Microbial Ecology Flashcards
What is LUCA ?
Last universal common ancestor (LUCA) lived around 4.2 billion years ago in the Haidean
What are the two main groups of oxygenic phototrophic organisms ?
plants and microorganisms
What are the 2 end-products of decomposition ?
methane and carbon dioxide
When does methane hydrates form ?
- Form when high levels of methane are under high pressure and low temperature
- Huge amounts of methane are trapped underground as methane hydrates
- Methane hydrates can absorb and release methane
- Methane hydrates fuel deep-sea ecosystems called cold seeps
What is methanogenesis ?
- Methanogenesis is central to carbon cycling in anoxic environments
- Most methanogens reduce CO2 to CH4 with H2 as an electron donor; some can reduce other substrates to CH4 (acetate)
- Methanogens team up with partners (syntrophs) that supply them with necessary substrates
What is syntropy ?
- Process whereby two or more microorganism degrade a substance neither can degrade alone
- Most syntrophic (symmetrical, repeated) reaction are secondary fermentations
- Most reactions are based on interspecies hydrogen transfer
- H2 production by one partner is linked to H2 consumption by the other
- Syntrophic reactions are important for the anoxic portion of the carbon cycle
What is acetogenesis ?
Acetogenesis is another H2-consuming process competing with methanogenesis in some environments
- Occurs in termite hindgut
- Methanogenesis is energetically more favourable than acetogenesis
- Acetogens can ferment glucose and methoxylated aromatic compounds whereas methanogens cannot
What are the 4 main nitrogen transformations ?
o Nitrification
o Denitrification
o Anammox
o Nitrogen fixation
What is denitrification ?
- Denitrification is the reduction of nitrate to gaseous nitrogen products and is the primary mechanism by which N2 is produced biologically
What are the cofactors for nitrogenase ?
cofactor of molybdenum or vanadium
What is anammox ?
Anammox is the anaerobic oxidation of ammonia to N2 gas
- Denitrification and anammox result in losses of nitrogen from the biosphere
- Performed by unusual group of obligate anaerobes
- Anammoxosome is a compartment where anammox reaction occurs
o Protects cell from reactions occurring during anammox
o Hydrazine is an intermediate of anammox - Anammox is very beneficial in the treatment of sewage and wastewater
What is nitrification ?
NH3 and NO2- are oxidized by nitrifying bacteria during the process of nitrification
- Two groups of bacteria work in concert to oxidize ammonia fully to nitrate
- Key enzymes are ammonia monooxygenase, hydroxylamine oxidoreductase, and nitrite oxidoreductase
- Only small energy yields from this reaction
o Growth of nitrifying bacteria is very slow
What is dissimulative metabolism ?
During anaerobic respiration, the reduction of inorganic compounds is called dissimilative metabolism because the reduced products are excreted
How can energy that is released during redox be measured ?
reduction potentials
What is the most common electron acceptors in anaerobic respiration ?
Inorganic nitrogen compounds are the most common electron acceptors in anaerobic respiration
What are all products of nitrate reduction ?
gases
What does a linear version of the nitrogen cycle look like ?
Nitrate to nitrite to nitric oxide to nitrous oxide to dinitrogen
What are some human impacts on the carbon and nitrogen cycle ?
- Carbon dioxide levels have increased, greenhouse gas
- Air and ocean water temperatures are increasing
- Humans produce large amount of nitrogenous fertilizers
- Ecological effects of fertilizers are unknown
- Nutrient cycles are coupled so a change in one cycle will affect other cycles
What is chemolithotrophy ?
using inorganic ions for electron donors for metabolism
- Hydrogen oxidation
- Oxidation of reduced sulphur compounds
- Iron oxidation
- Nitrification and anammox
What are chemolithotrophs ?
organisms that obtain energy from the oxidation of inorganic compounds
Mixotrophs: chemolithotrophs that require organic carbon as a carbon source
- Many sources of reduced molecules exist in the environment
- The oxidation of different reduced compounds yields varying amounts of energy
How does hydrogen oxidation happen ?
- Anaerobic hydrogen-oxidizing bacteria and archaea
- Catalysed by hydrogenase
- Calvin cycle and hydrogenase enzymes allow chemolithotrophic growth
How does oxidation of reduced sulphur compounds ?
- Many reduced sulphur compounds are used as electron donors
- Discovered by Sergei Winogradsky
- Hydrogen sulfide, S0, S2O3- are commonly used
- One product of sulphur oxidation is H+, which lowers the pH of its surroundings
- Sox system oxidizes reduced sulphur compounds directly to sulphate
- Usually aerobic, but some organisms can use nitrate as an electron acceptor
What are the oxidation states of sulfide, polysulfide, elemental sulfur, thiosulfate, sulfites, sulfates
-2,-1,0,-2,+6, +4, +6
How does iron oxidation happen ?
- Ferrous iron (Fe2+) is oxidized to ferric iron (Fe3+)
- Ferric hydroxide precipitates in water
- Many Fe oxidizes can grow at pH <1
o Often associated with acidic pollution from coal mining activities - Some anoxygenic phototrophs can oxidize Fe2+ anaerobically using Fe2+ as an electron donor for CO2 reduction
- Ferrous iron oxidation begins extracellularly, where a c-type cytochrome oxidizes Fe2+ to Fe3+, passing electrons to rusticyanin in the periplasm
- Rusticyanin then reduces cytochrome c, and this subsequently reduces cytochrome a
- Cytochrome a interacts with oxygen to form water
- ATP is synthesized from ATPase in the membrane
- Autotrophy in acidithiobacillus derrooxidans is driven by the calvin cycle
How does sulphate and sulphur reduction occur ?
- During sulphate reduction, electron transport reactions lead to proton motive force formation
o This drives ATP synthesis by ATPase
o Many different compounds can serve as electron donors in sulphate reduction
Examples, hydrogen, organic compounds, phosphite - Some sulphur-reducing bacteria can gain additional energy through disproportionation of sulphur compounds
- Sulphur transformations by microorganisms are complex
- The bulk of sulphur on earth occurs in sediments and rocks as sulphate and sulphide minerals (e.g., gypsum, pyrite)
- The oceans represent the most significant reservoir of sulphur (as sulphate) in the biosphere
- Hydrogen sulphide is a major volatile sulphur gas that is produced by bacteria via sulphate reduction or emitted from geochemical sources
- Sulphide is toxic to many plants and animals and reacts with numerous metals
- Sulphur-oxidizing chemolithotrophs can oxidize sulphide and elemental sulphur at oxic/anoxic interfaces
- Organic sulphur compounds can also be metabolized by microorganisms
- The most abundant organic sulphur compound in nature is dimethyl sulphide (DMS)
o Produced primarily in marine environments as a degradation product of dimethylsulphoniopropionate (an algal osmolyte) - DMS can be transformed via a number of microbial processes
What is the iron and manganese cycle ?
- Iron is one of the most abundant elements on the earth’s crust
- On earth’s surface, iron exists in 2 states:
o Ferrous (Fe2+)
o Ferric (Fe3+)
o The redox reactions in the iron cycle include both oxidations and reductions - Manganese (Mn) is also present on Earth’s surface
o Manganese exists mainly in two oxidation states
o Manganese is also oxidized and reduced - Fe3+ can be used by some microorganisms as an electron acceptor in anaerobic respiration
- In aerobic acidic pH environments, acidophilic chemolithotrophs can oxidize Fe2+
What phosphorus cycle ?
- Organic and inorganic phosphates
- Cycles through living organisms, water and soil
What is the calcium cycle ?
- Reservoirs are rocks and oceans
- Marine phototrophic microorganisms use Ca2+ to form exoskeletons
