Biogeochemical cycles: water, carbon, nitrogen and phosphorus – Concept of an Ecosystem (Senior 6 Biology) | Ganzaa

Concept of an Ecosystem

Lessons

Senior 6 · Biology

Concept of an Ecosystem

5 lessons

Lesson 4 of 5

Biogeochemical cycles: water, carbon, nitrogen and phosphorus

25 min

Where does a dead leaf go?

A leaf that falls on the floor of Nyungwe forest has gone within months. The carbon in it returns to the air as carbon dioxide, and its nitrogen and phosphorus return to the soil, ready for another tree. On the Rugezi wetland, by contrast, dead sedges and grasses have piled up for thousands of years as peat, because in waterlogged, oxygen-poor water the decomposers work very slowly.

Energy flows through an ecosystem once and is lost as heat (Lesson 3). Matter is different: the same atoms of carbon, nitrogen, phosphorus and water are used again and again. The pathways they follow between living things and the air, water, soil and rocks are the biogeochemical cycles.

Definition

Biogeochemical cycle: the pathway by which a chemical element or compound moves between the living (biotic) and non-living (abiotic) parts of the Earth, and back.

Reservoir (pool): a store in which an element is held, such as the atmosphere, the oceans, rocks or living biomass. Flux: the rate at which the element moves between two reservoirs.

Decomposer: an organism, mostly bacteria and fungi, that feeds saprotrophically on dead organic matter, releasing inorganic ions and carbon dioxide.

The water cycle

Water evaporates from lakes, rivers and soil, and transpires from leaves; the vapour condenses into clouds and falls as precipitation. On land, it either infiltrates into the soil and groundwater or runs off over the surface into rivers. Living things take part at every step: roots draw water up and leaves release it, so a forest returns much of its rain to the air, and its litter and roots help rain soak in rather than run off.

Nyungwe forest lies on the ridge that divides the Congo basin to the west from the Nile basin to the east, and its streams feed both. Clearing such a forest reduces infiltration and transpiration, so more rain runs off at once: floods and soil erosion in the rains, and less water in the streams in the dry season.

The carbon cycle

Carbon enters living things through photosynthesis, which turns carbon dioxide into sugars, and returns to the air through respiration by every organism, including decomposers. Figure 1 shows the main pathways.

Figure 1: The carbon cycle. Orange arrows: carbon dioxide released by respiration and combustion. Green arrow: carbon dioxide fixed by photosynthesis.

Two slow stores matter for today's climate:

Peat and fossil fuels. Where decomposers are held back by waterlogging, acidity or cold, dead matter accumulates as peat. Over millions of years, buried organic matter became coal, oil and natural gas. Burning them, or draining and burning peat, releases in years carbon that took thousands to millions of years to store.
Oceans and rocks. Carbon dioxide dissolves in water. Some is used by aquatic producers, and some is built into the calcium carbonate of shells, which can become limestone.

Figure 3 shows the result of burning fossil fuels and clearing forests faster than photosynthesis and the oceans can take the carbon back.

Figure 3: Annual mean CO₂ at Mauna Loa Observatory, every five years, 1960–2025. Data: NOAA Global Monitoring Laboratory.

Worked example 1: reading the carbon dioxide record

Use Figure 3. Calculate (a) the mean rate of increase in CO₂ concentration from 1960 to 1990 and from 2000 to 2025, and (b) the percentage increase from 1960 to 2025. (c) Suggest two reasons for the trend.

(a) 1960 to 1990: $\frac{354.45 - 316.91}{1990 - 1960} = \frac{37.54}{30} = 1.25\,\mathrm{ppm\,yr^{-1}}$ .
2000 to 2025: $\frac{427.35 - 369.71}{2025 - 2000} = \frac{57.64}{25} = 2.31\,\mathrm{ppm\,yr^{-1}}$ .
(b) $\frac{427.35 - 316.91}{316.91} \times 100 = 34.8\,\%$ (3 s.f.).
(c) The concentration is rising, and rising faster: the rate after 2000 is almost double the rate of 1960 to 1990. Reasons: the burning of more fossil fuels, which releases carbon stored for millions of years; and deforestation, which removes photosynthesis and often releases carbon by burning or decay.

Note: the monthly record also rises and falls every year. The concentration falls in the northern summer, when the large forests of the northern hemisphere photosynthesise fastest, and rises in winter, when respiration exceeds photosynthesis.

The nitrogen cycle

Nitrogen makes up 78 % of the air, but as $\mathrm{N_2}$ , whose triple bond most organisms cannot break. Plants need nitrogen as nitrate or ammonium ions to make amino acids, proteins and nucleic acids. Bacteria do almost every conversion in the cycle (Figure 2).

Figure 2: The nitrogen cycle. Nitrogen fixation (green arc): Rhizobium in the root nodules of legumes, free-living bacteria such as Azotobacter, lightning, and the Haber process.

Table 1: The steps of the nitrogen cycle

Step and change	Done by	Conditions
Nitrogen fixation $\mathrm{N_2} \rightarrow \mathrm{NH_4^+}$	Rhizobium in root nodules of legumes (beans, peas, groundnuts, soya); free-living Azotobacter; cyanobacteria; lightning; the Haber process	Needs much ATP; the enzyme nitrogenase works only without oxygen, so root nodules keep oxygen low (leghaemoglobin)
Ammonification organic N $\rightarrow \mathrm{NH_4^+}$	Saprotrophic bacteria and fungi, breaking down proteins and urea	Warm, moist soil
Nitrification $\mathrm{NH_4^+} \rightarrow \mathrm{NO_2^-} \rightarrow \mathrm{NO_3^-}$	Nitrosomonas, then Nitrobacter (chemoautotrophs)	Aerobic: needs oxygen
Assimilation $\mathrm{NO_3^-}$ or $\mathrm{NH_4^+} \rightarrow$ amino acids	Plants, by active transport into root hairs	Needs ATP from root respiration
Denitrification $\mathrm{NO_3^-} \rightarrow \mathrm{N_2}$	Denitrifying bacteria such as Pseudomonas	Anaerobic: waterlogged soil

Worked example 2: why waterlogged soil is short of nitrate

Soil samples from a drained field and from a waterlogged valley bottom nearby were analysed (illustrative data): nitrate $45\,\mathrm{mg\,kg^{-1}}$ in the drained field, $8\,\mathrm{mg\,kg^{-1}}$ in the waterlogged soil. Explain the difference.

Waterlogged soil has its air spaces filled with water, so it holds very little oxygen.
Nitrifying bacteria (Nitrosomonas, Nitrobacter) are aerobic: without oxygen they cannot oxidise ammonium to nitrate, so little nitrate is made.
Denitrifying bacteria are favoured in anaerobic conditions: they reduce the nitrate that is present to $\mathrm{N_2}$ , which escapes to the air.
Less nitrate is made and more is removed, so the waterlogged soil holds about a sixth as much ( $\frac{8}{45} = 0.18$ ).

Application: this is why farmers drain and dig heavy soils, and why ploughing, which lets air in, raises nitrate levels.

Worked example 3: the fertiliser value of a bean crop

A bean crop fixes about $60\,\mathrm{kg}$ of nitrogen per hectare (illustrative). Urea, $\mathrm{CO(NH_2)_2}$ , is a common nitrogen fertiliser. Calculate the mass of urea that contains the same mass of nitrogen. ( $A_{r}$ : C = 12, O = 16, N = 14, H = 1.)

$M_{r}$ of urea $= 12 + 16 + 2(14 + 2 \times 1) = 60$ .
Mass fraction of nitrogen $= \frac{2 \times 14}{60} = 0.467$ (46.7 %).
Mass of urea $= 60\,\mathrm{kg} \times \frac{60}{28} = 129\,\mathrm{kg}$ per hectare (3 s.f.).

Growing beans in rotation with maize or sorghum therefore saves a large amount of fertiliser, because some of the fixed nitrogen stays in the soil in the roots and crop remains.

The phosphorus cycle

Phosphorus is needed for ATP, DNA, RNA, phospholipid membranes and bones and teeth. Its cycle differs from the others in one important way: it has no gas phase. It moves only through rock, soil, water and living things:

Phosphate is released from rocks by weathering, very slowly.
Plants absorb phosphate ions ( $\mathrm{PO_4^{3-}}$ ) from the soil water; animals obtain phosphorus by feeding.
Decomposers return phosphate to the soil from dead matter, faeces and urine. Mycorrhizal fungi on roots help plants take it up.
Phosphate that washes into rivers and lakes, bound to eroded soil particles, settles in sediments. Over millions of years sediments become rock again and may be lifted up, which closes the cycle.

Because the cycle is so slow, phosphate often limits plant growth on old, weathered and acidic soils (you met this in Lesson 1). Where soil erodes from hillsides, its phosphate is lost from the farm and fertilises the lake below instead, feeding algae: the start of eutrophication, which Lesson 5 explains.

Warning

Three common mistakes

"Plants take nitrogen from the air." Plants cannot use $\mathrm{N_2}$ . Legumes gain fixed nitrogen from the Rhizobium bacteria in their nodules; all plants absorb nitrate or ammonium ions from the soil.
Mixing up nitrification and denitrification. Nitrification makes nitrate and needs oxygen; denitrification destroys nitrate and happens without oxygen.
"Decomposers only break things down." They also respire, releasing $\mathrm{CO_2}$ , and they release ammonium and phosphate: without them, nutrients would stay locked in dead matter.

CrashCourse: "Nitrogen & Phosphorus Cycles: Always Recycle! Part 2" (Crash Course Ecology #9). Watch for the role of bacteria at each step of the nitrogen cycle, and why phosphorus has no gas phase.

Tip

Memory hook for nitrification: follow the oxygen. Ammonium, $\mathrm{NH_4^+}$ , has no oxygen; nitrite, $\mathrm{NO_2^-}$ , has two; nitrate, $\mathrm{NO_3^-}$ , has three. Each step adds oxygen, so nitrification needs air. Denitrification takes the oxygen away again, so it happens where there is no air.

✦

Practice: nutrient cycles

Name the process that (a) removes carbon dioxide from the air, (b) converts ammonium ions to nitrite, (c) returns nitrogen to the air.
Explain why dead plant matter accumulates as peat in the Rugezi wetland but not on the floor of a well-drained forest.
State one way in which the phosphorus cycle differs from the carbon and nitrogen cycles, and one consequence for farmers.
The CO₂ concentration at Mauna Loa was 390.10 ppm in 2010 and 414.21 ppm in 2020. Calculate the mean annual increase over this decade, and compare it with the rate for 1960 to 1990.
Explain why a farmer might plant beans before maize on the same field.
A fertiliser is ammonium nitrate, $\mathrm{NH_4NO_3}$ . Calculate the percentage of nitrogen by mass. ( $A_{r}$ : N = 14, H = 1, O = 16.)
Predict and explain the effect of flooding a field for rice on (a) nitrification, (b) denitrification.
Evaluate the claim that "draining a peat wetland to grow crops is carbon-neutral, because crops photosynthesise."

Show answersHide answers

(a) Photosynthesis. (b) Nitrification (by Nitrosomonas). (c) Denitrification.
In waterlogged peat there is little oxygen (and the water is often acidic), so aerobic decomposers work very slowly and dead matter builds up faster than it decays. In well-drained forest soil, oxygen is plentiful, so bacteria and fungi decompose litter within months.
Phosphorus has no gas phase; it is released only slowly by rock weathering. So phosphate lost by erosion or harvest is not replaced quickly, and farmers must return it as manure, compost or fertiliser and prevent erosion.
$\frac{414.21 - 390.10}{10} = 2.41\,\mathrm{ppm\,yr^{-1}}$ , nearly double the 1960 to 1990 rate of $1.25\,\mathrm{ppm\,yr^{-1}}$ .
Beans are legumes: Rhizobium in their root nodules fixes nitrogen. When the roots and remains decompose, ammonium and then nitrate are released into the soil for the maize, so less fertiliser is needed.
$M_{r} = 2 (14) + 4 (1) + 3 (16) = 80$ ; $\frac{28}{80} \times 100 = 35\,\%$ .
(a) Nitrification decreases, because the flooded soil lacks oxygen and nitrifying bacteria are aerobic. (b) Denitrification increases, because denitrifying bacteria thrive without oxygen and convert nitrate to $\mathrm{N_2}$ .
Not valid. Draining lets oxygen into the peat, so decomposers oxidise carbon stored over thousands of years and release it as CO₂ for decades. A crop stores only a little carbon, and most of it returns to the air within a year when the crop is eaten or decays. So draining peat is a large net source of carbon dioxide.

Key points

Matter cycles between living things and the air, water, soil and rocks; decomposers are essential to every cycle.
Carbon: photosynthesis removes CO₂; respiration and combustion return it; peat and fossil fuels are slow stores. Atmospheric CO₂ rose from 316.91 ppm (1960) to 427.35 ppm (2025).
Nitrogen: fixation (N₂ → NH₄⁺), ammonification, nitrification (aerobic: NH₄⁺ → NO₂⁻ → NO₃⁻), assimilation and denitrification (anaerobic: NO₃⁻ → N₂).
Phosphorus has no gas phase; it moves slowly from rock to soil to organisms and back to sediments.

Sources and credits

8.3.4: Biogeochemical Cycles, from Biology 2e by OpenStax (Mary Ann Clark, Matthew Douglas, Jung Choi), via LibreTexts Biology, licensed under CC BY 4.0. Used for the water, carbon, nitrogen and phosphorus cycles. Adapted by Ganzaa.
Atmospheric CO₂: NOAA Global Monitoring Laboratory, Mauna Loa CO₂ annual mean data, US government work in the public domain. Values for 1960 to 2025, read on 30 September 2026.
Nyungwe National Park and Rugezi Marsh, Wikipedia contributors, licensed under CC BY-SA 4.0. Used for the Congo–Nile divide and the Rugezi peat. Adapted by Ganzaa.
Photo: Lake burera 07082024, Rogerirakoze, CC BY-SA 4.0, via Wikimedia Commons.
Video: Nitrogen & Phosphorus Cycles: Always Recycle! Part 2 - Crash Course Ecology #9, CrashCourse, embedded from YouTube.

Figures 1 to 3, Table 1, the worked examples and the practice questions are written by Ganzaa. Figure 3 is drawn from the NOAA values; the data in Worked examples 2 and 3 are illustrative.

This lesson adapts CC BY-SA material and is shared under CC BY-SA 4.0.

1Where does a dead leaf go?

2The water cycle

3The carbon cycle

4The nitrogen cycle

5The phosphorus cycle

Where does a dead leaf go?

The water cycle

The carbon cycle

The nitrogen cycle

The phosphorus cycle