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PubMed2026

Unlocking antifungal mechanisms of natural 3-(oxazole-5-yl) indole compound derived from Streptomyces syringium against plant gray mold caused by Botrytis cinerea.

BACKGROUND: Plant fungal diseases cause significant agricultural losses, and Streptomyces-derived antifungal compounds offer a promising biocontrol strategy. This study aimed to isolate and characterize bioactive metabolites from Streptomyces syringium LZ036 and evaluate their activity and mechanism of action against Botrytis cinerea. RESULTS: A strain LZ036 with broad-spectrum antifungal activity was identified as Streptomyces syringium. The 3-(oxazole-5-yl) indole compound NL3 isolated from this strain exhibited potent broad-spectrum antifungal activity, especially against Botrytis cinerea. Compound NL3 inhibited fungal growth and development by inducing severe oxidative damage and membrane disruption. And it could trigger jasmonic acid (JA)-dependent induced systemic resistance (ISR) in plants. Transcriptomic analysis of compound NL3-treated Botrytis cinerea revealed genome-wide transcriptional alterations, including disruption of energy metabolism and mitochondrial function. Key genes related to mitogen-activated protein kinase (MAPK) signaling pathway down-regulated significantly, among which the catalytic S_TKc domain of Bcste7 exhibited a predicted interaction with compound NL3 through hydrophobic interactions and hydrogen bonding. CONCLUSION: The Streptomyces syringium-derived compound NL3 shows high potential as a green fungicide, acting through multiple mechanisms. These findings advance the development of Streptomyces-based antifungal agents. © 2026 Society of Chemical Industry.

3‐(oxazole‐5‐yl) indole compo↗
PubMed2026

Novel Genomic Regions Associated with Multifungicide Resistance in Botrytis cinerea and Factors Impacting Greenhouse Population Structure.

The fungal plant pathogen Botrytis cinerea affects hundreds of valuable crops, including fruits, vegetables, and ornamental plants. In greenhouse production systems, B. cinerea disease management largely depends on the use of fungicides; however, the emergence of resistance to multiple fungicide classes has become a major challenge. An improved understanding of B. cinerea populations can contribute to the development of resistance management strategies. In this study, isolates (n = 276) of B. cinerea were collected from ornamental production greenhouses in Michigan, and whole-genome resequencing was performed to evaluate genetic differentiation among hosts, locations, growing cycles, and fungicide resistance. Discriminant analyses of principal components and analyses of molecular variance revealed limited genetic differentiation among isolates from different hosts, greenhouses, and years of isolate collection. In contrast, the same analyses alongside pairwise fixation indexes and an evaluation of population structure indicated significant genetic differentiation among isolates based on the number of fungicides to which they are resistant. There are two described mechanisms that confer resistance to multiple fungicides at the same time, both of which are mediated by efflux pumps. Results from a quantitative trait genome-wide association study revealed novel genomic regions associated with multifungicide resistance, including two genes that encode putative efflux pumps. An understanding of fungicide resistance patterns is essential for developing durable disease control measures. Our results highlight the importance of continued monitoring of B. cinerea populations, as the observed genetic differentiation linked to fungicide resistance emphasizes their ability to adapt to selection pressure.

Botrytis cinerea↗
PubMed2026

Genome-Wide Identification of NLP Family Genes in Cultivated Strawberry (Fragaria × ananassa Duch.) and Analysis of Their Expression Under Heat and Botrytis cinerea Stresses.

Nodule inception (NIN)-like proteins (NLPs) are plant-specific transcription factors regulating nutrient absorption, growth, and stress tolerance; however, their roles in stress responses remain largely uncharacterized. Cultivated strawberry (Fragaria × ananassa 'Camarosa') serves as an ideal model for dissecting the evolution and function of NLP genes. In this study, 37 FaNLP genes were identified genome-wide. Phylogenetic analysis classified them into three subfamilies, which are evenly distributed across seven chromosomes. Divergent exon-intron structures and conserved motif compositions suggest functional differentiation among FaNLPs. Quantitative real-time PCR (qRT-PCR) revealed distinct expression profiles under heat stress and Botrytis cinerea infection. Notably, FaNLPs were significantly more upregulated in the cultivar 'Shuxing' than in 'Benihoppe'. Heat stress inhibited photosynthesis and altered catalase activity (CAT), superoxide dismutase activities (SOD) and peroxidase activities (POD), whereas fungal infection enhanced chitinase activity in both cultivars. Comparative genomics with Arabidopsis and rice revealed strawberry-specific evolutionary patterns of NLPs. Subcellular localization prediction indicates that FaNLP proteins primarily localize to the nucleus, implying their potential roles as transcriptional regulators. This study links FaNLP sequence characteristics with stress response phenotypes, providing a foundation for elucidating NLP-mediated regulatory networks in strawberry. Future functional assays, including overexpression and knockout analyses, will further clarify the biological roles of FaNLPs.

Fragaria↗
PubMed2026

The genomic resource of Lysinibacillus fusiformis KBD-5, a biocontrol agent with antifungal activity against Botrytis cinerea.

Lysinibacillus fusiformis strain KBD-5, previously known for its antiviral activity against Tobacco mosaic virus, was investigated for its biocontrol potential against the fungal pathogen Botrytis cinerea. In plate assays, conducted with three independent biological replicates and incubated at 28 °C for 5 days, KBD-5 significantly inhibited the mycelial growth of B. cinerea by 76.42%. Whole-genome sequencing revealed a 4.69 Mb genome with a GC content of 37.28%, encoding 4719 proteins. Bioinformatics analysis identified genes involved in antimicrobial functions, including 195 carbohydrate-active enzymes (potentially aiding in fungal cell wall degradation) and 8 gene clusters for secondary metabolite synthesis (e.g., T3PKS with 30% similarity to bacillibactin biosynthetic clusters and NRPS), indicating the production of antifungal metabolites like bacillibactin-like polyketides. The strain also showed a high safety profile with no significant virulence or drug resistance risks. These findings indicate that genomic analysis of KBD-5 reveals the potential for multiple biocontrol mechanisms, supporting its potential development as a biocontrol agent. The draft genome sequence is available under NCBI accession PRJNA1335659.

Botrytis↗
PubMed2021

Spray-induced gene silencing for disease control is dependent on the efficiency of pathogen RNA uptake.

Recent discoveries show that fungi can take up environmental RNA, which can then silence fungal genes through environmental RNA interference. This discovery prompted the development of Spray-Induced Gene Silencing (SIGS) for plant disease management. In this study, we aimed to determine the efficacy of SIGS across a variety of eukaryotic microbes. We first examined the efficiency of RNA uptake in multiple pathogenic and non-pathogenic fungi, and an oomycete pathogen. We observed efficient double-stranded RNA (dsRNA) uptake in the fungal plant pathogens Botrytis cinerea, Sclerotinia sclerotiorum, Rhizoctonia solani, Aspergillus niger and Verticillium dahliae, but no uptake in Colletotrichum gloeosporioides, and weak uptake in a beneficial fungus, Trichoderma virens. For the oomycete plant pathogen, Phytophthora infestans, RNA uptake was limited and varied across different cell types and developmental stages. Topical application of dsRNA targeting virulence-related genes in pathogens with high RNA uptake efficiency significantly inhibited plant disease symptoms, whereas the application of dsRNA in pathogens with low RNA uptake efficiency did not suppress infection. Our results have revealed that dsRNA uptake efficiencies vary across eukaryotic microbe species and cell types. The success of SIGS for plant disease management can largely be determined by the pathogen's RNA uptake efficiency.

Ascomycota↗
PubMed2026

Mulberry-derived endophytic Bacillus velezensis suppresses gray mold and promotes mulberry growth via reshaping the root metabolism and microbiome.

INTRODUCTION: Gray mold is an important fungal disease caused by Botrytis cinerea which threatens global agriculture. As chemical control faces limitations, biological control using Bacillus has gained attention for its environmental friendliness and growth promotion. However, their ecological basis and application potential in mulberry gray mold control remain insufficiently understood. OBJECTIVE: This study aimed to evaluate the biocontrol efficacy of the mulberry derived endophytic strain Bacillus velezensis ZJU_268 and to investigate its associated effects on plant growth, root-associated microbiomes, and metabolic profiles. METHODS: Greenhouse assays were combined with genomic and comparative genomic analyses, amplicon sequencing, non-targeted metabolomics, and functional validation of isolated microbes and metabolites to assess the effects of ZJU_268 and its cell free supernatant (CFS) on mulberry seedlings. RESULTS: This study isolated a mulberry derived endophytic bacterium, B. velezensis ZJU_268, which exhibits strong antifungal activity and reduces the incidence of gray mold in mulberry seedlings. Whole-genome sequencing and comparative genomic analyses revealed strain-specific regions and genes associated with root colonization, stress adaptation, and antimicrobial biosynthesis. Both live cells and CFS significantly promoted seed germination, seedling growth, and biomass accumulation in a dose dependent manner. Amplicon sequencing showed that ZJU_268 and its supernatant reshaped the mulberry root microbiome, enriching beneficial bacterial and fungal taxa while reducing potentially pathogenic members. Cultivable members of the enriched microbiota displayed strong antifungal activity against B. cinerea and promoted mulberry growth. Metabolomic profiling further showed that ZJU_268 and its supernatant were associated with marked metabolic shifts in mulberry roots, accompanied by the accumulation of selected metabolites that supported the growth of representative enriched isolates. CONCLUSIONS: This study demonstrates that ZJU_268 suppresses gray mold and promotes mulberry growth in association with direct antagonistic activity, microbiome restructuring, and holobiont-level metabolic shifts, providing a promising biological strategy for sustainable mulberry disease management.

Bacillusvelezensis↗
PubMed2025

N-glycan remodeling by α-D-mannosidase and β-D-N-acetylhexosaminidase regulates fruit softening, redox balance, and post-harvest pathogen resistance.

Post-harvest loss of fruits and vegetables poses significant challenges to food security and economic sustainability, primarily due to ripening-associated excessive softening that shortens shelf life and increases susceptibility to pathogens. N-glycans, N-glycoproteins, and their processing enzymes are integral to various plant processes, including fruit ripening. Among these, α-D-mannosidase (α-Man) and β-D-N-acetylhexosaminidase (β-Hex) are key ripening-specific enzymes that modulate fruit softening. Previously, we have shown that RNAi-mediated suppression of α-Man or β-Hex improves fruit shelf life and firmness in both climacteric and non-climacteric fruits. However, the underlying molecular and biochemical basis of fruit softening regulation by α-Man and β-Hex was not well understood. In this study, we developed transgenic tomato (Solanum lycopersicum) plants by silencing α-Man and β-Hex simultaneously using RNAi. Suppression of these enzymes reduces N-glycoprotein degradation, downregulates pectin dissolution, and inhibits ripening-related gene expression. RNAi fruits exhibited enhanced shelf life, greater firmness, reduced reactive oxygen species (ROS) accumulation and increased resistance against post-harvest pathogens without affecting plant growth, fruit development, yield, or nutritional quality. To further explore the molecular mechanism of α-Man and β-Hex function, we purified and quantified N-glycans in RNAi fruits and other ripening-impaired mutants, identifying key N-glycan species. We also carried out iTRAQ-based quantitative proteome profiling to investigate the abundance of proteins in ripened fruit affected by silencing of α-Man and β-Hex. Molecular insights revealed that N-glycan processing and degradation are key events during ripening, influencing cell wall softening, fruit redox state, and post-harvest quality attributes. This study highlights the potential of co-silencing α-Man and β-Hex as a novel approach to extending the shelf life of fruits, regardless of their climacteric behavior, without compromising quality or yield.

Fruit↗