Coral Holobionts: A Secret Society under the Waves

From early classifications marking them as stones, to the gradual understanding of their plant-like morphology, you could say that corals have had a colourful history. In fact, medieval scholars from the 1st century AD used to believe that corals were ambiguous entities caught between plants, animals and minerals (1), explaining a possible evolutionary connection between the three, until prominent natural scientist William Herschel finally revealed their animal cell composition in the 18th century (2). But if not hardened ‘underwater flowers’ or some sort of ‘boundary organism’, what even are corals?

Essentially classified under the kingdom Animalia, corals are further categorised under the phylum Cnidaria (the same phylum to which jellyfish belong) and class Anthozoa, as they are considered aquatic invertebrate animals. They are made up of tiny animals called polyps, each with a mouth surrounded by tentacles and a central digestive cavity. Most reef-building corals secrete a hard skeleton of calcium carbonate (CaCO₃). Over generations, the accumulated skeletons of colonies form the foundation of coral reefs, creating habitats for an extraordinary diversity of marine life (3). So, when we’re talking about ‘coral reefs’…what exactly are we referring to? The hardened calcium-base structure? The fragile polyps inside? 

Neither. We’re referring to the countless partnerships that collectively sustain our Earth’s most biodiverse ecosystems: the coral holobiont.  

Each coral ‘colony’ can host a community of microorganisms, including bacteria, archaea, fungi, viruses and microscopic algae. Together, the coral and its associated organisms form a holobiont: an ecological partnership in which multiple forms of life coexist and interact (4). The combined genetic information of the host and its associated organisms is called the hologenome. Whether this collective should be considered a single unit of evolution remains debated, but the concept highlights an important point: coral health cannot always be understood by studying the animal alone (4).

Symbiosis: Partnerships built on mutual benefits

One of the best-known symbiotic relationships corals have is with photosynthetic dinoflagellates from the family Symbiodiniaceae. These microscopic algae live within coral tissues and use sunlight to convert carbon dioxide into organic compounds through photosynthesis. The coral receives some of this energy-rich material, helping support its metabolism, growth and skeleton formation. In return, the algae gain shelter, access to nutrients and a relatively stable environment (5).

Many other members of the coral microbiome may contribute to nutrient cycling, chemical defence and the breakdown of organic matter. However, these functions differ among coral species and microbial communities; the mere presence of a microorganism or a particular gene doesn't automatically prove that it benefits its coral host (4).

The ‘partnership’ between corals and microorganisms isn’t simply a fixed arrangement, but a network of exchanges shaped by the surrounding environment. Light, temperature, food availability and water chemistry can alter which organisms thrive and how they interact. Therefore, two corals that look similar may depend on very different biological relationships.

Two corals, two ways of life

1. Staghorn corals (Acropora millepora): Powered by sunlight

Acropora millepora, otherwise commonly known as staghorn coral, is a branching, reef-building coral found in shallow tropical waters, mostly in the western and central Indo-Pacific. Its relationship with Symbiodiniaceae illustrates how photosynthesis can power life in nutrient-poor environments. Sunlight penetrates the shallow water, allowing the dinoflagellates to fix inorganic carbon into organic compounds like glycerol, glucose, and amino acids. Some of these compounds are transferred to the coral, providing an important source of energy, and supporting growth and calcification (5).

The coral, in turn, offers the algae a protected place to live, and access to carbon dioxide and nutrients produced through the host’s metabolism. This exchange helps explain how tropical reefs can flourish in waters where nutrients are often scarce. Yet, there exists a glaring vulnerability: when seawater becomes excessively warm, their symbiosis can be disrupted. The coral may lose or expel its algae, or their pigments, causing the colony to appear white in a process known as coral bleaching (5,7).

2. Eye corals (Desmophyllum pertusum): Deep down in the dark

Far below the sunlit surface, the cold-water coral Desmophyllum pertusum, commonly known as eye coral but formerly known as Lophelia pertusa, builds reefs in darkness. Unlike many tropical reef-building corals, it doesn't rely completely on photosynthetic Symbiodiniaceae. Instead, it obtains energy by capturing zooplankton and organic particles from the surrounding water (8).

For the eye coral, like other deep-sea corals, its microbiomes include bacteria from groups historically classified as Bacteroidetes, Firmicutes and Actinobacteria. Also, research comparing deep-water and tropical coral-associated microbial communities found a greater representation of genes associated with chitin degradation in the deep-water communities examined (10). Chitin forms part of crustacean exoskeletons, so these genes suggest the potential to break down material from marine organisms. However, it isn’t fully clear whether those particular strains from all three groups directly digest crustacean remains for the coral’s benefit or for their own.

A further possibility emerges where cold-water corals occur near methane seeps, where microbial communities can use chemical energy rather than sunlight. Some sulfur-oxidising bacteria obtain energy by oxidising reduced sulfur compounds and use it to fix inorganic carbon into organic molecules. Research suggests that certain deep-sea corals may associate with these microbes, but the strength and significance of these relationships vary between species and locations (11). For D. pertusum, the contribution of seep-derived carbon to nutrition remains uncertain; thus, it shouldn’t be assumed that this coral routinely depends on sulfur-based chemosynthesis (11).

As illustrated in the image above, together, these two corals reveal different ways of life: one sustained by a sunlight-powered symbiosis with photosynthetic microalgae, the other by filter food capture and bacterial processing in the deep, dark sea, with possible additional chemical-energy pathways in seep-like environments. In all of this, the holobionts also provide shelter, nutrition and other resources to macroorganisms like marine animals and plants.  

Then, what makes an individual?

If a coral’s survival depends on organisms living within and around it, where does the individual begin and end? Is a coral the animal itself, or the broader community that sustains its survival and functionality?

Holobionts as a concept encourage scientists to consider the coral as part of a changing biological network. The organisms within that ecological network aren’t necessarily permanent, nor do they always share identical interests. Microbial communities can change with environmental conditions, and some associations may be beneficial in one context but less useful in another (4). A coral is, therefore, both an organism in its own right, and a participant in a wider ecological system. This complexity makes the idea of biological individuality less like a hard boundary, and more like a shifting mosaic.

How do holobionts get disrupted, and what happens then? 

Climate change is placing coral partnerships under increasing pressure. During marine heatwaves, elevated temperatures can disrupt the coral–algal relationship and trigger bleaching. Bleaching doesn't necessarily mean a coral is dead: if conditions improve quickly enough, surviving corals may regain their symbionts and recover in time. If stress is intense or prolonged, however, the entire reef may starve, become more vulnerable to disease, or die (5,7).

A recent investigation of living and fossil corals from the Galápagos Islands shows how reefs can preserve evidence of past environmental shocks. By analysing chemical signatures in coral skeletons, researchers reconstructed patterns of El Niño and La Niña over a long period. Their findings indicate that El Niño events during the past four decades were stronger than those recorded in the sampled millennium, with the intensification occurring alongside global warming (13). This association is concerning because El Niño can bring unusually warm waters and weaken nutrient-rich upwelling in the region.

The coral cores also contained “death horizons”: layers of calcified material produced by other reef organisms, including algae, gastropods and barnacles, that interrupted the coral skeleton during periods of mortality. Despite that, in some cases, coral growth later resumed over these surfaces (9). These layers reveal that reef recovery is possible, but not guaranteed. So, a surviving skeleton can provide a surface for new growth, but a reef’s future still largely depends on whether living corals can settle, grow and withstand further stress.

Moreover, other pressures compound the problem. Sediment runoff can cloud water, reduce light and smother coral tissue. Changes in ocean circulation can alter temperature, food supply and nutrient availability. Deep-sea mining may damage fragile cold-water coral habitats directly or disturb sediments that affect nearby ecosystems. Together, all these stressors can alter not only coral survival, but also the microbial communities and ecological relationships on which corals depend.

Understanding the holobiont and protecting it

Conservation researchers are exploring assisted evolution, selective breeding and the use of heat-tolerant algal partners to improve coral resilience, because understanding coral holobionts helps us know the nature of the interactions among various species. Microbiome manipulation, including introducing potentially beneficial microbes, is another area of investigation, although its effectiveness and ecological safety require further testing (14). These approaches may contribute to restoration, but they cannot replace our collective effort in reducing greenhouse gas emissions and protecting reefs from local stressors.

Furthermore, corals don’t need soil to establish a reef. Their planulae (coral’s larvae) can settle on suitable hard surfaces, including the calcium carbonate skeletons of earlier generations. As colonies grow, they build upon this foundation; other organisms, both micro and macro, can also colonise and reshape it. In a beautiful yet grim way, a coral’s skeleton is both a record of past life and a platform for future communities (3, 13). Unfortunately though, a dead reef structure alone doesn't guarantee recovery: successful regrowth depends on living corals, suitable conditions and the return of ecological relationships.

All in all, coral holobionts reveal that life is rarely an isolated journey. From tropical, sunlit branches to cold, dark seafloors, corals survive through different combinations of inter- and intra-species relationships, resources and environmental conditions. Like a kaleidoscope, each reef forms a distinctive pattern from many interacting parts. Protecting these ecosystems means preserving not only the coral animals, but also the intricate relationships that allow reefs to grow, adapt and endure while providing a place to sustain life for other organisms of varying shapes and sizes.

References

1. Why have corals long baffled scientists? [Internet]. Fondation Tara Océan. 2026 [cited 2026 Oct 23]. Available from: https://fondationtaraocean.org/en/scientific-news/the-history-of-science-and-coral/

2. Herschel W. The scientific papers of sir William Herschel. 1912.

3. National Oceanic and Atmospheric Administration. What are coral reefs made of? Silver Spring (MD): NOAA; [cited 2026 Oct 19]. Available from: https://oceanservice.noaa.gov/facts/coralmadeof.html 

4. van Oppen MJH, Blackall LL. Coral microbiome dynamics, functions and design in a changing world. Nat Rev Microbiol. 2019;17(9):557-567. doi:10.1038/s41579-019-0223-4.

5. Roth MS. The engine of the reef: photobiology of the coral-algal symbiosis. Front Microbiol. 2014;5:422. doi:10.3389/fmicb.2014.00422.

6. Acropora millepora acropora millepora or plate acropora [Internet]. Reeflex.net. 2026 [cited 2026 Oct 22]. Available from: https://reeflex.net/tiere/608_Acropora_millepora.htm

7. Weis VM. Cellular mechanisms of Cnidarian bleaching: stress causes the collapse of symbiosis. J Exp Biol. 2008;211(Pt 19):3059-3066. doi:10.1242/jeb.009597.

8. Roberts JM, Wheeler AJ, Freiwald A. Reefs of the deep: the biology and geology of cold-water coral ecosystems. Science. 2006;312(5773):543-547. doi:10.1126/science.1119861.

9. dfopacific. Deepwater coral (desmophyllum pertusum) [Internet]. iNaturalist. 2019 [cited 2026 Oct 22]. Available from: https://www.inaturalist.org/observations/42866226

10. Pratte Z, et al. Functional gene composition and metabolic potential of deep-sea coral-associated microbial communities. Coral Reefs [Internet]. 2023 [cited 2026 Oct 19]. Available from: https://link.sprhttps://doi.org/10.1186/s40168-025-02254-zinger.com/article/10.1007/s00338-023-02409-0 

11. Vohsen S, et al. Deep-sea corals near cold seeps associate with sulfur-oxidizing chemoautotrophs in the family Ca. Thioglobaceae. Microbiome [Internet]. 2025 [cited 2026 Oct 19]. Available from: https://link.springer.com/article/10.1186/s40168-025-02254-z 

12. Gong S, Liang J, Jin X, Xu L, Zhao M, Yu K. Unfolding the secrets of microbiome (Symbiodiniaceae and bacteria) in cold-water coral. Kormas KA, editor. Microbiology Spectrum. 2023 Oct 17;11(5).

13. Cole J. Galápagos corals show El Niño events are more extreme now than in past 1,000 years—here’s how my team made the discovery [Internet]. The Conversation. 2026 Aug 27 [cited 2026 Oct 19]. Available from: https://theconversation.com/galapagos-corals-show-el-nino-events-are-more-extreme-now-than-in-past-1-000-years-heres-how-my-team-made-the-discovery-272318

14. van Oppen MJH, Oliver JK, Putnam HM, Gates RD. Building coral reef resilience through assisted evolution. Proc Natl Acad Sci U S A. 2015;112(8):2307-2313. doi:10.1073/pnas.1422301112.