John A Burt

The nations on the shoreline of the Arabian/Persian Gulf are the world's largest users of desalination technologies, which are essential to meet their freshwater needs. Desalinated freshwater production is projected to rapidly increase in future decades. Thus, concerns have been raised that desalination activities may result in non-negligible long-term, basin-wide increases of salinity, which would have widespread detrimental effects on the Gulf marine ecosystems, with ripple effects on fisheries, as well as impacting the desalination activities themselves. We find that current yearly desalinated freshwater production amounts to about 2% of the net yearly evaporation from the Gulf. Projections to 2050 bring this value to 8%, leading to the possibility that, later in the second half of the century, desalinated freshwater production may exceed 10% of net evaporation, an amount which is comparable to interannual fluctuations in net evaporation. With the help of a model we examine several climatological scenarios, and we find that, under IPCC's SSP5-8.5 worst-case scenarios, end-of-century increases in air temperature may result in salinity increases comparable or larger to those produced by desalination activities. The same scenario suggests a reduced evaporation and an increased precipitation, which would have a mitigating effect. Finally we find that, owing to a strong overturning circulation, high-salinity waters are quickly flushed through the Strait of Hormuz. Thus, even in the worst-case scenarios, basin-scale salinity increases are unlikely to exceed 1 psu, and, under less extreme hypothesis, will likely remain well below 0.5 psu, levels that have negligible environmental implications at the basin-wide scale.

Echinometra is the most widespread genus of sea urchin and has been the focus of a wide range of studies in ecology, speciation, and reproduction. However, available genetic data for this genus are generally limited to a few select loci. Here, we present a chromosome-level genome assembly based on 10x Genomics, PacBio, and Hi-C sequencing for Echinometra sp. EZ from the Persian/Arabian Gulf. The genome is assembled into 210 scaffolds totaling 817.8 Mb with an N50 of 39.5 Mb. From this assembly, we determined that the E. sp. EZ genome consists of 2n = 42 chromosomes. BUSCO analysis showed that 95.3% of BUSCO genes were complete. Ab initio and transcript-informed gene modeling and annotation identified 29,405 genes, including a conserved Hox cluster. E. sp. EZ can be found in high-temperature and high-salinity environments, and we therefore compared E. sp. EZ gene families and transcription factors associated with environmental stress response ("defensome") with other echinoid species with similar high-quality genomic resources. While the number of defensome genes was broadly similar for all species, we identified strong signatures of positive selection in E. sp. EZ noncoding elements near genes involved in environmental response pathways as well as losses of transcription factors important for environmental response. These data provide key insights into the biology of E. sp. EZ as well as the diversification of Echinometra more widely and will serve as a useful tool for the community to explore questions in this taxonomic group and beyond.

Avicennia marina forests fulfill essential blue carbon and ecosystem services, including halting coastal erosion and supporting fisheries. Genetic studies of A. marina tissues could yield insight into halophyte adaptive strategies, empowering saline agriculture research. We compare transcriptomes from A. marina pneumatophores, stems, leaves, flowers, seeds, and transcriptomes across four widely divergent environments in the Indo-Pacific (Red Sea, Arabian Gulf, Bay of Bengal, and Red River Delta) to decipher the shared and location-, tissue-, and condition-specific functions. On average, 4.8% of transcripts per tissue were uniquely expressed in that tissue, and 12.2% were shared in all five tissues. Flowers' transcript expression was the most distinct, with domaincentric gene ontology analysis showing high enrichment for stimulus-responsive processes, as well as genes implicated in flowering (hydroxygeraniol dehydrogenase, TPM = 3687) and floral scent biosynthesis (e.g., benzoyl_coenzyme_A, 2497.2 TPM). Pneumatophores highly expressed antioxidant genes, such as glutathione S-transferase (GST, TPM = 4759) and thioredoxin (TRX, TPM = 936.2), as well as proteins in the GO term 'Hydroquinone:oxygen oxidoreductase activity'(enrichment Z = 7.69, FDR-corr. p = 0.000785). Tissue-specific metabolic pathway reconstruction revealed unique processes in the five tissues; for example, seeds showed the most complete expression of lipid biosynthetic and degradation pathways. The leaf transcriptome had the lowest functional diversity among the expressed genes in any tissue, but highly expressed a catalase (TPM = 4181) and was enriched for the GO term 'transmembrane transporter activity' (GO:0015238; Z = 11.83; FDRcorr. p = 1.58 × 10 −9), underscoring the genes for salt exporters. Metallothioneins (MTs) were the highest-expressed genes in all tissues from the cultivars of all locations; the dominant expression of these metal-binding and oxidative-stress control genes indicates they are essential for A. marina in its natural habitats. Our study yields insight into how A. marina tissue-specific gene expression supports halotolerance and other coastal adaptative strategies in this halophytic angiosperm.

The Regional Organization for the Protection of the Marine Environment (ROPME) Sea Area (RSA) in the northern Indian Ocean, which comprises the Gulf, the Gulf of Oman and the northern Arabian Sea, already experiences naturally extreme environmental conditions and incorporates one of the world’s warmest seas. There is growing evidence that climate change is already affecting the environmental conditions of the RSA, in areas including sea temperature, salinity, dissolved oxygen, pH, and sea level, which are set to continue changing over time. The cumulative impacts of these changes on coastal and marine ecosystems and dependent societies are less well documented, but are likely to be significant, especially in the context of other human stressors. This review represents the first regional synthesis of observed and predicted climate change impacts on marine and coastal ecosystems across the ROPME Sea Area and their implications for dependent societies. Climate-driven ecological changes include loss of coral reefs due to bleaching and the decline of fish populations, while socio-economic impacts include physical impacts from sea-level rise and cyclones, risk to commercial wild capture fisheries, disruption to desalination systems and loss of tourism. The compilation of this review is aimed to support the development of targeted adaptation actions and to direct future research within the RSA

During the summer the Arabian Gulf is the world's warmest sea, also characterized by hypersalinity and extreme annual temperature fluctuations (12–35oC), making it marginal for coral growth. Yet extensive reefs occur in all eight nations bordering the Gulf. Here we present data demonstrating recurrent summer hypoxia events [oxygen concentration (O2) <2 mg l−1] at a reef in the southern Gulf. Currently these episodes are short enough (median 3 h, max 10 h) to preclude mass mortality. Will this always be the case? Predicting future Gulf hypoxia risk for coral reef ecosystems requires diagnosing the underlying causes driving the timing and magnitude of O2 swings. To this end, we compare our data with the output of a simple coupled 1-D water column/biogeochemical model of the reef environment. This allows us to give quantitative estimates of the O2 fluxes produced by photosynthesis both in the water column and within the coral framework, by respiration processes in the benthos, and from the atmosphere. We demonstrate the role of turbulent mixing, and in particular of tides, in shaping the temporal variability of the amplitude of the diel O2 cycle. We find that, in spite of significant turbulent mixing, which maintains the temperature vertically well-mixed, the biological O2 production and consumption is dominant over the atmospheric O2 flux, and is sufficient to generate vertical differences of 1 to 5 mg l−1 between the bottom and 1.5 m above it. While estimating future trends of hypoxia frequency will require further study, the present findings single out the relevant physical and biological processes (and their interplay) which deserve further scrutiny. The Gulf today experiences temperatures expected to occur across much of the tropics by the end of the century, and the observation of recurrent hypoxia events in the Gulf suggests that similar hypoxic phenomena may represent an important, but to date underappreciated, threat to the future of global coral reefs.

The United Arab Emirates (UAE) has a long-term policy horizon, the financial capital, and a vision for a sustainable knowledge-based economy. These characteristics uniquely situate it as a potential leader for sea-level rise research. Climate science is already growing, and at the center of the UAE's pivot toward climate research is a burgeoning concern for sea-level rise. Over 85% of the UAE's population and more than 90% of the nation's infrastructure is within a few meters of present-day sea-level. With its low-lying and shallow-sloping geography (about 35 cm per km), this high-value coastline, including the rapidly expanding cities of Dubai and Abu Dhabi, is particularly vulnerable to sea-level rise. Meanwhile, limited regional research and data scarcity create deep uncertainty for sea-level projections. We set out a potential roadmap for the UAE to capitalize on its strengths to create usable and relevant sea-level projections for the region. With a newly established Climate Change Research Network, the UAE government is beginning to draw together universities and research centers for “furthering effective data collection and management, and advancing policy-relevant research on climate impacts and adaptation. By consolidating ideas from the science community within the UAE, we identify promoters and barriers to data gathering, information sharing, science-policy communication, and funding access. Our paper proposes pathways forward for the UAE to integrate sea-level science with coastal development and form best practices that can be scaled across climate science and throughout the region.

Determining the life-history consequences for fishes living in extreme and variable environments will be vital in predicting the likely impacts of ongoing climate change on reef fish demography. Here, we compare size-at-age and maximum body size of two common reef fish species (Lutjanus ehrenbergii and Pomacanthus maculo-sus) between the environmentally extreme Arabian/Persian Gulf ('Arabian Gulf') and adjacent comparably benign Oman Sea. Additionally, we use otolith increment width profiles to investigate the influence of temperature, salinity and productivity on the individual growth rates. Individuals of both species showed smaller size-at-age and lower maximum size in the Arabian Gulf compared to con-specifics in the less extreme and less variable environment of the Oman Sea, suggesting a life-history trade-off between size and metabolic demands. Salinity was the best environmental predictor of interannual growth across species and regions, with low growth corresponding to more saline conditions. However, salinity had a weaker negative effect on interannual growth of fishes in the Arabian Gulf than in the Oman Sea, indicating Arabian Gulf populations may be better able to acclimate to changing environmental conditions. Temperature had a weak positive effect on the interannual growth of fishes in the Arabian Gulf, suggesting that these populations may still be living within their thermal windows. Our results highlight the potential importance of osmoregulatory cost in impacting growth, and the need to consider the effect of multiple stressors when investigating the consequences of future climate change on fish demography.

The discovery of multi-species synchronous spawning of scleractinian corals on the Great Barrier Reef in the 1980s stimulated an extraordinary effort to document spawning times in other parts of the globe. Unfortunately, most of these data remain unpublished which limits our understanding of regional and global reproductive patterns. The Coral Spawning Database (CSD) collates much of these disparate data into a single place. The CSD includes 6178 observations (3085 of which were unpublished) of the time or day of spawning for over 300 scleractinian species in 61 genera from 101 sites in the Indo-Pacific. The goal of the CSD is to provide open access to coral spawning data to accelerate our understanding of coral reproductive biology and to provide a baseline against which to evaluate any future changes in reproductive phenology.

The gray mangrove [Avicennia marina (Forsk.) Vierh.] is the most widely distributed mangrove species, ranging throughout the Indo-West Pacific. It presents remarkable levels of geographic variation both in phenotypic traits and habitat, often occupying extreme environments at the edges of its distribution. However, subspecific evolutionary relationships and adaptive mechanisms remain understudied, especially across populations of the West Indian Ocean. High-quality genomic resources accounting for such variability are also sparse. Here we report the first chromosome-level assembly of the genome of A. marina. We used a previously release draft assembly and proximity ligation libraries Chicago and Dovetail HiC for scaffolding, producing a 456,526,188-bp long genome. The largest 32 scaffolds (22.4-10.5 Mb) accounted for 98% of the genome assembly, with the remaining 2% distributed among much shorter 3,759 scaffolds (62.4-1 kb). We annotated 45,032 protein-coding genes using tissue-specific RNA-seq data in combination with de novo gene prediction, from which 34,442 were associated to GO terms. Genome assembly and annotated set of genes yield a 96.7% and 95.1% completeness score, respectively, when compared with the eudicots BUSCO dataset. Furthermore, an F ST survey based on resequencing data successfully identified a set of candidate genes potentially involved in local adaptation and revealed patterns of adaptive variability correlating with a temperature gradient in Arabian mangrove populations. Our A. marina genomic assembly provides a highly valuable resource for genome evolution analysis, as well as for identifying functional genes involved in adaptive processes and speciation.

Tropical ectotherms are hypothesized to be vulnerable to environmental changes, but cascading effects of organismal tolerances on the assembly and functioning of reef fish communities are largely unknown. Here, we examine differences in organismal traits, assemblage structure, and productivity of cryptobenthic reef fishes between the world’s hottest, most extreme coral reefs in the southern Arabian Gulf and the nearby, but more environmentally benign, Gulf of Oman. We show that assemblages in the Arabian Gulf are half as diverse and less than 25% as abundant as in the Gulf of Oman, despite comparable benthic composition and live coral cover. This pattern appears to be driven by energetic deficiencies caused by responses to environmental extremes and distinct prey resource availability rather than absolute thermal tolerances. As a consequence, production, transfer, and replenishment of biomass through cryptobenthic fish assemblages is greatly reduced on Earth’s hottest coral reefs. Extreme environmental conditions, as predicted for the end of the 21st century, could thus disrupt the community structure and productivity of a critical functional group, independent of live coral loss.

The goal of this paper is to propose a screening method for assessing the environmental risk to aquatic systems in harbours worldwide. A semi-quantitative method is based on environmental pressures, environmental conditions and societal response. The method is flexible enough to be applied to 15 harbours globally distributed through a multinational test using standardised and homogenised open data that can be obtained for any port worldwide. The method emerges as a useful approach towards the foundation of a global environmental risk atlas of harbours that should guide the harbour sector to develop a more globally informed strategy of sustainable development.

Reef‐building corals are at risk of extinction from ocean warming. While some corals can enhance their thermal limits by associating with dinoflagellate photosymbionts of superior stress tolerance, the extent to which symbiont communities will reorganize under increased warming pressure remains unclear. Here we show that corals in the hottest reefs in the world in the Persian Gulf maintain associations with the same symbionts across 1.5 years despite extreme seasonal warming and acute heat stress (≥35°C). Persian Gulf corals predominantly associated with Cladocopium (clade C) and most also hosted Symbiodinium (clade A) and/or Durusdinium (clade D). This is in contrast to the neighbouring and milder Oman Sea, where corals associated with Durusdinium and only a minority hosted background levels of Cladocopium. During acute heat stress, the higher prevalence of Symbiodinium and Durusdinium in bleached versus nonbleached Persian Gulf corals indicates that genotypes of these background genera did not confer bleaching resistance. Within symbiont genera, the majority of ITS2 rDNA type profiles were unique to their respective coral species, confirming the existence of host‐specific symbiont lineages. Notably, further differentiation among Persian Gulf sites demonstrates that symbiont populations are either isolated or specialized over tens to hundreds of kilometres. Thermal tolerance across coral species was associated with the prevalence of a single ITS2 intragenomic sequence variant (C3gulf), definitive of the Cladocopium thermophilum group. The abundance of C3gulf was highest in bleaching‐resistant corals and at warmer sites, potentially indicating a specific symbiont genotype (or set of genotypes) that may play a role in thermal tolerance that warrants further investigation. Together, our findings indicate that co‐evolution of host–Symbiodiniaceae partnerships favours fidelity rather than flexibility in extreme environments and under future warming.

The perception that the inheritance of phenotypic traits operates solely through genetic means is slowly being eroded: epigenetic mechanisms have been shown to induce heri-table changes in gene activity in plants 1,2 and metazoans 1,3. Inheritance of DNA methylation patterns provides a potential pathway for environmentally induced phenotypes to contribute to evolution of species and populations 1-5. However, in basal metazoans, it is unknown whether inheritance of CpG methylation patterns occurs across the genome (as in plants) or as rare exceptions (as in mammals) 4. Here, we show that DNA methylation patterns in a reef-building coral are determined by genotype and developmental stage, as well as by parental environment. Transmission of CpG methylation from adults to their sperm and larvae demonstrates genome-wide inheritance. Variation in the hypermethylation of genes in adults and their sperm from distinct environments suggests intergenerational acclimatization to local temperature and salinity. Furthermore, genotype-independent adjustments of methylation levels in stress-related genes were strongly correlated with offspring survival rates under heat stress. These findings support a role of DNA methylation in the intergen-erational inheritance of traits in corals, which could extend to enhancing their capacity to adapt to climate change. Reef-building corals provide habitat for thousands of marine species , protect shorelines and support human livelihoods 6. However, as the oceans warm, repeated thermal stress events have driven cor-als into severe global decline 7,8 and the rapid rate of climate change threatens to overwhelm the capacity for adaptation by genetic means alone 9,10. Recent research demonstrates that stress-induced changes in the DNA methylome of corals correlate with phenotypic changes that explain increased organismal fitness 11,12. The increased methylation correlates with the reduction of spurious transcription and transcriptional noise, reflecting adjustments of expression in response to transcriptional needs under changing conditions 11,13. However, due to the low heritability of DNA methylation in mammals and its complete absence in popular model organisms (for example, Drosophila and Caenorhabditis elegans), the current perception is that this mechanism is unlikely to contribute to adaptive transgenerational plasticity in corals 10. Here, we provide evidence for inheritance of DNA methylation patterns in reef-building corals. The brain coral Platygyra daedalea shows traits that we expect to promote epigenetic acclimatization within generations and the transfer of these modifications between generations 9. Namely, individual colonies are stress-tolerant 14 , long-lived (Supplementary Table 1) and highly fecund 15. Samples of P. daedalea adults, their gametes and larval offspring, were sourced from two populations in the Arabian Peninsula (Fig. 1a,b). The Abu Dhabi population lives under extreme temperatures (winter <19 °C and summer >35 °C) and salinities (40-46 practical salinity units, psu; Supplementary Table 2), and has persisted through several major thermal stress events (coral bleaching) during the past two decades 16. In contrast, the neighbouring Fujairah population lives under comparatively milder conditions (22-33 °C, 36-39 psu) and has not experienced major coral bleaching in recent years. Using whole-genome bisulfite sequencing (WGBS), we identified 1.42 million CpG positions that were consistently methylated in the ~800 megabase pairs (Mb) P. daedalea genome (3.20% of all CpGs, mean coverage 49×; Supplementary Dataset 1b). These methylated positions have had single nucleotide polymorphisms (SNPs) excluded, preventing the misidentification of C-toT SNPs as fully unmethylated cytosines. Similar to other studied cnidar-ians, methylation in P. daedalea predominantly occurred in gene bodies 11-13,17,18. A larger fraction of CpGs in genic regions were methylated than in intergenic regions (3.9% versus 3.0% respectively ; Extended Data Fig. 1a). On a per-position basis, methyl-ated positions in genic regions were also, on average, more strongly methylated than in intergenic regions (mean of 35.4% versus 21.2% respectively; Extended Data Fig. 1b). Within genic regions, methyl-ated positions were more commonly found at both ends (Extended Data Fig. 1c). Colony identity proved to be a strong predictor of DNA meth-ylation patterns in corals. P. daedalea sperm samples were significantly more like their respective parents than like non-parental sperm (mean τ ± s.e.m., 64.8% ± 0.6% versus 53.0% ± 0.4%, t-test P < 10 −16 ; Fig. 1c and Supplementary Dataset 2). Sperm samples were also more like each other than adult samples are like each other (53.0% ± 0.4% versus 50.0% ± 0.4%, t-test P < 10 −6), visible as a 'che-querboard' pattern in the heatmap. This result probably reflects the heterogeneity of cell types in the adult samples and their tissue-specific methylation patterns 11. Inheritance of methylation patterns was further evident in the larval samples, which were more like their parental sperm samples (S7 and S8) than other sperm samples (S1-6; 62.9 ± 0.4% versus 52.4% ± 0.4%, t-test P < 10 −18). Larval samples from reciprocal crosses grouped together, suggesting that

Invasive non‐native species (NNS) are internationally recognised as posing a serious threat to global biodiversity, economies and human health. The identification of invasive NNS already established, those that may arrive in the future, their vectors and pathways of introduction and spread, and hotspots of invasion are important for a targeted approach to managing introductions and impacts at local, regional and global scales. The aim of this study was to identify which marine and brackish NNS are already present in marine systems of the northeastern Arabia area (Arabian Gulf and Sea of Oman) and of these which ones are potentially invasive, and which species have a high likelihood of being introduced in the future and negatively affect biodiversity. Overall, 136 NNS were identified, of which 56 are already present in the region and a further 80 were identified as likely to arrive in the future, including fish, tunicates, invertebrates, plants and protists. The Aquatic Species Invasiveness Screening Kit (AS‐ISK) was used to identify the risk of NNS being (or becoming) invasive within the region. Based on the AS‐ISK basic risk assessment (BRA) thresholds, 36 extant and 37 horizon species (53.7% of all species) were identified as high risk. When the impact of climate change on the assessment (CCA) was considered, the combined risk score (BRA + CCA) increased for 38.2% of all species, suggesting higher risk under warmer conditions, including the highest‐risk horizon NNS the green crab Carcinus maenas, and the extant macro‐alga Hypnea musciformis. This is the first horizon scanning exercise for NNS in the region, thus providing a vital baseline for future management. The outcome of this study is the prioritisation of NNS to inform decision‐making for the targeted monitoring and management in the region to prevent new bio‐invasions and to control existing species, including their potential for spread.

The United Arab Emirates (UAE) straddles 22–26 °N, positioning it in a latitudinal band well known across the globe for its desert biomes. The UAE is characterized by arid to hyper-arid conditions, but with marked variation in precipitation seasonally (highest in winter/spring) and across locations (highest near the Hajar mountains), representing a dramatic shift from the more humid conditions that characterized this region just six millennia ago. The low cloud cover, limited vegetation and poorly developed soil also result in extreme and highly variable temperatures across the year, particularly in areas distant from the coasts. Winds are typically dominated by daily land/sea breezes, but occasional brief ‘shamal’ wind events (particularly in late winter) or cyclones (in early summer) can have important implications for temperature, rainfall and biotic responses. Average temperatures have increased by 1 °C between the 1980s and the 2010s, and rainfall has declined by more than half; in addition, wet bulb temperatures associated with human health are increasing, and may exceed life-threatening levels by the end of the century. Today’s climate represents extremely marginal conditions for life, and the current trends suggest that the already vulnerable ecosystems and organisms of the UAE are coming under increasing climate-related pressure.

The United Arab Emirates (UAE) has had dramatic economic and population growth since its 1971 federation, with the built environment, green spaces, water features and other urban amenities growing to support its burgeoning population. These features, in turn, often provide unique habitats and microenvironments for a wide variety of resident and migratory species that benefit from their association with urban ecosystems, both on land and in nearshore coastal environments. While urbanization has undoubtedly caused important environmental challenges that should not be discounted, our growing cities have developed unique and important ecologies, much of which remains underappreciated and understudied in the UAE. Here we summarize the current understanding of urban ecology in the Emirates, providing insights into features that make cities amenable environments for organisms, particularly in the context of the UAE’s extreme environment. We also discuss several representative groups of organisms that benefit from the artificial environments provided by cities in both terrestrial and marine urban settings.