Enhancing seed quality and plant growth through modification of seed microbiome with beneficial endophytic bacteria

• It is believed to be most appropriate to present the results of both crops together within a single, comprehensive manuscript. • Missing data and details were fully integrated into the tables and main text. • The contradictory findings between the abstract and discussion were reconciled. • Necessary revisions have been made in the manuscript. The seed microbiome is able to perform an imperative key position in the germination and vigour of seedlings, regulating the growth of adult plants through vertical transmission. Accordingly, altering the seed microbiome with beneficial endophytic bacteria (EB) is a novel approach for stimulating seed quality and eliminating the problems related to the colonisation of bacteria in the host plant encountered in seed coating or biopriming practices. Yet, knowledge on the artificial modification of the seed microbiome is relatively meagre. Hence, aim of this research was to inoculate tomato and eggplant flowers with selected endophytic bacterial strains ( Pseudomonas fluorescens -L5b, Pseudomonas gessardii -L13, Bacillus subtilis -Bs1, Bacillus mojavensis -ApBm) to ensure the colonisation of the bacteria in developing seeds. Furthermore, the effects of altering the seed microbiome on germination, seedling growth and overall plant development compared with the seed coating method were examined in two consecutive years. Based on sequence analyses to detect the 16S rRNA gene region of strains, Pseudomonas species (strains L5b and L13) were successfully transferred into seeds of both species and vertically to progeny seedlings. The efficacy of altered seed microbiome with L5b and L13 strains on germination and seedling emergence rates remained limited, but improved stand establishment and biomass accumulation of mature plants in both species. In addition, similar pattern of results were taken from floral inoculation and seed coating methods. Consequently, these results provide evidence that altering the seed microbiome with beneficial endophytic bacteria is a promising tool for imparting growth-promoting aspects to the host plant.