Coral Symbiosis with Symbiodiniaceae

By the Coral Compass team · Last reviewed 2026-10-15

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A partnership that built the reefs

Almost every coral in a reef aquarium, including SPS, LPS and many soft corals, is really two organisms. The coral animal hosts single-celled dinoflagellate algae inside its gut-lining (gastrodermal) cells. Reefers call them zooxanthellae. Scientists now place them in the family Symbiodiniaceae.

The partnership works because each side supplies what the other lacks. The algae photosynthesize and pass most of the sugars and other carbon compounds they make to the coral. The coral gives the algae a protected, well-lit home, plus carbon dioxide and nitrogen- and phosphorus-rich waste from its own metabolism. In 1977, Leonard Muscatine and James Porter described reef corals as mutualistic symbioses "adapted to nutrient-poor environments." That idea still explains why coral reefs thrive in clear tropical water that holds very little dissolved food.

For aquarists, symbiosis is more than biology trivia. Nearly every lighting and nutrient decision you make is really a decision about keeping this partnership balanced. This guide walks through what the research shows and how it translates to a glass box.

Who the symbionts are: the 2018 reclassification

For decades, all coral symbionts were lumped into one genus, Symbiodinium, then split informally into "clades" A through I. In 2018, LaJeunesse and colleagues published a systematic revision in Current Biology that raised the group to family level, Symbiodiniaceae, and formally described several of the old clades as separate genera. They include Symbiodinium (formerly clade A), Breviolum (B), Cladocopium (C), Durusdinium (D) and others. Their genetic analysis suggested the family is ancient, with deep divergences among lineages, and that the "clades" differ about as much as genera do in other groups of dinoflagellates.

Why should a reefer care? Different symbionts behave differently. Research on trace metals, for example, found that Symbiodiniaceae genera differ in their iron and trace-metal needs (Reich et al., 2020). Durusdinium is widely studied because it's associated with heat tolerance in some corals. The same coral species can host different symbionts in different places. That helps explain why two frags of the "same" coral can respond differently to the same tank.

The carbon deal: how much food comes from light

The classic measurements come from a series of 1984 studies on the Red Sea coral Stylophora pistillata, a species many reefers keep. Muscatine, Falkowski, Porter and Dubinsky measured the full daily carbon budget of colonies growing in bright light and in shade:

• Less than 5% of the carbon the algae fixed went into growing more algae. More than 95% of net fixed carbon was translocated to the coral host (Muscatine et al., 1984).
• In high-light colonies, translocated carbon supplied about 143% of the animal's daily respiration needs. In other words, light alone could cover the coral's basic metabolism with some left over for growth. In shade colonies it covered about 58%.
• A companion paper summarized the consequence: shade colonies had to get about 60% of their reduced carbon heterotrophically, by feeding (Falkowski et al., 1984).

Falkowski and colleagues added a twist that matters a lot in aquariums. Although the coral gets plenty of carbon, very little of it is turned into new tissue, "apparently because the translocated products are deficient in nitrogen." Sugars are energy, not building material. To grow tissue, a coral needs nitrogen and phosphorus, either from the water or from food.

What this means for aquarium lighting

The 1984 numbers give a research-based rationale for something reefers learn by trial and error: light is food, but only up to a point.

More light is more energy, not unlimited growth

A coral under strong light can meet its whole energy budget from its algae. A coral in shade depends much more on feeding. That matches what reefers see. High-light SPS like Acropora generally need intense PAR. Many LPS and soft corals do well under moderate light, especially when they're fed. Our lighting and PAR guide covers typical hobby PAR ranges by coral type.

The research also shows that energy without nutrients doesn't build tissue. Turning up the lights in a tank with almost no nitrate and phosphate gives corals more sugar but not the nitrogen and phosphorus they need to use it. The next sections explain why that combination can cause trouble.

Light stress hits the algae first

In bleaching, the symbiosis breaks down and the coral loses its algae, its pigments or both. Weis (2008) reviewed the cell-level mechanisms. Under stress, the algae's photosynthetic machinery is damaged and produces reactive oxygen species that harm both partners, and the coral ends up expelling or digesting its symbionts. Heat is the main driver on wild reefs, but excess light makes it worse. That's why a sudden jump in light intensity, such as a new LED fixture at full power, can bleach aquarium corals even at normal temperature. Acclimate corals to new lighting gradually. See our bleaching science guide for details.

Nitrogen: the leash on the symbionts

Inside a healthy coral, the algae divide very slowly. In the Muscatine study, under 5% of fixed carbon went into new algal cells. What keeps them from multiplying out of control? A leading explanation is nitrogen limitation. In their 2015 review, Rädecker and colleagues argued that nitrogen cycling inside the coral holobiont (the coral, its algae and its microbes) is central to how the symbiosis works. By keeping its algae short of nitrogen, the coral keeps the algal population in check and receives more of their carbon as surplus.

A 2019 review by Morris, Voolstra, Quigley, Bourne and Bay in Trends in Microbiology built on this idea. Nutrient availability and metabolism affect how stable the coral–Symbiodiniaceae partnership is. Too much nutrient can tip the algae toward keeping resources for themselves. Too little, or the wrong balance, can starve the partnership.

This is one reason a tank with very high nitrate often grows corals that look brown. The algae multiply on the extra nitrogen and the tissue darkens, a familiar hobby pattern described in our browning out glossary entry.

Not all nitrogen is equal

In 2015, Ezzat, Maguer, Grover and Ferrier-Pagès tested how nitrogen form and N:P ratio affect the carbon deal in Stylophora pistillata. Under low phosphate (0.05 µM), adding 3 µM nitrate significantly decreased carbon fixation and carbon translocation to the host compared with controls. When nitrate was replaced by ammonium, those processes were enhanced. A combined enrichment of ammonium and phosphate shifted nutrients toward the symbionts "at the detriment of the host."

To put those lab concentrations in hobby units, 3 µM nitrate is about 0.19 ppm NO₃ and 0.05 µM phosphate is about 0.005 ppm PO₄. Both are low by aquarium standards. The finding isn't that nitrate is toxic. It's that nitrate added when phosphate is scarce changed how carbon moved through the symbiosis, and not in the coral's favor.

Phosphorus: the nutrient reefers forget

Phosphorus is needed for cell membranes (phospholipids), DNA and RNA, and the energy molecule ATP. Wiedenmann and colleagues (2013) showed in Nature Climate Change that elevated dissolved inorganic nitrogen combined with limited phosphate made corals more susceptible to heat- and light-induced bleaching. Lipid analysis of the algae showed a marked build-up of sulpholipids. Algae swap these in for phospholipids when they're short of phosphorus, and together with higher phosphatase activity this pointed to phosphate starvation of the symbionts. In short, an imbalanced N:P supply starved the algae of phosphorus and lowered their stress tolerance.

Our guide to ultra-low nutrient research covers the follow-up work, and our nitrate and phosphate guide covers practical targets and export methods.

Feeding: the other half of coral nutrition

Corals aren't just solar panels. Houlbrèque and Ferrier-Pagès (2009) reviewed decades of work on heterotrophy (feeding) in tropical scleractinian corals. Corals capture zooplankton, particles and dissolved organic matter, and this food can supply nitrogen and phosphorus that photosynthesis can't. Their review describes heterotrophy as an important source of nutrients that can support tissue growth and, in many studies, photosynthesis and calcification as well.

The bleaching literature makes the same point. Grottoli, Rodrigues and Palardy (2006) found that corals able to increase their feeding rates while bleached and recovering showed greater resilience. Some species can switch toward feeding when their algae fail.

In the aquarium, that supports a balanced approach: light for energy, plus regular feeding of fish (whose waste supplies nitrogen and phosphorus) and, where appropriate, target-feeding of LPS and other fleshy corals. Non-photosynthetic corals (NPS) are the extreme case. With no symbionts, they depend entirely on food.

Putting it into practice in your tank

The research doesn't hand us exact aquarium targets. Most experiments use a few species under controlled lab conditions. But it supports several practical principles:

1. Match light to nutrients. High light with near-zero nitrate and phosphate is a mismatch: lots of energy and no building material. If you push PAR up for SPS, make sure nutrients aren't bottoming out. Test with a low-range phosphate checker, not a kit that can't read below 0.1 ppm.
2. Keep nitrogen and phosphorus in proportion. Research points to imbalance, especially high nitrogen with very low phosphate, as a bleaching risk factor. Watch the ratio, not just each number.
3. Feed the reef. Fish food is the main nutrient input in most tanks. Shade-dwelling and fleshy corals rely more on feeding.
4. Change light slowly. Sudden intensity increases stress the algae's photosynthetic machinery. Ramp new fixtures up over weeks, and photo-acclimate new frags.
5. Keep conditions stable. Symbiosis is a balance, and sudden swings in temperature, light, alkalinity or nutrients push it off course. Use the dosing calculator to correct parameters in small daily steps.
6. Expect individuality. Different symbiont genera have different needs and tolerances, so the same coral species may respond differently in different tanks.

Summary

Reef corals depend on Symbiodiniaceae algae that pass most of their photosynthetic carbon to the host. Classic measurements put this at more than 95% of net fixed carbon in Stylophora. Light supplies energy, but coral tissue growth also needs nitrogen and phosphorus, which come from the water and from feeding. Research shows that the balance of those nutrients matters. Nitrogen-rich, phosphorus-starved conditions disrupt carbon sharing and raise bleaching risk. For reefers, that means matching light to nutrients, feeding sensibly, testing phosphate with a low-range method, and changing anything slowly.

Frequently asked questions

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More reef science guides

• Alkalinity, calcium & magnesium
• Nitrogen cycle & cycling
• Nitrate & phosphate
• Salinity & RO/DI
• Lighting & PAR
• Coral types & care
• Pests & diseases
• Reef conservation & science
• Coral bleaching science
• Ultra-low nutrient research
• Ocean acidification & calcification
• Coral restoration & microfragmentation
• ICP testing & trace elements

References

1. Ezzat L, Maguer JF, Grover R, Ferrier-Pagès C (2015). New insights into carbon acquisition and exchanges within the coral–dinoflagellate symbiosis under NH4+ and NO3− supply. Proceedings of the Royal Society B 282:20150610. doi:10.1098/rspb.2015.0610
2. Falkowski PG, Dubinsky Z, Muscatine L, Porter JW (1984). Light and the bioenergetics of a symbiotic coral. BioScience 34(11):705–709. doi:10.2307/1309663
3. Grottoli AG, Rodrigues LJ, Palardy JE (2006). Heterotrophic plasticity and resilience in bleached corals. Nature 440:1186–1189. doi:10.1038/nature04565
4. Houlbrèque F, Ferrier-Pagès C (2009). Heterotrophy in tropical scleractinian corals. Biological Reviews 84(1):1–17. doi:10.1111/j.1469-185X.2008.00058.x
5. LaJeunesse TC, Parkinson JE, Gabrielson PW, Jeong HJ, Reimer JD, Voolstra CR, Santos SR (2018). Systematic revision of Symbiodiniaceae highlights the antiquity and diversity of coral endosymbionts. Current Biology 28(16):2570–2580. doi:10.1016/j.cub.2018.07.008
6. Morris LA, Voolstra CR, Quigley KM, Bourne DG, Bay LK (2019). Nutrient availability and metabolism affect the stability of coral–Symbiodiniaceae symbioses. Trends in Microbiology 27(8):678–689. doi:10.1016/j.tim.2019.03.004
7. Muscatine L, Falkowski PG, Porter JW, Dubinsky Z (1984). Fate of photosynthetic fixed carbon in light- and shade-adapted colonies of the symbiotic coral Stylophora pistillata. Proceedings of the Royal Society of London B 222:181–202. doi:10.1098/rspb.1984.0058
8. Muscatine L, Porter JW (1977). Reef corals: mutualistic symbioses adapted to nutrient-poor environments. BioScience 27(7):454–460. doi:10.2307/1297526
9. Reich HG, Rodriguez IB, LaJeunesse TC, Ho TY (2020). Endosymbiotic dinoflagellates pump iron: differences in iron and other trace metal needs among the Symbiodiniaceae. Coral Reefs 39:915–927. doi:10.1007/s00338-020-01911-z
10. Rädecker N, Pogoreutz C, Voolstra CR, Wiedenmann J, Wild C (2015). Nitrogen cycling in corals: the key to understanding holobiont functioning?. Trends in Microbiology 23(8):490–497. doi:10.1016/j.tim.2015.03.008
11. Weis VM (2008). Cellular mechanisms of Cnidarian bleaching: stress causes the collapse of symbiosis. Journal of Experimental Biology 211:3059–3066. doi:10.1242/jeb.009597
12. Wiedenmann J, D'Angelo C, Smith EG, Hunt AN, Legiret FE, Postle AD, Achterberg EP (2013). Nutrient enrichment can increase the susceptibility of reef corals to bleaching. Nature Climate Change 3:160–164. doi:10.1038/nclimate1661

Ranges are common hobby targets compiled from reef chemistry literature (including Randy Holmes-Farley's articles), hobby consensus and manufacturer documentation. They're not rules. Last reviewed 2026-10-15.