1. Classification of Microorganisms
Chapter 10
Classification of Microorganisms

2. 1.7 million organisms identified so far
All Species Inventory ( )
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

3. Structure of cell organelles
Endosymbiotic Theory
Cyanophora paradoxa

4. 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.

5. Linnaeus kingdoms
Haeckel kingdoms
Chatton empires
Copeland kingdoms
Whittaker kingdoms
Woese et al kingdoms
Woese et al domains
(not treated)
Protista
Prokaryota
Monera
Eubacteria
Bacteria
Archaebacteria
Archaea
Eukaryota
Eukarya
Vegetabilia
Plantae
Fungi
Animalia

6. Mitochondrion degenerates
The Three-Domain System
Eukarya
Origin of mitochondria
Fungi
Animals
Bacteria
Origin of chloroplasts
Amebae
Mitochondria
Slime molds
Archaea
Cyanobacteria
Plants
Ciliates
Extreme
halophiles
Proteobacteria
Green
algae
Chloroplasts
Methanogens
Dinoflagellates
Hyperthermophiles
Diatoms
Gram-positive
bacteria
Euglenozoa
Thermotoga
Giardia
Horizontal gene transfer
occurred within the
community of early cells.
Mitochondrion degenerates
Nucleoplasm grows larger

7. Table 10.1

8. 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:

9. 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

10. 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

11. Scientific Names

12. 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
Species – single unique organism group
Domain
Kingdom
Phylum
Class
Order
Family
Genus
Species

13. 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

14. Figure 10.5 The taxonomic hierarchy.
All organisms
Eukarya
Archaea
Bacteria
Domain
Fungi
None assigned for archaea
None assigned for bacteria
Kingdom
Ascomycota
Euryarcheota
Proteobacteria
Phylum
Hemiascomycetes
Methanococci
Gammaproteobacteria
Class
Saccharomycetales
Methanococcales
Enterobacteriales
Order
Saccharomycetaceae
Methanococcaceae
Enterobacteriaceae
Family
Methanothermococcus
Saccharomyces
Escherichia
Genus
S. cerevisiae
Species
M. okinawensis
E. coli
Baker’s yeast
Methanococcus
E. coli

15. 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

16. 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

17. 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
Medical microbiology has dominant interest in microbes
Use many identification schemes.
High
G + C
Low
ARCHAEA
Chlamydias
Cyanobacteria
Gram-positive bacteria
BACTERIA
Spirochetes
Green sulfur
bacteria
Bacteroides
Proteobacteria
Green nonsulfur
Thermotoga
Hyperthermophiles
Methanogens
Extreme halophiles

18. 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

19. 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

20. 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.

21. Dichotomous Key
Dichotomous keys are used for the identification of organisms.

22. Numerical Identification
Figure 10.9

23. 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.
Combine known antiserum (Ab against Protein A) + unknown bacterium - Slide agglutination ( diagnostic method)
Staphylococcus aureus produce Coagulase and Protein A
Figure 10.10

24. 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
Known bacteria
Unknown presence of Ab
Antibody linked with an enzyme
Enzyme’s substrate is added

25. Immunological methods - Western Blot
Separates proteins in a specimen by electrophoresis
Use of antibodies linked with an enzyme for detection
Figure 10.12

26. 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

27. 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)

28. 5. Nucleic Acid Hybridization 5.A. Total DNA
Figure 10.15

29. 5.B. Nucleic Acid Hybridization- DNA probe
Figure 10.16

30. 5. C. Nucleic Acid Hybridization: DNA chip
Figure 10.17

31. 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

32. 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

33. References • Bergey’s Manual of Determinative Bacteriology
Once an organism is identified, it can be placed into a previously devised classification scheme
• Bergey’s Manual of Determinative Bacteriology
Provides identification schemes for identifying bacteria and archaea
Morphology, differential staining, biochemical tests
• Bergey’s Manual of Systematic Bacteriology
Provides phylogenetic information on bacteria and archaea
Based on rRNA sequencing
Lists species of known prokaryotes
• Approved Lists of Bacterial Names
Based on published articles

34. Learning objectives 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.