Nutrient cycles: nitrogen, phosphorus and eutrophication

Why nitrogen limits growth

Nitrogen is in every amino acid, so it is in every protein and every enzyme; in every nucleotide, so it is in DNA, RNA, ATP, NAD and NADP; and in the ring at the centre of chlorophyll. A plant short of nitrogen shows it as stunted growth and yellowing older leaves.

Nitrogen is also the commonest gas in the air, at about 78 per cent, and it is unavailable to plants and animals: the two atoms in N₂ are held by a triple bond that requires a great deal of energy to break, and neither plants nor animals have the enzyme to do it. A plant therefore takes its nitrogen from the soil, as nitrate ions absorbed by active transport into the root hairs, and to a lesser extent as ammonium. Four groups of microorganisms carry out the conversions that keep nitrate available in the soil.

Processes in the nitrogen cycle

Nitrogen fixation and nitrification are distinct processes with similar names. Fixation starts with nitrogen gas; nitrification starts with ammonium already dissolved in the soil.

Describe the drawing

The nitrogen cycle laid out as a horizontal ladder instead of a ring. Along the top, four boxes: nitrogen gas in the air, reduced to ammonium ions, then oxidised to nitrite, then nitrate, joined by arrows. The first arrow is labelled nitrogen fixation; the second and third are the two oxidation steps of nitrification, bracketed together and named with the bacteria that carry them out. Below the ladder, nitrate is taken into plant protein, passed to animals by eating and passed on again to dead remains and waste, from which ammonification returns it to the ammonium box. A long arrow round the bottom returns nitrate to the air as denitrification. The four bacterial processes are the only labels drawn in the same warm colour.

Nitrogen fixation. Nitrogen gas is reduced to ammonia, which picks up a hydrogen ion in the soil to become ammonium. The enzyme, nitrogenase, is highly oxygen-sensitive, and nitrogen-fixing organisms use several mechanisms to protect it, which determines where fixation occurs. Rhizobium lives inside nodules on the roots of legumes such as peas, beans and clover, in a mutualistic relationship: the plant supplies carbohydrate and a protein, leghaemoglobin, that mops up oxygen, and the bacterium supplies fixed nitrogen. Free-living fixers include Azotobacter in soil and cyanobacteria in water and flooded rice fields. Lightning fixes a little, and the Haber process fixes an industrial quantity.

Ammonification. Saprobiotic bacteria and fungi break down the nitrogen-containing compounds in dead organisms, faeces and urine, releasing ammonium into the soil: proteins are hydrolysed to amino acids and deaminated, urea is hydrolysed by urease. Nothing here comes from the air. Ammonification returns nitrogen that was already in the ecosystem.

Nitrification. Two oxidations, one after the other, carried out by two different genera. Nitrosomonas oxidises ammonium to nitrite; Nitrobacter oxidises nitrite to nitrate. Both are chemoautotrophs, using the energy released by these oxidations to fix carbon dioxide, and both need oxygen, because oxygen is what they are oxidising with. Nitrification is the process that produces the ion plants actually take up in quantity.

Denitrification. In soil with no oxygen in it, certain bacteria such as Pseudomonas respire using nitrate as the final electron acceptor in place of oxygen. The nitrogen ends up as nitrogen gas and leaves the soil. This is the only one of the four that returns nitrogen to the atmosphere, and the only one that requires oxygen to be absent. It is not the only way nitrogen leaves an ecosystem, though: leaching and the removal of crops carry it out too, as the fertiliser section below shows.

Three points separate the terms. Fixation combines nitrogen from the air with hydrogen, and it is the only route from the atmosphere into the soil. Nitrification starts and finishes with ions already in the soil, ammonium and nitrate. De-nitrification is the only route back to the atmosphere.

Oxygen accounts for two agricultural practices and fixation for a third. Ploughing and draining keep the soil aerated, favouring nitrification and suppressing denitrification, so nitrate builds up; compacted or waterlogged soil does the reverse and loses nitrogen as gas; and planting clover or beans in a rotation brings Rhizobium with them, adding fixed nitrogen without a bag of fertiliser.

The decomposers, and the fungi that trade with roots

Ammonification is done by saprobionts: organisms that feed on dead material by secreting enzymes onto it, digesting it outside themselves and absorbing the products. That extracellular digestion produces a zone of softened tissue around the hyphae in a rotting log. Without it, the nitrogen in dead organisms would not be returned to the soil.

Mycorrhizae are a separate association. A mycorrhiza is a mutualistic association between a fungus and a plant root: the fungal hyphae are far finer than root hairs and spread through a much larger volume of soil, greatly increasing the surface area available for absorbing water and mineral ions, and phosphate especially, which moves through soil very slowly. In return the fungus receives organic compounds the plant has made by photosynthesis. Mycorrhizae are named explicitly in AQA 7402's nutrient cycles content, and a plant with them typically takes up phosphate several times faster than one without.

Saprobiont

An organism that obtains its energy from dead material by secreting enzymes onto it and absorbing the soluble products.

Mycorrhiza

A mutualistic association between a fungus and a plant root, in which the fungus increases the surface area for absorbing water and mineral ions and receives organic compounds in return.

Phosphorus: the cycle with no gas in it

Phosphorus is in the phosphate groups of ATP, in the backbone of DNA and RNA, and in every phospholipid in every membrane. Plants take it up as phosphate ions from the soil solution, and animals get it by eating plants.

Describe the drawing

The phosphorus cycle drawn as a loop of four stores with a fifth hanging below it. Phosphate in rock is weathered into phosphate ions in the soil solution; those are taken up by plant roots and passed into animals; death and excretion move the phosphate into dead matter, where decomposers release it back to the soil. A separate pair of arrows leaves the loop: phosphate washed out to sea settles as sediment, and returns to rock only through geological uplift over millions of years. A note in the middle points out that no step in the cycle passes through a gas.

The structural difference from nitrogen is that no stage of the phosphorus cycle is gaseous. Phosphate has no volatile form under ordinary conditions, so the atmosphere plays no part, and the reservoir is rock rather than air. Phosphate is released from rock by weathering, dissolves in the soil solution, is taken into plants, passes into animals, and is returned to the soil by decomposers acting on dead material, urine and faeces.

Two consequences follow. The cycle is slow: the geological return, from sediment on the sea bed back to rock through uplift, takes millions of years, so phosphate washed into the ocean is lost from the land on any human timescale, and rock phosphate mined for fertiliser is a finite deposit. And phosphate is often the limiting nutrient in fresh water and on old, heavily weathered soils, precisely because there is no atmospheric source to top it up.

Bacteria matter here too, in one role rather than four: they decompose organic phosphorus compounds and release phosphate back into the soil. Mycorrhizal fungi then do much of the work of getting it into roots.

Exam-board note. AQA 7402 names the phosphorus cycle and requires the role of microorganisms in it. OCR Biology A H420 covers recycling through carbon and nitrogen. Cambridge International 9700 covers ecosystems, niche and the measurement of biodiversity.

Fertiliser loss and eutrophication

Every harvest removes nitrogen and phosphorus from a field in the crop. In an unharvested ecosystem the dead plant material decomposes in place and the nutrients return to the soil; in agriculture they are removed with the crop and must be replaced.

Natural fertilisers such as manure, slurry, compost and sewage sludge are organic matter, so their nitrogen is locked in protein and must be ammonified and then nitrified before a plant can use it. It becomes available slowly, over weeks, and the organic matter improves soil structure. The drawbacks are bulk and unknown composition. Artificial fertilisers are inorganic salts of known composition, whose nitrate is immediately available to the crop and equally available to be washed out of the soil by rain before the crop takes it up.

Leaching is what follows. Nitrate ions are very soluble and carry a negative charge, and clay particles and humus in soil also carry a net negative charge, so nitrate is not held and washes down through the soil with the rain into groundwater and streams. Ammonium, being positive, is held far more strongly, which is one reason it leaches less. Phosphate is much less soluble and travels mainly attached to eroded soil particles rather than in solution, so it reaches watercourses mostly when bare soil is washed off a field.

Eutrophication as a sequence

Eutrophication is nutrient enrichment of a body of water. It occurs naturally over centuries as lakes accumulate sediment; fertiliser runoff and treated sewage can produce the same enrichment within a season. The sequence below runs in order, and the oxygen is removed at step five.

Describe the drawing

Six stages of eutrophication animated over the same stretch of river. First, granules of fertiliser are spread on the bank while the water is clear, rooted plants stand on the bed, fish swim, and a bar at the top showing dissolved oxygen is full. Arrows then carry the fertiliser down through the soil into the water. A dense layer of algae spreads across the surface, and the oxygen bar has not moved. The rooted plants below the mat lose their light and die back to stumps. A swarm of bacteria fills the water as the dead material is decomposed, and the oxygen bar drops by half. In the last stage the swarm is denser still, the bar is empty and the fish are floating upside down.

One. Nitrate leaches off the land into the water, or phosphate arrives with eroded soil and treated sewage. In fresh water the nutrient in shortest supply is usually phosphate; in estuaries and coastal water it is usually nitrogen. Either way, the factor limiting the algae has just been relieved.

Two. Algae and cyanobacteria at the surface multiply rapidly in an algal bloom, because they already had light, carbon dioxide and warmth and now have the nutrient too.

Three. The bloom forms a dense mat and blocks the light. Submerged rooted plants and deeper algae are shaded, so photosynthesis falls below respiration and they die.

Four. Those dead plants, and the bloom itself once it exhausts the nutrient and dies back, are a vast supply of dead organic matter. Saprobiotic bacteria feed on it and their population grows enormously.

Five. Those bacteria respire aerobically, and this is the step at which oxygen is removed: they take dissolved oxygen out of the water faster than it can dissolve back in from the air, so the biochemical oxygen demand rises sharply and the dissolved oxygen concentration falls.

Six. Fish and invertebrates needing well-oxygenated water suffocate. Trout and the nymphs of mayflies and stoneflies go first; tolerant bloodworms and Tubifex worms survive and may become abundant, which is why stream invertebrates are used as indicator species. If the oxygen falls far enough, anaerobic bacteria take over and the water smells of hydrogen sulfide.

Two refinements follow. The algae themselves photosynthesise and release oxygen by day but only respire at night, so a living bloom makes the oxygen rise and fall between day and night; the large, sustained fall comes once the bloom dies and bacteria decompose it. And a mass mortality of fish is usually reported as sudden, because dissolved oxygen can fall past a lethal threshold within hours after weeks of change that is not visible at the surface.

The remedies follow the chain rather than the symptom: buffer strips of uncultivated land between field and watercourse; fertiliser applied in spring onto a growing crop rather than in autumn onto bare soil; soil tested first so that only what the crop needs is applied; and phosphate stripped at sewage works, since phosphate is usually the limiting nutrient in fresh water.