The marine animal eukaryome — Protist symbionts from mutualists to parasites

Almost every animal is also a habitat. Beyond the bacteria that dominate most microbiome studies, marine animals host a rich community of microbial eukaryotes — protists — that span the entire symbiotic spectrum, from mutualists and commensals to parasites and pathogens. This animal eukaryome remains poorly known: microeukaryotes are hard to detect against an overwhelming background of host DNA, many cannot be cultured, and most lack a genome or even a name. We study who these symbionts are, where they sit in the tree of life, how they evolved their host-associated lifestyles, and how a warming ocean reshapes their impact on animal health.

Parasites and partners across the animal tree

A recurring theme is parasitism by two of the most successful protist lineages in the sea — the apicomplexans and the dinoflagellates. We helped show that the enigmatic “X-cells”, long-known agents of tumour-like lesions in fish, are in fact globally distributed, genetically divergent parasites related to perkinsids and dinoflagellates, and that classic fish-infecting dinoflagellates such as Haidadinium and Piscinoodinium share a recent common ancestor. We traced Chytriodinium dinoflagellates that infect copepod eggs and the cryptic plastid they still carry, and more recently uncovered a new and widespread group of apicomplexan parasites of fish, as well as a sea-cucumber-infecting apicomplexan — Apostichocystis gudetama — that extends a distinct, marine-host-specific clade. Across these systems we use phylogenetically informed metabarcoding to map how apicomplexan parasites are partitioned between animal hosts and the free-living plankton.

Tools to read the eukaryome

Reading the eukaryome at all requires the right tools, because standard 18S primers are swamped by host sequence. We validated a universal primer set that selectively targets animal-associated microeukaryotic communities, and developed an improved high-throughput protocol for recovering eukaryotic symbionts from metazoan tissues and environmental DNA — approaches now used to survey the eukaryome across many hosts and environments and to place newly detected lineages in a common phylogenetic framework.

Primary research

Freeman MA, Fuss J, Kristmundsson Á, Bjorbækmo MFM, Mangot J-F, del Campo J, Keeling PJ, Shalchian-Tabrizi K, Bass D (2017). X-cells are globally distributed, genetically divergent fish parasites related to perkinsids and dinoflagellates. Current Biology 27, 1645–1651.

Hehenberger E, James ER, del Campo J, Buckland-Nicks JA, Reimchen TE, Keeling PJ (2018). Fish parasite dinoflagellates Haidadinium ichthyophilum and Piscinoodinium share a recent common ancestor. Journal of Eukaryotic Microbiology 65, 127–131.

Strassert JFH, Hehenberger E, del Campo J, Okamoto N, Kolisko M, Richards TA, Worden AZ, Santoro AE, Keeling PJ (2019). Phylogeny, evidence for a cryptic plastid, and distribution of Chytriodinium parasites (Dinophyceae) infecting copepods. Journal of Eukaryotic Microbiology 66, 574–581.

del Campo J, Heger TJ, Rodríguez-Martínez R, Worden AZ, Richards TA, Massana R, Keeling PJ (2019). Assessing the diversity and distribution of apicomplexans in host and free-living environments using high-throughput amplicon data and a phylogenetically informed reference framework. Frontiers in Microbiology 10, 2373.

Bonacolta AM, Krause-Massaguer J, Smit NJ, Sikkel PC, del Campo J (2024). A new and widespread group of fish apicomplexan parasites. Current Biology 34, 2748–2755.

Bonacolta AM, Krause-Massaguer J, Unuma T, del Campo J (2025). The sea cucumber-infecting parasite Apostichocystis gudetama gen. nov. sp. nov. expands a marine-host-specific clade of apicomplexans. Journal of Eukaryotic Microbiology 72, e70013.

Methods

del Campo J, Pons MJ, Herranz M, Wakeman KC, del Valle J, Vermeij MJA, Leander BS, Keeling PJ (2019). Validation of a universal set of primers to study animal-associated microeukaryotic communities. Environmental Microbiology 21, 3855–3861.

Minardi D, Ryder D, del Campo J, Garcia Fonseca V, Kerr R, Mortensen S, Pallavicini A, Bass D (2022). Improved high-throughput protocol for targeting eukaryotic symbionts in metazoan and eDNA samples. Molecular Ecology Resources 22, 664–678.

Reviews

del Campo J, Bass D, Keeling PJ (2020). The eukaryome: diversity and role of microeukaryotic organisms associated with animal hosts. Functional Ecology 34, 2045–2054.

Bass D, del Campo J (2020). Microeukaryotes in animal and plant microbiomes: ecologies of disease?. European Journal of Protistology 76, 125719.

Bonacolta AM, Li L, del Campo J, Keeling PJ (2026). Endosymbiotic apicomplexans of marine holobionts: microbial parasites in a warming ocean. Integrative and Comparative Biology 66, icag006.