Biogeochemistry - Life is redox

What enables life to exist at the chemical level?

Differences in redox potential that organisms exploit to move electrons

What is an exergonic reaction?

A reaction that releases energy (ΔG° < 0)

What is an endergonic reaction?

A reaction that requires energy (ΔG° > 0)

What is Gibbs free energy?

The thermodynamic potential that indicates whether a reaction releases or requires energy.

How to calculate Gibbs free energy?

ΔGo = Σ (G° products) – Σ (G° reactants)

What defines an organic species?

• Always have C (& often H, O)

• C oxidation state is -4 to +3

• Contain C-H or C-C bonds (mostly)

• Bonds mostly covalent

What defines an inorganic species?

• Do not always have C

• C oxidation state is +4 (mostly)

• No C-H or C-C bonds (mostly)

Examples of organic molecules:

Methane, benzene, lactate, glucose, acetaldehyde, tryptophan, chlorophyll, ATP, acetic acid.

Examples of inorganic molecules:

Sulfate, Ca²⁺, NH₃, O₂, HCl, CO₂, HCO₃⁻, CaCO₃, albite.

What is metabolism?

All the chemical processes of an organism

What are the two categories of metabolism?

Catabolism - degradative processes; breakdown of food to release energy

Anabolism - biosynthestic processes; formation of biomass which requires energy

How does ATP link catabolism and anabolism?

Catabolism puts ADP bact together to form ATP

Anabolism breaks apart ATP to from ADP

Why does ATP store energy?

The phosphate-oxygen bonds hold a lot of energy; the last phosphate bond releases the most energy when broken

Define heterotrophy and autotrophy

Heterotrophy - gets organic carbon from the environment

Autotrophy - takes in inorganic carbon and transforms it into organic carbon (carbon fixation)

What is biomass made of?

Primarily organic carbon, including amino acids, nucleotides, simple sugars, fatty acids and glycerol

What are examples of catabolic products?

Organic C compounds → builfings blocks for anabolism

Inorganic compounds → metabolic waste products

What is chemoheterotrophy?

Getting energy by oxidising organic carbon compounds, forming ATP via respiration or fermentation

What is chemolithotrophy?

Energy from oxidation of inorganic compounds, forming ATP by respiration

Why is photosynthesis not catabolism?

It doesn’t release anything; it harvests light energy and transforms it into ATP

What are the two components of a catabolic redox reaction?

• Primary electron donor (PED)

• Terminal electron acceptor (TEA)

What are examples of anabolic reactions?

• Carbon fixation

• Nitrogen fixation

• Biomolecule synthesis

What external reactants are needed for anabolism?

Organic or inorganic carbon, electron donors, and nutrients such as P, N, K, Ca, Fe, Mg, micronutrients

What is aerobic chemiheterotrophy?

Oxidation of organic carbon by O2, forming CO2 and H2O; produces the most ATP of all metabolism

What terminal electron acceptors are used in anaerobic chemoheterotrophy?

NO₃⁻, NO₂⁻, Mn⁴⁺/MnO₂, Fe³⁺/Fe(OH)₃, UO₂²⁺, SO₄²⁻.

What are faculative organisms?

Microorganisms that prefer oxygen because it yields more energy but can switch to anaerobic respiration.

What are common PEDs in chemolithoautotrophy?

H₂, CO₂/HCO₃⁻, H₂S, Fe²⁺/FeS₂, Mn²⁺, NH₄⁺, NO₂⁻

What is the TEA un aerobic vs anaerobic chemolithoautotrophy?

Aerobic: O2

Anaerobic: oxidsed species such as NO₃⁻, Mn⁴⁺, Fe³⁺, SO₄²⁻

What defines oxygenic photosynthesis?

• Used by all plants and many microorganisms

• Water is the electron donor

• Produces oxygen but does not use it

What defines anoxygenic photosynthesis?

• Microorganisms only

• Do not use or produce oxygen

• Electron donors include H₂, H₂S, S⁰, S₂O₃²⁻, Fe²⁺

What are the key prefixes for metabollic classification?

photo = light

chemo = chemical energy

Litho = inorganic electron donor

Hetero = organic carbon source

Auto = CO2 carbon source

Aerobic/anaerobic = oxygen use

Oxygenic/anoxygenic = O2 produced or not

What must a TEA not contain in chemolithoautotrophy?

No carbon

What environments favour nitrate reduction?

Soils/freshwaters with agricultural pollution (NO₃⁻, NH₄⁺) or sewage

What is denitrification?

Reduction of nitrate to nitrogen gases (NO₃⁻ → NO₂⁻ → NO → N₂O → N₂).

What is nitrate ammonification?

Reduction of nitrate to ammonium (NO₃⁻ → NO₂⁻ → NH₄⁺).

Which metals are commonly reduced

Fe(III), Mn(IV), plus radioactive/toxic contaminants like As(V), Se(IV), Cr(VI), U(VI).

What environmental impact do Fe(III)-reducers have?

Release of Fe2+ into anoxic groundwaters

What is the TEA in sulphate reduction?

SO₄²⁻ → HS⁻ or H₂S.

Where do sulphur reducing bacteria thrive?

Water-logged soils, brackish waters, sewage, mine waste, deap sea hydrothermal vents

What organisms perform methanogenesis?

strictly anaerobic archaea

Why does methanogenesis require low sulfate?

SRB outcompete methanogens if sulfate is present.

What are the four major anaerobic chemoheterotrophic pathways?

1. Dissimilatory nitrate reduction

2. Dissimilatory metal and mellaoid reduction

3. Dissimilatory sulfate reduction

4. Methanogenesis

What are typical PEDs for chemolithoautotrophs?

H₂, CH₄, H₂S, S⁰, S₂O₃²⁻, Fe²⁺, Mn²⁺, NH₄⁺, NO₂

Which PEDs are the most energy efficient? (highest to lowest)

1. H2 oxidation

2. Methane oxidation

3. sulfur oxidation

4. Iron oxidation

5. Manganese oxidation

6. Nitrogen oxidation

7. Chemolithoautrophic methanogenesis

TEAs for H2 oxidisers?

Aerobic: O2

Anaerobic: NO₃⁻, Mn(IV), Fe(III), SO₄²⁻, CO₂

Where do methanotrophs and methanogens co-occur>

In deep marine sediments → where methanogens make methan and methanotrophs eat it

Two types of sulfur oxidisers?

• Gradients (neutral pH, microaerophilic)

• Acidophilic (acidic, often H2S PED)

Two types of Fe-oxidisers?

• Neutrophilic (microaerophilic)

• Acidophilic (mine waste)

What conditions favour Mn oxidisers?

Suboxic environments

What are the two nitrogen-oxidising groups?

• Nitrifiers: NH₄⁺ → NO₂⁻ → NO₃⁻

• Anammox: NH₄⁺ + NO₂⁻ → N₂ + H₂O

What is the electron donor in oxygenic photosynthesis?

Water

What are the typical electron donors in anoxygenic photosynthesis?

H₂, H₂S, S⁰, S₂O₃²⁻, Fe²⁺.

Name examples of anoxygenic phototrophs?

GSB

GNB

PSB

PNB

Heliobacteria