On the culture-independent assessment of the diversity and distribution of Prochlorococcus

Much of our current knowledge on Prochlorococcus has derived from research on various genetic strains that have successfully been brought into culture. In particular, analyses of the complete genomes of 12 of those isolates have revealed the extent to which these strains differ from each other and the genetic means by which they are adapted to specific environmental niches. However, based on culture-independent studies it is now clear that the strains currently available in diverse culture collections do not represent the true diversity of Prochlorococcus geno- and phenotypes. Potential alternatives to overcome the limitations caused by difficulties in isolating Prochlorococcus may be provided by the whole-genome amplification of flow cytometrically isolated individual cells. The new information obtained in this way on various genetic types would, in turn, facilitate the correct identification of Prochlorococcus-derived sequences within metagenomic sequence data sets. However, culture-independent molecular population genetic approaches have also greatly furthered our understanding of the ecology and physiological capability of Prochlorococcus genetic groups. Based on this, I support the notion that such population genetic approaches to reveal the Prochlorococcus microdiversity are still of great value if appropriate marker genes providing a high genetic resolution are used. The comparison of the results from those culture-independent analyses of environmental marine samples with those from the measurement of relevant environmental and biotic parameters still has potential to uncover further parameters that control Prochlorococcus diversity and distribution. In this context, I will discuss those markers that have so far been used in population genetic studies of Prochlorococcus, which is followed by outlining a general approach to evaluate their use for resolving microbial microdiversity and for phylogenetic identification.