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Molecular Microbiology > Geomicrobiology > Flashcards

Geomicrobiology Flashcards

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1
Q

What is Geomicrobiology ?

A

a study of the role that microbes have played and are playing in process of fundamental importance to geology

  • relevance to pollutant responses ( and bioremediation)
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2
Q

What is the biosphere?

A

The portion of the planet that supports life

Restricted to uppermost part of the crust and the lower part of the atmosphere

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3
Q

What does the Biosphere include?

A
  • Lithosphere
  • Hydrosphere
  • atmosphere
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4
Q

What is the Lithosphere ?

A

the land surface, i.e. exposed sediment, soil and rock to a limited depth

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5
Q

What is the hydrosphere ?

A

the portion of the crust covered by water

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6
Q

Where has majority of life been seen to exist ?

A

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

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7
Q

What is different between the lithosphere and hydrosphere ?

A

Unlike lithosphere, life in the hydrosphere occurs at all water depths:
•the Marianas Trench - 11000m
•in marine sediments, microbes at 500mbsf

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8
Q

What does the Biosphere include?

A

Biosphere also includes lower portion of
atmosphere
Microbes recovered up to ~80 km

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9
Q

Why is the atmosphere important?

A

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)
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10
Q

What geological processes can be subject to microbial influence ?

A

• Mineral formation
• Mineral degradation:
weathering, bioleaching, soil and sediment formation
• Element cycling (Biogeochemical cycling)
• (Fossil Fuel Genesis and Degradation)

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11
Q

What are some bioremediation applications?

A

organics,

metals, radionuclides

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12
Q

examples of Bacterial involvement in geomicrobiology ?

A
  • H2-metabolizing bacteria
  • Iron-oxidizers and reducers
  • Manganese oxidizers and reducers
  • Nitrifying and denitrifying bacteria
  • Sulphate-reducing bacteria
  • Sulphur-oxidizing and –reducing bacteria
  • Anaerobic photosynthetic sulphur bacteria
  • O2-evolving cyanobacteria
  • Aerobic and anaerobic heterotrophs
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13
Q

examples of eukaryotic fungi involvement in geomicrobiology ?

A
  • Can attack silicates, carbonates and phosphates, and other minerals
  • Degrade recalcitrant organic molecules, e.g. lignin, cellulose, chitin
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14
Q

examples of eukaryotic algae involvement in geomicrobiology ?

A

• Major source of O2 in atmosphere
• Some promote CaCO3 dissolution or
precipitation
• Some precipitate silica

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15
Q

examples of eukaryotic protozoa involvement in geomicrobiology ?

A

• Some have siliceous or calcareous tests

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16
Q

Examples of archaea involvement in geomicrobiology?

A
  • Methanogens

* Extreme halophiles • Thermoacidophiles

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17
Q

can microbes affect concentrations ?

A

As agents of CONCENTRATION, microbes can

cause localized accumulation of inorganic matter

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18
Q

what ways can microbes allow an accumulation of inorganis matter?

A

(i) Deposition of inorganic products of metabolism in or on
parts of the

(ii) Passive accumulation involving surface adsorption or ion exchange
(iii) 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

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19
Q

give examples of Deposition of inorganic products of metablism in or on parts of the cell?

A
  1. sulphur deposition within chromatium cells
  2. magnetite (Fe3O4) in ‘magnetosomes’ in a magnetotatic bacterium
  3. silica deposition at diatom cell surface
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20
Q

give examples of passive accumulation involving surface adsorption or ion exchange?

A

• Net negative charge from PO43-, COO- and OH-
groups
•Small sizehighest surface-to-volume ratio of any life form

21
Q

give examples of promoting precipitation of inorganis compounds external to the cell - bound cations may react with CO3 , PO43- , S2- , forming salts that serve as nuclei for mineral formation ?

A

for example

  • p.aeruginosa with 1mM LaCl3 for 15 min at RT
  • bacterium and metal - rich precipitates - yellowstone hot spring !
  • bacterium and metal rich precipitates - acid mine drainage sediment ( in Ohio )
22
Q

What can agents of Dispersion microbes do?

A

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

23
Q

What can fractionation microbes do?

A

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

24
Q

How Do Microbes Act As Geomicrobial Agents?

A
  • Physical and Biochemical mechanisms
25
Q

what are some physical effects exerted by microbes ?

A
  • 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
  • By pressure exerted by growing biomass in small rock cracks and fissures

a combination of these activities

26
Q

What are some Biochemical effects exerted by microbes ?

A

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

these changes are effected through METABOLISM!

27
Q

What is metabolism ?

A

made up of catabolism and anabolism

both of these may play a geomicrobial role !

28
Q

What is anabolism?

A

Formation of organic polymers, e.g. proteins, polysaccharides, nucleic acids, lipids, and inorganic polymers, e.g. silicates, polyphosphate


29
Q

What is catabolism?

A

Energy-yielding metabolism

Supply of building blocks for polymers etc.

30
Q

What are examples of anabolisms?

A

Fossil fuels (peat, coal, oil) Siliceous sediments

31
Q

What are examples of catabolism?

A

Large-scale iron, manganese and sulphur oxidation

32
Q

Metabolic versatility in microorganisms ?

A
  • eukaryotic and prokaryotic differs
33
Q

What is eukaryotic versatility ?

A

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

34
Q

What is prokaryotic versatility ?

A

Prokaryotic versatility resides in metabolism
Requires a separate vocabulary for describing different metabolic groups based on energy source (light or chemical), though many overlaps
Bacteria therefore reside in a wide array of environments using a large variety of energy sources and oxidants not available to eukaryotes

35
Q

What are lithotrophs?

A

assimilate carbon as CO2 , HCO3- or CO32-

36
Q

What are photolithotrophs?

A

derive energy from photosynthesis

37
Q

What are chemolithotrophs?

A

derive energy from oxidation of inorganic compounds. Usually oxidized by oxygen but also possible to use other electron acceptors during anaerobic respiration (see Table above)

38
Q

What is heterotrophy ?

A

assimilate organic carbon

39
Q

What are photohetertrophs

A

derive energy from photosynthesis

40
Q

what are chemoheterotrophs?

A

derive energy from oxidation of organic compounds

41
Q

what is mixotrophy ?

A

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

42
Q

What is the Chemiostatic theory ?

A

How Living Organisms Harvest Chemical (Redox) Energy from the Environment and Conserve it as Biologically-Useful Energy (ATP)

43
Q

What are the three basic features of the Chemiostatic theory ?

A

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
( refer to diagram slide 21)

44
Q

where is the ETC ( electron transport chain ) located in prokaryotes ?

A
  • 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
45
Q

Where is the ETC located in eukaryotes?

A

In eukaryotes, ETC located in mitochondria and therefore lacks direct access to insoluble substances

46
Q

What are catabolic reactions?

A

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

slide 24- gives table with the bacteria !

47
Q

What is the relevance to organic matter breakdown?

A

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

48
Q

slide 26…

A

slide 26 ..

Molecular Microbiology (11 decks)

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