From Strains to Domains.

Two molecular methods have proven successful in determining the whole range of relationships between prokaryotic organisms, i.e. from the level of strains to the level of domains. DNA:DNA hybridization is suitable for the elucidation of relationships among closely related strains, while all other levels, from remote to distant relationships, can be unravelled by the analysis of conserved macromolecules, preferably the RNA of the small subunit of ribosomes or the genes coding for it (16S rRNA/DNA) (xcStackebrandt and Goebel, 1994). It is obvious that DNA reassociation methods require pure cultures, in order to determine the degree of relatedness between individual organisms, while 16S rDNA sequences can be obtained from mixed bacterial populations by analysis of cloned DNA restriction fragments or PCR products (xcGiovannoni et al., 1990; xcWard et al., 1990). The presence of rDNA in every organism, and the availability of a broad range of molecular methods, including amplification techniques and detection methods, e.g., the use of taxon- specific PCR primers and oligonucleotide probes, makes sequence analysis and/or detection of 16S rDNA the superior approach for the assessment of phylogenetic diversity (xcPace et al., 1985). The analysis of this molecule does not allow determination of morphological and physiological activities, hence information about the ecological role played by an organism in its environment; but it reveals information about approximate relationships between naturally occurring organisms and cultured strains, and it allows us to determine the presence of novel types of prokaryotes. [ABSTRACT FROM AUTHOR]