Metagenomic profiling of tobacco root endophytes reveals a disease-suppressive Enterobacter strain against Fusarium solani

Fusarium oxysporum-Induced Root Rot Severity Reshapes the Soybean Rhizosphere Microbiome and Affects Its Functional Potential

Soybean root rot caused by Fusarium oxysporum is an important soil-borne disease that affects soybean growth and disrupts rhizosphere microbial communities. However, how rhizosphere microbiomes respond to different levels of disease severity remains poorly understood. In this study, a five-level root rot severity gradient (F0–F4) was established using a carrier-matched inoculation design, and changes in soybean growth, rhizosphere soil properties, enzyme activities, microbial community composition, and functional potential were investigated using shotgun metagenomic sequencing. Increasing disease severity reduced soybean growth, with leaf area decreasing from 312.98 cm2 in F0 to 32.45 cm2 in F4. Root rot progression altered rhizosphere microbial communities, with fungal communities showing stronger responses than bacterial communities. The bacterial Chao1 richness index increased by 34.6% in F4 compared with F0, whereas fungal Shannon diversity decreased by 46.7%. Taxonomic analysis revealed clear shifts in microbial community composition, with Fusarium becoming strongly enriched under diseased conditions, increasing from 16.9% in F0 to maximum relative abundance of 68.8% in F2 and remaining highly abundant at 61.5% in F4, while Trichoderma decreased from 7.3% to 2.2% and Rhizophagus declined from 38.1% to nearly undetectable levels. Metagenomic functional profiling revealed disease-associated changes in microbial functional potential, particularly in pathways related to metabolism, membrane transport, signal transduction, and secondary metabolite biosynthesis. In addition, soil physicochemical properties and enzyme activities varied across the disease severity gradient, indicating changes in the rhizosphere environment during disease development. Overall, soybean root rot progression was associated with coordinated changes in plant performance, soil biochemical characteristics, microbial community structure, and functional potential, with fungal communities exhibiting stronger responses to disease-associated disturbance than bacterial communities.

Whole-genome sequencing and characterization of Pseudomonas stutzeri P1 endophyte isolated from potato unveils plant growth-promoting and other traits

The potential of P1 as a promising bioinoculant candidate for sustainable agriculture in the potato sector is demonstrated and the genome lacked major virulence factors and antimicrobial traits, supporting the non-pathogenic nature of the P1 strain.

Antifungal Activity and Transcriptomic Profiling of Equisetin from Endophytic Fusarium incarnatum Y2 Against Major Wheat Root and Crown Rot Pathogens

Background/Objectives: Wheat root and crown rot, caused by Fusarium pseudograminearum, Fusarium graminearum, and Bipolaris sorokiniana, are devastating soil-borne diseases that cause substantial yield losses worldwide. Endophytic fungi are promising sources of bioactive metabolites for agricultural applications. This study aimed to isolate and characterize an endophytic fungus with antifungal activity against major wheat pathogens, identify its active compound, and investigate the underlying transcriptional response. Methods: An endophytic strain Y2 was isolated from Hedyotis diffusa leaves and identified through morphological and phylogenetic analysis based on TEF-1α and RPB2 sequences. Pathogenicity of strain Y2 was evaluated on wheat stem bases. The bioactive compound was purified by HPLC and identified by HR-ESI-MS and NMR. Antifungal activity was assessed using dual-culture and microbroth dilution assays. Transcriptomic analysis (RNA-seq) was performed on F. pseudograminearum treated with equisetin, with qRT-PCR validation of seven representative differentially expressed genes. Results: Strain Y2 was identified as Fusarium incarnatum or a closely related member of the F. incarnatum–equiseti species complex (FIESC) and confirmed to be non-pathogenic to wheat. The purified bioactive compound was characterized as equisetin, which exhibited significant antifungal activity with MIC values of 16, 32, and 64 μg/mL against F. pseudograminearum, B. sorokiniana, and F. graminearum, respectively. Transcriptomic analysis revealed that equisetin treatment induced a polarized transcriptional response in F. pseudograminearum, characterized by strong upregulation of ribosome and translation-related genes and widespread downregulation of other metabolic pathways, particularly nitrogen metabolism. qRT-PCR validation of seven representative genes confirmed the reliability of the RNA-seq data. Conclusions: Our findings demonstrate that equisetin is the active antifungal metabolite produced by F. incarnatum Y2, with potent in vitro activity against major wheat root and crown rot pathogens. The transcriptomic data provide insights into the potential mechanism of action, while the non-pathogenic nature of strain Y2 supports its biosafety. Although these results highlight equisetin as a promising lead compound for antifungal development, further in planta efficacy and safety studies are required before it can be considered for practical biocontrol.

Comparative Insights into Bacterial Endophytome and Antifungal Metabolites in Fusarium Wilt-Resistant and -Susceptible Banana Cultivars Unveil the Resistance Toward Fusarium oxysporum f. sp. cubense

India contributes 26% of global banana production, yet cultivation is severely threatened by Fusarium wilt (Fusarium oxysporum f. sp. cubense, Foc), necessitating sustainable, eco-friendly management strategies. This study evaluated the biocontrol potential of endophytic bacteria isolated from Foc-resistant and -susceptible banana cultivars. Isolates from the pseudostem, corm, and root of the resistant cultivar showed significantly greater inhibitory activity than those from the susceptible cultivar, underscoring the role of host genotype in shaping functionally competent endophytic communities. Among all isolates, Bacillus sp. from the corm of cv. Rose (AB) showed the highest mycelial inhibition of Foc (70.37–76.54%) in vitro. GC-MS-based metabolite profiling revealed a chemically diverse array of secondary metabolites, fatty acid esters, steroids, terpenoids, siloxanes, and nitrogenous compounds. Corm-associated endophytes exhibited membrane-disruptive and cytotoxic activity, while root-associated endophytes contributed protective, defense-modulatory effects. Halomonas sp. RoRo2 and B. subtilis RoC1 showed the highest inhibition in both agar-well and in planta assays, with unsaturated fatty acids and organic acid derivatives implicated as key antifungal effectors acting through multiple biochemical pathways. These findings identify metabolically versatile endophytes as promising candidates for developing efficient, environmentally compatible bioinoculants as sustainable alternatives to chemical control of Fusarium wilt in banana.

ZmHPATR1 orchestrates phyllosphere organic acid flux to recruit Sphingomonas and enhance resistance of maize to Curvularia leaf spot

Leaf spots caused by Curvularia lunata infection pose a significant threat to global maize production. Although resistance gene breeding faces challenges due to pathogen evolution, the plant microbiome has emerged as a key modulator of disease resistance. However, the mechanisms via which plant genes regulate phyllosphere metabolites to recruit beneficial microbes remain poorly understood. Here, we combined gene mapping, metabolomics, microbiome analyses, cytological analysis, and in vitro and in vivo experiments to investigate the disease resistance mechanism of ZmHPATR1. We first identified that the loss‐of‐function mutation in ZmHPATR1 significantly increased the levels of fumaric acid, folic acid, and tetrahydrofolic acid in the leaves, leading to the enrichment of the genus Sphingomonas. We further demonstrated that the extracellular polysaccharide, welan gum, biosynthesized by Sphingomonas, effectively inhibited C. lunata growth and disrupted its cell structure. These results enable us to comprehensively understand the complicated mechanisms of plant resistance to disease through a four‐level regulatory network that links plant genes, metabolites, microbes, and pathogens. Our findings provide new strategies for targeted microbiome‐based disease‐resistant breeding and the development of novel biopesticides for maize.

Integrated biological and chemical strategies for sustainable management of Nigrospora coryli-induced tobacco leaf spot