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Metabolism Lectures. Outline: Part I: Fermentations (Monday) Part II: Respiration (Wednesday) Part III: Metabolic Diversity (Friday) Learning objectives are : Learn about anaerobic respiratory metabolisms. How can an inorganic compound be use as an energy source. Bacteria and Archaea.

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metabolism lectures
Metabolism Lectures


  • Part I: Fermentations (Monday)
  • Part II: Respiration (Wednesday)
  • Part III: Metabolic Diversity (Friday)

Learning objectives are:

  • Learn about anaerobic respiratory metabolisms.
  • How can an inorganic compound be use as an energy source.
agrobacterium species

Gram negative rods

Common in soil especially the root zone of plants

Some are plant pathogens

A. tumefaciens causes crown galls or plant tumors

Only if A. tumefaciens has the Ti (tumor inducing) plasmid.

Elements of Ti have been engineered to generate transgeneic plants using.

Agrobacterium species
neisseria species

Gram negative, diplococcal


Most nonmotile

N. gonorrhoeae


N. meningitidis

Spinal meningitis

Other Neisseria spp. are present in respiratory tract of animals.

Most rarely cause disease.

Cultivate on chocolate-blood agar with 3-10% CO2

Neisseria species

pseudomonas species
Pseudomonas species
  • Gram negative, (Gammaproteobact.)
  • Mostly obligate aerobes
    • Some can respire nitrate.
  • Present in soil, water, plant surfaces
  • Some can degrade pollutants
    • TNT for example
  • Produce secondary metabolites
    • siderophores or iron binding molecules
  • Some produce pigments:
    • Pyocyanin in P. aeruginosa
  • Some fluoresce:
    • P. fluorescence


sulfate reducing bacteria

Desulfovibrio speices

Strict anaerobes

Generate energy by respiration of sulfur compounds

Some can use H2 for energy

Many use lactate, acetate, and/or ethanol as carbon and energy sources.

Abundant in anaerobic aquatic environments where sulfate is high


Also abundant in anaerobic environments with lots of decomposing organic matter

Sulfate reducing bacteria

campylobacter jejuni
Campylobacter jejuni
  • Gram -, (Epsilonproteobact.)
  • Microaerophile
  • Most prevalent food-borne pathogen in US
    • Under cooked poultry, pork, shellfish
  • Prevalence of contamination:
    • 90% turkeys
    • 32% hogs
    • 89% chickens

  • Gram positive, Firmicutes
  • Pathogenic and non-pathogenic kinds
  • Non-pathogenic:
    • S. lactis common dairy organism
  • Oral Streptococcus
    • S. salivarius and mutans
    • Grow on sugars in the mouth
  • Pathogenic:
    • S. pyogenes: strains with hemolysins can cause scarlet fever
    • S. pneumoniae: strains with capsules can cause disease.
    • Some are “flesh eating”
  • Rod shap, Gram Negative
  • Strict anaerobe
  • Dominant microbe in human feces
  • 1010 per gram
  • Purely fermentative organisms
  • Normally commensal
  • Most anaerobic infections are Bacteroides species.
  • Big problem in GI tract surgeries


pyrococcus fireballs furiosus
Pyrococcus “fireballs” furiosus
  • Anaerobic, Crenarchaea
  • Stetter isolated these from a solfatara field in Vulcano Italy (1986).
  • Uses proteins, starch, sugars, maltose as electron donors for S0 reductions
  • Also ferments sugars to H2 and CO2
  • Growth temps:
    • 70-106˚C
    • 100˚C is optimum

thiobacillus ferrooxidans
Thiobacillus ferrooxidans
  • Gamma proteobacteria
  • 4 Fe(II) + 4 H+ + O2 −−>

4 Fe(III) + 2 H2O

  • Fe(II) is stable at acidic pH
    • Does not get oxidized in the presence of O2
  • T. ferrooxidans tolerates:
    • pH ~2.5
    • It’s an acidiphile
  • Can be found in acidic mine waters.
  • Add water to pyrite:
    • FeS2 −> Fe(III) + H2SO4
    • That’s sulfuric acid
anoxic photosynthetic iron ii oxidizing bacteria
Anoxic photosynthetic iron(II) oxidizing bacteria


1 μm


NO3−-dependent Fe(II)-oxidizer

(Acidovorax sp. strain BoFeN1)

Phototrophic Fe(II)-oxidizer

(R. ferrooxidans strain SW2)

Photos by Professor Andreas Kappler


Phototrophic Fe(II)-oxidizer

Chlorobium ferrooxidans strain KoFox

(co-culture with Geospirillum strain)

KoFox cells

How can they

avoid encrustation?


Geospirillum strain