Identification of prokaryotes

With taxonomy for prokaryotes in place the microbiologist can now start to place organisms within this framework, using the taxonomy to identify and describe species. When first purified an organism is define as an isolate and is commonly given a number which helps to distinguish it from others in the laboratory. Isolates may be genetically identical but have been taken from their natural environments at geographical locations or separate times.

Normally it is uncontroversial to place a new bacterium in an appropriate genus so this isolate may become example for, Paracoccus strain NCIMB 8944. The species concept is more hard to apply  to Archaea and Bacteria than in the  animal kingdom because of the  enormous genetic diversity so the  subspecies definition of biovar  is sometimes applied to organisms of the  similar species with  slightly  different properties; example for the  plague organism, Yersinia pestis  is divided into  biovars which include Orientalis and Mediaevalis. The differences among strains of the similar species are sometimes defined through subspecies for example the plant pathogen Pectobacterium carotovorum has subspecies including carotovorum and atroseptica. In this case the subspecies describe members of the similar species which cause various plant pathologies. In microbiological research the problem of species definition means that it is always best to leave the original isolate code in place when writing about an organism so that its history in several laboratories can be traced.

While the definition of the individual Archaeal and Bacterial taxa down to genus level has gained consensus between microbiologists there has since to be agreement on what constitutes the fundamental unit of biological diversity the species. The Species definition in one genus example for sharing less than a certain percentage of DNA homology does not necessarily hold true in another a problem particularly true in taxa dominated through human pathogens. If we cannot consistently and properly define a species then identification down to species level becomes problematic. The techniques used for prokaryotic identification which is the way in which we assign a classification to our new isolate are explored further in Section B2.