Taxonomy and Systematics

Lecture 02 [Notes]
TAXONOMY or SYSTEMATICS is a branch of biology which deals with the naming, describing and classifying of organisms. A good classification system will contain a workable classification which is easy to use. Normally a taxonomic system will begin by dividing groups of organisms on the basis of their most general characteristics and continue to work toward more specific characteristics which will separate the different species. Within the taxonomic system each species must have a name which is universally recognized and the same name must not be used for two different species of organisms. This second requirement was resolved by Carl von Linne', better known as Linnaeus, with his system of binomial nomenclature. Each organism is named by two technical names. These names are in Latin or are latinized and are used uniformly all over the world. The first word always identifies the genus to which the organism belongs and is capitalized. The second word designates the species or trivial name and is not capitalized. Both names are underlined separately, e.g. Escherichia coli.

Many types of evidence are used in the development of a classification system. They may include biochemical, structural (morphological), cytological, physiological, or ecological evidence. The vast majority of identification keys rely primarily on structural clues although other types may be included.

Schemes for classification have always been of great importance in biology. They are vital as means of communication among biologists, but also are functional as tools for developing generalizations, making predictions, and guiding experimentation. Early biologists grouped all living organisms into two huge kingdoms: one for plants and one for animals. When microscopic organisms were discovered, taxonomists tried to make all of them "fit" into either the plant or animal kingdoms. When this didn't seem to work, a third kingdom was invented for bacteria and other microscopic organisms. Traditions developed over many decades, with taxonomic "lumpers" favoring a two­kingdom scheme and "splitters" espousing three kingdoms.

During the last few decades, advances in cytological techniques and in general understanding of evolutionary biology have raised serious questions about the traditional two­ or three kingdom schemes. In 1969, Dr. R.H. Whittaker, proposed a five­ kingdom classification scheme that has been widely accepted by professional biologists. (see Science, 163: 150-160, 1969) Whittaker suggested the following kingdoms: MONERA, PROTISTA, ANIMALIA, FUNGI and PLANTAE.

The major insight upon which the five-kingdom classification is based is the recognition that the differences between prokaryotes and eukaryotes are probably the most profound in the living world. This distinction has been questioned most recently by Dr. Carl Woese of the University of Illinois. (see attached Woese, Carl R., Kandler, Otto and Mark L Wheelis. Towards a natural system of organisms: Proposal for the domains Archaea, Bacteria, and Eucarya, Proceedings of the National Academy of Sciences, Vol.87, pp. 4576-4579, June 1990)

The five-kingdom system is far superior to the traditional plant/animal one for anatomical, evolutionary, and even educational reasons. It far more closely represents the current living world and reflects the changes of organisms through time. Whittaker first introduced it because it suited his descriptions of ecosystems. Margulis has expanded upon it based on the concepts of the origins of eukaryotic cells organelles by symbiosis as embodied in her Serial Endosymbiotic Theory. The theory is built around the idea that the first eukaryotic cells arose from symbiotic combinations of prokaryotes. Three types of eukaryotic cellular organelles - mitochondria, plastids, and cilia - may have developed when smaller prokaryotic cells took up permanent residence inside larger eukaryotic cells. The smaller prokaryote gradually became functionally and structurally specialized and evolved into the familiar compartmentalized organelles of the eukaryotes. This theory is quite consistent with the acceptance of the Whittaker five-kingdom system.

Details concerning the relationship of the modified Whittaker five-kingdom scheme to concepts of the origins of eukaryotic cells by symbiosis are described in Symbiosis in Cell Evolution (Margulis 1981). In that work, recent advances in the interpretation of the early fossil record of organisms lead to the conclusion that the first billion years of Earth history were dominated by members of the MONERA Kingdom. Members of the PROTOCTISTA (formerly PROTISTA) and FUNGI Kingdoms have a poor fossil record, but it is clear that they emerged long after bacterial communities were well established. Members of the ANIMAL Kingdom probably appeared more than 680 million years ago and members of the PLANT Kingdom possibly not until about 450 million years ago. Although an understanding of the relatively late appearance of eukaryotes requires a multi-factored explanation, it is clear that the origin and evolution of mitotic cell division and major cell organelles preceded the appearance of FUNGI, ANIMALS, and PLANTS. It is thought that these organelles and cell functions appeared and evolved in the various groups of protoctists - organisms that today still show profound variations of themes that are relatively constant in the three kingdoms of large multicellular organisms.

Though all the problems of cell evolution and taxonomy have not been solved, it still may be said that the five-kingdom classification is more consistent with fossil record, cellular ultrastructure, and cellular biochemistry than the two kingdom system that preceded it.(Margulis, L., "How Many Kingdoms? Current Views of Biological Classification," American Biology Teacher, 43(9), 1981, 482-489)

Until recently, the most widely used reference for identification of microorganisms has been Bergey's Manual of Determinative Bacteriology. Since it was first published in 1923, it has undergone 8 revisions and is still the most frequently used manual for identification. As more and more information has been gathered by microbiologists regarding the relationships among bacteria, new classification schemes have been constructed that more accurately reflect the evolutionary relationships. The new classification has resulted in the expansion of the classical Bergey's Manual into a multi-volume series entitled Bergey's Manual of Systematic Bacteriology.

Earlier editions of the manual reflected a taxonomic classification for bacteria developed more for convenience than for evolutionary relationships. However, modern molecular evidence from studies of base composition, nucleic acid hybridization, and amino acid sequences have challenged many of the old ideas.

In addition, it has been suggested by Woese and others that a third broad division of living organisms should be considered. (Berry A., & Roy A. Jensen, "Biochemical evidence for Phylogene- tic Branching Patterns," BioScience, 38(2), 1988, 99-103) While this third group are bacteria, evidence indicates that they are a more ancient group and unrelated to other bacteria and eukaryotes. These microbes have been dubbed the ARCHAEBACTERIA.

Classification of bacteria differs from classification of eukaryotes in a number of ways. The term species, when applied to higher organisms, relates to geographical distribution and inter-breeding which result in distinctive morphological characteristics. A bacterial species is defined as a population of cells with similar characteristics. A basic problem arises because not all pure cultures of the same species are identical in all ways. Each such group in a species is called a strain, which is a group of cells all derived from a single cell. This homogeneous group from a single ancestral cell would also be called a clone. Strains are identified by numbers, letters, or names which follow the species name. It is therefore possible to define a bacterial species as a collection of closely related strains.

While more than 10,000 species of bacteria have been identified, only about 1,800 are known pathogens. Of that number only about 200 are known human pathogens. Within that group of 200+ human pathogens there may be several hundred thousand strains. For example, there are over 150 known strains of our old friend Escherichia coli.

Back to Homepage
Back to Menu Page
Back to Microbiology Start Page