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Nitrogen, phosphorus and the trouble with fertiliser

Energy passes through an ecosystem once and leaves as heat. Atoms do not: the same nitrogen has been in and out of living things many times, and four groups of bacteria do the moving. Get those four straight — which one starts in the air, which one needs oxygen, which one destroys the supply — and the rest of this topic, eutrophication included, follows from them.

Before this Proteins and the amino acid · Nucleotides and ATP · Aerobic respiration and the electron transport chain · Gross and net primary productivity

What you should be able to do

• Explain why plants cannot use nitrogen gas and must take up nitrate instead.
• Name the four bacterial processes of the nitrogen cycle and state what each converts into what.
• Say which of the four need oxygen and which needs its absence, and use that to explain a farming practice.
• Describe the phosphorus cycle and explain why it has no gaseous stage.
• Set out eutrophication as a sequence of consequences and identify the step that actually removes the oxygen.
• Calculate the nitrogen applied to a field from the mass of fertiliser, and estimate what leaches from it.

Why nitrogen is worth four bacteria

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 almost nothing can touch it: the two atoms in N₂ are held by a triple bond that takes a great deal of energy to break, and no plant or animal can do it. So a plant standing in an atmosphere four fifths made of the element it is short of takes its nitrogen from the soil instead, as nitrate ions absorbed by active transport into the root hairs, and to a lesser extent as ammonium. Four groups of prokaryotes fill that gap, and they are the reason a soil holds nitrate at all.

Four processes, and how to stop muddling them

More marks are lost here than anywhere else in ecology, and almost always to the same slip: writing 'nitrification' where the answer is 'nitrogen fixation'. The words look alike and the processes have nothing in common. Fixation starts with a gas; nitrification starts with something already dissolved in the soil.

Nitrogen fixation. Nitrogen gas is reduced to ammonia, which picks up a hydrogen ion in the soil to become ammonium. The enzyme, nitrogenase, is destroyed by oxygen, and that shapes where fixation happens. Rhizobium lives inside nodules on the roots of legumes — peas, beans, 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 — they use 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 takes nitrogen out of the ecosystem, and the only one that requires oxygen to be absent.

Three hooks keep the four apart under pressure. Fix means fasten: fixation fastens nitrogen from the air onto hydrogen, and it is the only way in. Nitrification has 'nitrite' and 'nitrate' inside the word, and both its start and its finish are already in the soil. De-nitrification undoes the lot and is the only way out.

The oxygen column explains three things a farmer does. 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 is why a rotting log has a soft wet zone around the fungus rather than a bite taken out of it, and without it every atom of nitrogen would end up locked in corpses.

Mycorrhizae are a different arrangement and a commonly confused one. 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 — 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.

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.

That has two consequences examiners like. 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.

One board difference is worth knowing. AQA 7402 names the phosphorus cycle and expects the role of microorganisms in it; OCR A H420 builds its recycling content round carbon and nitrogen; Cambridge 9700's A-level ecology leans towards ecosystems, niche and the measurement of biodiversity. Find out which you are sitting before deciding how much of this section to memorise.

Fertiliser, leaching and what happens downstream

Every harvest removes nitrogen and phosphorus from a field in the crop. In a natural ecosystem the dead plant would rot where it fell and the nutrients would return; agriculture breaks that loop on purpose and has to close it artificially.

Natural fertilisers — manure, slurry, compost, 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 — which is the point of them — and immediately available to the next rainstorm, which is the problem with them.

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, one consequence at a time

Eutrophication means nutrient enrichment of a body of water. It happens naturally over centuries as lakes silt up; fertiliser runoff and treated sewage compress that into a season. Running the chain in order is the difference between a two-mark answer and a six-mark one.

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 — 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 that does the killing: 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, mayfly and stonefly nymphs 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 are worth carrying into an exam. The algae themselves photosynthesise and release oxygen by day, so the bloom is not the thing removing it; the depletion is worst at night and worst of all once the bloom dies. And a fish kill is usually reported as sudden, because dissolved oxygen can fall past a lethal threshold in hours after weeks of nothing visible happening.

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.

In the exam

• Never write 'nitrification' for the conversion of nitrogen gas. Fixation is the only process that starts in the atmosphere, and denitrification is the only one that ends there.
• Name the organism where you can — Rhizobium, Nitrosomonas, Nitrobacter, saprobiotic bacteria and fungi. Boards differ on whether the genus is required, and it is never wrong.
• For any question about waterlogged, compacted or ploughed soil, reach for oxygen: nitrification needs it, denitrification needs it gone.
• In eutrophication, get the bacteria into the answer. 'The algae use up the oxygen' is the commonest wrong answer in the whole topic; the oxygen is used by decomposing bacteria respiring.
• Say what is blocked and what dies as a result. Light blocked by the mat, plants below die, bacteria decompose them — three separate marking points and each needs its own clause.
• Plants absorb nitrogen as nitrate, by active transport. Neither half of that sentence is optional in a mark scheme.
• The phosphorus cycle has no gaseous stage. If a question asks how it differs from the nitrogen cycle, that is the answer, with the slowness of the rock reservoir as the follow-up.

Questions

Written to the command words the boards use. Try them on paper before opening a scheme: the marks go to points made, not to length.

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