Seed Bacterial Communities of Three Pepper Varieties Are Influenced by Traditional Greenhouse and Hydroponic Growing Conditions

Peppers (Capsicum spp.) are one of the most important agricultural crops worldwide, but the bacterial communities present in their seeds are not yet well understood. Seedborne bacteria may represent taxa that can be vertically transmitted from parent to offspring, and understanding the composition of seed bacterial communities for different pepper varieties can accelerate the development of synthetic microbial communities that can be used to improve pepper cultivation. In this study, we used 16S amplicon sequencing to assess seeds from three pepper varieties—bell, jalapeño, and habanero—grown under two different cultivation methods: a traditional greenhouse cultivation method and a deep water culture hydroponic system. Our results showed that the seed microbiomes of peppers are influenced primarily by cultivation method and only weakly influenced by variety. Furthermore, we report the improved productivity of pepper plants grown in the hydroponic system and the different elemental compositions of their fruits. These findings suggest the importance of cultivation method in dictating the seed microbiome of peppers, regardless of variety, as well as the role of cultivation method in boosting pepper productivity.