The use of ribosomal markers in bacterial systematics intimately linked the Cytophaga-Flavobacteria-Bacteroides groups even though phenotypic studies classified them apart. With regard to phylogenetic evidence, they were circumscribed as the phylum Bacteroidetes but they stay principally studied as independent clades due lack of phenotypic coherence. The phenotypes foremost attributed to Bacteroidetes are the ability to decompose complex organic matter, gliding motility and pigmentation with flexirubins and carotenoids. The recent outburst of culture-independent methodologies and development of polynucleotide sequencing techniques has unveiled Bacteroidetes’ prevalence in many relevant ecosystems. For example, some saline environments seem to be selective of these bacteria out-competing other phyla. The goals of this doctoral thesis targets are (1) reviewing the taxonomy of the Bacteroidetes, (2) finding coding genes that could translate into an identifying phenotype and (3) finding what of their genes are selected in saline environments.For the taxonomic review of the phylum not only their 16S rDNA gene phylogeny has been updated, but also that of the 23S rDNA, signature nucleotides on their 16S rRNA sequence, insertion/deletion patterns in two of their proteins and a phylogeny based on the multilocus sequence analysis of 29 genes. This new taxonomy, on top of naming a new phylum, three classes, three orders, eight families and a genus (all of them with standing in bacterial nomenclature), paveda precise phylogenomic analysis of the Bacteroidetes, which on earlier studies included members ofthe new phylum Rhodothermaeota. However, it curtailed probabilities of finding salinity-relatedgenes, since most extreme halophiles belong to the new phylum.Through the compared genomics of 89 meticulously selected genomes we found that the most conserved genes in the phylum (in 90% of the genomes), not housekeeping, are those coding thetype-IX secretion system, hitherto only seen in the Bacteroidetes. This secretion system is involvedin the gliding motility of some Bacteroidetes, but it is also an excreting route for hydrolyticenzymes. Next, were genes coding the respiratory super-complex Alternative Complex III –cytochrome caa3 oxydoreductase at 83% of the genomes, all of aerobic species. The anaerobic lineage of the Bacteroidales can fulfill the aerobic respiration thanks to a cytochrome bdoxidoreductase with high oxygen affinity that helps detoxifying their surroundings. Genes of the Complex II, Succinate dehydrogenase, of the respiratory chain are single-copy through all Bacteroidetes’ genomes, and at the Bacteroidales other vestigial genes of the tricarboxylic acidcycle denote their aerobic past. Last, the genes of the respiratory Complex I are not arranged phylogenomically in the Bacteroidetes. These genes are substituted by an alternative complex I thatpumps sodium into the inter-membrane space instead of protons, the sodium pumping NADH: quinone oxydoreductase (Na+-NQR), only on marine species or gut microbiota species. Moreover, we found evidences of this complex being invented by the Bacteroidetes and its horizontal transmission within saline environments.The simultaneous expression of the type-IX secretion system and the respiratory chain of the Bacteroidetes, which is adapted to the environments they live at, is likely responsible for the adaptive radiation of the phylum. Some of these genes are horizontally transferred, but all together they predict the original bacteroidete was a heterotroph aerobic decomposer of complex organicmatter, likely living in freshwater.

This research was funded by the Max Planck Society, the Spanish Ministry of Economy and Competitivity projects CGL2012-39627-C03-03, CLG2015-66686-C3-1-P and PGC2018-096956-B-C41 that also supported the work with European Regional Development Fund (FEDER) funds,the preparatory phase of the Microbial Resource Research Infrastructure (MIRRI) funded by the EU (grant number 312251), and the financial support of Deep Blue Sea Enterprise S.L.

Tesis doctoral.-- Doctoral Programme of Environmental and Biomedical Microbiology.