Análisis del metabolismo, las funciones, la ecología y la taxonomía del género pseudomonas

Resum

Pseudomonas constitutes one of the most diverse and adaptable prokaryotic genera. Its metabolic versatility allows these bacteria to survive in many different environments. In this thesis, different approaches have been carried out in order to decipher novel functionalities and ecological aspects of the genus Pseudomonas. In the first chapter, 194 genomes from different Pseudomonas type strains were investigated to unravel the key secondary metabolism related pathways in the genus, as well as phylogenetic patterns that provide clues to understand the evolution of this metabolism. Based on this, some strains and biosynthetic gene clusters are suggested as interesting for further research. In the second chapter, Pseudomonas strains isolated from bark beetles are investigated for their potential to inhibit beetles’ fungal pathogens and other microbes, finding that several bacterial cyclodipeptides, likely produced by a cyclodipeptide synthase encoded in their genome, are involved in these antagonisms. Here, we also described 3 new bacterial species isolated from the insects. The third chapter pretends to unravel the interaction between the plant-beneficial strain Pseudomonas brassicacearum CDVBN10 and Brassica napus plants. For that, several approaches have been carried out: (I) an RNA-Seq analysis on the bacterial cells during the roots colonization has been performed, (II) the effect of this bacterium on the inner bacterial communities of the roots has been analyzed (through 16S rRNA amplicon metabarcoding sequencing), and (III) the in vitro and in vivo study of the biocontrol ability of this Pseudomonas strain to protect rapeseed plants against the fungal phytopathogen Leptosphaeria maculans has been showed. These methods facilitate to understand how this bacterium is able to promote the growth and to protect this crop. With the aim to study genes or functions related with the adaptation of Pseudomonas to different hosts or niches, in the fourth chapter, 3,274 high quality genomes from Pseudomonas strains for which their isolation origin is known have been used for comparative genomics purposes. The results show an extremely diverse Pseudomonas pan-genome, for which thousands of accessory genes, mainly hypothetical proteins, seem to be associated with some isolation source (plants, humans, soil, animals, etc.). These analyses include CAZY, COGs and antimicrobial resistances niche-associations as well as the dynamics of horizontally transferred genes and regions of genome plasticity in regards with the bacterial isolation source. Finally, in the last chapter, the taxonomy of the Pseudomonas genus is studied based on the genomes of their type strains. The results led to the description of different novel genera and several reclassification of species. In sum, this thesis aimed to shed light into ecological, metabolic, functional and taxonomic aspects of Pseudomonas and will help to a more deep understanding of the biology of this widely distributed genus.