Stucturation, dynamic and response of seed-associated microbial communities to transmission of phytopathogenic agents

La graine constitue le point de départ du cycle d’une plante et abrite une diversité de micro-organismes qui peuvent impacter négativement ou positivement la fitness de la plante. De plus, la graine permet la dispersion et la survie des agents phytopathogènes entre deux cycles de culture de la plante hôte. Dans ce contexte, l’objectif de ce travail était de : (i) décrypter les processus écologiques impliqués dans l’acquisition du microbiote des graines, (ii) analyser sa réponse à l’invasion par des agents phytopathogènes et(iii) suivre sa dynamique durant la germination de la graine et l’émergence de la plantule. Premièrement, nous avons analysé la structure du microbiote de graines de radis(Raphanus sativus) produites dans un même site sur trois générations successives. Ces analyses ont révélé une faible héritabilité du microbiote des graines avec peu de taxons dominants transmis d’une génération à l’autre. Ceci pourrait être expliqué par l’importance des processus neutres dans l’assemblage du microbiote des graines.Ensuite, nous avons étudié la réponse de ce microbiote à une invasion par Xanthomonas campestris pv. campestris(Xcc) et Alternaria brassicicola (Ab), deux agents phytopathogènes transmis par les graines. La transmission de Xcc aux graines n’impacte pas la composition globale du microbiote. En revanche, la transmission d’Ab modifie la structure des communautés fongiques. Ces différences de réponse sont probablement dues aux compétitions pour l’espace et les nutriments entre l’agent phytopathogène et les autres membres du microbiote. Finalement, la composition et la structure du microbiote des graines germées et des plantules ont révélé une transmission de la majorité des taxons associés à la graine y compris Xcc etAb. Globalement, les résultats de ce travail de thèse permettront à terme d’élaborer des stratégies de biocontrôle basées sur la modulation du microbiote des grainesSeed represents the initial step of the plant life cycle and harbors diverse microorganisms that can have detrimental or beneficial impacts on plant fitness. Moreover, seed represents an important means of pathogen dispersion and survival during intercrop periods. For those reasons, the aims of this work were to (i) unveil the ecological processes involved in the acquisition of the seedmicrobiota, (ii) to analyze its response against plant pathogens invasion and (iii) to monitor its dynamics during the first plant developmental stages, namely germination and emergence. First, we assessed the structure of the radish seed microbiota (Raphanus sativus) in the same experimental site across three successive plant generations. These analyses revealed a low heritability of the seed microbiota with few dominant taxa transmitted across generations. Neutral-based processes seem to be important in assembly of the seed microbiota. Second, we monitored the response of the seed microbiota to invasions by Xanthomonas campestris pv. campestris (Xcc) and Alternaria brassicicola (Ab), two seed-transmitted pathogens. While Xcc seed transmission do not change the composition of microbial communities, Ab transmission modified the structure of seed-associated fungal communities. This differences in response could be partly explained by competition for space and nutrients between the pathogenic agents and the members of the seed microbiota. Finally, composition and structure of microbial communities associated to germinating seed and seedling revealed transmission of most seed-borne microorganisms including Xcc and Ab from seed to seedling. Altogether, the results of this thesis could be helpful for designing future biocontrol strategies based on seed microbiota modulation

Differences in stability of seed-associated microbial assemblages in response to invasion by phytopathogenic microorganisms

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