Nitrogen and phosphorus are finite elements that ecosystems must recycle. Decomposers and specialist bacteria handle the conversions: dead material into ammonium, ammonium into nitrate, nitrate back to the air, and atmospheric nitrogen into ammonia. Phosphorus runs a simpler cycle with no atmospheric phase.
Nutrients cycle while energy flows; saprobionts make recycling possible.
Energy enters ecosystems as light and is ultimately lost as heat; it flows one way. Mineral nutrients behave differently. Nitrogen and phosphorus are finite elements essential in biological molecules — nitrogen in amino acids, proteins, nucleic acids, and chlorophyll; phosphorus in ATP, ADP, phospholipids, and nucleic acids. Ecosystems must recycle them, and that recycling depends on decomposers.
Saprobionts are decomposing microorganisms — bacteria and fungi. They secrete extracellular enzymes onto dead organic matter and absorb the soluble breakdown products. They do not ingest, engulf, or directly digest whole organisms. The absorbed products feed the saprobiont's own respiration.
Saprobionts secrete extracellular enzymes onto dead matter and absorb the soluble products. Don't write that they
ingest,engulf, ordirectly digest. The digestion happens outside the cell.
Nitrogen has a large atmospheric reservoir — N₂ makes up about 78% of air — acting as both source and sink, with four distinct bacterial conversions interconverting organic and inorganic forms. Phosphorus has no significant atmospheric phase. Phosphate enters only through the slow weathering of phosphate-bearing rocks and through decomposition of organic matter. There are no analogues of nitrogen fixation or denitrification.
Ammonification breaks organic nitrogen down to ammonium ions.
Ammonification is the conversion of organic nitrogen in dead matter and excreta into ammonium ions (NH₄⁺) in the soil. It is carried out by saprobionts and proceeds in two enzyme-catalysed stages.
- Saprobionts secrete extracellular protease enzymes onto dead organic matter. The proteases hydrolyse proteins into their constituent amino acids, breaking peptide bonds by addition of water and releasing free amino acids into the soil water.
- Deaminase enzymes then remove the amino group from each amino acid, releasing ammonia (NH₃). The ammonia dissolves in soil water to form ammonium ions (NH₄⁺). The carbon skeleton left behind feeds the saprobiont's own respiration.
Two-mark structure: named substrate plus named product. Acceptable substrates: proteins, amino acids, DNA, RNA, urea. The product is ammonium ions (or ammonium compounds). The one-word equivalent ammonification scores both marks on its own. Writing nitrogen-containing compounds unqualified earns nothing on the substrate mark.
Write a named nitrogen-containing substrate — proteins, amino acids, DNA, RNA, urea — and
ammonium ionsas the product.Nitrogen-containing compoundsunqualified earns zero on the substrate mark.
Write
ammonium ionsorammonium compounds, notnitrogenand notammonia gas. AQA wants the ion form for the product mark.
Nitrification and denitrification interconvert ammonium and nitrate under opposite oxygen conditions.
Nitrification converts ammonium ions to nitrate ions (NO₃⁻) — the form most plants absorb through their roots. Denitrification is the opposite: nitrate is reduced back to atmospheric N₂, removing nitrogen from the soil pool. Both are bacterial. The two processes operate under opposite oxygen conditions, so soil aeration determines which one dominates.
Nitrification and denitrification compared.
| Process | Bacteria | Conversion | Oxygen requirement |
|---|---|---|---|
| Nitrification | Nitrosomonas, then Nitrobacter | NH₄⁺ → NO₂⁻ → NO₃⁻ (two-step oxidation) | Aerobic (well-drained soil) |
| Denitrification | Denitrifying bacteria | NO₃⁻ → N₂ (returns nitrogen to atmosphere) | Anaerobic (waterlogged soil) |
Nitrosomonas and Nitrobacter
oxidiseorconvert. Don't writebreak down. Nitrification is oxidative conversion to a different ionic form, not degradation.
Nitrification is aerobic and proceeds rapidly only in well-drained soil. Denitrification is anaerobic and dominates in waterlogged soil. Drainage management therefore shifts the balance between gain (nitrification, producing usable nitrate) and loss (denitrification, removing nitrogen to atmosphere). Arable agriculture favours well-drained soils for this reason.
Nitrogen fixation captures atmospheric N₂ via nitrogenase, often in a mutualism with legumes.
Atmospheric N₂ is abundant but unusable to most organisms because the triple covalent bond between the two nitrogen atoms is extremely strong. Nitrogen fixation converts N₂ to ammonia, making atmospheric nitrogen biologically available. The process is carried out by nitrogen-fixing bacteria that possess the enzyme nitrogenase, which catalyses the reduction.
Live independently in the soil. They fix atmospheric N₂ from the soil air spaces and release ammonia when they die and decompose. They contribute to the soil ammonium pool from above and require no plant partner.
Rhizobium colonise the roots of leguminous plants — peas, beans, clover, soybeans — and induce root nodules. Inside the nodules, Rhizobium fix atmospheric nitrogen to ammonium and amino acids, which pass to the plant. In return, the plant supplies carbohydrates from photosynthesis to fuel the bacteria's energy-demanding fixation. Both partners gain; the relationship is mutualistic.
Write
carbohydrates,sugars, ororganic compoundsfor what the plant supplies the bacterium or fungus. Vaguer answers (food,energy,nutrients) are ignored, andstarchalone is rejected.
Crop rotation exploits this mutualism. Legumes are grown periodically in the rotation to replenish soil nitrogen without synthetic fertiliser. The Rhizobium-legume association is the classical worked example of mutualism in the AQA spec.
The phosphorus cycle runs without an atmospheric phase; mycorrhizae help plants reach phosphate.
Phosphorus is essential as a constituent of ATP, ADP, phospholipids, DNA, RNA, RuBP, TP, GP, and NADP. There is no atmospheric phase. Soil phosphate enters only through the slow weathering of phosphate-bearing rocks and through decomposition of dead organic matter. Plants take up inorganic phosphate ions (PO₄³⁻) through their roots.
Write a specific phosphate-containing molecule — ATP, ADP, phospholipids, DNA, RNA, RuBP, TP, GP, NADP. Don't write
proteinsas a phosphate-containing compound; proteins contain no phosphate group.
Mycorrhizae are mutualistic associations between fungi and plant roots. Fungal hyphae colonise root cells and extend into surrounding soil, far finer than root hairs and reaching pores roots cannot. They increase the effective surface area for water and phosphate uptake. In return, the plant supplies carbohydrates to the fungus. The exchange is mutualistic.
Excess fertiliser leaches into water and drives the eutrophication cascade.
Harvesting removes biomass — and the nutrients it contains — permanently from agricultural fields. Fertilisers replace those nutrients to maintain yields. Excess fertiliser beyond crop uptake is susceptible to leaching: mineral ions dissolve in rainwater and are carried into rivers and lakes. Eutrophication is the ecological cascade that follows.
- Excess nitrate and phosphate in the water stimulate rapid growth of algae and other aquatic plants, producing a dense algal bloom on the water surface.
- The algal bloom blocks light from reaching submerged plants and macroalgae below.
- The submerged plants die because they can no longer photosynthesise.
- Aerobic decomposers proliferate on the dead plant material. Their respiration depletes the dissolved oxygen in the water.
- Aerobic aquatic organisms — fish, invertebrates — suffocate and die as the oxygen concentration falls.
Soil sterilisation is a useful counter-example. Autoclaving kills the soil bacteria responsible for nitrification and ammonification; it does not remove inorganic nutrients, change soil pH, or alter soil structure. The dissolved nitrate and phosphate that were already in the soil remain there. The consequence is that newly-deposited organic nitrogen no longer gets converted to ammonium and nitrate, so over time the plant-available nitrogen pool collapses despite no physical removal.
Soil sterilisation kills bacteria; it does not remove nutrients, change pH, remove pesticides, or alter soil structure. The consequence is that bacterial conversions stop and plant-available nitrogen falls over time.
Investigations into bacterial activity in nutrient cycling often use a colorimeter, which measures the absorbance or transmission of light through a sample and tracks cloudiness change over time. A calorimeter measures heat and is the wrong instrument. Time-series fertiliser response data is read longitudinally: the credited conclusion is over time, the same level of fertiliser produces a smaller crop response, not the static more fertiliser produces less crops.
Use a
colorimeterfor cloudiness or absorbance investigations. Acalorimetermeasures heat — the wrong instrument. Useday⁻¹(negative-exponent), not/day(solidus). Use longitudinalover timeframing for fertiliser-response trends, not staticmore fertiliser produces less crops.
Key terms
- nitrogen
- ammonium
- phosphate
- saprobiont
- ammonification
- nitrification
- bacteria
- mycorrhizae
- amino acids
- decompose