Abstract
Summary Detailed analysis revealed fundamental differences between bacterial association with cucumber ( Cucumis sativus ) seeds and seedlings roots. Seed colonization by bacteria seems to result from passive encounter between bacteria, conveyed by imbibed soil solution, and the germinating seed. In accordance, the seed‐associated bacterial community composition directly reflected that of the germination medium and was characterized by low dominance. Transition from seed to root was marked by a shift in bacterial community composition and in an increase in dominance values. Furthermore, settlement of bacteria on roots was tightly controlled by the specific properties of each root segment. Size and richness of the seed‐associated bacterial community were clearly determinate by the community in the germination medium. In contrast, for fully developed and active roots, the medium effect on these parameters was negligible. Perturbation of the seed environment by a pathogen ( Pythium aphanidermatum ) had major consequences on the seed bacterial community. However, those were mostly related to direct pathogen–bacteria rather than seed–bacteria interactions. In conclusion, simple, even passive processes may determine the initial stage of plant–microbe association during seed germination, prior to extension of the primary root. Therefore, seed germination is a unique phase in the plant life cycle, with respect to its interaction with the below‐ground microbiome.