Classification of Microorganisms - Mt. San Antonio...
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Classification of MicroorganismsClassification of Classification of MicroorganismsMicroorganisms
ByByDr. Carmen Dr. Carmen RexachRexach
Mt San Antonio CollegeMt San Antonio CollegeMicrobiologyMicrobiology
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Taxonomy
• Science of classification of organisms– Aids in categorizing organisms not yet
studied in detail– Aids in identifying already classified
organisms– Provides common frame of reference when
organisms are discussed
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Phylogeny• Evolutionary history of
an organism• Father of taxonomy
– Linneaus– Grouped organisms by
characteristics into taxa = taxonomic categories
• Darwin– Studies on evolution– Readjustment of
organisms in taxa based on degrees of relatedness to each other
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How should we classify bacteria?• Originally in the Kingdom Plantae
– Division Schyzomycetes (Carl von Nageli, 1857)• Ernst Haeckel
– Kingdom Protista, suggested bacteria should be placed here, but remained in Kingdom Plantae
• Edward Chatton– Introduced term “prokaryotae” in 1937 = cells
without a nucleus• Roger Stanier
– Adjusted definition to include organisms without a nuclear envelope
• RGE Murray– Proposed Kingdom Prokaryotae in 1968
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• 1735 Plant & Animal Kingdoms• 1857 Bacteria & fungi put in the Plant Kingdom• 1866 Kingdom Protista proposed for bacteria,
protozoa, algae, and fungi• 1937 Prokaryote introduced for cells "without
a nucleus"• 1961 Prokaryote = cells in which nucleoplasm is
not surrounded by a nuclear membrane• 1959 Kingdom Fungi• 1968 Kingdom Prokaryotae proposed• 1978 Two types of prokaryotic cells found
Timeline
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The Three-Domain System
Table 10.1
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The Three-Domain System
Figure 10.1
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Five Kingdom System of RH Whittaker (1969)
• Kingdom Prokaryotae/Monera• Kingdom Protista• Kingdom Fungi• Kingdom Plantae• Kingdom Animalia
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Kingdom Prokaryotae/Monera• Precursor to all
eukaryotes• Eubacteria,
archaebacteria, cyanobacteria
Has now been reassigned to two Kingdoms: Bacteria and Archaea
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Kingdom Bacteria• Prokaryotes• Peptidoglycan cell
walls• Binary fission• Energy source:
organic chemicals, inorganic chemicals, or photosynthesis
H. influenza
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Kingdom Archaea• Extreme living
conditions• Unusual metabolism• No peptidoglycan in
cell walls• Examples
– Methanogens– Halophiles– thermoacidophiles
methanosarcinae
Anamox
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Kingdom Protista• Primarily
unicellular eukaryotes
• Protozoa, algae, slime molds, water molds
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Kingdom Fungi
• Unicellular yeasts• Multicellular molds• Mushrooms• Saprophytes with
hyphae
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Kingdom Plantae
• Some alga, mosses, ferns, conifers, flowering plants
• Multicellular• Photosynthetic
(autotrophs)
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Kingdom Animalia• Sponges, worms,
insects, chordates• Heterotrophic• multicellular
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Algae• Some unicellular,
some multicellular• Kingdom Protista,
Kingdom Archaea, and Kingdom Plantae!
• photoautotrophs
Tropical red algae
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Viruses• Acellular• DNA or RNA, not both
at same time• Protein capsid• Some have envelope
and other external structures
• Obligate intracellular parasites
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Three Domain System of Carl Woese (1978)
• Based on molecular biology and recognition that ribosomal differences suggest two types of prokaryotes
• Eukarya, prokarya, archaea• Sometimes organized as empires or
domains = a category above kingdom
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Kingdoms in three domain system• Recent discoveries in molecular biology have
suggested division in Kingdom Protista• New classification scheme
– Domain Bacteria• Kingdom Bacteria
– Domain Archaea• Kingdom Archaea
– Domain Eukarya• Kingdom Archaezoa Kingdom Plantae• Kingdom Euglenazoa Kingdom Fungi• Kingdom Alveolata Kingdom Animalia• Kingdom Stramenopila• Kingdom Rhodophyta
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Scientific Nomenclature
• Carolus Linnaeus• Binomial nomenclature: genus + species
– italicized or underlined. – genus is capitalized – specific epithet (species) is lower case.
• “Latinized”• used worldwide
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Scientific nomenclature• Naming bacteria
– Names can describe characteristics or honor pioneer in field
– Rules established by International Committee on Systemic Bacteriology = Bacteriological Code
– Bergey’s Manual contains description and rules• Compiled from publications in International Journal
of Systemic Bacteriology• Change as new techniques disclose similarities and
differences
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Examples• Staphylococcus aureus
– Describes the clustered arrangement of the cells (staphylo-) and the golden color of the colonies (aur-).
• Escherichia coli– Honors the discoverer,
Theodor Escherich, and describes the bacterium’s habitat–the large intestine or colon.
• After first use, can be abbreviated as: “S. aureus” and “E. coli”
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Scientific names
Honors OswaldoCruz
Corkscrew-like (trypano-, borer; soma-, body)
Trypanosoma cruzi
Produces a yellow (chryso-) pigment
Tuftlike (penicill-)Penicilliumchrysogenum
Forms pus (pyo-)Chains of cells (strepto-)
Streptococcus pyogenes
Stupor (typh-) in mice (muri-)
Honors Daniel Salmon
Salmonella typhimurium
Disease in fishHonors Lois Pfiester
Pfiesteria piscicida
The disease
Source of Specific Epithet
Honors Edwin KlebsKlebsiella pneumoniae
Source of Genus NameScientific Binomial
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Taxonomic hierarchy
• Kingdom• Phylum or Division• Class• Order• Family • Genus • Species
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What is a species?
• Eukaryotic species: A group of closely related organisms that breed among themselves
• Prokaryotic species: A population of cells with similar characteristics– Clone: Population of cells derived from a single cell– Strain: Genetically different cells within a clone
• Viral species: Population of viruses with similar characteristics that occupies a particular ecological niche
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How to determine phylogeneticheirarchy
• Generally determined by fossil records for higher organisms
• Not available for most microbes with following exceptions– White Cliffs of Dover in England
• Fossilized remains of marine protists
– Stromalites• Fossilized microbial
communities up to 2 billion years old
– Cyanobacterial fossils• Found in Australia• 3-3.5 billion years old
Stromalites: Hamilin Bay, Australia
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Classifying bacteria: Bergey’s Manual of Systematic Bacteriology
• 4 divisions– Distinguished by cell wall structure
• 7 classes– 3 eubacterial– 4 archaeobacterial
• Bacterial species– Population of cells with similar characteristics
• Strain– Variation within a species– Race, clade (ex) E. coli 0157:H7
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Viral classification• Viral species
– Population of viruses with similar characteristics occupying a particular ecological niche
• Where should they be placed?– Are they even alive?– Will you be able to
defend your position on an exam?
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Classification of bacteria
• Bergey’s manual• Morphology• Differential staining• Biochemical tests• Serology• Western Blot• Phage typing
• Amino acid sequencing• PAGE• Base composition of
nucleic acid• DNA fingerprinting• PCR• Nucleic Acid
hybridization• Flow cytometry
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Using Bergey’s Manual• Approx 1800 bacteria classified, <200
human pathogens• Four volumes
– 1. Wall-less eubacteria and some gram-negative eubacteria
– 2. Gram positive eubacteria– 3. Gram negative eubacteria
• Photosynthetic, chemolithotropic, sheathed, budding, appendaged, gliding, and fruiting bacteria
• archaeobacteria– 4. Actinomycetes
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Morphology
• Not as dominant in classification as in higher organisms because few shapes
• Many biochemical differences
• Structures that occasionally help in identification– Spore formation– Orientation of flagella, etc.
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Differential staining• Distinguish between
gram positive & gram negative, acid fast & non-acid fast
• Very general• Refers only to cell
wall structure• Some bacteria have
no cell wall, or unusual ones
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Biochemical tests• Distinctions based on biochemicals the organism
can utilize or metabolize• Ex) lactose or glucose fermentation, inositol
production, lipid utilization, production of gas, etc.
• API strips, Enterotube II– Degree of turbidity or color change
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Serology• Blood serum, looking at immune response
– Can distinguish strains in give species = very sensitive
– Antisera = contains antibodies for antigen of interest
• Slide agglutination test– Place unknown in saline on slide and add anti-
sera– Agglutinates if reaction is positive
• ELISA– Fast, can be scanned by computer– Antibodies embedded in wells– Add sera containing unknown antigen
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ELISA Latex Agglutination Test
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Latex agglutination
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Western Blot
• Electrophoresis separates proteins in patient’s serum
• Transfer proteins onto nitrocellulose filter by blotting
• Wash filter with antibodies tagged with dye
• Presence of antigen appears as colored band
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Western Blot
Western blot for lyme disease
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Phage typing
• Uses specificity of certain bacteriophage for particular bacteria to identify it
• Method– Grow a lawn– Inoculate– Look for plaques
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Phage typing
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Amino acid sequencing• More similar indicates closer phylogenetic
relationship• Farther apart = more distant• Compare the amino acid sequence of same
protein in two organisms to determine the degree of similarity
• Can only be used when organisms have common proteins
• Possibility exists that two unrelated organisms can produce same protein with same code
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Sequencer
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PAGEpolyacrylamide gel electrophoresis
• Premise: Genes determine protein sequence
• Procedure:– Lyse cells, extract protein and dissolve in
detergent– Place sample into a polyacrylamide gel– Electrophoresis separates out protein by
charge and size– Stain gel and compare banding patterns
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PAGE
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Base composition of nucleic acids
• Compare the percentage of certain bases in nucleic acids of two organisms
• Calculate the common ratio of:– G+C/A+T+G+C
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PCR= polymerase chain reaction
• Amplify DNA• Especially useful in microbes that
cannot be cultured• Also where limited amount of DNA is
available
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DNA fingerprinting
• Amplify specific regions of DNA using PCR, or cut DNA from organism with restriction enzymes
• Compare number and size of fragments after separation by gel electrophoresis
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DNA fingerprinting using primer/PCR
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Nucleic acid hybridization
• Separate double stranded DNA from two organisms into single strands by using heat
• Allow them to cool together• Will anneal at complementary bases• Measure degree of similarity• Can also compare DNA from one organism
with RNA from another = Southern Blotting
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Hybridization + Probe
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Flow cytometry• Run cells through narrow tube in
liquid medium so that only one cell moves through at at time
• Hit each cell with laser– Determines shape, size, surface,
density, fluorescence, etc.• Results recorded by computer• Determine similarity
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Flow cytometry
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Numerical taxonomy• Assign numerical values for each of
the tests• Put info into computer• Compare degrees of similarity for a
number of characteristics• 90% similarity or greater signifies
same species– Subjective because?
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Dichotomous Key
UN 10.2
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Cladogram
Figure 10.19, steps 1–2