Difficulty: Introductory | Prerequisites: Part 1 of these notes (Nutrient Cycles and Reservoirs) or equivalent understanding of abiotic/biotic transitions, reservoirs, and replenishment/removal processes.
Big Picture: This is the second half of Chapter 3. Where Part 1 covered the general framework of nutrient cycling, this document walks through five specific element cycles that the course expects you to know individually: carbon, nitrogen, magnesium, calcium, and phosphorus. Each has its own entry and exit routes, its own biological role, and its own exam-relevant quirks. If you are not yet comfortable with the concepts of reservoirs, upwelling, run-off, and decomposition, review Part 1 first.
Carbon cycles through the ocean via CO₂ dissolution, photosynthesis, respiration, sedimentary rock formation, and fossil fuel creation. Nitrogen must be converted from unusable N₂ gas into ammonia, nitrite, or nitrate before organisms can use it. Magnesium, calcium, and phosphorus each enter the ocean mainly through weathering and run-off, serve distinct biological roles (chlorophyll, skeletons, and DNA respectively), and are removed by sedimentation or biological incorporation.
Carbonic acid (H₂CO₃)
The weak acid formed when carbon dioxide dissolves in water. In simple terms, this is the first chemical product of CO₂ entering the ocean, and it kicks off the chain reaction that eventually produces carbonate ions.
Hydrogencarbonate ion (HCO₃⁻) / bicarbonate
The ion produced when carbonic acid dissociates, releasing a hydrogen ion. Think of it as the intermediate step between dissolved CO₂ and the carbonate ion that ends up in rocks and shells.
Carbonate ion (CO₃²⁻)
The ion produced when hydrogencarbonate dissociates further. This is the form of carbon that settles on the ocean floor and, over geological time, builds sedimentary rock such as limestone.
Diazotrophs
Marine organisms (mainly certain bacteria and cyanobacteria) that can convert molecular nitrogen gas (N₂) into ammonia (NH₃), a biologically usable form. Think of them as the ocean's nitrogen fixers.
Nitrogen fixation
The conversion of atmospheric N₂ into ammonia (NH₃). In simple terms, this is the gateway reaction that makes nitrogen available to the rest of the food web.
Nitrification
The oxidation of ammonia first into nitrite (NO₂⁻) and then into nitrate (NO₃⁻) by specialised bacteria. This is how fixed nitrogen is further processed into forms that phytoplankton readily absorb.
Saprophytic bacteria and fungi
Organisms that decompose dead consumers and producers, breaking proteins down into amino acids. Sometimes nicknamed "death eaters." In simple terms, they are the first link in the chain that recycles nitrogen from dead tissue back into the water.
Ammonifying bacteria
Bacteria that convert amino acids (from decomposed organisms) back into ammonia, completing the recycling loop.
Coccolithophores
A type of phytoplankton that builds tiny transparent calcium-carbonate plates called coccoliths. In simple terms, they are single-celled algae wearing armour made of calcium.
Coccoliths
The calcium carbonate "scales" or plates that coccolithophores produce. They are transparent, so they do not block light for photosynthesis.
Limiting nutrient
A nutrient whose scarcity directly restricts the growth of organisms in an ecosystem, even when other nutrients are abundant. Phosphorus and nitrogen are the classic limiting nutrients in marine systems.
CO₂ dissolution chain (carbon cycle):
CO₂ + H₂O → H₂CO₃ (carbonic acid) → HCO₃⁻ + H⁺ (hydrogencarbonate + hydrogen ion) → CO₃²⁻ + H⁺ (carbonate + hydrogen ion)
Approximately 90 gigatons of CO₂ dissolve into the ocean per year, and roughly the same amount diffuses back into the atmosphere.
Nitrogen fixation (nitrogen cycle):
N₂ → NH₃ (carried out by diazotrophs)
NH₃ dissolves in water to form NH₄⁺ (ammonium ions)
Nitrification (nitrogen cycle):
NH₃ → NO₂⁻ (nitrite) → NO₃⁻ (nitrate)
Phytoplankton can use both nitrite and nitrate, though breaking the N-O bond requires more energy than using ammonium.
All photosynthetic and chemosynthetic organisms take in carbon and fix it into glucose.
All organisms release CO₂ back into the environment through cellular respiration.
Biological uses of carbon: glucose, lipids, proteins.
CO₂ dissolves easily into seawater and immediately forms carbonic acid (H₂CO₃).
Carbonic acid dissociates into hydrogencarbonate ions (HCO₃⁻) and hydrogen ions (H⁺).
Hydrogencarbonate then dissociates further into carbonate ions (CO₃²⁻) and more hydrogen ions.
The system is in equilibrium: roughly 90 gigatons per year dissolve into the ocean, and roughly 90 gigatons diffuse back into the atmosphere.
When carbonate ions settle on the ocean floor, pressure and time compress the sediment into sedimentary rock.
Classic example: limestone.
Over geological time, sedimentary rocks are exposed on the Earth's surface through tectonic uplift.
Weathering and erosion then release the carbonate ions, and the cycle begins again.
Compressed carbonate ions and organic matter can also form fossil fuels.
Organic matter subjected to heat and pressure over millions of years becomes crude oil.
Most nitrogen on Earth exists as molecular nitrogen gas (N₂), which most organisms cannot use directly.
Biological uses of nitrogen: proteins, amino acids, DNA.
In the marine environment, diazotrophs (specialised bacteria and cyanobacteria) convert N₂ into ammonia (NH₃).
Ammonia dissolves in water to form ammonium ions (NH₄⁺), which organisms can absorb.
Phytoplankton can also take up nitrite (NO₂⁻) and nitrate (NO₃⁻) ions dissolved in seawater.
These ions are found in higher concentrations than ammonium, so organisms use them even though breaking the N-O bond requires more energy.
Saprophytic bacteria and fungi break down proteins in dead organisms and convert them to amino acids. They are sometimes called "death eaters."
Ammonifying bacteria then convert those amino acids back into ammonia (NH₃).
Ammonia is oxidised first into nitrite and then into nitrate through a process called nitrification.
This completes the recycling loop: nitrogen moves from dead organic matter back into forms that producers can absorb.
Biological use: magnesium is the central atom in the chlorophyll pigment, making it essential for photosynthesis.
Magnesium is found naturally in rocks.
It enters the water cycle primarily through weathering and erosion of those rocks.
It is also present in agricultural fertilisers.
The main entry route into the ocean is therefore run-off (carrying both weathered rock ions and fertiliser residue).
Removal: magnesium ions are removed from the nutrient cycle when they are deposited in sediment at the bottom of the ocean.
Biological uses: calcium is needed to build bones, coral skeletons, shells, and teeth.
Acid rain (carbonic acid in rainwater) helps weather calcium-containing rocks on land.
This adds dissolved calcium to run-off, which carries it to the ocean.
Calcium is also present in fertilisers, providing another run-off pathway.
Coccolithophores are a type of phytoplankton that use dissolved calcium to build tiny calcium carbonate plates called coccoliths.
The coccoliths are transparent, so they do not block the light the organism needs for photosynthesis.
When other organisms eat coccolithophores, they take in the calcium and pass it along the food chain.
Biological uses: phosphorus is essential for nucleic acids (DNA, RNA) and for bone structure.
Phosphorus is found in rocks. It attaches to water in soil and enters the ocean via run-off.
Also found in fertilisers, manure, and sewage.
Along with nitrogen, phosphorus is a limiting nutrient for life in the ocean. When it runs low, productivity drops regardless of how much of other nutrients is available.
Nutrient | Biological Uses |
|---|---|
Nitrogen | Proteins, amino acids, DNA |
Carbon | Glucose, lipids, proteins |
Magnesium | Chlorophyll (photosynthesis) |
Calcium | Bones, shells, coral |
Phosphorus | Bones, DNA |
The carbonic acid equilibrium is at the heart of ocean acidification: as atmospheric CO₂ rises, more dissolves into seawater, producing more H⁺ ions and lowering pH. This directly threatens organisms that build calcium carbonate structures (corals, coccolithophores, shellfish). Nitrogen and phosphorus from agricultural run-off are the primary drivers of eutrophication in coastal waters worldwide.
Students often think all nitrogen in the ocean is usable. Most nitrogen exists as N₂ gas, which the vast majority of organisms cannot metabolise. Only diazotrophs can fix it into ammonia.
Students sometimes confuse nitrification with nitrogen fixation. Nitrogen fixation converts N₂ to NH₃. Nitrification converts NH₃ to NO₂⁻ and then NO₃⁻. They are sequential but distinct processes carried out by different organisms.
Students assume magnesium and calcium enter the ocean the same way. While both arrive largely through run-off, calcium weathering is specifically aided by acid rain (carbonic acid), and magnesium is more closely associated with rock erosion and fertiliser.
Students forget that phosphorus is a limiting nutrient. Even when nitrogen is abundant, phosphorus scarcity can cap productivity.
⚠️ Know the CO₂ dissolution chain and be able to write out each step (CO₂ → carbonic acid → hydrogencarbonate + H⁺ → carbonate + H⁺).
⚠️ Be able to distinguish nitrogen fixation, ammonification, and nitrification, including which organisms carry out each.
⚠️ Know the biological use of each of the five nutrients (the summary table is a likely exam target).
⚠️ Understand why phosphorus and nitrogen are called limiting nutrients.
⚠️ Be prepared to explain the role of coccolithophores in the calcium cycle.
True or false: Most organisms can directly use molecular nitrogen (N₂) from the atmosphere. (False. Only diazotrophs can fix N₂ into ammonia.)
Fill in the blank: When CO₂ dissolves in seawater, the first product is __________. (Carbonic acid / H₂CO₃.)
True or false: Magnesium is essential for photosynthesis because it is the central atom in chlorophyll. (True.)
Fill in the blank: The process by which ammonia is converted to nitrite and then nitrate is called __________. (Nitrification.)
True or false: Coccoliths are opaque plates that block light for the organism. (False. They are transparent.)
Q: Trace the path of a carbon atom from the atmosphere to sedimentary rock on the ocean floor.
A: CO₂ dissolves into seawater and forms carbonic acid. Carbonic acid dissociates into hydrogencarbonate ions and hydrogen ions, then further into carbonate ions and hydrogen ions. Carbonate ions settle on the ocean floor, and over time, pressure compresses the sediment into sedimentary rock (e.g. limestone).
Q: What are diazotrophs, and why are they critical to the marine nitrogen cycle?
A: Diazotrophs are bacteria and cyanobacteria that convert molecular nitrogen gas (N₂) into ammonia (NH₃). They are critical because most organisms cannot use N₂ directly; without diazotrophs, fixed nitrogen would not enter the marine food web.
Q: Describe the sequence of processes that recycle nitrogen from a dead fish back into a form usable by phytoplankton.
A: Saprophytic bacteria and fungi decompose the fish's proteins into amino acids. Ammonifying bacteria convert the amino acids into ammonia. Nitrifying bacteria then oxidise the ammonia into nitrite and subsequently nitrate. Phytoplankton absorb the nitrite or nitrate from the water.
Q: Why is phosphorus described as a limiting nutrient in marine ecosystems?
A: Because even when other nutrients are abundant, a shortage of phosphorus directly restricts organism growth and overall productivity. It is essential for building nucleic acids and bone, and there is no atmospheric reservoir to replenish it quickly; it enters the ocean mainly through slow processes like run-off and rock weathering.
Q: How do coccolithophores contribute to the calcium cycle, and why are their coccoliths transparent?
A: Coccolithophores are phytoplankton that absorb dissolved calcium and use it to build calcium carbonate plates (coccoliths). The coccoliths are transparent so they do not block the light the organism needs for photosynthesis. When other organisms eat coccolithophores, the calcium passes along the food chain.
The carbon cycle links directly to ocean acidification and climate change topics later in the course: increasing atmospheric CO₂ shifts the carbonic acid equilibrium, lowering ocean pH and threatening calcifying organisms. The nitrogen cycle connects to marine productivity and food-web dynamics, because nitrogen availability often controls how much phytoplankton can grow in a given region. Phosphorus and calcium cycles tie into reef ecology and the biology of coral bleaching, since coral skeletons depend on both calcium carbonate and the nutrient balance maintained by zooxanthellae.
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