Molecular ecological interactions of bacterial endophytes with their host Vitis vinifera (L)

Bacterial endophytes are organisms that live asymptomatically within plants. Some endophytic bacteria display plant protection properties, such as synthesis of plant hormones, production of antibiotics against pathogens and deterrents against herbivores. All these capabilities have drawn the attention of agricultural research and agricultural industry, because of their potential and consequently imminent use as biotechnologies for better crop management. Such capabilities are the result of complex ecological interactions that endophytes engage in, including those with other organisms in the plant ecosystem. Thus, understanding the interplay between bacterial endophytes and co-inhabiting organisms may provide means of better exploiting such beneficial attributes. Functional analysis with enzymatic assays has been the classical method for studying the roles of endophytic bacteria in their plant hosts. Recently, sequencing of genomes and metagenomic studies have provided better insights into colonization, niche expansion and chromosome structure, all of which can be reflected in the beneficial properties of some endophytes. Additionally, metabolomics has allowed an in depth study of symbiosis, revealing the importance of chemical crosstalk with the plant. Evidence shows that the microbiota can have a strong influence on host fitness. In plants, several studies propose the use of microbes as probiotics, since in some soils the existence of a defined, beneficial microbiota can prevent the development of plant disease (these are called “suppressive soils”). Since endophytes harbor many beneficial properties, questions arise on whether the use of the endophytic microbiota can have a positive impact on crops. Also, contrary to their pathogenic counterparts, little is known about the horizontal transmission of entire endophytic communities and their possible use as probiotics. Thus, the aim of this thesis was to study the beneficial properties of endophytic bacteria isolated from grapevine and evaluate their genome structures to identify similarities and differences between these symbionts and plant pathogenic, free-living and epiphytic symbionts. Enzymatic and functional tests showed that a collection of more than 100 bacterial endophytes isolated from grapevine have beneficial properties for plants spanning from plant growth promotion to biocontrol against major grapevine pathogens. Using genome sequencing, chromosome organization was analyzed, revealing gene functions that might be important for plant – endophyte symbioses. Additionally, similarities between endophytic and non-endophytic bacteria at the genome level revealed the virulence potential that endophytes hold in their genomes, thus suggesting a role of ecological constraints in defining the lifestyle of these symbionts. Through 454 sequencing, the role of the insect, Scaphoideus titanus, as a vector was confirmed, showing that it could transfer entire endophytic communities between host plants and also indicating that both plant and insect hosts have an effect on bacterial endophytic community structure. Finally, with metabolomics, a possible “metabolic signature” exerted by endophytes on the grapevine plants they colonize was recognized and the ecological implications of this phenomenon on symbiosis was outlined. In summary, endophytes from grapevine harbor a great biotechnological potential reflected in their enzymatic activities, their genomes and in their interactions with other members of the ecosystem. Thus, investigations should be continued to develop them into possible plant probiotics.