week 2

• Autotrophy


  Building biomass by adapting CO2 as a carbon source and reducing it to generate complex cell constituents made of C, H and O
• Heterotrophy


  Building biomass by relying on other organisms to form organic nutrients such as glucose
• All of Earth's life forms are based on carbon which they acquire by a recycling process
• Oxygen requirements


  • Obligate aerobes
  • Obligate anaerobes
  • Facultative anaerobes
  • Microaerophiles
  • Capnophiles
  • Aerotolerant anaerobes
• Nitrogen


  Essential element found in many organic compounds, e.g. amine group of amino acids, makes up ~14% dry weight of microbial cells, a growth limiting nutrient for protein and nucleotides synthesis
• Nitrogen fixation


  1. Rhizobium reduce nitrogen gas (N2) to ammonia (NH3)

  2. Nitrogenase enzymes: two component protein - dinitrogenase and dinitrogenase reductase

  3. Essential for life on Earth - nitrogen fixers provide nitrogen in a usable form to other organisms
• Liquid media


  Organisms can move about freely, useful for studying growth characteristics in pure culture, microbial biochemistry at different growth phases, growth kinetics, DNA/protein extraction
• Solid media


  Useful for separating out different organisms, e.g. in clinical specimens, essentially liquid media with a solidifying agent (agar/agarose)
• Spread plate


  • Sample spread to grow bacteria, multiple species present
• Streak plate


  • Used to isolate single colonies, isolation of bacteria into pure cultures
• Media types


  • Defined (synthetic) media - exact chemical composition known
  • Complex media - not chemically defined, nutrients from digestion of beef, soy, yeast or proteins
• Minimal defined medium


  Only those nutrients essential for growth, useful for studying different conditions e.g. concentration of iron
• Enriched medium


  Some fastidious organisms require media to be enriched, e.g. blood provides chemical building blocks
• d (or broth) medium

  Organisms can move about freely, it is useful for studying growth characteristics in pure culture
• d (or broth) medium

  • Useful for microbial biochemistry at different growth phases, growth kinetics, DNA extraction, protein extraction etc.
• Solid media


  Agar plates
• Solid media


  • Useful for separating out different organisms in for example clinical specimens
  • Essentially liquid media with a solidifying agent (agar/agarose)
  • Agar – liquid at 100°C solid at 4°C
• Spread plate


  1. Sample spread to grow bacteria

  2. Multiple species present
• Streak plate


  1. Used to isolate single colonies

  2. Isolation of bacteria – pure cultures
• Defined media


  • Also called synthetic media
  • Exact chemical composition known
• Complex media


  • Not chemically defined
  • Nutrients from digestion of beef, soy, yeast or proteins
  • Contain variety of nutrients and growth factors
• Minimal defined medium


  • Only those nutrients essential for growth
  • Useful for studying different conditions e.g. concentration of iron
• Enriched medium


  • Some fastidious organisms require media to be enriched
  • E.g. Blood – provides chemical building blocks which the bacterial cells would otherwise need to synthesise
• Selective media


  • Favours growth of one organism over another (metabolic capabilities or toxicity)
  • e.g. Salmonella selective agar, Cetrimide selective agar for Pseudomonas spp.
• Differential media


  • Enable identification by visible change
  • e.g. mannitol salts agar - Bacteria which ferment mannitol become yellow
• Additional media types


  • Blood agar
  • CLED agar
• Blood agar


  • Whole red blood cells incorporated into agar
  • Detects haemolysis (α, β and γ)
• CLED agar


  • Cysteine lactose electrolyte-deficient agar
  • Detects lactose fermentation
  • Prevents swarming (e.g. Proteus)
• Colony morphology


  • Filamentous
  • Rhizoid
  • Round
• Binary fission


  1. Cell divides into 2 identical daughter cells

  2. 4 steps: Replication of genetic material, Elongation, Formation of new cell membrane and wall (septum), Cells either separate or remain attached (e.g. chains)
• Bacterial reproduction


  1. Circular chromosome begins to replicate at origin, or ori site

  2. Two replications forks are generated, which proceed outward in both directions

  3. As the termination site is replicated, the two forks separate from the DNA
• Generation time


  • Also known as doubling time
  • The time required for a bacteria to undergo binary fission - cell to grow and divide
  • Dependant on environmental conditions like temperature, resource availability, resident plasmid
• Factors affecting speed of bacterial growth
• Bacterial growth curve


  • 4 phases: Lag phase, Log phase, Stationary phase, Death phase
• Lag phase


  • Readjustment, Synthesize enzymes, Synthesize new cell structures
• Log phase


  • Cell optimised to environment, Exponential growth
• Stationary phase


  • Nutrient depletion, Increased waste, Cell growth = cell death
• Death phase


  • Cells die faster than produced, Depletion of nutrients, Build up of toxic waste
  • Some cells survive, Scavenge resources from dead cells, Sporulating bacteria may produce spores to assist survival
• Biphasic (Diauxic) growth curves

  • Two exponential growth phases, Bacteria cultured on two carbon sources - Easiest source utilised first, Secondary source utilised
• Chemostat culture


  • Postponement of stationary phase, Maintain exponential growth continuously: Adds fresh media, Removes waste, some cells and old media