1. BIO 244 GENERAL MICROBIOLOGY
Chapter 10
Identification and Classification of Microorganisms
_________________
The science of classifying organisms:
Provides ________________ for organisms
Provides a ______________ for identifying
organisms

2. CLASSIFICATION of MICROORGANISMS Systematics or phylogeny: The study of the _____________ history of organisms All Species Inventory ( ) To identify all species of life on Earth Taxonomic scheme favored by most microbiologists: ____________ system (before three domain system, five kingdom system used)
The three-domain system
Bacteria
Kingdoms and Domains
In the 18th Century, organisms were considered to belong to one of two kingdoms, Animalia or Plantae. As biologists gathered more information about the diverse forms of life on Earth, it became evident that the two-kingdom system did not accurately reflect relationships among different groups of organisms, and the number of kingdoms increased. In 1969, Robert Whittaker proposed a five-kingdom system consisting of monerans, protists, fungi, plants and animals. In the last few years, comparative studies of nucleotide sequences of genes coding for ribosomal RNA and other proteins have allowed biologists to recognize important distinctions between bacteria and archaebacteria. The graphic on this slide illustrates the phylogenetic relationships drawn from this information using a three-domain and a six-kingdom arrangement, compared to the traditional five kingdom system.
References:
Woese, C.R., Kandler, O. and M.L. Wheels Phylogenetic structure of the prokaryotic domain: the primary kingdoms. Proc. Natl. Acad. Sci. Nov;74(11):
Archaea
Eukarya
The six-kingdom system
Bacteria
Archaea
Protista
Plantae
Fungi
Animalia
The traditional five-kingdom system
Bacteria
Protista
Plantae
Fungi
Animalia

3. THE THREE _________ SYSTEM
Figure 10.1

4. TAXONOMIC HIERARCHY
Figure 10.5

5. PRINCIPLES of TAXONOMY
Taxonomic hierarchies
Classification categories arranged in hierarchical order
Species – group of ___________ isolates or strains
Most basic unit
Genus – group of related species
Family – collection of similar genera
Order – collection of similar families
Class – collection of similar orders
Phylum – collection of similar classes
Kingdom – collection of similar phyla
Domain – collection of similar kingdoms
Most ______________ unit
New taxonomic category

6. SPECIES DEFINITION ____________ SPECIES: PROKARYOTIC SPECIES:
A group of closely related organisms that _____ among themselves
PROKARYOTIC SPECIES:
A population of cells with similar characteristics
______: Population of cells derived from a single cell
Strain: ______________________ within a clone
VIRAL SPECIES:
Population of viruses with similar characteristics that occupies a particular ____________ niche

7. PROKARYOTE DOMAINS
Figure 10.6

8. DOMAIN EUKARYA KINGDOMS
_____________:
Multicellular; no cell walls; chemoheterotrophic
PLANTAE:
Multicellular; cellulose cell walls; usually photoautotrophic
FUNGI:
Chemoheterotrophic; unicellular or multicellular; cell walls of _______; may develop from spores or hyphal fragments
PROTISTA:
Unicellular, eukaryotic organisms; classification usually based on ____________

9. Source of Specific epithet
___________ NOMENCLATURE Names Given According to International Code for the Nomenclature of Bacteria
Scientific binomial
Source of Genus name
Source of Specific epithet
Klebsiella pneumoniae
Honors _________
The disease
__________________ typhimurium
Honors Daniel Salmon
Stupor (typh-) in mice (muri-)
Streptococcus pyogenes
Chains of cells (strepto-)
Forms pus (pyo-)
Penicillium notatum
Tuftlike (penicill-)
Spores spread in wind (nota)
_________ ________
Corkscrew-like (trypano-, borer; soma-body)
Honors Oswaldo Cruz

10. reference for classifying bacteria
__________________
BERGEY’S MANUAL
reference for identifying bacteria
reference for classifying bacteria
• Bergey’s Manual of Determinative Bacteriology
Provides identification schemes for _____________ bacteria and archaea
Morphology, differential staining, biochemical tests
• Bergey’s Manual of Systematic Bacteriology
Provides phylogenetic information (______________ history) on bacteria and archaea
Based on ________ sequencing
rRNA genes in DNA are sequenced using PCR
• Approved Lists of Bacterial Names
Lists species of known prokaryotes
Based on published articles

11. MAIN METHODS used in the IDENTIFICATION of _______________
PHENOTYPIC CHARACTERISTICS
CULTURAL CHARACTERISTICS
MICROSCOPIC MORPHOLOGY
___________ PROPERTIES
FATTY ACID ANALYSIS
___________ CHARACTERISTICS
NUCLEOTIDE SEQUENCES
rRNA SEQUENCES

12. MAIN METHODS used in BACTERIAL IDENTIFICATION
_____________ MORPHOLOGY
MORPHOLOGICAL CHARACTERISTICS:
(Very useful for identifying eukaryotic microorganisms)
______________ STAINING:
Gram staining, acid-fast staining
BIOCHEMICAL TESTS:
Determines presence of ________________
________________ TESTS:
Based on presence of an organism or immune response to organisms
Slide agglutination
______ (Enzyme Linked Immunosorbent Assay)
Figure 10.8

13. IDENTIFICATION BASED ON ________________
BACTERIAL MORPHOLOGY
NEMATODE MORPHOLOGY
ADULT WORM
OVUM

14. BACTERIAL IDENTIFICATION
______________ CHARACTERISTICS
_____________ ASSAYS

15. COMMON ____________ ASSAYS

16. BIOCHEMICAL ASSAYS
_________________

17. _________________ KEY
Used for _____________ identification
Based on series of _________ questions
Each question has one of ______
possible answers

18. Figure 10.7

19. ____________ ASSAYS Slide ___________________:
Combine known antiserum + ________________
Combine __________________ in patient serum with known antigen
Visualization of antigen antibody reactions through the formation of clumps
Figure 10.10

20. ENZYME LINKED IMMUNOSORBENT ASSAY
_____________
Antigen or antibody is tagged with an ___________
Enzyme substrate is added and ______ is produced

21. _____________ ANALYSIS
_____________ composition
Guanine + cytosine moles% (GC)
DNA _____________
Electrophoresis of restriction enzyme digests
rRNA sequencing
Polymerase Chain Reaction (PCR)
Figure 10.14

22. NUCLEIC ACID _________________
Figure 10.15

23. IDENTIFICATION of BACTERIA using DNA PROBES
Figure 10.16