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 new study, published in the journal Coral Reefs, was conducted by a team from the Australian Institute of Marine Science working across six macroalgal-influenced reef sites around the Keppel Islands, on Woppaburra sea Country in Queensland, Australia. The researchers tested whether a commercial, biocide-free foul-release coating, or FRC, applied to ceramic coral seeding devices could reduce fouling accumulation and improve the chances of survival for juvenile corals of the branching species Acropora millepora. The results were striking: devices treated with the coating carried roughly 24 percent fouling after 48 weeks in the water, compared with about 67 percent on untreated controls, and spat survival rose from roughly 22 percent to about 49 percent.

Foul-release coatings work very differently from the biocidal antifouling paints used on ships’ hulls. Rather than leaching toxic copper or organotin compounds, which are known to harm coral fertilisation and larval metamorphosis, these coatings rely on hydrophobic or amphiphilic surface chemistry that simply weakens the adhesion strength of fouling organisms. Algae and invertebrates struggle to grip the slick surface, and much of what does attach is easily sloughed off by water movement. That property has made FRCs increasingly popular in aquaculture and maritime applications, and earlier work by the same group had shown they reduced fouling on ceramic seeding devices by up to 70 percent at healthier, coral-dominated mid-shelf reefs, with a modest boost to spat survival of up to 12 percent.

What remained uncertain was whether such benefits would hold up under the far harsher conditions of degraded inshore reefs, where high macroalgal biomass, eutrophication and sedimentation create a fusillade of biological pressure on any artificial surface. To find out, the team collected gametes from 37 gravid Acropora millepora colonies around the Keppel Islands during the October 2022 spawning event, fertilised them on board an aquaculture-configured vessel, and reared the larvae in culture tanks. Once more than 70 percent of the larvae had reached settlement competency, roughly five days after fertilisation, they were induced to settle onto preconditioned concrete tabs carrying a crustose coralline algae biofilm, at a density of around 24,000 larvae per tank.

The settled spat, cut onto small 14 by 14 millimetre settlement tabs, were then slotted into alumina seeding devices, 216 in total, half coated with the commercial FRC Hempasil 77300 and half left as controls. Divers deployed the devices at six sites across the Keppels in December 2022 and retrieved them 48 weeks later. The sites spanned a gradient of benthic regimes: three were dominated by canopy-forming Sargassum macroalgae covering nearly two-thirds of the substrate, while the others were characterised by encrusting Lobophora and coral assemblages dominated by Montipora. At retrieval, divers recorded each device’s burial status, photographed the surrounding benthos, and brought the fouled devices back to the laboratory for detailed image analysis of fouling cover and spat survival.

The scale of the fouling difference was dramatic. The largest treatment effect appeared at Humpy, where control devices averaged nearly 72 percent fouling cover while coated devices carried only about 10 percent. Across all sites, the dominant foulers were crustose coralline algae and brown and red algae, both of which were substantially rarer on coated devices. Crucially, survival declined steeply with increasing fouling on the settlement tabs themselves: the model predicted survival of around 43 percent on completely clean tabs but under 4 percent where fouling approached total cover. Burial compounded the problem, with survival dropping to less than 1 percent on fully buried devices, whether they were buried by sediment, rubble, macroalgae or overgrowing coral.

Interestingly, the surrounding benthic community shaped outcomes in ways that were not always intuitive. Survival was generally higher at Sargassum-dominated sites than where understorey macroalgae such as Lobophora and Caulerpa, or encrusting corals, prevailed, possibly because these lower-growing competitors and sediment-retentive assemblages creep directly onto devices. Sediment accumulation of up to 25 percent on tabs at one site corresponded with sharply reduced survival regardless of treatment. Yet even across these environmental gradients, the FRC benefit remained consistent: coated devices maintained predicted survival above 30 percent across most benthic assemblages, while control survival fell to as little as 2 percent at coral-dominated locations. Posterior estimates suggested a 38 percent higher probability of finding live spat on FRC devices overall.

There was also a hint that the coating helped in an unexpected way, by discouraging burial. Fully buried devices were consistently less common among FRC treatments than controls, and the authors suggest that by limiting initial fouling accumulation, the slick surfaces may deny secondary colonisers, encrusting algae and corals the foothold they need to slowly overgrow and entomb the devices. Spat on coated devices also grew larger, with tissue covering up to about 24 percent of tabs compared with roughly 7 percent on controls, likely because reduced competitive pressure freed resources for growth, accelerating the recruits towards the size refuge at which they become far less vulnerable to overgrowth.

The findings carry practical weight for a restoration field that is racing against repeated mass bleaching. The 2024 bleaching event alone cut coral cover by more than 20 percent across the Great Barrier Reef and caused mortality approaching 90 percent on some reefs around Lizard Island, while inshore systems such as the Keppels face added pressure from flood plumes, turbidity and strong tidal extremes. Paradoxically, the same turbid conditions that buffer adult colonies against heat stress may worsen sediment deposition and fouling pressure at the millimetre scale where spat live. The Keppel Islands’ Acropora populations have repeatedly bounced back from six major bleaching events in three decades, but the authors caution that resilience at the colony level does not automatically protect the fragile post-settlement stages that determine whether a population can rebuild.

The team is quick to note that foul-release coatings are not a panacea. They mitigate one critical bottleneck, competition and overgrowth at the settlement surface, but they cannot override heavy sedimentation or poor site selection, and survival still fell sharply where tabs accumulated silt or were buried. The authors recommend pairing FRC-treated devices with site-prioritisation frameworks that minimise sediment and burial risk, testing coatings applied even closer to the settlement surface, trialling biologically inert settlement substrates, and refining device geometry to improve hydrodynamic performance. Longer-term monitoring will also be needed to capture seasonal swings in macroalgal cover. Still, as a scalable, non-toxic intervention, the approach offers something restoration has badly needed: a way to keep young corals alive long enough on degraded inshore reefs to give them a fighting chance of reaching adulthood.

Subject of Research: Testing biocide-free foul-release coatings on coral seeding devices to improve spat survival on macroalgal-dominated inshore reefs

Article Title: Coral spat survival on inshore reefs is enhanced by foul-release-coated seeding devices

Article References: Coral spat survival on inshore reefs is enhanced by foul-release-coated seeding devices. (n.d.). https://doi.org/10.1007/s00338-026-02953-5

Image Credits: AI Generated

DOI: 10.1007/s00338-026-02953-5

Keywords: coral restoration, coral spat survival, foul-release coating, Great Barrier Reef, Keppel Islands, larval seeding, macroalgae, biofouling, Acropora millepora, sedimentation, reef rehabilitation, early life-stage bottleneck