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Classification of Microorganisms
I. Microbial Diversity
• Evolution → large number of bacterial, archaeal and eukaryotic species
• Tree of life (Figure 10.1)
• >1.8 million species have been identified.
Systematics - The study of biodiversity in an evolutionary context (i.e., the study of the
evolutionary history of organisms)
1. Principles of classification
• organisms exist as real, separate groups
• natural ordering into the groups
• reflect genetic relationships
• established by evolutionary processes (phylogeny - evolutionary history = evolutionary
relatedness of organisms)
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Components of taxonomy
a) Classification
• Ordering organisms with like characteristics into groups or taxa (singular - taxon)
• Based on established procedures and rules
• Describes groups of organisms, their interrelationships and boundaries between groups.
b) Nomenclature
• Assignment of names for purposes of communication and identification
• Use a binomial systems of nomenclature
Rules for assigning names for various microorganisms are published in a variety of sources
Protozoa – International Code of Zoological Nomenclature
Fungi and Algae – International Code of Botanical Nomenclature
Prokaryotes
• The International Committee on Systematics of Prokaryotes establishes rules for naming
newly classified prokaryotes as well as assigning prokaryotes to taxa. These rules are
published in the Bacteriological Code
• Descriptions of prokaryotes are published in the International Journal of Systematic and
Evolutionary Microbiology
• The prokaryotic species descriptions are published in Bergey's Manual of Systematic
Bacteriology. A second major reference for descriptions of prokaryotic species is The
Prokaryotes
c) Identification
• Application of classification & nomenclature to assign proper name to unknown organism and
place it in its proper position within classification system.
2. Taxonomic Hierarchies
Ideally
• Represent a coherent degree of homology - genetic and evolutionary similarity
• Members of each taxa should be monophyletic - same evolutionary history. (i.e., members of
a genus had a common ancestor)
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Taxa
Domain
Kingdom
Phylum (Divisions)
Class
Order
Family
Genus
Species
Subspecies
Subspecies
Describes a specific clone of cells that differs from others within the same species
• physiologically - biovar
• morphologically - morphovar
• antigenically - serovar
• pathogenically - pathovar
strain - a population of cells that descended from a single cell - recall pure culture and the streak
plate technique
• For higher organisms a species is defined as a population that can naturally interbreed and
produce fertile offspring. This population is reproductively isolated from other species.
• A prokaryotic species is a collection of strains (i.e., populations) that share many stable
properties (i.e., have a high degree of overall similarity) and that differ considerably from
populations or strains in related groups. This is a subjective definition!
• New species or strains are deposited in an approved culture collection for future reference -
type culture
o ATCC - American Type Culture Collection
o DSMZ - Deutsche Sammlung von Mikrooganismen und Zellkulturen
Culture collections preserve deposited strains by either freeze drying (lyophilization) or ultra low
temperature storage (≤-80°C).
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i) Phenetic Classification
• Classification according to phenotypic characteristics
• Group analogously similar organisms
a. Morphology
• cell shape and size, arrangement of cells, arrangement of flagella, capsule, endospores,
mechanism of motility
• staining properties – e.g., Gram stain reaction and acid-fast stain reaction
c. Ecological Characteristics
• The ability of a microorganism to colonize a particular environment
• Life cycle patterns, the nature of symbiotic relationships, the ability to cause disease in a
particular host, habitat preferences (e.g., requirements for temperature, pH, oxygen, osmotic
concentration)
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The above approaches are useful but you must be able to grow the organism!
ii) DNA:DNA hybridization – genomic DNA from one organisms is labeled and hybridized with
the genomic DNA from another organism. This technique measures the similarity between the
two DNAs. Does not work well for comparing distantly related microorganisms.
• DNA chip technology has made it possible to “print” many different species specific probes
(> 10,000) onto a glass slide (i.e., the “chip”). Genomic DNA is extracted from an unknown
organism and labeled with a fluorochrome. The labeled genomic DNA is hybridized with the
probes on the chip. Hybridization reactions fluoresce and can be identified by reading the
DNA chip with an instrument known as a DNA chip reader
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iii) Ribosomal RNA sequence analysis – rRNA genes (i.e., rDNA) from an unknown is isolated,
sequenced and compared to database entries. The rDNA can easily be isolated by using rDNA
specific primers and PCR. The amplified rDNA gene fragments are sequenced and compared to
database entries (e.g., GenBank or Ribosomal Database project)
Species level
> 70% DNA re-association (DNA hybridization )
> 97% similarity between 16S rRNA sequences
Genus level
> 20% - 30% DNA re-association (DNA hybridization)
93% - 95% similarity in 16S rRNA sequences
Families
89 - 93 % similarity in 16S rRNA sequences
Family taxon is usually the highest level taxon used for prokaryotes
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proteins ATPase
DNA & RNA polymerases
Cytochromes & ferrodoxins
• The molecular chronometers are more reliable and objective tools for determining phylogeny
than past phenetic approaches. Bacterial phylogeny used to be largely intuitive.
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• These techniques have identified taxa specific sequences or signature sequences. These
sequences are used to produce phylogenetic probes and primers
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• Research by Woese and others suggests that life on earth evolved along three evolutionary
lineages called domains: Bacteria, Archaea and Eukarya
• Phylogenetic information along with other taxonomic information has been used to construct
the Universal Phylogenetic Tree or Tree of Life (Figure 10.1)
i) Cells Walls
Evolution of peptidoglycan cell walls is important to bacterial evolution.
• Unique feature of virtually all bacteria – few exceptions – Mycoplasma – Chlamydia and
Planctomyces – Pirella groups
• Peptidoglycan is a signature molecules for species of bacteria
• Gram negative cell wall evolved first - Gram-positive cell wall evolved later.
ii) Lipids
• Archaeal lipids consist of ether-linked molecules in contrast to the ester linked lipids of Bacteria and
Eukarya. A few Bacteria have ether linked lipids but no Archaea have ester linked lipids
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