Simoneau, P. | Search bioRxiv

bioRxiv2026

A Seed-Derived Multi-Kingdom Synthetic Community Enhances Radish Seedling Protection Against Alternaria brassicicola Abra43

Seed-associated microorganisms represent a promising resource for developing microbiome-based strategies against seed-borne pathogens. Here, we assembled synthetic microbial communities (SynComs) from cultivable members of the natural radish seed microbiota and evaluated their capacity to protect seedlings against the seed-transmitted fungal pathogen Alternaria brassicicola Abra43. Seven SynComs representing single- or multi-kingdom combinations of bacteria (B), filamentous fungi (F), and yeasts (Y) (B, F, Y, BF, BY, FY, and BFY) were inoculated onto radish seeds. We assessed their effects on disease incidence, seedling growth, microbial community assembly (ITS1 and gyrB gene metabarcoding) and pathogen colonization (metabarcoding and specific qPCR on dhn1 gene for A. brassicicola Abra43). Protection of radish seedlings against A. brassicicola Abra43 strongly depended on SynCom composition. The yeast fraction alone provided little protection, whereas the bacterial fraction partially reduced symptoms and maintained seedling growth despite substantial pathogen colonization, suggesting increased plant tolerance. SynComs containing filamentous fungi markedly reduced A. brassicicola Abra43 abundance, and the full multi-kingdom BFY SynCom provided the most consistent protection, combining reduced disease incidence, restored seedling growth, and low pathogen relative and absolute abundance. Inoculated strains, Alternaria alternata ABAI001 and Plectosphaerella sp. FL19 were enriched in protective SynComs and displayed antagonistic activity against A. brassicicola Abra43 in vitro. Together, these results show that seed-derived multi-kingdom communities can reshape early plant microbiota and that combining bacterial and fungal strains with complementary ecological functions can improve protection against a seed-borne fungal pathogen.

microbiology↗

bioRxiv2024

Unexplored Yeast diversity in Seed Microbiota

Yeasts are known to be fantastic biotechnological resources for medical, food, and industrial applications, but their potential remains untapped in agriculture, especially for plant biostimulation and biocontrol. In particular, yeasts have been reported as part of the core microbiome of seeds using next generation sequencing methods, but their diversity and functional roles remain largely undescribed. Focusing on yeasts and excluding filamentous fungi, this study aimed to characterize the diversity of seed-associated yeasts across nine plant species (crops and non-cultivated species) using culturomics and microscopy. Comparison with available metabarcoding data was performed to assess the representativeness of the strain collection in seed samples. Our results show that seed-associated yeasts largely belong to Basidiomycota phylum and more particularly to the Tremellomycetes class. This yeast collection covers 15 genera (2 of Ascomycota and 13 of Basidiomycota). Out of the 229 isolates described, the most frequently isolated yeasts were Holtermanniella, Vishniacozyma, Filobasidium, Naganishia and Sporobolomyces. The yeasts from these dominant genera were isolated from multiple plant species (4 to 8), except for Naganishia which only originated from Solanum lycopersicum L. These results are also consistent with the fact that these dominant taxa were recently identified as members of the core seed microbiome, indicating their high prevalence and abundance across diverse plant hosts and environments. Compared to previous plant yeast diversity surveys, the members from Ascomycota yeasts are less frequent in seeds and only represented here by the Aureobasidium and Taphrina genera. Altogether, these results suggest that yeasts are generally well-adapted to the aboveground habitats of plants, but seeds represent a specific habitat that diverse Basidiomycota yeasts can colonize. Take away messageO_LI229 yeasts isolated from seeds and seedlings of diverse plant species C_LIO_LIMost isolates are Basidiomycota yeasts, especially of the Tremellomycetes class C_LIO_LIThe most frequently isolated yeasts belong to Holtermanniella, Vishniacozyma, Filobasidium and Sporobolomyces genera C_LIO_LIThe collection is representative of taxa found in seed microbiota of multiple plant species, including core members C_LI

microbiology↗