Geomicrobiology Flashcards
What is geomicrobiology?
A study of the role that microbes have played and are playing in processes of fundamental importance to geology.
Relevance to pollutant response(s) and bioremediation.
What is the biosphere?
The portion of the planet that supports life.
Restricted to uppermost part of the crust and the lower part of the atmosphere.
Includes the land surface, i.e. exposed sediment, soil and rock to a limited depth – the LITHOSPHERE and the portion of the crust covered by water – the HYDROSPHERE.
Although most life exists at the surface of the lithosphere, significant populations of microbes have now been detected in various sedimentary rocks at >100s of meters. Withstand great pressure.
Unlike lithosphere, life in the hydrosphere occurs at all water depths:
•the Marianas Trench - 11000m.
•in marine sediments, microbes at 500mbsf.
Biosphere also includes lower portion of atmosphere.
Microbes recovered up to ~80 km.
However, atmosphere not capable of sustaining life but important as a: •Means of distribution •Source of oxygen for aerobes •Source of nitrogen for N2-fixers •Screen for UV-radiation (ozone layer)
Can’t sustain life on its own, but has other important properties.
Which geological processes can be subject to microbial processes?
•Mineral formation.
•Mineral degradation:
weathering, bioleaching (Removal of metals), soil and sediment formation.
- Element cycling (Biogeochemical cycling).
- (Fossil Fuel Genesis and Degradation).
- Bioremediation applications – organics, metals, radionuclides. How organism can be used to treat these kinds of pollution.
How can microbes cause localised accumulation of inorganic matter?
As agents of CONCENTRATION, microbes can cause localized accumulation of inorganic matter by:
- Deposition of inorganic products of metabolism in or on parts of the cell. For structure, energy source, degradation etc.
- Passive accumulation involving surface adsorption or ion exchange.
- Promoting precipitation of inorganic compounds external to the cell – bound cations may react with CO3, PO43-, S2- forming salts that serve as nuclei for mineral formation.
How can microbes promote mineral dissolution?
As agents of DISPERSION, microbes can:
- Promote mineral dissolution, e.g. dissolution of CaCO3 by respiratory CO2 (CO2(g) + CaCO3(s) + H2O → Ca2+(aq) + 2HCO3–(aq)) or by reduction of insoluble ferric oxide or manganese dioxide to soluble compounds.
Many metal reducers are anaerobic- good reducing environment.
Can react with other compounds to produce other minerals.
How can microbes act on a mixture of inorganic compounds?
As agents of FRACTIONATION, microbes can:
- Act on a mixture of inorganic compounds but selectively act on one or a few components of the mixture, e.g. preferential reduction of Mn(IV) over Fe(III) in ferromanganese nodules by bacteria.
What are physical and biomechanical mechanisms exerted microbes?
•Physical effects exerted by microbes - By creating anaerobic conditions by consuming oxygen in a closed space or in an open space into which air (O2) diffuses more slowly than O2 is consumed.
- By raising or lowering environmental pH. Based on pH of the compounds microbes are secreting.
- By pressure exerted by growing biomass in small rock cracks and fissures
•A combination of these activities.
Biochemical effects: Most influence that microbes have on geological processes is physiological and may involve:
•Enzyme catalysis: -mainly oxidases or reductases in case of minerals -range of enzymes for Corganic synthesis and degradation.
•Action by organic or inorganic products of metabolism, e.g. acids, bases, chelators, surface active agents.
Such changes are effected through METABOLISM.
Both anabolism and catabolism may play a geomicrobial role.
Metabolic versatility in microorganisms?
Eukaryotic versatility generally related to structure and the behaviours possible because of such structures.
Eukaryotic metabolism relatively limited – photosynthesis, organic carbon, O2 is the predominant oxidant.
Prokaryotic versatility resides in metabolism.
Requires a separate vocabulary for describing different metabolic groups based on energy source (light or chemical), though many overlaps. Alternative metabolisms.
Bacteria therefore reside in a wide array of environments using a large variety of energy sources and oxidants not available to eukaryotes.
What are lithotrophs, photolithotrophs and chemolithotrophs?
Lithotrophs – assimilate carbon as CO2, HCO3- or CO32-.
Photolithotrophs - derive energy from photosynthesis.
Chemolithotrophs – derive energy from oxidation of inorganic compounds. Usually oxidized by oxygen but also possible to use other electron acceptors during anaerobic respiration.
What is heterotrophy, photoheterotrophs, chemoheterotrophs, and mixotrophy?
Heterotrophy – assimilate organic carbon.
Photoheterotrophs - derive energy from photosynthesis.
(Chemo)heterotrophs – derive energy from oxidation of organic compounds.
Mixotrophy - some microbes may derive energy from simultaneous oxidation of carbon or inorganic compounds, or from CO2 and organic carbon, or from oxidation of an inorganic compound and carbon from organic compounds.
What are the basics of chemiosmotic theory?
How Living Organisms Harvest Chemical (Redox) Energy from the Environment and Conserve it as Biologically-Useful Energy (ATP).
Three basic features:
(I) a semi-permeable membrane which can separate charges.
(II) an e- transport chain in which H-carriers and e- carriers alternate in the flow of reducing power from substrate to oxidant – as e- flow, H+ are pumped to outside of membrane creating the pmf.
(III) an enzyme to convert pmf into energy, here an ATPase – allows H+ flow back inside and uses the energy to synthesise ATP.
Where is the electron transport chain located in prokaryotes and eukaryotes?
What is needed?
In prokaryotes, ETC located in the plasma membrane: therefore, if a bacterium has the appropriate oxidoreductases (enzymes that transfer H atoms or e-) it can oxidize or reduce insoluble substances, e.g. elemental S, iron sulphide, iron oxide, manganese oxide.
Because essential enzymes are located in the plasma membrane, periplasmic space or even the outer membrane, they can make direct contact with the substrate.
In eukaryotes, ETC located in mitochondria and therefore lacks direct access to insoluble substances.
Catabolic reaction?
In aerobic respiration, O2 always the terminal electron acceptor.
In anaerobic respiration, other reducible compounds, e.g. NO3-, SO42-, S, CO2, Fe(OH)3, MnO2 or organics, e.g. fumarate, serve as terminal electron acceptors – archaea and some bacteria.
What relevance is there of aerobic and anaerobic respiration to organic matter breakdown?
Aerobic respiration – O2 as terminal e- acceptor - organic matter completely degraded (oxidized) to CO2 and H2O. N,S and P in organic matter end up as NO3-. SO42- and PO43-
Anaerobic respiration – NO3-, Fe(III), Mn(IV), SO42-, CO2 act as terminal e- acceptors – products of organic matter degradation are CH4 and/or CO2, H2, NH3, PO43-
Single organisms or consortia.
In some environments, organic matter may accumulate if above processes inhibited or if organics are recalcitrant.
Result: stratification of microbial communities in subsurface.
Mineral transformations?
- Mineral attack - dissolution, degradation, (bio)deterioration, bioweathering. Mainly refers to organic substrates, but minerals too. (Degradation and biodeterioration).
- Mineral formation - mineralization, biomineralization.
