Chemistry and biomineralisation

Here we are at chapter 3. Now we enter the chemistry lab. I am not a chemist, best to make that clear first 🤣, so if I get a formula or a word wrong, I apologise. I want to get the concepts across, not be the "professor on duty": I hope you understand.

Let's go…

Having understood that the coral is a hungry animal (chapter 2) and that it lives under a rain of blue photons (chapter 1), let's work out what it is made of!

Years ago I thought dosing calcium was only needed to make the coral grow 🤣.

Aquarium chemistry is a battlefield. The coral has to extract ions from a liquid and turn them into rock (aragonite: the skeleton). And to do so it uses a crazy amount of energy.

The Triad: not just parameters

KH (alkalinity), calcium and magnesium. Everybody knows they must be stable, but let's see why, and how they balance each other.

1. 1KH · the brick bicarbonates the coral turns into carbonate: 7.5-8.5 dKH
2. 2Ca · the cement the skeleton itself: pumped in with a lot of energy, 420-440 mg/l
3. 3Mg · the additive stops the cement setting in the bucket: ~1,350 mg/l, Mg:Ca ≈ 3:1

Stability matters more than the number.

The skeleton's building site: KH, calcium and magnesium.

KH (alkalinity)

KH is not a "substance" the coral eats. It is the measure of the water's capacity to neutralise acids, given mainly by bicarbonates and carbonates.

As documented by Farmer et al. (2015), the coral takes up bicarbonate from the water and, through an enzyme called carbonic anhydrase, turns it into carbonate inside its "calcifying space".

Why it should be high (but not too high): the higher the KH in our tanks, the easier it is for the coral to "find" those bricks. But careful: if KH is too high (for example above 10) and nutrients are too low, the coral pushes on with growth but has no tissue to cover it. The result? Burnt tips.

Its ideal range is 7.5-8.5 dKH. Absolute stability: it is not the number itself that makes the difference between health and decline, but its stability over time.

Calcium (Ca)

Calcium is the physical building material of the skeleton.

The coral has to actively carry Ca²⁺ ions from seawater through its tissue to the skeleton. This happens through "protein pumps" called Ca-ATPases (we will look at them later).

This process "costs" the coral a great deal of ATP (energy). If calcium is too low, the pumps have to work twice as hard. If it is too high, the water becomes unstable and there is a risk of chemical precipitation.

Its ideal range, here too with stability making the difference, is 420-440 mg/l.

Magnesium (Mg)

Magnesium is often the "forgotten brother" of the Triad.

Let's stay on the building site 🤣. Suppose we have to build a wall: we need bricks and mortar. KH is the brick, calcium is the cement… magnesium is the additive that stops the cement from setting in the bucket before it reaches the wall. But it is not only needed in the water: it is needed inside every single cell of the coral.

In seawater, calcium and carbonates are supersaturated. In theory they should combine and instantly drop out as limescale powder, turning the water milky. That is why, when dosing Balling, there is always that little rule of dosing them at different times. Try it when you calibrate the dosing pumps: mix the KH and the calcium bottle, and after a few minutes you will see them clump into a whitish paste.

Magnesium has an ionic charge very similar to calcium. It "slips into" the first calcium carbonate crystals that try to form, stopping them from growing.

As Gregory Skomal (PhD) explains, without magnesium (or with levels below 1,100 mg/l) you would never manage to keep calcium at 420 and KH at 8: they would precipitate on the pumps, the heaters and the glass, leaving the coral short of bricks.

The biological role: the heart of chlorophyll

Here I quote Sorokin (Coral Reef Ecology). Have you ever wondered why Acropora turn pale and lose photosynthetic efficiency when magnesium drops?

The central atom of the chlorophyll molecule is a magnesium atom. Without Mg the zooxanthellae cannot build those famous solar panels we talked about in the previous chapter.

The study by Farmer et al. (2015) on biomineralisation highlights a critical point: the Ca-ATPase pumps are magnesium-dependent. If magnesium is low, calcium transport slows down and the coral uses more energy (ATP) to do the same work.

The result: a coral with low Mg grows slowly and has a more brittle and porous skeleton, prone to breaking.

The "magic" value of 1,350 mg/l is not made up: in nature the ratio between magnesium and calcium is about 3:1.

When Mg drops, Acropora often show suffering at the growing edges or loss of base tissue, which we often mistake for a nutrient deficiency or a bacterial attack.

The critical point: pH

For calcium to combine with carbonate under its tissue, the coral has to expel protons to raise the local pH.

In the marine aquarium we try to stay between 8.1 and 8.4. Why? It is not a random number: it is a question of electrochemical potential.

To build the skeleton the coral creates under its tissue a zone called the ECF (Extracellular Calcifying Fluid). To make calcium precipitate it has to raise the pH in this zone to about 9 (much higher than the water outside). To do so it uses protein pumps that "throw out" hydrogen ions (H⁺ protons). If your tank's pH is low (for example 7.8), the water outside is already loaded with protons and the coral has to push "uphill" against enormous chemical pressure.

The result, according to the study by Al-Horani et al. (2003): the higher the external pH, the less energy (ATP) the coral spends on calcifying. High pH = explosive growth. If you have perfect KH and calcium but low pH, growth will be slow. This is where boron (chapter 4) and gas exchange come in.

How is pH regulated in the aquarium? It is governed almost entirely by the amount of carbon dioxide (CO₂) dissolved in the water. The more CO₂ there is in the house (windows closed, lots of people), the more gets into the tank. The more CO₂ gets in, the more acidic the water becomes (H⁺ ions increase) and the pH crashes.

The paradox: even with KH at 12, if there is too much CO₂ in the water the pH will still be low. KH helps stop the pH crashing to 5, but it does not "push" it to 8.4 if the air is stale.

The day-night swing

By day the zooxanthellae photosynthesise and use up CO₂: pH rises.

At night photosynthesis stops, corals and fish respire and produce CO₂: pH falls.

Yuri Sorokin showed that corals grow up to 3 times faster during the day, not only because of the light, but because the higher pH makes the work of the proton pumps we saw earlier easier.

1. 1At night photosynthesis stops, corals and fish produce CO₂: pH falls
2. 2Lights on the zooxanthellae use up CO₂: pH rises

Under its tissue the coral raises pH to about 9. The lower the tank's pH, the harder it has to work.

pH rises with the lights on and falls at night: and how to help it.

How to go from low pH to high pH

If you want to see your Acropora "fly", you have to manage pH. Here is how:

CO₂ scrubber: connect the skimmer's air intake to a filter with soda lime. This removes CO₂ from the air before it gets into the water. It is the most effective method of all.

Reverse-cycle refugium: keep an area with algae (such as Chaetomorpha) lit at night. The algae will use up the CO₂ produced by the corals while they sleep, stabilising the pH.

Surface movement: gas exchange is essential. If the surface is still, CO₂ stagnates in the water.

Calcium hydroxide (kalkwasser): it is the king of pH. When you dose it, it reacts directly with the CO₂ in the water, turning it into… calcium carbonate (bricks!). It is the only supplement that raises KH and calcium while lowering CO₂ at the same time. But we will go into that in depth, because it would take too long now.

CO₂ scrubber

• Soda lime on the skimmer's air intake

Reverse-cycle refugium

• Algae lit at night

Moving surface

• More gas exchange

Kalkwasser

• Raises KH and Ca and removes CO₂

The more CO₂ you remove from the water, the less effort the coral needs to build its skeleton.

Sources: [3] [4]

Scientific sources cited by the author

• Farmer, J. R., et al. (2015). Effects of seawater-pH and biomineralization on corals. Geochimica et Cosmochimica Acta.
• Sorokin, Y. I. (1995). Coral Reef Ecology. Springer. (Ch. 3: Carbonate budget and Calcification).
• Skomal, G. (2020). Saltwater Aquariums For Dummies. (Section: The Chemistry of Calcification).
• Nature Scientific Reports (2025). Trace element accumulation and physiological stress in scleractinian corals.
• Morse, J. W., & Mackenzie, F. T. (1990). Geochemistry of Sedimentary Carbonates. (The bible on crystal precipitation).

Who wrote this article

Sources

1. Johnson K., Monterey Bay Aquarium Research Institute (MBARI) (2026). Periodic Table of Elements in the Ocean, Summary Table. MBARI.
2. Farmer J.R., Hönisch B., Robinson L.F., Hill T.M. (2015). Effects of seawater-pH and biomineralization on the boron isotopic composition of deep-sea bamboo corals. Geochimica et Cosmochimica Acta 155: 86-106.
3. National Center for Biotechnology Information, PubChem (2026). Soda lime (CID 66545795), GHS Classification. U.S. National Library of Medicine.
4. National Center for Biotechnology Information, PubChem (2026). Calcium Hydroxide (CID 6093208), GHS Classification. U.S. National Library of Medicine.