Genomics of brackish Actinobacteria

The broad taxonomic composition of bacteria in aquatic habitats of different salinity is well described, but the underlying population structures and genes involved in niche adaptation are poorly understood. Here, we present single-cell amplified genomes (SAGs) from actinobacterial cells sampled from the brackish waters of the Baltic Sea where salinity levels range from freshwater to saline conditions. A phylogenetic study of the brackish SAGs with genomes obtained from the freshwater acI lineage indicates multiple, independent transitions between freshwater and brackish habitats. Recruitments of metagenome reads from coastal habitats elsewhere support the hypothesis that there is a globally distributed brackish community, which consists of several distinct subgroups within the freshwater acI lineage. A phylometagenomic analysis confirmed that transitions between freshwater and brackish waters have occurred multiple times independently. One tribe of freshwater cells recruited reads exclusively from freshwater samples, suggesting that not all freshwater tribes have diversified into brackish waters. On the other extreme, one single cell genome obtained from a freshwater sample recruited mostly metagenomic reads from brackish waters. We hypothesize that additional environmental filters, such as phage predation, temperature, pH and/or nutritional availability, contribute to the selection of specific subgroups of acI Actinobacteria in brackish waters. Population-based genomic studies of Actinobacteria in the Baltic Sea are important sources of information for predictive models of how the microbiome changes in response to climate change, which has already had an impact on the temperature, pH and salinity levels of the Baltic Sea.