Biology · 19 Organisms and their environment

19.3 Nutrient cycles

Before you start

From 19.1: energy flows through an ecosystem and leaves as heat — atoms, by contrast, are used again and again.
Photosynthesis takes in carbon dioxide and water and makes glucose; respiration does the reverse and releases carbon dioxide.
Proteins are made of amino acids, and amino acids contain nitrogen as well as carbon, hydrogen and oxygen.
Plants absorb mineral ions from the soil through their root hair cells.
Decomposers are bacteria and fungi that get their energy from dead or waste organic material.

Syllabus objectives covered (3)

Describe the carbon cycle, limited to: photosynthesis, respiration, feeding, decomposition, formation of fossil fuels and combustion
Describe the nitrogen cycle with reference to: • decomposition of plant and animal protein to ammonium ions • nitrification • nitrogen fixation by lightning and bacteria • absorption of nitrate ions by plants • production of amino acids and proteins • feeding and digestion of proteins • deamination • denitrification
State the roles of microorganisms in the nitrogen cycle, limited to: decomposition, nitrification, nitrogen fixation and denitrification (generic names of individual bacteria, e.g. Rhizobium, are not required)

Part 1 of 7

Why anything cycles at all

Energy flows through an ecosystem once and leaves as heat, so it has to be resupplied. Atoms cannot leave — the Earth does not gain new carbon or nitrogen — so the same atoms have to be used over and over. That is what a nutrient cycle is.
So every cycle question is really the same question: how does an atom get from a store (the air, the soil, an organism) into a different store, and what process moves it? Learn the processes and the direction each one moves the atom, and you can answer any version of it.
The carbon cycle is limited, in your syllabus, to six processes: photosynthesis, respiration, feeding, decomposition, formation of fossil fuels and combustion. Nothing else is required, so a good answer names these and does not wander.

Part 2 of 7

The carbon cycle: one way in, three ways out

Start with the store that everything else connects to: carbon dioxide in the air. Ask two questions about it — what takes carbon out of it, and what puts carbon back in?
Only one process takes carbon dioxide out of the air: photosynthesis. Plants and other producers absorb carbon dioxide and use it to make glucose, so carbon that was in the air is now in an organic molecule inside a plant. Learn this as the one-way-in rule; it is a common one-mark question.
Carbon moves along the food chain by feeding. When an animal eats a plant, the carbon in the plant's carbohydrates, fats and proteins becomes carbon in the animal's molecules. No carbon dioxide is involved at this step — the carbon simply changes owner.
Now the ways back into the air. The first is respiration. Every living organism — plant, animal and decomposer — respires, breaking down glucose and releasing carbon dioxide into the air.
The second is decomposition. When organisms die, and in their waste material, the carbon is still locked in organic molecules. Decomposers (bacteria and fungi) feed on this dead and waste material and respire, releasing the carbon as carbon dioxide.
Notice what decomposition actually is, because this is where answers go wrong. Decomposers are not doing something separate from respiration — they break down the dead material and respire it, and that respiration is what returns the carbon dioxide to the air.
The third route back is combustion, and it needs a detour through fossil fuels. When organisms died in conditions where decomposers could not work, they were not broken down. Over millions of years, under heat and pressure, their remains formed fossil fuels — coal, oil and natural gas.
So a fossil fuel is a store of carbon that was taken out of the cycle. It sat underground, out of circulation, for millions of years, which is exactly why burning it matters.
Combustion is the burning of fossil fuels (or of wood). It releases that stored carbon into the air as carbon dioxide, returning carbon that had been locked away.
Now say the whole cycle back to yourself in one line, in the right directions: carbon dioxide in the air → (photosynthesis) → plants → (feeding) → animals → (respiration by all of them, or death then decomposition, or fossilisation then combustion) → back to carbon dioxide in the air.
Photosynthesis is the only arrow pointing away from the air. Fix its direction and the rest follow.

Part 3 of 7

Getting the carbon-cycle directions right

Almost every lost mark in the carbon cycle is a direction error, so drill the four sentences until they are automatic.
Photosynthesis removes carbon dioxide from the air. Respiration adds carbon dioxide to the air. Combustion adds carbon dioxide to the air. Decomposition adds carbon dioxide to the air, because the decomposers respire.
The commonest single error is writing that respiration takes in carbon dioxide. It does not — that is photosynthesis. Respiration takes in oxygen and gives out carbon dioxide.
The second commonest is treating plants as though they only photosynthesise. Plants respire all the time as well, so an arrow from plants back to carbon dioxide in the air is correct and is often a mark of its own.
If you are asked to describe a route rather than the whole cycle — say, how the carbon in a leaf ends up in the air — give the sequence with a named process at every step, and offer two routes if you have marks left to earn: eaten then respired, or died then decomposed.

Part 4 of 7

The nitrogen problem

Organisms need nitrogen because proteins are made of amino acids, and every amino acid contains nitrogen. No nitrogen, no protein, no growth.
The awkward fact is that about four-fifths of the air is nitrogen gas, and almost no organism can use it. Nitrogen gas is very unreactive, so plants cannot absorb it and animals cannot use it.
So plants get their nitrogen a different way: they absorb nitrate ions from the soil, through their roots. That is the sentence to remember — nitrate ions from the soil, not nitrogen gas from the air.
Having absorbed nitrate ions, a plant uses them, with the carbohydrates it made in photosynthesis, to produce amino acids, and joins those amino acids together into proteins.
Animals cannot absorb nitrate ions either. They obtain nitrogen by feeding: they eat plant or animal protein, digest it into amino acids, absorb those amino acids, and build their own proteins from them.
So the whole nitrogen cycle is about one thing — how nitrogen gets into the soil as nitrate ions, and how it gets back out again.

Part 5 of 7

Filling the soil: decomposition, nitrification and fixation

Route one into the soil is decomposition. When plants and animals die, and in their waste, there is protein. Decomposers break down this plant and animal protein and release the nitrogen as ammonium ions in the soil.
Excretion feeds the same route. In an animal, excess amino acids cannot be stored, so in the liver they undergo deamination: the nitrogen-containing part is removed and converted to urea, which is excreted in urine. Decomposers break the urea down to ammonium ions too.
Ammonium ions are not what plants absorb, so there is one more step. Nitrifying bacteria convert ammonium ions into nitrate ions. That conversion is called nitrification, and it is the step that makes the nitrogen available to plants.
Nitrifying bacteria need oxygen, so nitrification happens in well-aerated soil. Keep that fact — it explains a lot of the application questions.
Route two into the soil is nitrogen fixation, which means converting nitrogen gas from the air into nitrogen compounds that organisms can use. It happens in two ways, and the syllabus names both.
Lightning provides enough energy to make nitrogen and oxygen in the air combine. The compounds formed dissolve in rain water and are washed into the soil, where they add to the nitrate ions available to plants.
Nitrogen-fixing bacteria do the same job biologically. Some live free in the soil; others live inside root nodules on the roots of leguminous plants such as peas, beans and clover. They convert nitrogen gas into nitrogen compounds, which reach the soil when the plant dies and is decomposed.
You are not required to know the generic names of individual bacteria — Rhizobium and the rest. Write "nitrogen-fixing bacteria", "nitrifying bacteria", "denitrifying bacteria" and "decomposers", and you have everything the syllabus asks for.

Part 6 of 7

Emptying the soil: denitrification

There is one process that takes nitrogen out of the soil and returns it to the air. Denitrifying bacteria convert nitrate ions in the soil back into nitrogen gas. That is denitrification.
Denitrifying bacteria thrive where there is little oxygen — in waterlogged soil, where water fills the air spaces between the soil particles.
Put that together with what you already know and you can explain why crops grow badly in waterlogged soil. The denitrifying bacteria are active and remove nitrate ions, while the nitrifying and nitrogen-fixing bacteria, which need oxygen, become less active, so the nitrate is not replaced.
This is also why farmers plough and drain fields: aerating the soil favours the bacteria that make nitrate and works against the bacteria that destroy it.
Denitrification is the only one of the four microbial processes that moves nitrogen backwards, away from plants. If you can remember that, you will never mix it up with nitrification.

Part 7 of 7

The four microbial jobs, stated cleanly

The syllabus asks you to state the roles of microorganisms in the nitrogen cycle, limited to four. Questions on this are usually a table to complete or a four-mark list, so learn one crisp sentence for each.
Decomposition: decomposers (bacteria and fungi) break down plant and animal protein, and urea, releasing ammonium ions into the soil.
Nitrification: nitrifying bacteria convert ammonium ions into nitrate ions, which plants can absorb.
Nitrogen fixation: nitrogen-fixing bacteria convert nitrogen gas from the air into nitrogen compounds that can be used by plants.
Denitrification: denitrifying bacteria convert nitrate ions in the soil back into nitrogen gas, which returns to the air.
Two names that sound alike do opposite things. Nitrifying bacteria make nitrate; denitrifying bacteria destroy it. The prefix "de-" means undoing, which is the whole memory trick.
And keep fixation separate from nitrification. Fixation starts from nitrogen gas in the air; nitrification starts from ammonium ions already in the soil. Naming the starting substance in your answer proves you know which is which.

Worked examples

Example 1. Describe two different routes by which a carbon atom in the leaf of a growing tree could end up as carbon dioxide in the air. (4 marks)

Show the working

The instruction "two different routes" tells you the mark split: two marks per route. Plan the two before writing, so they do not overlap.
Route one, through an animal. The leaf is eaten by a herbivore, so the carbon becomes part of the animal's molecules — that step is feeding.
Complete route one with the process that releases it. The animal respires, breaking down glucose and releasing carbon dioxide into the air.
Route two, through death. The leaf falls and dies without being eaten, so it becomes dead organic material.
Complete route two the same way, naming the organisms. Decomposers, which are bacteria and fungi, feed on the dead leaf and respire, releasing carbon dioxide into the air.
Check that each route names a process at every step. "The leaf rots" without saying that decomposers respire will not get the second mark, because rotting is the observation, not the process.

Answer: Route one: the leaf is eaten by an animal (feeding), the carbon becomes part of the animal's molecules, and the animal respires, releasing carbon dioxide into the air. Route two: the leaf dies and decomposers — bacteria and fungi — break it down and respire, releasing carbon dioxide into the air.

Example 2. A dead rabbit lies on a field of grass. Describe how the nitrogen in the rabbit's protein could become protein in a blade of grass. (5 marks)

Show the working

This is the nitrogen cycle asked as a journey. Track the substance at each stage: protein, then ammonium ions, then nitrate ions, then amino acids, then protein again. Name the process and the organism that carries out each conversion.
First conversion: decomposers, which are bacteria and fungi, break down the animal protein in the dead rabbit.
Say what that produces, because the ion is the mark: decomposition releases ammonium ions into the soil.
Second conversion: nitrifying bacteria convert the ammonium ions into nitrate ions. Name the process as nitrification if you can, but the conversion itself is what scores.
Now the plant. The grass absorbs nitrate ions from the soil through its roots — not nitrogen gas, and not ammonium ions.
Finish inside the plant. The grass uses the nitrate ions to produce amino acids, and joins the amino acids together to make proteins.

Answer: Decomposers (bacteria and fungi) break down the protein in the dead rabbit, releasing ammonium ions into the soil. Nitrifying bacteria then convert the ammonium ions into nitrate ions (nitrification). The grass absorbs the nitrate ions from the soil through its roots and uses them to produce amino acids, which are joined together to form proteins.

Example 3. A farmer finds that a field which floods every winter produces a poor crop, and that adding clover to the field improves the yield the following year. Explain both observations. (4 marks)

Show the working

Two observations, so two explanations. Deal with the flooding first, and start from what flooding does to the soil rather than to the plants.
Waterlogged soil has water in the air spaces, so it contains little oxygen — it is anaerobic. That single fact drives both halves of the flooding answer.
Denitrifying bacteria are favoured by these low-oxygen conditions, and they convert nitrate ions in the soil back into nitrogen gas, so the soil loses nitrate.
At the same time the nitrifying and nitrogen-fixing bacteria, which need oxygen, become less active, so the nitrate is not replaced. With less nitrate, the crop makes fewer amino acids and proteins, so it grows poorly.
Now the clover. Clover is a legume, and nitrogen-fixing bacteria live in the root nodules on its roots.
State what those bacteria do and how the nitrogen reaches the next crop: they convert nitrogen gas into nitrogen compounds, which enter the soil when the clover dies and is decomposed, increasing the nitrate available.

Answer: Flooding makes the soil waterlogged and low in oxygen, which favours denitrifying bacteria that convert nitrate ions back into nitrogen gas, while the nitrifying and nitrogen-fixing bacteria that need oxygen become less active, so nitrate is removed and not replaced and the crop grows poorly. Clover has root nodules containing nitrogen-fixing bacteria, which convert nitrogen gas into nitrogen compounds; these enter the soil when the clover dies and is decomposed, increasing the nitrate available to the next crop.

Where people go wrong

Mistake: Writing that respiration takes carbon dioxide out of the air.

Instead: Photosynthesis removes carbon dioxide from the air; respiration, decomposition and combustion all return it.

Getting the direction of an arrow wrong reverses the whole cycle, and it is the single most common error in this topic. Only one process takes carbon dioxide out, and three put it back.

Mistake: Showing plants only photosynthesising, with no arrow from plants back to the air.

Instead: Plants respire as well, all the time, so they release carbon dioxide too.

A plant needs to release the energy stored in its glucose just as an animal does. Examiners often award a separate mark for recognising that producers respire.

Mistake: Treating decomposition as something separate from respiration, as in "the leaf just rots away".

Instead: Decomposers feed on the dead material and respire, and it is that respiration which releases carbon dioxide.

"It rots" describes what you see, not the process. Naming the decomposers and saying that they respire is what turns the observation into a marking point.

Mistake: Saying plants absorb nitrogen gas from the air.

Instead: Plants absorb nitrate ions from the soil, through their roots.

Nitrogen gas is very unreactive and plants cannot use it directly. Only nitrogen-fixing bacteria and lightning can convert nitrogen gas into a usable form.

Mistake: Confusing nitrifying with nitrogen-fixing and denitrifying bacteria.

Instead: Nitrogen-fixing bacteria convert nitrogen gas into nitrogen compounds; nitrifying bacteria convert ammonium ions into nitrate ions; denitrifying bacteria convert nitrate ions back into nitrogen gas.

The three names look similar but describe different starting substances. Naming the substance each one starts from proves which process you mean, and "de-" always signals the one that undoes the work.

Check yourself

Name the only process in the carbon cycle that removes carbon dioxide from the air, and three processes that return it.
Answer
Removed by photosynthesis. Returned by respiration, by decomposition (decomposers respiring as they break down dead and waste material) and by combustion of fossil fuels.
How are fossil fuels formed, and why does burning them change the amount of carbon dioxide in the air?
Answer
They formed over millions of years from the remains of organisms that were not decomposed, under heat and pressure. That carbon was stored out of the cycle, so combustion returns it to the air as carbon dioxide.
By which process does carbon move from a plant into an animal, and what happens to the carbon dioxide at that step?
Answer
By feeding. No carbon dioxide is involved — the carbon simply moves from the plant's organic molecules into the animal's.
In which form do plants absorb nitrogen, from where, and what do they make with it?
Answer
As nitrate ions, absorbed from the soil through the roots, and used to produce amino acids, which are joined together to make proteins.
What is deamination, and how does the nitrogen in it get back into the soil?
Answer
Deamination is the removal of the nitrogen-containing part from excess amino acids in the liver, forming urea, which is excreted in urine. Decomposers break the urea down to ammonium ions in the soil.
State the two ways in which nitrogen gas from the air is fixed.
Answer
By lightning, which provides enough energy for nitrogen and oxygen to combine, and the compounds formed are washed into the soil by rain; and by nitrogen-fixing bacteria, which live free in the soil or in root nodules of leguminous plants.
State what nitrifying bacteria and denitrifying bacteria each do, and say which soil conditions favour each.
Answer
Nitrifying bacteria convert ammonium ions into nitrate ions and need oxygen, so they are favoured by well-aerated soil. Denitrifying bacteria convert nitrate ions into nitrogen gas and are favoured by waterlogged, low-oxygen soil.
Do you need to know the name Rhizobium for this syllabus?
Answer
No. Generic names of individual bacteria are not required — "nitrogen-fixing bacteria" is all that is expected.

Exam questions

Try each part first. Open the mark scheme after you have written your answer.

Question 1. A tree in a woodland dies and falls to the ground. Nearby, a power station burns coal.

(a) Identify the process that removes carbon dioxide from the atmosphere. 1 mark No calculator

Mark scheme

B1 photosynthesis

(b) Describe how the carbon in the dead tree is returned to the atmosphere. 3 marks No calculator

Mark scheme

B1 decomposers / bacteria and fungi feed on the dead material
B1 they break down the organic molecules in the tree (decomposition)
B1 the decomposers respire, releasing carbon dioxide into the air

(c) Explain why burning coal returns carbon to the atmosphere that has not been part of the carbon cycle for a very long time. 3 marks No calculator

Mark scheme

B1 coal is a fossil fuel, formed over millions of years from the remains of organisms that were not decomposed
B1 the carbon in those organisms was stored underground, out of circulation
B1 combustion of the coal releases this stored carbon into the air as carbon dioxide

(d) State why an arrow is drawn from the living trees back to the carbon dioxide in the air. 1 mark No calculator

Mark scheme

B1 plants respire (as well as photosynthesise), releasing carbon dioxide

Question 2. A farmer tests the soil in two fields. Field A is well drained and has been planted with clover. Field B is frequently waterlogged.

(a) State the ion that plants absorb from the soil in order to make amino acids, and the part of the plant that absorbs it. 2 marks No calculator

Mark scheme

B1 nitrate ions
B1 the roots / root hair cells

(b) Describe how the protein in a dead plant is converted into a form that another plant can absorb. 3 marks No calculator

Mark scheme

B1 decomposers / bacteria and fungi break down the protein (decomposition)
B1 ammonium ions are released into the soil
B1 nitrifying bacteria convert the ammonium ions into nitrate ions (nitrification)

(c) Explain why the soil in field B is likely to contain fewer nitrate ions than the soil in field A. 3 marks No calculator

Mark scheme

B1 waterlogged soil contains little oxygen / is anaerobic
B1 denitrifying bacteria are favoured and convert nitrate ions into nitrogen gas (denitrification)
B1 nitrifying and nitrogen-fixing bacteria need oxygen, so they are less active and the nitrate is not replaced

(d) Suggest why planting clover increases the nitrate content of the soil in field A. 2 marks No calculator

Mark scheme

B1 clover has root nodules containing nitrogen-fixing bacteria
B1 these convert nitrogen gas from the air into nitrogen compounds, which enter the soil when the plant dies and is decomposed (naming a genus is not required)

How this is examined

Describing the carbon cycle as a set of named processes with the right directions: A four- to six-mark Describe, often with a partly labelled cycle diagram to complete, or "Describe how the carbon in a dead animal becomes carbon in a new plant". One mark per correct process, each stated with its direction: "photosynthesis removes carbon dioxide from the air and it is used to make glucose"; "respiration in plants, animals and decomposers releases carbon dioxide"; "feeding transfers carbon from plants to animals"; "decomposers break down dead material and respire, releasing carbon dioxide"; "combustion of fossil fuels releases carbon dioxide". A reversed direction cannot score.
The sequence protein to ammonium ions to nitrate ions to amino acids: A four- or five-mark Describe: "Describe how the nitrogen in a dead plant becomes protein in another plant." The named ion at each stage is the mark, so write "decomposers break down the protein, releasing ammonium ions", then "nitrifying bacteria convert ammonium ions to nitrate ions (nitrification)", then "the plant absorbs nitrate ions from the soil through its roots", then "the nitrate ions are used to make amino acids, which are joined to form proteins". Saying "nitrogen" where you mean "nitrate ions" loses the mark.
The four roles of microorganisms in the nitrogen cycle: A four-mark State, very often set as a table with the process named and the role left blank, or the reverse. One sentence each, each naming the substance converted: decomposition — decomposers break down protein and urea to ammonium ions; nitrification — nitrifying bacteria convert ammonium ions to nitrate ions; nitrogen fixation — nitrogen-fixing bacteria convert nitrogen gas to nitrogen compounds; denitrification — denitrifying bacteria convert nitrate ions to nitrogen gas. No credit is needed for naming a genus.
Why waterlogged soil gives poor crop growth: A three-mark Explain applying the nitrogen cycle to farming, often with data on crop yield or soil nitrate. "Waterlogged soil contains little oxygen / is anaerobic", then "denitrifying bacteria convert nitrate ions to nitrogen gas", then "nitrifying and nitrogen-fixing bacteria need oxygen so are less active, so nitrate is not replaced". A final link — less nitrate means fewer amino acids and proteins, so less growth — is often the fourth mark if there is one.
Fossil fuels as carbon taken out of the cycle, and combustion putting it back: A two- or three-mark Explain, usually the last part of a carbon-cycle question. "Fossil fuels formed from the remains of organisms that were not decomposed, over millions of years" plus "the carbon was stored and taken out of the cycle" plus "combustion releases it into the air as carbon dioxide". The mark is for recognising that this carbon had been locked away, not merely that burning makes carbon dioxide.

Words to know

Decomposition: The breakdown of dead organisms and waste material by decomposers, releasing carbon dioxide through their respiration and ammonium ions into the soil.
Combustion: The burning of a fuel. Burning fossil fuels releases carbon dioxide that had been stored out of the carbon cycle for millions of years.
Fossil fuel: Coal, oil or natural gas, formed over millions of years from the remains of organisms that were not decomposed.
Nitrogen fixation: The conversion of nitrogen gas from the air into nitrogen compounds that organisms can use, carried out by lightning and by nitrogen-fixing bacteria.
Nitrification: The conversion of ammonium ions in the soil into nitrate ions by nitrifying bacteria, which need oxygen.
Denitrification: The conversion of nitrate ions in the soil back into nitrogen gas by denitrifying bacteria, favoured by waterlogged, low-oxygen soil.
Deamination: The removal of the nitrogen-containing part of excess amino acids in the liver, forming urea, which is excreted in urine.

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