Complete genome sequences of freshwater acI actinobacterial isolates obtained by whole-genome amplification of dilution-to-extinction cultures

초록

The acI lineage of the phylum Actinobacteria is one of the most abundant bacterial groups in most freshwater lakes. However, due to difficulties in laboratory cultivation, only two mixed cultures and some incomplete single-amplified genomes have been reported for the acI lineage. Here, we report the initial cultivation and complete genome sequences of four novel strains of the acI lineage from the tribes acI-A1, -A4, -A7, and - C1. The four acI strains were initially isolated by dilution-to-extinction culturing using lownutrient liquid media, but eventually failed to be maintained as axenic cultures. However, the first complete genomes of the acI lineage were successfully obtained from these initial cultures, through the application of whole genome amplification (by multiple displacement amplification) to more than hundreds of cultured acI cells. The genome sequences exhibited features of genome streamlining and showed that the strains are aerobic chemoheterotrophs sharing central metabolic pathways, with some differences among tribes that may underlie niche diversification within the acI lineage. Actinorhodopsin was found in all strains, but retinal biosynthesis was complete in only A1 and A4 tribes.