Overall, Bacillus siamensis strain BACIII combines host-specific plant growth promotion with broad antifungal activity, supporting its potential for biological control in sustainable agriculture.
Abstract
Endophytic bacteria of the Bacillus subtilis species complex are known for plant growth promotion and antifungal activity, although strain-specific traits remain poorly understood. This study characterized the Bacillus siamensis strain BACIII, isolated from asymptomatic soybean roots in a charcoal rot-affected area, using whole-genome analysis and phenotypic assays. Genome sequencing identified BACIII as Bacillus siamensis and revealed a metabolically versatile genome containing twelve biosynthetic gene clusters linked to antimicrobial compounds such as difficidin, fengycin, and surfactin. Additionally, genomic islands associated with mobile elements, regulation, and stress response suggest adaptive potential. Inoculation with the BACIII strain significantly accelerated germination and increased early growth, biomass accumulation, and chlorophyll content in soybean and sunn hemp (p < 0.05), whereas no significant effects were observed in cotton or sunflower, indicating host-dependent responses. In vitro assays demonstrated consistent inhibition of several phytopathogenic fungi, including Sclerotinia sclerotiorum, Fusarium spp., and Macrophomina phaseolina, with variable intensity. Overall, BACIII combines host-specific plant growth promotion with broad antifungal activity, supporting its potential for biological control in sustainable agriculture.
Soybean is an important global crop, but its production is often limited by root rot, which causes severe yield and quality losses. In this study, a potent antagonistic bacterium, Bacillus velezensis B05, was isolated from the rhizosphere of healthy soybean plants. Genome analysis identified eight biosynthetic gene clusters, including bacilysin and macrolide H, as well as 34 carbohydrate-active enzymes, suggesting its biocontrol potential. Metabolomic analysis detected 621 metabolites, and KEGG enrichment results were consistent with the genomic predictions. The cell-free supernatant of B05 significantly inhibited the growth of Fusarium spp. by 65.85%, spore germination by 75.85%, and disease incidence by 62.5%. Scanning electron microscopy revealed severe damage to fungal cells, including spore deformation and hyphal disintegration. In addition, B05 produced lytic enzymes and siderophores related to plant growth promotion. These results indicate that B. velezensis B05 has potential as a multifunctional biocontrol agent for sustainable management of soybean root rot.
Gao Zhang, Yongsheng Jiang, Zhenshuo Zhang et al.· Journal of Agricultural and...· 0 citations
Endophytic bacteria play an important role in plant growth promotion and stress tolerance, offering sustainable alternatives to chemical inputs in agriculture. In this study, an endophytic bacterial strain P1 was isolated and identified as
Pseudomonas stutzeri
, a plant-associated bacterium exhibiting multiple plant growth–promoting traits (PGPTs). Biochemical (qualitative and quantitative) and
in vitro
analyses demonstrated nitrogen fixation, phosphate solubilization, ammonia production, indole-3-acetic acid (IAA) production, biofilm formation, and tolerance to abiotic stresses, including salinity and drought. Furthermore, the P1 strain displayed strong biocontrol activity against the fungal pathogen
Fusarium oxysporum
f. sp.
cumini,
indicating its potential to mitigate biotic stress. Whole-genome sequencing generated a high-quality complete genome of 4,758,235 bp. Functional annotation showed enrichment of metabolic pathways associated with plant-microbe interactions and environmental adaptation. Further analyses using KEGG and PGPT-pred data confirmed the presence of genes associated with direct and indirect PGPT, such as nitrogen fixation, phosphate solubilization, biofilm formation, and stress tolerance. The genome also contained genes related to CAZymes, adhesion, and motility, highlighting a strong plant association, whereas the genome lacked major virulence factors and antimicrobial traits, supporting the non-pathogenic nature of the P1 strain. Overall, these findings demonstrate the potential of P1 as a promising bioinoculant candidate for sustainable agriculture in the potato sector.
Poonam Patel, K. Raval, Satyamitra Shekh et al.· Frontiers in Microbiology· 0 citations
Seed-associated microbiota are emerging as key determinants of early plant establishment and resilience, yet their functional potential in wheat remains underexplored. Here, we isolated and functionally characterized culturable bacterial endophytes from seeds of Triticum aestivum cvs. Saekeumkang, Baeggang, and Ariheuk to assess plant growth promotion and pathogen suppression. Sixteen bacterial strains, belonging to Pseudomonadota, Actinomycetota, and Bacillota, were identified using 16S rRNA gene sequencing. Functional assays revealed the high prevalence of plant growth-promoting traits, with all isolates producing indole-3-acetic acid and 56.25% exhibiting phosphate-solubilizing activity, whereas siderophore production was restricted to Pseudomonas poae WSSR12. Despite this apparent functional redundancy, in planta assays demonstrated strong strain-specific effects on seedling biomass. Neobacillus cucumis WSSR17 consistently induced the highest increase in fresh weight. In parallel, dual culture assays against multiple Fusarium pathogens revealed that only one isolate, Calidifontibacillus erzurumensis WSSR11, showed consistent antifungal activity across all tested Fusarium strains. Notably, isolates combining multiple functional traits did not always correspond to the strongest growth promotion, underscoring the importance of host-microbe compatibility and trait expression in planta. Collectively, these findings reveal a functionally diverse seed endophytic community with complementary roles in plant growth and disease suppression. We propose that rational selection and combination of complementary strains, particularly N. cucumis WSSR17 (growth promotion), C. erzurumensis WSSR11 (biocontrol), and P. poae WSSR12 (multifunctional nutrient mobilization) could enable the development of targeted, multi-strain bioinoculant strategies for wheat. This study advances our understanding of seed microbiome functionality and provides a foundation for microbiome-informed crop improvement.
AIMS
To isolate and characterize a rhizosphere-derived Bacillus velezensis strain with biocontrol and plant growth-promoting potential, and to evaluate its efficacy against plant pathogens together with its genomic basis.
METHODS AND RESULTS
A bacterial strain (BJ-1141) was isolated from the rhizosphere and identified as B. velezensis based on morphological characteristics and phylogenetic analyses of 16S rRNA and gyrA gene sequences. The strain exhibited broad-spectrum antagonistic activity against 24 plant pathogenic fungi, inhibiting 23 pathogens by more than 50%, with a maximum inhibition rate of 95.57%. BJ-1141 produced hydrolytic enzymes (amylase, protease, cellulase and pectinase) and plant growth-promoting factors, including siderophores and indole-3-acetic acid (IAA). It also demonstrated phosphorus solubilization, nitrogen fixation and biofilm formation. Greenhouse experiments showed that root application of BJ-1141 effectively controlled tomato Fusarium wilt caused by Fusarium oxysporum f. sp. lycopersici, achieving control efficacies of 81.13 - 85.93%, which were higher than those of chemical and commercial microbial treatments. In addition, BJ-1141 significantly increased plant height, biomass and chlorophyll content in tomato and lettuce seedlings. Whole-genome sequencing revealed a 3 902 965 bp genome containing 13 biosynthetic gene clusters associated with antimicrobial secondary metabolites, including surfactin, fengycin, bacillaene, difficidin, macrolactin H, bacillibactin and bacilysin.
CONCLUSIONS
B. velezensis BJ-1141 is a multifunctional bacterial strain with strong biocontrol efficacy and plant growth-promoting traits, supported by genomic evidence, and represents a promising candidate for sustainable crop disease management.
Yunyun Chen, Mei Liu, Wei Zhang et al.· Journal of Applied Microbiol...· 0 citations
Endophytic bacteria represent a promising, sustainable alternative to synthetic agrochemicals for plant disease management by actively antagonizing phytopathogens and stimulating host immune responses. Despite its traditional use as an antimicrobial remedy, Wedelia chinensis remains underexplored as a source of beneficial endophytes. This study aimed to isolate and screen endophytic bacteria from W. chinensis for their antifungal activity against Fusarium oxysporum. Among 14 endophytic isolates, Bacillus subtilis LS1-5 showed the strongest antifungal activity by dual culture assay. Its cell-free culture filtrate effectively inhibited fungal spore germination by 91.3% at a 20% concentration. Crucially, B. subtilis LS1-5 produced several extracellular enzymes, including cellulase, amylase, chitinase, pectinase, gelatinase, lipase, and protease. Furthermore, the LS1-5 strain exhibited a broad array of plant growth-promoting and environmental resilience traits. Notably, it synthesized indole-3-acetic acid (IAA) at 2.11 ± 0.27 µg/mL in an LB medium without L-tryptophan, significantly promoted a 34.19% increase in root elongation, and demonstrated remarkable tolerance to extreme conditions, including high salinity (11% NaCl) and broad pH levels ranging from 6 to 12. Additionally, volatile organic compounds (VOCs) emitted by LS1-5 significantly inhibited the severe bacterial pathogens Xanthomonas oryzae (45.83%) and Xanthomonas citri (47.99%). These findings highlight B. subtilis LS1-5 as a highly effective candidate for biological control and sustainable agricultural applications.
D. Nguyen, Dong Tang Vien, Ngoc-Minh Truong Bui et al.· IOP Conference Series: Earth...· 0 citations
Fungi are major phytopathogens that have a strong impact on agricultural productivity. Recently, biological control has gained attention for managing plant pathogenic fungi due to its eco-friendly characteristics. Hence, using biological agents to replace chemical fungicides is a viable alternative approach in sustainable agriculture systems. In this study, we demonstrated the potentiality of Streptomyces sp. VNUA24 as a promising biocontrol agent. The strain strongly inhibited mycelial growth of several common pathogenic fungi. Its culture filtrate also altered fungal morphology, restricted hyphal elongation, inhibited spore germination, and suppressed fungal virulence. Biochemical assays and genomic analysis revealed the productions and encoding genes for several hydrolytic enzymes. The antiSMASH analysis identified 38 biosynthetic gene clusters in the genome. Interestingly, many of these exhibited strong homologies to clusters responsible for producing established antifungal metabolites such as ɛ-poly-L-lysine, concanamycin A, informatipeptin, and humidimycin. These findings highlight the strong antifungal potential of Streptomyces sp. VNUA24 and suggest that it is a promising candidate for developing microbial control agents in sustainable fungal disease management.
T. Dang, Thu Thi Nguyen, Giang Van Nguyen et al.· Plant Pathology Journal· 0 citations