Seed-Borne Endophytic Bacteria of Tomato: Dynamic Colonization and Implications in Plant Health

Seed-borne endophytic bacteria are essential for seed germination, plant growth, and stress tolerance. However, their functional diversity remains elusive because of difficulties in maintaining sterile conditions and amplifying the bacterial community without amplifying the plant genome. Using tomato ( Solanum lycopersicum L.) as a model, we designed a novel culture system to study this bacterial community from seed to seedling, investigating its colonization and impact on plant health. Our workflow combined metabarcoding and culture-based approaches to capture the most accurate picture of the tomato seed-associated bacteria. An advanced metabarcoding protocol involving sequencing of the 16S-ITS-23S rRNA operon and the use of newly designed peptide nucleic acid clamps specific for tomato var. Moneymaker revealed a core microbiota consistently transmitted from seeds to shoots and roots. Key bacteria included Ralstonia pickettii, Sphingomonas aerolata, Bradyrhizobium spp., Paucibacter aquatile, Microbacterium spp., and Stenotrophomonas spp. Culture-dependent approaches isolated endophytic strains such as Rummeliibacillus stabekisii, Peribacillus frigoritolerans, and Pseudomonas protegens, which increase plant osmotic stress resistance. Using quantitative PCR, confocal microscopy, and colony counting, we demonstrated that P. protegens tagged with mCherry colonizes root, shoot, and leaf tissues. Overall, our study supports the hypothesis that a rich and stable core of endophytic bacteria, capable of enhancing drought resistance, is transferred from seeds to plant organs. Our study provides the most detailed investigation to date of the diversity of the seed-borne microbial community of tomato and offers new approaches to better assess the diversity of plant-associated microorganisms, a key step to improve crop resistance and productivity. [Formula: see text] Copyright © 2025 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .