Genomic Insights Into the Freshwater Genus Aquirufa (Bacteroidota): Taxonomic Diversity, Proteorhodopsins and Their Associated Genes, Including the Description of Eight Novel Species

Abstract Aquirufa is a widespread and diverse bacterial genus inhabiting freshwater ecosystems. Analyses of genomes from cultured strains and metagenome-assembled genomes (MAGs) of the genus revealed four phylogenetically distinct branches that differed markedly in the proportions of cultured strains and MAGs they contained. In total, 56 species or species-like taxa were identified, including eight novel species described here. Proteorhodopsin genes were detected in many of the genomes and were found across a wide range of habitat types, but their prevalence differed considerably among the four phylogenetic branches. Detailed analyses of two branches with markedly different proteorhodopsin gene frequencies suggested differences in the occurrence, size, structure, and pangenomes of their populations. Comparative whole-genome analyses showed that proteorhodopsin genes in Aquirufa consistently co-occurred with two key genes involved in retinal chromophore biosynthesis. These three genes exhibited distinct evolutionary patterns, most likely reflecting differences in recombination and co-evolution. Phylogenetic analyses placed the Aquirufa proteorhodopsins within the proteorhodopsin-xanthorhodopsin clade, specifically in a lineage comprising proteorhodopsins from species of the phylum Bacteroidota . Extending the analyses to related proteorhodopsins revealed additional patterns. Thirteen distinct gene arrangement types and all three common spectral-tuning residues were identified, with variation occurring not only among genera but occasionally even among species within the same genus. Overall, our findings indicated that the evolution, acquisition, horizontal transfer, and recombination of proteorhodopsin genes and associated genes have proceeded differently across taxonomic groups.