Environmental Flashcards
Pure culture (culture-dependent) methods
- Nutrients available in lab culture are typically higher than in nature
- Difficult to replicate environmental conditions in lab
- Only minor components of ecosystem
16S rRNA gene
- Functions as part of small subunit (SSU)
- Good marker gene
- Extensive databases with sequences from a large number of microorganisms
- PCR
- Align rRNA gene sequences
- Find number of differences in gene
- Less differences –> closer in evolution
- Three distinct lineages of cells called domains
- Bacteria (prokaryotic)
- Archae a (prokaryotic)
- Eukarya (eukaryotic)
- Archaea more closely related to Eukarya than Bacteria
Domain Bacteria
- 60 phyla
- Majority defined from environmental sequences
- Many groups are phenotypically diverse
- Physiology and phylogeny not necessarily linked
Domain Archaea
Euryarchaeota
Crenarchaeota
Euryarchaeota
- Methanogens: degrade organic matter, produce methane - Extremophiles: require high salt concentrations for metabolism and reproduction - Grow in moderately high temperatures and low pH environments
Crenarchaeota
- Vast majority of cultured Crenarchaeota grow in high temperatures (extremophiles)
Marine, freshwater, soil, etc
Extremophiles
Temperature
Psychrophile: min <0oC, optimum 15oC, max <20oC
Psychrotolerant: can grow 0oC, optimal 20oC-40oC
Thermophile: optimal 45-80oC
Hyperthermophile: optimal >80oC
Extremophiles
pH
Acidophile: optimum pH <6
Alkaliphile: optimal pH >8
Extremophiles
Salinity
Halophile: optimal 1-15% NaCl
Extreme halophile: optimal 15-30% NaCl
Halotolerant: can tolerate some, but grow best in absence
Extremophiles
Pressure
Barophile: thrives at high pressure, typically light sensitive
Barotolerant: can survive high pressures, but can exist in less extreme
Obligate barophiles: cannot survive outside of high pressure
Chemical energy store
ATP
Phosphoenolpyruvate
Long term energy storage
Insoluble polymers that can be oxidised to generate ATP
- Glycogen
- Poly-B-hydroxybutyrate
- Elemental sulfur
Long term energy storage
Insoluble polymers that can be oxidised to generate ATP
- Glycogen
- Poly-B-hydroxybutyrate
- Elemental sulfur
Chemoorganotrophy
Fermentation
- Anaerobic
- Substrate level phosphorylation
- ATP directly synthesised from energy-rich intermediate
- Glycolysis
- Glucose –> 2 pyruvate + 2 ATP + fermentation products
Fermentation product: Lactic acid, ethanol, CO2
Chemoorganotrophy
Respiration
- Aerobic and anaerobic
- Oxidative phosphorylation
- ATP produced from proton motive force formed by transport of electrons
- Oxidation using O2 as terminal electron acceptor
Higher ATP yield than fermentation
Associated Electron Carriers
NADH dehydrogenases
Flavoproteins
Quinones
Cytochromes
-NADH dehydrogenases: active site binds NADH and accepts 2 electrons and 2 protons and passes to flavoproteins
Proteins bound to inside surface of cytoplasmic membrane
-Flavoproteins: accepts 2 electrons and 2 protons, donates only electrons to the next protein
-Quinones: Accept electrons and protons but only pass on electrons
Non-protein-containing molecules that participate in electron transport
-Cytochromes: Accept and donate a single electron via the iron atom in heme
Proteins that contain heme prosthetic groups
Proton Motive Force
- pH gradient
- Electrochemical potential across membrane
- ATP synthase (ATPase) converts proton motive force to ATP
- 38 ATP
The Citric Acid Cycle (CAC)- Krebs Cycle
-Pyruvate completely oxidised to CO2
- Glucose –> pyruvate (same as glycolysis)
- 1 Glucose –> 6 CO2 + NADH + FADH
- Key role in catabolism
Energetic advantage to aerobic respiration over fermentation
Anaerobic Respiration
-Use electron acceptors that aren’t oxygen
Nitrate (NO3-), ferric ion (Fe3+), sulphate (SO4-), carbonate (CO32-)
-Less energy released than aerobic respiration
-Dependent on electron transport, generation of proton motive force, ATPase activity
Nitrogen
- Inorganic nitrogen compounds are the most common electron acceptors in anaerobic respiration (nitrate reduction, denitrification)
- Denitrification is the main biological source of gaseous N2
Nitrate (NO3-) –> Nitrite (NO2-) –> Nitric oxide (NO) –> Nitrous oxide (N2O) –> Dinitrogen (N2)
Manganese Oxide
Insoluble MgO2 + 4H+ + 2e- –> soluble Mn2+ + 2H2O
Manganese Oxide
Insoluble MgO2 + 4H+ + 2e- –> soluble Mn2+ + 2H2O
Chemolithotrophy
-Uses inorganic molecules as electron donors (oxidation)
Hydrogen Sulphide (H2S), Hydrogen gas (H2), ferrous iron (Fe+), ammonia (NH3)
- Aerobic (oxygen as electron acceptor)
- Oxidation of inorganic electron donor
- Different inorganic compounds yield different energy
- Uses phosphorylation (electron transport chain and proton motive force)
- Autotrophic (uses CO2 as carbon source)
Sulfur Oxidisers
- Many reduced sulfur compounds are used as electron donors
- Sulfur-oxidising bacteria
- Oxidise sulfide (H2S/HS-), sulfur (S), thiosulphate (S2O32-) and sulfite (SO32-)
- Sulfate (SO42-) is the final product of sulfur oxidation
- Deposit internal granules of sulfur
- Oxidation –> respiratory electron transfer + generate proton motive force
Nitrifiers (ammonia and nitrite oxidisers)
- NH3 and NO2- are oxidised by nitrifying bacteria through nitrification
- Two groups of bacteria work in concert to fully oxidise ammonia –> nitrate
- Nitrosomonas: oxidise NH3 –> NO2- (ammonia oxidisers)
- Nitrobacter: oxidise NO2- –> NO3- (nitrite oxidisers)
- Nitrate is a key nutrient for plants
- Nitrification in aerobic zones –> nitrate –> denitrification in anaerobic zones
Iron Oxidisers
- Oxidise ferrous iron Fe2+ –> ferric iron Fe3+
- Fe2+ is a weak electron donor
- Acidophiles use ferrous iron (Fe2+ is unstable at neutral pH)