Frontiers in Marine Science

There is growing interest in manipulating coral-associated bacteria to enhance coral thermal bleaching tolerance. Reactive oxygen species (ROS), particularly hydrogen peroxide (H2O2), are major drivers of coral bleaching, therefore, coral-associated bacteria capable of scavenging H2O2 may help reduce bleaching. Bacterial candidates are commonly selected through genome inference and occasionally phenotypic assays, but how well these approaches predict H2O2-scavenging capacity is unknown. We screened 29 bacterial strains isolated from the scleractinian corals Acropora loripes and Galaxea fascicularis for genome-inferred H2O2-scavenging pathways and in vitro activity using an ABTS radical-scavenging assay, H2O2 tolerance (the highest H2O2 concentration that allows bacterial growth), H2O2 removal from the medium, and qualitative catalase activity. Although all strains encoded at least two complete H2O2-scavenging pathways, genomic prediction did not consistently align with in vitro scavenging activity. Growth under H2O2 exposure was strongly coupled with H2O2 scavenging, but these traits showed no correlation with ABTS inhibition or catalase activity inferred from bubble formation. The top-ranked phenotypes, based on H2O2 tolerance and scavenging, were observed in Roseovarius, Roseibium, Ruegeria, and Muricauda strains, which tolerated 5-50 mM H2O2. These genera are common associates of microalgae, including coral endosymbionts, which are key sources of excess ROS during thermal stress. Among these, Roseovarius and Muricauda also showed high ABTS inhibition (>97%), indicating broader antioxidant capacity that may be advantageous within the complex oxidative environment of thermally stressed corals. Strains combining strong H2O2 scavenging with broad antioxidant activity may therefore represent the most promising candidates for subsequent validation within the coral holobiont.

The identification and use of stress-tolerant coral in outplanting efforts has been proposed as a method of restoring and bolstering reef health under increasing environmental change. Prior research has focused on understanding survival in cross-reef transplantation, but evidence of long term resiliency of outplanted corals remains limited. Here, we report data at a five-year timepoint of a reciprocal transplant study of the stress-tolerant Caribbean corals Pseudodiploria strigosa and Siderastrea siderea between a nearshore and offshore site in Belize. Extreme marine heat wave conditions in August of 2024 revealed species and site-specific bleaching patterns. Through assessments of mortality, energy reserves, and chlorophyll concentrations, P. strigosa appear to be more limited in long-term acclimatization potential to the nearshore environment while S. siderea maintain acclimatization capacity displayed 17 months post transplant to nearshore. This work conveys information relevant to managers in selecting species for restoration efforts based on short-term growth and long-term resilience in native versus non-native sites, offers insight into potential mechanisms driving these trends, and takeaways on site specific management decisions for successful coral outplanting success.

Diatoms are major contributors to marine primary production, yet current approaches for monitoring their abundance and function rely on coarse satellite chlorophyll estimates or sparse cell count and carbon fixation measurements. Molecular markers are a promising approach for high-resolution measurement of both abundance and metabolic activity through analysis of environmental DNA (eDNA) and RNA (eRNA). We present an isothermal quantitative recombinase polymerase amplification (qRPA) assay targeting rbcL gene copies and transcripts of marine diatoms, operating at low temperature and producing results in less than 15 min. We demonstrate specificity and calibration across diverse diatom taxa, then apply the assay to eDNA and eRNA samples from the Mare Chiara Long-Term Ecological Research site in the Bay of Naples, Italy, alongside microscopy, chlorophyll, physicochemical, and carbon-fixation data. Diatom rbcL DNA tracked abundance across five orders of magnitude despite seasonal shifts in community composition. Combining molecular and optical data revealed increased cellular rbcL copies and chlorophyll in low-light winter populations, suggesting enhanced photosynthetic capacity despite lower abundance. Furthermore, rbcL RNA reflected total carbon fixation rates and identified populations with differing carbon fixation activity. These results support rapid, RPA-based rbcL quantification as a robust approach for biomolecular ocean observing.

The marine biodiversity inhabiting rocky shores in the Colombian Pacific remains largely undocumented, primarily due to geographic isolation, logistical challenges, and socio-political constraints. To address the existing knowledge gap, we conducted an expedition to enhance baseline biodiversity knowledge in rocky shores by integrating multiple complementary approaches, including visual censuses, specimen collection with morphological identification, environmental DNA (eDNA) metabarcoding and DNA barcodes. eDNA samples were collected at four coastal sites adjacent to rocky substrates, along with biological specimens obtained from fourteen locations through SCUBA diving at depths ranging from 1 to 25 meters. Tissue samples were subjected to genomic DNA isolation, followed by the generation and validation of cytochrome c oxidase subunit I (COI) barcode sequences, which were subsequently corroborated through taxonomic assessment to ensure accurate species identification. eDNA metabarcoding analyses yielded over 7 million high-quality sequence reads. Although taxonomic resolution at the species level was constrained by the limited completeness of reference sequence databases, a total of 106 species and 83 families were successfully identified, predominantly within the classes Actinopteri, Chondrichthyes, and marine mammals. From the 769 specimens obtained we generated 871 sequences, including 414 validated COI barcodes representing 76 species across 64 families. The integration of DNA barcoding and eDNA approaches resulted in over 1,400 taxonomic detections spanning five phyla, with only six species shared between methodologies. Richness and diversity varied among sites, and revealed significant differences along the coastline between Jurado and Cupica Gulf. All sequences were deposited in BOLDsystems database under the CCBIO project and were visualized through OBIS and GBIF databases. These findings provide the first molecular-based baseline for rocky shore biodiversity in the Colombian Pacific, highlighting the value of integrative approaches for monitoring and conservation.

Populations are exposed to multiple anthropogenic stressors simultaneously; however, the combined effects are poorly understood. Climate change is starkly impacting marine ecosystems and consequently fishes, with warming temperatures and increases in frequencies and durations of extreme climate events. Concurrently, plastics, such as nylon used in fishing industries, are contaminating marine waters at unprecedented levels, with detrimental effects on fishes. Here we studied the cumulative effects of warming and nylon microplastic fibres on the behavior and physiology of threespine stickleback (Gasterosteus aculeatus) by exposing fish to conditions of 15{degrees}C and 20{degrees}C and nylon concentrations of 0, 1, 10, and 100 mg/g (mg nylon/g food) for 4 weeks. Feeding rates responded complexly to multiple stressors, as increasing concentrations of plastic reduced feeding rates, with warming having an antagonistic effect. Furthermore, we observed "coughing" behaviors in response to ingestion of microfibres and a unique reselection tendency of food items previously selected by conspecifics. Under warming conditions, critical thermal maximum (CTmax) increased; however, exposure to plastics led to reductions in CTmax and thermal safety margins. Given these results, we anticipate reduced acclimation capacities, greater anxiety, and reductions in foraging efficiencies with increasing concentrations of plastic. Cumulatively, these stressors will yield greater energetic trade-offs and decreased accuracy in food selection with stark implications for marine ecosystem dynamics.

Climate change is threatening coral reef ecosystems around the world, causing significant declines in reef organisms, including sponges. The health of sponges is intimately linked to their symbiosis with microorganisms, yet little is known about their integrated response to ocean warming. Here, we present a comprehensive view of the effect of elevated sea surface temperatures (SST) on the model sponge Ianthella basta. I. basta individuals were exposed to temperatures up to 32 {degrees}C, 2-3 {degrees}C above the mean annual maxima. Host gene expression profiles showed an initial response to heat stress after 2 days, and a decreased expression of genes involved in maintaining tissue integrity, pumping capacity, vitamin transport, and stable symbioses after 4 to 8 days. Congruently, heat stressed samples started to show tissue regression and a reduced abundance of the dominant symbionts after 4 days. A significant loss of the symbionts occurred after 8 days, together with a reduction in microbially driven nitrogen cycling and amino-acid transport and an introduction of opportunistic microbes, which could lead to nutrient imbalance and further destabilisation of the holobiont. Together, this work provides important insights into the avenues through which future SST can impact host-microbe interactions in coral reef sponges.

Experimentally evolved, heat-tolerant algal symbionts (heat-evolved; HE) offer a promising means of enhancing coral holobiont thermotolerance under rapidly warming oceans. However, translating their benefits into restoration practices requires scalable delivery methods. Coral tissue fusion may provide one such pathway by facilitating HE symbiont transfer to wild corals; however, its feasibility remains largely untested. As an initial test, we paired adult isografts of Galaxea fascicularis and Psammocora columna hosting HE Cladocopium proliferum (SS8) with chemically bleached, SS8-naive recipients. Fusion was first observed after three days in G. fascicularis and nine days in P. columna. In both species, fusion was followed by increased pigmentation and photochemical efficiency at the recipients fusion interface relative to distal tissue and unfused controls. After [~]50 days, SS8 was detected at low levels (<3.5%) in 15/19 fused G. fascicularis recipients, although detection was also common among unfused horizontal-transmission controls maintained in the same water column (13/18). These findings provide the first empirical evidence that conspecific coral tissue fusion is associated with localised physiological recovery and can coincide with HE symbiont acquisition, while highlighting the need to distinguish tissue-mediated transfer from background horizontal transmission. Fusion may therefore represent a complementary pathway for beneficial symbiont delivery in assisted-evolution frameworks.

As climate change continues to disrupt marine ecosystems, reliable body condition indices (BCIs) for sentinel megafauna species such as dolphins will become increasingly important tools for long-term ecosystem monitoring. We developed novel BCIs from routinely collected morphometric measurements and applied them to a 22-year dataset (1998-2019) of 597 stranded common dolphins (Delphinus delphis) from Northwest Spain. BCIs were calculated as residuals from Generalized Additive Models relating body length to girth and blubber thickness measurements, thereby controlling for body size effects. The indices were first validated against visually assessed nutritional status and then used to investigate long-term trends and potential environmental and trophic drivers of body condition. The girth-based BCI outperformed the blubber thickness-based index in predicting nutritional status. The indices differed in their sensitivity to confounding variables. Both indices revealed an increase in male body condition until 2009-2010 followed by a sustained decline through 2019, whereas no long-term trend was detected in females. By integrating data on climate variability (North Atlantic Oscillation), oceanographic conditions (upwelling intensity, sea surface temperature, chlorophyll-a), prey availability, and prey quality, we found evidence that changes in body condition was associated with climate- and oceanography-driven changes in prey communities and reductions in the quality of prey available to dolphins. Our findings suggest that body condition in common dolphins integrates signals across multiple components of marine ecosystems and can serve as a sensitive indicator of ecosystem change. Given growing reports of declining body condition in marine predators worldwide, the approach presented here provides a practical and transferable framework for long-term ecosystem monitoring using existing stranding network datasets.

Coral reef monitoring needs scalable, non-invasive tools to complement resource-intensive traditional survey methods. Passive Acoustic Monitoring (PAM) offers a promising supplement, but its effectiveness is limited by the difficulty of attributing recorded sounds to species outside of previously well-characterized taxa. Using Omnidirectional Underwater Passive Acoustic Cameras (UPAC-360), we identified sounds from 31 reef fish species across 14 families on the Kona coast of Hawaii Island, including 13 not previously documented as soniferous. By releasing video and audio specimens, we have created the largest open-access collection of in-situ reef fish sounds to date for the Pacific. A subset of acoustically distinctive taxa--such as Hawaiian Dascyllus (Dascyllus albisella), Lei Triggerfish (Sufflamen bursa), soldierfishes (Myripristis spp.), wrasses, and herbivorous grazers--were identifiable in PAM recordings through manual acoustic and spectrogram review. Through identifying particular sounds linked to species with different ecological roles, these sounds have the potential to serve as indicators of reef function to increase the information and value coming from PAM surveys of Hawaiian and Pacific coral reefs.

1. Protecting and restoring corals is critical to conserve marine biodiversity and ecosystem services in the Anthropocene. Knowledge of coral larval dispersal dynamics can be used to identify important sites for coral metapopulation connectivity and to spatially optimise coral conservation efforts. However, we know little regarding the larval dispersal of many coral species and our understanding of the relationships between coral larval dispersal and life-history traits (e.g., reproductive mode, colony morphology), phylogenetic relationships, and biogeography is incomplete. These knowledge gaps impede coral conservation. 2. In this research, we systematically reviewed the species, regions, and methodologies of studies of coral larval dispersal. Additionally, we conducted a meta-analysis to quantify the heterogeneity in reported coral larval duration values and identified the roles of life-history traits in driving that heterogeneity. 3. We found that various methods (experimental, biophysical modelling, and population genetics) were used to study 221 coral species across many regions. Soft and temperate corals received comparatively lower research attention. Our meta-analysis reveals that reproductive mode and colony morphology explain significant heterogeneity in larval settlement times, and that closely-related species have more similar larval settlement times. 4. Our findings suggest that reproductive mode and colony morphology could be used to predict larval duration in under-studied coral species, and that larval duration could be approximated from closely-related corals when trait data is unavailable. Our results support strategies focused on modelling differing larval durations across corals with different life-history traits to predict realised dispersal in under-studied coral species and identify conservation priority sites.

The picocyanobacterium Prochlorococcus is a fundamental contributor to ocean primary productivity. While its free-living population has been extensively studied, primarily using flow cytometric analyses, the size and distribution of its particle-associated population is not well understood. Using filter fractionated samples from cruises in the Pacific Ocean, Atlantic Ocean, and Mediterranean Sea, we generated metagenomic data using internal standards, yielding absolute genome equivalent counts of Prochlorococcus cells in different size fractions. We used these data to model a relationship between relative and absolute genome equivalent counts, yielding a correction factor that we validated using published datasets. We then applied the correction factor to size-fractionated global metagenomic data from the TARA Oceans Project, which has widespread Prochlorococcus cells in size fractions >1.6 m throughout the transects, to calculate the fraction of the total Prochlorococcus population in large size fractions. The ''particle-associated'' population fraction increased with net primary productivity. Dissolved inorganic carbon was also directly correlated with increased particle association, which, combined with other evidence, could indicate an association with upwelling. We also examined the relationship between particle-associated population and carbon export at 150 m by incorporating published estimates of carbon flux based on TARA optical scattering data. This study highlights the potential importance of particle-associated Prochlorococcus to carbon flux in marine ecosystems and offers a way to convert relative to absolute genome equivalents of microorganisms in archival metagenomic datasets.

Tidal flats cover less than 1% of the surface of our planet, but they provide important ecosystem functions and services, like carbon sequestration and nutrient (re-)mineralization, primary, sec-ondary, and food production, and habitats for a variety of species. Despite their importance, they are threatened by environmental stressors and anthropogenic impacts. Hence, a better under-standing of the interaction between macrozoobenthos, their metabolic activity, and their contri-bution to carbon and nitrogen cycling is important. Therefore, we conducted in-situ pulse-chase tracer experiments at a Pacific oyster (Magallana gigas) reef in the Eastern Scheldt (Southwest Dutch Delta, Netherlands) in summer and autumn 2020. During these experiments, we provided the submerged benthic community with 13C and 15N-enriched bacterioplankton and incubated it in seawater enriched in 1% deuterium oxide (2H2O) for one tidal cycle (~9 h), before the benthic community was kept at in situ conditions for another 14 d. Our aim was (1) to assess seasonal variations in 13C and 15N processing by macrozoobenthos, (2) to evaluate potential life-stage de-pendent differences in 2H uptake - a proxy for metabolic activity, and (3) to identify the macro-zoobenthos taxon which had the highest metabolic turnover rate (MTR). In summer, most bacte-rioplankton-derived 13C- and 15N was taken up by sponges (Halichondria panicea), limpets (Crepidula fornicata), and clams (Ruditapes philippinarum), whereas in autumn, H. panicea, C. fornicata and the sponge Hymeniacidon perlevis dominated 13C and 15N incorporation. Statisti-cally significant differences in 2H uptake between life stages (juvenile/ small vs. adult) was de-tected in Malacostraca (i.e., Rhithropanopeus harrisii), but not in Polychaeta or Bivalvia. There-fore, this difference between taxonomic classes might be linked to mold-intermolt periods. Sea-sonal differences in MTR of H. panicea and M. gigas (i.e., the species with the highest MTRs in summer and autumn) might be linked to seasonal environmental variability, such as temperature and food availability.

Cell-type-specific molecular responses are obscured in bulk RNA sequencing, whereas generating matched single-cell datasets across environmental conditions remains costly and technically challenging, particularly in non-model organisms. Here, we present a workflow that integrates existing bulk and single-cell RNA-seq resources to prioritize cell-type-associated environmental-response genes. We demonstrate the workflow by examining heat-stress-associated neuronal genes in the reef-building coral Stylophora pistillata. Neuronal genes were first identified based on cell type-specific expression in single-cell transcriptomic data and then intersected with differentially expressed genes from bulk RNA-seq datasets under heat-stress. In parallel, we applied a deconvolution approach to infer cell type-specific expression changes directly from bulk data, independently capturing neuronal transcriptional responses. This integrated pipeline reduced thousands of heat-responsive genes previously identified in bulk RNA-seq studies to nine heat-associated, neuron-enriched candidates. Eight of the nine candidates showed their highest mean expression in the same neuronal subcluster. Targeted sequence-based characterization supported the identification of a TRPA-family ion channel, two calmodulin/centrin-family Ca2+-binding proteins, and a Class A/rhodopsin-like GPCR of unresolved ligand specificity. Two additional candidates were predicted secreted proteins belonging to conserved coral protein families, while the molecular functions of the remaining candidates remained unresolved. Their coordinated regulation suggests heat-associated remodeling of neuronal sensory and intracellular signaling processes. Our workflow provides a scalable framework for extracting cell type-associated molecular responses from existing transcriptomic resources and prioritizing candidates for further investigation. More broadly, it offers a generalizable strategy for investigating cell type-specific gene expression responses across organisms, cell types, and environmental conditions without requiring new single-cell datasets.

Nitrogen source and availability can modulate thermal stress responses in marine macroalgae, yet the transcriptional mechanisms underpinning these effects in green seaweeds remain poorly understood. We tested how three N sources (ammonium, nitrate, urea) at low (5 M) and high (100 M) concentrations influence the thermal physiology and gene expression of Codium cylindricum. Thermal performance curves were constructed for growth, photosynthesis, and pigment content across a 5-29 {degrees}C gradient, coupled with transcriptomic analysis at three key temperatures. At high concentrations, ammonium reduced maximum growth rate by 25% and lowered the thermal optimum relative to nitrate and urea, while nitrate supported the broadest thermal performance. Urea constrained thermal breadth regardless of concentration. These responses were linked to differential expression of Nitrogen assimilation genes. Ammonium suppressed nitrate transporter genes (NRT) and nitrite transporter (FNT), and drove pigment accumulation with rising temperature despite reduced growth, suggesting resource reallocation from growth to photoprotection. In contrast, nitrate upregulated photosystem and phosphorylation-related genes. Our findings demonstrate that Nitrogen source and concentration jointly determine the thermal threshold of C. cylindricum, with high ammonium reducing both maximum growth and the temperature at which it is achieved. This highlights how shifting coastal nutrient regimes may alter macroalgal resilience under ocean warming.

Bottom trawls have been used for centuries, yet studies of their impact on marine ecosystems have largely been restricted to recent decades. Here, we reconstruct fishing effort for the international trawler fleets in the North Sea from the age of sail to early steam trawling, by synthesising historical data describing vessel numbers and specifications, gear dimensions, fishing grounds, and operational characteristics. The trawler fleet increased from ca 800 sailing vessels in the 1820s to ca 3500 at the peak in sail trawling in the 1880s. Subsequently, steam trawling fleets emerged, increasing to almost 2000 vessels in the 1910s, while sailing fleets declined. Trawling grounds, covering ca 7% of the North Sea in 1820s, expanded from coastal to offshore grounds, reaching ca 25% in the 1880s, and 46% in the 1910s after the transition to steam trawling. Using a hydro- and aerodynamic approach to model the wind conditions required for sail trawling, we show that about 55% to 80% of the time at sea was suitable for trawling, providing a new quantitative basis for estimating historical fishing effort. The surface area swept by the trawl per year increased from 35,000 km2 in 1820s to 225,000 km2 in 1880s and 500,000 km2 in 1910s, corresponding to ca 60% of present levels. The trawling intensity (swept area ratio) varied between 0.9-1.7 year-1 in the era of sail, increasing to ca 2.0 in the 1910s. The trawling footprint (unique area trawled) increased to 160,000 km2, about half the present level.

Here, oyster larval developmental abnormalities within a New England hatchery were linked to a common UV sterilization technique that has been used for over 20 years. Because of the known link between phytoplankton oxylipins and egg mortality in copepods, we hypothesized that UV pretreatment of seawater results in the production of oxylipins that inhibit larval digestion of microalgae. We used lipidomics to observe changes in the organic compounds dissolved in estuarine seawater when filtered and when filtered and pretreated with UV. UV treatment resulted in an increase in the relative abundance of oxylipins associated with cyanobacteria, fungi, and macroalgae in 2020, whereas oxylipins typically produced by diatoms were more abundant in the UV treatments from 2021. Oxylipin concentrations were higher in 2020, when the hatchery reported the most severe problems with larval development. Removing the UV step allowed continued larval production in both years. However, the lack of UV sterilization led to an unidentified bacterial pathogen in 2021, which nearly decimated the overall seasonal production of oyster seed. To follow up in a more controlled environment, the larvae were exposed to exogenous oxidized lipids, which resulted in the same digestive syndrome and histological symptoms as the endogenous suite of compounds produced by UV. Further investigation of the lipidomes revealed that oxylipins were only one class of potentially harmful compounds linked to UV sterilization, and the dissolved concentrations of secondary metabolites associated with higher plants, a wide range of pharmaceuticals, and anthropogenic organic pollutants also increased under UV light. Future efforts will explore the sources of these compounds, the mechanisms by which they inhibit oysters, and whether this is an emerging environmental problem for other ecosystems and shellfish hatcheries. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=137 SRC="FIGDIR/small/738347v1_ufig1.gif" ALT="Figure 1"> View larger version (37K): org.highwire.dtl.DTLVardef@43d06corg.highwire.dtl.DTLVardef@2894daorg.highwire.dtl.DTLVardef@449e59org.highwire.dtl.DTLVardef@f81983_HPS_FORMAT_FIGEXP M_FIG C_FIG

Sexual coral propagation is an emerging technique capable of producing large numbers of corals for coral transplantation and reef rehabilitation. In contrast to asexual coral propagation, sexual propagation increases genotypic diversity and can be used for selective breeding to enhance coral heat tolerance or other desirable traits. However, implementation at meaningful ecological scales is hindered by high mortality during early life stages, high costs associated with nursery rearing facilities, and labour-intensive outplanting methods. To overcome these issues, we developed the CoralAssist Plug (CAP), a ceramic device designed for the rapid and cost-effective outplanting of sexually propagated corals in large numbers that maximises post-outplant survivorship. CAPs combine three important functional features: 1) built-in microrefugia to protect juvenile corals from grazing, 2) a relatively small size, 3 by 1 cm, that is easy to handle and stack efficiently without compromising the survivorship of corals, and 3) a hole in the middle that facilitates handling and attachment. CAPs were settled with Acropora aff. digitifera and outplanted to a reef crest after 1 to 6 months of ex situ nursery rearing. A 3-person dive team was able to outplant ~120 CAPs in one 90-minute shallow dive (just over 2 minutes per CAP per person). With longer nursery durations of 6 months, it was possible to achieve 36 % yield (i.e., the proportion of devices with a surviving coral) 4-years post-outplant. With nursery durations shortened to 1 month, we were able to attain 24 % yield 3-years post-outplant. Microrefugia significantly enhanced post-outplant survivorship leading to an 11 % increase in yield 4 years post outplant compared to devices without microrefugia. Outplanted corals that had reached adult size, were self-attached and were reproductively mature after 4 years. Our results suggest that CAPs can play a meaningful role in reef rehabilitation by efficiently introducing sexually propagated corals into natural populations with clear applications to assisted evolution techniques, such as selective breeding.

Understanding the consequences of global change for our ecosystems requires reliable, accurate, and scalable tools for detecting ecological change. To this end, recent efforts have focused on scaling up the quantification of demographic processes from individual organisms (the fundamental ecological unit) to the larger spatial scales they inhabit to yield more precise and informative estimations of ecological change, especially in response to disturbance. Here, we describe a transferable workflow that combines robust underwater photogrammetry techniques with machine-learning-assisted image analysis to quantify demographic changes in coral colonies (growth, stasis, partial mortality, and complete mortality) through time on the reef landscape. We then demonstrate several analytical applications of this workflow that can be broadly applied to sessile and/or clonal organisms in other ecosystems. First, we tracked the fates of 3,162 coral colonies through a marine heatwave that caused substantial mortality. Second, our approach enabled detection of size- and taxon-dependent patterns in demographic changes from before to after the heatwave. Finally, for a subset (425) of these colonies, we further demonstrated how our method can be used to track fates across multiple years, including a year of change before and after the heatwave took place, revealing nuanced patterns of survival and mortality, as well as changes in size structure that occurred before and after the disturbance. Our workflow offers an important advance for increasing the accuracy of change detection on coral reefs and other ecosystems by linking demographic changes in individual organisms with spatially extensive image-based surveys through time.

Rising ocean temperatures disrupt previously stable coral-microbe interactions, leading to widespread coral mortality and threatening reef ecosystems worldwide. Growing evidence demonstrates the coral microbiome, including protists, plays a critical role in the host response to thermal stress. Specifically, corallicolids (Phylum: Apicomplexa) are positively correlated with thermal stress mortality in soft corals. This study investigates changes in the eukaryotic microbiome of the stony coral, Pocillopora damicornis, across an experimental thermal stress event. Using anti-metazoan 18S rRNA gene metabarcoding, protist communities were assessed at four time-points during experimental thermal stress. Outside of the Symbiodiniaceae, a prominent shift in microbiome composition during thermal stress was observed, most notably a significant increase and dominance in Corallicolida abundance in heat-stressed corals, while other protists declined substantially. Increased corallicolid abundance concurrent with bleaching suggests an overlooked compounding stressor beyond the loss of algal symbionts during heat stress. These results contrast with previous research on Pocillopora microbiomes showing prokaryotic community stability throughout stress, and support the hypothesis that thermal stress may alter the coral-corallicolid relationship, potentially shifting corallicolids from a commensal to a parasitic role, and synergistically contributing to coral mortality during and after heat stress. This work provides critical insight into the role of protists in marine holobionts, supports their inclusion in future microbiome studies, and informs strategies to improve coral resilience under climate change.

The increased frequency and intensity of coral bleaching events expose reefs to disturbance-recovery cycles that threaten their long-term dynamics. Understanding the impact of thermal stress requires evaluating coral mortality and recovery rates after disturbances. By integrating two long-term monitoring datasets, we examined coral mortality and recovery patterns at 13 sites in Mo'orea, French Polynesia, following the 2019 bleaching event, the most severe heat stress on record for the island. The maximum accumulated heat stress (AHSmax) varied from 5.76 to 6.26 {degrees} C weeks and enabled a direct analysis of heat-stress-related mortality. One year after bleaching, Pocillopora mortality increased with AHSmax, reducing mean coral cover from 35% to 17%. Regardless of AHSmax, Acropora mortality was high at all sites (median: 84%), reducing mean cover from 5% to 1% and indicating greater heat tolerance of Pocillopora than Acropora. Within four years after the bleaching event, no recovery occurred, and coral cover further declined relative to pre-bleaching levels. This decline was stronger for sites exposed to more intense heat stress. The impact of colony size was assessed by tracking 3090 individual Pocillopora colonies over six years and estimating size-dependent mortality and growth with a Bayesian mixed model. Immediately after the bleaching event, large Pocillopora corals exhibited a higher probability of complete and partial mortality than smaller colonies, highlighting size-specific consequences of bleaching. Even three years after the heat stress ended, large Pocillopora corals remained stressed, as evidenced by the continuously high probability of partial mortality. The lack of recovery observed here may be related to increased spatial competition with macroalgae. The disappearance of large fecund colonies and high mortality of coral recruits could have catastrophic consequences for the resilience of Mo'orea's reefs.