Tomato seeds preferably transmit plant beneficial bacteria

Endophytes with plant growth-promoting activity are opening the way for sustainable agriculture. However, less is known about their stability across plant genotypes, habitats and generations. To understand how plant growth-promoting bacteria (PGPB) are distributed across a whole tomato plant and two generations, an integrative approach combining analyses of bacterial communities and isolates was employed. Our results showed that the bacterial community of each plant microhabitat and genotype had distinct fingerprints and harboured distinct PGPB. Soil, endosphere and rhizosphere were the microhabitats with the highest diversity, while seeds hosted more selective communities in both generations. Commercially obtained seeds (first generation) generated under field conditions showed traces of a bacterial setup connected to the suppression of plant pathogens, while seeds of the second generation in a pathogen-free and low-nutrient environment showed a predominance of bacteria able to increase the uptake of nutrients. This seed bacteriome modification across the two generations can be explained by an adaptation to prevalent environmental conditions. Cultivation approaches revealed microhabitat-specific PGPB that were assigned to distinct species of Bacillus, Stenotrophomonas, and Ralstonia. Tracking these bacteria across the whole plant system allowed us to identify the seed as a primary vehicle of PGPB transmission as well as a hotspot for their isolation.