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Geomicrobiology > Biomineralisation > Flashcards

Biomineralisation Flashcards

1
Q

does dissolution involve breaking or making bonds

A

breaking

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2
Q

does precipitation involve making or breaking bonds

A

making bonds

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3
Q

what do you need to overcome to make a bond

A

activation energy barrier

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4
Q

what needs to happen for biomineralisation

A
  • overcome electrostatic repulsions
  • eliminate hydrogen shells around solutes
  • remove ligands from solutes
  • form new interface: nucleation
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5
Q

process of mineral nucleation and growthq

A
  1. Nucleation: formation of the nucleus of a new phase (the mineral) within the old phase (solution)
  2. Growth of initial phase: ions adsorb, starting at the nucleus (initial phase is usually amorphous)
  3. Growth of crystalline phase/dehydration and internal rearrangement
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6
Q

what does amorphous mean

A

not crystalline

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7
Q

what is saturation state defined by

A

the saturation index

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8
Q

Q=Ksp: SI=0:

A

Equilibrium

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9
Q

Q<Ksp: SI<0:

A

Undersaturated, can dissolve

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10
Q

Q>Ksp: SI>0:

A

Supersaturated, won’t dissolve, can precipitate

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11
Q

What is Q

A

ion activity product (IAP): same form as Ksp but for actual concentrations of ions in solution whereas Ksp is at equilibrium

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12
Q

what does Ksp mean

A

solubility product

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13
Q

what is biologically induced mineralisation

A

minerals form as a by-product of metabolic activity or other interactions between cells and their environment

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14
Q

what is biologically controlled mineralisation

A

the microorganism controls all stages of
mineralization to serve a physiological
purpose

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15
Q

2 mechanisms of biologically induced biomineralisiation

A
  1. cell surface reactivity - ionised surface functional groups (ligands) have low interfacial energies for nucleation
  2. metabolism - affecting saturation states and pH
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16
Q

examples of induced biomineralised products

A

ferrihydrite

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17
Q

mechanism and facilitated mechanisms for ferrihydrite

A

Totally passive mechanism (even dead cells can do this):
*Step 1: Fe adsorbed to EPS or cell wall
*Step 2: Nucleation - bacteria serve as nucleation sites
Cells become encrusted with ferrihydrite over time

Facilitated mechanisms (but not totally controlled by microbes):
1.Chemoheterotrophic iron mineralization
2.Anoxygenic photoautotrophic iron mineralization (photoferrotrophy)
3.Chemolithoautotrophic iron mineralization

18
Q

Chemoheterotrophic iron mineralization

A

– “iron-depositing bacteria” – not true (metabolic) Fe-oxidisers because they don’t obtain energy from the process
– Have surface ligands that promote Fe(II)-oxidation
– Leptothrix ochracea – most common
– Sphaerotilus (image), Crenothrix, Clonothrix,
Metallogenium, Siderocapsaceae

19
Q
  1. Anoxygenic photoautotrophic iron mineralization
    (Photoferrotrophic growth):
A

-some GSB, PSB, PNB
– How does this happen without O2?
– E0 for Fe3+/Fe2+ too + to be PED except with very good TEA
– E0 for Fe(OH)3+HCO3/FeCO3 much less +, can be PED with various other TEAs.

20
Q

3.Chemolithoautotrophic iron mineralization

A
  • Using Fe(II) as an energy source (PED), TEA: O2 usually
  • Most occurs at low pH, but this usually doesn’t form minerals
  • At neutral pH, low O2, Gallionella ferruginea forms lots of ferrihydrite
  • Form ferrihydrite stalks (top image)
  • Ferrihydrite from G. ferruginea clogs wells, water pipes, drains etc.
21
Q

Hydrothermal ferrihydrite precipitation

A
  • Found along low O2 zones, from 2-50°C.
  • Extensive deposits – some Gallionella (chemolithoautotrophs), others may be Leptothrix or other chemoheterotrophs
22
Q

Magnetite

A

mixed Fe(II)-Fe(III) oxide: Fe3O4
- can be biologically induced or controlled

23
Q

Induced biomineralization products are:

A
  • poorly crystalline, small magnetite grains, mostly non-magnetic
24
Q

Biogenic Mn-oxides are very common

A
  • Form at the same oxic-anoxic interfaces as many ferrihydrites form
  • At ca. pH 7, most Mn(IV)-oxide minerals attributed to microorganisms.
25
Q

Carbonates are formed by

A

either induced or controlled biomineralization

26
Q

Photosynthetic cyanobacteria have 2 primary roles in induced carbonate biomineralization.
What are they?

A
  1. C-fixation increases pH, leading to supersaturation and precipitation (Eukaryotic algae can also do this)
  2. Cell surface catalyses nucleation
27
Q

Induced Biomineralization: S-minerals - sulfides

A

Sulfate Reducing Bacteria (SRB) reduce SO42- to HS- or H2S, which then reacts with metals, to produce sulfide minerals (cells can nucleate sulfide minerals too)

28
Q

what is a whiting event

A

aragonite deposits - a phenomenon that occurs when a suspended cloud of fine-grained calcium carbonate precipitates in water bodies - microorganisms play an integral role in this

29
Q

Induced Biomineralization: Calcrete (carbonates)

A

common in arid and semi-arid areas
fungi aids the process of calcrete formation

30
Q

Induced Biomineralization: S-minerals - sulfides

A
  • Sulfate Reducing Bacteria (SRB) reduce SO4
    2- to HS- or H2S, which then reacts
    with metals, to produce sulfide minerals (cells can nucleate sulfide minerals too)
  • SRB role in low-temp metal sulfide ore deposits
31
Q

4 stages of controlled biomineralisation

A
  1. Seal off a site from the environment - can be inter or intracellular
  2. Transport ions of choice to the mineralization site until supersaturated
  3. Nucleation controlled by organic ligands with specific properties tailored to interact with mineralizing ions
  4. Crystals grow, highly ordered, orientation and size governed by structure of the membrane-bound compartment where they grow
32
Q

Controlled biomineralization: what are the most well know magnetite-making bacteria and what is a key characteristic of them

A
  • magnetotactic bacteria
  • microaerophilic
33
Q

Controlled biomineralization: where does the process that creates Magnetite occur and who does it

A
  • oxic-anoxic interfaces
  • chemoheterotrophic (O2 as TEA)
34
Q

How does magnetite navigate to optimum oxygen conditions

A

using the Earth’s magnetic field

35
Q

What can magnetotactic biomineralised magnetite help us do

A

the contribute to palaeomagnetic record in deep-sea sediments

36
Q

Controlled biomineralization: Greigite (Fe3S4)

A

Formed the same way as intracellular magnetite, also in chains, also by magnetotactic bacteria, but in an anoxic environment

37
Q

Controlled biomineralization: Amorphous silica:

Why do they form these shells in silica undersaturated environments - why don’t they form CaCO3 , which would be easier?

A

Possibly genetic holdover from evolution in silica-rich world

38
Q

Controlled biomineralization: Amorphous silica:

How does it form?

A
  • Extract Si(OH)4 from water, pump it into intracellular silica deposition vesicle (SDV) that lines the inside of the plasma membrane.
  • Inside SDV, silica added until supersaturated
    -OH- and NH3+ containing amino acids (functional groups!) in the SDV react with silica, catalysing nucleation. The SDV acts as a template.
39
Q

what are coccolithophores

A
  • unicellular algae
  • Calcite
40
Q

what do coccolithophores effect

A

atmosphere-ocean C transfer and marine Ca budget

41
Q

what are foraminifera

A
  • calcite
  • marine micro-omnivores, eat bacteria, protozoa and small invertebrates

Geomicrobiology (12 decks)

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