Molecular Revolution & Microbial Controversies

For 5 decades, Prokaryotes’ subdivision into Bacterial and Archaeal kingdoms remained unknown. Carl Woese became the first to resolve the taxonomic mystery thanks to developing 16s rRNA method classifying organisms based on sequence variation of the highly conserved and essential 16s rRNA gene. Significant divergence in prokaryotic 16s rRNA genes led Woese to divide the prokaryotic domain into archaeal and bacterial kingdoms which are also significantly divergent in physiology and ecology. Moreover, 16s rRNA method emerged to successfully assign taxa to eukaryotic organisms at a species resolution. The 16s method’s success in eukaryotic taxonomic identification, as well as prokaryotes’ subdivision into archaeal and bacterial kingdoms, led people to think about the branches of bacterial and archaeal domains into lower ranks of taxonomy, ie. phylum. Therefore, Woese attempted to identify the branch order of bacterial phyla using the 16s technique. Although the branch order of bacterial phyla is still debated, Woese’s attempt revealed that bacteria and archaea shared a common ancestor and archaea created a monophyletic group with eukaryotes. Consequently, Woese’s attempt to characterize bacterial phyla led him to divide 2 main domains (Prokaryote and Eukaryote, into 3 domains (Archaea, Bacteria and Eukarya).

Woese’s phlyogenetic ToL showing three domains of life, Towards a natural system of organisms: Proposal for the domains Archaea, Bacteria, and Eucarya, Woese et al. 1990

Woese’s successors tried to identify evolutionary bacterial phyla branches based on cell wall morphology, conserved coding mutations or conserved protein sequences. Yet, none was to have a verdict on the status of bacterial phyla branchings. Therefore, the scientific community welcomed a novel molecular method: whole-genome sequencing (WGS), to identify branchings in the lower ranks of bacterial taxonomy. WGS emerges as a more powerful technique as it compares and contrasts species’ whole genome sequences, instead of a single gene’s. Novel phylogenetic trees were also generated using WGS, but WGS arose new questions rather than resolving the issue on bacterial phyla branchings. WGS revealed that bacterial genes were interchangeable meaning that bacteria could transfer genes amongst themselves. Gene transfer amongst bacteria being common in nature, as well as some bacteria being unculturable,or cryptic in extreme environments further confounded how bacteria branched into lower phylum ranks of taxonomy. There is still an ongoing debate on bacterial phyla branching, as there is still also no common definition of what a bacterial species is. Understanding bacterial phyla branching order would resolve a mystery in evolutionary biology which may then focus our efforts on resolving bacterial taxonomy in finer ranks. To do that, it appears in order to understand what a bacterial phylum is and what is bacterial phyla’s ecological significance.