Ch. 1-23

• The Carbon Cycle


  While the sediments and rocks in the Earth's crust are the largest carbon reservoir, CO2 in the atmosphere is the most rapidly transferred carbon reservoir

  
• CO2 is removed from the atmosphere by

  Photosynthetic land plants and marine microbes
• Syntrophy


  Two or more organisms cooperate to benefit nutritionally from the presence of the other
• Biochemical oxygen demand (BOD)


  The microbial oxygen-consuming capacity of a body of water
• Methanogens


  Team up with partners (syntrophs) that supply them with substrates and remove products
• Influx of organic material (e.g., from sewage)


  Increases BOD, then decreases over time
• Most microbes cannot be cultivated in the lab due to environmental factors, nutritional factors, and syntrophy
• The Nitrogen Cycle


  Nitrogen is a key constituent of cells and exists in a number of oxidation states, with four major nitrogen transformations: nitrification, denitrification, anammox, and nitrogen fixation

  
• Open ocean environment


  • Saline
  • Low in nutrients (oligotrophic), especially with respect to nitrogen, phosphorus, and iron
  • Cooler
• Microbial activities taking place in the oceans are major factors in Earth's carbon balance
• Nitrification


  NH4+ to NO3-
• Oligotroph


  An organism that grows best at very low nutrient concentrations
• Denitrification


  NO3- to N2
• Pelagibacter


  The most abundant marine heterotroph
• Anammox


  Anaerobic oxidation of ammonia to N2 gas
• Proteorhodopsin


  A form of rhodopsin that allows cells to use light energy to drive ATP synthesis
• Fermentations


  • Energy conservation depends on substrate-level phosphorylation
  • Defined by lack of external electron acceptor
  • No ETC or PMF
  • Achieve redox balance by donating electrons to metabolic intermediates excreted as fermentation products
  • Conserve much less energy (via Substrate-Level Phosphorylation) than respiratory organisms
  • Tremendous reaction diversity
• Nitrogen Fixation


  N2 + 8 H → 2 NH3 + H2

  
• Deep-sea hydrothermal vents


  • Thriving animal and microbial communities are associated with them
  • Chemolithotrophic bacteria predominate at vent
  • Thermophiles and hyperthermophiles are present
  • Chemolithotrophic prokaryotes utilize inorganic materials from the vents
• Common Fermentations


  • Alcoholic
  • Homolactic
  • Heterolactic
  • Propionic acid
  • Mixed acid
  • Butanediol
  • Butyric acid
  • Butanol
  • Caproate/Butyrate
• Key Processes and Microbes in the Nitrogen Cycle


  • Nitrification: Comammox (Nitrospira), Nitrosomonas, Nitrosopumilus (Archaea), Nitrobacter
  • Denitrification: Bacillus, Paracoccus, Pseudomonas
  • N2 Fixation: Azotobacter (aerobic), Clostridium, purple and green phototrophic bacteria, Methanobacterium (Archaea) (anaerobic), Rhizobium, Bradyrhizobium, Frankia (symbiotic)

  
• Chemolithotrophic Bacteria and Archaea Present Near Deep-Sea Hydrothermal Vents


  • Sulfur-oxidizing
  • Nitrifying
  • Sulfate-reducing
  • Methanogenic
  • Hydrogen-oxidizing
  • Iron- and manganese-oxidizing
  • Methylotrophic
• N2 is the most stable form of nitrogen and is a major reservoir, as it is ~70 percent of the Earth's air

  
• Alcoholic fermentation


  Hexose gives 2 ethanol + 2 CO2
• Only a few prokaryotes have the ability to use N2 as a cellular nitrogen source. They convert inorganic to organic nitrogen through an energy-intensive process called nitrogen fixation.
• Homolactic fermentation


  Hexose gives 2 lactate + 2 H+
• Heterolactic fermentation


  Hexose gives lactate- + ethanol + CO2 + H+
• Propionic acid fermentation


  3 lactate- gives 2 propionate- + acetate- + CO2 + H2O
• Point mutations


  • Change only one base pair
  • Occur via single base-pair substitution
  • Phenotypic change depends on exact location
• Mixed acid fermentation


  Hexose gives lactate- + acetate- + succinate2- + formate- + ethanol + H2 + CO2
• Insertions or deletions


  Shift the reading frame of mRNA
• Butanediol fermentation


  Hexose gives 2,3 butanediol + ethanol + lactate- + acetate- + succinate2- + formate- + H2 + CO2
• Transformation: Horizontal gene transfer


  1. Via transformation

  2. Conjugation

  3. Transduction

  
• Butyric acid fermentation


  Hexose gives butyrate- + 2 H2 + 2 CO2 + H+
• Generalized transduction


  • Lytic cycle
  • Any host genes can be transduced

  
• Butanol fermentation


  2 Hexose gives butanol + acetone + 5 CO2 + 4 H2
• Specialized transduction


  • Lysogenic cycle
  • Only genes near the prophage can be transduced

  
• Caproate/Butyrate fermentation


  6 ethanol + 3 acetate- gives 3 butyrate- + caproate- + 2 H2 + 4 H2O + H+
• Conjugation


  1. Horizontal gene transfer that requires cell-to-cell contact

  2. Plasmid-encoded (F plasmid)

  3. Occurs between closely related or distantly related cells

  4. Donor cell: contains conjugative plasmid (F+)

  5. Recipient cell: does not contain plasmid (F-)

  6. F+ conjugates with F- to make 2 F+

  
• Beer is produced by yeast fermentation of grain


  The process of beer production is anaerobic