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, http://www.cme.msu.edu/RDP/).
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