Nutrient cycles (A-level only) — AQA A-Level Biology

Nutrients are recycled within ecosystems, whereas energy flows through and is lost. Nitrogen and phosphorus follow this pattern: producers absorb inorganic ions from soil or water, building them into organic molecules. Elements pass along food chains, and microorganisms return them to the inorganic pool when organisms die. Nitrogen enters mainly as nitrate, absorbed by active transport into roots, and is used to make amino acids, proteins, ATP and DNA. It has a vast atmospheric reservoir of nitrogen gas, fixed mainly by nitrogen-fixing bacteria and archaea, though lightning also contributes. Phosphorus has no significant gaseous stage; its reservoir is rock, which weathers to release phosphate ions into soil water. Phosphate is needed for phospholipids, ATP, DNA and RNA.

Soil microorganisms recycle nitrogen and phosphorus. Saprobionts (saprobiotic bacteria and fungi) secrete hydrolytic enzymes onto dead organisms and waste, digest the material extracellularly and absorb the products, releasing ammonia that forms ammonium ions in soil water (ammonification). Nitrifying bacteria oxidise ammonium to nitrite and nitrite to nitrate, using the released energy; these oxidations need well-aerated soil. Nitrogen-fixing bacteria, free-living or mutualistic in legume root nodules, reduce atmospheric nitrogen to ammonia using nitrogenase and ATP. Denitrifying bacteria reduce nitrate to nitrogen gas in waterlogged, anaerobic soil. Saprobionts also release phosphate ions from dead matter. In a valid experiment, sterilising soil removes other microorganisms so the test organism is the only variable changed.

Saprobionts, also called saprobiotic or saprophytic bacteria and fungi, feed on dead organic material and on faeces and urine. They cannot ingest solid food, so they use extracellular digestion: hydrolytic enzymes, including proteases, lipases, carbohydrases and nucleases, are secreted out of the cell onto the substrate, the enzymes hydrolyse the polymers there, and the soluble products, amino acids, sugars, fatty acids and glycerol, are absorbed across the cell surface membrane by diffusion and active transport. The nitrogen in those amino acids is surplus to the saprobiont's needs, so it is deaminated and released as ammonia, which dissolves to give ammonium ions, and that step is ammonification. Phosphate is released in the same way from nucleic acids and phospholipids.

Mycorrhizae are mutualistic associations between fungal hyphae and plant roots. The hyphae are extremely fine and grow far out into the soil, adding an enormous absorbing surface area to the root system and reaching water and ions in soil pores too small for root hairs to enter. This increases uptake of water and of inorganic ions, particularly phosphate, which diffuses very slowly through soil and is quickly depleted in the zone immediately around a root. The hyphal network also holds water around the root, helping the plant resist drought. In return the plant supplies the fungus with organic compounds, principally sugars from photosynthesis, so both partners gain. The effect is largest when a resource is scarce: with plenty of water, mycorrhizal and untreated plants may show no significant difference in yield, but under water shortage the treated plants grow significantly better.

The nitrogen cycle involves five key processes. Saprobiotic nutrition and ammonification are performed by saprobiotic bacteria and fungi, which secrete enzymes onto dead matter and waste, releasing nitrogen as ammonia that forms ammonium ions in soil. Nitrification involves nitrifying bacteria oxidising ammonium to nitrite, then to nitrate. This requires oxygen, so it stops in waterlogged soil. Nitrogen fixation uses nitrogen-fixing bacteria (free-living or mutualistic in legume root nodules) to reduce atmospheric nitrogen gas to ammonia. Finally, denitrification occurs in anaerobic, waterlogged soils where denitrifying bacteria reduce soil nitrates into nitrogen gas, returning it to the atmosphere and reducing soil fertility.

In a natural ecosystem, plants and animals die where they grew, so saprobionts return their nitrogen and phosphorus to the soil. Agriculture breaks that loop: the crop is harvested and the livestock are walked off the field, so the nitrate and phosphate locked in that biomass leave with them and the soil is progressively depleted. Fertilisers replace it. Natural fertilisers are organic, including manure, slurry, compost and bone meal, and the ions they contain are not immediately available because saprobionts must first digest the organic matter and release them; release is therefore slow and sustained, and the organic matter also improves soil structure and water retention. Artificial fertilisers are inorganic salts of known composition that dissolve quickly, so the ions are immediately available and the dose can be matched precisely to the crop.

Leaching is the washing of soluble ions down through the soil by rain or irrigation water, and it matters most for nitrate: every nitrate salt is soluble and nothing in the soil binds it, so it moves with the drainage water. Phosphate is an anion too, so repulsion by the negatively charged clay cannot be the difference; phosphate is fixed in place by adsorption onto, and precipitation with, iron, aluminium and calcium compounds, so it reaches water mainly on eroded soil in run-off. Leached nitrate reaches groundwater and then rivers and lakes, where it fertilises the water. Eutrophication then follows a fixed sequence. The extra nitrate and phosphate remove the limiting factor on algal growth, so algae multiply rapidly and form a surface bloom. The bloom blocks light from reaching submerged plants, which die.