Background and aims Seeds are involved in the transmission of microorganisms from one plant generation to another and consequently may act as the initial inoculum source for the plant microbiota. In this work, we assessed the structure and composition of the seed microbiota of radish (Raphanus sativus) across three successive plant generations.Methods Structure of seed microbial communities were estimated on individual plants through amplification and sequencing of genes that are markers of taxonomic diversity for bacteria (gyrB) and fungi (ITS1). The relative contribution of dispersal and ecological drift in inter-individual fluctuations were estimated with a neutral community model. Results Seed microbial communities of radish display a low heritability across plant generations. Fluctuations in microbial community profiles were related to changes in community membership and composition across plant generations, but also to variation between individual plants. Ecological drift was an important driver of the structure of seed bacterial communities, while dispersal was involved in the assembly of the fungal fraction of the seed microbiota. Conclusions These results provide a first glimpse of the governing processes driving the assembly of the seed microbiota.

Seeds are involved in the vertical transmission of microorganisms from one plant generation to another and consequently act as reservoirs for the plant microbiota. However, little is known about the structure of seed-associated microbial assemblages and the regulators of assemblage structure. In this work, we have assessed the response of seed-associated microbial assemblages of Raphanus sativus to invading phytopathogenic agents, the bacterial strain Xanthomonas campestris pv. campestris (Xcc) 8004 and the fungal strain Alternaria brassicicola Abra43. According to the indicators of bacterial (16S rRNA gene and gyrB sequences) and fungal (ITS1) diversity employed in this study, seed transmission of the bacterial strain Xcc 8004 did not change the overall composition of resident microbial assemblages. In contrast seed transmission of Abra43 strongly modified the richness and structure of fungal assemblages without affecting bacterial assemblages. The sensitivity of seed-associated fungal assemblage to Abra43 is mostly related to changes in relative abundance of closely related fungal species that belong to the Alternaria genus. Variation in stability of the seed microbiota in response to Xcc and Abra43 invasions could be explained by differences in seed transmission pathways employed by these micro-organisms, which ultimately results in divergence in spatio-temporal colonization of the seed habitat.

Seeds are involved in the vertical transmission of microorganisms in plants and act as reservoirs for the plant microbiome. They could serve as carriers of pathogens, making the study of microbial interactions on seeds important in the emergence of plant diseases. We studied the influence of biological disturbances caused by seed transmission of two phytopathogenic agents, Alternaria brassicicola Abra43 (Abra43) and Xanthomonas campestris pv. campestris 8004 (Xcc8004), on the structure and function of radish seed microbial assemblages, as well as the nutritional overlap between Xcc8004 and the seed microbiome, to find seed microbial residents capable of outcompeting this pathogen. According to taxonomic and functional inference performed on metagenomics reads, no shift in structure and function of the seed microbiome was observed following Abra43 and Xcc8004 transmission. This lack of impact derives from a limited overlap in nutritional resources between Xcc8004 and the major bacterial populations of radish seeds. However, two native seed-associated bacterial strains belonging to Stenotrophomonas rhizophila displayed a high overlap with Xcc8004 regarding the use of resources; they might therefore limit its transmission. The strategy we used may serve as a foundation for the selection of seed indigenous bacterial strains that could limit seed transmission of pathogens.

31Seeds are involved in the vertical transmission of microorganisms in plants and act as 32 reservoirs for the plant microbiome. They could serve as carriers of pathogens, making the 33 study of microbial interactions on seeds important in the emergence of plant diseases. We 34 studied the influence of biological disturbances caused by seed transmission of two 35 phytopathogenic agents, Alternaria brassicicola Abra43 (Abra43) and Xanthomonas 36 campestris pv. campestris 8004 (Xcc8004), on the structure and function of radish seed 37 microbial assemblages, as well as the nutritional overlap between Xcc8004 and the seed 38 microbiome, to find seed microbial residents capable of outcompeting this pathogen. 39According to taxonomic and functional inference performed on metagenomics reads, no shift 40 in structure and function of the seed microbiome was observed following Abra43 and 41Xcc8004 transmission. This lack of impact derives from a limited overlap in nutritional 42 resources between Xcc8004 and the major bacterial populations of radish seeds. However, 43 two native seed-associated bacterial strains belonging to Stenotrophomonas rhizophila 44 displayed a high overlap with Xcc8004 regarding the use of resources; they might therefore 45 limit its transmission. The strategy we used may serve as a foundation for the selection of 46 seed indigenous bacterial strains that could limit seed transmission of pathogens. 47 average, 3,850 species (SD + 385) were detected in seed-associated microbial assemblages 128 collected from control plots (Fig. 1b). This estimation is one order of magnitude higher than 129 the richness predicted with 16S rRNA gene or gyrB 24 . According to Kruskal-Wallis non 130 parametric analysis of variance followed by Dunn's post-hoc test, the observed species 131 richness, the predicted species richness and the species diversity were not significantly 132 affected (P > 0.01) by seed transmission of both phytopathogenic agents (Fig. 1b). 133Differences in community membership and community composition between seed samples 134were assessed with Jaccard and Bray-Curtis indexes, respectively ( Fig. 1e and Fig.1f). 135