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
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.