Biogeochemistry - Minerals

What is nucleation?

Formation of a new mineral phase nucleus in solution:

• requires SI>0

How do surfaces affect nucleation?

Surfaces lower activation energy by reducing surface tension, increasing nucleation rate.

What characterises the initial amorphous growth phase?

Highly hydrated, high surface area, very soluble, no crystal lattice

What happens in crystalline growth?

Crystalline phases grow using amorphous phases as templates, bypassing activation barriers

What is induced biomineralisation?

Minerals form as metabollic by-products or cell-environmental interactions (extrcellular)

What is controlled biomineralisation?

Organisms control all stages of mineral formation for physiological purposes intra/epicellular

What conditions are required for controlled biomineralisation?

Organisms actively concentrate ions until SI > 0, enabling precipitation.

What are two induced biomineralisation mechanism?

1. Cell surface nucleation

2. Metabolism-driven changes in pH and ion concentrations

What are the two roles of cyanobacteria in induced carbonate biomineralisation?

1. C-fixation increases pH → supersaturation

2. Cell surfaces catalyse nucleation

What is controlled carbonate biomineralisation?

Organisms (e.g: coccolithophores) pump ions into vesicles until supersaturated, then nucleate minerals.

What are metal (hydr)oxides used for?

Remediation, wastewater treatement, Carbon capture storage, and as TEAs for microbes.

What are the passive mechanisms of ferrihydrite biomineralisation?

Fe²⁺ adsorbs to EPS/cell walls → nucleation → cells become encrusted.

How is magnetite formed by induced biomineralisation?

Fe(III)-reducers expel Fe(II), producing poorly crystalline, small, non‑magnetic grains.

What is sorption?

Removal of solutes (ions, gases, compunds) from solution by adsorption or absorption

What is the difference between adsorption and absorption?

aDsorption → solutes bind to surface of a solid

aBsorption → solutes are incorporated into a solid

What is desorption?

Release of sorbates (adsorbed ion) back into solution when bonds break

What is outer-sphere complexation?

Adsorbate held in place by electrostatic forces or H-bonds between hydration shell and surface

What is inner-sphere complexation?

Adsorbate forms dircet ionic or covalent bonds with the surface

What controls surface reactivity?

Surface area, grain size, crystallinity, lattice structure, roughness, vacancies, damage

Why are secodnary minerals good sorbents?

High SA, fine grained, often amorphous, layered, rough surfaced

What is pHzpc?

pH at which net surface charge = 0.

How does pH affect surface charge?

• pH = pHzpc → neutral

• pH > pHzpc → negative

• pH < pHzpc → positive

Why do microbial cells act as sorbents?

Their functional groups ionise, giving surfaces an EC

What is the typical pHzpc of bacteria?

Between pH 2 and pH 4

Why are most bacterial surfaces charge?

Most bacteria grow best at circumneutral pH – most bacteria surfaces negatively charged

What are microbial envelopes?

Structures that modify surface charge and protect cells; can be neutral or positive even if cell wall is negative.

Some capsules protect from toxic metals

What are the 5 types of chemical weathering?

• Dissolution

• Hydration

• Oxidation

• Ion exchange

• Precipitation of secondary minerals

What is the difference between congruent and incongruent dissolution?

• Congruent - the mineral dissolves stoichimetrically

• Incongruent -not all products are soluble so solid is left behind

What controls dissolution rates?

Temperature, water flow, reactants (H⁺, O₂, ligands), and product concentrations.

What is hydrolysis?

Proton-promoted dissolution where H+ replaces cations in minerals

What is ligand-promoted dissolution?

Ligands complex mineral‑bound cations, breaking bonds and enhancing dissolution

What are siderophores?

Microbial, multidentate organic ligands with extremely high Fe(III) affinity

How do microbes influence weathering indirectly?

By altering pH, redox, CO₂, ligand concentrations, and saturation state.

How do microbes influence weathering directly?

By attaching to minerals, forming biofilms, drilling with hyphae, or wedging into pores.

What are endolithic bacteria?

Microbes living inside rock pores, dissolving cement and increasing erosion.

What do lichens do in weathering?

Attach with hyphal structures and produce organic acids (e.g., oxalic acid).

What are etch pits?

Microscopic dissolution features left after microbial removal.