Germination Modulates Diversity and Network Connectivity in Tomato Seed Bacterial Endophytes

Seeds are increasingly recognized not only as vectors of plant genetic information but also as reservoirs of vertically transmitted microbial communities that influence early development and plant performance. Seed borne endophytes are promising targets for sustainable crop protection, particularly through seed priming approaches leveraging beneficial microbes. In this study, we investigated the endophytic bacterial communities associated with commercial tomato seeds, aiming to assess shifts occurring during early germination. Following surface sterilization, seeds were examined either in their dry state or after pregermination on moist blotting paper at 25 °C under official germination testing conditions until at least 50% germination was reached. Eight commercial seed lots, each represented by five biological replicates and encompassing four tomato varieties (80 samples total), were examined. Bacterial communities were characterized using an amplicon based metagenomic approach targeting the 16S rRNA gene, and a parallel culture based analysis was conducted by plating seed extracts on standard bacteriological media. Across seed lots, Pseudomonadota, Actinomycetota and Bacillota dominated both seed endosphere and pregerminated samples, together accounting for at least 90% of the total bacterial composition. Overall, α diversity was higher in the seed endosphere than in pregerminated seeds, with differences influenced by seed origin (organic vs. conventional). β diversity analysis further indicated compositional shifts between the two sample types. Co occurrence network analysis revealed that endospheric communities had a more complex and interconnected structure, with more nodes and edges, higher cohesion, and a more articulated modular organization than the simpler, less connected networks of pregerminated seeds. Recovering the cultivable fraction proved challenging and required liquid medium enrichment, yielding higher recovery from pre-germinated seeds. A subset of isolates was screened for plant growth promoting traits and in vitro antagonism against major tomato pathogens, revealing substantial variability. When selected strains were used to inoculate tomato seeds, effects were heterogeneous, although some isolates consistently promoted seedling growth.