Nutrient cycles

In a nutshell

Living things constantly pull nitrogen and phosphorus out of their surroundings to build proteins, nucleic acids (DNA and RNA), ATP and phospholipids. If nothing ever put those elements back, the supply would run out.

Nutrient cycles are how nitrogen and phosphorus are recycled within an ecosystem, passing between the non-living environment, producers, consumers and decomposers, over and over.

This note covers the nitrogen cycle and the phosphorus cycle, the microorganisms (bacteria and fungi) that drive them, and the trade-offs of adding fertilisers to replace the nutrients that harvesting removes.

Assumed knowledge: Proteins, Nucleic acids and ATP, so you know why organisms need nitrogen and phosphorus at all.

Core content

The big picture: nutrients are recycled

Nutrients are recycled within natural ecosystems. A single nitrogen or phosphorus atom moves out of the soil or air, into a plant, along a food chain, and eventually back to the soil, then round again.

Microorganisms make the recycling happen. Groups of bacteria, and decomposer fungi, carry out the conversions that shift nitrogen and phosphorus between their inorganic forms (ions in soil, or nitrogen gas in air) and their organic forms (locked inside living things).

AQA tests the nitrogen cycle in the most detail. The trick is to learn it as four bacterial jobs, plus the plant taking up nitrate:

• Ammonification (saprobionts) puts nitrogen back into the soil as ammonium ions.
• Nitrification (nitrifying bacteria) upgrades ammonium to nitrate.
• Nitrogen fixation (nitrogen-fixing bacteria) pulls nitrogen gas out of the air into ammonia.
• Denitrification (denitrifying bacteria) loses nitrate back to the air as nitrogen gas.

Saprobionts and ammonification

When organisms die, and in their waste (urea and faeces), nitrogen is trapped inside organic molecules: proteins, amino acids and nucleic acids. That nitrogen has to be released before anything else can use it.

Saprobionts are the decomposer microorganisms (bacteria and fungi) that release it. A saprobiont feeds by saprobiotic nutrition:

• it secretes enzymes onto the dead material and digests it outside its body (extracellular digestion), then
• it absorbs the soluble products.

Ammonification is the production of ammonium ions from nitrogen-containing organic compounds (such as proteins and nucleic acids) by saprobionts. This returns nitrogen to the soil as the ammonium ion, NH₄⁺.

Note the wording examiners want: name a specific nitrogen-containing compound (protein, amino acids, DNA), not just "dead matter", and name saprobionts, not "decomposers".

Nitrification

Nitrification is the oxidation of ammonium ions to nitrate ions by nitrifying bacteria, and it happens in two separate steps:

1. ammonium ions (NH₄⁺) are oxidised to nitrite ions (NO₂^-);
2. nitrite ions are oxidised to nitrate ions (NO₃^-).

Both steps are oxidations, so nitrifying bacteria need oxygen. Nitrification therefore only happens well in well-aerated soil. This is why farmers plough and drain fields: adding oxygen speeds up nitrification and slows denitrification, so more nitrate is available to crops.

Plants absorb nitrate ions (by active transport) and use them to make amino acids, proteins and nucleic acids. Animals then get their nitrogen by eating plants or other animals.

Nitrogen fixation

Nitrogen fixation is the reduction of nitrogen gas to ammonia (and ammonium ions) by nitrogen-fixing bacteria. It is how new nitrogen enters the living world from the atmosphere.

Two groups do it:

• Free-living nitrogen-fixing bacteria in the soil.
• Mutualistic nitrogen-fixing bacteria in the root nodules of leguminous plants (peas, beans, clover). The bacteria fix nitrogen the plant can use; in return the plant supplies them with carbohydrates from photosynthesis. Both partners benefit, so the relationship is mutualistic.

Because legumes carry their own nitrogen supply, they grow well in nitrogen-poor soil, which is why farmers grow them in crop rotation.

Still don't get it? · keeping the four nitrogen processes straight

Forget the biology names for a second. Think of nitrogen as money, and picture three places it can sit: a locked vault (nitrogen gas in the air, which nothing can spend), a wallet (ammonium in the soil), and a bank account (nitrate in the soil, the form plants prefer to draw on).

Now the four jobs are just money moving between those places:

• Fixation cracks the locked vault open and puts cash in the wallet. Air nitrogen becomes ammonium. Only special bacteria have the key.
• Ammonification empties a dead body's pockets back into the wallet. The nitrogen in dead protein becomes ammonium again, done by saprobionts.
• Nitrification pays the wallet cash into the bank account. Ammonium becomes nitrate. It needs oxygen, like a bank that is only open in good weather (well-aerated soil).
• Denitrification is money leaking back into the locked vault and lost. Nitrate becomes nitrogen gas. It happens when the soil is waterlogged and airless.

Back to the exam words: fixation is the reduction of nitrogen gas to ammonia by nitrogen-fixing bacteria; ammonification is organic nitrogen to ammonium ions by saprobionts; nitrification is the oxidation of ammonium to nitrite to nitrate by nitrifying bacteria; denitrification is nitrate to nitrogen gas by denitrifying bacteria in anaerobic conditions. Mix up "nitrifying" and "nitrogen-fixing" and you lose the mark, so anchor each name to where the money is going.

Denitrification

Denitrification is the conversion of nitrate ions to nitrogen gas by denitrifying bacteria. These bacteria are anaerobic, so they thrive in waterlogged, oxygen-poor soil.

Denitrification removes nitrate from the soil, so it reduces the nitrogen available to plants. Good drainage limits it.

Mycorrhizae

Mycorrhizae are mutualistic associations between certain fungi and the roots of plants.

• The fungus grows a web of fine threads (hyphae) around and into the root.
• The hyphae hugely increase the surface area for absorption, acting like an extension of the root system.
• This facilitates the uptake of water and inorganic ions (especially phosphate, and also nitrate) by the plant, which matters most in nutrient-poor soil.
• In return, the plant gives the fungus carbohydrates (sugars from photosynthesis).

The phosphorus cycle

Phosphorus behaves very differently from nitrogen: it has no gaseous phase. There is essentially no phosphorus in the air, so the whole cycle runs through rock, soil, water and living things. Phosphorus is held and moved as the phosphate ion, PO₄^3-.

The stages:

1. Weathering of phosphate-containing rock slowly releases phosphate ions into the soil and water.
2. Plants absorb phosphate ions from the soil (by active transport) and build them into DNA, RNA, ATP and phospholipids. Mycorrhizae help this uptake.
3. Animals get phosphorus by feeding on plants or other animals.
4. Death and excretion return organic phosphate to the soil, where saprobionts decompose it and release phosphate ions again.
5. In water, dissolved phosphate can settle as sediment and, over very long timescales, form new rock. This return is extremely slow.

Fertilisers: replacing what harvesting removes

In a natural ecosystem the nutrients in a dead plant return to the same soil. On a farm they do not: when a crop is harvested, or livestock are removed, the nitrogen and phosphorus locked in that biomass leaves the field for good. The soil steadily loses nitrate and phosphate.

Fertilisers replace the nitrates and phosphates lost by harvesting plants and removing livestock, raising the mineral ion content of the soil so crops grow faster (higher net primary productivity). There are two types:

Environmental issues: leaching and eutrophication

Leaching is the washing of soluble ions (especially nitrate) out of the soil, into rivers and lakes, by rainwater. Nitrate ions are very soluble and are not held by the soil, so they leach readily, more so from artificial fertiliser applied in excess. Leached nitrate can pollute drinking water, and it triggers eutrophication.

Eutrophication is what happens when those mineral ions enrich a body of water. It is a chain of events, and the key exam point is that the fish are not poisoned: they suffocate.

1. Leached nitrate (and phosphate) enriches the water.
2. Algae grow rapidly at the surface: an algal bloom.
3. The bloom blocks light from reaching plants below.
4. Those plants cannot photosynthesise, so they die.
5. Saprobiotic microorganisms decompose the dead plants and algae and increase in number.
6. These decomposers respire aerobically, using up the dissolved oxygen.
7. The oxygen concentration falls, so fish and other aerobic organisms die (no oxygen for respiration). Biodiversity drops.

The inverse relationship between the bloom and the oxygen is the whole story:

Still don't get it? · why eutrophication kills fish

Imagine a pond with a thick green blanket of algae floating on top. It is tempting to think the algae, or the fertiliser, poison the fish. They do not. The killer is a lack of oxygen, and the real culprits are the decomposers.

Build it up one step at a time. Extra nitrate is basically fertiliser for algae, so the algae explode in number and form a mat over the surface. That mat is like pulling a blanket over a window: the plants living deeper down are now in the dark, so they stop photosynthesising and die. Dead plants and dead algae are food for decomposer microorganisms, which multiply. Like any living thing, those decomposers respire, and aerobic respiration uses up oxygen. There are now huge numbers of them, all pulling oxygen out of the water at once. The dissolved oxygen crashes, and fish, which need oxygen to respire, suffocate.

For the marks, say it in this order: nitrate leached in, algal bloom, light blocked, plants die, saprobiotic microorganisms decompose them and increase, they respire and use up the oxygen, oxygen concentration falls, fish die from lack of oxygen for respiration. Naming saprobionts (not just "decomposers") and pinning the death on oxygen (not toxicity or lack of food) is what separates a full-mark answer from a half one.

Worked examples

Model 5-mark answer: "Describe how nitrogen in a dead animal's protein is converted into nitrate in the soil."

A 5-mark "describe" needs five distinct, ordered points. Notice the answer never says "decomposers" and always names the microorganism and the compound:

1. Saprobionts (saprobiotic microorganisms) break down the protein / amino acids in the dead animal.
2. They carry out extracellular digestion, secreting enzymes and absorbing the products.
3. This produces ammonium ions (ammonification).
4. Nitrifying bacteria then oxidise the ammonium ions to nitrite, and then nitrite to nitrate (nitrification).
5. These steps require oxygen (they are oxidations).

Model 5-mark answer: "Explain how leaching of fertiliser can lead to the death of fish in a lake."

A causal-chain question: each link must be stated in order, and the final cause must be oxygen.

1. Nitrate ions are leached from the soil into the lake, enriching the water.
2. Algae grow rapidly and form an algal bloom at the surface.
3. The bloom blocks light, so plants below cannot photosynthesise and die.
4. Saprobiotic microorganisms decompose the dead material and increase in number.
5. Their aerobic respiration uses up the oxygen, the oxygen concentration falls, and fish die from lack of oxygen for respiration.

Common exam mistakes

• Confusing nitrifying and nitrogen-fixing bacteria. This is the single most common slip on this topic. Nitrogen-fixing bacteria turn nitrogen gas into ammonia; nitrifying bacteria turn ammonium into nitrate. Learn the two names as opposites.
• Saying nitrogen-fixing bacteria produce nitrate. They produce ammonia / ammonium ions, not nitrate. Nitrate is made later, by nitrifying bacteria.
• Saying root-nodule bacteria give the plant protein or amino acids. They supply ammonia / a usable nitrogen source; the plant makes its own amino acids and protein from it.
• Writing "decomposers" instead of "saprobionts". AQA credits saprobionts / saprobiotic; "decomposers" is often treated as neutral and may not earn the mark.
• Not naming a nitrogen-containing compound in ammonification. Answers that say "dead matter" or "faeces" lose the mark; you must name protein, amino acids, nucleic acids (DNA/RNA) or urea.
• Forgetting nitrification is two steps. It is ammonium to nitrite, then nitrite to nitrate. Skipping the nitrite step loses a mark.
• Bringing in lightning or the Haber process. Only biological fixation by bacteria is on the AQA specification; industrial or atmospheric fixation earns nothing.
• Giving phosphorus a gaseous phase. There is no atmospheric phosphorus. Do not describe phosphorus moving through the air.
• Thinking dying plants add lots of "new" phosphate or nitrate. Decomposition only returns the nutrients the plant took from the soil; it does not create extra. On a farm, harvesting removes those nutrients, which is why fertiliser is needed.
• Saying nitrate "poisons" fish in eutrophication. Fish die from lack of oxygen, because saprobionts using up the oxygen, not from toxicity, and not from lack of food.
• Saying algae "feed on" the nitrate. Algae are producers: they absorb the ions and grow / photosynthesise. Also remember to mention that light is blocked and plants die, not just that oxygen falls.

Key definitions

• Saprobiont (saprobiotic nutrition): a microorganism that feeds on dead organisms and organic waste by secreting enzymes onto the material and absorbing the soluble products of this extracellular digestion.
• Ammonification: the production of ammonium ions from nitrogen-containing organic compounds (such as proteins and nucleic acids) by saprobionts.
• Nitrification: the oxidation of ammonium ions to nitrite ions, and then to nitrate ions, by nitrifying bacteria (in aerobic conditions).
• Nitrogen fixation: the reduction of nitrogen gas to ammonia (ammonium ions) by nitrogen-fixing bacteria.
• Denitrification: the conversion of nitrate ions to nitrogen gas by denitrifying bacteria, in anaerobic (waterlogged) conditions.
• Mycorrhizae: mutualistic associations between fungi and the roots of plants that increase the plant's uptake of water and inorganic ions (such as phosphate).
• Leaching: the washing of soluble ions (especially nitrate) out of the soil and into watercourses by water.
• Eutrophication: the enrichment of water by mineral ions (such as nitrate), which causes an algal bloom, the blocking of light and the death of organisms as decomposers deplete the dissolved oxygen.

Specification

• I can state that nutrients are recycled within natural ecosystems, using the nitrogen and phosphorus cycles as examples, and that microorganisms recycle nitrogen and phosphorus.
• I can explain the role of saprobionts in decomposition (saprobiotic nutrition and extracellular digestion).
• I can explain the role of mycorrhizae in facilitating the uptake of water and inorganic ions by plants.
• I can describe the roles of bacteria in the nitrogen cycle in enough detail to illustrate saprobiotic nutrition, ammonification, nitrification, nitrogen fixation and denitrification (species names not required).
• I can explain the use of natural and artificial fertilisers to replace the nitrates and phosphates lost by harvesting plants and removing livestock.
• I can explain the environmental issues arising from fertiliser use, including leaching and eutrophication.

Related notes

• Photosynthesis: where producers fix the energy that builds the biomass whose nutrients are recycled here.
• Respiration: the process saprobionts and denitrifying bacteria use, and the oxygen demand behind eutrophication.
• Energy and ecosystems: how energy (unlike matter) flows through and is lost from an ecosystem rather than cycled.