Genomics of saltwater Actinobacteria

Marine Actinobacteria have ultra-small bacterial cells, but no cultivated bacterial strains and only partial genome data are available. Here, we describe 13 amplified genomes of the newly proposed sub-class “Candidatus Actinomarinidae” assembled from single bacterial cells isolated from high salinity waters at the west coast of Sweden. Based on the high sequence similarity and conserved genome architecture of the single cell genomes we constructed a composite, virtual genome of 1.26 Mb, which is the first high-quality complete genome with a nearly complete set of genes from this lineaeg. A phylogeny of the Actinobacteria inferred from a concatenated alignment of 89 core proteins indicates a sister relationship of Ca. Actinomarinidae and the Acidimicrobiales. By mapping gene contents onto the phylogeny, we infer that Ca. Actinomarinidae has evolved by a massive loss of genes. Proteins such as photolyase, cyanophycinase and actino-opsin represent adaptive gains that are uniquely associated with the aquatic members of the Actinobacteria. The actino-opsins are predicted to absorb green light, consistent with adaptations to freshwater, coastal waters and the deep chlorophyll maximum in marine habitats. However, while freshwater Actinobacteria and Acidimicrobiales have leucine at the frequency-tuning site of the actino-opsin, Ca. Actinomarinidae have methioninie at this site, possibly reflecting adaptations to slightly more alkaline environments. Taken together, the results suggest that Ca. Actinomarinidae is not the most deeply branching lineage of Actinobacteria, as previously thought. Rather, we suggest that Ca. Actinomarinidae has evolved by accelerated substitution rates and gene loss from a bacterial ancestor shared with the Acidimicrobiales, and that subsequently diversified into habitats of different pH and salinity.