Investigating the potential of seed microbiome enhancement in controlling damping-off caused by Pythium ultimum

Seed health is a crucial part of a sustainable agri-food system and is indispensable to food security, but this status is often threatened by various abiotic and biotic factors. Due to limited options of chemical control and their negative impact on the environment, the development of more sustainable alternatives is necessary. Research showed that microbiome exhibited disease suppressive potential on spinach – Pythium ultimum pathosystem, and the subsequent study suggested the positive effect on disease suppressiveness through seed microbiome enhancement. This study aimed to validate and further investigate the role of seed microbiome in suppressing the disease using the same pathosystem. A series of plant-pathogen bioassays were conducted, in which the seeds were addressed to microbiome enhancement or transplantation by soaking them in culturable microbial suspensions derived from original or different spinach seed lots. These treated seeds were then challenged with or without P. ultimum to assess growth-promoting and disease-suppressing effects. Additionally, dual culture was performed to select isolates exhibiting antagonism against P. ultimum from the cultured seed microbiome. The results revealed the change in disease tolerance after seed microbiome enhancement or transplantation, indicating the alteration of microbial composition of the treated seeds. The disease-suppressing effect, however, was not persistent across the bioassays. Unhomogenized infection and varied seed microbiome composition deriving from the same seed lot was observed, indicating methodological shortcomings. The two isolates selected from dual culture were identified as Pseudomonas viridiflava and Erwinia persicina. Despite their antagonistic effect on P. ultimum mycelial growth, they led to insignificant or deleterious effect on the plant. This study gave an insight into the dynamic nature of the seed microbiome and paved the way for further relevant studies. Improvement of the current design and the integration of alternative approaches are necessary to reveal the taxonomic composition of the seed microbiome as well as investigating its role in disease suppressiveness, which eventually contribute to a more sustainable cropping system and better food security.