5 Classification of microorganisms

Definitions
Taxonomy the science of biological classification
Classification grouping organisms into taxa based on mutual similarity or evolutionary
relatedness
Identification characterization of an isolate to determine what species it is
Nomenclature assignment of names to taxonomic groups in agreement with published
rules
Systematics Study of the diversity of life (both past and present) and the relationships among living things
through time; uses taxonomy as a means to understand organisms
Bacterial Species collection of strains that share many stable properties in common and
differ significantly from other group of strains
Strain population of organisms that descends from a pure culture isolate or from a species
Classification
Artificial classification based upon the expressed characteristics or the phenotype of the organism
Natural/ Phylogenetic classification based upon the purported evolution of the organism,
i.e. those that share a common ancestor
5 kingdoms: Monera, Protista, Fungi, Plantae, Animalia
3 Domains: (Eu)bacteria, Archaea, Eukarya
Principles of nomenclature
Each distinct kind of organism is designated as a species.
List of species of prokaryotes: Bergeys Manual of Systematic Bacteriology
The species is designated by a Latin binomial to provide a characteristic international label.
Binomial System (Carl von Linn or Carolus Linnaeus)
Genus (generic) name and species (specific) name: Escherichia coli
Names are descriptive
The application of names is regulated.
A law of priority ensures the use of the oldest available legitimate name.
Specific Name: stable; the oldest epithet for a particular organism takes precedence and must be used
Generic Name: can change if the organism is assigned to another genus because of new information
e.g. Pseudomonas solanacearum to Rhalstonia solanacearum
Designation of categories is required for classification of organism.
Taxon = group; taxa = groups
Example of Taxonomic Ranks and Names
Domain
Bacteria
Phylum
Proteobacteria
Class
Gammaproteobacteria
Order
Enterobacteriales
Family
Enterobacteriaceae
Genus
Escherichia
Species
coli
Criteria are established for effective publication of new specific names, as well as guidance for
forthcoming new names.
Rules for naming bacteria: International Code for the Nomenclature of Bacteria (1991)
Question on Nomenclature: International Journal of Systematic Bacteriology (IJSB)
Characterization and Identification
- Involves the study, not of a single cell, but of a population of identical cells
Pre-requisite: pure culture

5 Classification of microorganisms

Reasons for doing characterization

1. identification purposes
2. comparison with other organisms
3. exploit characteristics which may be beneficial
Major Characteristics Used in Taxonomy
A.CULTURAL refer to the nutrients required for growth and the physical conditions of an
environment that will favor growth
Nutritional types
1. based on E source
phototrophs
chemotrophs
2. based on C source
autotrophs
heterotrophs (organotrophs)
3. based on both C & E sources
photoautotroph
photoheterotroph
chemoautotroph
chemoheterotroph (chemoorganotroph)
Based on physical conditions
1. temperature requirement (minimum, maximum, optimum)
psychrophile
mesophile
thermophile
2. O2 requirement
Aerobe
strict/obligate aerobe
microaerophile
Anaerobe
strict/obligate anaerobe
facultative anaerobe
aerotolerant anaerobe
3. pH requirement (~ opt: 6.5 7.5)
acidophile
neutrophile
alkalophile
4. other examples of cultural characteristics
type of growth in agar media: margin, elevation, color, consistency, etc.
type of growth in broth: ring, pellicle, flocculent, etc.
salt requirement/tolerance: halotolerant, halophile (require 10 15% salt)
B.MORPHOLOGICAL microscopic characteristics (size, shape, arrangement, structures)
C.METABOLIC biochemical/ physiological characteristics; the manner in which the population carry out the
chemical processes of life
e.g.
presence of enzymes, fermentation of sugar
D.CHEMICAL COMPOSITION CHARACTERISTICS the identification of major characteristic chemical
constituents of the cell
e.g.
capsule chemistry, chemistry of CW and CM, etc.
E. ANTIGENIC CHARACTERISTICS the detection of cell components (Ag) w/c provide evidence for
similarities between species (specificity of Ag-Ab rxn)
F. GENETIC CHARACTERISTICS DNA composition analysis, detection of the likeness or homology
between DNA of cells