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Taxonomy of Cellular Life
Know domains:
(Tables 10.1 & 10.2)
Taxonomy: classification (hierarchical
grouping based on characteristics);
nomenclature (naming); identification
(define characteristics that match taxa).
Phylogeny: study of evolutionary
relationships. Comparison of
rRNA base sequences is most
common.
Classification: Taxa Hierarchy
Eukaryote (e.g. Humans)
• Domain: Eukarya
• Kingdom: Animalia
• Phylum: Chordata
• Class: Mammalia
• Order: Primata
• Family: Hominidae
• Group: Homo
• Species: sapiens
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Prokaryote (e.g. E. coli)
Domain: Bacteria
(no kingdom)
Phylum: Proteobacteria
Class: γ-proteobacteria
Order: Enterobacteriales
Family: Enterobacteriaceae
Genus: Escherichia
Species: coli
Binomial nomenclature: Genus species (italic or underlined)
Just like varieties of apples, or races of people, there are strains of
a prokaryote species (e.g. the harmless Escherichia coli K12 versus
the deadly pathogenic E. coli O157:H7). Why so?
Phenetic Characters:
Very useful in identification!
1) Ecological Characters
2) Morphological
Characters
3) Physiological and
Metabolic Characters
Phenetic Identification
Use of dichotomous keys for bacteria
Manually run individual analyses
of phenotype (staining, metabolic
tests, etc…) needed in the key.
Sequentially progress through the key
until you reach an end point. The
example here stops at the genus level.
Phenetic Identification
Use of multi-test kits and their databases.
This is the EnteroTube II
test for members of the
Enterobacteriaceae
Different media are used
to determine specific
metabolic capabilities
(e.g. lactose fermentation
or citrate use)
Numerical code is
interpreted from an
established database.
Often there are different
kits for different groups;
mostly restricted to
medically important
bacteria.
Molecular Characters
• Fatty acid profiles (FAME analysis)
• Proteins
– Electrophoretic Mobility
– Immuno-Reactivity (Serotyping)
– A.A. Sequence Data
• Nucleic Acids
– Nucleotide composition (G+C content ≈ Tm)
– Degree of Hybridization (>70% ≈ species)
– Nucleotide Sequence Data
Small subunit rRNA of the
three domains of life.
Bacteria
16SrRNA
Archaea
16SrRNA
Eucarya
18SrRNA
Phylogenetic Classification
Molecular Chronometers
• Phylogeny refers to grouping based on evolutionary
relatedness; regardless of phenetic characters.
• Phylogeny is inferred from changes in protein or rRNA
sequence over time.
• Attributes of an Ideal “Molecular Chronometer”:
Universally distributed.
– Functionally homologous.
– Ease of analysis (get enough information quickly).
– Sequence changes reflects a measurement of evolutionary
distance between organisms.
• Similarity between organisms’ sequences are used to
create a graphical representation, called a cladogram or
phylogenetic tree. (See example Fig 10.17.)
Microbial Diversity Assignment
Complete by Exam #3 on April 9th, 2003, for participation marks
(2% final grade). You may work in groups of three or fewer.
(1% Extra Credit if completed by Friday, March 21st, 2003.)
Know these 13 prokaryote groups,
including five classes of
Proteobacteria, and selected fungi,
algae, protozoa and helminths.
Total Extra Credit Ops: 4% STSS;
2% Ch 7; 1% M.D.A. (Ch 11 & 12) =
7% (about two grade intervals).