Evolutionary history of prokaryotes: Tree or no tree?

Prokaryotes are likely to be the most numerous and species rich organisms on the planet(1), occupying a more diverse set of ecological niches than eukaryotes. Knowledge of prokaryote diversity is severely limited by our inability to recreate the conditions in the laboratory that are needed to cultivate the majority. Discrepancies between direct microscopical counts and the numbers of colony-forming units can be as much as 100-fold, leading to speculation concerning how much we really know about prokaryotes. In contrast, genomic studies of prokaryotes are advanced. So, while on one hand we know that we have a poor overview of prokaryotic life on the planet, we have, paradoxically, succeeded in obtaining more completed genomic sequences of prokaryotes than of eukaryotes. Therefore, even though taxon sampling has been restricted, we have now reached the stage where we can evaluate whether there is a meaningful prokaryotic phylogenetic tree or taxonomy. Questions remain as to whether the history of prokaryotic life has been overwritten by continuous and random interspecies gene transfer and occasional genome fusions, or whether these events have only been minor contributors, thereby enabling prokaryotic evolutionary history to be adequately described by a tree.