Microbiome (bacteria and fungi) data for eight spinach seed lots based on amplicon sequencing

Samenvatting

Using a bioassay setup, we recently demonstrated that eliminating the seed microbiota of certain spinach (Spinacia oleracea) seed lots makes them more susceptible to damping-off caused by Pythium ultimum. This indicates that the presence of an intact seed microbiome can confer disease suppression against this pathogen which attacks seedlings during germination. This study aimed at identifying the key actors associated with seed microbiome suppressiveness by correlating the bioassay results with the taxonomy and relative abundance of bacteria and fungi present in eight spinach seed lots differing in suppressive potential. Seed lots shared core taxa, but 81 % of all taxa were rare and a large proportion of variance between samples was explained by seed lot identity. Additionally, 7.1 % of bacterial and 6.2 % of fungal community variance between samples correlated with the trait of disease suppression. High fungal diversity was a characteristic of highly suppressive seed lots. More specifically, a higher relative abundance of basidiomycetous dimorphic yeasts such as Vishniacozyma, Papiliotrema and Filobasidium was a key feature of suppressive seed microbiomes. The same was true for the bacterial genera Massilia and Paenibacillus which are known for their antagonistic properties. Consequently, we suggest for the abundance of these genera to be used as an indicator of seed lot suppressive potential. As a result, seed processing and treatment can become more targeted with indicator taxa being used to evaluate the presence of beneficial seed-associated microbial functions. This process in turn would contribute to the sustainable management of seedling diseases. Finally, this study highlights the ubiquity of yeasts in spinach seed microbiota and their potential beneficial roles for seed health.