Endophytic bacterial communities of tomato seeds produced in organic and conventional systems.

Seeds carry vertically transmitted microbes that shape the plant microbiome and influence plant health and resilience. Understanding seed-associated bacterial communities is key to developing microbiome-based strategies for crop improvement. We analyzed the endophytic bacterial communities in seeds, endosphere and spermosphere of four tomato cultivars produced under organic and conventional system by amplicon-based metagenomics. Alpha-diversity metrics revealed that seeds from organically cultivated genotypes exhibited greater richness and microbial diversity in both compartments. Notably, diversity remained stable across compartments in organic seeds, whereas conventional seeds showed a marked decline in richness and diversity from endosphere to spermosphere. Principal component analysis based on ASV abundances indicated a significant separation between the two compartments, independent of farming practice. Although cultivation system exerted a moderate but non-significant effect on overall community composition, differences in phyla were observed between compartments within the same system. The seed microbiota was primarily dominated by Pseudomonadota, Actinomycetota, and Bacillota (up to 90%), with organic spermospheres exhibiting a notable reduction in Actinomycetota. At finer taxonomic resolution, dominant families included Burkholderiaceae, Microbacteriaceae, Sphingomonadaceae, Staphylococcaceae, and Pseudomonadaceae, known for their plant-associated functional traits. Core microbiome analysis identified 25 core bacterial genera, with seven exhibiting high relative abundance, suggesting ecological dominance and potential functional relevance in tomato seed microbiomes. These findings offer a comprehensive snapshot of seed-associated bacterial communities under different cultivation regimes, laying the groundwork for isolating functionally beneficial strains. Future efforts will focus on the cultivation and characterization of promising taxa for use as bioinoculants in sustainable tomato production. This research was funded by the project Quali.Gene “Piattaforma Analitica Molecolare per la Sicurezza, la Qualità e la Genuinità Agroalimentare” (CUP: B69J24001490005).