Symbionts and the survival of corals

New research reports raise hopes that assisted evolution of coral holobionts may help protect them from bleaching due to global warming.

Many corals depend on photosynthetic symbionts. It’s been known for almost 140 years that many corals harbour symbiotic microbes known colloquially as zooxanthellae within their tissues. Although corals possess tentacles and stinging cells that enable them to can feed on prey (varying from plankton to small fish), many coral species depend for most of their nutrition on the photosynthetic activities of the zooxanthellae. This is especially important in tropical and sub-tropical waters, where the high yield of photosynthetic activity leads to the building of reefs due to deposition of the calcium carbonate skeleton. Secretion of mucus also provides a major source of nutrients — this is why coral reefs provide such productive and diverse “oases” in the “deserts” of oligotrophic oceans. These symbionts are members of the group of protists known as dinoflagellates and are assigned to the family Symbiodiniaceae. Many studies have revealed extensive phylogenetic diversity within this family, enabling strains to be grouped into different clades (A-I), which differ in their host range and physiological properties. In particular, differences in their sensitivity to light, temperature. pH and other stressors have critical implications for the survival of coral species in response to rapidly changing environmental threats from climate change and pollution. The basis of the differences between different clades proved exceptionally difficult to unravel due to the complexity of dinoflagellate genomes. However, by combining analysis of morphological and physiological features with molecular analysis of multiple genes, LaJeunesse et al. (2018) and Nitschke et al. (2020) have now classified Symbiodiniaceae clades A-G into distinct named genera. The most important genera (clades) in corals are Symbiodinium (A), Breviolum (B), Cladocopium (C) and Durusdinium (D).

Left, golden-brown zooxanthellae. Individual cells are 6-10 µm. [Credit: Todd LaJeunesse]. Right, Diagrammatic representation of a coral polyp with cross-section showing the habitats of microbes within the mucus and tissues (not to scale). Zooxanthellae are represented as large gold cells within the gastroderm. Aggregates of bacteria observed in some corals are shown as black clusters. [Credit: Colin Munn].

Coral bleaching occurs when host-symbiont interactions are disturbed. The importance of the Symbiodiniaceae endosymbionts to many tropical corals is shown dramatically by the phenomenon of bleaching, for which the main triggers are increased sea surface temperature (SST) and solar irradiation. Photo-oxidative stress on the photosynthetic system and leakage of damaging reactive oxygen species (ROS) leads to expulsion of the symbionts. Prolonged or intense bleaching leads to mortality of the corals and major shifts in the reef ecosystem. Until the 1980s, mass bleaching events occurring over a large region were rare, but they now occur with increased frequency and severity due to global climate change (Hughes et al., 2018; Sully et al., 2019). There is now insufficient time between bleaching events for corals to recover, and the situation will worsen as global CO2 emissions continue to rise. Mass bleaching — as well as diseases and other phase shifts in microbial activity due to pollution and overfishing — is leading to irreversible degradation of major reef systems. This will have profound implications for marine biodiversity and for the safety and livelihoods of millions of people in affected areas.

Early (left) and late stages of coral bleaching on the Great Barrier Reef. [Credit: Mary Wakeford, AIMS].

Symbiont diversity affects nutrition and environmental tolerance of the coral holobiont. A coral colony can be described as a “holobiont” — an assemblage of different organisms that functions as an ecological unit. Besides the photosynthetic zooxanthellae (note that not all corals contain these), we now know that the tissues, skeleton and secreted mucus layer of the animal host also contain many other kinds of intra- and extracellular microbes — these include other protists, bacteria, archaea, fungi, and viruses — which contribute to the nutrition and health of the host. Some of these organisms are core members of niche microhabitats (different tissues, mucus, and skeleton) within particular coral species, while others form more transient associations. Many studies have provided evidence to support the concept first proposed by Buddemeier & Fautin (1993) that bleaching is a natural process, by which corals can adapt to changing environmental conditions by “shuffling” or re-assortment of symbionts already present, or by acquiring new types of symbiont better suited to the conditions. Of special interest is the finding that Durusdinium (formerly clade D) is more resilient to higher temperatures. It is one of the most dominant endosymbionts in corals inhabiting reefs with warmest waters (such as the Persian Gulf) and experiments show that it has a that members of this clade are often acquired as a temporary replacement to Symbiodinium, Breviolum or Cladocopium (formerly clades A, B and C). Several studies have shown that there is a physiological cost to hosting the thermotolerant clade, because it results in lower provision of nutrients to the coral — Durusdinium can be regarded as more of an opportunist (more “selfish”?) symbiont than a well-adapted mutualist. The abundance of different symbionts in coral colonies often varies at different depths, depending on water temperature and light availability.

A recent paper by scientists from the Hawaii Institute of Marine Biology (HIMB) showed that the relative distribution of Cladocopium and Durusdinium in the coral Montipora capitata varies with depth in Kaneh’oe Bay, with the heat-tolerant strains more abundant in colonies at shallower depths (Wall et al., 2020). The reefs of Kaneh’oe Bay have a long history of human impacts like pollution, dredging and heatwaves, and the authors conclude that this may have allowed a niche for the stress-tolerant Durusudinium to exploit, thus becoming dominant in the shallower water. Corals obtain nutrition from both their photosynthetic symbionts (autotrophy) and from ingestion of plankton prey (heterotrophy). Wall and colleagues asked whether the balance of autotrophy and heterotrophy varied with depth and the relative distribution of the symbiont types. To determine this, they used analysis of stable isotopes of carbon and nitrogen — this revealed that the shallower corals dominated by Durusudinium had lower rates of photosynthesis and carbon fixation into their tissues, despite having higher density of symbionts. Surprisingly, the corals did not compensate by increasing the amount of nutrition obtained from heterotrophic feeding. Wall et al. (2020) concluded that the functional diversity of Symbiodiniaceae clades results in distinct holobionts with different nutritional capacities.

Reefs of Kaneh’oe Bay, showing HIMB on Coconut Island [credit: NASA Earth Right Now, via flickr]. B. Montipora capitata [credit: Wall et al. (2020) CC-BY-4.0].

Can we help corals to adapt to climate change? We know that corals have adapted to survive major environmental upheavals since their evolution began over 500 million years ago. Some recent insights into the evolution of the coral holobiont come from studies revealing how the microbial communities are shaped by environmental variables and the phylogeny and functional traits of the host (e.g. Pollock et al. 2018). This gives us some hope that we might be able to use knowledge of the microbiome for  “assisted evolution” of coral holobionts by breeding them to be more resistant to environmental stressors like increased SST. This idea has been championed by the late Ruth Gates (HIMB) and Madeleine van Oppen (Australian Institute of Marine Science/ University of Melbourne). Although careful risk-benefit analysis is needed before introducing such organisms into a natural ecosystem, such an approach can be compared to the successful use of genetic and epigenetic modification successfully used for breeding plants and animals in agriculture and aquaculture (van Oppen, 2015). Several research groups are now pursuing different approaches to explore the feasibility of this concept, focusing on different components of the microbiome (see Torda et al., 2017; Donelson et al., 2018, NAS, 2019; van Oppen & Blackall, 2019).

One strategy is to increase the thermal tolerance of Symbiodiniaceae strains. This can be achieved by growing the dinoflagellates over multiple asexual generations in lab cultures by applying stepwise 1oC temperature increases and isolating strains with the highest growth rates. This selects for adapted strains due to mutations and epigenetic changes. Using this approach, Chakravaty et al. (2017) obtained strains of Cladocopium C1 after 80 cycles that had higher photosynthetic performance and growth rate than the wild-type at 31oC; they also produced much lower levels of ROS. In vitro, the selected strains grew as well at 27oC as they did at 31oC. However, when the thermal-adapted (“heat-evolved”) symbionts were transferred to coral larvae (from three species of Acropora) at 27oC before shifting to 31oC, they didn’t confer any significant resistance to bleaching. That might have been the end of the story but the team, together with colleagues from the CSIRO Synthetic Biology lab, conducted further experiments and have reported some very promising results in a new paper (Buerger et al., 2020). In this study, tests were performed using 10 heat-evolved strains of the same C1 strain from the clonal culture after 120 generations over 4 years at 31oC, together with two wild-type strains from cultures maintained in the same way at 27oC. Like before, the heat-adapted strains grew well for three weeks at the elevated temperature in vitro (66% increase), whereas the wild-type did not (79% decline). Photochemical stress and ROS productions was minimal in all the heat-evolved strains. In this study, all 10 heat-evolved strains were then used to infect coral larvae and this showed big differences in their performance within the coral host. During the week after transfer of the corals to 31oC from 27oC, three of the heat-evolved strains showed increases (26% average) in density and protected the corals from bleaching, whereas all other strains gave no protection. (The strain used in the earlier experiments of Chakravaty et al. (2017) again showed no protection from bleaching). All strains produced by the prolonged lab treatment had similar in vitro properties, but they clearly behaved very differently when inside the host. To understand the basis of this, Patrick Buerger and colleagues looked at the gene expression profiles of the heat-tolerant and heat-sensitive holobionts containing different heat-evolved or wild-type symbionts, by extracting, amplifying and sequencing messenger RNA. This transcriptomics analysis showed great differences in the patterns of up-regulation or down-regulation among the different holobionts. The main effect displayed in the heat-evolved strains was the down-regulation of Cladocopium genes connected with the photosynthetic process. But when in symbiosis with the coral larvae, one strain (SS8) had 165 uniquely up-regulated and 227 uniquely down-regulated genes compared with other heat-evolved strains and the wild-type. The up-regulated genes include those involved in carbon fixation and synthesis of high-energy sugar molecules. This suggests that the enhanced bleaching tolerance of the coral-SS8 symbiosis is due to increased expression of genes encoding enzymes in these processes, in combination with reduced photosynthesis and active photoprotection. Gene expression of the coral host also showed distinct patterns depending on the type of symbiont present. Of special note was the finding that the transcriptomes of coral-SS8 holobionts taken before temperature increase showed up-regulation of genes associated with heat stress response genes. This suggests that strain SS8 may elicit a “front-loading” response in the host, providing benefits for avoiding the harmful affects of elevated temperature. This study suggests that detailed studies and careful evaluation of the properties of laboratory-evolved Symbiodiniaceae strains could lead to effective candidates to restore damaged reefs by introducing coral colonies better able to resist bleaching due to marine heat waves. Obviously, further studies will be needed to determine gene expression, physiological and protective effects in different coral species/symbiont partners and to test whether increased tolerance is maintained in adult colonies and their progeny long term in the field. However, these results are very welcome news to boost our hopes that assisted evolution can help in the conservation of corals until humanity can bring CO2 emissions and global warming under control.


Buerger, P., Alvarez-Roa, C., Coppin, C.W., Pearce, S.W., Chakravarti, L.J., Oakeshott, J.G., Edwards, O.R. & van Oppen, M.J.H. Heat-evolved microalgal symbionts increase coral bleaching tolerance. Science Advances, 13 May 2020, eapba2498.

Chakravarti, L. J., Beltran, V. H., & van Oppen, M. J. (2017). Rapid thermal adaptation in photosymbionts of reef‐building corals. Global Change Biology23(11), 4675-4688.

Donelson, J. M., Salinas, S., Munday, P. L., & Shama, L. N. (2018). Transgenerational plasticity and climate change experiments: Where do we go from here?. Global Change Biology24(1), 13-34.

Hughes, T. P., Kerry, J. T., Baird, A. H., Connolly, S. R., Dietzel, A., Eakin, C. M., … & McWilliam, M. J. (2018). Global warming transforms coral reef assemblages. Nature556, 492-496.

NAS (2019). Interventions to increase the resilience of coral reefs. National Academies of Science, Engineering and Medicine. Online at Accessed 15 May 2020.

Nitschke, M. R., Craveiro, S. C., Brandão, C., Fidalgo, C., Serôdio, J., Calado, A. J., & Frommlet, J. C. (2020). Description of Freudenthalidium gen. nov. and Halluxium gen. nov. to formally recognize clades Fr3 and H as genera in the family Symbiodiniaceae (Dinophyceae). Journal of Phycology, 08 April 2020,

Pollock, F. J., McMinds, R., Smith, S., Bourne, D. G., Willis, B. L., Medina, M., Thurber, R.V. & Zaneveld, J. R. (2018). Coral-associated bacteria demonstrate phylosymbiosis and cophylogeny. Nature communications9(1), 1-13.

Sully, S., Burkepile, D. E., Donovan, M. K., Hodgson, G., & Van Woesik, R. (2019). A global analysis of coral bleaching over the past two decades. Nature communications10(1), 1-5.

Torda, G., Donelson, J. M., Aranda, M., Barshis, D. J., Bay, L., Berumen, M. L., … & Miller, D. J. (2017). Rapid adaptive responses to climate change in corals. Nature Climate Change7(9), 627-636.

Wall, C. B., Kaluhiokalani, M., Popp, B. N., Donahue, M. J., & Gates, R. D. (2020). Divergent symbiont communities determine the physiology and nutrition of a reef coral across a light-availability gradient. The ISME Journal, 14, 945-958.

van Oppen, M. J., & Blackall, L. L. (2019). Coral microbiome dynamics, functions and design in a changing world. Nature Reviews Microbiology17(9), 557-567.

van Oppen, M. J., Oliver, J. K., Putnam, H. M., & Gates, R. D. (2015). Building coral reef resilience through assisted evolution. Proceedings of the National Academy of Sciences112(8), 2307-2313.

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