Deep sequencing of evolving populations in bacterial biofilms
Bacterial communities growing as biofilms are subject to a distinct lifecyle, featuring initial surface attachment, microcolony formation and dispersal of cells. Bacterial biofilms are sometimes characterised by high levels of heritable phenotypic variants, presumably resulting from genetic diversification during the biofilm lifecyle. As biofilms are a favoured lifestyle of many environmental and pathogenic bacteria, identifying the evolutionary processes responsible for this diversification has important implications, both for our understanding of ecological processes, such as niche adaptation, and to clinically relevant questions, such as the evolution of antibiotic resistance.
I've used longitudinal genome-wide deep sequencing to reveal the underlying genetic structure of bacterial populations growing as biofilms, for the model organisms Phaeobacter gallaeciensis 2.10 (an abundant marine bacterium) and Pseudomonas aeruginosa 18A (a clinical Cystic Fibrosis isolate). Biofilms were grown under defined laboratory conditions known to generate reproducible phenotypic diversification. Samples from different stages of biofilm development were then sequenced to very high coverage (>800x). By accounting for sequencing errors using a matched-sample approach, variants with population frequencies as low as 0.5% could be accurately identified.
In general, the extent and nature of genetic variation was comparable for biofilms of both model organisms, being driven by selection for a small number of non-synonymous variants within key genes involved in biofilm- and competition-related pathways. These results also demonstrate that genome-wide deep sequencing can rapidly, accurately and comprehensively describe genetic variation within evolving populations.