Plant colonization: exploring the genetic basis of rhizobial symbiotic performance and bacterial invasion

Plant growth can be influenced by a large variety of biotic and abiotic factors. Among these factors, the microrganisms associated with plants play an important role. Plant-associated microrganisms (fungi and bacteria) can be present on the surface of plant tissue (rhizospheric and epiphytic), or colonize the internal tissues of the plants (endophytes). Rhizobia represent a paradimantic group of microrganisms which have peculariar plant-association. They are soil bacteria, which colonize also the rhizosphere of plants, and on some of them (legumes) can enter the root or stem tissues establishing a symbiotic interaction. Under this interaction, rhizobia positively influence the host's growth thanks to the nitrogen fixation process, by which the bacterium is able to fix nitrogen from the atmosphere, making it bioavailable for the plant. The symbiosis is a highly specific process and it is strongly regulated by genetic and chemical factors, which allow the formation of new organs, the root (or stem) nodules. A well-established model used for the nitrogen-fixing symbiosis is that involving the rhizobium Sinorhizobium meliloti and the host legume Medicago sativa (alfalfa). S. meliloti is a particularly interesting study model for its high genetic and phenotypic variability and for the multipartite nature of its genome. This thesis is focused on three main aspects which characterize S. meliloti biology: the interaction and competition for the symbiosis (sociomicrobiology), the relevance of dispensable genes in such interaction, the functional meaning of the multipartite genome. From the sociomicrobiological point of view, the study mainly focused on the cooperative interactions established among different strains, which are able to colonize the same plant and, interestingly, the same root nodule. This capability allowed the evolutionary persistence of strains with highly different symbiotic phenotypes. Concerning the dispensable genome fractions which may affect strain competition, we focused on acdS, an accessory gene present in S. meliloti strains and in some other rhizobia. This gene encodes the enzyme 1-aminocyclopropane-1-carboxylate (ACC) deaminase, which is postulated to be involved in the decrease of ethylene production by the host plant and in the improvement of the symbiotic performance. Actually, its role in the symbiosis has not been completely elucidated. In our work, we present a phylogenetic and a functional analysis of acdS that allowed to hypothesize a role linked to rhizospheric or endophytic colonization. The last part of the thesis focuses on the bacterial cell metabolic reconstruction, which allowed to deep of the proposed step-by-step evolutionary scenario of S. meliloti multipartite genome. The study assessed the contribution of each replicon (which composes the multipartite genome of S. meliloti) to its life cycle, in particular in relation with the main three colonized environments (soil, rhizosphere and the root nodule). Overall, this thesis aimed to design a social, molecular and metabolic profile of S. meliloti, trying to improve its application in agriculture and biotechnology and to understand the ecology and the evolution of plant-microbe symbiotic interaction.