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Chapter 10
Classification of Microorganisms
• 1.7 million organisms identified so far
• All Species Inventory (2001-2025)
– To identify all species of life on Earth
– Estimates data from Aug 2011 are 8.7 million (with 6.5 million species found on
land and 2.2 million dwelling in the ocean depths)
– 86% of all species on land and 91% of those in the seas have yet to be
discovered, described and catalogued
• Theory of evolution
• 1895 – Charles Darwin proposed that natural selection was
responsible for the similarities as well as the differences among
organisms
• Phylogenetics is the study of evolutionary relation among groups of
organisms
– Grouping organisms according to common properties implies that a group of
organisms evolved from a common ancestor
– Similar plasma membrane
– Use ATP for energy
– DNA is genetic storage
Structure of cell organelles
Endosymbiotic Theory
Cyanophora paradoxa
Taxonomy – Science of classification
• Taxonomy - Systematic - the science of the classification of
organisms.
– The goal of showing relationships among organisms.
– Also provides a means of identifying organisms.
Linnaeus
1735
2 kingdoms
Haeckel
1866
3
kingdoms
Chatton
1937
2 empires
Prokaryota
(not treated)
Copeland
1956
4 kingdoms
Monera
Whittaker
1969
5 kingdoms
Woese et al.
1977
6 kingdoms
Woese et
al.
1990
3
domains
Eubacteria
Bacteria
Archaebacteria
Archaea
Monera
Protista
Protista
Protista
Fungi
Fungi
Protista
Vegetabilia
Animalia
Plantae
Animalia
Eukaryota
Eukarya
Plantae
Plantae
Plantae
Animalia
Animalia
Animalia
The Three-Domain System
Eukarya
Fungi
Origin of mitochondria
Bacteria
Origin of chloroplasts
Animals
Amebae
Mitochondria
Slime molds
Cyanobacteria
Proteobacteria
Chloroplasts
Archaea
Methanogens
Plants
Extreme
halophiles
Ciliates
Green
algae
Dinoflagellates
Diatoms
Hyperthermophiles
Gram-positive
bacteria
Euglenozoa
Thermotoga
Horizontal gene transfer
occurred within the
community of early cells.
Giardia
Mitochondrion degenerates
Nucleoplasm grows larger
Table 10.1
Genetic study in Classification
• In Genetic - Homologous genes means that the genes have similar
sequences.
• In systematic homologous means that genes have a common
ancestor
– Orthologs are homologous genes that belong to different species but still retain
their original function
– Ortholog genes can be used in the construction of phylogenetic trees.
• The classical example is the
16S ribosomal RNA gene
Figure by Jamie Cannone, courtesy of Robin Gutell;
data from the Comparative RNA Web Site: www.rna.icmb.utexas.edu
Taxonomy
• Three major areas of activity.
1. Nomenclature – naming of organisms
2. Classification – the process of ordering of organisms in
group based on common properties
3. Identification of unknown organisms
1. Nomenclature
• Every recognized species on earth (at least in theory) is given a
two-part scientific name. This system is called "binomial
nomenclature.“
• The scientific name of each species is made up of a generic
name (generic epithet) and a specific name (specific epithet).
•
• The genus is the first level of taxonomic organization, in a
way, because all species that are thought to be most closely
related, are placed together in a genus.
• Genus is capitalized; whole name in italic, Latinized
Scientific Names
2. Classification -Taxonomic Hierarchy
•Taxa (taxon) – taxonomic category designed to show degrees
of similarities among organisms. (Groups based on similarity)
•Higher taxa – very general
•Lower taxa – more restricted
Domain
Kingdom
Phylum
Class
Order
Family
Genus
Species
•Species – single unique organism group
The Taxonomic Hierarchy
•
Example:
• Canus latrans (coyote)
• Canus aureau (jackal)
• Canus lupus (wolf)
• Canus familiaris
(common dog)
Kingdom Animalia
Phylum Chordata
Class
Mammalia
Order
Primates
Family Hominidae
Genus Homo
Species H. sapiens
Figure 10.5
Figure 10.5 The taxonomic hierarchy.
All organisms
Eukarya
Archaea
Bacteria
Fungi
None assigned for archaea
None assigned for bacteria
Ascomycota
Euryarcheota
Proteobacteria
Hemiascomycetes
Methanococci
Gammaproteobacteria
Saccharomycetales
Methanococcales
Enterobacteriales
Saccharomycetaceae
Methanococcaceae
Enterobacteriaceae
Domain
Kingdom
Phylum
Class
Order
Family
Genus
Species
Saccharomyces
S. cerevisiae
Baker’s yeast
Methanothermococcus
M. okinawensis
Methanococcus
Escherichia
E. coli
E. coli
Species Definition
• Eukaryotic species:
– A group of closely related organisms that breed among
themselves and produce fertile offspring
• 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
Domain Eukarya
• Kingdom Protista: A catchall for eukaryotic organisms that do
not fit other kingdoms, 200,000 species.
• Unicellular and multicellular
• Nutritionally quite diverse. Autotrophs, heterotrophs, intracellular parasites
• Kingdom Fungi:
• Unicellular or multicellular; cell walls of chitin;
• Develop from spores or fragments of hypha
• Chemoheterotrophic
• Kingdom Plantae:
• Multicellular; cellulose cell walls;
• Usually photoautotrophic
• Cells are organized into tissues
• Kingdom Animalia:
• Multicellular; no cell walls;
• Chemoheterotrophic, ingest food through a mouth
• Cells are organized into tissues
Prokaryotes
• Historically, prokaryotes were classified on the basis of their
phenotype.
• Phenotypic characterization is based on the information carried in the
products of the genes.
• Modern characterization is based on the sequence of the genes i.e.
the genome.
• Can also tell us something
about the phylogenetic
relationships of prokaryotes
BACTERIA
Gram-positive
bacteria
High
G+C
Low
G+C
ARCHAEA
Methanoge
ns
Cyanobacteria
Proteobacteria
Chlamydias
Spirochetes
Green nonsulfur
bacteria
Green sulfur
bacteria
Extreme
halophiles
Hyperthermophil
es
Thermotoga
Bacteroides
• Medical microbiology has dominant interest in microbes
• Use many identification schemes.
Viruses
• Viruses are acellular organisms – do not fit the three domain
system
• Obligate intracellular parasites, usually infect one type of
cells
• Classified by Family and Genus
– Often referred to by common name
Methods of Classifying and Identifying
Microorganisms
• Morphological characteristics
• Useful for identifying prokaryotes and eukaryotes
• Differential staining
• Gram staining, acid-fast staining
– Cell wall structure
• Biochemical tests
• Determine presence of bacterial enzymes, metabolic
activities
• Immunological tests
• Determine antigens
– toxins
• Genetic tests
• Determine presence and structure of genes
Figure 10.8
Biochemical tests
• Determine presence of specific enzymes
Enzyme (?)
Substrate
Product (presence or absence)
–
–
–
–
–
–
–
–
Carbohydrate fermentation, gas production, acid production
Citrate fermentation
Nitrogen fixation
Sulfur oxidation
Nitrate reduction
Hydrogen sulfide production
Starch hydrolysis
Catalase production, etc.
Dichotomous Key
Dichotomous keys are used for the identification of organisms.
Numerical Identification
Figure 10.9
Immunological methods - Serology
• Serology is the scientific study of blood serum. In practice, the term
usually refers to the diagnostic identification of antibodies in the
serum
– Antibody - Proteins made by animals in response to exposure to bacteria
and other pathogens, toxins, plant pollen and red blood cells that the body
recognized as alien, or non-self.
Staphylococcus aureus produce
Coagulase and Protein A
• Combine known antiserum (Ab against Protein A) + unknown
bacterium - Slide agglutination ( diagnostic method)
Figure 10.10
Immunological methods - ELISA
• Enzyme-Linked Immunosorbent Assay - biochemical technique
used mainly in immunology to detect the presence of an antibody
or an antigen in a sample
– Antibody linked with an enzyme
– Enzyme’s substrate is added
•
•
•
•
Known antibodies
Unknown presence of bacterium
Antibody linked with an enzyme
Enzyme’s substrate is added
•
•
•
•
Known bacteria
Unknown presence of Ab
Antibody linked with an enzyme
Enzyme’s substrate is added
Immunological methods - Western Blot
• Separates proteins in a specimen by electrophoresis
• Use of antibodies linked with an enzyme for detection
Figure 10.12
Phage Typing
• Bacteriophages are viruses that infect bacteria ("phages" for short)
and some of these can only infect a single strain of bacteria.
• Phage typing is a method used for detecting different strains of
bacteria within a single species.
Figure 10.13
Genetics
1.DNA base composition
– Guanine + cytosine moles% (GC)
2.DNA fingerprinting
– Electrophoresis of restriction enzyme
digested DNA
3. rRNA sequencing
4. Polymerase Chain Reaction (PCR)
5. Nucleic Acid Hybridization
5.A. Total DNA
Figure 10.15
5.B. Nucleic Acid Hybridization- DNA probe
Figure 10.16
5. C. Nucleic Acid Hybridization: DNA chip
Figure 10.17
Cladogram
• A cladogram is a diagram much like a family tree showing the
phylogenic tree of different species and demonstrating where
they evolved from common ancestors.
– Once taxonomists based cladograms on physical, easily-observed
characteristics;
– Today, they can use more reliable information like genetic and
biochemical analysis to show phylogenetic relationships among
organisms.
Figure 10.18.1
Classification and Identification
• Classification of unknown
• Differential staining
• DNA analyses
• rRNA sequencing
• PCR
• Identification of an unknown
microbe previously discovered
and classified
• requires combined methods
Figure 10.5
References
Once an organism is identified, it can be placed into a previously
devised classification scheme
•• Bergey’s Manual of Determinative •Morphology,
Bacteriology
differential staining,
•Provides identification schemes for
biochemical tests
identifying bacteria and archaea
•• Bergey’s Manual of Systematic
Bacteriology
•Provides phylogenetic information on
bacteria and archaea
•Lists species of known prokaryotes
•• Approved Lists of Bacterial Names
•Based on rRNA
sequencing
•Based on published
articles
Learning objectives
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Define taxonomy, taxon, and phylogeny.
Discuss the advantage of the three-domain system.
List the characteristics of the Bacteria, Archaea, and Eukarya domains.
Differentiate among eukaryotic, prokaryotic, and viral species.
Explain why scientific names are used.
List the major taxa.
Differentiate between culture, clone, and strain.
List the major characteristics used to differentiate the three kingdoms of
multicellular Eukarya.
Compare and contrast classification and identification.
Explain the purpose of Bergey’s Manual.
Describe how staining and biochemical tests are used to identify bacteria.
Differentiate Western blotting and Southern blotting.
Explain how serological tests and phage typing can be used to identify an
unknown bacterium.
Describe how a newly discovered microbe can be classified by: DNA base
composition, DNA fingerprinting, and PCR.
Describe how microorganisms can be identified by nucleic acid hybridization,
Southern blotting and DNA chips.
Differentiate a dichotomous key from a cladogram.