Coral Reefs

Reef restoration practitioners aim to preserve coral genetic diversity by protecting reefs and cultivating diverse genotypes in coral nurseries. However, cryptic genetic lineages in most corals complicate restoration strategies, as the role of between-lineage genetic divergence remains unclear regarding adaptation. In Montastraea cavernosa, researchers have identified cryptic lineages, some strongly segregated by depth. We conducted a ten-week reciprocal transplantation experiment using two cryptic lineages restricted to shallow water (<10m depth), with one lineage more common on nearshore reefs and the other on offshore reefs. We aimed to quantify lineage-specific responses to the environment that explain the genetic and ecological divergence between the two lineages. Surprisingly, the strongest response was not lineage-specific. Instead, both lineages exhibited strong and similar changes in growth and metabolomic profiles, depending on the transplantation habitat. These results suggest that cryptic lineages employ similar mechanisms of adaptation and acclimatization to environmental challenges, despite their genetic distinction.

The rariphotic zone, typically spanning depths of approximately 130 to 300 meters, represents a key transition between light-dependent coral reef ecosystems and the aphotic deep sea. Despite its potential ecological importance, including its proposed role as a refuge for species exposed to climate-driven stress, rariphotic ecosystems remain poorly understood. In this study, we conducted a systematic review and synthesis of the scientific literature on these habitats from 1970 to 2025. Following the PRISMA 2020 protocol, we analyzed 185 studies to characterize the historical development of research, identify geographic and methodological biases, and assess shifts in research priorities over five decades.Our results show a marked increase in research effort over the last decade, driven in part by advances in underwater technologies such as Remotely Operated Vehicles (ROVs), Human Occupied Vehicles (HOVs), and Baited Remote Underwater Video Station (BRUVS). However, this growth remains uneven, with persistent biases toward benthic rather than pelagic studies and a strong concentration of research in geographically accessible regions. Multivariate analyses of research novelty indicate that technological innovation and the formal recognition of the rariphotic zone in 2018 corresponded with major structural shifts in literature. Although the rariphotic zone is now increasingly recognized as an ecologically distinct component of the reef continuum, it remains underrepresented in ecological theory and conservation frameworks. Future research should move beyond descriptive taxonomic mapping toward integrative, data-driven functional ecology, with particular emphasis on long-term monitoring and depth-stratified connectivity.

Crown-of-thorns sea star (CoTS), Acanthaster cf. solaris, outbreaks are a major cause of hard coral cover decline across the west Pacific, threatening coral reefs. Coral taxa vary in susceptibility to CoTS predation from preferred (Acropora spp.) to non-preferred (Porites spp.), yet the mechanisms underlying these differences are poorly understood. We investigated coral defenses during an ongoing CoTS outbreak in Mo'orea, French Polynesia by examining gene expression (including putative toxin genes) in healthy and actively predated colonies of a preferred (Acropora hyacinthus) and a non-preferred (Porites sp.) coral prey species. During predation, A. hyacinthus exhibited molecular signatures of cellular stress responses involving oxidative stress signalling, inflammation, and tissue proteolysis. In contrast, Porites sp. showed enrichment of genes involved in mitochondrial metabolic adjustment and aerobic metabolism, suggesting metabolic compensation to maintain cellular function. Furthermore, A. hyacinthus demonstrated a reactive defense behaviour by differentially expressing toxins (e.g., kunitz-type neurotoxins) while Porites sp. employed constitutive expression of all putative toxins regardless of active predation, suggesting a proactive defense strategy. Together, these findings suggest that preferred and non-preferred coral prey exhibit fundamentally different molecular and defensive strategies during CoTS predation, shedding light on the evolutionary arms race between corals and their predators.

Near-shore coral reefs in southern Guam (Mariana Islands) experience severe sedimentation, in particular during the wet season when rainfall and erosion are high. We sampled fragments of the reef-forming coral Porites lobata from opposite ends of a sedimentation gradient in Fouha Bay, southern Guam, during dry and wet seasons. Using DNA metabarcoding, we characterized the diversity and composition of P. lobata-associated Symbiodiniaceae and bacterial microbiome communities. As in many species of Porites, Symbiodiniaceae communities of P. lobata were dominated by variants of Cladocopium C15 with sites showing differences in Symbiodiniaceae communities attributable to variation in these Cladocopium C15 variants. Bacterial microbiomes of P. lobata were dominated by Endozoicomonadaceae, a family of putative coral bacterial endosymbionts involved in nutrient cycling. Site and seasonal differences in bacterial diversity and community composition were apparent. In close proximity to the mouth of the river draining into Fouha Bay, bacterial diversity was highest during the wet season when sedimentation is generally severe. Microbiome reorganization in response to sedimentation may explain this result, but we also found overrepresentation of bacteria associated with terrestrial origin close to the river mouth and/or during the wet season. Together these patterns highlight that coral Symbiodiniaceae and bacterial communities are both spatially and temporally structured in this disturbed system. IMPORTANCEThis study provides a time series dataset of coral-associated microorganisms, including dinoflagellate algae and bacteria, from a tropical bay impacted by sedimentation that results from upstream erosion of disturbed soils. Characterizing temporal patterns of coral-associated microbes provides insights into the dynamic nature of these communities. While microbiome variability across sites and seasons may be a result of acclimatization to different environmental conditions, we identified bacterial groups of putative terrestrial origin in sampled coral microbiomes that may have been exported from eroded soils to the near-shore reef. Considering that disturbed soils act as hotspots for the proliferation of potentially harmful substances, such as antimicrobial resistance genes, understanding microbial community connections at the marine-freshwater-terrestrial interface is an important step toward evaluating environmental impacts across connected ecosystems from ridge to reef.

Global marine heatwaves have devastated tropical coral reefs, and further mortality is projected under ongoing climate change. Identifying thermally tolerant coral colonies is therefore a priority for conservation, restoration, and research. Portable acute heat stress assays (e.g., CBASS) enable rapid, standardized estimates of coral thermal tolerance under field conditions. However, it remains unresolved whether such experimentally derived metrics (ED5, ED50, DW) predict bleaching and mortality in situ. Here, we quantified acute thermal tolerance metrics for 2,068 coral colonies across 12 common Indo-Pacific species, six months prior to an unprecedented heat stress event in northeastern Peninsular Malaysia and compared experimentally derived ED and DW values to subsequent bleaching severity and mortality in the field. Experimental thermal tolerance metrics explained only a limited proportion of variation in bleaching outcomes and survival. Predictive power varied among species and was higher in slow-growing species. Our findings suggest that while acute heat stress assays capture substantial variation in coral thermal tolerance, their ability to predict in situ outcomes is context-dependent and diminishes under severe thermal stress. Ultimately, in situ coral bleaching under severe heat stress may reduce the discriminatory capacity of acute assay-derived tolerance metrics.

Coral reefs deliver vital services via a complex three-dimensional framework sustained by the balance between calcium carbonate production and erosion, or the net carbonate budget state. In many tropical western Atlantic reefs, ecological decline has reduced carbonate production, yielding near-neutral or negative budgets. Yet some reefs retain high coral cover and, theoretically, should also have high net positive budgets, yet often show modest carbonate accumulation. We used the remote reef of Cayo Arenas in the Campeche Bank, Gulf of Mexico, to test whether in reefs under suboptimal (variable) environmental conditions, high coral production is offset by robust bioeroder communities, producing neutral budgets. At 14 sites, we quantified carbonate producers and bioeroders to estimate gross production, bioerosion, and net budget states. Despite relatively high live coral cover, mean net carbonate budgets were approximately neutral. Crucially, this neutrality arose not from depressed biological activity (as in degraded reefs) but from an active equilibrium: vigorous carbonate production coupled with substantial bioerosion. These reefs, therefore, represent a contemporary, functional reef state in net stasis. Distinguishing active-neutral from impoverishment-neutral regimes is critical for predicting reef trajectories under environmental change and for targeting management, although near-stasis emerging from high carbonate turnover can appear functionally intact yet operate with limited buffering capacity against net carbonate loss.

Oxygen minimum zones (OMZs) are among the most significant abiotic environmental gradients found in the ocean. Yet, fine-scale species distribution patterns of organisms inhabiting OMZs are still spatially limited, hindering our understanding on how these oceanographic features influence species diversity and community structure. Cold-water corals are ecologically important habitat-forming species that are often considered to be sensitive to low seawater dissolved oxygen concentration and thus likely to be useful indicators for exploring change in megafaunal abundance and biodiversity across the OMZ. In the eastern tropical Pacific Ocean, widespread oxygen minimum zones and oxygen limiting zones encompass several thousand square kilometers of area and span several hundred meters of the water column, but typically are strongest between 300-700 m depth. A January 2019 cruise aboard the R/V Falkor using the ROV SuBastian, conducted video transects along 7 seamounts between the Costa Rica Margin and Isla del Coco, as well as within one submarine incised canyon on the north side of Isla del Coco. In this study, we analyzed survey data for patterns in cold-water coral species distribution, diversity, and coral community structure relative to abiotic oceanographic variables in order to gain biogeographic insights to this area. Across all sites, we identified 3675 coral occurrences and 75 unique morphospecies between 177-1565 m. Rapid species turnover with increasing depth occurred primarily across the upper (300 m) and lower OMZ boundaries (700 m). Coral assemblages within the OMZ depths were observed to contain distinct groups of species compared to those below at deeper bathyal depths. Stylasterid hydrocorals were disproportionately abundant above and within the OMZ, while octocoral and black coral species dominated in the more well-oxygenated waters below. Coral assemblage diversity and abundance was depressed within the OMZ, but bathyal diversity peaked at intermediate water depths between 1200-1500 m. In addition to assessing the impact of OMZs on coral communities, these results provide unique insights to the abundance, diversity, and environmental drivers of deep-water coral community assembly in a data-deficient locality, thus improving biodiversity metrics and informing marine conservation efforts off Costa Rica. These baseline data are particularly salient in the light of projected expansion and shoaling of eastern tropical Pacific oxygen minimum zones as a result of decreasing ocean oxygen concentrations driven by ocean warming and other climate drivers.

Ocean warming is currently leading to distributional shifts of species and an alternation of coastal communities. Vulnerable species that are most sensitive to ocean warming are able to use several acclimation mechanisms, with one of the fastest being a shift in and shuffling of their partnerships with symbiotic microorganisms. Assessing symbiosis-focused mechanisms of acclimation and adaptation in response to ocean warming is a technical challenge due to the difficulty of accurately simulating the de novo formation of coastal communities. Here, we use the Kiel Outdoor Benthocosm facility to assess which sponges species are experimentally recruited and whether they exhibit symbiosis-focused mechanisms of acclimation following selection to ocean warming. We observed one sponge species (Haliclona sp.) and found that this sponge exhibited significant shifts in the membership and composition of its associated microbiome in response to ocean warming, with much of this being attributed to the rare microbiota. Moreover, Haliclona sp. maintained the diversity and dominance of its microbiome members. Four bacteria taxa were differentially abundant at elevated temperatures, with two being a Francisella sp. that is a suspected pathogen and an uncultured Francisellaceae that is most closely related to sulfur-oxidizing endosymbionts. Changes to the Haliclona sp. microbiome are largely consistent with a limited acclimation response, which could indicate that this sponge may use microbial symbionts as part of a mechanism to acclimate and adapt to a warmer future ocean.

Stony coral tissue loss disease (SCTLD), a coral pathology with rapid tissue loss and high mortality rate has affected nearly 30 species with a variable degree of susceptibility across species. It has been suggested that SCTLD has a systemic effect within coral colonies, but little is known about within-colony changes of the microbial communities associated with this disease. Here we evaluate the microbial shifts within coral colonies: apparently healthy tissue and SCTLD tissue. The study was done in three species following a gradient of susceptibility to the disease: Dendrogyra cylindrus (Dcyl, n = 11) and Pseudodiploria strigosa (Pstr, n = 6) two highly susceptible species; and Orbicella faveolata (Ofav, n = 8), a moderately affected species. 16S rRNA Illumina sequences analysis showed differential microbial community structure within two species (Dcyl, p = 0.01, Pstr, p = 0.01) but not for Ofav (p = 0.28). Taxonomic profiles of bacterial groups were species-specific in SCTLD tissue, but healthy tissue shared similarities between species including Pirelullales, NB1-J and SAR324. Our results reveal that the microbial communities effects associated to the disease follow a similar pattern to the species susceptibility to SCTLD, providing new insights into the disease dynamics in the Mexican Caribbean.

Pocillopora is a widespread, dominant reef-building coral genus in the Indo-Pacific that exhibits high morphological similarity and plasticity. Given this, genetic tools are needed to robustly identify Pocillopora individuals to the species level. Quick and accurate identification approaches for Pocillopora species are critical to estimating biodiversity patterns under current and future environmental challenges. In recent years, the mitochondrial open reading frame (mtORF) and a histone region (PocHistone) have been validated using genome-wide data to become the most widely used species-level markers for Pocillopora. However, Sanger sequencing of a large number of samples can be prohibitively expensive and sequencing facilities are not always readily available. Therefore, we present restriction fragment length polymorphism (RFLP) digests here that identify the six species of Pocillopora (P. acuta, P. cf. effusa, P. grandis, P. meandrina, P. tuahiniensis, and P. verrucosa) found in French Polynesia, without sequencing. In uninformed validation tests (in silico and in vitro), our protocol identified each Pocillopora species with 100% accuracy. Given their cost-effective, rapid nature, the tailoring of additional RFLP digest protocols to identify cryptic coral species in reef regions around the world will support foundational reef science, conservation and restoration initiatives.

Corals harbor a diverse bacterial community that facilitates adaptation and sustains their health. In coral holobiont research, culture-independent approaches have transformed the existing paradigm. Molecular techniques, such as metabarcoding, revealed a high diversity of previously unrecognized bacterial symbionts. Coral microbiota characterization has relied on these techniques over the last decade, but relying solely on them does not provide a detailed understanding of the dynamics of the coral holobiont complex. Returning to classic microbiological methods and in vitro experimentation can yield novel insights into symbiont roles, physiology, and interactions within the holobiont. Under this premise, we aimed to isolate and culture bacteria from four Mediterranean corals. The recovery of 84 pure bacterial isolates and their initial classification based on the 16S rRNA gene revealed substantial diversity among symbionts amenable to culture. Several isolates represent novel species within relevant genera, such as Vibrio, underscoring the value of culture-based studies. All cultures were cryopreserved to guarantee long-term accessibility for future projects. This represents a key step towards describing the roles of bacteria within the coral holobiont, as cultures enable in-depth morphological and physiological characterization of the symbionts and experimental ecology studies.

Octocoral colonies with unusual morphology were detected in September 2022 and October 2023 in two coastal areas east of Havana, Cuba, and tentatively identified as Unomia stolonifera. U. stolonifera is an invasive octocoral from the Indo-Pacific that was first reported in the Caribbean off Venezuela in the 2000s, where it has spread rapidly, smothering coral reefs and substantially altering benthic communities. After obtaining tissue samples from a Cuban octocoral colony, we re-examined the specimen using molecular barcoding of three mitochondrial regions (16S/ND2, mtMutS, COI) and the nuclear large ribosomal subunit (28S rRNA), and we unequivocally identified it as Xenia umbellata. X. umbellata, a native of the Red Sea, was first identified in southern Puerto Rico in October 2023 and has since been found in various marine ecosystems along the southern coast of the island. The presence of either invasive octocoral species in Cuba or elsewhere in the Caribbean would be of a serious environmental concern due to their documented tolerance, totipotentiality, propagation capacity and significant negative interactions with local benthic fauna. Attempts to eradicate the invasive soft coral colonies from Cuban waters have been initiated with apparent success, helping to control further expansion. The most likely introduction pathway is the accidental or intentional releases from the aquarium trade but transport via ballast water cannot be ruled out. We cannot discount the possibility of independent invasion events from different routes to Puerto Rico and Cuba occurring within a year of each other. Propagation from Cuba to Puerto Rico, or vice versa, which we consider highly improbable, would likely imply that soft coral populations may also have been established on Hispaniola but have remained undetected in the Dominican Republic and Haiti to date.

The global coral reef crisis has prompted restoration initiatives worldwide. Targeting the coral larval stage is among the most scalable approaches as recruitment operates over large spatial scales. It thus represents one of the best levers for coral population recovery. Active coral larval seeding has shown considerable success, and passive substrate engineering has emerged as a promising complementary strategy. Coral settlement modules featuring helix recesses have increased settlement and survival by up to 80-fold on small experimental units, but whether these results translate to tools deployable at the scale of thousands of units, remains yet an open question. Here, we transferred structural features from successful experimental coral settlement designs into production-ready concrete modules to (i) evaluate coral recruitment on five designs at four reef sites differing in flow regime and coral cover over one year; (ii) compare production-scale performance against experimental clay modules and natural reef substrate; and (iii) identify key parameters for large-scale production. The helix recess geometry of coral settlement modules outperformed the featureless control design approximately 20-fold and exceeded natural reef recruitment at least 3- to 32-fold. The helix features were successfully transferred from experimental clay to production-scale concrete modules, yielding comparable settlement densities when standardized to crevice length, which proved to be the biologically relevant unit of available habitat. Production feasibility was demonstrated by producing 690 modules for deployment on a hybrid reef on the west side of Oahu, Hawaii. The passive coral larval recruitment approach presented here could substantially improve the logistical and economic feasibility of large-scale coral reef restoration. This approach requires neither coral larval rearing, handling, nor coral fragmenting, and is compatible with active larval seeding where genetic diversity or larvae supply are limiting factors. The coral settlement modules can be cast in standardized concrete molds at precast facilities. Modules have demonstrated consistent coral recruitment enhancement across reef environments with contrasting flow and coral cover. Deploying mixed arrays of helix-recess structures with designs offering multi-level complexity and three-dimensional rugosity maximizes outcomes for coral, fish, and invertebrate communities simultaneously. Site selection is the most critical deployment decision and should consider larval supply, hydrodynamics, and substrate stability which drive recruitment outcomes more than design choice alone. The modules offer a range of application potential, ranging from integration into existing coastal infrastructure over stand-alone reef restoration approaches, to substrate-consolidating interconnected arrangements.

Resilient turbid coral reefs, found 1{degrees} north of the equator, experience fewer and less intense bleaching events despite being situated within the worlds busiest shipping port in highly urbanised Singapore. We hypothesised that bacteria within the coral holobiont play a role in maintaining coral diversity within this extreme environment by conferring traits that enhance host tolerance. Eleven Pseudovibrio isolates, whose genomes differ by only four SNPs, were isolated from the scleractinian coral Pachyseris speciosa. A [~]490 kbp megaplasmid (pCJH) was found in 7 of the 11 Pseudovibrio isolates. This study identified an opportunistic Pseudovibrio sp. pathogen of P. speciosa, accelerating bleaching disease. However, presence of the megaplasmid alters the ecological strategy of Pseudovibrio sp. toward mutualism, delaying coral bleaching. The megaplasmid enhances Pseudovibrios host colonisation and establishment of symbiosis through increased attachment and extends its bioactive genetic potential, but reduces fecundity. The Pseudovibrio genomes and megaplasmid encode several diffusible antibiotic biosynthetic gene clusters and contact-dependent inhibition mechanisms, with both types of inhibitory activity shown against local (i.e. P. speciosa) and type-strain Vibrio spp. Interaction analyses in experimentally heat-stressed corals revealed negative associations between Pseudovibrio and Vibrio ASVs corresponding to these cultured isolates. They also showed increased coral thermal tolerance by a full degree (1{degrees}C) when it is associated with the megaplasmid-bearing strain. Together, these findings support the Coral Probiotic Hypothesis that bacteria enhance coral resilience through chemical defense and identifies additional aspects to this symbiosis by a mobile genetic element which could play an important role in coral reef resilience.

This study presents a systematic revision of the suborder Astrophorina for the temperate Pacific coast of the United States and Canada. Major findings include a reduction in the number of species previously thought to range into the region from Japan; validation of most Geodia species erected by Lendenfeld (1910), which were later synonymized by de Laubenfels (1932); the formal description of 10 new species (Poecillastra alaskensis sp. nov., Vulcanella explorata sp. nov., Vulcanella rupta sp. nov., Stelletta cardenasi sp. nov., Stelletta nicolenya sp. nov., Stelletta limuwensis sp. nov., Dercitus (Stoeba) giveni sp. nov., Penares anyapax sp. nov., Penares foxi sp. nov., and Thenea diastra sp. nov.); and one new combination, Penares orientalis comb. nov. Extensive SCUBA-based collection efforts yielded new samples for 11 of the 26 species identified in the region, which enabled an integrative taxonomic approach that combined field photography, fresh material for DNA sequencing, and improved characterization of species ranges and morphological variability in previously described taxa. Illumina sequencing generated complete nuclear ribosomal haplotypes for five species, while Sanger sequencing of the 28S and cox1 loci placed 20 of the 26 species within molecular phylogenies. The use of very short "mini-barcode" amplicons also enabled sequence recovery from historic type specimens up to 137 years old. This study additionally reports the discovery of sponge grounds of abundant, large Geodia at diving depths in Southern California. Together, these results substantially advance our understanding of global astrophorid diversity and systematics, and the biogeography of sponge diversity in the Northeast Pacific. Note about species names: this pre-print is not intended to be a publication of the associated species names for the purposes of zoological nomenclature.

Linking animal movements to environmental drivers is essential for understanding ecological processes and anticipating species responses to climate change. We investigated habitat-specific movements in a globally significant aggregation of loggerhead turtles (Caretta caretta) nesting in Cabo Verde. Satellite tags on 15 adults (12 females, 3 males) provided multi-year tracks spanning breeding, migration, and foraging habitats. Movements and phenology differed by habitat. During the breeding season, females used either coastal areas, remaining within [~]20 m depth, or undertook long looping forays up to 360 km. Males showed two strategies: two remained resident in Cabo Verde waters, including Fra, the largest male tracked (Curved carapace length of 105 cm compared with a male mean of 90.7 {+/-} 10.3 cm), while the third migrated annually to distant foraging grounds and returned ahead of the subsequent breeding season. In foraging habitats, turtles adopted neritic or oceanic strategies: neritic turtles remained localised in warm, productive waters, whereas oceanic turtles ranged widely in deeper, less productive areas. Time- and space-shift analyses showed that oceanic foragers used intermediate sea surface temperature and chlorophyll-a conditions relative to nearby or temporally shifted alternatives, consistent with movement within a thermal-trophic trade-off. Together, these results show how sex, body size, and energy balance drive habitat-specific movement dynamics in a changing ocean.

BackgroundCoral reefs are among the most biodiverse ecosystems on Earth yet face an increasing risk of collapse under climate change and intensifying anthropogenic pressures. Although there is strong evidence that stressors such as overfishing, sedimentation, and wastewater runoff can drive shifts in coral community structure, few studies have investigated the molecular mechanisms underlying these shifts. Integrating data across multiple layers of biological organization, from the genome to the proteome and metabolome, offers a powerful approach to understanding how coral physiology and resilience are impacted by human activities. FindingsHere, we present high-coverage whole genome sequencing (Montipora only) together with untargeted metabolomic and proteomic datasets from three coral genera (Acropora, Pocillopora, and Montipora) that inhabit Ulithi Atoll, Yap State, FSM. Ulithi Atoll is an ideal system for investigating how anthropogenic pressures influence coral molecular ecology and adaptation, with extensive historical ecological data available through the long-term research program of the One People One Reef collaborative to connect multi-omics data with macroecological trends. Following data cleaning and quality control, all datasets exhibited minimal technical variation among samples, providing a comprehensive baseline for future research on coral resilience across a mosaic of natural and anthropogenic stressors. ConclusionsThese data provide a resource for examining how anthropogenic pressures influence coral physiology and resilience across environmental gradients. They also allow the identification of biomarkers of chronic stress that may inform the development of point-of-care diagnostic tools for coral health and contribute to evidence-based reef conservation and management strategies.

Acropora spp. are the dominant reef-builders of the Indo-Pacific but are also amongst the most stress-sensitive corals. For these reasons, Acropora spp. have become the most studied of corals, two species (A. digitifera and A. millepora) often essentially serving as the basis for understanding molecular responses and processes across the sub-order Refertina and corals in general. The early development of these species has been well-characterised in terms of morphology and gene expression but as yet we have a limited understanding of how transcription is regulated during development. In "higher" animals (bilaterians) microRNAs (miRNAs) are critical regulators of gene expression but until now their involvement in coral development has not been investigated. Building on the existing developmental data for Acropora spp., we catalogued microRNAs (miRNAs) expressed during the early development of Acropora digitifera and profiled their expression in 21 stages from unfertilised eggs to 24h after treatment with a natural settlement cue (CCA chips). 157 miRNAs were recognised, many of which ([~]60%) were novel. These fell into three distinct groups, corresponding to three distinct developmental phases: (1) those present in eggs through to gastrulation (2) a larvally expressed group and (3) those expressed following settlement induction. Exposure of competent larvae to a natural settlement inducer resulted in major changes in the miRNA profile within 10 minutes, indicating that miRNAs may be particularly important in mediating the larva/polyp transition but are also likely to play important regulatory roles throughout early coral development in addition to possible roles in disease resistance.

Benthic communities form the foundation of food webs in coastal and shelf seas worldwide. However, these communities face severe threats from anthropogenic bottom-disturbing activities. Marine Protected Areas (MPAs) effectively safeguard benthic communities against such disturbances. Nevertheless, the effectiveness of MPAs for the recovery of benthic communities in highly dynamic soft-bottom areas is much debated, as these communities are thought to be adapted to natural dynamics and therefore resistant to human impacts. In this study, we examine whether MPAs in highly dynamic seas support sensitive communities that are affected by bottom-disturbing fishing gear. Utilising a Before-After-Control-Impact (BACI) experimental design, we investigated the effects of disturbance caused by a shrimp trawl gear on macrozoobenthic communities within MPAs in a dynamic coastal soft-bottom sea over two years. We assessed changes in taxonomic and functional diversity, as well as community composition, across three levels of trawling intensity and frequency (low intensity and high frequency, high intensity and low frequency, and high intensity and high frequency) compared with undisturbed control areas. The study was carried out in the lower dynamic areas of the study system, where we found that, even light trawling gear impacted functional diversity and community assembly of macrozoobenthic communities, leading to shifts in functional groups. Contrastingly, taxonomic diversity metrics were not affected. We found that taxonomic and functional turnover increased stronger over time than the undisturbed control, with the highest turnover in the most frequently disturbed treatments. Long-living species were negatively impacted by disturbance, and the abundance of scavengers and predators increased in trawled areas, with possible radiating effects into undisturbed areas, while suspension feeders declined. Our findings demonstrate that anthropogenic disturbance remains a relevant ecological pressure, even in areas that may appear resilient due to their dynamic nature. MPAs can then provide ecological benefits by protecting sensitive and functionally important species. Article Impact StatementMarine Protected Areas are effective in safeguarding sensitive communities from anthropogenic disturbance.

Ocean warming is altering abiotic environments and biotic interactions experienced by marine organisms, where sensitive early developmental windows occur in biologically complex seawater communities. The impact of these interactions on developmental processes and fitness in hosts is not well understood, but likely contingent on the establishment of a host-associated microbiome. Here, we hypothesize that temperature and microbial exposure during embryogenesis influence larval microbiome assembly and host morphology. Strongylocentrotus purpuratus embryos were raised in low microbial richness (LMR) or high microbial richness (HMR) seawater at ambient (14 {degrees}C) or elevated (18 {degrees}C) temperature, then collected at 2, 4, and 6 days post-fertilization (dpf) following multiple feedings. Higher microbial diversity was observed in larvae that developed in HMR seawater when compared to LMR. Differences in relative abundances of dominant microbial families between seawater and larvae suggest some degree of host selectivity in microbiome assembly. Temperature did not strongly alter microbiome composition, but both temperature and microbial condition led to differences in larval morphology by 6 dpf, potentially due to enrichment of microbes with chemoheterotrophic functions. By linking how temperature and microbial communities interact with host development, we contribute novel insights into how early-life environmental conditions impact holobiont formation and morphology. One sentence summaryEarly developmental temperature and microbial conditions shape larval microbiome establishment and morphology.