Targeted population genomics of marine Synechococcus cyanobacteria

Large-scale sequencing of nucleic acids extracted from diverse sources is now widely used to study the structure and function of bacterial communities. However, the biological complexity of natural environments, combined with both technical and practical difficulties in analysing large datasets often means the full potential of this technique is rarely achieved. In this respect, we present a targeted metagenomic pipeline, focusing on extracting one component of a complex bacterial community. We used a 3 step process: flow cytometric sorting, followed by direct whole genome amplification on purified cells, then high throughput sequencing. We selected Synechococcus, a ubiquitous marine picophytoplankton, as a target and tested our methods on defined mixtures of cultivated isolates before applying the approach on environmental samples. We show that this targeted approach can provide precise and in-depth assessment of the genomic potential of a selected group where low environmental abundance would limit the return of metagenomic information from community-wide DNA surveys. This approach will help to explore fine-scale population structure and biogeography in a genomic context and therefore the underlying mechanisms that allow specific keystone populations, e.g., marine Synechococcus, to cohabit and contribute to nutrient cycling across a range of habitats.