Principles of Taxonomy

Taxonomy is the science that studies organisms in order to arrange them into groups; those organisms with similar properties are grouped together and separated from those that are different. Taxonomy can be viewed as three separate but interrelated areas:

■ Identification—the process of characterizing organisms

■ Classification—the process of arranging organisms into similar or related groups, primarily to provide easy identification and study

■ Nomenclature—the system of assigning of names to organisms

Strategies Used to Identify Prokaryotes

In practical terms, identifying the genus and species of a prokary-ote may be more important than understanding its genetic relationship to other microbes. For example, a food manufacturer is most interested in detecting the presence of microbial contaminants that can spoil a food product. In a clinical laboratory, it is critical to quickly identify the microbes that are isolated from patients so the best possible treatment can be given.

To characterize and identify microorganisms, a wide assortment of technologies is used including microscopic examination, culture characteristics, biochemical tests, and nucleic acid analysis. While each of these methods is best suited for detecting certain kinds of organisms in specific types of specimens, combinations of the tests may provide the most accurate identification. The number and type of tests used depends on the microbe to be detected or identified and the specimen being examined.

In a clinical laboratory, the patient's disease symptoms play an important role in identifying the infectious agent. For example, pneumonia in an otherwise healthy adult is typically caused by Streptococcus pneumoniae, an organism that is easily differentiated from others using a few specific tests. In contrast, diagnosing the cause of a wound infection is often more difficult, because many different microorganisms could be involved. Often, however, it is only necessary to rule out the presence of organisms known to cause a particular disease, rather than to conclusively identify each and every organism in the specimen. For example, a fecal specimen from a patient complaining of a diarrhea and fever would generally only be tested for the presence of specific organisms that cause those symptoms. ■ Streptococcus pneumoniae, p. 576

The various methods used to identify prokaryotes will be discussed in detail later in the chapter.

Strategies Used to Classify Prokaryotes

Understanding the evolutionary relatedness, or phylogeny, of prokaryotes is important in constructing a classification scheme that reflects the actual evolution and biology of these organisms. Such a scheme is more useful than one that simply groups organisms by arbitrary characteristics, because it is less prone to the bias of human perceptions. It also makes it easier to classify newly recognized organisms and allows scientists to make predictions, such as which genes are likely to be transferred between organisms.

Unfortunately, determining genetic relatedness among prokaryotes is more difficult than it is for plants and animals. Not only do prokaryotes have few differences in size and shape, they do not undergo sexual reproduction. In higher organisms such as plants and animals, the basic taxonomic unit, a species, is generally considered to be a group of morphologically similar organisms that are capable of interbreeding to produce fertile offspring. Obviously, it is not possible to apply these same criteria to prokaryotes, thus making classification problematic.

Historically, taxonomists have relied heavily on phenotyp-ic attributes to classify prokaryotes; however, the development and application of molecular techniques such as nucleotide sequencing is finally making it possible to determine the genetic relatedness of microorganisms. The techniques used to classify prokaryotes based on phenotype and genotype will be discussed in detail later in the chapter. Regardless of the methods employed to assess relatedness, the objective of classification is to arrange organisms into structured categories that reflect the similarities of individuals within the groups. ■ genotype, p. 192 ■ phenotype, p. 192

Taxonomic Hierarchies

Taxonomic classification categories are arranged in a hierarchical order, with the species being the basic unit. The species designation gives a formal taxonomic status to a group of related isolates or strains, which, in turn, permits their identification. Without classification, scientists and others would not be able to communicate about organisms with any degree of accuracy. Taxonomic categories include:

■ Species—a group of related isolates or strains. Note that members of a species are not all identical; individual strains may vary in minor properties. The difficulty for the taxonomist is to decide how different two isolates must be in order to be classified as separate species rather than strains of the same species.

■ Genus—a collection of related species.

■ Family—a collection of similar genera. In prokaryotic nomenclature, the name of the family ends in the suffix -aceae.

■ Order—a collection of similar families. In prokaryotic nomenclature, the name of the family ends in the suffix -ales.

■ Class—a collection of similar orders. In prokaryotic nomenclature, the name of the family ends in the suffix -ia.

■ Phylum or Division—a collection of similar classes.

■ Kingdom—a collection of similar phyla or divisions. The number of different kingdoms varies according to the classification system used.

■ Domain—a collection of similar kingdoms. The domain is a relatively new taxonomic category that reflects the characteristics of the cells that make up the organism.

Note, however, that microbiologists often group prokaryotes into informal categories rather than utilizing the higher taxonomic ranks such as order, class, and phylum. Examples of such

Table 10.1 Taxonomic Ranks of the Bacterium Escherichia coli

Formal Rank

Example

Domain

Bacteria

Phylum

Proteobaderia

Class

Gammaproteobacteria

Order

EnterobaCter'ales

Family

Enterobaderiaceae

Genus

Escherichia

Species

coli

informal groupings include the lactic acid bacteria, the anoxy-genic phototrophs, the endospore-formers and the sulfate reducers. Organisms within these informal groupings share similar phenotypic and physiological characteristics, but may not be genetically related. ■ lactic acid bacteria, p. 275 ■ anoxygenic phototrophs, p. 276 ■ sulfate reducers, p. 274

An example of how a particular bacterial species is classified is shown in table 10.1. Note that the table intentionally omits the taxonomic category of kingdom. This is because the use of kingdoms within the Bacteria is still in a state of flux.

Classification Systems

Taxonomy is still an evolving discipline, with systems of classification that change over the years as new information is discov-

10.1 Principles of Taxonomy 247

ered. There is no such thing as an "official" classification system, and, as new ones are introduced, others fall into disfavor. The classification scheme currently favored by most micro-biologists is the three-domain system. This designates all organisms as belonging to one of the three domains—Bacteria, Archaea, and Eucarya (figure 10.1). The system is based on the work of Carl Woese and colleagues who compared the sequences of nucleotide bases in ribosomal RNA from a wide variety of organisms. They showed that prokaryotes could be divided into two major groups that differ from one another as much as they do from the eukaryotic cell. The ribosomal RNA data are consistent with other observed differences between the Archaea and Bacteria, including the chemical compositions of their cell wall and cytoplasmic membrane (table 10.2). ■ Bacteria, p. 8 ■ Archaea, p. 8 ■ Eucarya, p. 8

Before the three-domain classification system was introduced, the most widely accepted system was the five-kingdom system, proposed by R. H. Whittaker in 1969. The five kingdoms in this system are the Plantae, Animalia, Fungi, Protista (mostly single-celled eukaryotes) and Prokaryotae. While the five-kingdom system recognizes the obvious morphological differences between plants and animals, it does not reflect the recent genetic insights of the ribosomal RNA data, which indicates that plants and animals are more closely related to each other than Archaea are to Bacteria.

The genetic insights provided by the ribosomal RNA techniques are causing significant upheaval in classification of microorganisms, as evidenced by the creation of the new taxonomic rank, domain. This new information is resulting in the need to shuffle some organisms within taxonomic categories, causing both confusion and controversy. In addition, the transition from the five-kingdom system to the three-domain system of classification causes significant change in itself. This is because the new system simultaneously elevates and splits what was once

Bacteria

Archaea

Eucarya

Green nonsulfur bacteria

Entamoebae Slime

Gram-Spirochetes positive

Proteobacteria

Flavobacteria

Bacteria

Archaea

Eucarya

Green nonsulfur bacteria

Entamoebae Slime

Gram-Spirochetes positive

Proteobacteria

Animals

Flavobacteria

Microsporidia

Flagellates Trichomonads

Microsporidia

Animals

Figure 10.1 The Three-Domain System of Classification This classification system separates prokaryotic organisms into two domains—Bacteria and Archaea. The third domain, Eucarya, contains all organisms composed of eukaryotic cells.This system of classification is based on ribosomal RNA sequence data.

248 Chapter 10 Identification and Classification of Prokaryotes

Table 10.2 A Comparison of Some Properties of the Three Domains—Archaea, Bacteria, and Eucarya

Cell Feature Archaea Bacteria Eucarya

Peptidoglycan Cell Wall

No

Yes

No

Cytoplasmic Membrane Lipids

Hydrocarbons (not fatty acids)

Fatty acids linked to glycerol

Fatty acids linked to glycerol

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