Urban coral reefs: Degradation and resilience of hard coral assemblages in coastal cities of East and Southeast Asia

Shifts in dominance of benthic communities along a gradient of water temperature and turbidity in tropical coastal ecosystems

Tropical coastal benthic communities will change in species composition and relative dominance due to global (e.g., increasing water temperature) and local (e.g., increasing terrestrial influence due to land-based activity) stressors. This study aimed to gain insight into possible trajectories of coastal benthic assemblages in Raja Ampat, Indonesia, by studying coral reefs at varying distances from human activities and marine lakes with high turbidity in three temperature categories (<31 °C, 31-32 °C, and >32 °C). The benthic community diversity and relative coverage of major benthic groups were quantified via replicate photo transects. The composition of benthic assemblages varied significantly among the reef and marine lake habitats. The marine lakes <31 °C contained hard coral, crustose coralline algae (CCA), and turf algae with coverages similar to those found in the coral reefs (17.4-18.8% hard coral, 3.5-26.3% CCA, and 15-15.5% turf algae, respectively), while the higher temperature marine lakes (31-32 °C and >32 °C) did not harbor hard coral or CCA. Benthic composition in the reefs was significantly influenced by geographic distance among sites but not by human activity or depth. Benthic composition in the marine lakes appeared to be structured by temperature, salinity, and degree of connection to the adjacent sea. Our results suggest that beyond a certain temperature (>31 °C), benthic communities shift away from coral dominance, but new outcomes of assemblages can be highly distinct, with a possible varied dominance of macroalgae, benthic cyanobacterial mats, or filter feeders such as bivalves and tubeworms. This study illustrates the possible use of marine lake model systems to gain insight into shifts in the benthic community structure of tropical coastal ecosystems if hard corals are no longer dominant.

Genome-wide analysis to uncover how Pocillopora acuta survives the challenging intertidal environment

Characterisation of genomic variation among corals can help uncover variants underlying trait differences and contribute towards genotype prioritisation in coastal restoration projects. For example, there is growing interest in identifying resilient genotypes for transplantation, and to better understand the genetic processes that allow some individuals to survive in specific conditions better than others. The coral species Pocillopora acuta is known to survive in a wide range of habitats, from reefs artificial coastal defences, suggesting its potential use as a starter species for ecological engineering efforts involving coral transplantation onto intertidal seawalls. However, the intertidal section of coastal armour is a challenging environment for corals, with conditions during periods of emersion being particularly stressful. Here, we scanned the entire genome of P. acuta corals to identify the regions harbouring single nucleotide polymorphisms (SNPs) and copy number variations (CNVs) that separate intertidal colonies (n = 18) from those found in subtidal areas (n = 21). Findings revealed 74,391 high quality SNPs distributed across 386 regions of the P. acuta genome. While the majority of the detected SNPs were in non-coding regions, 12% were identified in exons (i.e. coding regions). Functional SNPs that were significantly associated with intertidal colonies were found in overrepresented genomic regions linked to cellular homeostasis, metabolism, and signalling processes, which may represent local environmental adaptation in the intertidal. Interestingly, regions that exhibited CNVs were also associated with metabolic and signalling processes, suggesting P. acuta corals living in the intertidal have a high capacity to perform biological functions critical for survival in extreme environments.

Reduction of small-prey capture rate and collective predation in the bleached sea anemone Exaiptasiadiaphana

Cnidarians may dominate benthic communities, as in the case of coral reefs that foster biodiversity and provide important ecosystem services. Polyps may feed by predating mesozooplantkon and large motile prey, but many species further obtain autotrophic nutrients from photosymbiosis. Anthropogenic disturbance, such as the rise of seawater temperature and turbidity, can lead to the loss of symbionts, causing bleaching. Prolonged periods of bleaching can induce mortality events over vast areas. Heterotrophy may allow bleached cnidarians to survive for long periods of time. We tested the reinforcement of heterotrophic feeding of bleached polyps of Exaiptasia diaphana fed with both small zooplantkon and large prey, in order to evaluate if heterotrophy allows this species to compensate the reduction of autotrophy. Conversely to expected, heterotrophy was higher in unbleached polyps (+54% mesozooplankton prey and +11% large prey). The increase of heterotrophic intake may not be always used as a strategy to compensate autotrophic depletion in bleached polyps. Such a resilience strategy might be more species-specific than expected.

Coral transplantation in urban environments: Insights from colony survival and growth on artificial frames versus the seabed

Urban and green transitions require infrastructures that can cause pressure on coastal ecosystems. In northern Taiwan, plans to convert an oil-fired power plant to gas would necessitate a port terminal construction, threatening nearby corals and marine life. To mitigate construction impacts, the relocation of affected corals was proposed. We conducted a transplantation study, prior to such a large-scale coral relocation, to assess its feasibility and to identify potential risks associated with the marginal location of northern Taiwan for tropical corals. Five coral species, representative of the different ecological strategies, were selected. We used two methods (artificial frames and seabed cementation) to transplant 246 colony fragments to two pre-selected sites. Over a year, we monitored fragment survival and growth, in parallel with environmental conditions. We found that survival and growth were significantly influenced by transplantation methods, sites, and species. The difference between methods revealed biotic (predation by corallivorous snails) and abiotic (mechanical damage by waves) factors affecting coral survival and growth. Acropora species exhibited high growth, but also high mortality, consistent with their known ecology. Other species presented slower growth but higher survival. One site provided a better environment for corals, which we attributed to topography and reduced exposure. Overall, this study provides interesting insights into relocating corals in a high-latitude and urban coral ecosystem, highlighting risks related to mechanical damages and predation.

Current status of coral disease prevalence at Karimunjawa Island: correlation between land zonation and lesion occurrence

Coral diseases have contributed significantly to the decline of coral populations at both local and global scales. The Karimunjawa Archipelago, located off the coast of Java in Indonesia, is a marine national park with a zonation-based approach, designated by the local government due to its rich coral reef biodiversity. Unfortunately, there is a limited amount of research regarding the prevalence of coral diseases in coral reefs located on the islands. We analyzed the coral reef lesion assemblages at 6 sites within 3 designated zones, namely Tourism, Aquaculture, and Core zones. Our investigation aimed to determine (1) the types, prevalence, and patterns of coral lesions, (2) the correlation between coral cover and lesion prevalence, and (3) the susceptibility of coral taxa to lesions. A significant difference of 80.54% in the total number of coral lesions was observed between the tourism zone (24.34%) and the core zone (10.36%). Fourteen different lesion types were identified; among the non-disease lesions, sediment damage was the most prevalent (9.95%), followed by disease lesions caused by white syndrome (3.7%). A correlation was found between the cover of dominant coral taxa and the prevalence of lesions (disease and non-disease) at all sites. Mean lesion prevalence across all zones ranged from moderate to high categories. These findings present current data on the distribution of coral lesions and their patterns across zones around Karimunjawa Island. Research on the etiology and epidemiology of coral lesions should be promoted to identify ways to prevent the spread of coral diseases in Karimunjawa.

Bunkering for change: Knowledge preparedness on the environmental aspect of ammonia as a marine fuel

Nitrogen cycling is essential to ecosystem functioning and the overall health of our planet. Ammonia, a nitrogen-containing product, as well as a nutrient, is promoted as a low-carbon fuel for the maritime sector, with spectacular production increase in plan. Similar to any other widespread fuels in the past, it is paramount to be prepared for the potential environmental impact of ammonia fuel. Here, through our preliminary calculations using literature data, we suggest that the amount of ammonia to be produced to fulfil the maritime energy need by 2050 may entail large alterations in global nitrogen cycling. Currently, the literature based on limited known cases of ammonia excess is insufficient to quantify the environmental impacts caused by the probable increase in bunkering ammonia release at global scale. With a few knowledge gaps identified, we call on the marine science community to investigate the potential environmental impact related to substantial ammonia excess, contributing new knowledge to a more environmentally sustainable future.

Assessment of macrobenthos diversity and a zoning proposal for Seixas coral reefs (northeastern Brazil)

Coral reefs worldwide are under severe threat due to their inherent fragility and urgent need for conservation. The escalating tourism in coral reefs significantly impacts the marine ecosystem's biodiversity and conservation. This study analyzed the diversity and conservation status of macrobenthos in the Seixas coral reef, located in northeastern Brazil, and proposed a zoning plan. We employed monitoring protocols adapted from the Reef Check Program, the Rapid Assessment Protocol for Atlantic and Gulf Reefs, and the Protocol for Monitoring Coastal Benthic Habitats. Species identification was carried out by analyzing 25 transects, each divided into 1 m2 grids, with photos recorded for each grid, totaling 625 photos. Margalef, Shannon-Weaver, Simpson, and Pielou indices were used to analyze species distribution and diversity. The results indicated Dictyotaceae, Sargassaceae, and Corallinaceae as prevalent families. This research offers decision-makers a snapshot of species distribution in the Seixas coral reefs, providing a non-destructive, efficient methodology for assessing environmental impacts on coastal coral reefs.

Implementing a transformative approach to the coral reefs' recovery phase

Mitigation and rehabilitation are responses to climate change and human misuse. However, many regions worldwide still lose coral reefs even after implementing these responses. We chose Hurghada city, on the Red Sea, and Weizhou island, on the South China Sea, as sample regions to assess their various modes of coral community structure loss against the combined climatic and human impact drivers that led to this shift. Despite the former being considered a regional coral refuge, while the latter was limited, both regions have previously intervened with coral restoration. We found that even after three decades of impact cessation by forcing laws, most coral reef states are still declining (about a third and a half in both cities), have not harnessed the existing crowded larval density, and are unrecovered. Such findings imply that the combined impacts will persist, necessitating a broad connectivity analysis that enables a suitable intervention (hybrid solutions hypothesis). Each state of coral categories was connected to certain combined stressor factors using our broad connectivity analysis to grasp the extent and relative contribution of coral community shift since our data obtained from comparable sites were widely varied. Moreover, destructive emerged changes have transformed the coral community structure under the forced adaptation scenario of the community structure, boosting those who can resist at the expense of others. To prove our hypothesis, we used the connectivity findings in determining the optimal technique and spots for coral rehabilitation around the two cities. We then compared our findings with the outcomes of two other existing adjacent restoration projects related to other endeavors. Our hybrid approach harvested coral larvae that had been wasted in both cities. Thus, hybrid solutions are globally required for such cases, and proper early interventions are needed to maintain the genotype power to boost coral adaptability throw global ecological settings.

Decadal stability in coral cover could mask hidden changes on reefs in the East Asian Seas

Coral reefs in the Central Indo-Pacific region comprise some of the most diverse and yet threatened marine habitats. While reef monitoring has grown throughout the region in recent years, studies of coral reef benthic cover remain limited in spatial and temporal scales. Here, we analysed 24,365 reef surveys performed over 37 years at 1972 sites throughout East Asia by the Global Coral Reef Monitoring Network using Bayesian approaches. Our results show that overall coral cover at surveyed reefs has not declined as suggested in previous studies and compared to reef regions like the Caribbean. Concurrently, macroalgal cover has not increased, with no indications of phase shifts from coral to macroalgal dominance on reefs. Yet, models incorporating socio-economic and environmental variables reveal negative associations of coral cover with coastal urbanisation and sea surface temperature. The diversity of reef assemblages may have mitigated cover declines thus far, but climate change could threaten reef resilience. We recommend prioritisation of regionally coordinated, locally collaborative long-term studies for better contextualisation of monitoring data and analyses, which are essential for achieving reef conservation goals.

Two centuries of sponges (phylum Porifera) taxonomic studies in Indonesia (1820-2021): checklist and bibliography

Sponges in Indonesia have been studied since the 19th century during several historical expeditions and international collaborations. Hundreds of new species were reported from various locations, e.g., Ambon, Ternate, Sulawesi, Aru, and Kei Islands. This study aimed to create a sponge (Porifera: Calcarea, Demospongiae, Hexactinellida, and Homoscleromorpha) species checklist from Indonesia based on World Porifera Database. With a total of 731 species, our checklist comprises approximately 45 species of Calcarea, 566 species of Demospongiae, 115 species of Hexactinellida, and five species of Homoscleromorpha. The number of species are recorded from 12 marine ecoregions across the Indonesian Archipelago and freshwater habitats (Spongillida) between 1820-2021. The species composition indicates higher regional endemism or poorly studied since no other report after the original description. However, several marine ecoregions of Indonesia remain highly overlooked (e.g., Northeast Sulawesi, Papua, Southern Java, Western Sumatra), including freshwater habitats. Therefore, a taxonomic biodiversity baseline study, particularly on Porifera, is necessary to better understand the aquatic and marine biodiversity in the Indonesia Archipelago.

Response of coral bacterial composition and function to water quality variations under anthropogenic influence

Microbial communities play key roles in the adaptation of corals living in adverse environments, as the microbiome flexibility can enhance environmental plasticity of coral holobiont. However, the ecological association of coral microbiome and related function to locally deteriorating water quality remains underexplored. In this work, we used 16S rRNA gene sequencing and quantitative microbial element cycling (QMEC) to investigate the seasonal changes of bacterial communities, particularly their functional genes related to carbon (C), nitrogen (N), phosphorus (P) and sulfur (S) cycle, of the scleractinian coral Galaxea fascicularis from nearshore reefs exposed anthropogenic influence. We used nutrient concentrations as the indicator of anthropogenic activities in coastal reefs, and found a higher nutrient pressure in spring than summer. The bacterial diversity, community structure and dominant bacteria of coral shifted significantly due to seasonal variations dominated by nutrient concentrations. Additionally, the network structure and nutrient cycling gene profiles in summer under low nutrient stress was distinct from that under poor environmental conditions in spring, with lower network complexity and abundance of CNPS cycling genes in summer compared with spring. We further identified significant correlations between microbial community (taxonomic composition and co-occurrence network) and geochemical functions (abundance of multiple functional genes and functional community). Nutrient enrichment was proved to be the most important environmental fluctuation in controlling the diversity, community structure, interactional network and functional genes of the coral microbiome. These results highlight that seasonal shifts in coral-associated bacteria due to anthropogenic activities alter the functional potentials, and provide novel insight about the mechanisms of coral adaptation to locally deteriorating environments.

Coral persistence despite marginal conditions in the Port of Miami

Coral cover has declined worldwide due to anthropogenic stressors that manifest on both global and local scales. Coral communities that exist in extreme conditions can provide information on how these stressors influence ecosystem structure, with implications for their persistence under future conditions. The Port of Miami is located within an urbanized environment, with active coastal development, as well as commercial shipping and recreational boating activity. Monitoring of sites throughout the Port since 2018 has revealed periodic extremes in temperature, seawater pH, and salinity, far in excess of what have been measured in most coral reef environments. Despite conditions that would kill many reef species, we have documented diverse coral communities growing on artificial substrates at these sites-reflecting remarkable tolerance to environmental stressors. Furthermore, many of the more prevalent species within these communities are now conspicuously absent or in low abundance on nearby reefs, owing to their susceptibility and exposure to stony coral tissue loss disease. Natural reef frameworks, however, are largely absent at the urban sites and while diverse fish communities are documented, it is unlikely that these communities provide the same goods and services as natural reef habitats. Regardless, the existence of these communities indicates unlikely persistence and highlights the potential for coexistence of threatened species in anthropogenic environments, provided that suitable stewardship strategies are in place.

Species richness and the dynamics of coral cover in Bangka Belitung Islands, Indonesia

Pressures on the world's tropical coral reefs that threaten their existence have been reported worldwide due to many stressors. Loss of coral cover and declines in coral richness are two of the most common changes often reported in coral reefs. However, a precise estimate of species richness and the coral cover dynamics for most Indonesian regions, particularly in the Bangka Belitung Islands, have been poorly documented. Annual monitoring data from 2015 to 2018 at 11 fixed sites in the Bangka Belitung Islands using the photo quadrat transect method identified 342 coral species from 63 genera. Of these, 231 species (>65%) were rare or uncommon, occurring in <40% of all sites. The species richness of hard corals was categorized as moderate compared to other studies in Indonesia, averaging 53 species across sites and years, and there was an increasing number of sites with high species richness. The percent cover of live and dead hard corals was greater than other benthic and substrate categories in all sites; revealing a live-dead hard corals pattern with dead coral cover averaged 12% higher than live hard coral across the years, but they did not show a significant difference (P > 0.05). There was a slightly increasing trend in hard coral cover in ten out of 11 sites in 2018, indicating the reefs are in a recovery process. The results support the need to identify recovering or stable areas despite apparent anthropogenic and natural variations recently. This vital information is essential for early detection and preparation for management strategies in the current context of climate change and for ensuring future coral reef survival.

Coral diversity matches marine park zonation but not economic value of coral reef sites at St. Eustatius, eastern Caribbean

Stony corals play a key role in the marine biodiversity of many tropical coastal areas as suppliers of substrate, food and shelter for other reef organisms. Therefore, it is remarkable that coral diversity usually does not play a role in the planning of protected areas in coral reef areas. In the present study we examine how stony coral diversity patterns relate to marine park zonation and the economic value of reefs around St. Eustatius, a small island in the eastern Caribbean, with fisheries and tourism as important sources of income. The marine park contains two no-take reserves. A biodiversity survey was performed at 39 sites, 24 inside the reserves and 15 outside; 22 had a maximum depth >18 m and 17 were shallower. Data on economic value per site were obtained from the literature. Corals were photographed for the verification of identifications made in the field. Coral species richness (n = 49) was highest in the no-take reserves and species composition was mainly affected by maximum depth. No distinct relation is observed between coral diversity and fishery value or total economic value. Based on the outcome of this study we suggest that in future designs of marine park zonation in reef areas, coral diversity should be taken into consideration. This is best served by including reef areas with a continuous depth gradient from shallow flats to deep slopes.

Sediment trap height affects mass, particle size, and biogeochemical composition of material collected in an equatorial coral reef

Anthropogenic sedimentation is a major contributor to the worldwide decline in coral cover. Resuspension of benthic material can exacerbate the threat to corals, but evidence of vertical sediment gradients is limited. Here, we installed sediment traps at 10, 20, 30, 40, and 50 cm above the substrate at three equatorial reef sites for three months and determined the dry mass, particle size, and biogeochemical composition of the material collected. As the trap mouth height increased from 10 to 50 cm, dry mass decreased as sediments became finer, poorer in carbonate, and richer in silicate. Despite among-site differences in collected sediment, this vertical gradient was present in all trap arrays, likely driven by resuspension mechanisms on seabed sediments. These results have implications for coral vertical ecology and underline the importance of standardising sediment collection protocols.

Unraveling Moreton Bay reef history: An urban high-latitude setting for coral development

High-latitude habitats have become increasingly recognized as a potential climate refuge for coral communities, supporting both tropical and sub-tropical corals. Despite the increasing interest in the ecology of high-latitude corals, our current knowledge of their temporal dynamics is limited, especially within urbanized settings. Here, we examined the entire history of a high-latitude coral reef ecosystem in an urbanized setting. We surveyed Holocene fossil and modern coral communities along a water quality gradient in Moreton Bay, southeast Queensland, Australia, representing near-river (Wellington Point), intermediate (Peel Island) and near-oceanic (Myora Reef) environmental conditions. Reef accretion occurred during three discrete episodes from 7,400 to 5,800, 4,900 to 3,000, and 2,100 to 300 years BP, each separated by roughly 1,000-year hiatuses, where conditions were probably not favorable enough for reef accretion to occur. Episodic reef initiation and termination suggests strong environmental controls over reef development. Eastern Australian Holocene reef growth and cessation has been linked previously to sea level fluctuations and climatic regimes (e.g., ENSO). Within each reef building episode, there were few changes in coral assemblages over time. The fast growing and branching Acropora had a relative abundance greater than 90% in ten of the 13 sediment cores and all the submerged terrace excavations. However, substantial modification of adjacent coastal catchments from European colonization in the mid 1800’s resulted in increased sediment and nutrient discharge into the bay. This perturbation coincided with a greater abundance of stress-tolerant coral species (e.g., Dipsastraea, Goniastrea, and Goniopora) and the near extirpation of Acropora in the modern coral communities of near-river and intermediate sites due to poor water quality. In contrast, the modern coral assemblage at the near-oceanic site (Myora Reef) continues to be dominated by Acropora, likely due to the consistent oceanic input, resulting in lower sediment loading and higher water quality. In order for conditions for reef growth to improve, especially within the near-river portions of the bay, further sediment and nutrient runoff from anthropogenic land-use changes need to be mitigated. Given the historical abundance of Acropora, we recommend this genus be used as an indicator of natural resource management success in the bay.

A half-century record of coral skeletal P/Ca reveals late 20th century nutrient pollution in Port Dickson, Malaysia

Anthropogenic nutrient pollution has been identified as one of the key stressors of coastal ecosystems. However, the paucity of long-term nutrient records limits our understanding of both the extent of nutrient pollution as well as of the ecological impacts. Here, using coral skeletal phosphorus (P/Ca), we reconstructed a half-a-century record of seawater phosphate at Port Dickson, Malaysia. The P/Ca in the coral revealed an up to 8-fold increase in coral P/Ca from the late 1970s to 2000s, likely linked to increases in fertilizer use (R² = 0.47) and variabilities in rainfall (R² = 0.17). The rise in coral P/Ca in coincided with a contemporaneous 18 % decrease in coral skeletal density, suggesting phosphate enrichment may impact the growth and structural integrity of reef-building corals. Given the importance of both agriculture and heavy reliance on coral reefs by populations in Southeast Asia, our study highlights continue the need to develop environmental management upstream of coastal zones.

Urban coral communities and water quality parameters along the coasts of Guangdong Province, China

Coral communities in China's Great Bay Area (GBA) have experienced severe degradation, but only limited information is available about their community structure. We surveyed 20 sites across three regions (Daya Bay, Dapeng Bay, Wanshan Islands) in GBA to provide an updated baseline of these urban coral communities. Live coral cover varied substantially, with the lowest values (<2 %) found inside the highly urbanized Daya Bay, and highest values (40-47 %) from offshore islands that are less affected by human activities. The two sites with the lowest live coral cover had a high percentage of dead coral. Five groups of coral communities could be identified, with most of them characterized by dominance of massive and encrusting coral species. Both coral cover and generic richness were negatively correlated with dissolved inorganic nitrogen in the water column, indicating that nutrient pollution could potentially constrain the development of these urban coral communities.

Temporal and spatial dynamics of tropical macroalgal contributions to blue carbon

Blue carbon ecosystems are a vital part of nature-based climate solutions due to their capacity to store and sequester carbon, but often exclude macroalgal beds even though they can form highly productive coastal ecosystems. Recent estimates of macroalgal contributions to global carbon sequestration are derived primarily from temperate kelp forests, while tropical macroalgal carbon stock in living biomass is still unclear. Here, using Singapore as a case study, we integrate field surveys and remote sensing data to estimate living macroalgal carbon stock. Results show that macroalgae in Singapore account for up to 650 Mg C biomass stock, which is greater than the aboveground carbon found in seagrass meadows but lower than that in mangrove forests. Ulva and Sargassum dominate macroalgal assemblages and biomass along the coast, with both genera exhibiting distinct spatio-temporal variation. The annual range of macroalgal biomass carbon is estimated to be 450 Mg C yr^-1, or 0.77 Mg C ha^-1 yr^-1. Noting the uncertainties of the fate of macroalgal biomass carbon, we estimate the potential sequestration rate and find that it is comparable to mature terrestrial ecosystems such as tropical grasslands and temperate forests. This study demonstrates that macroalgal seasonality allows for a consistent amount of biomass carbon to either be exported and eventually sequestered, or harvested for utilization on an annual basis. These findings on macroalgal growth patterns and their considerable contributions to tropical coastal carbon pool add to the growing support for macroalgae to be formally included in blue carbon assessments.

A 3D perspective on sediment turnover and feeding selectivity in blennies

Sediments in algal turfs can modify a wide variety of key ecological processes on coral reefs. While some larger reef fishes can remove these turf-bound sediments, the role of small, yet abundant, cryptobenthic fishes is currently unclear. To address this knowledge gap, we explored the extent to which the blenny, Ecsenius stictus, can shape sediment dynamics on coral reefs by quantifying their sediment ingestion and space use. Per unit body mass, E. stictus process sediments at comparable rates to key parrotfish and surgeonfish species. However, in absolute terms, E. stictus has a negligible influence on net sediment dynamics, despite their abundance. Behavioural observations and 3D photogrammetry reveal that E. stictus preferentially feed and rest on elevated surfaces; potentially because of low sediment loads on these surfaces. Overall, E. stictus may be responding to sediment loads rather than manipulating them; it is a passenger rather than a driver in reef processes.

Monsoonal variations of lead (Pb) in coastal waters around Singapore

Anthropogenic lead (Pb) has been the overwhelming Pb source to the global ocean, primarily contributed from Pb gasoline and industrial emissions. However, since Pb gasoline has been phased out globally, questions about whether there was a decrease in seawater Pb concentration, or if there are other sources taking over remains unclear in Southeast Asia. Here, combining Pb concentrations in seawater from Singapore Strait in 2010-2017; trap sediment in 2018-2019; and the previously published coral reconstruction covering 1975-2010; we found that the seawater Pb concentration in Singapore Strait over past decades followed the regional gasoline emissions, and no additional major source had contributed the Pb in the seawater since ~2010. The present-day Pb in Singapore Straits' water mainly follows the monsoonal current reversals, with variable degrees of scavenging that peak in inter-monsoon season. Minor Pb sources still contribute to some local-scale variabilities, despite a decadal-scale decreasing trend of Pb in seawater.

Behaviour broadens thermal safety margins on artificial coastal defences in the tropics

Tropical species are predicted to be among the most vulnerable to climate change as they often live close to their upper limits to thermal tolerance and in many cases, behavioural thermoregulation is required to persist in the thermal extremes of tropical latitudes. In concert with warming temperatures, near-shore species are faced with the additional threat of shoreline hardening, leading to a reduction in microhabitats that can provide thermal refuges. This situation is exemplified in Singapore, which lies almost on the equator and so experiences year-round hot temperatures, and much of its coastline is now seawall. To investigate the thermal ecology of a common intertidal gastropod, Nerita undata, on these artificial structures, we measured thermal conditions on two seawalls, the temperatures of habitats occupied by the snail, and compared these with the snail's thermal tolerance by measuring heart rate and behavioural thermoregulation (as preferred temperature, Tpref). At one of the two seawalls (Tanjong Rimau), temperatures experienced by N. undata exceeded all measures of thermal tolerance in the sun, while at the other (Palawan Beach), they did not. Temperatures in habitats occupied by the snails on the seawalls were similar to their measured Tpref in the laboratory and were lower than all measures of thermal tolerance. Behavioural thermoregulation by the snails, therefore, significantly increased the thermal safety margins of N. undata on the relatively homogenous seawalls in Singapore, and at one of the two seawalls were necessary to allow snails to survive. Accordingly, to facilitate motile species to maintain broad thermal safety margins through behavioural regulation, the provision of additional refuges from thermal stress is recommended on artificial coastal defences such as seawalls.

Urbanization comprehensively impairs biological rhythms in coral holobionts

Coral reefs are in global decline due to climate change and anthropogenic influences (Hughes et al., Conservation Biology, 27: 261-269, 2013). Near coastal cities or other densely populated areas, coral reefs face a range of additional challenges. While considerable progress has been made in understanding coral responses to acute individual stressors (Dominoni et al., Nature Ecology & Evolution, 4: 502-511, 2020), the impacts of chronic exposure to varying combinations of sensory pollutants are largely unknown. To investigate the impacts of urban proximity on corals, we conducted a year-long in-natura study-incorporating sampling at diel, monthly, and seasonal time points-in which we compared corals from an urban area to corals from a proximal non-urban area. Here we reveal that despite appearing relatively healthy, natural biorhythms and environmental sensory systems were extensively disturbed in corals from the urban environment. Transcriptomic data indicated poor symbiont performance, disturbance to gametogenic cycles, and loss or shifted seasonality of vital biological processes. Altered seasonality patterns were also observed in the microbiomes of the urban coral population, signifying the impact of urbanization on the holobiont, rather than the coral host alone. These results should raise alarm regarding the largely unknown long-term impacts of sensory pollution on the resilience and survival of coral reefs close to coastal communities.

Light availability regulated by particulate organic matter affects coral assemblages on a turbid fringing reef

Recently, increasing evidence suggests that reef-building corals exposed to elevated suspended solids (SS) are largely structured by changes in underwater light availability (ULA). However, there are few direct and quantitative observations in situ support for this hypothesis; in particular, the contribution of SS to the diffuse attenuation coefficient of the photosynthetically active radiation (K_d-PAR) variations is not yet fully understood. Here, we investigated the variations in ULA, the structure of coral assemblages, and the concentration and composition of SS on the Luhuitou fringing reef, Sanya, China. Light attenuation was rapid (K_d-PAR: 0.60 ± 0.39 m^-1) resulting in a shallow euphotic depth (Z_eu-PAR) (<11 m). Benthic PAR showed significant positive correlations with branching and corymbose corals (e.g. Acropora spp.), while massive and encrusting species (e.g. Porites spp.) dominated the coral communities and showed no significant correlations with PAR. These results indicate that the depth range available for coral growth is shallow and the tolerance to low-light stress differs among coral species. Notably, K_d-PAR showed no significant correlations with the grain size fractions of SS, whereas significant positive correlations were found with its organic fraction content, demonstrating that the light attenuation of SS is mainly regulated by particulate organic matter (POM). Intriguingly, our isotopic evidence revealed that POM concentration contributed the most to changes in K_d-PAR, with its source being slightly less important. Combined, our results highlight ULA regulated by POM is an important factor in contributing to changes in coral assemblages on inshore turbid reefs, and reducing the input of terrestrial materials, especially POM, is an effective measure to alleviate the low-light stress on sensitive coral species.

Characterization of anthropogenic marine macro-debris affecting coral habitat in the highly urbanized seascape of Mumbai megacity

Marine debris has become a major form of pollution and a serious ecosystem health concern. The present study evaluates the accumulation, origin, and fate of debris in intertidal coral habitats of Mumbai-one of the world's highly populated coastal cities on the west coast of India. Predominantly, seven hermatypic coral species belonging to seven genera and five families were identified and mainly represented by Pseudosidastrea, Porites, and Bernardpora. In terms of number, the mean density of marine debris was 1.60 ± 0.13 SE items/m², which is higher than the global average. The mean density of plastic debris was 1.46 ± 0.14 SE items/m². Approximately 9% of total coral colonies were in physical contact with debris, and 22% of these colonies showed visible signs of partial bleaching. Single use plastic bags and wrappers were dominant plastic debris. The study area was characterized as 'very poor cleanliness' according to the Beach Quality Indexes, which include the Clean Coast Index, General Index, and Hazardous Items Index. The numerical model indicates the influence of river discharge and probable areas of plastic accumulation with high tidal currents in this region, maneuvering the spatial advection of litter in the nearshore areas. Combined analysis of ground-truthing and model simulation implies that the possible contributing sources of litter were representatives of land-based and sea-originated. The overall results point to increasing anthropogenic stressors threatening coastal coral communities, including marine debris pollution. It is advocated to adopt an integrated coastal zone management approach supported by coordinated policy frameworks could guide the mitigation of the debris footprint in coastal environments.

Differential Response of the Microbiome of Pocillopora acuta to Reciprocal Transplantation Within Singapore

As corals continue to decline globally, particularly due to climate change, it is vital to understand the extent to which their microbiome may confer an adaptive resilience against environmental stress. Corals that survive on the urban reefs of Singapore are ideal candidates to study the association of scleractinians with their microbiome, which in turn can inform reef conservation and management. In this study, we monitored differences in the microbiome of Pocillopora acuta colonies reciprocally transplanted between two reefs, Raffles and Kusu, within the Port of Singapore, where corals face intense anthropogenic impacts. Pocillopora acuta had previously been shown to host distinct microbial communities between these two reefs. Amplicon sequencing (16S rRNA) was used to assess the coral microbiomes at 1, 2, 4, and 10 days post-transplantation. Coral microbiomes responded rapidly to transplantation, becoming similar to those of the local corals at the destination reef within one day at Raffles and within two days at Kusu. Elevated nitrate concentrations were detected at Raffles for the duration of the study, potentially influencing the microbiome's response to transplantation. The persistence of corals within the port of Singapore highlights the ability of corals to adapt to stressful environments. Further, coral resilience appears to coincide with a dynamic microbiome which can undergo shifts in composition without succumbing to dysbiosis.

A community and functional comparison of coral and reef fish assemblages between four decades of coastal urbanisation and thermal stress

Urbanized coral reefs experience anthropogenic disturbances caused by coastal development, pollution, and nutrient runoff, resulting in turbid, marginal conditions in which only certain species can persist. Mortality effects are exacerbated by increasingly regular thermal stress events, leading to shifts towards novel communities dominated by habitat generalists and species with low structural complexity.

There is limited data on the turnover processes that occur due to this convergence of anthropogenic stressors, and how novel urban ecosystems are structured both at the community and functional levels. As such, it is unclear how they will respond to future disturbance events.

Here, we examine the patterns of coral reef community change and determine whether ecosystem functions provided by specialist species are lost post‐disturbance. We present a comparison of community and functional trait‐based changes for scleractinian coral genera and reef fish species assemblages subject to coastal development, coastal modification, and mass bleaching between two time periods, 1975–1976 and 2018, in Nakagusuku Bay, Okinawa, Japan.

We observed an increase in fish habitat generalists, a dominance shift from branching to massive/sub‐massive corals and increasing site‐based coral genera richness between years. Fish and coral communities significantly reassembled, but functional trait‐based multivariate space remained constant, indicating a turnover of species with similar traits. A compression of coral habitat occurred, with shallow (<5 m) and deep (>8 m) coral genera shifting towards the mid‐depths (5–8 m).

We show that although reef species assemblages altered post disturbance, new communities retained similar ecosystem functions. This result could be linked to the stressors experienced by urban reefs, which reflect those that will occur at an increasing frequency globally in the near future. Yet, even after shifts to disturbed communities, these fully functioning reef systems may maintain high conservation value.

Abandoned, lost, or discarded fishing gear at urban coastlines

Abandoned, lost, or discarded fishing gear (ALDFG) is considered a major threat to ocean biodiversity. Yet, little is known of the interactive impacts of ALDFGs and urban nearshore biodiversity and habitats, especially in Southeast Asia where fisheries efforts are increasing. We identified ALDFG hotspots around Singapore-where 80% of coastal areas are urbanized or anthropogenically modified. Fishing lines and nets were the most common ALDFGs recovered; with strong correlations between ALDFG presence and beaches, intertidal, mangroves, as well as sites with significant coastal modifications. Plastic polymer nets trapped the highest organism diversity and abundance. A total of 1052 trapped individuals comprising 124 species were recovered, the majority in classes Merostomata, Actinopterygii and Malacostraca. The most abundant trapped species was Carcinoscorpius rotundicauda and the highest mortality presentation was in Class Actinopterygii. This study demonstrates that ALDFGs remain a threat to marine biodiversity within urban coastal habitats and at heavily modified shorelines.

Large host anemones can be shelters of a diverse assemblage of fish species, not just anemonefish

The mutualistic relationships between anemonefish (Amphiprion; Pomacentridae) and host sea anemones are well known, but host anemones are also used as shelter by damselfish (Pomacentridae), wrasses (Labridae) and cardinalfish (Apogonidae). The threespot dascyllus Dascyllus trimaculatus (Pomacentridae) is known to live on or near host anemones in their immature phase. Nonetheless, detailed studies on the use of host anemones by other fish species have not yet been conducted. To understand the factors that influence the use of host anemones by other fish species, this study investigated the fish biota around host anemones in the Ryukyu Archipelago. Other than Amphiprion spp. and D. trimaculatus, 10 additional species of fish (9 species of damselfish and 1 species of cardinalfish) were confirmed to temporarily use host anemones as shelter, and five species of wrasse including Labroides dimidiatus came to clean anemonefish. Logistic regression analyses (independent variable: presence or absence of other species of fish; dependent variables: anemonefish aggressiveness, size of host anemone, number of D. trimaculatus) indicated that the size of host anemones is important for the presence of fish, both in species using the anemone as temporary shelter and in cleaner species. Large host anemones can provide shelter and food resources for other species of coral reef fish as well as for anemonefish.

Marine litter pollution on coral reefs of Darvel Bay (East Sabah, Malaysia)

Marine litter is recognized as an increasing component of marine ecosystem pollution. In this baseline study, we document the magnitude, types, sources, and potential impacts of litter on six coral reefs in East Sabah. We applied a simplified classification of litter to extract abundance data from video transects. The average density was 10.7 items per 100 m². Plastics represent 91% and the remaining 9% were metal, glass, and wood. Most (~70%) plastics are single-use items derived from dumping. Discarded fishing gear accounts for ~25%. Litter pollution increases closer to urban developments, with Sakar reef having higher densities (51 items per 100 m²), and higher Clean Coast Index (CCI = 10.2, dirty) and higher Plastic Abundance Index (PAI = 4.68) scores. This method could and should be readily integrated into ongoing monitoring programs to support assessments of the extent and magnitude of marine litter pollution on reefs worldwide.

An urban intertidal reef is dominated by fleshy macroalgae, sediment, and bleaching of a resilient coral (Siderastrea stellata)

We provide a baseline assessment of benthic cover, salinity, temperature, and bleaching in an urban intertidal reef. The cover is composed of a weedy coral (Siderastrea stellata), algae, and sand sediments. Fleshy macroalgae provided the most of the cover (23% to 43%), followed by coral (16% to 24%), and sediment (6% to 19%). Most of the tidal pools presented high algae cover with seasonal differences; whereas, the coral and sediment cover did not differ significantly over time. The bleached colonies ranged from 6% (November) to 76% (March) over the months according to the stress levels (warming and runoff). Temperature (30.3 to 33.5 °C), and salinity (35.2 to 43.2) characterized an extreme reef habitat. S. stellata resistance to chronic and acute stress makes it a bioindicator of environmental stress. The results highlight those marginal reefs may be simplified habitats, composed of monospecific coral populations and morphogically-simple macroalgae adapted to current pressures but its long-term survival is unlikely due to climate change.

Antagonistic effects of seawalls and urban sedimentation on epilithic algal matrix (EAM)-feeding fishes

Marine urbanisation often results in the proliferation of artificial coastal defences and heavy sedimentation, adversely impacting coral reef systems in tropical coastal cities. Knowledge of how motile organisms, such as reef fish, respond to novel human-made habitats and high sedimentation is limited. Here, we examine the role of sloping granite seawalls in supporting reef fishes that utilise the epilithic algal matrix (EAM) as a food resource. We surveyed fish assemblages and feeding activities on seawalls and reef flats, and conducted a field experiment to examine the effects of sediment on EAM feeding rates. Seawalls and reef flats supported distinct fish assemblage composition with significantly greater feeding activity on seawalls. However, reduced feeding activity on EAM with elevated sediment loads suggests that urban sedimentation may limit the utility of this novel feeding ground for nearshore communities. These findings illustrate the complexities and interactive effects of anthropogenic changes driven by coastal urbanisation.

Untangling the molecular basis of coral response to sedimentation

Urbanized coral reefs are often chronically affected by sedimentation and reduced light levels, yet many species of corals appear to be able to thrive under these highly disturbed conditions. Recently, these marginal ecosystems have gained attention as potential climate change refugia due to the shading effect of suspended sediment, as well as potential reservoirs for stress-tolerant species. However, little research exists on the impact of sedimentation on coral physiology, particularly at the molecular level. Here, we investigated the transcriptomic response to sediment stress in corals of the family Merulinidae from a chronically turbid reef (one genet each of Goniastrea pectinata and Mycedium elephantotus from Singapore) and a clear-water reef (multiple genets of G. pectinata from the Gulf of Aqaba/Eilat). In two ex-situ experiments, we exposed corals to either natural sediment or artificial sediment enriched with organic matter and used whole-transcriptome sequencing (RNA sequencing) to quantify gene expression. Analysis revealed a shared basis for the coral transcriptomic response to sediment stress, which involves the expression of genes broadly related to energy metabolism and immune response. In particular, sediment exposure induced upregulation of anaerobic glycolysis and glyoxylate bypass enzymes, as well as genes involved in hydrogen sulphide metabolism and in pathogen pattern recognition. Our results point towards hypoxia as a probable driver of this transcriptomic response, providing a molecular basis to previous work that identified hypoxia as a primary cause of tissue necrosis in sediment-stressed corals. Potential metabolic and immunity trade-offs of corals living under chronic sedimentation should be considered in future studies on the ecology and conservation of turbid reefs.

Spatio-temporal dynamics of coral-macroalgal interactions and their impacts on coral growth on urbanised reefs

Interactions between corals and macroalgae are important in influencing benthic community structures on coral reefs and have become increasingly common occurrences. However, little is known about their temporal variation as most studies have only documented them from single surveys. To investigate the dynamics of coral-macroalgal interactions, we surveyed three urbanised reefs in Singapore bi-monthly for three years. We found that the frequency of coral-macroalgal interactions varied greatly across sites and seasons. The extent of coral-macroalgal contact was positively correlated with macroalgal abundance, but the correlation differed significantly among macroalgal genera. The growth rates of Goniopora, Montipora and Pavona corals, but not Platygra, were also negatively correlated with the extent of macroalgal interactions. Overall, our results highlight that coral-macroalgal interactions are spatially and temporally dynamic, with varying effects among coral species. It is critical to consider seasonal fluctuations of macroalgae if the overall long-term impacts of macroalgae are to be understood.

Seeing through sedimented waters: environmental DNA reduces the phantom diversity of sharks and rays in turbid marine habitats

BACKGROUND

Sharks and rays are some of the most threatened marine taxa due to the high levels of bycatch and significant demand for meat and fin-related products in many Asian communities. At least 25% of shark and ray species are considered to be threatened with extinction. In particular, the density of reef sharks in the Pacific has declined to 3-10% of pre-human levels. Elasmobranchs are thought to be sparse in highly urbanised and turbid environments. Low visibility coupled with the highly elusive behaviour of sharks and rays pose a challenge to diversity estimation and biomonitoring efforts as sightings are limited to chance encounters or from carcasses ensnared in nets. Here we utilised an eDNA metabarcoding approach to enhance the precision of elasmobranch diversity estimates in urbanised marine environments.

RESULTS

We applied eDNA metabarcoding on seawater samples to detect elasmobranch species in the hyper-urbanised waters off Singapore. Two genes-vertebrate 12S and elasmobranch COI-were targeted and amplicons subjected to Illumina high-throughput sequencing. With a total of 84 water samples collected from nine localities, we found 47 shark and ray molecular operational taxonomic units, of which 16 had species-level identities. When data were compared against historical collections and contemporary sightings, eDNA detected 14 locally known species as well as two potential new records.

CONCLUSIONS

Local elasmobranch richness uncovered by eDNA is greater than the seven species sighted over the last two decades, thereby reducing phantom diversity. Our findings demonstrate that eDNA metabarcoding is effective in detecting shark and ray species despite the challenges posed by the physical environment, granting a more consistent approach to monitor these highly elusive and threatened species.

Natural experiments and long-term monitoring are critical to understand and predict marine host-microbe ecology and evolution

Marine multicellular organisms host a diverse collection of bacteria, archaea, microbial eukaryotes, and viruses that form their microbiome. Such host-associated microbes can significantly influence the host’s physiological capacities; however, the identity and functional role(s) of key members of the microbiome (“core microbiome”) in most marine hosts coexisting in natural settings remain obscure. Also unclear is how dynamic interactions between hosts and the immense standing pool of microbial genetic variation will affect marine ecosystems’ capacity to adjust to environmental changes. Here, we argue that significantly advancing our understanding of how host-associated microbes shape marine hosts’ plastic and adaptive responses to environmental change requires (i) recognizing that individual host–microbe systems do not exist in an ecological or evolutionary vacuum and (ii) expanding the field toward long-term, multidisciplinary research on entire communities of hosts and microbes. Natural experiments, such as time-calibrated geological events associated with well-characterized environmental gradients, provide unique ecological and evolutionary contexts to address this challenge. We focus here particularly on mutualistic interactions between hosts and microbes, but note that many of the same lessons and approaches would apply to other types of interactions.

This Essay argues that in order to truly understand how marine hosts benefit from the immense diversity of microbes, we need to expand towards long-term, multi-disciplinary research focussing on few areas of the world’s ocean that we refer to as “natural experiments,” where processes can be studied at scales that far exceed those captured in laboratory experiments.

A centuries-old manmade reef in the Caribbean does not substitute natural reefs in terms of species assemblages and interspecific competition

With increasing maritime activities in the proximity of coral reefs, a growing number of manmade structures are becoming available for coral colonisation. Yet, little is known about the sessile community composition of such artificial reefs in comparison with that of natural coral reefs. Here, we compared the diversity of corals and their competitors for substrate space between a centuries-old manmade structure and the nearest natural reef at St. Eustatius, eastern Caribbean. The artificial reef had a significantly lower species richness and fewer competitive interactions than the natural reef. The artificial reef was dominated by a cover of crustose coralline algae and zoantharians, instead of turf algae and fire corals on the natural reef. Significant differences in species composition were also found between exposed and sheltered sites on both reefs. Our study indicates that even a centuries-old manmade reef cannot serve as a surrogate for natural reefs.

Turbid Coral Reefs: Past, Present and Future—A Review

Increasing evidence suggests that coral reefs exposed to elevated turbidity may be more resilient to climate change impacts and serve as an important conservation hotspot. However, logistical difficulties in studying turbid environments have led to poor representation of these reef types within the scientific literature, with studies using different methods and definitions to characterize turbid reefs. Here we review the geological origins and growth histories of turbid reefs from the Holocene (past), their current ecological and environmental states (present), and their potential responses and resilience to increasing local and global pressures (future). We classify turbid reefs using new descriptors based on their turbidity regime (persistent, fluctuating, transitional) and sources of sediment input (natural versus anthropogenic). Further, by comparing the composition, function and resilience of two of the most studied turbid reefs, Paluma Shoals Reef Complex, Australia (natural turbidity) and Singapore reefs (anthropogenic turbidity), we found them to be two distinct types of turbid reefs with different conservation status. As the geographic range of turbid reefs is expected to increase due to local and global stressors, improving our understanding of their responses to environmental change will be central to global coral reef conservation efforts.

Experimental Techniques to Assess Coral Physiology in situ Under Global and Local Stressors: Current Approaches and Novel Insights

Coral reefs are declining worldwide due to global changes in the marine environment. The increasing frequency of massive bleaching events in the tropics is highlighting the need to better understand the stages of coral physiological responses to extreme conditions. Moreover, like many other coastal regions, coral reef ecosystems are facing additional localized anthropogenic stressors such as nutrient loading, increased turbidity, and coastal development. Different strategies have been developed to measure the health status of a damaged reef, ranging from the resolution of individual polyps to the entire coral community, but techniques for measuring coral physiology in situ are not yet widely implemented. For instance, while there are many studies of the coral holobiont response in single or limited-number multiple stressor experiments, they provide only partial insights into metabolic performance under more complex and temporally and spatially variable natural conditions. Here, we discuss the current status of coral reefs and their global and local stressors in the context of experimental techniques that measure core processes in coral metabolism (respiration, photosynthesis, and biocalcification) in situ, and their role in indicating the health status of colonies and communities. We highlight the need to improve the capability of in situ studies in order to better understand the resilience and stress response of corals under multiple global and local scale stressors.

Among-genotype responses of the coral Pocillopora acuta to emersion: implications for the ecological engineering of artificial coastal defences

Stony corals are promising transplant candidates for the ecological engineering of artificial coastal defences such as seawalls as they attract and host numerous other organisms. However, seawalls are exposed to a wide range of environmental stressors associated with periods of emersion during low tide such as desiccation and changes in salinity, temperature, and solar irradiance. All of these variables have known deleterious effects on coral physiology, growth, and fitness. In this study, we performed parallel experiments (in situ and ex situ) to examine among-genotype responses of Pocillopora acuta to emersion by quantifying growth, photophysiological metrics (F_v/F_m, non-photochemical quenching [NPQ], endosymbiont density, and chlorophyll [chl] a concentration) and survival, following different emersion periods. Results showed that coral fragments emersed for longer durations (>2 h) exhibited reduced growth and survival. Endosymbiont density and NPQ, but not F_v/F_m and chl a concentration, varied significantly among genotypes across different durations of emersion. Overall, the ability of P. acuta to tolerate emersion for up to 2 h suggests its potential to serve as a 'starter species' for transplantation efforts on seawalls. Further, careful characterisation and selection of genotypes with a high capacity to withstand emersion can help maximise the efficacy of ecological engineering using coral transplants.

Hong Kong's subtropical scleractinian coral communities: Baseline, environmental drivers and management implications

We surveyed 41 sites to provide an updated baseline of Hong Kong coral communities. Five community types were identified, among them the most common one inhabited oceanic waters and dominated by both massive and upward-plating corals. The 41 sites had 2.1-⁠79% coral cover; among them 21 in the eastern waters had >40% coral cover. Corals in several sites showed signs of external bioerosion or bleaching-induced damage. Sites in the southern waters had low coral cover. Both coral cover and generic richness correlated negatively with several water quality parameters including total inorganic nitrogen concentration and turbidity, indicating the development of Hong Kong's coral communities is constrained by water quality parameters. Management actions are proposed to reduce bioerosion, and to monitor sites affected by bleaching.

Coral community composition and carbonate production in an urbanized seascape

Coastal urbanization causes environmental modifications that directly and indirectly influence the distribution and functioning of coral reefs. However, the capacity of urban infrastructure to support corals and vertically accrete is less understood. Here, we investigated if coral communities on reefs and seawalls in Singapore are distinct, and examined the environmental variables influencing coral carbonate production. Surveys at 22 sites yielded 134 coral species, with richness significantly higher on reefs. Coral cover and Shannon index did not differ between habitat types. Community composition was distinct between habitat types, with seawalls supporting a higher proportion of massive and thick-plating species. 'Distance from mainland' was the single most important variable influencing normalized carbonate production rates (a function of species-specific linear extension rate and skeletal bulk density and site coral cover), which were higher further from the mainland where human activity and development pressures were greater. Our results indicate that environmental filtering strongly shapes coral communities and may influence ecosystem functioning in Singapore's urbanized reef system. The findings will guide the management of reefs on increasingly urbanized coastlines.

Uranium-thorium dating of coral mortality and community shift in a highly disturbed inshore reef (Weizhou Island, northern South China Sea)

Inshore coral habitats are at high risk of loss due to a combination of climate warming and regional-scale human impacts. As a result, they have undergone significant declines. Direct evidence of acute and chronic disturbance on most inshore coral assemblages is limited. Long-term, periodical surveys and historical baseline data essential for effective management are lacking. Using high-precision uranium-thorium (UTh) dating, we reconstruct a ~100-year-long history of extensive coral loss, changes in coral community structure, and a shifting baseline. The data were collected at Weizhou Island, northern South China Sea (SCS), which has highly disturbed inshore coral habitats that are typical globally. According to our UTh dates, major coral mortalities around Weizhou Island have occurred since the 1950s, with increasing frequency and severity since the 1980s. The extensive loss of branching Acropora and collapse of coral communities with peaks around 1960, 1984, and 1998 are accompanied by a shift toward low coral cover and noncoral-dominated assemblages. Prior to this collapse, the local coral community structure sustained remarkable long-term stability over millennia. The timing of the Acropora loss and massive coral mortalities coincides with multiple acute and chronic, natural and anthropogenic disturbance events. We suggest that priority should be given to directly addressing the causes of degradation and effectively controlling chronic disturbances before attempting to restore reef ecosystems. This is probably the only way to solve the "wicked problem" of sustaining the key functions and ecosystem services of inshore coral habitats such as those of Weizhou Island, northern SCS.

Community structure and size-frequency distribution of soft corals in a heavily disturbed reef system in northwestern Philippines

Soft corals in the Philippines have received little attention. In this study, community structure and size-frequency distribution of soft corals were assessed via quantitative surveys in a heavily disturbed reef system in northwestern Philippines. Relationships between selected environmental parameters and benthic components were also investigated. Results reveal that soft coral cover, density, and taxa richness were lowest at stations nearest a fish farming area, characterized by the poorest water quality. Differences in dominance of taxonomic groups may indicate differences in environmental preference or tolerance. Exposure to waves and water clarity were determined to have high correlations with the distribution of different taxa. Symmetrical size distributions of selected alcyoniids were indicative of healthy populations. However, the negative skewness of Lobophytum may indicate an eventual population decline caused by unfavorable environmental conditions. The study's findings suggest the need to conduct a detailed analysis of the different soft coral variables during coral reef surveys to improve data interpretations necessary for coral reef management in the Philippines.

Reproduction in Urbanised Coastal Waters: Shallow-Water Sea Anemones (Entacmaea quadricolor and Stichodactyla haddoni) Maintain High Genetic Diversity and Panmixia

Sea anemones are sedentary marine animals that tend to disperse via planktonic larvae and are predicted to have high population connectivity in undisturbed habitats. We test whether two sea anemone species living in two different tidal zones of a highly disturbed marine environment can maintain high genetic connectivity. More than 1000 loci with single-nucleotide polymorphisms (SNPs) were obtained with double-digest RADseq for 81 Stichodactyla haddoni and 99 Entacmaea quadricolor individuals to test for population genetic structure. We find evidence that both species predominantly propagate via sexual reproduction, and asexual reproduction is limited. We observe panmixia that indicates the absence of effective dispersal barriers for these species living in a highly anthropogenically disturbed environment. This is positive news for both species that are also found in the aquarium trade. More fundamentally, our results suggest that inhabiting different parts of a shallow reef may not affect a species’ population connectivity nor favour asexual reproduction.

Synergic effect of global thermal anomalies and local dredging activities on coral reefs of the Maldives

We investigated possible synergic effects on coral reefs of the local land reclamation activities in the Himmafushi Island (North Malè atoll, Maldives) and the global bleaching event that affected the Maldives in 2016. A BACI (Before-After Control-Impact) sampling design was adopted to contrast effects of dredging activities before and after the occurrence of both dredging and bleaching. The Reef Check protocol, a standardised and worldwide survey method, was applied to collect data through underwater visual surveys on corals, macro-zoobenthos, and fish communities. The bleaching in 2016 hit all the reefs investigated, but only in the reefs around Himmafushi (i.e., the impact sites) the live hard coral reduced significantly its cover and the sand deposited on reefs showed a fourfold increase. Substrate indicators (i.e., coral community and abiotic components) turned out to be more effective than macro-zoobenthos and fish in this short-term environmental impact study.

Population dynamics and growth rates of free-living mushroom corals (Scleractinia: Fungiidae) in the sediment-stressed reefs of Singapore

The reefs of Singapore provide an excellent opportunity to study the population dynamics and growth rates of free-living mushroom corals (Fungiidae) under sediment-stressed conditions. Transect surveys at four study sites revealed a total of 11 free-living mushroom coral species-the same 11 species as those found by local studies since the 1980s. The abundance of the four most common species ranged from 1.0 to 68.3 Ind. per 100m², while their population size-structure showed a common pattern of a higher proportion of small-sized corals than large-sized ones (i.e. positively skewed size-structure), although very few individuals of the smallest-size classes were recorded for any of the four species. A more positively skewed size-structure for each of the four most common species was observed at the reef slope (5-6m depth) than at the reef crest (2-3m depth), possibly due to a slower growth rate caused by light reduction with depth. All the mushroom corals studied exhibited a decline in growth rate with increasing size and weight, indicating determinate growth. Growth rate of each of the four most common species was similar among the study sites, despite variation in environmental conditions. Our results demonstrate species richness stability over the past three decades, suggesting that these free-living mushroom coral assemblages comprise species that are well-adapted to the chronic high sedimentation characteristic of Singapore's reefs. However, if the paucity of individuals of the smallest-size classes reflects poor recruitment and/or early mortality, there may be some cause for concern. Our robust baseline data can contribute to a long-term monitoring strategy for determination of changes in mushroom coral population dynamics.