Microbial Evolution and Diversity

PART V Microbial Evolution and Diversity This material cannot be copied, disseminated, or used in any way without the express written permission of the publisher. Copyright 2007 Sinauer Associates Inc. The objectives of this chapter are to: N Provide information on how bacteria are named and what is meant by a validly named species. N Discuss the classification of Bacteria and Archaea and the recent move toward an evolutionarily based, phylogenetic classification. N Describe the ways in which the Bacteria and Archaea are identified in the laboratory. This material cannot be copied, disseminated, or used in any way without the express written permission of the publisher. Copyright 2007 Sinauer Associates Inc. 17 Taxonomy of Bacteria and Archaea It’s just astounding to see how constant, how conserved, certain sequence motifs—proteins, genes—have been over enormous expanses of time. You can see sequence patterns that have per- sisted probably for over three billion years. That’s far longer than mountain ranges last, than continents retain their shape. —Carl Woese, 1997 (in Perry and Staley, Microbiology) his part of the book discusses the variety of microorganisms that exist on Earth and what is known about their characteris- Ttics and evolution. Most of the material pertains to the Bacteria and Archaea because there is a special chapter dedicated to eukaryotic microorganisms. Therefore, this first chapter discusses how the Bacte- ria and Archaea are named and classified and is followed by several chapters (Chapters 18–22) that discuss the properties and diversity of the Bacteria and Archaea. When scientists encounter a large number of related items—such as the chemical elements, plants, or animals—they characterize, name, and organize them into groups. Thousands of species of plants, animals, and bacteria have been named, and many more will be named in the future as more are discovered. Not even the most brilliant biologist knows all of the species. Organizing the species into groups of similar types aids the scientist not only in remembering them but also in comparing them to their closest relatives, some of which the scientist would know very well. In addition, biologists are interested in evolution, because this is the process through which organisms became diverse. Unraveling the route of evolution leads to an understanding of how one species is related to another. As discussed in subsequent text of this chapter, evolutionary relationships are assessed by molecular phylogeny, the analysis of gene and protein sequences to determine the relatedness among organisms. To date, approximately 5,000 bacterial and archaeal species have been named and, based on their characteristics, placed This material cannot be copied, disseminated, or used in any way without the express written permission of the publisher. Copyright 2007 Sinauer Associates Inc. 486 Chapter Seventeen within the existing framework of other known species. The branch of bacteriology that is responsible for char- Hierarchical classification acterizing and naming organisms and organizing them TABLE 17.1 of the bacterium into groups is called taxonomy or systematics. Spirochaeta plicatilis Taxonomy can be separated into three major areas Taxon Name of activity. One is nomenclature, which is the naming of bacteria. The second is classification, which entails the Domain Bacteria ordering of bacteria into groups based on common prop- Phylum Spirochaetes (vernacular name: spirochetes) erties. In identification, the third area, an unknown bac- Class Spirochaetes terium, for example, from a clinical or soil sample, is Order Spirochaetales characterized to determine its species. This chapter cov- Family Spirochaetaceae ers all three of these areas. Genus Spirochaeta Species plicatilis 17.1 Nomenclature The International Journal of Systematic and Evolutionary Microbiology (IJSEM) is a journal devoted to the taxon- Bacteriologists throughout the world have agreed on a omy of bacteria that is published by the Society for Gen- set of rules for naming Bacteria and Archaea. These rules, eral Microbiology. IJSEM publishes papers that describe called the “International Code for the Nomenclature of and name new bacterial taxa and contains an updated Bacteria” (1992), state what a scientist must do to de- listing of all new bacteria whose names have been scribe a new species or other taxon (taxa, pl.), which is validly published. Thus, although bacterial species may a unit of classification, such as a species, genus, or fam- be described in other scientific journals, they are not con- ily. Each bacterium is placed in a genus and given a sidered validly published until they have been included species name in the same manner as are plants and an- on a validation list in IJSEM. imals. For example, humans are Homo sapiens (genus IJSEM also provides a forum to debate specific con- name first, followed by species), and a common intes- troversies in nomenclature by allowing a scientist to tinal bacterium is named Escherichia coli. This binomial challenge the current nomenclature of an organism or system of names follows that proposed for plants and group of organisms. Such challenges, if accepted by peer animals by the Swedish taxonomist Carl von Linné (Lin- review, are then published as a question in the IJSEM. naeus; 1707–1778). The question is then evaluated by the Judicial Commis- According to the rules of bacterial nomenclature, the sion of the International Union of Microbiological Soci- root for the name of a species or other taxon can be de- eties, which subsequently publishes a ruling in the jour- rived from any language, but it must be given a Latin end- nal. One typical example of a problem considered by the ing so that the genus and species names agree in gender. Judicial Commission was the question about Yersinia For example, consider the species name Staphylococcus pestis, the causative agent of bubonic plague. Scientific aureus. The first letter in the genus name is capitalized, evidence indicates that Y. pestis is really just a subspecies the species name is lowercase, and they are both itali- of Yersinia pseudotuberculosis, a species name that has cized to indicate that they are Latinized. When writing precedence over Y. pestis because of its earlier publica- species names in longhand, as for a laboratory notebook, tion. Because of the potential confusion and possible they should be underlined to denote that they are itali- public health issues that could arise by renaming Y. cized. The genus name Staphylococcus is derived from pestis, Y. pseudotuberculosis subspecies pestis, the Judi- the Greek Staphyl from staphyle, which means a “bunch cial Commission ruled against renaming the bacterium of grapes,” and coccus, from the Greek, meaning “a despite its scientific justification. berry.” The o (“oh”) between the two words is a joining vowel used to connect two Greek words together. The figurative meaning of the genus name is “a cluster of SECTION HIGHLIGHTS cocci,” which describes the overall morphology of mem- Nomenclature is concerned with naming or- bers of the genus. The species name aureus is from the ganisms. For Bacteria and Archaea, specific Latin and means “golden,” the pigmentation of mem- rules must be followed in order to name and bers of this species. The -us ending of the genus and describe new species. Organisms that are species names is the Latin masculine ending for a noun placed on the approved or validated lists are (Staphylococcus in this case) and its adjective (aureus). officially recognized species. Successively higher taxonomic categories are family, order, class, phylum, and domain (Table 17.1) This material cannot be copied, disseminated, or used in any way without the express written permission of the publisher. Copyright 2007 Sinauer Associates Inc. Taxonomy of Bacteria and Archaea 487 17.2 Classification otic organisms exist—the Bacteria and the Archaea—versus only one domain for eukaryotes, Eukarya. In addition, Classification is that part of taxonomy concerned with the Eukarya may have evolved more recently as the result the grouping of bacteria into taxa based on common of symbiotic events between different early prokaryotic characteristics. The earliest classifications did not con- forms of life (see Chapter 1). Because of the long period of sider microorganisms. There were two kingdoms of life: evolution of bacteria and archaea, the various groups Plants and Animals. In 1868, Ernst Haeckel, a German within these domains exhibit considerable diversity, par- scientist, proposed a third kingdom specifically for mi- ticularly metabolic and physiological. In contrast, the croorganisms. Approximately a century later, in 1969, metabolic diversity of the Eukarya is limited, especially Robert Whittaker proposed a five-kingdom system of with respect to energy generation. The vast diversity of classification. His classification included Plants (Plan- metabolic types of prokaryotes is discussed more fully in tae), Animals (Animalia), Fungi, Protista, and Monera. In Chapter 5 and in Chapters 18–22. This chapter first dis- this system, the eukaryotic microorganisms were placed cusses the traditional system of classification and then cov- in the Protista kingdom and the fungi had their own spe- ers what is being done to make it phylogenetic. cial kingdom. The bacteria and archaea were placed, as prokaryotes, in the kingdom Monera. Organisms were Artificial versus Phylogenetic Classifications separated from one another on the basis of nutrition and cell structure. Therefore, plants are photosynthetic eu- Conventional artificial taxonomy uses phenotypic tests karyotes, fungi are heterotrophs that use dissolved nu- to determine differences between strains and species. trients, and animals are heterotrophs that ingest their These tests are typically weighted so that characteristics food. The five-kingdom classification remained popular that are considered to be more important are given until recently. Then, in 1990, Carl Woese and colleagues higher priority. For example, in traditional taxonomy, proposed an entirely new classification, the Tree of Life the Gram stain has been given more weight in determin- (see Chapter 1).

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