The definition of a bacterial or archaeal species is widely debated, as discussed in Next Article Nonetheless, for practical reasons it is essential that the established rules of taxonomy are followed.
Microbes are placed in taxonomic levels arranged in a nonoverlapping hierarchy so that each level includes not only the traits that define the rank above it but also a new set of more restrictive traits (See chart).
Thus within each domain—Bacteria, Archaea, or Eukarya— each organism is assigned (in descending order) to a phylum, class, order, family, genus, and species epithet or name. Some microbes are also given a subspecies designation. Microbial groups at each level have a specific suffix that indicates rank or level.
The application of Linnaeus’s classification system to bacteria began in Pasteur and Koch’s time, about 1872. However, within 20 years microbiologists became dissatisfied, considered it haphazard, and called for more uniform criteria in organizing phyla, classes, orders, families, genera, and species.
With the ongoing explosion in metagenomic analysis, some would argue that history is repeating itself. Within the last decade or so, thousands of 16S rRNA genes and protein-coding genes have been sequenced that cannot convincingly be affiliated with any previously defined taxa.
This data explosion has led to the recent development of the taxo nomic classification “superphylum,” below domain and above phylum (e.g., in figure 19.1, superphylum would be placed between Bacteria and Proteobacteria).
Ideally a superphylum includes organisms of several phyla that share a number of distinctive characteristics, such as unusual morphological or metabolic features. However, some feel that the term is being loosely applied based on insufficient data—for instance, to SSU rRNA sequences alone.
At the other end of the classification scheme is the most fundamental definition of a bacterial or archaeal species. A species is a collection of strains that share many stable properties and differ significantly from other groups of strains. A strain consists of the descendants of a single, pure microbial culture.
Strains within a species may be described in a number of different ways. Biovars are variant strains characterized by biochemical or physiological differences, morphovars differ morphologically, and serovars have distinctive antigenic (immunologically reactive) properties.
Because changes in species assignment are not uncommon, one strain is designated as the type strain for each species. The type strain is the holder of the species name. This ensures permanence of names when nomenclature revisions occur because the type species must remain within the original species.
It is usually one of the first strains studied and often is more fully characterized than others; however, it does not have to be the most representative member. Only those strains very similar to the type strain or type species are included in a species.
Each species is assigned to a genus, the next rank in the taxonomic hierarchy. A genus is a well-defined group of one or more species that is clearly separate from other genera. In practice, considerable subjectivity occurs in assigning species to a genus, and taxonomists may disagree about the composition of genera.
Hierarchical Arrangement in Taxonomy. In this example, members of the genus Shigella are placed within higher taxonomic ranks. Not all classification possibilities are given for each rank to simplify the diagram. Note that -ales denotes order and -ceae indicates family
Microbiologists name microorganisms using the binomial system of Linnaeus. The Latinized, italicized name consists of two parts. The first part is the generic name (i.e., the genus), and the second is the species name (e.g., Yersinia pestis, the causative agent of plague).
The species name is stable; the oldest epithet for a particular organism takes precedence and must be used. In contrast, a generic name can change if the organism is assigned to another genus. For example, some members of the genus Streptococcus were placed into two new genera, Enterococcus and Lactococcus, based on rRNA analysis and other characteristics.
Thus Streptococcus faecalis is now Enterococcus faecalis. To be recognized as a new species, genomic, metabolic, morphological, reproductive, and ecological data must be accepted and published in the International Journal of Systematic and Evolutionary Microbiology; until that time, the new species name will appear in quotation marks.
Microbes that have not been grown in pure culture but for which there is sufficient genetic characterization may be given a provisional genus and species name preceded by the term Candidatus, meaning candidate. For instance, a novel aerobic phototrophic member of the phylum Acidobacterium has been grown only in coculture with another isolate.
It has been given the provisional name Candidatus Chloracidobacterium thermophilum (note that the genus and species are not italicized). Bergey’s Manual of Systematic Bacteriology contains only recognized bacterial and archaeal species