Bacterial taxonomics: finding the wood through the phylogenetic trees

Bacterial taxonomy comprises systematics (theory of classification), nomenclature (formal process of naming), and identification. There are two basic approaches to classification. Similarities may be derived between microorganisms by numerical taxonomic methods based on a range of present-day observable characteristics (phenetics), drawing in particular on conventional morphological and physiological test characters as well as chemotaxonomic markers such as whole-cell protein profiles, mol% G+C content, and DNA-DNA homologies. By contrast, phylogenetics, the process of reconstructing possible evolutionary relationships, uses nucleotide sequences from conserved genes that act as molecular chronometers. A combination of both phenetics and phylogenetics is referred to as polyphasic taxonomy, and is the recommended strategy in description of new species and genera. Numerical analysis of small-subunit ribosomal RNA genes (rDNA) leading to the construction of branching trees representing the distance of divergence from a common ancestor has provided the mainstay of microbial phylogenetics. The approach has some limitations, particularly in the discrimination of closely related taxa, and there is a growing interest in the use of alternative loci as molecular chronometers, such as gyrA and RNAase P sequences. Comparison of the degree of congruence between phylogenetic trees derived from different genes provides a valuable test of the extent they represent gene trees or species trees. Rapid expansion in genome sequences will provide a rich source of data for future taxonomic analysis that should take into account population structure of taxa and novel methods for analysis of nonclonal bacterial populations.