DNA-DNA Reassociation Methods Applied to Microbial Taxonomy and Their Critical Evaluation

TL;DR: It is still too soon to substitute DNA-DNA reassociation techniques for circumscribe species because of several reasons: (a) the use of whole genome hybridizations in the definition of species has been of paramount influence and has actually determined the size and shape of what the authors call ‘species’, (b) there are almost 5,000 species described, many of them based on reassociation experiments, and the legitimacy of new circumscription methods should be validated.

Abstract: DNA-DNA reassociation techniques are used for many purposes, but in the field of microbial systematics they are in most cases linked to the circumscription of prokaryotic species. Actually, as we will see, the use of whole genome hybridizations in the definition of prokaryotic species has had an enormous influence since the origin of the polythetic classification system (Rossello-Mora and Kampfer 2004). The importance of morphology in the middle of the eighteenth century was substituted for that of biochemical properties at the beginning of the nineteenth century; and subsequently the emerging “modern spectrum” techniques emphasized the importance of genetic measurements, such as DNA-DNA reassociation experiments. However, after almost 50 years of the application of these techniques to circumscribe species, there is increasing reluctance to use them because of the intrinsic pitfalls in the methods (e.g. Stackebrandt 2003; Stackebrandt et al. 2002). Consequently, the question that arises is: if DNA reassociation techniques are to be substituted, what will take their place? However, in my opinion, it is still too soon to substitute these techniques because of several reasons: (a) the use of such parameters in the definition of species has been of paramount influence and has actually determined the size and shape of what we call ‘species’, (b) there are almost 5,000 species described (Garrity et al. 2004), many of them based on reassociation experiments, and the legitimacy of new circumscription methods should be validated and (c) the alternatives proposed are not yet standardized and tested sufficiently enough to offer a reliable, pragmatic and easy to use circumscription tool.