Frontiers in Marine Science

The study explores the effects of elevated pCO2 on shell calcification, microbiome composition, and gene expression in a strain of Pacific oyster (Magallana gigas) selectively bred for low-pH resistance. Juvenile oysters reared under low-pH conditions exhibited increased shell mass compared to the control population by 51 days post-fertilization, despite high variance in shell size at earlier stages. Microbiome analyses revealed significant shifts in community composition under low-pH conditions, particularly in bacterial taxa involved in CO2 production and biogeochemical cycling, which could influence carbonate chemistry within oyster tissues. Gene expression profiling demonstrates differential regulation of genes related to biomineralization, immunity, and microbial interactions under low-pH conditions. For example, multiple carbonic anhydrases exhibited treatment-specific expression patterns, suggesting a role in adapting to low-pH environments. Observed changes in immune-related genes imply a relaxation of immune responses, potentially reflecting resource reallocation toward calcification processes. These results collectively support the "dysbiosis hypothesis," where oysters adapt to environmental stress by modulating their microbiomes and gene expression. Future studies should investigate whether these responses are consistent across oyster strains and environmental conditions, providing insights into the resilience of aquaculture species to ocean acidification. SUMMARY STATEMENTElevated pCO2 impacts Pacific oyster calcification, microbiome composition, and gene expression, suggesting genetic adaptation and microbiome shifts may be crucial for resilience to ocean acidification.

Coastal acidification leads to widespread impacts on calcifying organisms across the worlds oceans, which could result in decreased calcium carbonate deposition and the dissolution of calcium carbonate. As an abundant group of calcifying organisms, some protists within the phylum Foraminifera demonstrate potential success under elevated partial pressure of carbon dioxide (pCO2) due to their ability to modulate intracellular pH. However, little is known about their responses under more extreme acidification conditions that are already seen in certain coastal environments. Here we exposed Haynesina, a foraminiferal genus that is prevalent in temperate coastal salt marshes, to moderate (pCO2 = 2386.05+/-97.14 atm) and high acidification (pCO2 = 4797.64+/-157.82 atm) conditions through the duration of 28 days. We demonstrate that although this species is capable of withstanding moderate levels of coastal acidification with little impact on their overall test thickness, they could experience deposition deficiency and even dissolution of the calcareous test under highly elevated pCO2. Interestingly, such a deficit was primarily seen among live foraminifera, as compared to dead specimens, throughout the four-week experiment. We propose that a combination of environmental stress and the physiological process of test formation (i.e., calcite precipitation) could induce thinning of the test surface. Therefore, with the acceleration of coastal acidification due to anthropogenic production of CO2, benthic foraminifera amongst coastal ecosystems could reach a tipping point that leads to thinning and dissolution of their calcareous tests, which in turn, will impair their ecological function as a carbon sink. ImportanceThe calcareous foraminifera protists are responsible for large proportions of calcium carbonate production across the global ocean. Their responses to ocean and coastal acidification are essential for understanding carbon and mineral cycling in diverse marine ecosystems. However, relatively few studies have examined more extreme conditions related to what is seen in coastal habitats (e.g. pCO2 > 2,500 atm), and the response of individual test chambers have never been inspected. Here, we consider the response of Haynesina sp., a benthic foraminifera obtained from temperate coastal sediments to moderate and high acidification regimes. Comparison of test thicknesses across treatment conditions and among individual chambers of Haynesina sp. revealed potential tolerance under moderate acidification but demonstrated impaired new chamber formation and test dissolution under high acidification. Our results suggest that with growing anthropogenic CO2 production, foraminifera could reach a tipping point that leaves their ecological function as a carbon sink at greater risk.

Ocean warming and acidification are among the biggest threats to the persistence of coral reefs. Organismal stress tolerance thresholds are life stage specific, can vary across levels of biological organization, and also depend on natural environmental variability. Here, we exposed the early life stages of Pocillopora acuta in K[a]ne ohe Bay, Hawai i, USA, a common reef-building coral throughout the Pacific, to projected ocean warming and acidification scenarios. We measured ecological, physiological, biomineralization, and molecular responses across the critical transition from larvae to newly settled recruits following 6 days of exposure to diel fluctuations in temperature and pH in Control (26.8-27.9{degrees}C, 7.82-7.96 pHTotal), Mid (28.4-29.5{degrees}C, 7.65-7.79 pHTotal) and High conditions (30.2-31.5{degrees}C, 7.44-7.59 pHTotal). We found that P. acuta early life stages are capable of survival, settlement, and calcification under all scenarios. The High conditions, however, caused a significant reduction in survival and settlement capacity, with changes in the skeletal fiber deposition patterns. In contrast to a limited impact on the expression of biomineralization genes, the dominant transcriptomic response to the High conditions relative to the two other treatments included depressed metabolism, reduced ATP production and increased activity of DNA damage-repair processes. Collectively, our findings indicate that corals living in environments with large diurnal fluctuations in seawater temperature and pH, such as K[a]ne ohe Bay, can tolerate exposure to moderate projected increased temperature and reduced pH. However, under more severe environmental conditions significant negative effects on coral cellular metabolism and overall organismal survival jeopardize species fitness and recruitment.

Understanding how marine species tolerate acidified conditions is critical for predicting biological responses to ocean change. A recent one-year experiment (Long 2026) found that juvenile snow crab (Chionoecetes opilio) maintain growth and molting under acidification (pH 7.8, 7.5), and survival begins to decline only after [~]250 days under severe acidification (pH 7.5). In this companion study, we characterized whole-transcriptome responses after 8 hours and 88 days of exposure to identify molecular mechanisms underlying short-term tolerance and chronic effects of ocean acidification. The immediate transcriptional response involved strong activation of genes associated with mitochondrial metabolism and biogenesis, protein homeostasis, cuticle maintenance, and immune modulation, processes shared between moderate and severe treatments but of greater magnitude under severe acidification. After 88 days, expression patterns diverged, revealing sustained upregulation of stress- and damage-mitigation pathways in the severe treatment (pH 7.5) compared to the moderate treatment (pH 7.8). These findings indicate that crabs in severe acidification are likely to experience chronic OA stress that precedes outward physiological effects, and provides a mechanistic basis for delayed mortality. We further highlight potential early indicators of chronic acidification stress in snow crab, among which a gene likely coding for carbonic anhydrase 7 (CA7, GWK47_031192) appears to be the most promising biomarker. Summary StatementJuvenile snow crabs tolerate ocean acidification through flexible gene expression, but prolonged exposure reveals hidden cellular stress that helps explain delayed mortality.

Rising atmospheric CO2 reduces seawater pH causing ocean acidification (OA). Understanding how resilient marine organisms respond to OA may help predict how community dynamics will shift as CO2 continues rising. The common slipper shell snail Crepidula fornicata is a resilient marine gastropod native to eastern North America, which has been a successful invader along the western European coastline and elsewhere. To examine its potential resilience to OA, we conducted two controlled laboratory experiments. First, we examined several phenotypes and genome-wide gene expression of C. fornicata in response to pH treatments (7.5, 7.6, 8.0) throughout the larval stage and then tested how conditions experienced as larvae influenced juvenile stages (i.e. carryover effects). Second, we examined genome-wide gene expression patterns of C. fornicata larvae in response to acute (4, 10, 24 and 48 hours) pH treatment (7.5, 8.0). Both C. fornicata larvae and juveniles exhibited resilience to OA and gene expression responses highlight the role of transcriptome plasticity in OA resilience. Larvae did not exhibit reduced growth under OA until they were at least 4 days old. These phenotypic effects were preceded by broad transcriptomic changes, which likely serve as an acclimation mechanism for combating reduced pH conditions frequently experienced in littoral zones. Delayed metamorphosis was observed for larvae reared at reduced pH. Although juvenile size reflected larval rearing pH conditions, no carryover effects in juvenile growth rates were observed. Transcriptomic analyses suggest increased metabolism under OA, which may indicate compensation in reduced pH environments. Time course transcriptomic analyses suggest energetic burdens experienced under OA eventually dissipate, allowing C. fornicata to reduce metabolic demands and acclimate to reduced pH. This study highlights the importance of assessing the effects of OA across life history stages and demonstrates how transcriptomic plasticity can allow highly resilient organisms, like C. fornicata, acclimate to reduced pH environments.

The importance of infaunal bioturbators for the functioning of marine ecosystems cannot be overstated. Inhabitants of estuarine and coastal habitats are expected to show resilience to fluctuations in seawater temperature and pH, which adds complexity to our understanding of the effects of global change drivers. Further, stress responses may be propagated through chemical cues within and across species, which may amplify the costs of life and alter species interactions. Research into the molecular mechanisms underlying this resilience has been limited by a lack of annotated genomes and associated molecular tools. In this study, we present the first chromosome-level, annotated draft genome of the marine ragworm Hediste diversicolor, specifically mapping genes important for chemical communication, sensing and pH homeostasis. Using these resources, we then evaluate the transcriptomic and behavioural responses of two distinct populations -- one field-sampled from Portugal (Ria Formosa) and one laboratory-acclimated and -bred from the United Kingdom (Humber) -- to changes in seawater pH, temperature, and odour cues from a low pH-stressed predator. Both populations displayed adaptive responses to future oceanic conditions, with targeted acid-base regulation in the Ria Formosa population experiment, and broader changes in metabolism and growth genes in the Humber population experiment. Chemical cues from stressed fish predators induced genes related to Schreckstoff biosynthesis in ragworms. Additionally, under future ocean conditions including increased temperature, the Humber population exhibited signs of cellular stress and damage. Our findings using the new annotated genome offer novel insights into the molecular arsenal of acid-base regulation which aids in predicting the impacts of an increasingly acidified and unstable ocean, and to transfer this knowledge to investigate these mechanisms in species with less tolerance.

Uncontrolled carbon dioxide emissions from human activities contribute to ocean warming and acidification. These alterations in ocean chemistry threaten marine organisms, such as the true giant clam, Tridacna gigas, which is already imperiled due to overharvesting and habitat destruction. To gain an understanding of the physiological and molecular responses of T. gigas and its symbiotic dinoflagellates to ocean warming and acidification, we subjected juvenile individuals to different treatments simulating predicted seawater pH (7.6 and 8.0) and temperature (28{degrees}C, 30{degrees}C, 32{degrees}C and 34{degrees}C) levels for the next century. Juvenile giant clams were able to tolerate sustained exposure to temperatures of up to 32{degrees}C and pH as low as 7.6, while exposure to higher temperature (34{degrees}C), regardless of pH level, resulted in total mortality after a week. However, symbiosis was compromised even in the sublethal treatments, as indicated by the decrease in Symbiodiniaceae density and changes in symbiont gene expression. Symbionts significantly upregulated genes involved in splicing, translation, fatty acid metabolism, and DNA repair, which may constitute an adaptive response, while downregulating genes involved in photosynthesis and transmembrane transport, suggests impaired transfer of photosynthates to the host. These findings demonstrate the vulnerability of the juvenile T. gigas holobiont to heat stress, highlighting the critical importance of continued conservation and management alongside efforts to mitigate global changes in ocean conditions to safeguard this iconic marine bivalve. Summary StatementThis study investigates physiological and molecular responses of Tridacna gigas to seawater warming and acidification, providing insights into the potential future of endangered giant clam populations in a changing ocean.

Variation in light and temperature can influence the genetic diversity and structure of marine plankton communities. While open ocean plankton communities receive much scientific attention, little is known about how environmental variation affects tropical coral reef plankton communities. Here, we characterize eukaryotic plankton communities on coral reefs across the Bocas del Toro Archipelago in Panama. Temperature loggers were deployed for one year and mid-day light levels were measured to quantify environmental differences across reef zones at four inner and four outer reef sites: Inner: Punta Donato, Smithsonian Tropical Research Institute (STRI) Point, Cristobal, Punta Laurel and Outer: Drago Mar, Bastimentos North, Bastimentos South, and Popa Island. Triplicate vertical plankton tows were collected mid-day and high-throughput 18S ribosomal DNA metabarcoding was leveraged to investigate the relationship between eukaryotic plankton community structure and reef zones. Plankton communities from STRI Point were additionally characterized in the morning ([~]08:00), mid-day ([~]12:00), and evening ([~]16:00) to quantify diel variation within a single site. We found that inshore reefs experienced higher average seawater temperatures, while offshore sites offered higher light levels, presumably associated with reduced water turbidity on reefs further from shore. However, these significant reef zone-specific environmental differences did not correlate with overall plankton community differences or changes in plankton genetic diversity. Instead, we found that time of day within a site and diel vertical migration played structuring roles within these plankton communities, and therefore conclude that the time of community sampling is an important consideration for future studies. Overall, plankton communities in the Bocas del Toro Archipelago appear relatively well mixed across space; however, follow-up studies focusing on more intensive sampling efforts across space and time coupled with techniques that can detect more subtle genetic differences between and within communities will more fully capture plankton dynamics in this region.

Environmental DNA (eDNA) offers a powerful, non-invasive means of assessing biodiversity in marine ecosystems, yet the spatial resolution of eDNA remains poorly understood. We investigated the vertical and horizontal dispersion of eDNA from an isolated mesophotic coral reef (Bright Bank) in the stratified offshore waters of the northern Gulf of Mexicos shelf edge. We conducted comprehensive vertical and horizontal water column eDNA sampling across multiple radial directions and depths. We characterized invertebrate communities using a paired metabarcoding approach targeting broad (18S) and taxon-specific (28S) markers. We found that vertical transport of benthic eDNA was limited by water column stratification, with distinct benthic community signals confined to the near-bottom layers. In contrast, horizontal dispersal of eDNA extended beyond at least 1.5 km, though the prevalence of eDNA from benthic invertebrates declined with increasing distance from the bank. Taxon-specific primers showed greater detection sensitivity and dispersal range, particularly for benthic corals, than primers that are used to broadly assess eukaryotic biodiversity. These findings demonstrate that water column structure and marker selection critically influence the spatial interpretation of marine eDNA data. The study represents a snapshot of late-summer conditions. Seasonal variability should be considered in future studies. Our results provide a realistic framework for integrating eDNA into offshore environmental surveillance, biodiversity monitoring, and spatial management.

Reef-building cold-water-corals (CWC) form deep-sea habitats that can create biodiversity hotspots. As live coral and dead intact framework provide disparate ecosystem services and are vulnerable to different anthropogenic stressors, it is important to quantify the proportions of each on CWC reefs. We analysed 1,160 images of Solenosmilia variabilis reefs at four sites off New Zealand (Valerie and Forde Guyots at the Louisville Seamount Chain & Ghoul and Gothic Seamounts at the Graveyard Seamount Complex) to determine the ratio of live coral to the whole reef area (termed live:reef). We found live:reef ratios are significantly different between sites at the offshore Louisville Seamount Chain and onshore Graveyard Seamount Complex. This could be driven by reef position relative to the aragonite saturation horizon (ASH) as corals in the Louisville Seamount Chain live below the ASH in colder and deeper waters than those at the Graveyard Seamount Complex, which live above the ASH. In the southwest Pacific, depth is a driver of live:reef ratios, with a larger proportion of live coral at shallow depths and dead intact framework at deeper depths. The live:reef ratios at Gothic Seamount within the Graveyard Seamount Complex remained stable between 2015 and 2020 despite significant differences in live coral, dead intact framework, and reef structure surface area. Our results indicate live:reef ratios can be used to estimate the amount of dead intact framework threatened by shoaling ASH due to ocean acidification at each site, which can help inform which sites could be protected as possible climate change refugia.

Antarctic Krill (Euphausia superba) is a pivotal keystone species in the Southern Ocean ecosystem, with immense ecological and commercial significance. However, its vulnerability to climate change necessitates urgent investigation of its population genetics and adaptive responses. Historical spirit collections of Antarctic krill from the early 20th century represent an ideal opportunity for genomic research, to investigate how krill have changed over time and been impacted by predation, fishing and climate change. In this study, we assessed the utility of shotgun sequencing and exome capture for genomic analyses with historical spirit collections of Antarctic krill. Because the krill genome is very large (48Gb) two full-length transcriptomes were generated and used to identify putative targets for targeted resequencing. Skim genome sequencing allowed sample and library quality control. By comparing genome to exome resequencing of the same libraries we calculate enrichment and variant calling metrics. Full-length mitochondrial and nuclear ribosomal sequences were successfully assembled from genomic data demonstrating that endogenous DNA sequences could be assembled from historical collections. We find that exome capture provided enrichment of on-target sequence data, with increased depth and higher variant quality for targeted loci. Our findings demonstrate the feasibility of extracting genomic information from historical krill samples, despite the challenges of fragmented DNA and huge genome size unlocking such collections to provide valuable insights into past and present krill diversity, resilience, and adaptability to climate change. This approach unlocks the potential for broader genomic studies in similar samples, and for enhancing conservation efforts and fisheries management in the Southern Ocean ecosystem.

Coral spawning has evolved to occur during relatively calm hydrodynamic conditions. However, moderate to high surface winds are often present on spawning nights in specific regions, with many unknown impacts to the early life-history stages of corals. Here, we mechanistically examine the sensitivity of fertilisation and larval development to increasing wind speeds for four common species of hermaphroditic corals on the Great Barrier Reef: Acropora kenti, A. millepora, A. spathulata, and Platygyra daedalea. Wind intensities relevant to coral spawning seasons were simulated by downscaling location-specific, historical wind speeds to laboratory flumes. Generally, fertilisation success declined as duration of exposure increased and was often lowest at the highest wind intensity equating to 15 knots in situ. Embryo damage, deformity, and fragmentation increased with exposure time, but varied across species. Four days following spawning, damaged and fragmented embryos had the highest mortality rates (76-82% and 70-73%) compared to intact embryos (26% and 52%) for A. kenti and A. spathulata, respectively. Experimental parameters were used to fit a 3D Fluid Dynamics model with outputs confirming that water surface elevations, velocity, and turbulence energy increased by up to 10%, 40%, and 50% respectively as winds intensified, likely explaining the physical drivers of the deleterious effects observed. Overall, results from this study indicate that suboptimal spawning conditions reduce propagule production, which may diminish recovery potential, thus require consideration when planning management strategies to safeguard coral reproduction.

Increasing ocean temperatures are causing dysbiosis between coral hosts and their symbionts. Previous work suggests that coral host gene expression responds more strongly to environmental stress compared to their intracellular symbionts; however, the causes and consequences of this phenomenon remain untested. We hypothesized that symbionts are less responsive because hosts modulate symbiont environments to buffer stress. To test this hypothesis, we leveraged the facultative symbiosis between the scleractinian coral Oculina arbuscula and its symbiont Breviolum psygmophilum to characterize gene expression responses of both symbiotic partners in and ex hospite under thermal challenges. To characterize host and in hospite symbiont responses, symbiotic and aposymbiotic O. arbuscula were exposed to three treatments: 1) control (18{degrees}C), 2) heat (32{degrees}C), and 3) cold (6{degrees}C). This experiment was replicated with B. psygmophilum cultured from O. arbuscula to characterize ex hospite symbiont responses. Both thermal challenges elicited classic environmental stress responses (ESRs) in O. arbuscula regardless of symbiotic state, with hosts responding more strongly to cold challenge. Hosts also exhibited stronger responses than in hospite symbionts. In and ex hospite B. psygmophilum both downregulated genes associated with photosynthesis under thermal challenge; however, ex hospite symbionts exhibited greater gene expression plasticity and differential expression of genes associated with ESRs. Taken together, these findings suggest that O. arbuscula hosts may buffer environments of B. psygmophilum symbionts; however, we outline the future work needed to confirm this hypothesis.

Despite evidence of their importance to marine ecosystems, at least 25% of all chondrichthyan species are estimated or assessed as threatened with extinction. In addition to the logistical difficulties of effectively conserving wide-ranging marine species, shark conservation is believed to have been hindered in the past by public perceptions of sharks as dangerous to humans. Shark Week is a high-profile, international programming event that has potentially enormous influence on public perceptions of sharks, shark research, shark researchers, and shark conservation. However, Shark Week has received regular criticism for poor factual accuracy, fearmongering, bias, and inaccurate representations of science and scientists. This research analyzes the content and titles of Shark Week episodes across its entire 32 years of programming to determine if there are trends in species covered, research techniques featured, expert identity, conservation messaging, type of programming, and portrayal of sharks. We analyzed titles from 272 episodes (100%) of Shark Week programming and the content of all available (201; 73.9%) episodes. Our data demonstrate that the majority of episodes are not focused on shark bites, although such shows are common and many Shark Week programs frame sharks around fear, risk, and adrenaline. While anecdotal descriptions of disproportionate attention to particular charismatic species (e.g. great whites, bull sharks, and tiger sharks) are accurate and supported by data, 79 shark species have been featured briefly at least once. Shark Weeks depictions of research and of scientists are biased towards a small set of (typically visual and expensive) research methodologies and (mostly white, mostly male) scientists, including presentation of many white male non-scientists as experts. While sharks are more often portrayed negatively than positively, limited conservation messaging does appear in 53% of episodes analyzed. Results suggest that as a whole, while Shark Week is likely contributing to the collective perception of sharks as monsters, even relatively small alterations to programming decisions could substantially improve the presentation of sharks and shark science and conservation issues.

Clam gardens traditionally established and maintained by coastal Indigenous Peoples of northwest North America are habitat modifications to enhance intertidal clam productivity for reliable local food production. In this study, phenotypic and transcriptomic responses of Pacific littleneck clams (Leukoma staminea) were evaluated 16 weeks after transplantation to either unmaintained clam gardens or reference (unmodified) clam beaches. Beach sediment characteristics including grain size and organic content were examined across all beaches. Large differences in abiotic characteristics and phenotypic responses were observed among beaches; however, differences were not related to the clam garden/reference beach effect. Clam survival and growth were negatively associated with small rocks, very fine sand, and silt, along with carbonate and organic content, and positively associated with coarse sand, sand, and fine sand. To investigate molecular responses to unmaintained clam gardens, a de novo transcriptome containing 52,000 putative transcripts was assembled for L. staminea and was used to test for differential expression between transplanted clams in unmaintained clam gardens or on reference beaches. As expected, given the lack of significant phenotypic differences between treatments, transcriptomic responses to unmaintained clam gardens were minor, although several weakly-associated transcripts were identified. By contrast, the strong survival gradient across beaches was used to identify genes associated with survival and, combined with characterization of tissue-specific expression in the gill and digestive gland, contributes to our understanding of molecular processes in this non-model species.

Large commercial ports facilitate the introduction of non-indigenous species (NIS), while smaller harbours and marinas contribute to their regional spread. Harbour networks are thus important drivers of introductions. Despite extensive research effort on NIS in recent years, no study has yet assessed genetic connectivity among harbours considering whole-community composition. Here, we analysed spatio-temporal patterns of metazoan communities over one year in four medium-size harbours along the NW Mediterranean coast sampled by deploying standardised biological collectors. Using cytochrome c oxidase subunit I (COI) metabarcoding, we identified 1,770 metazoan molecular operational taxonomic units (MOTUs), of which 82 were classified as NIS based on a custom database of Mediterranean NIS. Despite their lower species count compared to natives, NIS accounted for 34-70% of reads in harbours. The southernmost harbour had the highest NIS number of reads, likely due to its proximity to aquaculture facilities. While we observed some variation in the spatial structure of metazoan communities across harbours, NIS showed consistently low differentiation values, sharing significantly more MOTUs among sites. Seasonal patterns influenced both NIS and the rest of the community. Haplotype diversity was significantly higher in NIS, which also exhibited lower genetic differentiation across harbours compared to native species, indicating NIS spread via local boating and likely recurrent introductions. These findings highlight distinct dynamics between NIS and native species in artificial environments, emphasising the importance of continued monitoring in harbour networks to manage coastal NIS proliferation. HIGHLIGHTSCOI metabarcoding of standardised collectors detected over 1,700 MOTUs of marine metazoans in ports over a year. Less than 4% were NIS MOTUs, but they comprised 34-71 % of the reads. NIS were more homogeneously distributed among ports than other MOTUs. NIS showed higher genetic variability but lower genetic differentiation than native species. Different dynamics underpin NIS and native assemblages in port communities. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=77 SRC="FIGDIR/small/688838v1_ufig1.gif" ALT="Figure 1000"> View larger version (32K): org.highwire.dtl.DTLVardef@fa0a5corg.highwire.dtl.DTLVardef@1be29ccorg.highwire.dtl.DTLVardef@1aa4e85org.highwire.dtl.DTLVardef@91842_HPS_FORMAT_FIGEXP M_FIG C_FIG

Pinctada radiata, commonly known as the Gulf pearl oyster, is a species of pearl oyster found primarily in the warm waters of the Red Sea, the Persian Gulf, and parts of the Indian Ocean. Pinctada radiata contributes to marine ecosystems by filtering water, which helps maintain water quality and supports other marine life. This species is the first bivalve Lessepsian migrant, having migrated from the Red Sea to the Mediterranean Sea via the Suez Canal. The reference genome of Pinctada radiata could help identify genes enabling adaptation to varying temperatures and salinities, facilitating survival in diverse and newly colonized habitats allowing comparisons with other bivalves to uncover shared and unique genetic adaptations. Additionally, the genome could support targeted management practices and conservation initiatives, such as habitat restoration and selective breeding, ensuring the long-term sustainability of P. radiata. The entirety of the genome sequence was assembled into 14 contiguous chromosomal pseudomolecules. This chromosome-level assembly encompasses 0.93 Gb, composed of 220 contigs and 44 scaffolds, with contig and scaffold N50 values of 8.1 Mb and 63.8 Mb, respectively.

The marine heatwave in the summer of 2023 was the most severe on record for Floridas Coral Reef, with unprecedented water temperatures and cumulative thermal stress precipitating near 100% coral bleaching levels. An existing SCTLD coral fate-tracking program assessed over 4200 coral colonies across five offshore and four inshore reef sites approximately every two months, allowing for analyses of bleaching-related mortality and diseases during and after the marine heatwave. Across the vast majority of assessed corals, including multiple sites and species, there was no partial or full mortality as a result of the 2023 bleaching event. The two sites that did experience substantial bleaching-related mortality were those experiencing the highest levels of cumulative thermal stress. However, the substantial acute mortality at one of them occurred at relatively low levels of cumulative stress, suggesting death was the result of exceeding thermal maxima. At the two sites with notable mortality, 43% and 24% of all monitored corals died, but mortality varied among species. Brain corals fared worse than boulder corals, with Pseudodiploria strigosa the most heavily impacted species. The health status of corals before the bleaching event had little impact on whether they experienced disease or bleaching-related mortality during the event. At three sites, we observed unusual lesions on Orbicella faveolata colonies shortly after color returned to the corals; the lesions were only observed for a few months but on some colonies led to substantial tissue loss. Though not part of the coral monitoring program, we also observed substantial losses and local extinctions of Acroporid corals at most sites, as well as probable local extinctions of octocorals at three of the four inshore reefs. Though most reef-building corals came through the 2023 event with no mortality, continually rising temperatures are likely to make these temperature regimes more common and widespread. We encourage future research on what the unusual O. faveolata lesions are, and why the brain and boulder corals fared differently at highly-impacted sites. Our results also provide perspective on how restoration strategies, particularly those focused on species likely to die under current and future climate regimes, should consider shifting focus to species likely to survive. Finally, these results highlight the importance of this type of monitoring, with a focus on fate-tracking individuals through disturbance events, including a large number of individuals of multiple species across a geographic range and multiple habitats.

Natural bleaching events provide an opportunity to examine how local scale environmental variation influences bleaching severity and recovery. During the 2020 marine heatwave, we documented widespread and severe coral bleaching (75 - 98% of coral cover) throughout the Keppel Islands in the Southern inshore Great Barrier Reef. Acropora, Pocillopora and Porites were the most severely affected genera, while Montipora was comparatively less susceptible. Site-specific heat-exposure metrics were not correlated with Acropora bleaching severity, but recovery was faster at sites that experienced lower heat exposure. Despite severe bleaching and exposure to accumulated heat that often results in coral mortality (degree heating weeks [~] 4 - 8), cover remained stable. Approximately 94% of fate-tracked Acropora millepora colonies survived, perhaps owing to reduced irradiance stress from high turbidity, heterotrophic feeding, and large tidal flows that can increase mass transfer. Severe bleaching followed by rapid recovery, and the continuing dominance of Acropora populations in the Keppel Islands is indicative of high resilience. These coral communities have survived an 0.8 {degrees}C increase in average temperatures over the last 150 years. However, recovery following the 2020 bleaching was driven by the easing of thermal stress, which may challenge their recovery potential under further warming. Open Research StatementData are not yet provided but are being compiled. Upon acceptance data will be archived on GitHub.

Coral cover on tropical reefs has declined during the last three decades due to the combined effects of climate change, destructive fishing, pollution, and land use change. Drastic reductions in greenhouse gas emissions combined with effective coastal management and conservation strategies are essential to slow this decline. Innovative approaches, such as selective breeding for adaptive traits combined with large-scale sexual propagation, are being developed with the aim of pre-adapting reefs to increased ocean warming. However, there are still major gaps in our understanding of the technical and methodological constraints to producing corals for such restoration interventions. Here we propose a framework for selectively breeding corals and rearing them from eggs to 2.5-year old colonies using the coral Acropora digitifera as a model species. We present methods for choosing colonies for selective crossing, enhancing early survivorship in ex situ and in situ nurseries, and outplanting and monitoring colonies on natal reefs. We used a short-term (7-day) temperature stress assay to select parental colonies based on heat tolerance of excised branches. From six parental colonies, we produced 12 distinct crosses, and compared survivorship and growth of colonies transferred to in situ nurseries or outplanted to the reef at different ages. We demonstrate that selectively breeding and rearing coral colonies is technically feasible at small scales and could be upscaled as part of restorative assisted evolution initiatives. Nonetheless, there are still challenges to overcome before selective breeding can be implemented as a viable conservation tool, especially at the post-settlement and outplanting phases. Although interdisciplinary approaches will be needed to overcome many of the challenges identified in this study, selective breeding has the potential to be a viable tool within reef managers toolbox to support the persistence of selected reefs in the face of climate change.