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Kenneth Todar currently teaches Microbiology 100 at the University of Wisconsin-Madison.  His main teaching interests include general microbiology, bacterial diversity, microbial ecology and pathogenic bacteriology.

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Overview of Bacteriology (page 3)

(This chapter has 6 pages)

© Kenneth Todar, PhD

TAXONOMY AND CLASSIFICATION OF PROCARYOTES

Haeckel (1866) was the first to create a natural Kingdom for the microorganisms, which had been discovered nearly two centuries before by van Leeuwenhoek. He placed all unicellular (microscopic) organisms in a new kingdom, "Protista", separated from plants (Plantae) and animals (Animalia), which were multicellular (macroscopic) organisms. The development of the electron microscope in the 1950's revealed a fundamental dichotomy among Haeckel's "Protista": some cells contained a membrane-enclosed nucleus, and some cells lacked this intracellular structure. The latter were temporarily shifted to a fourth kingdom, Monera (or Moneres), the procaryotes (also called Procaryotae). Protista remained as a kingdom of unicellular eucaryotic microorganisms. Whittaker refined the system into five kingdoms in 1967, by identifying the Fungi as a separate multicellular eucaryotic kingdom of organisms, distinguished by their absorptive mode of heterotrophic nutrition.


Figure 9 (above) The structure of a typical procaryotic cell, in this case, a Gram-negative bacterium, compared with (below) a typical eucaryotic cell (plant cell). The procaryote is about 1 micrometer in diameter and about the size of the eucaryotic chloroplast or mitochondrion. Drawings by Vaike Haas, University of Wisconsin-Madison.


In the 1980's, Woese began phylogenetic analysis of all forms of cellular life based on comparative sequencing of the small subunit ribosomal RNA (ssrRNA) that is contained in all organisms. A new dichotomy was revealed, this time among the procaryotes: there existed two types of procaryotes, as fundamentally unrelated to one another as they are to eucaryotes. Thus, Woese defined the three cellular Domains of life as they are displayed in Figure 3 (above): Eucarya, Bacteria and Archaea. Whittaker's Plant, Animal and Fungal Kingdoms (all of the multicellular eucaryotes) are at the end of a very small branch of the tree of life, and all other branches lead to microorganisms, either procaryotes (Bacteria and Archaea), or protists (unicellular algae and protozoa), thus establishing clearly that  microbial life is the predominant form of life on the planet.

Sequence analysis of macromolecules such as the small subunit ribosomal RNA found in all cells has allowed bacteriologists to classify bacteria into a typical hierarchal scheme based on genetic relatedness. The current edition (2001) of Bergey's Manual of Systematic Bacteriology has established 24 phyla of bacteria, systematically ordered into class, order, family, genus and species. For example, E. coli is in the Domain Bacteria, Phylum Proteobacteria, Class Gamma Proteobacteria, Order Enterobacteriales, Family Enterobacteriaceae, Genus Escherichia, Species E. coli. You can download Bergey's 400-page taxonomic outline of the procaryotes at Bergey's Manual of Systematic Bacteriology 2nd ed (2001), or you can back in to a taxonomic outline of bacteria in Wikipedia by looking up the scientific name of any well-known bacterium and viewing the right-hand frame, Scientific classification.

Although the definitive difference between Woese's Archaea and Bacteria is based on fundamental differences in the nucleotide base sequence in the 16S ribosomal RNA, there are many biochemical and phenotypic differences between the two groups of procaryotes. (Table 1). The phylogenetic tree indicates that Archaea are more closely related to Eucarya than are Bacteria. This relatedness seems most evident in the similarities between transcription and translation in the Archaea and the Eucarya. However, it is also evident that the Bacteria have evolved into chloroplasts and mitochondria, so that these eucaryotic organelles derive their lineage from this group of procaryotes. Perhaps the biological success of eucaryotic cells springs from the evolutionary merger of the two procaryotic life forms.

Table 1. Phenotypic properties of Bacteria and Archaea compared with Eucarya.
Property Biological Domain

Eucarya Bacteria Archaea
Cell configuration eucaryotic procaryotic procaryotic
Nuclear membrane present absent absent
Number of chromosomes >1 1 1
Chromosome topology linear circular circular
Murein in cell wall - + -
Cell membrane lipids ester-linked glycerides; unbranched; polyunsaturated ester-linked glycerides; unbranched; saturated or monounsaturated ether-linked branched; saturated
Cell membrane sterols present absent absent
Organelles (mitochondria and chloroplasts) present absent absent
Ribosome size 80S (cytoplasmic) 70S 70S
Cytoplasmic streaming + - -
Meiosis and mitosis present absent absent
Transcription and translation coupled - + +
Amino acid initiating protein synthesis methionine N-formyl methionine methionine
Protein synthesis inhibited by streptomycin and chloramphenicol - +
Protein synthesis inhibited by diphtheria toxin + - +

IDENTIFICATION OF BACTERIA

Classic Methods

The criteria used for microscopic identification of procaryotes include cell shape and grouping, Gram-stain reaction, and motility. Bacterial cells almost invariably take one of three forms: rod (bacillus), sphere (coccus), or spiral (spirilla and spirochetes). Rods that are curved are called vibrios. Fixed bacterial cells stain either Gram-positive (purple) or Gram-negative (pink); motility is easily determined by observing living specimens. Bacilli may occur singly or form chains of cells; cocci may form chains (streptococci) or grape-like clusters (staphylococci); spiral shape cells are almost always motile; cocci are almost never motile. This nomenclature ignores the actinomycetes, a prominent group of branched bacteria which occur in the soil. But they are easily recognized by their colonies and their microscopic appearance.


Figure 10. Gram stain of Bacillus anthracis, the cause of anthrax. K. Todar.

Such easily-made microscopic observations, combined with knowing the natural environment of the organism, are important aids to identify the group, if not the exact genus, of a bacterium - providing, of course, that one has an effective key. Such a key is Bergey's Manual of Determinative Bacteriology 9th ed, the "field guide" to identification of the bacteria. Bergey's Manual describes affiliated groups of Bacteria and Archaea based on a few easily observed microscopic and physiologic characteristics. Further identification requires biochemical tests which will distinguish genera among families and species among genera. Strains within a single species are usually distinguished by genetic or immunological criteria.

A modification of the Bergey's criteria for bacterial identification, without a key, is used to organize the groups of procaryotes for discussion in a companion chapter Important Groups of Procaryotes

Figure 11. Size and fundamental shapes of procaryotes revealed by three genera of Bacteria (l to r): Staphylococcus (spheres), Lactobacillus (rods), and Aquaspirillum (spirals).


Streptococcus pyogenes by Maria Fazio and Vincent A. Fischetti, Ph.D. with permission. The Laboratory of Bacterial Pathogenesis and Immunology, Rockefeller University.

Molecular Techniques

The sciences of genomics and bioinformatics have led to a radical reclassification of procaryotes based on comparative analysis of organismal DNA. Genomics involves the study of all of the nucleotide sequences, including structural genes, regulatory sequences, and noncoding DNA segments, in the chromosomes of an organism. To date over 200 bacterial genomes have been sequenced. We have seen how highly conserved genetic sequences, such as those that encode for the small subunit ribosomal RNAs (16S rRNA) of an organism, can be analyzed to specifically relate two organisms. So can the identification of certain genes provide information about specific properties of an organism, and analysis of specific nucleotide sequences may be used to indicate identity and degrees of genetic relatedness among organisms.

The newest editions of Bergey's Manual are adapted to the new phylogenetic classification. This has resulted in the formation of several new taxa of bacteria and archaea at every hierarchical level. Occasionally, organisms thought to be more or less distantly related become unified; but more likely, organisms thought to be closely-related due to similar phenotypic properties are found to be genetically distinct and warrant separation into a new taxa.

Metagenomics. Sequencing of 16S rRNA genes obtained from environmental samples produces a broad profile of microbial diversity and reveals that the vast majority of microbes present have been missed by reliance on cultivation-based methods. This observation has given rise to the field of metagenomics. Metagenomics (also called environmental genomics) is the application of modern genomics techniques to the study of communities of microorganisms directly in their natural environments, bypassing the need for isolation and lab cultivation of individual species. Metagenomics provides a means to identify and quantify microbes from environmental samples based on the presence of distinctive genes. This enables studies of organisms that are not easily cultured in the laboratory, as well as studies of organisms in their natural environment.

"Shotgun" metagenomics is capable of sequencing nearly complete microbial genomes directly from the environment. Because the collection of DNA from an environment is largely uncontrolled, the most abundant organisms in a sample are most highly represented in the resulting sequence data. To achieve the high coverage needed to fully resolve the genomes of underrepresented community members, large samples, often prohibitively so, may be needed. However, the random nature of shotgun sequencing ensures that many of these organisms will be represented by at least some small sequence segments. Due to the limitations of microbial isolation methods, the majority of these organisms would go unnoticed using traditional culturing techniques.

Shotgun sequencing and screens of clone libraries reveal genes present in environmental samples. This provides information both on which organisms are present and what metabolic processes are possible in the community. This can be helpful in understanding the ecology of a community, particularly if multiple samples are compared to one other.




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Kenneth Todar is an emeritus lecturer at University of Wisconsin-Madison. He has taught microbiology to undergraduate students at The University of Texas, University of Alaska and University of Wisconsin since 1969.

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