Beyond the Symbiodiniaceae — Protist symbionts of the coral holobiont

The coral holobiont — the animal host together with its associated microbes — has been studied mostly through two of its members: the photosynthetic dinoflagellates of the Symbiodiniaceae and the coral-associated bacteria. The microbial eukaryotes are the great enigma of the system. Protists and fungi are abundant and widespread in corals, yet only a handful have been characterised, fewer still have been cultured, and fewer again have genomes available. Most of what we know about their identity comes from ribosomal RNA metabarcoding, leaving their biology and their contribution to the holobiont largely unresolved. Our work aims to bring this hidden eukaryome into focus — to establish who these symbionts are, where they live, how they evolved, and what they do for, or to, their hosts.

A central thread has been the corallicolids, a group of apicomplexans — the same eukaryotic lineage that includes the agents of malaria and toxoplasmosis. We contributed to the discovery that these parasites are core members of the coral microbiome: widespread across coral groups, at times nearly as abundant as the Symbiodiniaceae, and carrying a non-photosynthetic plastid that nonetheless retains the genes for chlorophyll biosynthesis. More recent phylogenomic work has placed the corallicolids firmly among the apicomplexans, close to the coccidians, and traced a surprising evolutionary history in which the ability to make chlorophyll was retained long after photosynthesis itself was lost, then shed repeatedly and independently across the group. We have also begun to map how these parasites move through reef ecosystems, identifying the bearded fireworm as a probable non-coral reservoir and vector. Alongside the corallicolids, we have worked to characterise other overlooked partners, including Ostreobium, the endolithic green alga that bores into coral skeletons and represents one of the most prevalent yet least understood “other” coral symbionts.

Scaling these questions from single lineages to whole communities, we carried out the first global survey of the coral eukaryome, using an anti-metazoan 18S rRNA primer set that suppresses host DNA so that the rarer microbial-eukaryote signal can be read. Sampling corals and other anthozoans across the Caribbean, the Red Sea, and the Pacific — spanning robust and complex scleractinians, black corals, octocorals, anemones, zoanthids, and more — this work shows that protist communities are structured by host and geography: corallicolids dominate in robust corals, for instance, while distinct dinoflagellates and Ichthyodinida prevail in black corals and octocorals. Complementary analyses of the Tara expedition datasets place this diversity in a wider oceanic context, distinguishing the corallicolids that stay with coral hosts from the broader sweep of marine apicomplexans found across plankton and sediments, and resolving how that parasite diversity is partitioned across ocean basins.

These symbionts are not biological curiosities; they bear on coral health under the climate crisis. In the Mediterranean gorgonian Paramuricea clavata, we found that the presence of apicomplexans predicts mortality under thermal stress, and during the 2022 Mediterranean marine heatwaves the eukaryome of the red coral Corallium rubrum shifted in step with colony health, with corallicolids and other microeukaryotes tracking the intensity of heat stress. Increasingly, these microeukaryotes also feature in integrative, holobiont-scale studies from the lab — from in situ diel-rhythm transcriptomics to single-cell atlases of coral bleaching — where the protist community is read alongside the host and its bacterial and algal partners. Because most of these organisms resist cultivation, we lean on genomics, transcriptomics, and phylogenomics — including the recovery of symbiont sequence hidden in published coral datasets — to move from cataloguing diversity toward understanding function and resolving the precise position of these lineages in the tree of life.

Selected publications

• Leboine C, del Rio-Hortega L, Henry N, … del Campo J, … Porcel BM (2026). Hidden apicomplexan parasite diversity links coral and plankton microbiomes across reef seascapes. bioRxiv. Preprint
• Jacko-Reynolds VKL, Kwong WK, Livingston SJ, Trznadel M, Bonacolta AM, Lax G, Shivak J, Irwin NAT, Vermeij MJA, del Campo J, Keeling PJ (2025). Phylogenomics of coral-infecting corallicolids reveal multiple independent losses of chlorophyll biosynthesis in apicomplexan parasites. Current Biology 35:1156–1163.e4. doi:10.1016/j.cub.2025.01.028
• Bonacolta AM, Weiler BA, Grimes CJ, Trznadel M, Vermeij MJA, Keeling PJ, del Campo J (2025). Fireworms are a reservoir and potential vector for coral-infecting apicomplexans. The ISME Journal 19:wraf078. doi:10.1093/ismejo/wraf078
• Prioux C, Ferrier-Pagès C, del Campo J, Guillou L, Estaque T, Allemand D, Tignat-Perrier R (2025). Unraveling the impact of marine heatwaves on the eukaryome of the emblematic Mediterranean red coral Corallium rubrum. ISME Communications 5:ycaf035. doi:10.1093/ismeco/ycaf035
• Weiler BA, Kron N, Bonacolta AM, Vermeij MJA, Baker AC, del Campo J (2026). Global diversity and distribution of coral-associated protists. bioRxiv. Preprint
• Bonacolta AM, Miravall J, Gómez-Gras D, Ledoux JB, López-Sendino P, Garrabou J, Massana R, del Campo J (2024). Differential apicomplexan presence predicts thermal stress mortality in the Mediterranean coral Paramuricea clavata. Environmental Microbiology 26:e16548. doi:10.1111/1462-2920.16548
• Bonacolta AM, Weiler BA, Porta-Fitó T, Sweet M, Keeling PJ, del Campo J (2023). Beyond the Symbiodiniaceae: diversity and role of microeukaryotic coral symbionts. Coral Reefs 42:567–577. doi:10.1007/s00338-023-02352-0
• Kwong WK, del Campo J, Mathur V, Vermeij MJA, Keeling PJ (2019). A widespread coral-infecting apicomplexan with chlorophyll biosynthesis genes. Nature 568:103–107. doi:10.1038/s41586-019-1072-z
• del Campo J, Pombert J-F, Šlapeta J, Larkum A, Keeling PJ (2017). The ‘other’ coral symbiont: Ostreobium diversity and distribution. The ISME Journal 11:296–299. doi:10.1038/ismej.2016.101

Related work — holobiont-scale studies with a microeukaryote component

• Weiler BA, Kron N, Bonacolta AM, Vermeij MJA, Baker AC, del Campo J (2026). Temporal transcriptional rhythms govern coral-symbiont function and microbiome dynamics. Cell Host & Microbe 34:304–323.e4. doi:10.1016/j.chom.2026.01.004
• Bonacolta AM, Snyder GA, Karp RF, Yeager E, Wen ADE, Dykman CE, Nonell J, Traylor-Knowles N, Baker AC, del Campo J (2024). A single-cell atlas of coral bleaching. Research Square (preprint). doi:10.21203/rs.3.rs-5397639/v1