Prokaryotic Species

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.

Figure 10.6 Three-dimensional surface: visualizing prokaryotic species as more stable (valleys), and hence more likely, combinations of characteristics, although intermediates may exist.

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).

10.4.3 Naming of Microorganisms

When microorganisms were first discovered, there were only two kingdoms, Plant and Animal. Thus, protozoans were considered "single-celled animals'' studied by zoologists, and fungi, algae, and bacteria were "plants," studied by botanists. As a result, the latter organisms are still sometimes referred to as "flora" (and protozoans as "fauna"). However, based on our improved knowledge of their taxonomy, a better term today is biota.

The formal assignment of the Latin and Greek names (nomenclature) used in microbial taxonomy is now closely controlled. The official journal for publication of new pro-karyote species is the International Journal of Systematic Bacteriology (note the holdover from the time when all prokaryotes were considered bacteria). If the new species description is first published elsewhere, it must be forwarded to IJSB to be formally accepted and included in the next approved list of names. The official representative, or type, culture of a newly labeled microorganism is held in an approved culture collection such as that maintained in the United States by the American Type Culture Collection (ATCC) or in Germany by the Deutsche Sammlung von Mikroorganismen und Zellkulturen (DSMZ). Rediscovered species (original type culture lost or never saved) are deposited as neotype strains. Species of some microorganisms have been subdivided further as specific cell strains, subspecies, or types (e.g., Escherichia coli type 0157:H7).

When a new bacterial or archaeal strain is isolated and characterized, it is compared to the existing information on described species, and/or directly to the type species. Traditional (mainly phenotypic) comparisons are made using keys (Figure 10.7) and standard references, particularly Bergey's Manual of Determinative Bacteriology. Genotypic information is included in Bergey's Manual, but large databases are also now available online (e.g., the Ribosomal Database Project maintained by the Center for Microbial Ecology at Michigan State University, for ribosomal RNA sequences,

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