CHAPTER 10

Classification of Microorganisms

I.          Taxonomy – the science of classification, especially the classification of living things, thereby establishing the relationships between them and allowing differentiation of individuals.

II.         The Study of Phylogenetic Relationships

            A.        Definitions

1.         Taxa – hierarchical organization structures in taxonomy (i.e. genus, species, etc.)

2.         Systematics, or Phylogeny – the study of evolutionary relationships between organisms.

3.         Phenotypic – characteristics based on definable and/or testable traits (i.e. fermentation tests, endospores, etc.)… these may or may not have a phylogenetic basis.

B.         The ideal taxonomy is based on phylogenetic relationships, however modern microbiology taxonomy is a mix of phylogenetics and phenotypic characteristics.

C.        The original taxonomies were based mainly on phenotypic characteristics, with little concern for evolutionary connections. (i.e. the five kingdom system).

III.       The Three Domains

A.        In 1978 Carl Woese developed a theory that utilized the structure of the ribosome to develop evolutionary relationships between the major classes of cells.

B.         Three Domains

1.         Eukarya – All eukaryotic cell types – Fungi, Animals, Plants, and Protists

2.         Eubacteria (or Bacteria) – Common bacteria (prokaryotic)

3.         Archaea – Prokaryotic microorganisms that lack peptidoglycan and typically reside in extreme environment.

            C.        The Three Domain system is a phylogenetic system.

D.        According to this theory life originates from a common ancestor approximately 3.5 billion years ago, and eukaryotes arose approximately 1.4 billion years ago. 

E.         Phylogeny does not allow for theorizing on the nature of life before the last common universal ancestor (LUCA).

F.         According to the theory the LUCA would have been prokaryotic cells.

1.         Eukaryotic cells developed from enfolded prokaryotes (evidence to support this in the Gemmata bacteria).

2.         Mitochondria and Chloroplasts develop as captured endosymbiotes (the Endosymbiotic Hypothesis)

G.        Current theory has suggested that the bacterial genus Thermotoga may be one of the oldest lineages, though there is some dispute about this.

H.        Evolutionary history is difficult to discern in microorganism due to the fact that bacteria don’t fossilize (except for a few incidents listed in the book).

IV.       Classification of Organisms

A.        Remember from chapter one that all biological nomenclature is based on the binomial nomenclature idea (genus and species).

B.         There are more levels of taxonomy above the genus level.

C.        Taxonomy levels from highest to lowest.

            1.         Domain

            2.         Kingdom (not used in Prokaryotes)

            3.         Phylum

            4.         Class

            5.         Order

            6.         Family

            7.         Genus

            8.         Species

D.        Bacterial species are difficult constructs since there is no sexual isolation mechanism present. 

            1.         Without recombination all prokaryotic reproduction is clonal.

2.         The bacterial species is a collection of bacteria that have limited phenotypic or genetic diversity and survive in the same environmental niche.

E.         Eukaryotic organisms have sexual isolation mechanisms and a more constructive idea of species.

F.         The viral species is defined in a similar fashion to the bacterial species.

V.        Methods of Classifying and Identifying Microorganisms

            A.        Morphological Characteristics – Phylogeny: NO, Phenotype: YES

            B.         Differential Stain – Phylogeny: YES, Phenotype: YES

            C.        Biochemical Testing – Phylogeny: NO, Phenotype: YES

            D.        Serology – Phylogeny: NO, Phenotype: YES

            E.         Phage Typing – Phylogeny: NO, Phenotype: YES

            F.         Fatty Acid Profiles – Phylogeny: NO, Phenotype: YES

            G.        Flow Cytometry – Phylogeny: NO, Phenotype: YES

            H.        DNA Base Composition – Phylogeny: YES, Phenotype: NO

            I.          DNA Fingerprinting – Phylogeny: YES, Phenotype: YES

            J.          PCR – Phylogeny: YES, Phenotype: YES

            K.        Nucleic Acid Hybridization – Phylogeny: YES, Phenotype: YES

            L.         rRNA Sequencing - Phylogeny: YES, Phenotype: NO

VI.       Putting This All Together

A.        Dichotomous Keys – method used for identification, based mainly on phenotypes. 

B.         Cladograms – shows evolutionary relationships between organisms, not very useful in identification… more for research.

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