2.3 Biogeochemical Cycles

Since 1990, skeletal cores drilled from more than 300 Great Barrier Reef coral colonies show calcification rates have fallen by 14.2%, a decline unprecedented in at least the past 400 years of coral growth records.

Warmer water and bleaching are the reef's best-known threats. This particular decline has a different, quieter cause. What is it?

The Great Barrier Reef and ocean acidification

Global average surface ocean pH has dropped from about 8.2 pre-industrial to about 8.1 today, roughly a 30% increase in acidity on the logarithmic pH scale.
A 2009 study in Science (De'ath, Lough and Fabricius) examined 328 Porites coral colonies across 69 Great Barrier Reef locations and found calcification had declined 14.2% since 1990.
A separate ten-year monitoring record (2009-2019) on the Great Barrier Reef continental shelf recorded steadily rising seawater CO₂ and steadily falling pH and aragonite saturation, the direct chemical measure of how easily corals can calcify.
Acidification does not act alone: it compounds with the thermal stress that causes coral bleaching, but works through an entirely separate chemical pathway.

Sources: De'ath, G., Lough, J.M. and Fabricius, K.E. (2009) "Declining Coral Calcification on the Great Barrier Reef," Science; Great Barrier Reef Marine Park Authority, Outlook Report 2024; Scientific Reports (2020), "Progressive seawater acidification on the Great Barrier Reef continental shelf."

Coral and reef fish on the Great Barrier Reef off Queensland, Australia, the world's largest coral reef system. Rising dissolved CO₂ is making it progressively harder for corals like these to build calcium carbonate skeletons.

2.3.1

Why biogeochemical cycles matter

Biogeochemical cycles ensure that chemical elements essential to life, carbon, nitrogen, phosphorus and others, continue to be available to living organisms rather than being permanently locked away. Human activity can disrupt these cycles, and disrupting them can directly threaten the sustainability of entire ecosystems.

2.3.2

Stores, sinks and sources

Every biogeochemical cycle can be described using three terms. A store (storage) is in equilibrium with its surroundings: what enters roughly balances what leaves. A sink indicates a net accumulation of the element, absorbing more than it releases. A source indicates a net release, releasing more than it absorbs.

🔗Linking across the ESS course

Store, sink and source are just a more specific vocabulary for the storages and flows introduced generally back in 1.2. Every biogeochemical cycle is, underneath the specific chemistry, a system of storages connected by flows.

2.3.3

Carbon stores

Carbon exists in both organic and inorganic stores. Organic stores include living organisms, crude oil and natural gas. Inorganic stores include the atmosphere, soils and oceans. A store is in equilibrium when absorption is balanced by release, and residence time is the average length of time a carbon atom stays within a given store before moving on. Without human interference (mining and extraction), the residence time of carbon in fossil fuels would be measured in hundreds of millions of years.

Limestone cliffs along a coastline — Carboniferous limestone cliffs near Buckspool on the Pembrokeshire coast of Wales, built from calcium carbonate accumulated by marine organisms roughly 330 million years ago. Limestone is the largest single carbon store in Earth systems.

2.3.4

How carbon flows between stores

Carbon flows between stores in ecosystems through photosynthesis, feeding, defecation, cellular respiration, death and decomposition. As with the nitrogen flows covered later in this subtopic's HL content, some of these flows are transformations, chemically converting carbon from one compound into another, while others are simple transfers, physically moving the same carbon compounds from one organism or store to another without changing their chemical form.

🛠Application of skills

Statement 2.3.4 explicitly asks you to create a systems diagram of the carbon cycle, showing which of its flows are transfers and which are transformations. Try this yourself in the Skills tab.

2.3.5

Carbon sequestration

Carbon sequestration is the process of capturing gaseous, atmospheric carbon dioxide and storing it in a solid or liquid form. Trees do this naturally, absorbing CO₂ through photosynthesis and converting it into biomass. Over geological time, organic matter can also become fossilized into coal, oil and natural gas, sequestering carbon on a far longer timescale.

2.3.6

Ecosystems as stores, sinks or sources

Whether an ecosystem behaves as a store, sink or source of carbon depends on the balance between photosynthesis (which removes CO₂ from the atmosphere) and cellular respiration (which releases it). If photosynthesis exceeds respiration, there is a net uptake of carbon dioxide: a sink. If respiration exceeds photosynthesis, there is a net release: a source. A forest can occupy any of these three roles at different points in its life.

Classify each forest scenario as a sink, a store, or a source.

A young forest regrowing on former farmland, adding new biomass rapidly every year.

A mature, old-growth forest whose total biomass has stopped increasing year to year.

A forest recently cleared by fire, with burned and decomposing wood releasing carbon dioxide across the site.

2.3.7

Fossil fuels: stores with unlimited residence time

Fossil fuels are carbon stores that, left undisturbed, have effectively unlimited residence times: they formed when ancient ecosystems acted as carbon sinks over millions of years, then remained locked away. Burning them releases that stored carbon almost instantly, turning a store built up over geological time into an active carbon source within a human lifetime.

A pumping unit extracting oil from an underground borehole — A pumping unit drawing oil from an underground borehole. Fossil fuels take millions of years to form; extraction and burning release that stored carbon within a single human lifetime.

2.3.8

Agriculture: store, sink or source, depending on method

Agricultural systems can act as any of the three roles depending on the techniques used. Crop rotation, cover crops and no-till farming all promote soil acting as a carbon sink. Wetland drainage, monoculture and heavy tillage all promote soil acting as a carbon source instead, releasing carbon that had been stored for far longer.

🔗Linking across the ESS course

5.1 covers exactly this trade-off from the soil-science side, including the Rothamsted long-term field trials, and 5.2 covers it from the food-systems side, including the Green Revolution's effect on soil management. Both pages ground the same sink-versus-source choice this statement describes.

2.3.9

The oceans as a carbon sink

Carbon dioxide is absorbed into the oceans by simply dissolving into seawater, and is released back as a gas when it comes out of solution. Oceans act as a major carbon sink overall, but human fossil fuel use now releases inorganic carbon into the atmosphere faster than the oceans can absorb it, so atmospheric concentrations keep rising even as the oceans absorb a large share of the total.

2.3.10

Ocean acidification

Rising concentrations of dissolved carbon dioxide cause ocean acidification, directly harming marine life. Even small decreases in seawater pH interfere with the calcium carbonate deposition that corals and molluscs rely on to build shells and skeletons, exactly the mechanism behind the Great Barrier Reef's declining calcification rates introduced in the hook.

Diagram of coral polyp anatomy — Anatomy of a coral polyp. The basal plate and theca are the calcium carbonate skeleton structures that ocean acidification makes harder to build.

🔗Linking across the ESS course

2.1 covers biodiversity loss and tipping points in ecosystem stability generally; ocean acidification is one concrete, chemistry-driven mechanism that can push a reef system toward exactly that kind of tipping point.

2.3.11

Alleviating human impact on the carbon cycle

Measures are required to alleviate the effects of human activity on the carbon cycle. At least three broad categories are worth knowing: adopting low-carbon technologies (renewable energy, electrification); reducing fossil fuel burning, soil disruption and deforestation directly; and actively capturing carbon, whether through reforestation or through artificial (engineered) carbon capture and storage.

Quick check. Which of these is an example of artificial carbon capture, rather than a natural or behavioral measure?

A coastal mangrove forest

A coastal town is deciding whether to protect a mangrove forest at the edge of its harbor or clear it to expand a marina. The mangroves have grown steadily denser over the past 30 years.

A waterway through a dense mangrove forest — A waterway through the Pichavaram mangrove forest in Tamil Nadu, India, often cited as the world's second-largest mangrove forest. Dense root systems and waterlogged soil beneath mangroves like these store large amounts of carbon, the scenario behind the question below.

Think it through, then check your reasoning against the model answer below. Using the vocabulary of stores, sinks and sources, explain what role the mangrove forest plays in the carbon cycle right now, and what would happen to that role if it were cleared.

Sources: this tab

Great Barrier Reef ocean acidification and coral calcification decline: De'ath, Lough and Fabricius (2009), "Declining Coral Calcification on the Great Barrier Reef," Science; Great Barrier Reef Marine Park Authority, Outlook Report 2024; Scientific Reports (2020).
Global ocean pH figures: NOAA Climate.gov, "Ocean Acidification, Today and in the Future"; Smithsonian Ocean Portal.
IB Environmental Systems and Societies Guide, first assessment 2026, Topic 2, Subtopic 2.3, statements 2.3.1-2.3.11.
Photos and diagrams: via Wikimedia Commons, individually credited beneath each image.

2.3.4 · skill

Transfer or transformation?

Application of skills, statement 2.3.4: create a systems diagram of the carbon cycle, distinguishing transfers from transformations. A transformation chemically converts carbon from one compound into another. A transfer physically moves the same carbon compound from one place to another without changing its chemical form. Sort each carbon cycle flow correctly.

Photosynthesis: a plant converts atmospheric CO₂ into glucose.

Feeding: a caterpillar eats a leaf, taking in the carbon compounds it contains.

Defecation: an animal excretes undigested plant material.

Cellular respiration: an organism converts stored glucose back into CO₂ and usable energy.

Death: an organism dies, and its stored carbon compounds become part of the dead organic matter store.

Decomposition: fungi and bacteria break down dead organic matter into simpler compounds.

2.3.3 · skill

Rank carbon stores by residence time

Statement 2.3.3 introduces residence time, how long a carbon atom typically stays in a given store. Click the stores below, in order, from shortest average residence time to longest.

Click each store above, shortest residence time first.

Sources: this tab

IB Environmental Systems and Societies Guide, first assessment 2026, Topic 2, Subtopic 2.3, statements 2.3.3, 2.3.4.

Glossary

Biogeochemical cycle: The movement of a chemical element through living organisms and the physical environment, keeping it available to life.
Store (storage): A reservoir of an element in equilibrium: absorption balances release.
Sink: A reservoir with a net accumulation of an element: it absorbs more than it releases.
Source: A reservoir with a net release of an element: it releases more than it absorbs.
Residence time: The average length of time a given atom remains within a particular store.
Carbon sequestration: The process of capturing atmospheric carbon dioxide and storing it in a solid or liquid form.
Transfer: A flow that physically moves a compound from one place to another without changing its chemical form.
Transformation: A flow that chemically converts a compound from one form into another.
Fossil fuel: A carbon store formed from ancient organic matter, with an effectively unlimited residence time unless extracted by humans.
Ocean acidification: The fall in ocean pH caused by increasing amounts of dissolved carbon dioxide, which interferes with calcium carbonate formation in shells and skeletons.
Aragonite saturation: A chemical measure of how readily calcium carbonate can form in seawater; falls as the ocean acidifies.
Lithosphere (HL): The solid outer layer of the Earth, including rocks such as limestone, that contains major carbon stores.
Methanogenesis (HL): The production of methane from dead organic matter by methanogenic bacteria under anaerobic conditions.
Nitrogen fixation (HL): The conversion of atmospheric nitrogen gas into ammonia, usable by living organisms.
Nitrification (HL): The conversion of ammonia into nitrates.
Denitrification (HL): The conversion of nitrates back into nitrogen gas, occurring only in anaerobic conditions.
Ammonification (HL): The conversion of amino acids and other organic nitrogen compounds into ammonium during decomposition.
Mutualistic nitrogen-fixing association (HL): A relationship, such as between legumes and Rhizobium bacteria, in which a plant hosts nitrogen-fixing bacteria in exchange for usable nitrogen compounds.
Haber process (HL): An industrial process producing ammonia from nitrogen and hydrogen gas, used to manufacture synthetic nitrogen fertilizer.
Planetary boundary (HL): A scientifically defined limit for an Earth system process, beyond which the risk of abrupt, irreversible change increases sharply.

2.3.12 through 2.3.25 are HL only. This tab covers additional carbon cycle detail, then the entire nitrogen cycle, which the 2026 Guide places entirely at HL.

2.3.12-2.3.14

Carbon in the lithosphere

The lithosphere, the solid outer layer of the Earth, contains major carbon stores in fossil fuels and in rocks such as limestone, which contains calcium carbonate. Reef-building corals and molluscs build hard parts from calcium carbonate that can eventually become fossilized into limestone, the largest single carbon store in Earth systems, though not all limestone forms this way. In past geological eras, partially decomposed plants became fossilized into coal, and partially decomposed marine organisms became fossilized into the oil and natural gas held within porous rocks. Formation of coal, oil and gas was greatest during specific geological eras with especially favorable conditions, and took tens of millions of years to accumulate into significant stores.

2.3.15-2.3.16

Methane

Methane is produced from dead organic matter under anaerobic conditions by methanogenic bacteria, in environments such as swamps, rice paddies, and the stomachs of cattle and other ruminants. Methane has a much shorter atmospheric residence time than carbon dioxide, about 10 years, after which it is oxidized into carbon dioxide. Despite this shorter residence time, methane is a potent greenhouse gas while it remains in the atmosphere.

Flooded rice terraces — The Banaue Rice Terraces in Ifugao province, the Philippines, carved into the mountainside by hand roughly 2,000 years ago by the ancestors of the Ifugao people and often called the "stairway to heaven." Flooded rice paddies like these are anaerobic environments where methanogenic bacteria produce methane, one of the main non-livestock sources of agricultural methane.

Batad Rice Terraces, an amphitheater-shaped rice terrace system — The nearby Batad Rice Terraces, shaped like a natural amphitheater to distribute irrigation water evenly down the slope. Banaue and Batad are both part of the UNESCO World Heritage Rice Terraces of the Philippine Cordilleras.

2.3.17

Nitrogen stores

The nitrogen cycle, like the carbon cycle, has both organic and inorganic stores. Organic nitrogen stores consist of proteins and other nitrogenous carbon compounds within living organisms and dead organic matter. Inorganic nitrogen stores consist of nitrogen gas in the atmosphere, along with ammonia and other nitrogen compounds, nitrites and nitrates, in soil and water.

🛠Application of skills

Statement 2.3.17 explicitly asks you to create a systems diagram of the nitrogen cycle. Use the process definitions below as your building blocks.

2.3.18-2.3.20

Bacteria and the nitrogen cycle

Bacteria carry out the essential chemical conversions of the nitrogen cycle. Nitrogen fixation converts atmospheric nitrogen gas into ammonia. Nitrification converts ammonia into nitrates. Denitrification converts nitrates back into nitrogen gas, and only happens under anaerobic conditions, such as waterlogged soils. Decomposition converts amino acids in dead organic matter into ammonium, a process also called ammonification.

In waterlogged, anaerobic soils, plant growth is reduced or stopped, and denitrification and nutrient leaching both increase. In these nitrogen-poor conditions, some plants, such as pitcher plants and sundews, have evolved to capture and digest insects as an alternative nitrogen source.

Since plants cannot fix nitrogen themselves, atmospheric nitrogen gas is unavailable to them unless they form mutualistic associations with nitrogen-fixing bacteria, legumes hosting Rhizobium bacteria in root nodules being the classic example. This mutualism gives such plants a competitive advantage in ecosystems where nitrogen is a limiting factor on growth.

Scanning electron micrograph of nitrogen-fixing bacteria inside a legume root nodule cell — A scanning electron micrograph of nitrogen-fixing bacteria inside a legume root nodule cell. The bacteria are wrapped in plant membranes and trade fixed nitrogen for carbon and protection.

Match each nitrogen cycle process to its correct definition.

Bacteria convert nitrogen gas from the atmosphere into ammonia.

Soil bacteria convert ammonia into nitrates.

In a waterlogged, oxygen-poor soil, bacteria convert nitrates back into nitrogen gas.

Decomposers break down amino acids in dead organic matter into ammonium.

2.3.21

Nitrogen cycle flows

The nitrogen cycle's flows include mineral uptake by producers, photosynthesis, consumption, excretion, death, decomposition and ammonification. Of these, photosynthesis, decomposition and ammonification are transformations, chemically converting nitrogen compounds. Mineral uptake, consumption, excretion and death are transfers, physically moving nitrogen compounds without changing their chemical form, exactly the same transfer/transformation distinction covered for the carbon cycle earlier on this page.

2.3.22-2.3.23

Human impact and the Haber process

Human activities including deforestation, agriculture, aquaculture and urbanization all change the nitrogen cycle, typically by adding far more reactive nitrogen to ecosystems than would occur naturally. The single largest source is the Haber process, an industrial process that produces ammonia from atmospheric nitrogen and hydrogen gas, for use as synthetic fertilizer.

Schematic diagram of the Haber-Bosch process — A schematic of the Haber-Bosch process: nitrogen and hydrogen gas are combined under heat and pressure with an iron catalyst to synthesize ammonia for fertilizer.

Reading the numbered diagram. This level of industrial detail goes beyond what's needed for the exam, useful only if you want to see how the process actually runs at scale.

1. Adding of methane: natural gas (CH₄) enters the plant as feedstock.
2. Adding of water: steam (H₂O) is added as the second reactant.
3. Primary reformer: methane and steam react over a catalyst to form carbon monoxide and hydrogen: CH₄ + H₂O → CO + 3H₂.
4. Adding of air: oxygen and nitrogen are introduced for the next stage.
5. Secondary reformer: remaining methane reacts with the added oxygen (2CH₄ + O₂ → 2CO + 4H₂), and the nitrogen needed later for ammonia synthesis is introduced.
6. Catalyst: the catalyst bed that drives the reforming reactions.
7. Compressor: raises the gas mixture to the high pressure the process requires, appearing at several points in the diagram.
8. Washing: the gas mixture is scrubbed to remove carbon dioxide, leaving a purified nitrogen-hydrogen mixture.
9. Pre-heating: the purified gas is warmed before entering the reactor.
10. Reactor: nitrogen and hydrogen combine over an iron catalyst to form ammonia: N₂ + 3H₂ → 2NH₃.
11. Heat exchanger: recovers heat from the hot reactor output to preheat incoming gas.
12. Cooling: the gas mixture is cooled until the ammonia condenses into a liquid.
13. Storage tank: the liquid ammonia product is collected and stored.

The Haber process and the Baltic Sea dead zone

Developed by Fritz Haber and industrialized by Carl Bosch between 1909 and 1913, the Haber process combines nitrogen and hydrogen gas under high heat and pressure, using an iron catalyst, to produce ammonia.
Synthetic nitrogen fertilizer made possible by this process now supports an estimated 48% of the global population, roughly half of everyone alive today, through increased crop yields.
The process is highly energy-intensive: producing roughly 180 million tonnes of ammonia a year consumes an estimated 1-2% of global energy and generates around 1.4% of global CO₂ emissions.
Excess nitrogen fertilizer that runs off farmland drives eutrophication downstream. The Baltic Sea, fed by agricultural runoff from nine surrounding countries, now has the largest human-caused (anthropogenic) dead zone on Earth, an anoxic seafloor area of roughly 70,000 km², about 20% of the Baltic's total seafloor.

Sources: C&EN (Chemical & Engineering News), "The industrialization of the Haber-Bosch process"; Our World in Data, "How many people does synthetic fertilizer feed?"; Race for the Baltic, "State of the Baltic Sea"; Wikipedia-cited HELCOM (Baltic Marine Environment Protection Commission) monitoring data.

The Shahjalal Fertilizer Factory in Bangladesh at night — The Shahjalal Fertilizer Factory in Fenchuganj, Sylhet, Bangladesh, the country's largest urea plant, built on Haber-Bosch chemistry to cut Bangladesh's reliance on imported fertilizer. Plants like this now help feed an estimated 48% of the global population.

Satellite image of algal blooms swirling across the Baltic Sea — A Copernicus Sentinel-2 satellite image of algal blooms swirling around the island of Gotland, Sweden, in the Baltic Sea, fed by nutrient runoff from farmland across nine surrounding countries. The Baltic now hosts the largest human-caused dead zone on Earth.

2.3.24-2.3.25

The nitrogen planetary boundary

Human-driven increases in nitrates across the biosphere, overwhelmingly from inorganic fertilizer use, have already pushed the biogeochemical flows planetary boundary for nitrogen well past its safe limit, making irreversible changes to Earth systems more likely. Because nitrogen pollution crosses national borders freely through rivers, coastlines and the atmosphere, addressing it requires global collaboration, not action by any single country, to bring the nitrogen cycle back within a safer planetary boundary.

🔗Linking across the ESS course

1.3 covers the planetary boundaries framework as a whole, including the finding that 7 of 9 boundaries were assessed as transgressed as of September 2025. The nitrogen cycle (alongside biosphere integrity) was among the very first boundaries confirmed crossed, well before most of the others, specifically because of fertilizer use enabled by the Haber process described here.

Quick check. The Baltic Sea's dead zone and the nitrogen planetary boundary being crossed both trace back to the same root cause. What is it?

Sources: this tab

Haber process history and figures: C&EN, "The industrialization of the Haber-Bosch process"; Our World in Data, "How many people does synthetic fertilizer feed?"
Baltic Sea dead zone: Race for the Baltic, "State of the Baltic Sea"; HELCOM monitoring data.
Planetary boundaries status: covered in full on 1.3 Sustainability, citing the Stockholm Resilience Centre's Planetary Health Check, September 2025.
IB Environmental Systems and Societies Guide, first assessment 2026, Topic 2, Subtopic 2.3, statements 2.3.12-2.3.25.
Photos and diagrams: via Wikimedia Commons, individually credited beneath each image.

2.3 Biogeochemical Cycles

Why biogeochemical cycles matter

Stores, sinks and sources

Carbon stores

How carbon flows between stores

Carbon sequestration

Ecosystems as stores, sinks or sources

Fossil fuels: stores with unlimited residence time

Agriculture: store, sink or source, depending on method

The oceans as a carbon sink

Ocean acidification

Alleviating human impact on the carbon cycle

A coastal mangrove forest

Transfer or transformation?

Rank carbon stores by residence time

Glossary

Quick quiz

Written practice questions

Carbon in the lithosphere

Methane

Nitrogen stores

Bacteria and the nitrogen cycle

Nitrogen cycle flows

Human impact and the Haber process

The nitrogen planetary boundary