabolic rearrangement of compatibilisers in ZS-3 and combined the findings with genomic data to reveal how ZS-3 survives in stressful environments, induces plant growth, and tolerates stress. The results showed that ZS-3 tolerated salinity levels up to 9%. In addition, glutamate and trehalose help ZS-3 adapt to osmotic stress under low NaCl stress, whereas proline, K+, and extracellular polysaccharides regulate the osmotic responses of ZS-3 exposed to high salt stress. Potting experiments showed that applying the ZS-3 strain in saline and neutral soils could effectively increase the activities of soil acid phosphatase, urease, and invertase in both soils, thus improving soil fertility and promoting plant growth. In addition, strain ZS-3-GFP colonised the rhizosphere and leaves of Cinnamomum camphora well, as confirmed by confocal microscopy and resistance plate count analysis. Genomic studies and in vitro experiments have shown that ZS-3 exhibits a variety of beneficial traits, including plant-promoting, antagonistic, and other related traits (such as resistance to saline and heavy metal stress/tolerance, amino acid synthesis and transport, volatile compound synthesis, micronutrient utilisation, and phytohormone biosynthesis/regulatory potential). The results support that ZS-3 can induce plant tolerance to abiotic stresses. These data provide important clues to further reveal the interactions between plants and microbiomes, as well as the mechanisms by which micro-organisms control plant health.

Bioprospecting and Challenges of Plant Microbiome Research for Sustainable Agriculture, a Review on Soybean Endophytic Bacteria

This review evaluates oilseed crop soybean endophytic bacteria, their prospects, and challenges for sustainable agriculture. Soybean is one of the most important oilseed crops with about 20-25% protein content and 20% edible oil production. The ability of soybean root-associated microbes to restore soil nutrients enhances crop yield. Naturally, the soybean root endosphere harbors root nodule bacteria, and endophytic bacteria, which help increase the nitrogen pool and reclamation of another nutrient loss in the soil for plant nutrition. Endophytic bacteria can sustain plant growth and health by exhibiting antibiosis against phytopathogens, production of enzymes, phytohormone biosynthesis, organic acids, and secondary metabolite secretions. Considerable effort in the agricultural industry is focused on multifunctional concepts and bioprospecting on the use of bioinput from endophytic microbes to ensure a stable ecosystem. Bioprospecting in the case of this review is a systemic overview of the biorational approach to harness beneficial plant-associated microbes to ensure food security in the future. Progress in this endeavor is limited by available techniques. The use of molecular techniques in unraveling the functions of soybean endophytic bacteria can explore their use in integrated organic farming. Our review brings to light the endophytic microbial dynamics of soybeans and current status of plant microbiome research for sustainable agriculture.

Exploring plant growth-promoting, biocatalytic, and antimicrobial potential of salt tolerant rhizospheric Georgenia soli strain TSm39 for sustainable agriculture

To explore the in vivo and in vitro plant growth promoting activities, biocatalytic potential, and antimicrobial activity of salt tolerance rhizoactinobacteria, rhizospheric soil of a halotolerant plant Saueda maritima L. was collected from Rann of Tiker, near Little Rann of Kutch, Gujarat (India). The morphology analysis of the isolated strain TSm39 revealed that the strain belonged to the phylum actinobacteria, as it was stained Gram-positive, displayed filamentous growth, showed spore formation and red pigment production on starch casein agar (SCA). It was identified as Georgenia soli based on 16S rRNA gene sequencing. The Georgenia soli strain TSm39 secreted extracellular amylase, pectinase, and protease. It showed in vitro plant growth-promoting (PGP) activities such as indole acetic acid (IAA) production, siderophore production, ammonia production, and phosphate solubilization. In vivo plant growth-promoting traits of strain TSm39 revealed 30% seed germination on water agar and vigor index 374.4. Additionally, a significant increase (p ≤ 0.05) was found in growth parameters such as root length (16.1 ± 0.22), shoot length (15.2 ± 0.17), the fresh weight (g), and dry weight (g) of the roots (0.43 ± 0.42 and 0.32 ± 0.12), shoots (0.62 ± 0.41 and 0.13 ± 0.03), and leaves (0.42 ± 0.161 and 0.14 ± 0.42) in treated seeds of Vigna radiata L. plant with the strain TSm39 compared to control. The antibiotic susceptibility profile revealed resistance of the strain TSm39 to erythromycin, ampicillin, tetracycline, and oxacillin, while it displayed maximum sensitivity to vancomycin (40 ± 0.72), chloramphenicol (40 ± 0.61), clarithromycin (40 ± 1.30), azithromycin (39 ± 0.42), and least sensitivity to teicoplanin (15 ± 0.15). Moreover, the antimicrobial activity of the strain TSm39 was observed against Gram's positive and Gram's negative microorganisms such as Shigella, Proteus vulgaris, and Bacillus subtilis. These findings indicated that the Georgenia soli strain TSm39 has multiple plant-growth-promoting properties and biocatalytic potential that signifies its agricultural applications in the enhancement of crop yield and quality and would protect the plant against plant pathogens.

Termite Nest Associated Bacillus siamensis YC-9 Mediated Biocontrol of Fusarium oxysporum f. sp. cucumerinum

The antagonistic potential of bacteria obtained from the nest of Odontotermes formosanus was assessed against Fusarium oxysporum f. sp. cucumerinum (FOC). Of 30, seven termite nest-associated bacteria strains had biocontrol potential. Among them, the strain YC-9 showed the strongest antifungal activity toward FOC. Phylogenetic analysis of the 16S rRNA amplified product of YC-9 revealed its identification as Bacillus siamensis. The in vivo antifungal activity experiment showed that the application of YC-9 at 10⁸ cfu/ml significantly reduced the cucumber wilt incidence with a control efficacy of 73.2%. Furthermore, plant growth parameters such as fresh weight, dry weight, plant height, and root height were significantly improved by 42.6, 53.0, 20.8, and 19.3%, respectively. We found that inoculation with B. siamensis YC-9 significantly increased the activity of defensive enzymes such as peroxidase (POD), polyphenol oxidase (PPO), and phenylalanine ammonia-lyase (PAL) in diseased cucumber roots, thereby raising the resistance. PCR using gene-specific primers revealed that B. siamensis YC-9 contains biosynthetic genes for known antibiotics, including bacillomycin, iturin, and surfactin. Chemical analysis of the cultivation of B. siamensis YC-9 resulted in the isolation of five metabolites, including hexadecanoic acid (1), cyclo-(L-phenylalanylglycine) (2), cyclo-(L-trans-Hyp-L-Leu) (3), C₁₅-surfactin (4), and macrolactin A (5), the structures of which were identified by the analysis of NMR spectroscopic data and MS. Among them, the compound 4 showed significant antifungal activity against conidial germination of FOC with an IC₅₀ value of 5.1 μg/ml, which was comparable to that of the positive control, cycloheximide (IC₅₀ value of 2.6 μg/ml). Based on these findings, this study suggests that termite-nest associated B. siamensis YC-9 could be a potential biological control agent for integrated control of soil-borne diseases like cucumber Fusarium wilt.

Pangenome analyses of Bacillus pumilus, Bacillus safensis, and Priestia megaterium exploring the plant-associated features of bacilli strains isolated from canola

Previous genome mining of the strains Bacillus pumilus 7PB, Bacillus safensis 1TAz, 8Taz, and 32PB, and Priestia megaterium 16PB isolated from canola revealed differences in the profile of antimicrobial biosynthetic genes when compared to the species type strains. To evaluate not only the similarities among B. pumilus, B. safensis, and P. megaterium genomes but also the specificities found in the canola bacilli, we performed comparative genomic analyses through the pangenome evaluation of each species. Besides that, other genome features were explored, especially focusing on plant-associated and biotechnological characteristics. The combination of the genome metrics Average Nucleotide Identity and digital DNA-DNA hybridization formulas 1 and 3 adopting the universal thresholds of 95 and 70%, respectively, was suitable to verify the identification of strains from these groups. On average, core genes corresponded to 45%, 52%, and 34% of B. pumilus, B. safensis, and P. megaterium open pangenomes, respectively. Many genes related to adaptations to plant-associated lifestyles were predicted, especially in the Bacillus genomes. These included genes for acetoin production, polyamines utilization, root exudate chemoreceptors, biofilm formation, and plant cell-wall degrading enzymes. Overall, we could observe that strains of these species exhibit many features in common, whereas most of their variable genome portions have features yet to be uncovered. The observed antifungal activity of canola bacilli might be a result of the synergistic action of secondary metabolites, siderophores, and chitinases. Genome analysis confirmed that these species and strains have biotechnological potential to be used both as agricultural inoculants or hydrolases producers. Up to our knowledge, this is the first work that evaluates the pangenome features of P. megaterium.