Seed-borne endophytic bacteria of tomato dynamic colonization and implication in plant health

The ecological importance of seed-transmitted endophytic bacteria is well recognized, as they play critical roles in promoting seed germination, enhancing plant growth, and conferring stress tolerance. Detailed characterization of this microbial component remains challenging due to difficulties in maintaining sterile conditions and complexities in amplifying bacterial communities without amplifying the plant genome. These issues have limited our understanding of the transmission dynamics and functional roles of these microbial communities. To address this, we engineered a new culture system to study these communities directly from seeds to plantlets and performed metabarcoding and culture-dependent approaches to generate an accurate picture of the tomato seed microbiota. Our advanced metabarcoding protocol, involving sequencing 16S-ITS-23S rrn operon and employing a newly designed PNA clamp specific for tomato var. Moneymaker, revealed a core microbiota consistently transmitted from seeds to shoots and roots. Key bacteria identified include Ralstonia picketti, Sphingomonas aerolata, Bradyrhizobium sp., Paucibacter aquatile, Microbacterium sp., and Stenotrophomonas sp. Culture-dependent approaches isolated bacterial strains, including Rummeliibacillus stabekisii, Peribacillus frigoritolerans, and Pseudomonas protegens, that enhance plant resilience to osmotic stress. By creating mCherry-tagged mutants of two strains, we confirmed their endophytic colonization of roots, shoots, and leaves when coated on seeds, using quantitative PCR, confocal microscopy, and colony counting. Our findings confirm that a stable core of endophytic bacteria, capable of enhancing drought resistance, is transferred from seeds to plant organs. This study advances our understanding of microbial transmission and its implications for plant health, opening new avenues for harnessing endophytes to improve crop resilience and productivity.