Nutrient Cycles

Biogeochemical cycles describe how chemical elements move through the biotic and abiotic compartments of an ecosystem and the planet as a whole. Energy flows through ecosystems in one direction — lost ultimately as heat — but matter is conserved and recycled. The carbon and nitrogen cycles are the canonical A-Level biogeochemical cycles, complemented at AQA 7402 by the phosphorus cycle. A confident grasp of these cycles links biochemistry (photosynthesis, respiration, nitrogen-containing biomolecules) to organism-level physiology and to ecosystem and global-scale dynamics.

Spec mapping: This lesson sits in AQA 7402 Section 3.5.4 (nutrient cycles — carbon, nitrogen, phosphorus), with strong forward links into Section 3.7.5 (succession changes the rate of biogeochemical cycling) and applied content on agricultural impacts (lesson 5) and climate change (lesson 6). Refer to the official AQA specification document for exact wording.

Connects to: Photosynthesis and respiration (course 7 — biochemistry of CO₂ fixation and release); succession and the closing of nutrient cycles in late-successional communities (lesson 1 of this course); agricultural impacts of fertiliser inputs on N and P cycles (lesson 5 of this course); climate change and the perturbed carbon cycle (lesson 6 of this course).

Key Definition: A biogeochemical cycle is the pathway by which a chemical element circulates between the biotic and abiotic components of an ecosystem — atmosphere, hydrosphere, lithosphere and biosphere — driven by both biological transformations and abiotic processes. Matter is conserved within the cycle; the input of fresh nutrients to the biosphere balances losses to long-term geological storage.

---

The Carbon Cycle

Carbon is the structural element of all organic molecules — carbohydrates, lipids, proteins and nucleic acids. The carbon cycle is the canonical biogeochemical cycle for A-Level because every metabolic step on the syllabus is a transfer between carbon pools: photosynthesis (inorganic → organic), respiration (organic → inorganic), and decomposition (return to inorganic). Atmospheric CO₂ is the small but biologically critical pool that links the cycle's biotic and abiotic reservoirs.

Reservoirs

Reservoir	Approximate scale	Form of carbon
Atmosphere	Smallest of the major reservoirs	CO₂ (and trace CH₄)
Terrestrial biosphere	Large	Organic molecules in living biomass and soil organic matter
Oceans	Very large	Dissolved CO₂, HCO₃⁻, CO₃²⁻; dissolved organic carbon; marine biomass
Lithosphere — fossil fuels	Very large	Hydrocarbons (coal, oil, gas)
Lithosphere — carbonate rocks	Largest reservoir	CaCO₃ (limestone, chalk)

Carbon moves between reservoirs along well-characterised pathways; the cycle is in dynamic balance on geological timescales but is currently being perturbed by anthropogenic emissions, the focus of lesson 6.

Key Processes

flowchart LR
  A["Atmospheric CO2"] -- "Photosynthesis" --> B["Producer biomass"]
  B -- "Feeding" --> C["Consumer biomass"]
  B -- "Respiration" --> A
  C -- "Respiration" --> A
  C -- "Death + egestion" --> D["Detritus + soil organic matter"]
  B -- "Death" --> D
  D -- "Decomposition (respiration)" --> A
  D -- "Sedimentation + burial" --> E["Fossil fuels + sedimentary rock"]
  E -- "Combustion (anthropogenic)" --> A
  A -- "Dissolution" --> F["Ocean DIC pool"]
  F -- "Sedimentation" --> G["Carbonate rock"]

1. Photosynthesis. Producers (green plants, algae, cyanobacteria) absorb atmospheric CO₂ and fix it into organic molecules using light energy. The overall equation 6CO₂ + 6H₂O → C₆H₁₂O₆ + 6O₂ understates the biochemical detail: the Calvin–Benson cycle catalyses the actual CO₂-incorporation step via RuBisCO, with the light-dependent reactions supplying ATP and reduced NADP. This is the primary entry point of inorganic carbon into the biosphere and the basis of every food chain.

2. Respiration. All living organisms — plants, animals, fungi, bacteria — carry out aerobic respiration, returning CO₂ to the atmosphere. C₆H₁₂O₆ + 6O₂ → 6CO₂ + 6H₂O is the overall equation; the biochemistry is glycolysis → link reaction → Krebs cycle → oxidative phosphorylation. Anaerobic respiration also returns carbon, in incompletely-oxidised forms (lactate, ethanol).

3. Decomposition. When organisms die or excrete, decomposers (saprobiotic fungi and bacteria) digest the organic remains. Saprobionts secrete extracellular enzymes — proteases, lipases, cellulases, ligninases — that break down complex polymers into soluble products absorbed across the cell membrane. Decomposer respiration then returns CO₂ to the atmosphere. Decomposition rate depends on:

• Temperature (Q₁₀ ≈ 2 — see biochemistry, course 1 lesson 4).
• Moisture — water is needed for enzymatic reactions and microbial growth.
• Oxygen availability — aerobic decomposition is much faster than anaerobic.
• pH — extreme pH inhibits decomposer enzymes.
• Substrate quality — soft, low-lignin tissues decompose in weeks; lignified woody tissue takes years; bone takes decades to centuries.
• C:N ratio of detritus — high-C, low-N material (straw, wood) is decomposed slowly because nitrogen is limiting for microbial growth.

4. Combustion. Anthropogenic burning of fossil fuels releases carbon that has been locked away on geological timescales (10⁶–10⁸ years). Biomass burning — wildfires, slash-and-burn agriculture, biofuel use — also returns biospheric carbon to the atmosphere on much shorter timescales.

5. Fossil-fuel formation. Where dead organisms accumulate in anaerobic conditions (deep marine basins, swamps, peat bogs), decomposition is incomplete. Over millions of years, heat and pressure transform the partially-decomposed material into coal, oil and natural gas. This represents a slow but very large long-term carbon sink, now being rapidly re-mobilised.

6. Ocean dissolution. CO₂ dissolves in seawater, forming carbonic acid that dissociates into bicarbonate and carbonate ions. The ocean is a major sink for atmospheric CO₂ (paraphrased from IPCC literature — quantitative claims about the fraction taken up annually should be referred to the published primary literature rather than asserted as fixed values). Marine calcifying organisms — corals, molluscs, planktonic foraminifera and coccolithophores — combine Ca²⁺ with CO₃²⁻ to build CaCO₃ shells and skeletons. On death these settle to the seafloor and, on geological timescales, become carbonate rock (limestone, chalk). This is the largest carbon reservoir on Earth, though turnover is glacially slow.

Long-Term Sinks vs Short-Term Flux

Distinguishing fast and slow components of the carbon cycle is the hinge concept for understanding anthropogenic climate change (lesson 6):

• Fast cycle — photosynthesis ↔ respiration ↔ decomposition. Timescales of seconds to decades. Net effect on atmospheric CO₂ on annual scales is small and roughly balanced.
• Slow cycle — fossil-fuel formation, carbonate sedimentation, weathering of silicate rocks. Timescales of 10⁵–10⁹ years.

Anthropogenic emissions take carbon out of the slow cycle (combustion of fossil fuels) and add it to the fast cycle (atmosphere, ocean surface, biosphere) at rates much faster than the slow cycle can compensate. The atmospheric CO₂ pool is small, so even modest net flux from the slow cycle changes its size measurably.

Human Impact on the Carbon Cycle

• Fossil-fuel combustion is the largest single anthropogenic flux into the atmosphere.
• Deforestation reduces standing biomass (less carbon stored in living trees), reduces ongoing photosynthetic uptake, and — through clearance burning or post-clearance decomposition — releases stored carbon directly.
• Land-use change (drainage of peat bogs, conversion of pasture to arable) lowers soil organic carbon.
• Cement manufacture releases CO₂ from CaCO₃ decarbonation, separately from its energy emissions.

The biological consequences are developed in lesson 6 — atmospheric CO₂ accumulation enhances the greenhouse effect, contributing to warming; the dissolved-CO₂ fraction lowers ocean pH (ocean acidification), threatening calcifying organisms.

---

The Nitrogen Cycle

Nitrogen is the central element of amino acids, proteins, nucleotides and nucleic acids — every cell of every organism. Despite N₂ comprising ~78% of the atmosphere, biological availability is severely limited because the N≡N triple bond is one of the strongest chemical bonds in nature, requiring enormous activation energy to break. Most organisms cannot use atmospheric N₂ directly; they depend on the activity of nitrogen-fixing prokaryotes and on the rest of the recycling network maintained by soil microbes.

Reservoirs and Forms

Form	Where	Biological role
N₂	Atmosphere	Inaccessible to most organisms
NH₃ / NH₄⁺	Soil, water	Product of fixation and ammonification
NO₂⁻	Soil	Transient intermediate in nitrification
NO₃⁻	Soil, water	Main form absorbed by plants
Organic N	Living biomass, detritus	Amino acids, proteins, nucleic acids, urea

Key Processes

flowchart LR
  A["Atmospheric N2"] -- "Nitrogen fixation<br/>(Rhizobium, Azotobacter, lightning, Haber)" --> B["NH3 / NH4+"]
  C["Organic N<br/>(dead organisms, urea)"] -- "Ammonification<br/>(saprobionts)" --> B
  B -- "Nitrification<br/>(Nitrosomonas)" --> D["NO2-"]
  D -- "Nitrification<br/>(Nitrobacter)" --> E["NO3-"]
  E -- "Assimilation<br/>(plant uptake)" --> F["Plant amino acids and proteins"]
  F -- "Feeding" --> G["Animal protein"]
  F -- "Death" --> C
  G -- "Death + excretion" --> C
  E -- "Denitrification<br/>(Pseudomonas, anaerobic)" --> A

1. Nitrogen fixation. Conversion of atmospheric N₂ into a biologically usable form (NH₃ or NH₄⁺).

• Free-living N-fixing bacteria — Azotobacter, Clostridium and others fix N₂ directly in soil and water.
• Mutualistic N-fixing bacteria — Rhizobium species inhabit root nodules on leguminous plants (peas, beans, clover, alfalfa). The bacteria fix N₂ to NH₃ using the nitrogenase enzyme complex; the plant supplies sugars as an energy source. Nitrogenase is severely inhibited by O₂, so root nodules contain leghaemoglobin (a plant-encoded oxygen-binding protein structurally and functionally analogous to animal haemoglobin) that maintains low free-O₂ conditions while supplying O₂ to bacterial respiration. The relationship is mutualistic: both partners gain.
• Cyanobacteria — fix N₂ in heterocysts; ecologically critical in waterlogged rice paddies and in early-succession terrestrial systems.
• Lightning — discharge provides activation energy to combine N₂ with O₂; the resulting nitrogen oxides dissolve in rainwater and reach the soil as nitrate. A small but persistent flux.
• Industrial Haber process — N₂ + 3H₂ → 2NH₃ at high temperature (~450 °C) and pressure (~200 atm) with an iron catalyst. NH₃ is the precursor to most synthetic fertilisers (ammonium nitrate, urea, NPK formulations). This anthropogenic flux now rivals or exceeds the natural biological fixation rate, doubling the available reactive nitrogen in the biosphere — a key driver of the agricultural and eutrophication impacts developed in lesson 5.

2. Ammonification (mineralisation). Decomposers digest organic nitrogen — proteins, nucleic acids, urea, uric acid — releasing NH₄⁺ to the soil. Saprobionts (the same fungi and bacteria that drive the carbon cycle decomposer step) secrete proteases and deaminases; ammonia released from amino acid deamination dissolves to NH₄⁺ at biological pH.

3. Nitrification. A two-step oxidation of ammonium to nitrate, carried out by chemoautotrophic nitrifying bacteria that derive energy from these oxidations:

• Nitrosomonas: NH₄⁺ + 1.5 O₂ → NO₂⁻ + H₂O + 2H⁺
• Nitrobacter: NO₂⁻ + 0.5 O₂ → NO₃⁻

Nitrification is strictly aerobic. Waterlogged soils have suppressed nitrification because diffusion of O₂ through saturated pore space is too slow to keep up with microbial demand. Soils that are well-drained and well-aerated maintain rapid nitrification and high NO₃⁻ availability — a key reason farmers value good soil structure.

Nitrate is the form of nitrogen most readily taken up by plant roots (via H⁺-coupled symport — active transport).

4. Assimilation. Plants absorb NO₃⁻ across root cells by active transport, reduce it back to NH₄⁺ via nitrate and nitrite reductases, then incorporate the N into amino acids through transamination (glutamate synthase pathway). Plant amino acids are polymerised into proteins, contribute the N skeleton of nucleotides, and are passed up the food chain when herbivores eat plants. Animals deaminate excess amino acids in the liver, excreting nitrogen as urea (mammals), uric acid (birds, reptiles, insects) or ammonia directly (freshwater fish — the cheapest form energetically but only feasible where water is abundant to dilute it).

5. Denitrification. Conversion of NO₃⁻ back to N₂, returning nitrogen to the atmosphere. Carried out by denitrifying bacteria (e.g. Pseudomonas denitrificans) under anaerobic conditions — typically waterlogged or compacted soils. Denitrification reduces soil fertility by removing plant-available nitrogen; intermediate gaseous products (N₂O — nitrous oxide) are also potent greenhouse gases, linking the nitrogen cycle to lesson 6. Farmers minimise denitrification by maintaining drainage and aeration.

Bacterial Roles — Quick Reference

Process	Bacteria	Substrate → Product	Conditions
Nitrogen fixation (free-living)	Azotobacter	N₂ → NH₃	Aerobic soil
Nitrogen fixation (mutualistic)	Rhizobium	N₂ → NH₃	Anaerobic (leghaemoglobin-protected)
Ammonification	Saprobionts (various)	Organic N → NH₄⁺	Variable
Nitrification step 1	Nitrosomonas	NH₄⁺ → NO₂⁻	Aerobic
Nitrification step 2	Nitrobacter	NO₂⁻ → NO₃⁻	Aerobic
Denitrification	Pseudomonas	NO₃⁻ → N₂	Anaerobic

---

The Phosphorus Cycle