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High-throughput sequencing (HTS) of DNA barcodes (metabarcoding), particularly when combined with standardized sampling protocols, is one of the most promising approaches for censusing overlooked cryptic invertebrate communities. We present biodiversity estimates based on sequencing of the cytochrome c oxidase subunit 1 (COI) gene for coral reefs of the Gulf of Aqaba, a semi-enclosed system in the northern Red Sea. Samples were obtained from standardized sampling devices (Autonomous Reef Monitoring Structures (ARMS)) deployed for 18 months. DNA barcoding of non-sessile specimens >2 mm revealed 83 OTUs in six phyla, of which only 25% matched a reference sequence in public databases. Metabarcoding of the 2 mm - 500 μm and sessile bulk fractions revealed 1197 OTUs in 15 animal phyla, of which only 4.9% matched reference barcodes. These results highlight the scarcity of COI data for cryptobenthic organisms of the Red Sea. Compared with data obtained using similar methods, our results suggest that Gulf of Aqaba reefs are less diverse than two Pacific coral reefs but much more diverse than an Atlantic oyster reef at a similar latitude. The standardized approaches used here show promise for establishing baseline data on biodiversity, monitoring the impacts of environmental change, and quantifying patterns of diversity at regional and global scales.

The stability and persistence of coral reefs in the decades to come is uncertain due to global warming and repeated bleaching events that will lead to reduced resilience of these ecological and socio-economically important ecosystems. Identifying key refugia is potentially important for future conservation actions. We suggest that the Gulf of Aqaba (GoA) (Red Sea) may serve as a reef refugium due to a unique suite of environmental conditions. Our hypothesis is based on experimental detection of an exceptionally high bleaching threshold of northern Red Sea corals and on the potential dispersal of coral planulae larvae through a selective thermal barrier estimated using an ocean model. We propose that millennia of natural selection in the form of a thermal barrier at the southernmost end of the Red Sea have selected coral genotypes that are less susceptible to thermal stress in the northern Red Sea, delaying bleaching events in the GoA by at least a century., (© 2013 John Wiley & Sons Ltd.)

Accumulating data on the increasing degradation of coral reefs worldwide has led to a focus on the unique mesophotic coral ecosystem (MCE) as a potential refuge for threatened shallow-water species (i.e., the deep reef refugia hypothesis: DRRH). Sponges play a crucial role in coral-reef functioning but are often overlooked in benthic surveys. This knowledge gap is especially true for the Red Sea, where data on sponge abundance, coverage and species composition are scarce. Furthermore, to date, no study has examined mesophotic sponges in the Red Sea. Here we compared sponge abundance and diversity metrics between shallow and mesophotic reefs at two sites in the Gulf of Aqaba, northern Red Sea. We also examined the role of biotic and abiotic parameters in determining sponge variability between sites and depths. Sponge diversity metrics significantly varied with increasing depth and between sites. Sponge species composition also differed significantly between depth and sites. However, parameters measured in the water column, that is, Total Organic Carbon (TOC), Particulate Organic Carbon (POC), NOx, etc., did not differ between depths and sites, except for Synechococcus and Prochlorococcus concentration, which did. The findings indicated that site characteristics and biotic interactions may play an essential role in determining sponge diversity and community composition. Between-site differences in sponge fauna revealed in the study highlight the importance of considering the variability in the benthic communities and the factors controlling it when designing management tools for coral reefs, particularly for the northern Red Sea. [ABSTRACT FROM AUTHOR]

Coral reefs are among the most diverse ecosystems on our planet, and essential to the livelihood of hundreds of millions of people who depend on them for food security, income from tourism and coastal protection. Unfortunately, most coral reefs are existentially threatened by global climate change and local anthropogenic pressures. To better understand the dynamics underlying deterioration of reefs, monitoring at high spatial and temporal resolution is key. However, conventional monitoring methods for quantifying coral cover and species abundance are limited in scale due to the extensive manual labor required. Although computer vision tools have been employed to aid in this process, in particular structure‐from‐motion (SfM) photogrammetry for 3D mapping and deep neural networks for image segmentation, analysis of the data products creates a bottleneck, effectively limiting their scalability.This paper presents a new paradigm for mapping underwater environments from ego‐motion video, unifying 3D mapping systems that use machine learning to adapt to challenging conditions under water, combined with a modern approach for semantic segmentation of images.The method is exemplified on coral reefs in the northern Gulf of Aqaba, Red Sea, demonstrating high‐precision 3D semantic mapping at unprecedented scale with significantly reduced required labor costs: given a trained model, a 100 m video transect acquired within 5 min of diving with a cheap consumer‐grade camera can be fully automatically transformed into a semantic point cloud within 5 min. We demonstrate the spatial accuracy of our method and the semantic segmentation performance (of at least 80% total accuracy), and publish a large dataset of ego‐motion videos from the northern Gulf of Aqaba, along with a dataset of video frames annotated for dense semantic segmentation of benthic classes.Our approach significantly scales up coral reef monitoring by taking a leap towards fully automatic analysis of video transects. The method advances coral reef transects by reducing the labor, equipment, logistics, and computing cost. This can help to inform conservation policies more efficiently. The underlying computational method of learning‐based Structure‐from‐Motion has broad implications for fast low‐cost mapping of underwater environments other than coral reefs. [ABSTRACT FROM AUTHOR]

In March 2020, an unusually intense storm system struck the Gulf of Aqaba‐Eilat, resulting in severe shoreline damage. This brief account examines post‐storm observations of inconsistent damage patterns and structural changes along a specific coastal stretch located at the south beach of Eilat. Certain sections of the coastline experienced direct impact from extreme waves on the south‐southeast‐facing shallow reef, resulting in areas where rocks were completely stripped of corals due to sediment backwash. Conversely, areas characterized by ridges and deep troughs saw the loss of branching corals and some massive colonies, while many small corals survived. A neighboring area with a well‐developed fringing reef suffered lesser damage. Between the severely affected shallow reef and the robust fringing reef lies an unconsolidated slope that migrated eastward by at least 2 m following the storm, incorporating numerous coral colonies dislodged by the event. We propose that this slope advances with each major storm occurrence, influencing the characteristics of nearby shores and coral reefs. This case demonstrates how storm events, in conjunction with geomorphology, have a cumulative and significant impact not only on the structure of coral communities but also on the fundamental shape of coral reefs themselves. As climate change amplifies the range, intensity, and frequency of storms, comprehending these processes becomes increasingly crucial. [ABSTRACT FROM AUTHOR]

Understanding the role of coral reefs on air‐sea CO2 exchange is essential to accurately estimate carbon budgets throughout the tropical and subtropical oceans. Results from research conducted in humid marine environments show coral reefs are mainly net sources of CO2 to the atmosphere due to calcification being dominant over respiration and dissolution. However, coral reefs are also found bordering deserts in the subtropical high‐pressure belt. Here, we present results from concurrent direct measurements of air‐sea CO2 exchange over fringing coral reefs and open sea bordered by hyper‐arid deserts in the Gulf of Eilat (Aqaba). The fringing coral reefs were found to be a net sink of CO2 at −1.62 ± 4 μmol m−2 s−1 sequestering 1.96 times more CO2 than adjacent open sea. The CO2 fluxes showed a negative correlation with some local meteorological parameters such as humidity, wind speed, and net radiation but were positively correlated to air temperature. The air‐sea CO2 fluxes were also found to be correlated with dust, which is believed to trigger metabolic processes in bacteria and phytoplankton in the low‐nutrient, low‐chlorophyll sea of the study site. Results are compared to measurements from the humid marine setting of the Great Barrier Reef, Australia. Plain Language Summary: Quantifying air‐sea exchange of CO2 is critical to developing accurate carbon budgets for the world oceans. However, uncertainty remains as to whether coral reefs are net sinks or sources of atmospheric CO2. Here we present direct measurements of air‐sea CO2 exchange over the desert fringing coral reefs in the northern Gulf of Eilat (Aqaba), Israel. Unlike coral reefs in humid tropical and subtropical locations, which have been found to be mainly net sources of CO2 to the atmosphere, our results indicate that the fringing coral reefs in the northern Gulf of Eilat (Aqaba) are net sinks of atmospheric CO2. This net influx of CO2 correlates with periods of increased dust concentrations in the atmosphere. The deposition of this dust into the low‐nutrient, low‐chlorophyll waters of the coral reef triggers an increase in metabolic processes in the reef ecosystem through fertilization. We conclude that dust may influence air‐sea CO2 exchange at other coral reefs regularly impacted by dust deposition, such as in the Caribbean and northwest Australia. Key Points: Results from the first direct measurements of air‐sea CO2 exchange with the atmosphere over desert fringing coral reefs are presentedFringing coral reefs in the Gulf of Eilat were found to be a net sink of atmospheric CO2 during the summerFertilization of the low‐nutrient, low‐chlorophyll sea by dust was identified as a possible major influence on air‐sea CO2 exchange [ABSTRACT FROM AUTHOR]

Coral reefs are in global decline and anomalously hot temperatures shoulder the blame. Foraminferal bioindicators are important because they record historical reef stress over periods of centuries to millennia, as compared to the few decades offered by diver surveys. For a region lacking systematic long-term reef monitoring programs, the use of bioindicators in the Red Sea is compelling. Whereas foraminfera-based indices exist to reconstruct histories of nutrient stress on reefs, there is a paucity of equivalent bioindicators that respond to temperature. Capitalizing on a portfolio of surficial sediment samples collected along the eastern margin of the N. Red Sea and Gulf of Aqaba, this study shows that the relative abundance of Amphisteginidae foraminifera—specifically Amphistegina lobifera—closely track heat stress, as has recently been reported for this family in the S. Pacific. This result is consequential for at least three reasons. First, the Red Sea hosts some of the most northerly coral reefs on Earth. Establishment of a thermal bioindicator here confirms the strategy can be deployed on high latitudes reefs, which are disproportionally afflicted with heat extremes. Second, the considered reefs, and the foraminifera they host, are famed for their thermal resilience. Foraminiferal bioindicators have not previously been trialed on reefs that have adapted in this way. Finally, as a restricted offshoot of the Indian Ocean, the level of endemism in the Red Sea is especially high. The bioindicator that we propose is apparently not compromised by endemism. Our findings advocate for an expanded deployment of Amphistegina-based reef bioindicators. [ABSTRACT FROM AUTHOR]

Rising ocean temperatures are pushing reef-building corals beyond their temperature optima (Topt), resulting in reduced physiological performances and increased risk of bleaching. Identifying refugia with thermally resistant corals and understanding their thermal adaptation strategy is therefore urgent to guide conservation actions. The Gulf of Aqaba (GoA, northern Red Sea) is considered a climate refuge, hosting corals that may originate from populations selected for thermal resistance in the warmer waters of the Gulf of Tadjoura (GoT, entrance to the Red Sea and 2000 km south of the GoA). To better understand the thermal adaptation strategy of GoA corals, we compared the temperature optima (Topt) of six common reef-building coral species from the GoA and the GoT by measuring oxygen production and consumption rates as well as photophysiological performance (i.e. chlorophyll fluorescence) in response to a short heat stress. Most species displayed similar Topt between the two locations, highlighting an exceptional continuity in their respective physiological performances across such a large latitudinal range, supporting the GoA refuge theory. Stylophora pistillata showed a significantly lower Topt in the GoA, which may suggest an ongoing population-level selection (i.e. adaptation) to the cooler waters of the GoA and subsequent loss of thermal resistance. Interestingly, all Topt were significantly above the local maximum monthly mean seawater temperatures in the GoA (27.1°C) and close or below in the GoT (30.9°C), indicating that GoA corals, unlike those in the GoT, may survive ocean warming in the next few decades. Finally, Acropora muricata and Porites lobata displayed higher photophysiological performance than most species, which may translate to dominance in local reef communities under future thermal scenarios. Overall, this study is the first to compare the Topt of common reef-building coral species over such a latitudinal range and provides insights into their thermal adaptation in the Red Sea. [ABSTRACT FROM AUTHOR]

The dinoflagellate family Symbiodiniaceae comprises numerous divergent genera containing species whose ecologies range from endosymbiotic to freeliving. While many associate with invertebrates including corals, sea anemones, jellyfish, giant clams, and flatworms, others occur within the cytoplasm of large protists, most notably benthic foraminifera in the sub-family Soritinae. Recent systematic revisions to the Symbiodiniaceae left out formal naming of some divergent lineages because each lacked a representative type species to erect new genus names. Here we provide genetic, morphological and ecological evidence to describe a new genus and species. Miliolidium n. gen. is closely related to the genus Durusdinium and contains several genetically divergent ecologically distinct lineages found in distant geographic locations indicating an Indo-Pacific wide distribution. One of these, Miliolidium leei n. sp., is represented by an isolate cultured from Amphisorus sp. originally collected in the Gulf of Eilat, northern Red Sea. Its peripheral chloroplast extensions are uniquely petal- or lobe-shaped, and cells possess a pyrenoid with three stalks connecting to chloroplasts, and without thylakoid intrusions. It is related to an isolate cultured from an azooxanthellate sponge from Palau and another that is commonly harbored by the soritid Marginopora vertebralis in shallow reef habitats from Guam. Research on Symbiodiniaceae diversity including free-living species in benthic habitats and those mutualistic with soritid foraminifera remains extremely limited as does our knowledge of their diversity, physiology, biogeography, and ecology. [ABSTRACT FROM AUTHOR]

Increases in the frequency and intensity of acute and chronic disturbances are causing declines of coral reefs world‐wide. Although quantifying the responses of corals to acute disturbances is well documented, detecting subtle responses of coral populations to chronic disturbances is less common, but can also result in altered population and community structures.We investigated the population dynamics of two key reef‐building Merulinid coral species, Dipsastraea favus and Platygyra lamellina, with similar life‐history traits, in the Gulf of Eilat and Aqaba, Red Sea from 2015 to 2018, to assess potential differences in their population trajectories.Demographic processes, which included rates of survival, growth, reproduction and recruitment were used to parametrize integral projection models and estimate population growth rates and the likely population trajectories of both coral species.The survival and reproduction rates of both D. favus and P. lamellina were positively related to coral colony size, and elasticity analyses showed that large colonies most influenced population dynamics. Although both species have similar life‐history traits and growth morphologies and are generally regarded as 'stress‐tolerant', the populations showed contrasting trajectories—D. favus appears to be increasing whereas P. lamellina appears to be decreasing.As many corals have long‐life expectancies, the process of local and regional decline might be subtle and slow. Ecological assessments based on total living coral coverage, morphological groups or functional traits might overlook subtle, species‐specific trends. However, demographic approaches capable of detecting subtle species‐specific population changes can augment ecological studies and provide valuable early warning signs of decline before major coral loss becomes evident. [ABSTRACT FROM AUTHOR]

Sea urchins are primary herbivores on coral reefs, regulating algal biomass and facilitating coral settlement and growth. 1,2,3,4,5,6,7,8,9,10,11,12 Recurring mass mortality events (MMEs) of Diadema species Gray, 1825 have been recorded globally, 13,14,15,16,17,18,19,20,21,22,23 the most notorious and ecologically significant of which occurred in the Caribbean in 1983, 14,17,19,20 contributing to the shift from coral to algal-dominated ecosystems. 17,24,25 Recently, first evidence of Diadema setosum mass mortality was reported from the eastern Mediterranean Sea. 23 Here, we report extensive mass mortalities of several diadematoid species inhabiting the Red Sea and Western Indian Ocean (WIO) 26,27,28 including first evidence of mortalities in the genus Echinothrix Peters, 1853. Mortalities initiated in the Gulf of Aqaba on December 2022 and span the Red Sea, the Gulf of Oman, and the Western Indian Ocean (Réunion Island), with population declines reaching 100% at some sites. Infected individuals are characterized by spine loss and tissue necrosis, resulting in exposed skeletons (i.e., tests) and mortality. Molecular diagnostics of the 18S rRNA gene confirm the presence of a waterborne scuticociliate protozoan most closely related to Philaster apodigitiformis in infected specimens—identical to the pathogen found in the 2022 Caribbean mass mortality of Diadema antillarum. 13,15,18 Collapse of these key benthic grazers in the Red Sea and Western Indian Ocean may lead to algal dominance over corals, threatening the stability of coral reefs on a regional scale. 29,30,31,32 We issue a warning regarding the further expansion of mortalities and call for immediate monitoring and conservation efforts for these key ecological species. • Mass mortalities of diadematoid sea urchins spread through the Red Sea and WIO • Species of both Diadema and Echinothrix are susceptible to mortalities • Population declines in D. setosum and E. calamaris in the Gulf of Aqaba reach 100% • Molecular analyses confirm the presence of a Philaster -like scutocilliate protozoan Roth et al. report regional-scale mass mortalities of diadematoid sea urchins in the Red Sea and Western Indian Ocean, driving population declines of up to 100% in Diadema and Echinothrix species since December 2022. Genetic analyses confirm the presence of the Caribbean D. antillarum pathogen, a Philaster- like scuticociliate, in infected specimens. [ABSTRACT FROM AUTHOR]

Evaluating the efficacy of artificial structures in enhancing or sustaining biodiversity on tropical coral reefs is key to assessing their role in reef conservation or management. Here, we compare spatial and temporal patterns of colonization and succession of the benthic assemblage on settlement collectors (ceramic tiles) in a 13-mo mensurative experiment on a suspended artificial reef, a seafloor artificial reef, and two nearby natural reefs at Eilat, Gulf of Aqaba. We also conducted a concurrent 7-mo manipulative experiment on the suspended reef and one of the natural reefs, and monitored fish feeding behaviour on experimental collectors, to examine effects of large mobile consumers on these patterns. In both experiments, taxonomic composition as percent planar cover for the whole community or biomass for the invertebrate component differed between collector topsides, dominated by a filamentous algal matrix, and shaded undersides with a profuse assemblage of suspension- or filter-feeding invertebrates. In the mensurative experiment, we found differences in final community and invertebrate composition between sites, which clustered according to reef type (artificial vs. natural) for collector undersides. Invertebrate biomass was greater at both artificial reefs than at one (undersides) or both (topsides) natural reefs. In the manipulative experiment, we found similar differences in composition between sites/reef types as well as between treatments (exclusion vs. control), and the invertebrate biomass was greater on the artificial reef. Invertebrate biomass was greater in the exclusion treatment than the control on collector undersides, suggesting mobile consumers can affect community composition and abundance. Predominant fish species observed interacting with collectors differed between artificial and natural reefs, likely contributing to differences in patterns of colonization and succession between sites and reef types. Our findings suggest artificial reefs have the potential to enhance cover and biomass of certain reef-associated assemblages, particularly those occupying sheltered microhabitats. [ABSTRACT FROM AUTHOR]

Abstract Seawater reverse osmosis (SWRO) is becoming an increasingly important source of potable water in arid and semi-arid regions worldwide. Discharge of brine-effluent from desalination facilities has been shown to significantly impact coastal marine ecosystems ranging from seagrass meadows to microbial communities. In this study, we examined the impacts of increased salinity (10% above ambient) and presence of antiscalants (0.2 mg L−1, polyphosphonate-based) on three reef-building coral species; Stylophora pistillata , Acropora tenuis and Pocillopora verrucosa , from the Gulf of Aqaba (northern Red-Sea). Our results indicate that the corals, as well as associated bacteria and algae, were significantly impaired by the elevated salinity and antiscalants, leading to partial bleaching. Specifically, the abundance of bacteria and symbiotic algae as well as calcification rates were typically lower (20–85%, 50–90% and 40–50%, respectively) following incubations with both amendments. However, the impact of desalination brine was often species-specific. Thus, we propose that the ecotoxicological criteria used for hard corals should be determined based on the sensitivity of key species in the community dominating the area affected by desalination discharge. Highlights • Salinity 10% above ambient and polyphosphonate antiscalants have clear impacts on coral's physiology. • Salinity 10% above ambient and polyphosphonate antiscalants significantly reduced bacteria and Symbiodinium abundances. • Calcification rates decreased following the addition of salt and polyphosphonate antiscalants. • Variable responses to increased salinity among coral species suggests species-specific sensitivity. [ABSTRACT FROM AUTHOR]

Although the Gulf of Aqaba-Eilat is located in the tectonically active northern Red Sea, it has been described as low-risk with regard to tsunami activity because there are no modern records of damaging tsunami events and only one tsunami (1068 AD) referred to in historical records. However, this assessment may be poorly informed given that the area was formed by and is located along the seismically active Dead Sea Fault, its population is known to fluctuate in size and literacy in part due to its harsh hyper-arid climate, and there is a dearth of field studies addressing the presence or absence of tsunamigenic deposits. Here we show evidence from two offshore cores for a major paleotsunami that occurred ~2300 years ago with a sedimentological footprint that far exceeds the scarce markers of the historically mentioned 1068 AD event. The interpretation is based on the presence of a laterally continuous and synchronous, anomalous sedimentological deposit that includes allochtonous inclusions and unique structural characteristics. Based on sedimentological parameters, these deposits could not be accounted for by other transport events, or other known background sedimentological processes. [ABSTRACT FROM AUTHOR]

The photosymbiotic ascidianDiplosoma simileis characterized by a wide global distribution. The current study provides the first record ofD. similein the Red Sea, with remarks on its spatial distribution and phylogeny. Partial COI and 18S rDNA sequences ofD. similefrom the Red Sea revealed high similarity to those from the West Pacific, indicating a much broader range than previously recorded. In the Red SeaD. simileis common on natural coral reefs at depths ranging from 1–35 m.Diplosoma similecolonies were found to overgrow and would appear to suffocate several species of live stony corals, though this does not appear to cause mass coral mortality in the Red Sea, unlike that recorded in other locations. [ABSTRACT FROM AUTHOR]

For coral reef fish with an obligate relationship to their habitat, like Pomacentrid damselfish, choosing a suitable home amongst the reef structure is key to survival. A surprisingly small number of studies have examined patterns in adult damselfish distributions compared to other ontogenetic phases. The aim of this study was to determine which reef and coral colony characteristics explained adult damselfish distribution patterns in a Red Sea reef. The characteristics investigated were reef type (continuous or patchy), coral species (seven species of Acropora), and coral morphology (coral size and branching density). The focal damselfish species were Dascyllus aruanus, D. marginatus, Chromis viridis, and C. flavaxilla. Occupancy (presence or absence of resident damselfish), group size and fish species richness were not significantly different between the seven Acropora species. However, within each coral species, damselfish were more likely to occupy larger coral colonies than smaller coral colonies. Occupancy rates were also higher in patchy reef habitats than in continuous sections of the reef, probably because average coral colony size was greater in patchy reef type. Fish group size increased significantly with coral colony volume and with larger branch spacing. Multi-species groups of fish commonly occurred and were increasingly likely with reduced branching density and increased coral size. [ABSTRACT FROM AUTHOR]

The northern Gulf of Aqaba is an oligotrophic water body hosting valuable coral reefs. In the Gulf, phytoplankton dynamics are driven by an annual cycle of stratification and mixing. Superimposed on that fairly regular pattern was the establishment of a shallow-water fish-farm initiative that increased gradually until its activity was terminated in June 2008. Nutrient, water temperature, irradiation, phytoplankton data gathered in the area during the years 2007–2009, covering the peak of the fish-farm activity and its cessation, were analyzed by means of statistical analyses and ecological models of phytoplankton dynamics. Two datasets, one from an open water station and one next to the fish farms, were used. Results show that nutrient concentrations and, consequently, phytoplankton abundance and seasonal succession were radically altered by the pollution originating from the fish-farm in the sampling station closer to it, and also that the fish-farm might even have influenced the open water station. [ABSTRACT FROM AUTHOR]

Abstract: The current state of health of the coral reefs in the northern Gulf of Aqaba (Red Sea), notably the Eilat reefs, is under debate regarding both their exact condition and the causes of degradation. A dearth of earlier data and unequivocal reliable indices are the major problems hinder a clear understanding of the reef state. Our research objective was to examine coral–algal dynamics as a potential cause and an indication of reef degradation. The community structure of stony corals and algae along the northern Gulf of Aqaba reveal non-seasonal turf algae dominancy in the shallow Eilat reefs (up to 72%), while the proximate Aqaba reefs present negligible turf cover (<6%). We believe that turf dominancy can indicate degradation in these reefs, based on the reduction in essential reef components followed by proliferation of perennial turf algae. Our findings provide further evidence for the severe state of the Eilat coral reefs. [Copyright &y& Elsevier]

The article presents a research study which monitors the coral reefs and the influence of natural and anthropogenic factors in South Sinai, Egypt. It examines the possible impacts to coral reefs related to the growth of tourism in the South Sinai region of the Egyptian Red Sea. The study covers nine stations that were established at the key reef sites over 2002-2003. It utilizes a video survey method at depths ranging three, seven and 16 meters and with fish abundance by underwater visual census at depths of three and ten meters. Furthermore, it explores the abundances of hard and soft coral genera and growth forms of significant reef fish families on a series of South Sinai reefs.