Nutrient Cycles and Succession

Spec Mapping — OCR H420 Module 6.3.1 — Ecosystems, content statements covering the carbon and nitrogen biogeochemical cycles, the microorganisms responsible for nitrogen fixation, nitrification and denitrification, the impact of human activity on these cycles, and ecological succession (primary and secondary, leading to climax communities; the concept of plagioclimax) (refer to the official OCR H420 specification document for exact wording). This lesson completes Module 6.3.1.

Ecosystems recycle chemical elements through biogeochemical cycles, and develop over time through the process of succession. OCR A-Level Biology A specification 6.3.1 requires you to describe the carbon and nitrogen cycles in detail, name the microorganisms involved, and explain how communities change through primary and secondary succession to a climax community.

The conceptual framing of succession comes from two near-contemporary schools that disagreed sharply on the underlying mechanism. Frederic Clements at the University of Nebraska (1916) framed plant communities as superorganisms that develop in deterministic stages toward a single climax community determined by climate alone — the "monoclimax" theory. Paraphrased: Clements held that succession is teleological, with each seral stage paving the way for the next in a directional sequence. Henry Gleason (1926) and later Arthur Tansley (1935) rejected this view, framing communities instead as statistical assemblages of species each responding individualistically to environmental conditions; the resulting climax community is contingent on local conditions, history and disturbance regime — the "polyclimax" or "individualistic" theory. Modern ecology largely follows the Gleason-Tansley framing, but the OCR specification still uses the Clementsian language of "climax community" and "seral stages", so you must master both. Treat Clements's framework as a useful pedagogical abstraction; recognise its paradigm-superseded status in the academic literature.

Key Definitions:

• Nutrient cycle — the circulation of an element between living organisms and the abiotic environment.
• Decomposer — a heterotroph (usually bacterium or fungus) that breaks down dead organic matter.
• Fixation — conversion of an element from an unusable form (e.g. N₂) into a biologically useful form (e.g. NH₃).
• Succession — the change in community structure over time as one community replaces another.
• Pioneer species — the first species to colonise a new area.
• Climax community — the stable, self-perpetuating community at the end of a successional sequence.

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The Carbon Cycle

Carbon is the backbone of every organic molecule. It cycles between the atmosphere, oceans, soil and living organisms through four main processes.

The Processes

1. Photosynthesis — plants, algae and cyanobacteria fix CO₂ into organic molecules, using light energy: $6\text{CO}_2 + 6\text{H}_2\text{O} \rightarrow \text{C}_6\text{H}_{12}\text{O}_6 + 6\text{O}_2$6CO2​+6H2​O→C6​H12​O6​+6O2​
2. Respiration — all living organisms release CO₂ back to the atmosphere by breaking down organic molecules.
3. Decomposition — bacteria and fungi break down dead material, releasing CO₂.
4. Combustion — burning of wood, coal, oil and gas releases CO₂ from long-term stores.

flowchart TD
    A[Atmosphere CO2] -->|Photosynthesis| B[Producers organic C]
    B -->|Respiration| A
    B -->|Eaten by| C[Consumers]
    C -->|Respiration| A
    B -->|Death| D[Detritus]
    C -->|Death faeces| D
    D -->|Decomposition by saprotrophs| A
    D -->|Long-term burial + heat + pressure| E[Fossil fuels]
    E -->|Combustion anthropogenic| A
    A -->|Dissolution| F[Ocean dissolved CO2 + bicarbonate]
    F -->|Marine organisms| G[Carbonate sediments limestone]
    F -->|Outgassing| A

Long-Term Carbon Stores

Carbon is stored on geological timescales in:

• Fossil fuels (coal, oil, natural gas).
• Carbonate rocks (limestone, chalk) formed from marine organisms.
• Deep ocean dissolved CO₂ and bicarbonate ions.
• Peat and permafrost.

Burning fossil fuels transfers carbon from these long-term stores to the atmosphere at a rate that natural processes cannot offset, causing the rise in atmospheric CO₂ from around 280 ppm (pre-industrial) to over 420 ppm today. This is the primary driver of anthropogenic climate change.

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The Nitrogen Cycle

Although nitrogen gas (N₂) makes up 78% of the atmosphere, most organisms cannot use it directly because the triple bond in N₂ is extraordinarily strong. Four groups of microorganisms transform nitrogen between forms plants and animals can use.

flowchart TD
    A[N2 atmospheric nitrogen] -->|Nitrogen fixation Rhizobium Azotobacter| B[NH3 ammonia]
    C[Dead plants animals urine faeces] -->|Ammonification saprotrophs| B
    B -->|Nitrification Nitrosomonas| D[NO2- nitrite]
    D -->|Nitrification Nitrobacter| E[NO3- nitrate]
    E -->|Plant uptake| F[Plant proteins]
    F -->|Feeding| G[Animal proteins]
    G --> C
    F --> C
    E -->|Denitrification Pseudomonas anaerobic| A

1. Nitrogen Fixation

Converts N₂ to ammonia (NH₃) or ammonium (NH₄⁺). Carried out by:

• Rhizobium — lives symbiotically in root nodules of legumes (peas, beans, clover, alfalfa). It fixes atmospheric nitrogen using the enzyme nitrogenase (which is destroyed by oxygen — hence the pink pigment leghaemoglobin in root nodules, which binds free O₂).
• Azotobacter — free-living soil bacteria.
• Cyanobacteria — in water and soil; major nitrogen source in paddy rice fields.
• Lightning — converts a small but significant amount of N₂ to nitrate.
• Industrial fixation (Haber process) — man-made production of ammonia fertilisers; now rivals biological fixation in scale.

2. Ammonification (Putrefaction)

Decomposer bacteria and fungi (saprotrophs) break down proteins and other nitrogen-containing molecules in dead organisms, faeces and urine, releasing ammonia into the soil. Ammonia dissolves as ammonium ions (NH₄⁺).

3. Nitrification

Ammonium ions are oxidised to nitrate by chemoautotrophic bacteria that use the released energy to fix carbon:

• Nitrosomonas — oxidises ammonium (NH₄⁺) to nitrite (NO₂⁻).
• Nitrobacter — oxidises nitrite (NO₂⁻) to nitrate (NO₃⁻).

Both require oxygen, so nitrification only happens in well-aerated soils. Plants absorb nitrate through their roots (active transport) and use it to make amino acids, nucleotides and chlorophyll.

4. Denitrification

Under anaerobic conditions (waterlogged soils, landfill, anaerobic sediments, the anoxic interior of large soil aggregates), Pseudomonas and similar denitrifying bacteria use nitrate as a terminal electron acceptor (in place of oxygen, which is absent) and reduce it back to N₂ gas through a series of intermediates (NO₃⁻ → NO₂⁻ → NO → N₂O → N₂). The N₂ escapes to the atmosphere. This is a loss from the ecosystem's usable nitrogen pool — bad for farmers, because fertiliser is wasted, and bad for the climate because nitrous oxide (N₂O) is a potent greenhouse gas with ~300× the warming effect of CO₂ per molecule on a 100-year time horizon.

Waterlogging encourages denitrification and discourages nitrification, which is why farmers drain fields. Conversely, controlled wetland creation can be used deliberately to remove nitrate from agricultural runoff before it enters waterways — constructed wetlands at field edges exploit denitrification as an ecosystem service.

Nitrogen Cycle Summary Table

Process	Microorganism	Input	Output	Aerobic/anaerobic
Nitrogen fixation	Rhizobium, Azotobacter, cyanobacteria	N₂	NH₃ / NH₄⁺	Aerobic (in nodules)
Ammonification	Saprotrophs	Proteins / urea	NH₃ / NH₄⁺	Aerobic
Nitrification step 1	Nitrosomonas	NH₄⁺	NO₂⁻	Aerobic
Nitrification step 2	Nitrobacter	NO₂⁻	NO₃⁻	Aerobic
Denitrification	Pseudomonas	NO₃⁻	N₂	Anaerobic

Exam Tip: OCR loves naming. Learn the four genus names (Rhizobium, Nitrosomonas, Nitrobacter, Pseudomonas) and what each does. Most marks in nitrogen-cycle questions go to students who give the right genus for the right process.

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Fertilisers and Nitrogen

Modern intensive agriculture depends on nitrogen fertilisers (ammonium nitrate, urea, anhydrous ammonia). The industrial Haber-Bosch process — N₂ + 3 H₂ → 2 NH₃ at ~450 °C, ~200 atm, iron catalyst — fixes more than 150 million tonnes of nitrogen per year globally, comparable in scale to the entire biological nitrogen-fixation flux. The Haber-Bosch invention (Fritz Haber 1909, Carl Bosch industrial scale-up 1913, Nobel Prizes 1918 and 1931) is one of the most consequential chemical breakthroughs in history; it has been estimated that food produced via Haber-Bosch nitrogen feeds approximately half of the world's current population — a fact that the OCR examiner expects you to handle with appropriate gravity.

Overuse of nitrogen fertilisers causes:

• Eutrophication — runoff into rivers and lakes stimulates algal blooms; when the algae die, decomposer bacteria multiply rapidly and respire, stripping oxygen from the water (BOD spike), creating anoxic zones in which fish suffocate. The dead-zone in the Gulf of Mexico, attributable to Mississippi-basin agricultural runoff, varies between ~10,000 and 22,000 km² in size depending on year.
• Leaching — nitrate is soluble and washes into groundwater, contaminating drinking water. The EU nitrate-in-water directive limits drinking water to 50 mg/L NO₃⁻; agricultural areas of eastern England regularly exceed this.
• Denitrification of excess fertiliser releases nitrous oxide (N₂O), a potent greenhouse gas. Agriculture is the largest anthropogenic source of N₂O globally.
• Soil acidification — ammonium fertiliser lowers pH as nitrification produces protons; this can require regular liming to neutralise.

Sustainable alternatives include crop rotation with legumes (which host Rhizobium and restore soil nitrogen biologically), green manures (legume cover crops ploughed into the soil), precision fertiliser application (variable-rate technology that matches input to crop demand), and controlled-release urea formulations that reduce leaching and denitrification losses.

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Ecological Succession

Succession is the sequence of changes in a community over time. It occurs because each community of organisms modifies the environment, making it more (or less) suitable for different species.

Primary Succession

Begins on bare substrate never previously colonised — a new volcanic island, a glacial retreat, a lava flow, a sand dune, a newly exposed cliff. There is no soil and no existing organisms.

Stages of primary succession:

1. Pioneer species — the first colonisers. They must tolerate harsh conditions (wind, drought, no soil, low nutrients). Typical pioneers include lichens (a symbiosis of fungus and alga, acting as a single organism), cyanobacteria and moss.
2. Soil formation — pioneers die, decompose, and add organic matter. Weathering of rock by acids released from lichens adds minerals. A thin soil develops.
3. Secondary colonisers — herbaceous plants (grasses, small flowering plants) establish in the new soil.
4. Intermediate communities — shrubs and small trees move in, further enriching the soil and providing shade.
5. Climax community — eventually a stable community of tall trees (in temperate latitudes, usually oak or beech) persists. This is the climatic climax community — determined by the regional climate.

Each stage is called a seral stage, and the whole sequence is a sere. A sere on bare rock is a lithosere; on water it is a hydrosere; on sand a psammosere; on salt marsh a halosere.

Secondary Succession

Begins where soil is already present but the existing community has been destroyed — after a forest fire, a flood, deforestation, or ploughing. Secondary succession is much faster than primary because soil (and a seed bank) are already present. Farmland left fallow can reach a climax community in 50–150 years; primary succession on bare rock may take 1000 years or more.

Deflected Succession (Plagioclimax)

Sometimes human activity prevents succession reaching its natural climax. Grazing by sheep keeps a grassland as grassland, preventing scrub and trees from establishing. Mowing keeps lawns short. Regular burning of moorland (managed for grouse) suppresses tree colonisation. These communities are called plagioclimax communities (deflected climax). The UK is almost entirely plagioclimax — nearly all grasslands, moorlands, chalk downs and lowland heaths are maintained in their current state only by grazing, burning or mowing. If left alone for several decades, the majority of UK landscape would revert to broadleaved woodland (oak, birch, ash in lowland areas; Scots pine and birch in upland areas).

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Worked Example: Succession on a Glacial Moraine

When a glacier retreats (as in Glacier Bay, Alaska, studied since 1794 when George Vancouver's expedition documented the original ice margin, providing a 230-year chronosequence that has become the textbook case study of primary succession):

1. Bare rock, gravel, silt — no vegetation.
2. Within a few years: mosses, lichens establish. Cyanobacteria fix nitrogen.
3. Within 20–40 years: nitrogen-fixing shrubs (alder, Alnus) take over, enriching the soil further.
4. After 100 years: spruce forest begins to replace alder.
5. After 200–300 years: mature spruce–hemlock climax forest — the stable community of the region.