Dal microbiota delle piante ai batteri simbionti azotofissatori: indizi per lo sviluppo di nuovi approcci biotecnologici per soluzioni l’agricoltura sostenibile

This thesis is the result of a three-years “journey” into the plant microbiome, from the complexities of the microbial communities to the intimate relationships between strains and plant genotypes. The central focus has been to understand the connections (through microbial ecology, ecological genetics and molecular approaches) between the microbiome and the host, to rationally develop novel approaches for low input agriculture. Many actors were playing a role in this journey; the microbiome change, depending on the host genotype and the environmental conditions, even a single microbial species can show dramatic differences among strains in the behaviour with the plant. Which are the players? Microbial taxa, microbial genes, plant genotypes, edaphic conditions, climate, agronomic practices, and even randomness. The chapters of this thesis are aimed at presenting the investigations and obtained results done part of such players. - Chapter 1 is dealing with microbial taxa and plant genotypes asking the question about the specificities of the plant microbiomes with respect to plant species (and varieties) and the way to improve its services to plant in terms of bioinoculant use. - Chapter 2 is moving to a specific taxon, where genotypes of single strains and plant genotypes display interactions and single bacterial genes in epistatic combinations contribute to plant phenotypes. - Chapter 3 enters into the genetic details of such combinations and investigates the ecological genetics of genetic transfer of symbiotic and nitrogen-fixation genes between plant symbiotic bacteria, which bring to strains with different symbiotic properties. - Chapter 4 continues the journey into the molecular aspects of the genetics below the differences in symbiotic behaviour of bacterial strains, presenting the results of investigations on epigenomic signatures of mutualistic interactions and strain-by-strain differences. The appendix is then reporting two case studies where methods and expertise gained during this “journey” have been applied to phytoremediation and the study of animal model microbiomes. Finally, the works in progress and the drafts of future publications are reported in the thesis.