Phylogenetic analysis of aquatic microbiomes : Evolution of the brackish microbiome

Sammanfattning: Microorganisms play crucial roles in aquatic environments in determining ecosystemstability and driving the turnover of elements essential to life. Understanding thedistribution and evolution of aquatic microorganisms will help us predict how aquaticecosystems will respond to Global Change, and such understanding can be gained bystudying these processes of the past. In this project, we investigate the evolutionaryrelationship between brackish water bacteria from the Baltic Sea and Caspian Seawith freshwater and marine bacteria, with the goal of understanding how brackishwater bacteria have evolved. 11,276 bacterial metagenome-assembled genomes(MAGs) from seven metagenomic datasets were used to conduct a comparativeanalysis of freshwater, brackish and marine bacteria. When clustering the genomes bypairwise average nucleotide identity (ANI) at the approximate species level (96.5%ANI), the Baltic Sea genomes were more likely to form clusters with the Caspian Seagenomes than with Swedish lakes genomes, even though geographic distancesbetween Swedish lakes and the Baltic Sea are much smaller. Phylogenomic analysisand ancestral state reconstruction showed that approximately half of the brackishMAGs had freshwater ancestors and half had marine ancestors. Phylogeneticdistances were on average shorter to freshwater ancestors, but when subsampling thetree to the same number of freshwater and marine MAG clusters, the distances werenot significantly different. Brackish genomes belonging to Acidimicrobiia,Actinobacteria and Cyanobacteriia tended to originate from freshwater bacteria, whilethose of Alphaproteobacteria and Bacteroidia mainly had evolved from marinebacteria.