Another problem besides size complicates the taxonomy of prokaryotes: What exactly is a species? In the long-used definition developed for plants and animals, a species is considered a grouping of similar organisms that under natural conditions is capable of mating to produce fertile offspring. However, this definition is not very useful for organisms that reproduce asexually. Perhaps an even greater difficulty is that the genetic exchange that does occur among prokaryotes can be between organisms that are obviously not closely related to each other. This can lead to cross-linkings of otherwise unrelated species in taxonomic trees: organisms that, in a sense, are not close relatives of one of their biological "parents"! (The human genome has been found to contain considerable bacterial DNA, for example.)
Yet the idea of a species is still useful for prokaryotes. Some individual cells clearly are very similar, sharing numerous traits, and having a name to describe this grouping is desirable. Salmonella typhi causes typhoid fever, Pseudomonas putida does not; Bacillus stearothermophilus is a thermophilic sporeformer, whereas Nitrosomonas europaea is a mesophilic autotroph. Some organisms exist that appear to be intermediate between closely related species, and arguments arise among taxonomists between "splitters," who think that even minor differences are sufficient to define a new species, and "lumpers," who feel that various strains can be included in a single species unless there are numerous substantial differences. A strain is a group of cells that have all derived from a single cell in the not-too-distant past and are thus genetically identical except for any random mutations that might have occurred; molecular biologists call a strain recently obtained from a single cell a clone.
One view taken by some microbiologists is that nearly unlimited genetic variation can occur among microorganisms, but that some of the potential combinations of characters are more successful and stable than others. This can be pictured (Figure 10.6) as a surface in three-dimensional space, with hills and valleys. A marble dropped on the surface potentially could end up on a hillside or even the peak of a hill, but most will end up in the valleys. Incorporating every potentially useful trait is not necessarily the best survival strategy for a microorganism, in the same way that the camper who takes every potentially useful item is not likely to be the one who does the best on a backpacking trip.
The new genetic tools (Section 10.4.4) have provided some quantitative means of determining whether individual strains of prokaryotes belong to the same species. One approach compares the degree of DNA homology (similarity in sequence of DNA base pairs) among microorganisms. Generally, if the DNA homology of two organisms is more than 70%, they will be considered the same species. If homology exceeds 20%, they may be considered to belong to the same genus. Using another tool, similarities of ribosomal RNA sequences of greater than 97% has led to considering two organisms to be the same species, while similarities of greater than 93 to 95% usually indicates the same genus. [The higher similarity for the rRNA analysis stems from the more highly conserved (less variable) nature of these sequences.]
The use of such techniques has led to the renaming of a number of microorganisms, as well as the "discovery" of the Archaea (Section 10.2.5). For example, the well-established species Pseudomonas cepacia was renamed Burkholderia cepacia when it was realized that it belonged to a different group of Proteobacteria than (and thus was not a close (relative of) other Pseudomonas species (Section 10.5.6).
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