Defining taxonomic ranks

Abstract

Taxonomic ranks are subjectively defined constructs based on dissimilarities between individuals or groups of organisms, with higher ranks representing higher-order groupings. The establishment of a Linnaeus-type hierarchy and binomial nomenclature for bacteria originated from the botanical background of the first microbiologists in the nineteenth century and the desire to establish a system comparable to those of plants and animals. Anatomical/morphological similarities, reflecting evolutionary relationships, are common among plants and animals, allowing their classification into a hierarchic structure. In contrast, as bacterial relatedness is not typically characterized by distinctive morphological and physiological similarities, the first 100 years of bacteriology witnessed several different hierarchic structures, often discussed in parallel, depending upon the emerging discoveries at the time. It was not until the semantic nature of DNA, RNA, and proteins was described that scientists were able to present the outline of a hierarchic structure of the prokaryotes. This structure is primarily based on the phylogenetic tree of the small subunit ribosomal RNA gene, a universally present molecule of about 1,500 nucleotides long, and so far represents the most convincing reflection of the evolutionary relationships among prokaryotic taxa. Although the evolution of several housekeeping genes is in support of the rRNA gene tree, indicating that an average consensus phylogeny may have been obtained, the phylogenies of many other genes depart from the rRNA phylogeny due to extensive horizontal gene transfer, making it clear that the true evolutionary history of organisms is probably not reflected by the present prokaryotic tree. It must also be remembered that taxonomy is not fixed but prone to changes as a result of research on established and new taxa. Only the naming of taxa but not the science of classification is regulated, resulting in taxonomy in flux with regular changes of ranks due to their splitting and merging and introduction of novel ranks at all levels as new information becomes available. This chapter describes the main principles underlying the delineation of the higher ranks (phylum-class-order-family) and discusses the finding that not all taxa related at the same rank are comparable units in terms of intrataxon genetic relatedness. Special attention is given to the species rank, the fundamental unit of biological organization, and the recent advances in genomics and ecology that call into question the pragmatic but artificial species definition that is in use today. Only when these issues will be addressed, the promise for a more predictive, genome-based prokaryotic taxonomy will be realized. We believe time and technology needed may have arrived.