Taxonomic Characterization of Prokaryotic Microorganisms

Prokaryote microorganisms constitute a major part of the genetic diversity of our planet and they play a pivotal role in the biochemical processes of the biosphere. In addition, they find application in a broad array of industrial and biotechnological applications. In the search for new industrial strains and catalysts, prospecting of natural diversity has greatly intensified over the last decades. Improved cultivation techniques and newly emerging (meta)genomic tools have provided access to sources of microbial diversity that were previously uncovered. The interest of biotechnologists in what microorganisms can do is not always accompanied by a serious investigation on who they are. Identification of the isolates is of primary importance, not only for the exchange of scientific knowledge, but also in an applied context, because names are crucial for regulations in biotechnology and biosafety. A survey of species names associated with published genome sequences has, in several cases, revealed incorrect, out-of date, or incomplete strain names. This suggests that reductionism brought about by molecular biology and the interests of single research groups could significantly affect the coherence of names, with negative consequences on accessibility of microbiological data.Taxonomy provides the framework for correct identification of prokaryotic strains. The aim of this chapter is to present microbiologists in biotechnology and molecular biology with the basic conceptual framework and the currently accepted procedures for characterization and consistent naming of newly isolated prokaryotic strains.