The research, led by Teresa Bednarek of the University of Western Australia and the Australian Institute of Marine Science, focused on two closely related corymbose corals, Acropora millepora and Acropora digitifera. Corals are not solitary organisms but holobionts, integrated ecological units comprising the animal host, its photosynthetic dinoflagellate symbionts of the family Symbiodiniaceae, and a diverse community of bacteria, archaea and fungi. The algal partners supply the bulk of the coral’s energy through photosynthesis, while the bacterial associates contribute to nutrient cycling, immune function and metabolite exchange. Understanding how external partners such as resident fish perturb this internal ecosystem is a frontier in coral biology, particularly as reefs face intensifying thermal stress.

In May 2023, the team sampled 155 healthy adult colonies across two sites near Coral Bay, at depths of two to five metres. Before collecting tissue, divers conducted visual censuses of every damselfish swimming between the branches or hovering immediately above each colony, recording species, abundance and estimated body length. Five damselfish species were documented, including Dascyllus reticulatus, Dascyllus aruanus, Dascyllus trimaculatus, Pomacentrus moluccensis and Pomacentrus coelestis. Branch tips were snapped from the centre of each colony, flash-frozen in liquid nitrogen and later processed for symbiont cell counts, chlorophyll quantification and DNA extraction from the intact coral fragment, skeleton included.

The molecular work relied on amplicon sequencing of two genetic markers. The internal transcribed spacer 2 region, or ITS2, was used to characterise the Symbiodiniaceae communities, while the V5-V6 hypervariable regions of the 16S rRNA gene profiled the bacterial and archaeal assemblages. Sequences were denoised into amplicon sequence variants using the DADA2 pipeline, taxonomy was assigned against the SILVA and GeoSymbio reference databases, and the LULU algorithm was applied to curate the highly variable ITS2 variants. Statistical models then tested whether damselfish presence, abundance or biomass explained variation in symbiont density, pigmentation and community composition, while controlling for colony size and sampling site.

The first major finding was that host identity, not fish residency, is the dominant force shaping the holobiont. A. millepora carried roughly twice the symbiont cell density of A. digitifera, at 2.36 million cells per square centimetre versus 1.25 million. Chlorophyll a per symbiont cell was similar between species, but A. digitifera packed significantly more of the accessory pigment chlorophyll c2 into each algal cell, suggesting a distinct light-harvesting strategy that extends absorption into spectral ranges where chlorophyll a performs poorly. Because chlorophyll c2 is among the first pigments lost during thermal stress, this baseline difference could influence how each species approaches bleaching thresholds.

Both corals were dominated by symbionts of the genus Cladocopium, yet at finer resolution their assemblages diverged sharply. A. millepora hosted predominantly the C21 type, which averaged 91.67 percent of its symbiont community, while A. digitifera was dominated by C3k at 85.23 percent. Bacterial communities told a parallel story. Both species were overwhelmingly dominated by members of the family Endozoicomonadaceae, bacteria often regarded as markers of coral health, but the specific strains differed. A. millepora harboured a richer and more even bacterial community, with Endozoicomonadaceae comprising 83.48 percent of its microbiome, whereas A. digitifera’s community was more narrowly concentrated, with the family accounting for 95.27 percent. Coral species alone explained nearly a quarter of the variation in bacterial community composition across all colonies.

The damselfish themselves were not evenly distributed. A. millepora colonies hosted significantly more fish than A. digitifera, averaging 11 individuals per occupied colony compared with 6, although total fish biomass was similar between the two coral species. The assemblage composition also differed, with D. reticulatus dominating on A. millepora at 73 percent of recorded individuals, while D. aruanus and P. moluccensis were proportionally more common on A. digitifera. In total, 573 damselfish were counted on A. millepora colonies and 168 on A. digitifera, underscoring how strongly fish settlement preferences track coral architecture and species identity.

When the researchers tested whether fish occupancy altered the algal symbionts, the answer was largely no. Symbiont density, chlorophyll a content and overall symbiont community composition remained essentially unaffected by damselfish presence, abundance or biomass in both coral species. The one exception was chlorophyll c2 per cell, which responded in opposite directions: increasing fish numbers were associated with higher chlorophyll c2 in A. digitifera but lower chlorophyll c2 in A. millepora. The authors suggest this divergence may reflect photoacclimation to improved light availability, as damselfish remove sediment and algae from their host colonies, or nutrient-stimulated pigment production, with the direction of the response shaped by the different symbiont types each coral harbours.

The bacterial communities, by contrast, told a more nuanced story. In A. millepora, colonies hosting damselfish showed significantly lower Shannon diversity, and both diversity and evenness declined steadily as the number of resident fish increased. Remarkably, the interspecies gap in bacterial diversity that distinguished A. millepora from A. digitifera in fish-free colonies disappeared entirely in fish-occupied ones, as though the damselfish pulled A. millepora’s microbiome down to levels comparable with its neighbour. Crucially, bacterial richness was unaffected, meaning the fish did not eliminate taxa but rather shifted their relative abundances, allowing certain bacteria to dominate. Damselfish-occupied colonies also showed significantly lower community heterogeneity, a pattern that contrasts with the erratic, high-variability microbiomes typically associated with dysbiosis under stress.

The authors propose that fish-derived nutrients, primarily ammonium and phosphate excreted directly onto the colony, act as a consistent selective pressure favouring particular bacterial taxa, while the physical agitation of water within the branches and direct microbial transfer via contact or waste deposition may further reshape the local microbial environment. Notably, Terasakiellaceae, a bacterial family associated with nitrogen fixation in coral tissue, was weakly enriched in fish-occupied A. millepora colonies, consistent with nutrient-enriched conditions. In A. digitifera, where fish were fewer and the assemblage composition differed, bacterial communities remained essentially untouched, and the authors caution that host morphology or the species’ inherently lower bacterial diversity may also contribute to its apparent resistance.

The study offers an initial snapshot rather than a definitive causal account, and the authors are explicit about its limits. The observations were made under non-stressful autumn conditions, and whether the damselfish-associated microbial shifts confer resilience benefits under thermal stress remains a critical open question. Long-term monitoring would clarify whether these community changes persist as fish populations turn over through recruitment and mortality, and experimental manipulations using clonal coral genotypes would help isolate mechanisms from the variability inherent in observational work. Still, the message is clear: the coral holobiont is not an isolated system, and the animals that live in and around a colony are active participants in its microbial architecture. For reef conservation and restoration programmes, the implication is that transplant success may depend not only on choosing the right coral species but on understanding the fish tenants that come with it.

Subject of Research: Species-specific effects of resident damselfish on the coral holobiont microbiome of Acropora corals

Article Title: Resident damselfish influence the coral holobiont: species-specific responses in Acropora millepora and Acropora digitifera

Article References: Bednarek, T., Brooker, R. M., Martin, B. C., Gleeson, D. B., & Thomas, L. (2026). Resident damselfish influence the coral holobiont: species-specific responses in Acropora millepora and Acropora digitifera. Coral Reefs. https://doi.org/10.1007/s00338-026-02938-4

Image Credits: AI Generated

DOI: 10.1007/s00338-026-02938-4

Keywords: coral holobiont, damselfish, Acropora millepora, Acropora digitifera, Symbiodiniaceae, Cladocopium, Endozoicomonadaceae, microbiome, Ningaloo Reef, coral reefs, symbiosis, 16S rRNA sequencing

The central insight of the review is that corals live on a metabolic knife edge. Essential metals serve as cofactors in metalloproteins that drive electron transport, antioxidant defense, calcification, and nitrogen cycling. Iron sits at the core of the photosynthetic machinery of Symbiodiniaceae, the single-celled dinoflagellates that supply corals with most of their energy. Zinc and copper activate superoxide dismutase enzymes that neutralize reactive oxygen species, the damaging molecules that accumulate during heat stress. Manganese has been shown in experimental work to mitigate coral bleaching, while nickel supports urease activity and has been linked to enhanced calcification through its role in nitrogen recycling. Remove these micronutrients, and the symbiosis falters; studies of symbiont transcriptomes reveal strong metabolic responses when iron and other trace metals become scarce.

But the dose makes the poison, and the review documents how quickly essentiality flips into toxicity. Elevated copper, zinc, cadmium, lead, mercury, and nickel induce oxidative stress, disrupt metabolism, impair the coral-algal partnership, and can contribute to bleaching and mortality. Copper is among the best-studied offenders: laboratory exposures reduce fertilization success in spawning corals, impair larval settlement, and lower the thermal tolerance of even highly resistant Red Sea species such as Stylophora pistillata. Cadmium triggers systemic stress responses in Pocillopora damicornis, and high zinc exposure reduces levels of dimethylsulfoniopropionate, a compound involved in coral stress signaling and symbiosis maintenance. Non-essential metals are particularly insidious because the holobiont has no evolved use for them and limited mechanisms to render them harmless.

What makes the problem scientifically difficult is that metal toxicity is not a fixed property of any element. The review emphasizes that coral responses depend on external concentration, chemical speciation, the physiological regulation capacity of the organism, and environmental context. The free ion concentration of a metal, not its total dissolved amount, largely determines how much crosses biological membranes, and organic ligands in reef waters can bind metals and dramatically alter their bioavailability. Toxicity thresholds measured in one season, at one life stage, or at one temperature may not apply elsewhere. Research on the coral Montipora capitata, for example, found that the timing of spawning relative to copper exposure influenced fertilization success, and studies across life stages show that gametes and larvae are often far more sensitive than adult colonies.

The holobiont concept adds another layer of complexity. Different partners in the symbiosis have different metal demands and different accumulation capacities. Radiotracer experiments with Stylophora pistillata demonstrated that the animal host, the algal symbionts, and even the skeleton sequester metals to different degrees, meaning that bulk measurements of a whole colony can obscure where a metal actually resides and what it is doing. Work on the model anemone Exaiptasia pallida showed that zooxanthellae play a significant role in the uptake and depuration of essential metals, and comparative studies reveal that different Symbiodiniaceae lineages have distinct iron and trace metal requirements. A coral hosting a high-iron-demand symbiont may be more vulnerable to iron limitation, and possibly to bleaching, than one hosting a less demanding strain.

This metal economy connects directly to one of the most pressing questions in reef science: why do corals bleach under heat stress? One influential hypothesis, supported by elemental analysis of coral tissues, links bleaching to the capacity of the animal host to supply essential metals to its symbionts. If heat stress disrupts the transport of iron, zinc, or copper to the algae, their photosystems degrade, carbon transfer to the host collapses, and the symbiosis breaks down. Intriguingly, natural metal inputs can sometimes help. Studies from the Red Sea found that desert dust deposition, a major source of iron and other bioelements, improved the photophysiology of heat-stressed corals, suggesting that atmospheric supply of micronutrients may partially buffer some reefs against thermal stress.

The review also highlights how climate change is rewriting the rules of metal availability. Ocean acidification alters metal speciation and can increase the free ion concentrations of some elements while changing uptake pathways; experiments combining acidification with copper exposure have produced antagonistic, additive, and even protective effects depending on species and conditions. Warming changes stratification and upwelling patterns that govern the delivery of metals to reef waters, while deoxygenation shifts redox conditions that control whether metals are dissolved or locked into sediments. Coastal development, mining, industrial discharge, and agricultural runoff add anthropogenic loads on top of these shifting natural baselines, meaning that many reefs face simultaneous changes in both metal supply and the stressors that determine whether that supply helps or harms.

Corals, remarkably, keep records of all of this. Their skeletons grow in annual bands and incorporate trace elements as they calcify, creating archives that researchers can read with techniques such as laser ablation inductively coupled plasma mass spectrometry. Lead profiles in Porites skeletons have tracked industrialization in Hong Kong over two centuries, cadmium ratios in Galapagos corals record seasonal upwelling, and growth bands from the Philippines and Indonesia have documented mine tailings and gold mining impacts. Coral records even captured the elemental signature of the Fundão dam collapse in Brazil. These geochemical archives, the review notes, are invaluable for reconstructing pollution histories and land-use change, but interpreting them requires understanding the biological regulation that governs metal incorporation, since corals do not record seawater chemistry passively.

New analytical tools are rapidly expanding what is possible. Inductively coupled plasma mass spectrometry and its laser ablation variant allow multi-element mapping at fine spatial resolution, while isotope signatures of copper and zinc in coral skeletons offer new windows into metal cycling in modern and ancient oceans. On the biological side, transcriptomic and elemental profiling approaches, sometimes framed as studies of the coral elementome, reveal species-specific metal handling by hosts and symbionts and show that colonies persisting in different reef environments diverge in their elemental composition. These methods, combined with pollution indices such as enrichment factors and geoaccumulation indices applied to reef sediments, are building a multi-scale picture of metal exposure from the molecule to the ecosystem.

The authors are candid about the gaps that remain. Scientists still lack robust thresholds separating essentiality from toxicity for most metals in most coral species, particularly under the combined stressors that characterize real reefs. Holobiont-level metal cycling, including the roles of bacteria and fungi, remains poorly quantified, and interactions between metals and climate stressors such as warming, acidification, and deoxygenation are only beginning to be explored experimentally. Closing these gaps, the review argues, is essential for interpreting coral metal records accurately, predicting which reefs are most vulnerable, and designing conservation strategies for an ocean whose chemistry is being altered at unprecedented speed. In an era when reefs face mounting thermal and chemical pressure, the trace metal budget may prove to be one of the most important, and most overlooked, determinants of their survival.

Subject of Research: The roles, regulation, and toxicity of trace metals in the coral holobiont under changing ocean conditions

Article Title: Trace metals in the coral holobiont: roles and regulation in a changing ocean

Article References: Versola, J. J. N., & Rodriguez, I. B. (2026). Trace metals in the coral holobiont: roles and regulation in a changing ocean. Coral Reefs. https://doi.org/10.1007/s00338-026-02968-y

Image Credits: AI Generated

DOI: 10.1007/s00338-026-02968-y

Keywords: coral reefs, coral holobiont, trace metals, metal toxicity, Symbiodiniaceae, metal bioaccumulation, biogeochemical cycling, ocean acidification, coral bleaching, skeletal geochemistry, oxidative stress, marine pollution