Metabolism. The coral is a holobiont

If we think our Acropora are light-dependent, we are ignoring their nature as predators.

The coral is not an individual, but a holobiont.

The concept of the holobiont described by Yuri Sorokin in his book Coral Reef Ecology is essential to understanding how Acropora dominate coral reefs. Sorokin does not see the coral as a single animal, but as a complex, integrated entity.

Sorry for the lecture 🤣, but we need it to understand what follows…

The definition of the holobiont according to Sorokin

For Sorokin the holobiont is the union of three pillars:

• the animal polyp, which provides the physical structure and captures prey;
• the symbionts, dinoflagellates (zooxanthellae) that live in the tissues and turn solar energy into nutrients;
• the microbiome, a microscopic community that lives in the mucus and tissues, essential for immune defence and the nutrient cycle.

1. 1Polyp hunts and builds
2. 2Zooxanthellae light → sugars
3. 3Microbiome bacteria in the mucus: defences, vitamin B12, phosphorus

We are not feeding a single animal: we are keeping an alliance in balance.

Polyp, zooxanthellae and microbiome: three organisms, one coral.

The internal energy cycle

Sorokin analyses how the holobiont is a "zero waste" machine: the zooxanthellae supply the animal with glycerol and glucose. Sorokin calculates that in clear, well-lit water this source covers almost the entire metabolic cost of the animal's respiration.

The polyp's metabolic waste (ammonium and phosphates) is not expelled, but immediately taken back up by the zooxanthellae for their growth. This makes the coral an almost self-sufficient system in nutrient-poor (oligotrophic) ocean environments.

The role of bacteria (bacteriotrophy)

One of Sorokin's most innovative contributions concerns the role of bacteria in feeding the holobiont.

The mucus: the coral secretes mucus that acts as a substrate for bacterial growth.

Capture and ingestion: the bacteria in the mucus or in the plankton are ingested by the polyps or absorbed. Sorokin shows that bacteria supply the holobiont with essential vitamins (such as B12) and organic phosphorus that photosynthesis cannot produce.

The holobiont and calcification

Calcification is a process helped along by the whole holobiont.

The zooxanthellae's photosynthesis removes CO₂ from the tissues, raising the local pH and helping calcium carbonate (CaCO₃) to precipitate, as we saw in the previous chapters with boron.

Without the energy supplied by the symbionts, the polyp would not have enough ATP (cell energy) to actively pump calcium ions to the calcification site.

So the holobiont is a dynamic system. Sorokin explains that under stress (thermal or chemical) the balance breaks: if the zooxanthellae produce too many oxygen free radicals, the host expels them (bleaching). In this state the holobiont survives only if its heterotrophic side (catching food and bacteria) is strong enough to make up for the loss of solar energy. The famous "solar panels".

All in all, keeping an Acropora means managing a microbiological ecosystem. We are not feeding just an animal: we are keeping a complex alliance in balance.

Into the practical heart of it

An Acropora is a machine that consumes and recycles. In the aquarium we have to try to reproduce the energy flows that are constant in nature, but that in our closed system risk becoming bottlenecks.

Bacteria are the primary source of organic phosphorus and vitamins. In the aquarium it is not enough for bacteria to be there: they must be available. Dosing a carbon source is not only about cleaning the water, but about creating bacterial biomass.

Sorokin stresses that corals absorb DFAA (free amino acids) with incredible efficiency.

The energy budget: carbon versus nitrogen

Photosynthesis supplies plenty of organic carbon (sugars), but it is extremely poor in nitrogen (N) and phosphorus (P).

• Autotrophy (sugars): the zooxanthellae pass glycerol and glucose to the host. This covers basal metabolism and respiration.
• Heterotrophy (proteins): to grow tissue and build the skeleton's organic matrix the coral has to take in nitrogen. Sorokin points out that under strong light the heterotrophic supply is what limits growth. Without proteins, the energy from light turns into oxidative stress instead of growth.

The three pillars of feeding

Based on the writings of Sorokin and Hovland, let's look at the three pillars of feeding.

Absorbing DOM (Dissolved Organic Matter): Acropora can absorb dissolved molecules directly through the epidermis.

Free amino acids (DFAA): molecules such as glycine or aspartic acid are taken up by active transport. This is why the feeding mash left to stand for 4 hours is so important: enzymatic breakdown releases these building blocks, making them immediately available, without the coral having to "chew".

Bacteriotrophy: Sorokin revolutionised the field by showing that corals "eat" bacteria. The coral secretes polysaccharide-rich mucus that acts as a substrate for bacterial growth (biofilm), and this biofilm traps particles and bacterioplankton. The coral periodically takes its own mucus back in, ingesting a bacterial biomass rich in vitamin B12 and organic phosphorus. In the aquarium, carbon dosing (tiger, vodka) increases the density of this bacterioplankton, feeding the holobiont indirectly.

Capturing particles (POM): despite their small polyps, Acropora hunt micro-zooplankton. The nematocysts inject toxins that paralyse the prey. Hovland points out how the branching shape of Acropora creates micro-turbulence that helps the polyp meet the food particle (the feeding mash).

The biochemistry of feeding: the role of ammonium

A crucial technical point is the difference between nitrate and ammonium.

• Nitrates (NO₃): to be used they must be reduced enzymatically by the coral, a process that is costly in terms of ATP.
• Ammonium (NH₄⁺): it is the protein "fast food". It is absorbed directly and turned into amino acids at minimal energy cost.

And here is the link with fish, and why a balanced fish population helps, and not a little. Fish excrete ammonium through their gills. That is why tanks with plenty of (well-managed) fish have Acropora with denser colours: they receive ready-to-use nitrogen.

1. 1Fish excrete ammonium through their gills
2. 2Ammonium (NH₄⁺) the protein "fast food": absorbed straight away, little energy
3. 3Nitrates (NO₃) must be reduced by the coral: a process costly in ATP

Well-managed fish give the coral ready-to-use nitrogen.

Sources: [2]

The phosphorus cycle and calcification

Phosphorus is a double-edged sword.

It is essential for making ATP, the energy molecule: without phosphorus the coral does not have the strength to pump calcium ions.

But if inorganic phosphate (PO₄) is too high (for example 0.30), it binds to the growth sites of aragonite crystals, physically blocking calcification.

We must supply organic phosphorus (with food) and keep inorganic phosphorus low (with bacteria and skimming).

The feeding mash: why I prepare it this way

On this subject, let me explain why I prepare the feeding mash you have seen.

The feeding mash is not just a mix of food: it is a bioavailable concentrate that turns inert powders (the classic SPS powdered food you see everywhere) into an active feast for the Acropora. What I do is simply add amino acids, bacteria and the powders to about 20-30 ml of tank water, and leave it all to stand for 4-5 hours at room temperature.

1. 1
   Mix

   20-30 ml of tank water + amino acids + bacteria + powders.

2. 2
   Wait 4-5 hours

   At room temperature: the bacteria break down the food and free amino acids form.

3. 3
   A trail forms

   The water fills with chemical signals the coral "smells".

4. 4
   Into the tank

   The polyps open and the mucus captures live particles, ready to be assimilated.

From "dead" food to a bio-active purée: less waste in the skimmer.

The feeding mash step by step.

Why don't I throw it straight into the tank? Because the coral is an animal with limited "external" digestion. This is what happens in those 4 hours:

• the bacteria release enzymes (proteases and lipases) that soften the powders' membranes and turn the food's complex proteins into fresh bacterial biomass;
• leaving the food to soak starts hydrolysis: complex proteins start to split into peptides and free amino acids (DFAA).

When we dose it, the coral does not have to struggle to digest.

Corals do not see food: they "smell" it. The organic molecules that dissolve in the water while soaking create a chemical trail. After 4 hours the mash water is saturated with signals: as soon as you pour in a drop, the Acropora's receptors detect the amino acids and force the polyps to extend (feeding response). We are literally telling the holobiont to "open wide".

In those 4 hours the beneficial bacteria also start colonising the food particles, and the Acropora get much of their phosphorus and vitamin B12 precisely from digesting the bacteria.

Result: we are not giving just "powder", but live particles enriched with fresh bacterial biomass.

In short: why do I do it?

I make the feeding mash because I want to turn a "dead" (freeze-dried) food into a bio-active purée.

Without soaking, a lot of food is spat out or ends up in the skimmer because it is too hard or inert.

With soaking, every particle is a granule of energy ready to be assimilated by the holobiont.

Capture by interception and the mucus

Bacteria are too small to be "harpooned" one by one by the polyps (by the stinging cells) as if they were little shrimps.

The coral constantly expels a thin layer of mucus that coats the tentacles and the tissue between the polyps. When the water flow passes through the Acropora's branches, the bacteria (and the particles of our feeding mash) literally get stuck in the mucus, like flies on flypaper.

The role of the polyps: the "conveyor belt"

Here we answer the doubt I used to have too: yes, the polyps are essential, but they act in a coordinated way.

On the surface of the tissue and on the tentacles there are microscopic hairs called cilia. Once the mucus has trapped the enriched bacteria (thanks also to the 4 hours of incubating the feeding mash), the cilia start beating in sync. This creates a surface current that moves the food-laden mucus towards the polyp's mouth, which simply "swallows" the package of mucus and bacteria.

Pinocytosis: absorption "without a mouth"

Sorokin goes into another aspect: not everything is absorbed through the mouth.

The cells of the ectoderm (the outer "skin") can engulf tiny droplets of liquid loaded with bacteria or dissolved amino acids, through pinocytosis. In practice the coral tissue "drinks" the smallest bacterial particles of the feeding mash, even without the polyp acting as a grasping tentacle.

Why this can change the way we feed

Knowing that capture is muco-ciliary (that is, based on glue and transport): flow is life. If the water is still, the mucus does not intercept new bacteria. The pumps must push the food against the coral.

The bacteria in the feeding mash are the "primer": by adding live bacteria to the mix that stands for 4 hours, we create particles of the perfect size to get stuck in the mucus net.

Polyp extension is a signal, not the only means: even if the polyps are not fully extended the coral can feed through its tissue, but with the polyps open the mucus's "fishing" surface increases enormously.

The author's scientific references

• Yuri Sorokin, Coral Reef Ecology (holobiont concept, bacteriotrophy, nutrient cycle).
• Martin Hovland (hydrodynamic flow and interaction with the coral).

Who wrote this article

Sources

1. NOAA National Ocean Service (2026). Corals Tutorial: What is Zooxanthellae?. National Oceanic and Atmospheric Administration.
2. Grover R., Maguer J.-F., Allemand D., Ferrier-Pagès C. (2008). Uptake of dissolved free amino acids by the scleractinian coral Stylophora pistillata. Journal of Experimental Biology 211(6): 860-865.
3. Houlbrèque F., Ferrier-Pagès C. (2009). Heterotrophy in tropical scleractinian corals. Biological Reviews 84(1): 1-17.
4. Houlbrèque F., Tambutté E., Allemand D., Ferrier-Pagès C. (2004). Interactions between zooplankton feeding, photosynthesis and skeletal growth in the scleractinian coral Stylophora pistillata. Journal of Experimental Biology 207(9): 1461-1469.