2.2 Identification, Classification and Nomenculture (Taxonomy))

Question 1

Taxonomy of microorganisms

1. Conventional (Classical) Taxonomy
2. Molecular (Chemo) Taxonomy

Answer 1

1. Early Days: Discovery, Medical and General Microbiology

• VanLeeuwenhoek (1687)
• Pasteur (1864)
• Koch (1895)
• Winogradsky (1864 - 1900)

2.1 Era of molecular Biology / General Microbiology

• DNA is genetic material (1941)
• Streptomycin (1944)
• Bacterial genetics (1946)
• Structure of DNA (1953)
• Genetic Code (1966)
• DNA sequencing / Discovery of Archaea (1977)
• PCR (1985)

2.2 Molecular Microbiology, Genomics, and Proteomics

• Molecular microbial ecology (1986)
• First genome (1995)
• Over 500 genomes (2006)

Question 2

Nomenclature and Classification

Answer 2

Domain - Bacteria
Kingdom - Monera
Phylum - Proteobacteria
Class - Gammaproteobacteria
Order -  Enterobacteriales
Family - Enterobacteriaceae

Genus - Escherichia
Species - E. Coli

Genus + Species:
Esterichia Coli (E. Coli)

Binominal system

Question 3

Concentional (Classical) Taxonomy

Answer 3

Emphasis on analysis of phenotopic properties of the microorganism

Some phenotypic properties of taxonomic value:

I. Morphology
Shape, size, cell wall (gram), arrangement of flagella

II. Motility
flagella, gliding, gas, vesicles, non-motile

III. Nutrition and Physiology
mechanism of energy conservation, relation to oxygen, temperature, pH, salt, requirements/tolerances, ability to use carbon, nitrogen and sulfur sources, growth factors

IV. Other factors
pigments, cell inclusions, pathogenicity, antibiotic sensitivity

Question 4

Microbial cells share basic structures

Answer 4

Cell membrane:
lipid and protein layer surrounding the cytoplasm

Cell wall:
rigid outer layer of the cell

Nuclear material:
the hereditary materia, DNA

Cytoplasm:
contains organelles, enzymes, chemicals

Question 5

I. Morphology

Answer 5

Prokaryotic cell

Cytoplasm 
nucleotis 
ribosomes 
plasmid 
cytoplasmic membrane

Membrane
Wall
DNA

Eukaryotic cell

Cytoplasmic membrane
Nucleus
Cell Wall
Internal membrane
Mitochondrion

Eukaryotic cells have a more complex internal structure than prokaryotic cells

Question 6

I. Morphology

Bacterial Cell Wall - Staining

Answer 6

Gram staining:

Structure: Distinguishes groups of bacteria

Cells that gram stain:
gram sensitive and gram negative

Cells that resist gram staining:

• Genus Mycobacterium and Norcardia
• Stained using acid-fast staining techniques

Cells that lack cell walls:
Will retain counterstain (second colour applied during differential staining)

Question 7

I. Morphology

Cell Wall - Gram staining

Answer 7

Gram-positive cell wall - purple

Lipoteichoic Acid (LTA)

• > Peptidoglycan
• > Cytoplasmic membrane

Gram-negative cell wall - pink

Lipopolysaccharide (LPS)

• > Outer membrane
• > Periplasmic space
• > inner membrane

Question 8

I. Morphology

Shape

Answer 8

Coccus:

• > Spherical or ovoid (diplococcus - two)
• > Chain of cocci
• > Streptococcus
• > Streptococcus pneunomia

Rod:

• > Bacillus
• > Cylindrical shape
• > Chain of rods - Streptobacillus

Spirillum:

• > Spiral shape
• > Rhodospirillum rubrum

Spirochete:

• > tightly coiled shape
• > Spirochaeta stenostrepta

Budding and appendaged bacteria:

• > stalk and hypha
• > with extensions

Filamentous bacteria:
-> long and thin shape

Pckages - staphylococcus aureus

Question 9

I. Morphology

size matters

Answer 9

-

Question 10

II. Motility

Flagella

Answer 10

Peritichorus
(randomly on surface)

Monotrichous
(monopolar or bipolar)

Iophotrichous
(polar tufts or several flagella)

Question 11

II. Nutrition

Energy source

Answer 11

All microorganisms need energy sources

Chemicals -> Chemotrophy -> 1. organic chemicals (chemoorganotrophs) / 2. inorganic chemicals (Chemolithotrophs)

Sun -> Phototrophy -> Phototrophs => Pigments

light ~ ATP

Question 12

III. Nutrition

Carbon sources / Electron Acceptors

Answer 12

Microbial cells need carbon sources:

• > Autotrophs use CO2 (Carbon fixation)
• > Heterotrophs use organic carbon

Microbial cells need (terminal) electron acceptors:

• > Aerobe microorganisms use O2
• > Anaerobe microorganisms grow in the absence of O2

(may be facultative, obligate or microaerophilic)

Question 13

Facultative

Answer 13

microorganism grow in either the presence or absence of an environmental factor

Question 14

Obligate

Answer 14

microorganism grows only in the presence of an environmental factor

Question 15

III. Physiology

Adaptation to Environmental extremes

1. extremophiles

Answer 15

1. Thrive under environmental conditions in which other organisms cannot survive

Question 16

Mirobial identification in conventional taxonomy

Answer 16

Assessment of its phenotopic properties, from general to specific

I. Isolation and microscopy

Isolation -> Pure culture -> Gram reaction / morphology

II. General physiology

Gram-negative rod -> Facultative -> Ferments lactose to acid / gas

III. Detailed Physiology

Facultative lactose fermenter -> Perfom series of biochemical tests -> Positive (indole, methyl red, mucate) Negative (citrate, Voges - Proskauer, H2S)

IV. Conclusion -> Esterichia coli