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Major trade-offs often manifest as axes of diversity in organismal functional systems. Overarching trade-offs may result in high trait integration and restrict the trajectory of diversification to be along a single axis. Here, we explore the diversification of the feeding mechanism in coral reef fishes to establish the role of trade-offs and complexity in a spectacular ecological radiation. We show that the primary axis of variation in the measured musculo-skeletal traits is aligned with a trade-off between mobility and force transmission, spanning species that capture prey with suction and those that bite attached prey. We found weak or no covariation between about half the traits, reflecting deviations from the trade-off axis. The dramatic trophic range found among reef fishes occurs along the primary trade-off axis, with numerous departures that use a mosaic of trait combinations to adapt the feeding mechanism to diverse challenges. We suggest that morphological evolution both along and independent of a major axis of variation is a widespread mechanism of diversification in complex systems where a global trade-off shapes major patterns of diversity. Significant additional diversity emerges as systems use weak integration and complexity to assemble functional units with many trait combinations that meet varying ecological demands.

The National Marine Sanctuary Foundation (the Foundation) is developing a new Blue Economy program and associated strategy to help envision and provide sustainable revenue generation for the benefit of Sanctuary conservation work across our nation’s 15+ Sanctuaries. This Blue Economy Strategy will be first applied within the Florida Keys National Marine Sanctuary in support of its Mission: Iconic Reefs restoration initiative, by building critical revenue-generating initiatives that also support restoration work. Within this first overarching Florida Keys application, work will center around the native Caribbean king crab and its potential to become a novel fishery alongside its primary purpose as a coral reef restoration species. This project will contribute to the Florida Keys application of the Foundation’s Blue Economy Strategy by providing critically necessary background market analysis research for a viability study of the Caribbean king crab (CKC) fishery within the Florida Keys.

Coral reefs are facing unprecedented threats due to climate change and local stressors,necessitating a better understanding of their responses and resilience mechanisms regionally. This study examines the impacts of the 2020 mass bleaching event on coral reef dynamics in Kenting National Park, Taiwan, using large-area imaging (LAI) technology. Four sites were analyzed, revealing insights into coral abundance, planar area, size distribution, and survivalrates of two common coral taxa, corymbose Pocillopora and massive Porites. Whilerestricted in scope, our findings highlight the resilience and adaptability of coral species inthe face of environmental stressors. Despite limitations, our study underscores the importance of LAI data in providing detailed insights into coral reef demography and dynamics, serving as both a scientific analysis tool and a means of effective science communication. Further research is needed to fully understand underlying mechanisms and ensure the long-termsustainability of coral reef ecosystems in Kenting National Park.

Coral bleaching is a well-documented and increasingly widespread phenomenon in reefs across the globe, yet there has been relatively little research on the implications for reef water column microbiology and biogeochemistry. A mesocosm heating experiment and bottle incubation compared how unbleached and bleached corals alter dissolved organic matter (DOM) exudation in response to thermal stress and subsequent effects on microbial growth and community structure in the water column. Thermal stress of healthy corals tripled DOM flux relative to ambient corals. DOM exudates from stressed corals (heated and/or previously bleached) were compositionally distinct from healthy corals and significantly increased growth of bacterioplankton, enriching copiotrophs and putative pathogens. Together these results demonstrate how the impacts of both short-term thermal stress and long-term bleaching may extend into the water column, with altered coral DOM exudation driving microbial feedbacks that influence how coral reefs respond to and recover from mass bleaching events.

Biting to obtain attached benthic prey characterizes a large number of fish species on coral reefs, and is a feeding mode that contributes to important ecosystem functions. We use high-speed video to reveal the mechanisms used by a surgeonfish, Acanthurus leucosternon, to detach algae. After gripping algae in its jaws, the species pulls it by ventrally rotating both the head and the closed jaws, in a novel use of the intra-mandibular joint. These motions remain in the plane of the fish, reducing the use of a lateral head flick to detach the algae. The novel ability to bite and pull algae off the substrate without bending the body laterally minimizes exposure to high water flows, and may be an adaptation to feeding in challenging reef habitats such as the crest and flat. Therefore, our results could potentially represent a key milestone in the evolutionary history of coral reef trophodynamics.

An alarming amount of damage has occurred to coral reefs in Indonesia, with the causes of such damage either from human activities (anthropogenic causes) or natural processes. This study investigated the long-term dynamic changes in coral reef habitats in eight selected islands in the Spermonde archipelago, Indonesia, using remote sensing and historical information. A series of Landsat images recorded in different years (i.e. 1990, 1996, 2002, 2008, 2013, 2016, 2018, 2019, and 2022) were used to map the benthic habitats of each island (i.e. live coral, dead coral, seagrass, sand, rubble, mix bottom). The analysis estimated a total of 303.47 hectares or 76.26% loss of live coral in studied islands since 1990. In contrast, there was a substantial increase in dead coral algae and rubble, estimated at around 108.63 and 101.91 hectares, respectively. Strong and similar negative coefficient determination between live coral cover with both dead coral algae (R2 = 0.96, Y = -2.95) and rubble (R2 = 0.94, Y = -2.85) suggested that human activities (e.g. destructive fishing activities, damage from anchors, coral mining) and natural processes (e.g. sedimentation, coral bleaching, coral diseases, and coral predation) played comparable roles in coral reef degradation in Spermonde Archipelago. Furthermore, this study revealed that destructive fishing occurred on the island regardless it was inhabited or uninhabited and was influenced by the extent of its live coral cover. This study overall highlighted the ongoing degradation and factors contributing to coral loss in the Spermonde archipelago. Further research and monitoring efforts are necessary to understand the mechanisms driving the decline in live coral and the factors contributing to increases in dead coral algae and rubble. This knowledge will aid in developing targeted conservation strategies and management plans to protect the coral reef ecosystem in the Spermonde Archipelago and other affected regions in Indonesia. [ABSTRACT FROM AUTHOR]

Recurrent climate-driven warming events, which can induce severe coral bleaching and mortality on tropical reefs, are predicted to cause homogenisation of coral communities and loss of ecosystem functions in shallow reef systems (< 30 m). However, data documenting the variation in coral carbonate production across depth are limited. Here we explore differences in coral cover, community composition, coral colony size structure and carbonate production rates between two depths (10 m and 17.5 m) across four atolls in the remote Chagos Archipelago. We show higher coral carbonate production rates at 10 m (4.82 ± 0.27 G, where G = kg CaCO3 m−2 yr−1) compared to sites at 17.5 m (3.1 ± 0.18 G). The main carbonate producers at 10 m consisted of fast-growing branching and tabular corals (mainly Acroporids) and massive corals (mainly Porites), with high abundances of medium- and large-sized colonies. In contrast, coral carbonate production at 17.5 m was driven by slow-growing encrusting and foliose morphotypes and small colony sizes. Utilising a dataset following 6–7 years of recovery after the 2015–2017 bleaching event, our results show that depth-homogenisation of coral communities was temporary and carbonate production rates at 10 m depth recovered quicker at 3 of 4 studied atolls. The exception is Great Chagos Bank where slower recovery of branching and tabular corals at 10 m has led to a longer-lasting depth-homogenisation of carbonate production rates. The latter example cautions that more frequent bleaching events may drive increasing homogenisation of carbonate production rates across depth gradients, with implications for vital reef geo-ecological functions. [ABSTRACT FROM AUTHOR]

Reef-building corals live in close mutualism with dinoflagellate algae (family Symbiodiniaceae), which play key roles in coral physiological performance and survival. Association patterns between host species and endosymbiont algae and their significance are still not fully understood, but they seem to affect the ability of hosts to inhabit different environments and their resilience to climate change. In this work, we used next-generation sequencing of the Internal Transcribed Spacer 2 region of ribosomal DNA to determine the diversity and composition of the Symbiodiniaceae community in Pocillopora corals from Colombia, in the Eastern Tropical Pacific (ETP). We sampled 243 colonies from four localities characterized by distinct sea surface temperature, turbidity, and proximity to the coast. Two genera of Symbiodiniaceae, Durusdinium and Cladocopium were found associated with Pocillopora mitochondrial Open Reading Frame (mtORF) types. Cladocopium latusorum was highly specific to Pocillopora mtORF type 1, while C. pacificum was found exclusively associated with Pocillopora mtORF type 3. In contrast, Durusdinium glynnii was found in both Pocillopora mtORF types. Furthermore, a Cladocopium-dominated symbiont community occurred in cooler and less turbid localities, while a Durusdinium- dominated community was found in localities with high sea surface temperature and high water turbidity, irrespective of mtORF type. These results suggest that Pocillopora mtORF lineages associate with different Symbiodiniaceae genera in response to local environmental conditions. The ability to associate with a different partner under particular environmental conditions (Pocillopora-Durusdinium combination), and also maintain a specific partnership (Cladocopium species and Pocillopora mtORF types) may be key to understanding the resilience of the genus Pocillopora on ETP coral reefs. [ABSTRACT FROM AUTHOR]

ABSTRACT Corals residing in habitats that experience high‐frequency seawater pCO2 variability may possess an enhanced capacity to cope with ocean acidification, yet we lack a clear understanding of the molecular toolkit enabling acclimatisation to environmental extremes or how life‐long exposure to pCO2 variability influences biomineralisation. Here, we examined the gene expression responses and micro‐skeletal characteristics of Pocillopora damicornis originating from the reef flat and reef slope of Heron Island, southern Great Barrier Reef. The reef flat and reef slope had similar mean seawater pCO2, but the reef flat experienced twice the mean daily pCO2 amplitude (range of 797 v. 399 μatm day−1, respectively). A controlled mesocosm experiment was conducted over 8 weeks, exposing P. damicornis from the reef slope and reef flat to stable (218 ± 9) or variable (911 ± 31) diel pCO2 fluctuations (μatm; mean ± SE). At the end of the exposure, P. damicornis originating from the reef flat demonstrated frontloading of 25% of the expressed genes regardless of treatment conditions, suggesting constitutive upregulation. This included higher expression of critical biomineralisation‐related genes such as carbonic anhydrases, skeletal organic matrix proteins, and bicarbonate transporters. The observed frontloading corresponded with a 40% increase of the fastest deposited areas of the skeleton in reef flat corals grown under non‐native, stable pCO2 conditions compared to reef slope conspecifics, suggesting a compensatory response that stems from acclimatisation to environmental extremes and/or relief from stressful pCO2 fluctuations. Under escalating ocean warming and acidification, corals acclimated to environmental variability warrant focused investigation and represent ideal candidates for active interventions to build reef resilience while societies adopt strict policies to limit climate change. [ABSTRACT FROM AUTHOR]

Society relies on intact marine ecosystems for ecosystem services such as nutrition, livelihoods, health and well‐being. Yet, to obtain these benefits, we carry out activities, introducing pressures to ecosystems, damaging and degrading habitats and reducing their capacity to optimally provide ecosystem services. Biodiversity and ecosystem services are consequently being lost globally but impact chains from these activities are poorly understood, especially in tropical marine ecosystems. We identified for the first time impact chains linking activities with pressures they introduce in five tropical coastal and marine habitats, specifically through application in four Southeast Asian case study sites. Using expert elicitation based on existing evidence, we weighted each impact chain according to pressure extent, frequency and persistence, and habitat resistance and resilience. Assigning each impact chain an impact risk score allowed identification of activities and pressures introducing most risk, and habitats most under threat. Of 26 activities we considered, we found fishing activities, specifically trawling, gill nets and seine nets introduce most risk, along with tourism and recreation. Litter and pollution were among the greatest pressures on habitats, with coral reefs being most vulnerable overall. Destructive fishing practices were associated with physical pressures like abrasion, smothering and siltation and total habitat loss, while tourism activities were associated with organic enrichment, litter and pollution. The risk levels depended on the habitat and on local case study context. Synthesis and applications: A contextualised risk‐based approach can help to prioritise sustainability issues for management in data‐poor regions by making use of a range of knowledge types from local experts to broader scientific knowledge. A multisectoral, and ecosystem‐based risk assessment can help decision makers to consider trade‐offs in marine resource management and highlight priorities transparently, where coordination of multiple administrative organisations, sectors and local actors is required to meet multiple sustainability objectives. Physical pressures from fishing activities combined with pollution from tourism indicate effective management requires a multi‐use zoning approach that not only considers impacts at the site of activities but also integrates regional coordination to tackle dispersive pressures from pollution or sediment disturbance that occur at a distance from the source. [ABSTRACT FROM AUTHOR]

Background: Subtropical coral reefs are comparatively understudied compared to tropical coral reef ecosystems, yet also host a diverse and abundant array of marine life and provide substantial socio-economic benefits to communities. Research into the impacts of ocean warming on subtropical coral reefs has increased over the past two decades due to increase frequency and intensity of bleaching and degradation of these ecosystems. Understanding the extent of research effort and type of evidence assessing the response of subtropical corals and reefs to ocean warming provides valuable insight into global patterns in research efforts allowing critical knowledge gaps to be identified. A comprehensive understanding the impact of ocean warming on these systems will underpin our ability to predict and respond to future changes on subtropical coral reefs. Here, a systematic-map approach is used to identify recent research effort, from 2010 to 2023, and highlight patterns in the type, scale, and location of research conducted and as well as identify the availability of data and evidence reported. Methods: Primary literature was identified by searching Scopus and Science Citation Index Expanded through Web of Science Core Collection databases. The methodologies provided in a previously published systematic map protocol were applied, and 90 primary research publications were subsequently identified. Data extraction from the identified literature included bibliometric data, discipline and type of research, type of data reported and how it was recorded, and data availability. Findings: The identified literature consisted primarily of experimental (49%) and observational (39%) studies. The majority of the primary literature investigated corals in the ecoregions of Southern China (13%), Western Mediterranean (10%) and across a total of seven ecoregions grouped within Oceania (29%). Stressors reported in the literature as drivers of ocean warming reflect the standardisation of methods applied in reporting of events within the literature. Standardised metrics related to degree heating weeks (DHW) and marine heatwaves (MHW) have been reported when assessing the occurrence and severity of drivers, and are increasing in recent years, particularly in Australia. Finally, the need for increased research effort across much of the subtropics is evident, particularly for understudied regions such as the Western Indian Ocean where there are far fewer studies than other similar subtropical coral reef ecosystems. Conclusions: Climatic change, increasing ocean temperatures, and the impacts to subtropical and temperate coral reefs are of increasing concern to policy makers and researchers alike. This systematic map provides a broad overview of research topics and effort around the globe since 2010 and identifies areas where more research effort is urgently needed. Our study has identified major research clusters in Asia, Australia, the Mediterranean, and North America and gaps of research in regions such as the East Indian Oceans. Of the research conducted to date approximately one third reports on evidence related to marine protected areas and the vast majority of evidence is from close/territorial sea locations, providing important knowledge base for management of these areas. Of the 17 studies reporting on specific extreme events (rather than experimental studies which is the majority of evidence identified here) 13 have been published since 2019, with the majority reporting on events occurring in 2019/20 indicating a trend of increasing evidence in recent years (a total of 7 studies from 2010 to 2013, compared to over 10 studies published annually since 2019 up to mid-2023). [ABSTRACT FROM AUTHOR]

Ecologists have long sought general explanations for the co‐occurrence of ecologically similar taxa. Niche theory explains co‐occurrence via functional differences among taxa that reduce competition and promote resource partitioning. Alternatively, the unified neutral theory of biodiversity and biogeography suggests that co‐occurrence can be attributed to stochastic processes, and thus, presupposes that ecologically similar species that occur in sympatry are functionally analogous. We test these hypotheses using the most diverse crustacean‐sea anemone symbiosis from coral reefs in the Tropical Western Atlantic. δ13C and δ15N stable isotope analyses of six crustacean symbionts that co‐occur around the host anemone Bartholomea annulata exhibit highly differentiated isotopic niche space spanning several trophic levels. As multiple crustacean species within the symbiosis have been documented as cleaners that remove parasites from reef fishes, we extended our investigation into the broader cleaner community. Our stable isotope analyses of cleaners shows that Pederson's cleaner shrimp Ancylomenes pedersoni exhibits the highest δ15N isotopic values‐ significantly higher than all other putative cleaner species and consistent with expectations of a dedicated cleaning lifestyle. However, for other species previously described or observed to clean reef fishes, including Periclimenes yucatanicus, Stenopus hispidus and Stenorhynchus seticornis, δ15N isotopic values were substantially lower, raising questions about the degree to which these species rely on cleaning interactions to meet their nutritional requirements. Taken together, our data are consistent with the expectations of niche theory: co‐occurring symbiotic crustaceans have highly partitioned niche space with low levels of functional redundancy. [ABSTRACT FROM AUTHOR]

Understanding of non-geniculate coralline algal (NGCA) diversity, prevalence, and distribution in the tropical western North Atlantic is currently limited by reliance on morphological and anatomical features that are inadequate for species identifications. Reef surveys from two study sites, the Florida Keys (Florida, USA) and Roatán (Honduras), provided prevalence data for the main benthic organisms as well as relative abundance for NGCA genera. NGCA collected during these surveys and from additional sites and depths were identified using DNA sequences from two plastid genes, psbA and rbcL, and two nuclear genes, SSU and LSU, and supported by morphological and anatomical descriptions. Bayesian and Maximum Likelihood phylogenetic analyses, along with species delimitation and genetic distance methods, resolved 11 genera within two orders. Within the Corallinales, the genera Dawsoniolithon, Porolithon and Spongites each had one species, Harveylithon and Lithophyllum had two, Titanoderma three, Hydrolithon four, Neogoniolithon eight, and an unknown genus within the subfamily Neogoniolithoideae had 11 putative species. Within the Hapalidiales, the genera Phymatolithon and Roseolithon each had one species. This study reinforces the inability of morphological and anatomical features to distinguish NGCA species in the tropical western North Atlantic, resulting in substantial underestimations of species richness and diversity. [ABSTRACT FROM AUTHOR]

ABSTRACT Aim Location Method Results Main Conclusion As climate change increasingly threatens the world's coral reefs, enhancing their resilience by improving population connectivity for key reef species is crucial for ensuring their persistence. Here, we evaluate the population genomic structure of two common coral species, Pocillopora acuta and Porites sp., chosen due to their divergent life histories. Thousands of single‐nucleotide polymorphisms (SNPs) were sequenced and analysed to infer regional connectivity patterns in Southeast Asia, a region that harbours a tremendous diversity of marine life.Coasts of the Malay Peninsula and northern Borneo, covering ~1 million km2.NextRAD genotyping‐by‐sequencing of 185 Porites sp. and 221 Pocillopora acuta colonies. Libraries were prepared and sequenced on Illumina NovaSeq 6000. Genotyping involved initial quality controls, allele frequency filtering and checks for contamination. Genetic structure was assessed with Bayesian clustering, and relationships between genetic variation and environmental factors were studied through redundancy analysis. Contemporary gene flow was estimated using BayesAss.We observed panmixia among the broadcasting Porites sp. populations, while for the brooding Pocillopora acuta, the Malay Peninsula acts a strong barrier to dispersal between the Malacca Strait and the southern South China Sea. Moreover, its genomic structure seems to follow current marine ecoregion delineation. By analysing contemporary migrant movement, we can prioritise reef localities for conservation. In particular, localities at the Andaman Coral Coast are contemporarily isolated from the other localities, and Tioman is identified as a major larval source for both species.Our analyses highlight contrasting population differentiation patterns between the two species that can be explained by the disparity in their reproductive strategies. These findings are important for biodiversity managers in Southeast Asia; incorporation of regional connectivity considerations into conservation planning can help safeguard ecosystem resilience and persistence. [ABSTRACT FROM AUTHOR]

Worldwide, coral reefs are facing risk from climate change. The Western Indian Ocean (WIO) harbours about 16% of global coral reefs with highly reef-dependent local communities. Coastal protection and food security depend on effective conservation management, which requires understanding species abundances. Here, we explore how fish group distribution and abundance across the WIO, categorized by their trophic function, are explained by oceanographic connectivity, sea surface temperature (SST), and chlorophyll a. We designed a proportional oceanographic connectivity metric describing the relative strength of connectivity between all WIO coral reefs and each survey site. We created statistical models for four trophic groups: grazers and detritivores, herbivorous excavators, corallivores, and primary piscivores across 51 sites in the WIO. We show that SST and chlorophyll a are strong predictors of all trophic fish groups and that the proportional oceanographic connectivity metric improved the model predictions significantly for grazers and detritivores and excavators. For excavators, peak abundances were predicted at medium connectivity, and for grazers and detritivores, at low and medium connectivity, suggesting that larvae dispersal predominates at a local scale. Decision making should include connectivity for efficient conservation area prioritization, for which our proportional oceanographic connectivity metric is a valid and useful parameter. [ABSTRACT FROM AUTHOR]

Understanding an organism's niche and ecological role in its ecosystem is critical for conservation, especially for species that use multiple habitats at different life stages. The hawksbill sea turtle (Eretmochelys imbricata) is one such migratory animal that plays an ecologically important role in imperiled coral reef habitats. Hawksbill resource use strategies (e.g., generalism vs. specialism) in these foraging grounds are poorly understood, yet stable isotope analysis of carbon (δ13C) and nitrogen (δ15N) can provide information on the trophic niche and foraging location of consumers. Additionally, when a single sample is taken from a tissue that accretes through time, such as keratin, analyses can reveal information on the long-term foraging patterns of individuals. Here, we evaluate resource use strategies for 98 females within a nesting aggregation of hawksbills on the island of Antigua (17.159, -61.756) in the Eastern Caribbean. Stable isotope analysis of scute tissue collected from 2017 to 2019 revealed population-level generalism and varying degrees of individual specialization. Additionally, reproductive age was significantly related to niche width, with younger turtles showing higher variability in their isotopic record. Older turtles displayed overall smaller ranges in isotope values, indicating a narrowing of resource use with increased reproductive age amongst breeding adult females. These findings provide evidence of high variability in hawksbill diet, illustrate differences in ecological niche use across different ages, and highlight the necessity of evaluating multiple life stages to inform the conservation of this critically endangered species. [ABSTRACT FROM AUTHOR]

Coral reefs face threats from climate change and local pressures that lead to reductions in their physical structure, impacting biodiversity by limiting habitat availability. Despite many efforts to actively restore damaged reefs, few projects provide thorough evaluations of their success. This study measured the success of the "Reef Star" method at the Mars Coral Reef Restoration Project in Indonesia in reestablishing the physical structure of reef habitats that were destroyed by blast fishing. We used photogrammetry surveys to measure the physical habitat structure of 17 large sites (1000 m2 each), calculating three complementary measures of small‐ and large‐scale habitat complexity across degraded, restored, and naturally healthy coral reefs. We demonstrate that the restoration efforts have successfully restored small‐scale habitat complexity, as described by surface complexity metrics (3.22 ± 0.27 on restored reefs; 2.85 ± 0.26 on healthy reefs) and fractal dimension (2.27 ± 0.02 on restored reefs; 2.24 ± 0.02 on healthy reefs). This demonstrates the capacity for restored reefs to recover important ecosystem functions that are lost in degradation. However, while restoration has delivered some increases in large‐scale habitat complexity compared to degraded reefs, restored reefs still exhibit lower values of maximum vertical relief than healthy reefs, due to a lack of large physical structures. This lack of available large‐scale habitat might impact fish populations, meaning that restored reefs with limited large‐scale complexity may only support a restricted range of ecosystem functions. Effective reef restoration strategies must use a mixture of different methods that target the recovery of structural complexity at multiple scales. [ABSTRACT FROM AUTHOR]

The zoantharian genus Umimayanthus consists largely of species that live in obligate symbioses with sponges. Although zoantharians have often been overlooked in field collecting campaigns and in research, sponges are usually well-collected, and many natural history museums harbor numerous sponge specimens. Thus, these sponge collections may also include previously overlooked zoantharian species. Such is the case in this research, in which we examined sponge specimens in museum collections from Western Australia and eastern Indonesia. Based on our morphological and molecular analyses, we herein describe six species of Umimayanthus new to science, and redescribe another species described over a century ago. These species can be distinguished by their sponge associations, gross polyp and colony morphology, and depth ranges. Based on these findings, it appears that the Central Indo-Pacific region of Western Australia and Indonesia can be considered a hotspot for sponge-associated zoantharian diversity. We provide a key for the identification of all formally described species in the genus, but caution that there are likely more Umimayanthus species awaiting discovery. [ABSTRACT FROM AUTHOR]

Coral reef roughness produces turbulent boundary layers and bottom stresses that are important for reef metabolism monitoring and reef circulation modeling. However, there is some uncertainty as to whether field methods for estimating bottom stress are applicable in shallow canopy environments as found on coral reefs. Friction velocities (u∗ ${u}_{\ast }$) and drag coefficients (CD ${C}_{D}$) were estimated using five independent methods and compared across 14 sites on a shallow forereef (2–9 m deep) in Palau with large and spatially variable coral roughness elements (0.4–1 m tall). The methods included the following: (a) momentum balance closure, (b) log‐fitting to velocity profiles, (c) Reynolds stresses, (d) turbulence dissipation, and (e) roughness characterization from digital elevation models (DEMs). Both velocity profiles and point turbulence measurements indicated good agreement with log‐layer scaling, suggesting that measurements were taken within a well‐developed turbulent boundary layer and that canopy effects were minimal. However, u∗ ${u}_{\ast }$ estimated from the DEMs, momentum budget and log‐profile fitting were consistently larger than those estimated from direct turbulence measurements. Near‐bed Reynolds stresses only contributed about 1/3 of the total bottom stress and drag produced by the reef. Thus, effects of topographical heterogeneity that induce mean velocity fluxes, dispersive stresses, and form drag are expected to be important. This decoupling of total drag and local turbulence implies that both rates of mass transfer as well as values of fluxes inferred from concentration measurements may be proportional to smaller, turbulence‐derived values of u∗ ${u}_{\ast }$ rather than to those based on larger‐scale flow structure. Plain Language Summary: Bottom stress plays a primary role in the dynamics of coral reef flows and is therefore critical to parameterize correctly in reef circulation models. These models are often used to examine transport of the larvae of reef biota, for example. Bottom stress is also important for coral metabolism, as turbulent mixing enhances nutrient uptake and potentially alleviates coral bleaching severity. However, it is difficult to measure directly in the field and there is some uncertainty as to whether commonly used methods are applicable in shallow, canopy environments as might be found on coral reefs. We estimated bottom stress on a shallow forereef with high coral cover in Palau using five common methods at 14 different locations. The methods included point‐measurements of near‐bed turbulence, velocity profile fitting to expected boundary layer scaling, large‐scale momentum budgets, and roughness characterization from digital elevation models of the reef. Estimates of bottom stress derived from "local" measurements of turbulence were consistently smaller than those from more "spatially distributed" methods such as momentum balance closure. Care should be taken in choosing the appropriate measurement of bottom stress to use in circulation modeling or reef health studies. Key Points: Bottom stress was estimated using 5 methods and compared across 14 sites on a shallow forereef in Palau with large coral roughness elementsMeasurements indicate that Reynolds stresses contributed only about 1/3 of the total bottom stress and drag produced by the reefCirculation models should use drag coefficients from momentum budgets; reef metabolism studies should use direct turbulence measurements [ABSTRACT FROM AUTHOR]

Florida's coral reef is the third-largest barrier reef system in the world and provides valuable ecosystem services, such as recreation and tourism, erosion protection, and other services. Florida's reefs have been declining due to impacts from climate change, pollution, and other pressures. In response, various conservation strategies have been implemented, including education and outreach, growing corals in nurseries and transplanting them to degraded reef sites, and deploying artificial reefs. However, few studies have estimated an explicit value for different strategies to attain conservation goals. Understanding economic values for reef restoration and enhancement is needed to help inform decision-making and support marine policy. This study conducted a stated preference choice experiment survey to examine the way U.S. residents make economic trade-offs among different restoration strategies, including increasing coral cover, deploying artificial reefs, and limiting visitor access to reef sites. The results suggest that, on average, the economic value of increasing coral cover is about twice as high as the value of increasing the number of artificial reef sites. Economic values for reducing visitation were similar to values for increasing the number of artificial reefs. These results provide essential information to policy analysts concerning reef use, reef importance, and economic values for reef restoration. [ABSTRACT FROM AUTHOR]

The back-reef depressions, or lagoons, of Reunion Island (western Indian Ocean) host a high abundance of organisms living amongst the coral reefs and are critical sites for artisanal fishing, tourism, and shoreline stability for the island. Over time, increasing degradation of Reunionese reefs has been observed due to overexploitation, beach erosion and eutrophication. Efforts to mitigate the impact of these pressures on aquatic organisms include biodiversity surveys primarily performed through visual censuses that can be logistically complex and may unintentionally overlook organisms. Surveys integrating environmental DNA (eDNA) collections have provided rapid biodiversity assessments, while helping to circumvent some limitations of visual surveys. The present study describes the results of an exploratory eDNA survey, which aims to characterize metazoan communities of four Reunionese lagoons located along the west coast of the island. As eDNA surveys first require deliberate study design and optimization for each new context, we sought to establish a modernized workflow implementing specialized equipment to collect and preserve samples to facilitate future studies in these lagoons. During the austral summer of 2023, samples were pumped directly from surface and bottom depths at each site through self-preserving filters which were then processed for DNA metabarcoding using regions of the 12S ribosomal RNA (12S), small ribosomal subunit 18S (18S) and Cytochrome Oxidase I (COI) genes. The survey detected high species richness that varied by site, and in a single collection period, recovered the presence of 60 teleost families and numerous invertebrate taxa, including members of the coral faunal community that are less studied in Reunion. Distinct biological communities were observed at each site, and within a single lagoon, suggesting that these differences are due to site-specific factors (e.g., environmental variables, geographic distance, etc.). Although continued protocol optimization is needed, the present findings demonstrate the successful application of an eDNA-based survey for biodiversity assessment within Reunionese lagoons. [ABSTRACT FROM AUTHOR]

Bioerosion plays a crucial factor in shaping the structure and function of coral reef ecosystems, with bioeroders actively altering both the physical and ecological dynamics of coral substrates. Despite their importance, studying internal bioeroders in corals presents significant challenges owing to their cryptic nature within the skeletal structures. Additionally, invasive methods are often required to reveal the subtle and microscopic bioerosive alterations they induce in calcium carbonate substrates. Here, we demonstrate the effectiveness of high-resolution micro-computed tomography (mCT) in quantifying the abundance, size, distribution, and growth directions of coral bioeroders such as cryptic calcareous bivalves in the northern Red Sea. We scanned three coral species inhabited by bioeroders, followed by the utilization of three-dimensional image analysis software to identify, count, and measure each bivalve within the coral skeleton, along with quantifying boring cavity volumes. We revealed that mCT captures small boring cavities (< 1mm), providing more accurate abundance estimates of live and dead boring bivalves than the skeleton decalcification technique, with the added benefits of being rapid and non-destructive in contrast to traditional methods. Furthermore, measurements of empty cavity volumes enabled the estimations of the contribution of bioeroders to the overall coral skeletal porosity. Overall, our study highlights mCT as a practical and effective tool for studying cryptic coral bioeroders, providing novel ecological insights into bioeroder population ecology and coral-bioeroder interactions. [ABSTRACT FROM AUTHOR]

The collection of a dead specimen of the coral Heterocyathus cf. sulcatus on a sandy beach in southern Odisha highlights the importance of exploring offshore waters along this coast. The specimen was identified based on prominent taxonomic characters and association with coral boring worm. This genus was previously known to occur along the eastern coast of India, from the Gulf of Mannar/Palk Bay and off the Chennai coast. The presence of rocky offshore outcrops and a sandy substratum in the vicinity suggests that the specimen likely originated from that location. [ABSTRACT FROM AUTHOR]

Animal gut microbiomes are critical to host physiology and fitness. The gut microbiomes of fishes—the most abundant and diverse vertebrate clade—have received little attention relative to other clades. Coral reef fishes, in particular, make up a wide range of evolutionary histories and feeding ecologies that are likely associated with gut microbiome diversity. The repeated evolution of herbivory in fishes and mammals also allows us to examine microbiome similarity in relationship to diet across the entire vertebrate tree of life. Here, we generate a large coral reef fish gut microbiome dataset (n = 499 samples, 19 species) and combine it with a diverse aggregation of public microbiome data (n = 447) to show that host diet drives significant convergence between coral reef fish and mammalian gut microbiomes. We demonstrate that this similarity is largely driven by carnivory and herbivory and that herbivorous and carnivorous hosts exhibit distinct microbial compositions across fish and mammals. We also show that fish and mammal gut microbiomes share prominent microbial taxa, including Ruminoccocus spp. and Akkermansia spp., and predicted metabolic pathways. Despite the major evolutionary and ecological differences between fishes and mammals, our results reveal that their gut microbiomes undergo similar dietary selective pressures. Thus, diet, in addition to phylosymbiosis must be considered even when comparing the gut microbiomes of distantly related hosts. [ABSTRACT FROM AUTHOR]

The back-reef depressions, or lagoons, of Reunion Island (western Indian Ocean) host a high abundance of organisms living amongst the coral reefs and are critical sites for artisanal fishing, tourism, and shoreline stability for the island. Over time, increasing degradation of Reunionese reefs has been observed due to overexploitation, beach erosion and eutrophication. Efforts to mitigate the impact of these pressures on aquatic organisms include biodiversity surveys primarily performed through visual censuses that can be logistically complex and may unintentionally overlook organisms. Surveys integrating environmental DNA (eDNA) collections have provided rapid biodiversity assessments, while helping to circumvent some limitations of visual surveys. The present study describes the results of an exploratory eDNA survey, which aims to characterize metazoan communities of four Reunionese lagoons located along the west coast of the island. As eDNA surveys first require deliberate study design and optimization for each new context, we sought to establish a modernized workflow implementing specialized equipment to collect and preserve samples to facilitate future studies in these lagoons. During the austral summer of 2023, samples were pumped directly from surface and bottom depths at each site through self-preserving filters which were then processed for DNA metabarcoding using regions of the 12S ribosomal RNA (12S), small ribosomal subunit 18S (18S) and Cytochrome Oxidase I (COI) genes. The survey detected high species richness that varied by site, and in a single collection period, recovered the presence of 60 teleost families and numerous invertebrate taxa, including members of the coral faunal community that are less studied in Reunion. Distinct biological communities were observed at each site, and within a single lagoon, suggesting that these differences are due to site-specific factors (e.g., environmental variables, geographic distance, etc.). Although continued protocol optimization is needed, the present findings demonstrate the successful application of an eDNA-based survey for biodiversity assessment within Reunionese lagoons. [ABSTRACT FROM AUTHOR]

ABSTRACT Giant clams are invertebrates that form mutualistic associations with Symbiodiniaceae dinoflagellates. Despite their ecological significance, gaps persist regarding our understanding of their trophic ecology. Specifically, it is unknown whether Symbiodiniaceae‐derived photosynthates are metabolized differently according to species and organ. Therefore, we maintained Tridacna derasa and T. noae for 3 months in a well‐lit recirculated system without food supply. Samples were taken from eight organs and underwent lipid extraction and fatty acid esterification before analysis of three symbiont‐derived fatty acids (stearidonic acid, docosapentaenoic acid, and docosahexaenoic acid—SDA, DPA, and DHA, respectively) using gas chromatography. Results show considerable variation in fatty acids concentration among species and organs. SDA was found in higher concentrations in T. noae, especially in the adductor muscle. DPA was detected in low concentrations across T. noae organs and absent for T. derasa. DHA did not vary significantly among species and organs. Our findings indicate that Symbiodiniaceae supply clams with fatty acids, which are stored differentially according to species and organs. This demonstrates that these compounds are translocated to multiple organs throughout the complex giant clam anatomical system, in contrast to simpler hosts like corals. These results advance our understanding of the physiological dynamics of the mollusk‐algae association. [ABSTRACT FROM AUTHOR]

Coral reefs, widely distributed in tropical and subtropical waters, generally have uneven flat topography. Sudden changes in reef flat topography significantly impact the propagation and evolution characteristics of tsunami-like waves; however, related studies are rare. This study systematically investigates the propagation and evolution of tsunami-like waves over uneven islands and reefs through wave flume physical experiments, analyzing the influences of incident wave height and reef flat water depth on these characteristics. The experimental results show that an uneven reef flat blocks the propagation of solitary waves and generates reflected waves. The slope, reef margin, and first reef flat in front of the reef are deep underwater, causing solitary waves to undergo shallow deformation without breaking. The wave height increases to a maximum at the step of the reef flat at shallower water depths and then breaks on the second reef flat. After breaking, the solitary wave propagates over the second reef flat as a swell, with wave height slowly attenuated due to energy dissipation from breaking in the limited water depth. As the incident wave height increases, the local wave height at each measuring point rises, with the increase in wave surface further amplified by the shallowing effect at the reef flat step. An increase in incident wave height causes the uneven reef flat to dissipate more wave energy and enhances wave attenuation. Consequently, the spatial distribution of local wave height Hi/H0 decreases with an increase in incident wave height. Increasing the water depth of the reef flat gradually weakens the shallowing effect, resulting in a decrease in the range and peak value of the maximum wave height near the reef flat step. When the water depth of the reef flat exceeds a certain limit, such as hr = 0.05 m in this study, the influence of the uneven reef flat on local wave height diminishes. An increase in the water depth leads to a reduction in wave energy consumed by the uneven reef flat, while the maximum wave height on the second reef flat increases monotonically with deeper water. During the propagation of solitary waves over uneven islands and reefs, two reflections from reef margins and flat steps occur. The reflection coefficient CR1 decreased with increasing incident wave height and reef flat water depth, while the reflection coefficient CR2 decreases significantly with increasing water depth. When the reef flat water depth is low, sudden changes in reef flat terrain greatly enhance the reflection intensity of incident waves. In particular, when hr = 0 m, the reflection coefficient CR2 reaches approximately 0.3. [ABSTRACT FROM AUTHOR]

Anthropogenic pressure is increasing the variety and frequency of environmental disturbance events, limiting recovery and leading to long‐term declines in wild plant and animal populations. Coral reefs and associated fish assemblages are inherently dynamic due to their susceptibility to a host of disturbances, but regional‐scale nuances in the drivers of long‐term change frequently remain poorly resolved. Here, we examine the effects of multiple potential drivers of change in coral reef fish assemblages across 4 inshore regions of the Great Barrier Reef Marine Park (GBRMP), Australia, over 12–14 years (2007–2021). Each region had a unique disturbance history, in conjunction with long‐term changes in physical and habitat variables. Phases of recovery were apparent in the years between disturbance events at all locations, but these were not long enough to prevent substantial declines in reef fish density (by 33%–72%) and species richness (by 41%–75%) throughout the study period. The main drivers of change in fish assemblages varied among regions; however, the most rapid changes followed cyclone and flood events. Limited recovery periods resulted in temporal shifts in fish species composition from typically coral‐associated to algae‐associated. Most trophic groups declined in density except farmers, grazers, omnivores and parrotfish. No‐take marine reserves (NTMRs) had small and inconsistent effects on total fish assemblages, but delivered benefits for fishery‐targeted piscivores. Our findings suggest that coral reef responses to local stressors and cumulative escalating climate change impacts are highly variable at regional scales, and that small NTMRs are unlikely to mitigate the impacts of increasingly frequent climatic disturbances. Nearshore coral reefs worldwide are high‐value habitats that are either already degraded or vulnerable to degradation and the loss of important fish groups. Global efforts to reduce greenhouse gas emissions must be coupled with effective local management that can support the functioning and adaptive capacity of coral reefs. [ABSTRACT FROM AUTHOR]

Biodiversity changes and habitat shifts are two phenomena substantially reshaping marine life on our present and future planet. Although those phenomena are well recognized on the macrobial level, they currently do not receive similar attention on the microbial level. Generally, microbiome diversity and function, associated with and governing the health and fitness of their host organisms, are neglected in conservation efforts. This is especially problematic as previous research has highlighted that host‐associated microbes (microbiomes) may display distribution patterns that are not only correlated with host animal biogeographies but also with other factors such as prevailing environmental conditions. Here, marine spatial planning for socio‐ecological management of animal‐associated microbiomes is discussed, using deep‐sea sponge and coral‐associated microbiomes as an example of how to incorporate microbial diversity into conservation planning. We advocate for a holistic and integrative approach to marine spatial planning that incorporates the larger habitat, the host, the microbiome, as well as the socio‐economic and cultural perspective, throughout the whole decision‐making process. A general workflow containing the needed steps to establish microbiome‐integrated marine protected areas is presented, as well as the analytical steps and results underlying the implementation of the world's first microbiome‐considered marine conservation network on the Scotian Shelf off eastern Canada. [ABSTRACT FROM AUTHOR]

This review comprehensively covers the development of viable unmanned underwater vehicles based on their technical capabilities, in particular those designed to conduct research exploration in underwater ecosystems and address environmental issues through analysis of coral reef vulnerability. The most important elements to be obtained are in situ data samples for analysis and characterization, supported by molecular biomarkers and marine ecology indicators. The following aspects are considered in this study: first, the geographic distribution of coral reefs for the study of marine ecology and molecular biological approaches for the detection of biomarkers to evaluate the vulnerability of coral reefs are detailed; then, the technologies currently available for the study of coral reefs are briefly described, ranging from large-scale capture to local-scale capture directly in the study region, taking advantage of remote sensing systems assisted by aerial technologies, marine vehicles, and artificial intelligence for the mapping, monitoring, and management of coral reefs as well as the characterization of their vulnerability; following this, existing marine vehicle technologies are generally explained, including a categorical description and an updated and highlighted list of innovative and robust marine vehicles that have been used in coral reef applications; the technical capabilities of such vehicle throughout the missions they have been subjected to are presented based on bibliographic references; finally, this review promotes multidisciplinary work to integrate the developments in the associated knowledge areas in order to obtain synergies in the face of challenges related to the massive scale of coral reef degradation worldwide. [ABSTRACT FROM AUTHOR]

Extreme wildfire events and cyclones are on the rise across tropical regions in response to climate change. Despite assumptions about their impact on phytoplankton through nutrient supplies, field evidence is lacking, and their combined effects remain unclear. In an on‐site microcosm experiment conducted in the Xisha Islands, South China Sea (SCS) after Typhoon Noru, we observed enhanced phytoplankton growth in response to exposure to total suspended particulates (TSP) from wildfires (2 mg/L and 6 mg/L) under wind‐driven upwelling conditions. Upwelled nutrients had a limited effect on Chl‐a concentration due to phosphate depletion, by contrast, wildfire TSP contributed nutrients enriched in nitrogen and phosphate, resulting in a 3.30–5.61‐fold increase in Chl‐a. However, upwelled nutrients increased the diatom‐to‐dinoflagellate ratio from the initial 11.0 to 12.7, TSP at low and high levels reduced the ratio to 0.3–0.8 and significantly altered the communities, with 61.8% of species, including two dominant diatoms, negatively correlated with N and/or P supplies. Species diversity declined significantly at high TSP levels. These findings suggest that enhanced primary productivity by wildfires may come at the cost of an altered phytoplankton community. This field study improves understanding of the effects of simultaneous occurrences of multiple extreme climate events on marine ecosystems. Plain Language Summary: Increasing wildfires and typhoons in tropical regions due to global warming are believed to affect algae growth by altering nutrient inputs from atmospheric deposition and upwelling. Tropical coral reefs rely on algae to sustain high biomass in the food web. However, there is limited evidence of how wildfires impact algae under upwelling conditions. This study in the coral reef regions of the SCS found that wildfires provide nutrients including nitrogen and phosphorus, which enhance algae growth more effectively under upwelling compared to upwelling alone. However, when typhoon and wildfire particles are combined, they tend to alter the types of algae present. Some algae become less competitive, leading to reduced species diversity overall. Given the potential variations in carbon export efficiency among species, wildfires may influence carbon sequestration by algae. This field study suggests that the simultaneous occurrence of wildfires and tropical cyclones may enhance productivity but pose potential risks to coral reef ecosystems. Key Points: Wildfire particulates (2–6 mg/L) alleviated P limitation and extended the promotion of phytoplankton growth under wind‐driven upwellingWhen combined with upwelling, wildfire particulates altered the phytoplankton community, lowering the diatom‐to‐dinoflagellate ratioNearly 60% of algal species displayed a negative relationship with N and/or P provided by wildfire particulates [ABSTRACT FROM AUTHOR]

Coral reefs are among the most diverse and productive ecosystems, teeming with life and providing many benefits to marine life and human communities. Coral reef classification is popular for many important reasons, such as assessing biodiversity, prioritizing conservation actions to protect vulnerable species and their habitats, and many other objectives related to scientific research and interdisciplinary studies on marine ecosystems. Classifying images of coral reefs is challenging due to their great diversity and subtle differences in morphology. Manually classifying them is a time-consuming process, especially when dealing with large datasets. This can limit the scalability and efficiency of scientific research and conservation efforts. This study proposes an automated classification approach using computer vision and deep learning techniques to address these challenges, employing models such as YOLOv5l, YOLOv8l, and VGG16 to classify images of coral reefs. The dataset, comprising 1,187 images of five coral species, was augmented for robustness. YOLOv8l demonstrated superior performance with an accuracy of 97.8%, significantly outperforming the other models in terms of speed and accuracy. These results demonstrate the potential of advanced deep-learning models to improve coral reef monitoring and conservation efforts. This approach aims to streamline classification processes, improving the efficiency and scalability of coral reef research and conservation initiatives worldwide. [ABSTRACT FROM AUTHOR]

Coral reefs are among the most biodiverse ecosystems on Earth, largely due to the structural complexity created by corals. Coral habitat is crucial refuge for numerous small animals, and competition for habitat can structure populations if in short supply. Reefs in Hawai'i are largely dominated by the small branching coral Pocillopora meandrina, which supports diverse communities of fishes and invertebrates. Two species of nocturnal scorpionfishes, Sebastapistes coniorta and S. galactacma, are particularly common in P. meandrina, inhabiting the complex branching morphology of their host corals during the day and feeding in and around these corals at night. Surveys of scorpionfishes in 458 P. meandrina between 3 and 22 m deep along the south and west shores of O'ahu revealed inverse depth distributions over which these species occurred in P. meandrina. Sebastapistes coniorta almost exclusively occurred in coral colonies between 5 and 10 m deep, while S. galactacma were found across all depths surveyed, though were far more common and abundant in deeper coral colonies (15–20 m) below the range of S. coniorta. Further, measurements of host colony morphometrics revealed that these species appeared to use microhabitat in subtly different ways. The larger-bodied species, S. coniorta, was more commonly found in P. meandrina with wider spaces between branches, while the smaller-bodied species was negatively associated with wider branch spacing. These patterns indicate habitat partitioning between S. coniorta and S. galactacma at both the reef and colony scale, which may explain how these species are able to coexist on reefs in Hawai'i. [ABSTRACT FROM AUTHOR]

Periodic outbreaks of crown‐of‐thorns starfish have led to severe coral reef degradation, with one hypothesized cause being eutrophication. Phosphorus (P) is one of the driving factors for eutrophication, but researches on the spatiotemporal distributions of P in coral reefs are limited, impeding our understanding of the P cycling in coral reefs and its correlation with starfish outbreaks. This study undertook an analysis of various P species, migration and transformation in seawater, sediments, and crown‐of‐thorns starfish within the coral reefs of the Xisha Islands, northern South China Sea. The results show that in seawater, P predominantly existed in the dissolved phase, with organic P constituting the largest fraction (>67%). Conversely, in sediments, P primarily existed as inorganic form (43%−95%), with calcium‐bound P comprising the majority (26%−46%). Notably, exchangeable P accounted for a relatively smaller fraction (9%−20%) but played a significant role as a source of P released from sediments into seawater (0.01−0.17 mmol m−2 hr−1). During starfish outbreaks, starfish (1,000 individuals per hectare) assimilated P from seawater via phytoplankton or corals, resulting in substantial accumulation of both organic and inorganic P in their tissues (69−315 μmol g−1). Meanwhile, starfish excretion released P back into the seawater, which contributes to the migration and transformation of various P forms. Historical data also show a close relationship between P content and starfish density. These findings highlight the interactions between starfish and P cycling within coral reefs, and provide valuable insights into conservation and restoration on coral reefs, especially those severely affected by starfish outbreaks. Plain Language Summary: The coral reefs of the Xisha Islands, northern South China Sea have experienced periodic outbreaks of crown‐of‐thorns starfish, causing severe degradation of the coral reefs. However, the reasons for the outbreak of starfish remain unclear. This study aims to investigate the relationship between P content and starfish outbreaks, and examines where and how P migrates and transforms in seawater, sediments, and crown‐of‐thorns starfish. This study discovered that the majority of P in seawater existed in a dissolved state, primarily as organic compounds. In sediments, P existed mostly in inorganic forms, particularly bound to calcium, which is commonly found in coral reef sediments. The proportion of exchangeable P which can easily migrate from the sediments into the seawater was the least. During starfish outbreaks in the Xisha Islands, the density of starfish can hit 1,000 individuals per hectare. These starfish assimilated P from seawater via phytoplankton or corals, resulting in significant amounts of both organic and inorganic P within their tissues. Yet, starfish excretion releases P back into the seawater. This study linked starfish outbreaks to DIP levels, which helps us understand the P cycling in coral reefs and provides some outlooks on coral reef conservation in the context of starfish outbreaks. Key Points: Water P in Xisha's coral reefs mainly existed in DOP, as a significant DIP source via degradationPorous calcium carbonate boosted Ca‐P and Ex‐P proportion and DIP release in reef sedimentsCrown‐of‐thorns starfish stored and released OP and IP, affecting P cycle and starfish outbreaks [ABSTRACT FROM AUTHOR]

Abstract Background Subtropical coral reefs are comparatively understudied compared to tropical coral reef ecosystems, yet also host a diverse and abundant array of marine life and provide substantial socio-economic benefits to communities. Research into the impacts of ocean warming on subtropical coral reefs has increased over the past two decades due to increase frequency and intensity of bleaching and degradation of these ecosystems. Understanding the extent of research effort and type of evidence assessing the response of subtropical corals and reefs to ocean warming provides valuable insight into global patterns in research efforts allowing critical knowledge gaps to be identified. A comprehensive understanding the impact of ocean warming on these systems will underpin our ability to predict and respond to future changes on subtropical coral reefs. Here, a systematic-map approach is used to identify recent research effort, from 2010 to 2023, and highlight patterns in the type, scale, and location of research conducted and as well as identify the availability of data and evidence reported. Methods Primary literature was identified by searching Scopus and Science Citation Index Expanded through Web of Science Core Collection databases. The methodologies provided in a previously published systematic map protocol were applied, and 90 primary research publications were subsequently identified. Data extraction from the identified literature included bibliometric data, discipline and type of research, type of data reported and how it was recorded, and data availability. Findings The identified literature consisted primarily of experimental (49%) and observational (39%) studies. The majority of the primary literature investigated corals in the ecoregions of Southern China (13%), Western Mediterranean (10%) and across a total of seven ecoregions grouped within Oceania (29%). Stressors reported in the literature as drivers of ocean warming reflect the standardisation of methods applied in reporting of events within the literature. Standardised metrics related to degree heating weeks (DHW) and marine heatwaves (MHW) have been reported when assessing the occurrence and severity of drivers, and are increasing in recent years, particularly in Australia. Finally, the need for increased research effort across much of the subtropics is evident, particularly for understudied regions such as the Western Indian Ocean where there are far fewer studies than other similar subtropical coral reef ecosystems. Conclusions Climatic change, increasing ocean temperatures, and the impacts to subtropical and temperate coral reefs are of increasing concern to policy makers and researchers alike. This systematic map provides a broad overview of research topics and effort around the globe since 2010 and identifies areas where more research effort is urgently needed. Our study has identified major research clusters in Asia, Australia, the Mediterranean, and North America and gaps of research in regions such as the East Indian Oceans. Of the research conducted to date approximately one third reports on evidence related to marine protected areas and the vast majority of evidence is from close/territorial sea locations, providing important knowledge base for management of these areas. Of the 17 studies reporting on specific extreme events (rather than experimental studies which is the majority of evidence identified here) 13 have been published since 2019, with the majority reporting on events occurring in 2019/20 indicating a trend of increasing evidence in recent years (a total of 7 studies from 2010 to 2013, compared to over 10 studies published annually since 2019 up to mid-2023).

Coral reefs, widely distributed in tropical and subtropical waters, generally have uneven flat topography. Sudden changes in reef flat topography significantly impact the propagation and evolution characteristics of tsunami-like waves; however, related studies are rare. This study systematically investigates the propagation and evolution of tsunami-like waves over uneven islands and reefs through wave flume physical experiments, analyzing the influences of incident wave height and reef flat water depth on these characteristics. The experimental results show that an uneven reef flat blocks the propagation of solitary waves and generates reflected waves. The slope, reef margin, and first reef flat in front of the reef are deep underwater, causing solitary waves to undergo shallow deformation without breaking. The wave height increases to a maximum at the step of the reef flat at shallower water depths and then breaks on the second reef flat. After breaking, the solitary wave propagates over the second reef flat as a swell, with wave height slowly attenuated due to energy dissipation from breaking in the limited water depth. As the incident wave height increases, the local wave height at each measuring point rises, with the increase in wave surface further amplified by the shallowing effect at the reef flat step. An increase in incident wave height causes the uneven reef flat to dissipate more wave energy and enhances wave attenuation. Consequently, the spatial distribution of local wave height Hi/H0 decreases with an increase in incident wave height. Increasing the water depth of the reef flat gradually weakens the shallowing effect, resulting in a decrease in the range and peak value of the maximum wave height near the reef flat step. When the water depth of the reef flat exceeds a certain limit, such as hr = 0.05 m in this study, the influence of the uneven reef flat on local wave height diminishes. An increase in the water depth leads to a reduction in wave energy consumed by the uneven reef flat, while the maximum wave height on the second reef flat increases monotonically with deeper water. During the propagation of solitary waves over uneven islands and reefs, two reflections from reef margins and flat steps occur. The reflection coefficient CR1 decreased with increasing incident wave height and reef flat water depth, while the reflection coefficient CR2 decreases significantly with increasing water depth. When the reef flat water depth is low, sudden changes in reef flat terrain greatly enhance the reflection intensity of incident waves. In particular, when hr = 0 m, the reflection coefficient CR2 reaches approximately 0.3.

Filamentous viruses are hypothesized to play a role in stony coral tissue loss disease (SCTLD) through infection of the endosymbiotic dinoflagellates (Family Symbiodiniaceae) of corals. To evaluate this hypothesis, it is critical to understand the global distribution of filamentous virus infections across the genetic diversity of Symbiodiniaceae hosts. Using transmission electron microscopy, we demonstrate that filamentous virus-like particles (VLPs) are present in over 60% of Symbiodiniaceae cells (genus Cladocopium) within Pacific corals (Acropora hyacinthus, Porites c.f. lobata); these VLPs are more prevalent in Symbiodiniaceae of in situ colonies experiencing heat stress. Symbiodiniaceae expelled from A. hyacinthus also contain filamentous VLPs, and these cells are more degraded than their in hospite counterparts. Similar to VLPs reported from SCTLD-affected Caribbean reefs, VLPs range from ~150 to 1500 nm in length and 16-37 nm in diameter and appear to constitute various stages in a replication cycle. Finally, we demonstrate that SCTLD-affected corals containing filamentous VLPs are dominated by diverse Symbiodiniaceae lineages from the genera Breviolum, Cladocopium, and Durusdinium. Although this study cannot definitively confirm or refute the role of filamentous VLPs in SCTLD, it demonstrates that filamentous VLPs are not solely observed in SCTLD-affected corals or reef regions, nor are they solely associated with corals dominated by members of a particular Symbiodiniaceae genus. We hypothesize that filamentous viruses are a widespread, common group that infects Symbiodiniaceae. Genomic characterization of these viruses and empirical tests of the impacts of filamentous virus infection on Symbiodiniaceae and coral colonies should be prioritized.

Coral reefs are both exceptionally biodiverse and threatened by climate change and other human activities. Here, we review population genomic processes in coral reef taxa and their importance for understanding responses to global change. Many taxa on coral reefs are characterized by weak genetic drift, extensive gene flow, and strong selection from complex biotic and abiotic environments, which together present a fascinating test of microevolutionary theory. Selection, gene flow, and hybridization have played and will continue to play an important role in the adaptation or extinction of coral reef taxa in the face of rapid environmental change, but research remains exceptionally limited compared to the urgent needs. Critical areas for future investigation include understanding evolutionary potential and the mechanisms of local adaptation, developing historical baselines, and building greater research capacity in the countries where most reef diversity is concentrated.

Accurate species identification, based on DNA barcoding, can be achieved when sufficient sequence variations are present amongst species in the sampled marker. In general, the ability to discriminate species decreases with shorter sequences; however, shorter regions have a merit in amplification success by the polymerase chain reaction. In either case, it is important to investigate sequence variations amongst species before barcoding to understand its reliability and limitations. In this study, we investigate how accurately short, but hypervariable portion of the mitochondrial 12S ribosomal RNA (12S) gene (MiFish region with approximately 180 bp) is used to identify each species in diversified pomacentrid fishes compared with the longer region of the same gene (approximately 750 bp). We prepared three datasets with 301 sequences of the MiFish region for 150 species, the same 301 of sequences of the longer 12S region and 476 sequences of the MiFish region for 183 species. Neighbour-joining (NJ) analyses and genetic distance analyses revealed several indistinguishable pairs of species in these DNA regions. Although the number of such pairs was larger in the MiFish region, 83.6% (153 of 183) of species possessed respective unique sequences even in the MiFish region (versus 96.0% [144 of 150 species] in the longer 12S region). A part of indistinguishable pairs of species might have caused by mitochondrial DNA introgressions and taxonomically unresolved problems. Our analysis clarified the effectiveness and limitations of species identification using DNA barcoding for Pomacentridae and the sequences we provided here contribute to the expansion of references for pomacentrid mitochondrial 12S sequences.

Abstract Background Marine benthic prokaryotic communities play crucial roles in material recycling within coastal environments, including coral reefs. Coastal sedimentary microbiomes are particularly important as potential reservoirs of symbiotic, beneficial, and pathogenic bacteria in coral reef environments, and therefore presumably play a core role in local ecosystem functioning. However, there is a lack of studies comparing different environments with multiple sites on the island scale, particularly studies focusing on prokaryotic communities, as previous investigations have focused mainly on a single site or on specific environmental conditions. In our study, we collected coastal sediments from seven sites around Okinawa Island, Japan, including three different benthic types; sandy bottoms, seagrass meadows, and hard substratum with living scleractinian corals. We then used metabarcoding to identify prokaryotic compositions and estimate enzymes encoded by genes to infer their functions. Results The results showed that the three substrata had significantly different prokaryotic compositions. Seagrass meadow sites exhibited significantly higher prokaryotic alpha-diversity compared to sandy bottom sites. ANCOM analysis revealed that multiple bacterial orders were differentially abundant within each substratum. At coral reef sites, putative disease- and thermal stress-related opportunistic bacteria such as Rhodobacterales, Verrucomicrobiales, and Cytophagales were comparatively abundant, while seagrass meadow sites abundantly harbored Desulfobacterales, Steroidobacterales and Chromatiales, which are common bacterial orders in seagrass meadows. According to our gene-coded enzyme analyses the numbers of differentially abundant enzymes were highest in coral reef sites. Notably, superoxide dismutase, an important enzyme for anti-oxidative stress in coral tissue, was abundant at coral sites. Our results provide a list of prokaryotes to look into in each substrate, and further emphasize the importance of considering the microbiome, especially when focusing on environmental conservation. Conclusion Our findings prove that prokaryotic metabarcoding is capable of capturing compositional differences and the diversity of microbial communities in three different environments. Furthermore, several taxa were suggested to be differentially more abundant in specific environments, and gene-coded enzymic compositions also showed possible differences in ecological functions. Further study, in combination with field observations and temporal sampling, is key to achieving a better understanding of the interactions between the local microbiome and the surrounding benthic community.

ABSTRACT Ostreobium comprises endolithic algae commonly seen in conjunction with scleractinian corals. In the past, it was solely recognized as a coral skeleton bioeroder. Their relationship with corals is critical because they give photosynthetic byproducts and help the coral when it loses its primary symbionts due to stress. The variety of these algae in coral species of the genus Porites in the Tropical Eastern Pacific and western Atlantic was investigated. Ostreobium samples from seven Porites species including two from the Tropical Eastern Pacific (TEP) (P. panamensis and P. lobata) and five from the Caribbean (P. furcata, P. porites, P. colonensis, P. branneri, and P. astreoides) were extracted. Published rbcL sequences from algae found within various coral species from other parts of the world were also compared. A biogeographic analysis and two methodologies, PTP (Poisson tree process) and GMYC (general mixed Yule‐coalescent), were used to delineate the different species. The findings revealed a significant degree of genetic diversity within Ostreobium, with more than 15 groups of not more than three individuals and 40 individual lineages. Its origins date back to the Ordovician, 500 Ma, and it does not appear to preserve host specificity. The sampled locations still have a wide variety of Ostreobium. Biogeographically patterns were also confirmed, making it impossible to pinpoint the precise origins of most clades. The ancestry analyses revealed convergent events for not only the emergence of Ostreobium in a few genera of local corals, but also the phenomenon occurred in genera from far‐off places. [ABSTRACT FROM AUTHOR]

The coral reef ecosystem is one of the most productive ecosystems in the ocean, and is also an important calcium carbonate deposition region. Because excess production is very low in coral reefs, organic carbon reservoirs are very limited. During the calcification process, each mole of CaCO3 will produce 1 mol of CO2, approximately 60% of which will be released into the atmosphere through the sea-air interface. This causes coral reefs to be large inorganic carbon reservoirs, but at the same time, most coral reefs act as atmospheric CO2 sources (which also act as sinks in some coral reefs). Therefore, clarifying the sea-air CO2 exchange flux and carbon storage is critical for understanding the carbon cycle in coral reef ecosystems. In this paper, we summarize the carbon cycle processes in the coral reefs of the South China Sea (SCS) and estimate the total CO2 budget and carbon reserves. According to current research, the coral reefs in this area act as a source of atmospheric CO2, releasing 0.37-1.59 × 1011 g C a-1 into the atmosphere. Owing to their extremely high biological productivity and carbonate productivity, the carbon reserves of coral reefs in the SCS range from 1.66-3.78 × 1012gCa-1, which is an order of magnitude greater than the CO2 emissions at the sea-air interface. Overall, coral reefs in the SCS are important carbon storage areas. As the current results are still approximate, a more comprehensive and indepth investigation is needed to clarify the carbon source/sink processes, regulatory mechanisms, and carbon storage capacity of SCS coral reefs. [ABSTRACT FROM AUTHOR]

The local stability and resilience of 13 eco-social keystone species complexes (eco-social KSCs)—considered as conservation and monitoring units—were quantified in coastal marine ecosystems located in the Caribbean and eastern Pacific. Based on Routh–Hurwitz's criterion and Levins' criteria, the eco-social KSCs corresponding to Islas Marietas National Park (Mexico) emerged as the most locally stable and resilient ecosystem. To the contrary, the eco-social KSCs determined for Guala Guala Bay (Chile) and Xcalak Reef National Park (Caribbean) were the least stable and resilient, respectively. In terms of sensitivity, the eco-social KSCs corresponding to El Cobre Bay (Chile) presented the greatest number of sensitive components. The ecological section of the KSCs is formed by a tri-trophic network, dominating self-negative feedbacks. In the case of the socio-economic section, the fisher could exhibit the three types of self-feedbacks, and instead, the demand should be controlled. The identification of eco-social KSCs and the quantification of their stabilities and resiliences allow us to approach ecosystem-based fisheries management under a climate change context. Therefore, we suggest assessing and monitoring the persistence of the eco-social KSCs herein analysed over time, as a way to conserve the fundamental network structure of these ecosystems intervened by fishing. This article is part of the theme issue 'Connected interactions: enriching food web research by spatial and social interactions'. [ABSTRACT FROM AUTHOR]

Adaptation of reef-building corals to global warming depends upon standing heritable variation in tolerance traits upon which selection can act. Yet limited knowledge exists on heat-tolerance variation among conspecific individuals separated by metres to hundreds of kilometres. Here, we performed standardized acute heat-stress assays to quantify the thermal tolerance traits of 709 colonies of Acropora spathulata from 13 reefs spanning 1060 km (9.5° latitude) of the Great Barrier Reef. Thermal thresholds for photochemical efficiency and chlorophyll retention varied considerably among individual colonies both among reefs (approximately 6°C) and within reefs (approximately 3°C). Although tolerance rankings of colonies varied between traits, the most heat-tolerant corals (i.e. top 25% of each trait) were found at virtually all reefs, indicating widespread phenotypic variation. Reef-scale environmental predictors explained 12–62% of trait variation. Corals exposed to high thermal averages and recent thermal stress exhibited the greatest photochemical performance, probably reflecting local adaptation and stress pre-acclimatization, and the lowest chlorophyll retention suggesting stress pre-sensitization. Importantly, heat tolerance relative to local summer temperatures was the greatest on higher latitude reefs suggestive of higher adaptive potential. These results can be used to identify naturally tolerant coral populations and individuals for conservation and restoration applications. [ABSTRACT FROM AUTHOR]

The intensifying loss of coral reefs from global climate change and local stressors has seen international commitments targeted at conservation and repair, for example the Kunming–Montreal Global Biodiversity Framework. Fulfilling these targets requires decisions to be made on where, when, and how to act, ultimately dictating where limited resources will be deployed. Every choice on action or inaction toward our ocean has direct and indivisible consequences not only for the health of marine ecosystems but also for the health of humans, particularly those who directly depend on marine habitats, both culturally and economically. The well‐being of the environment, humans, and animals is interlinked, co‐dependent, and even co‐produced, as has already been acknowledged by One Health approaches, which endorse a cross‐ and trans‐disciplinary view to health. Coral reefs epitomie how tightly intertwined ecosystem health and the fate of the human and nonhuman communities that depend on them are. A field that thus far remains poorly considered is a human rights‐based approach to coral reef protection. A human rights‐based approach implements human rights obligations, including the recently affirmed right to a clean, healthy, and sustainable environment, while embedding principles of accountability, nondiscrimination, participation, and empowerment for local and Indigenous communities that ensure effectiveness and meaningful stakeholder engagement. Tying the protection of coral reef ecosystems to human rights emphasises the importance of healthy ecosystems to human well‐being and thus the inevitable connection between nonhuman and human life. The general failure to consider coral reef protection through a human rights‐based approach is a missed opportunity to expedite reef protection while simultaneously advancing climate justice for both humans and nonhumans. [ABSTRACT FROM AUTHOR]

Ecosystem responses to disturbance depend on the nature of the perturbation and the ecological legacies left behind, making it critical to understand how climate‐driven changes in disturbance regimes modify resilience properties of ecosystems. For coral reefs, recent increases in severe marine heat waves now co‐occur with powerful storms, the historic agent of disturbance. While storms kill coral and remove their skeletons, heat waves bleach and kill corals but leave their skeletons intact. Here, we explored how the material legacy of dead coral skeletons modifies two key ecological processes that underpin coral reef resilience: the ability of herbivores to control macroalgae (spatial competitors of corals), and the replenishment of new coral colonies. Our findings, grounded by a major bleaching event at our long‐term study locale, revealed that the presence of structurally complex dead skeletons reduced grazing on turf algae by ~80%. For macroalgae, browsing was reduced by >40% on less preferred (unpalatable) taxa, but only by ~10% on more preferred taxa. This enabled unpalatable macroalgae to reach ~45% cover in 2 years. By contrast, herbivores prevented macroalgae from becoming established on adjacent reefs that lacked skeletons. Manipulation of unpalatable macroalgae revealed that the cover reached after 1 year (~20%) reduced recruitment of corals by 50%. The effect of skeletons on juvenile coral growth was contingent on the timing of settlement relative to the disturbance. If corals settled directly after bleaching (before macroalgae colonized), dead skeletons enhanced colony growth by 34%, but this benefit was lost if corals colonized dead skeletons a year after the disturbance once macroalgae had proliferated. These findings underscore how a material legacy from a changing disturbance regime can alter ecosystem resilience properties by disrupting key trophic and competitive interactions that shape post‐disturbance community dynamics. [ABSTRACT FROM AUTHOR]

Compact bushy and expansive branching Acropora survival rates were compared in an experimental restoration setting. Coral fragments were sourced as corals of opportunity (CoPs) or refragmented from CoPs reared on a floating mid‐water rope nursery. Fragments were attached in single‐species and mixed‐species aggregations to modular substrate stabilization structures (reef stars) on degraded, unconsolidated dead coral rubble slopes in Wakatobi Marine National Park, central Indonesia. In total, 1440 Acropora fragments were outplanted to 96 reef stars across five experimental restoration blocks at 14 m depth. Fragment survival was recorded 40–44 months post‐attachment. Survival had a significant relationship with fragment morphology (p < 0.001) and aggregation type (p < 0.01). Sourcing fragments as CoPs or from the nursery did not have a significant relationship with survival. No significant relationships were found with fragment survival for any interactions between morphology, outplanted aggregation, and source. Survival rates for bushy Acropora were 3.44 times and 5.25 times higher than for expansive species for direct CoP outplants and nursery‐reared corals, respectively. The results demonstrate the potential efficacy of returning complex bushy branching Acropora morphologies to mid‐depth reef slopes previously dominated by the genus, using single‐species aggregations interspersed with mixed‐species aggregations. The study also supports using mid‐water nurseries to create a closed or semi‐closed nursery cycle to scale up restoration, and proposes introducing the term "biomass production system" to distinguish this as a process distinct from other coral nursery approaches. [ABSTRACT FROM AUTHOR]

Sea hares are cryptic, herbivorous sea slugs present on many coral reefs worldwide. Although they are known to consume high quantities of macroalgae, they are rarely considered or quantified in assessing algal suppression. Their role as algal suppressors is not well understood, therefore this study sought to quantify sea hare herbivory on the abundant red algal genus Laurencia. The sea hares Aplysia dactylomela, Dolabella auricularia and Dolabella sp. were collected and used in herbivory trials in aquaria at Heron Island on the Southern Great Barrier Reef to quantify their rate of consumption. A. dactylomela consumed 76.9 g partially dried weight of Laurencia per 24-h, which was significantly more than the other species, with D. auricularia consuming an average of 22.5 g and Dolabella sp. consuming 37.4 g partially dried weight. Consumption of Laurencia by A. dactylomela increased with body size, with the exception of the smallest animals, which ate up to 12.5 times their body weight. D. auricularia consumed significantly more algae than was lost in control tanks. Although we observed Dolabella sp. feeding on Laurencia, the amount consumed was not significantly different to loss of algae in control tanks. The rate of herbivory on Laurencia by A. dactylomela is comparable or greater than that of more commonly studied reef herbivores such as fishes and urchins, which suggests that they may contribute to algal suppression on coral reefs and further studies are warranted to evaluate their possible role in coral-algal phase shift dynamics. [ABSTRACT FROM AUTHOR]