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Definitions

Taxonomy – the science of biological classification; describing, identifying, classifying,

and naming of organisms
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
Species (in prokaryotes) – collection of strains that share many stable properties in common
and differ significantly from other group of strains
Species (in eukaryotes) - a group of closely related organisms that breed among themselves
Strain – population of organisms that descends from a pure culture isolate or from a species;
eg., E. coli O157:H7 vs E. coli O111

Classification
 Artificial classification – based upon the expressed characteristics or the phenotype of the
organism
 Natural/ Phylogenetic classification – based upon the suggested evolution of the organism
(i.e. those that share a common ancestor)

5 kingdoms: Monera, Protista, Fungi, Plantae, Animalia

- Robert Whittaker (1969)
- groupings based on mode of nutrition and number of cells (uni-/multicellular)
6 kingdoms: Eubacteria, Archaebacteria, Protista, Fungi, Plantae, Animalia
- Carl Woese (1977)
3 Domains: Bacteria, Archaea, Eukarya
- Carl Woese (1990)
- groupings based on differences in 16S rRNA genes

Summary of the proposed classification schemes:

Image lifted from: http://haylingbillyheritage.org/wp-content/uploads/2015/09/Timeline.png

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Principles of nomenclature
 Each distinct kind of organism is designated as a species.
List of species of prokaryotes: Bergey’s Manual of Systematic Bacteriology
 The species is designated by a Latin binomial to provide a characteristic international
label.
Binomial System (Carl von Linnè or Carolus Linnaeus)
Genus (generic) name and species (specific) name: Escherichia coli
 Names are descriptive (e.g. Diplococcus salivarius, Thiomargarita namibiensis, Caldivirga
maquilingensis, Caldisphaera lagunensis)
 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
eg., Pseudomonas solanacearum to Ralstonia solanacearum
Pseudomonas cepacia to Burkholderia cepacia
Aquaspirillum magnetotacticum to Magnetospirillum magnetotacticum
 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

Reasons for doing characterization

1. identification purposes
2. comparison with other organisms
3. exploit characteristics which may be beneficial
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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)

Type Energy Source Carbon Source

Photoautotroph Sunlight CO
2
Photoheterotroph Sunlight Organic compounds
- 2+
Chemoautotroph Inorganic chemicals (H , NH , NO , Fe , H S)‫‏‬ CO
2 3 2 2 2

Chemoheterotroph Organic compounds (sugars, amino acids, etc)‫‏‬ Organic compounds

Based on physical conditions:

1. temperature requirement (minimum, maximum, optimum)
psychrophile -5 to 15°C
mesophile 25 to 45°C
thermophile 45 to 70°C
psychrotroph: 20 to 30°C, (but grows well at lower temperatures)
hyperthermophile: 70 to 110°C

2. pH requirement (~ opt: 6.5 – 7.5)

acidophile opt pH below 5.5
neutrophile opt pH 5-8
alkalophile opt pH above 8.5

3. O2 requirement
Aerobe
strict/obligate aerobe
microaerophile
Anaerobe
strict/obligate anaerobe
facultative anaerobe
aerotolerant anaerobe
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4. other examples of cultural characteristics
type of growth on agar media: margin, elevation, form, color, consistency, etc.
growth pattern on slants: filiform, arborescent, beaded, effuse, rhizoid, echinulate
type of growth in broth: turbid (cloudy), ring, pellicle, sediment, flocculent, etc.
salt requirement/tolerance: halotolerant, halophile (require 10 – 15% salt)

B. MORPHOLOGICAL – microscopic characteristics (size, shape, arrangement, structures)

Stella: star-shaped bacteria
Haloarcula: rectangular bacteria

C. METABOLIC – biochemical/ physiological characteristics; (e.g., presence of enzymes,

fermentation of sugar)

D. CHEMICAL COMPOSITION – the identification of major characteristic chemical

constituents of the cell (e.g., capsule chemistry, chemistry of cell wall and cell
membrane, etc.)

E. ANTIGENIC – antigen (molecule capable of inducing an immune response on the part of

the host organism);
- antigens in flagella (H antigen), capsule (K antigen) and cell wall (O antigen)
- the detection of cell components (Ag) w/c provide evidence for similarities
between species (specificity of Ag-Ab rxn)

F. GENETIC – DNA composition analysis, detection of the likeness or homology between

DNA of cells