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Synchronous multispecific coral spawning generally occurs annually and forms an integral part of the coral life cycle. Apart from spawning times and species participation, however, much else remains unknown. Here, we applied environmental DNA (eDNA) metabarcoding to study two tropical reef sites of contrasting coral cover before, during and after coral spawning. Using coral‐ITS2 and vertebrate‐12S markers, we evaluated eDNA as an alternative monitoring tool by assessing its capabilities in detecting spawning species and tracking relative abundances of coral and fish eDNA. Over 3 years, elevated eDNA coral signals during the event (proportional read increase of up to five‐fold) were observed, detecting a total of 38 coral and 133 fish species with all but one of the coral species visually observed to be spawning. This is also the first demonstration that eDNA metabarcoding can be used to infer the diurnal partitioning of night‐ and day‐time spawning, spawning in coral species overlooked by visual surveys, and the associated changes in fish trophic structures as an indicator of spawning events. Our study paves the way for applied quantitative eDNA metabarcoding approaches to better study ephemeral and important biological events. [ABSTRACT FROM AUTHOR]

• Understanding spatial and temporal trends of diversity is crucial for conservation. • This study analyses long-term data from 1986 to 2020 on Singapore reefs. • Taxonomic and phylogenetic diversity increased but functional diversity declined. • Reefs shifted towards dominance of stress-tolerant traits such as slow growth. • Trait-based approaches at finer taxonomic resolution will enhance reef monitoring. Coral reefs provide a multitude of ecosystem functions owing to the high levels of biodiversity they host. Coral species, as the foundation of shallow-water reefs, differ in their contributions toward the functioning of the ecosystem due in part to the disparate phylogenetic histories of scleractinian lineages. Understanding the spatial patterns and temporal trajectories of these biodiversity facets, as well as their interrelationships, is critical for more targeted conservation strategies in the face of widespread habitat degradation and climate change. Here, we analyse long-term benthic data spanning 1986 through 2020 on coral reefs in Singapore, which have been impacted by decades of urbanisation-related and thermal stressors, to test for differences between coral biodiversity facets—specifically, taxonomic, phylogenetic (evolutionary relatedness between species), and functional (occupancy of functional trait space) richness and diversity. Analyses show that taxonomic and phylogenetic richness and diversity measures increased over the 35-year period despite declines during major bleaching events. Yet, while taxonomic and phylogenetic diversity increased, functional richness and diversity declined over the same period. Community-weighted trait measures indicate a shift towards dominance of more stress-tolerant traits such as slower growth rates, smaller corallite sizes, and massive colony forms. Together, these trends highlight the effects of chronic urban stressors alongside major bleaching events impacting reef assemblages. Critically, such assemblage shifts and functional diversity declines were masked by increasing taxonomic diversity, which is most commonly assessed, and could erode ecosystem resilience. The temporal decoupling of the biodiversity facets examined here underscore the need for more comprehensive monitoring of reefs through a combination of trait-based approaches alongside traditional field surveys at finer taxonomic resolution. [ABSTRACT FROM AUTHOR]

Rapid urbanization has resulted in the loss of coastal and marine habitats in cities worldwide. The effective conservation of urban coastal ecosystems requires detailed knowledge of their spatial distribution, necessitating high-resolution mapping. Our study produces a high-resolution coastal and marine habitat map and shoreline map for the tropical city-state of Singapore created through pixel-based supervised classification of satellite imagery, bathymetry data and expert ground knowledge. These maps can be used as a base reference for multiple applications including ecological research, conservation and urban planning. They also help identifiy trends in the extent of key coastal habitats, providing insight into their differing levels of vulnerability to loss and potential for restoration to ensure long-term resilience. The method used for mapping shoreline typologies and resulting insights gained, can guide other rapidly urbanizing coastal cities on strategies to assemble useful spatial knowledge for effective conservation of their urban coastal ecosystems. [ABSTRACT FROM AUTHOR]

Discovered in 1819 in the tropical waters off Singapore, the magnificent Neptune's cup sponge Cliona patera (Hardwicke, 1820) was harvested for museums and collectors until it was presumed extinct worldwide for over a century since 1907. Recently in 2011, seven living individuals were rediscovered in Singapore with six relocated to a marine protected area in an effort to better monitor and protect the population, as well as to enhance external fertilisation success. To determine genetic diversity within the population, we sequenced the complete mitochondrial genomes and nuclear ribosomal DNA of these six individuals and found extremely limited variability in their genes. The low genetic diversity of this rediscovered population is confirmed by comparisons with close relatives of C. patera and could compromise the population's ability to recover from environmental and anthropogenic pressures associated with the highly urbanised coastlines of Singapore. This lack of resilience is compounded by severe predation which has been shrinking sponge sizes by up to 5.6% every month. Recovery of this highly endangered population may require ex situ approaches and crossbreeding with other populations, which are also rare. [ABSTRACT FROM AUTHOR]

Reefs in Southeast Asia, such as those in Indonesia's Riau archipelago, are among the most diverse habitats in the sea, but limited baseline data pose a severe challenge for their conservation. Here, we surveyed five reef sites along the northern coast of Bintan Island to determine the most recent condition of the benthic and fish communities. Fourteen years of resort development on the island have elapsed since the last survey in 1993. Using several diversity measures to compare the reefs then and in 2007, we found that abundances of hard corals and fish remained high (average of >50% coral cover and >0.7 fish/m3), but taxonomic richness was compromised. The most common taxa now account for greater proportions of fish counts at all sites and of coral cover at three of four comparable sites. These shifts in coral and fish assemblages may be explained by freshwater influences and development along the north coast of Bintan Island. Because the local community and tourism industry still rely heavily on the reefs, we advocate implementing a comprehensive, integrated coastal management plan that mitigates further reef declines and promotes sustainable use. [ABSTRACT FROM AUTHOR]

The American charru mussel Mytella strigata (Hanley, 1843) is an invasive species of great concern along the shores of North America and Asia. As with most invasive mussels, it is very difficult to eradicate once established. Surveillance therefore plays a vital role in controlling its spread. Molecular tools like environmental DNA (eDNA) have proved to be useful in recent years to assist in the early detection and management of invasive species, with considerable advantages over conventional methods like substrate monitoring and sampling, which can be relatively laborious and time-intensive. This technique can be particularly useful in the initial stages of invasion when the population density is often too low to be detected by visual surveys alone. In the present study, we developed a species-specific quantitative polymerase chain reaction (qPCR) approach targeting a cytochrome c oxidase subunit I (COI) DNA fragment aimed at detecting the presence of M. strigata from water samples. We also investigated the relationship between mussel cover and eDNA concentration. Our approach was tested on coastal seawater samples from 14 sites in Singapore, supported by conventional visual quadrat surveys. The results showed clear, positive M. strigata eDNA detection for all sites where this species was observed visually during field surveys. However, there was a weakly negative correlation between percent mussel cover and eDNA concentration, indicating that mussel abundance could not be estimated reliably using seawater eDNA alone. Nevertheless, this study underscores the effectiveness of eDNA in informing the presence and distribution of M. strigata along extensive coastlines comprising different habitats. This approach contributes to a robust toolkit for routine surveillance at sites where invasion may be impending to control the spread of the invasive mussel. [ABSTRACT FROM AUTHOR]

Impending anthropogenic climate change will severely impact coastal organisms at unprecedented speed. Knowledge on organisms' evolutionary responses to past sea‐level fluctuations and estimation of their evolutionary potential is therefore indispensable in efforts to mitigate the effects of future climate change. We sampled tens of thousands of genomic markers of ~300 individuals in two of the four extant horseshoe crab species across the complex archipelagic Singapore Straits. Carcinoscorpius rotundicauda Latreille, a less mobile mangrove species, has finer population structure and lower genetic diversity compared with the dispersive deep‐sea Tachypleus gigas Müller. Even though the source populations of both species during the last glacial maximum exhibited comparable effective population sizes, the less dispersive C. rotundicauda seems to lose genetic diversity much more quickly because of population fragmentation. Contra previous studies' results, we predict that the more commonly sighted C. rotundicauda faces a more uncertain conservation plight, with a continuing loss in evolutionary potential and higher vulnerability to future climate change. Our study provides important genomic baseline data for the redirection of conservation measures in the face of climate change and can be used as a blueprint for assessment and mitigation of the adverse effects of impending sea‐level rise in other systems. [ABSTRACT FROM AUTHOR]

• This study presents one of the first agent-based models to evaluate dispersal potential of seagrass vegetative fragments. • Vegetative fragments could be an effective mode of dispersal for pioneer species Halophila ovalis. • Vegetative fragments from Halophila ovalis had similar establishment patterns to seeds from Thalassia hemprichii and established at greater distances on average. • Most meadows around Singapore are well connected locally and regionally, regardless of the mode of dispersal. Understanding how populations in the marine environment exchange genetic material is vital for the implementation of suitable conservation measures. However, dispersal can be challenging to empirically assess as it can occur over huge distances. Increasingly, agent-based models (ABMs) are being used to predict the dispersal pathways of populations of many taxa, including seagrasses. Most seagrass ABMs have been based on sexual propagules (i.e. fruits, seeds, spathes), and overlook the potential role of asexual vegetative fragments in long-distance dispersal. In this study, we developed two contrasting ABMs, one for vegetative fragments and another for fruits and seeds using Halophila ovalis and Thalassia hemprichii respectively as model species, to evaluate (i) the dispersal potential of these two dispersal strategies, and (ii) the local and regional seagrass connectivity around Singapore. Our models demonstrate that vegetative fragments could be an effective mode of dispersal for H. ovalis , having similar establishment patterns to T. hemprichii fruits/seeds and establishing at greater distances on average. The models also show that most meadows are well connected locally and regionally, regardless of the mode of dispersal. The ABMs identified possible source and sink meadows that should be conserved to provide a repository of genetic material, as well as a supply of propagules for recruitment. We highlight the need to include vegetative fragments alongside sexual propagules when evaluating seagrass connectivity in future modeling efforts. [ABSTRACT FROM AUTHOR]

Suspended and deposited sediments can negatively impact coral health by reducing light penetration and smothering coral tissue. As coral sediment thresholds vary among species and between locations, setting sediment thresholds for the management of activities that increase sediment loads continues to be a challenging goal. Static threshold values used to date do not take into account temporal and spatial variations in a coral’s ability to acclimate to high sediment loads leading to either management approaches that are overly conservative or do not protect corals. This study presents a numerical model that quantifies the relationship between coral photosynthesis and growth potential under varying turbidity-driven light regimes. The model accounts for coral acclimation potential as well as a dynamic energy transfer between host and symbiont using field data collected from nearshore reefs in Singapore combined with both established and novel mathematical relationships. The model yielded photosynthetic and respiratory outputs that were comparable to in situ data collected, illustrating the predictive capability of modelling coral growth potential to declines in light driven by suspended sediments. The inclusion of more than one coral species into the model allows for variations in responses to sediments among different coral morphologies and taxa, and will strengthen the predictive capacity for management of sediment related events. As demonstrated here, the model can be used to identify least risk scenarios for dredging operations as a means of both conserving coral reefs as well as ensuring cost-effective management practices. [ABSTRACT FROM AUTHOR]

• Bacterial communities are temporally dynamic whereas Symbiodiniaceae are stable in an equatorial reef system. • No monsoonal or environmental effect on any directional shifts in bacterial communities. • Partnerships between bacteria and Symbiodiniaceae members are associated with biogeochemical and physiological processes. • Long-term studies shed insight into holobiont community dynamics and are critical in guiding restoration efforts. Coral-associated bacteria and Symbiodiniaceae are critical for maintaining the health of their coral hosts. Factors that are known to affect the coral microbiome include biogeography, seasonality, and environmental change, but longitudinal studies are sorely lacking. Many temporal studies rarely extend beyond a year, limiting the conclusions that can be drawn. In this study, we characterised both the bacterial and Symbiodiniaceae communities in three species of corals— Merulina ampliata , Pachyseris speciosa , and Porites lutea —found in an equatorial reef over a two-year period. Furthermore, we investigated the effect of monsoon seasons on the pattern of bacterial and Symbiodiniaceae communities using metabarcoding methods. We found significant differences in bacterial communities through time and space, but no consistent patterns of diversity between seasons and environmental conditions (temperature and rainfall) were observed. Conversely, Symbiodiniaceae communities did not differ over time and space. Taken together, our results suggest that bacterial communities, even within a stable climate regime, were highly dynamic through time, but were not affected by monsoonal variations. Finally, network analyses of bacteria and Symbiodiniaceae revealed multiple potential biogeochemical processes that worked in tandem between the members of the coral holobiont to support holobiont functioning. Longitudinal studies on host-associated microbial diversity are critical for drawing relevant conclusions about the long-term effects of environmental change on the coral holobiont, and for directing conservation efforts. [ABSTRACT FROM AUTHOR]

We studied the plankton dynamics of two semi-enclosed marine coastal inlets of the north of Jurong Island separated by a causeway (SW Singapore; May 2012–April 2013). The west side of the causeway (west station) has residence times of ca. one year and is markedly eutrophic. The east side (east station) has residence times of one month and presents lower nutrient concentrations throughout the year. The higher nutrient concentrations at the west station did not translate into significantly higher concentrations of chlorophyll a , with the exception of some peaks at the end of the South West Monsoon. Microzooplankton were more abundant at the west station. The west station exhibited more variable abundances of copepods during the year than did the east station, which showed a more stable pattern and higher diversity. Despite the higher nutrient concentrations at the west station (never limiting phytoplankton growth), the instantaneous phytoplankton growth rates there were generally lower than at the east station. The phytoplankton communities at the west station were top-down controlled, largely by microzooplankton grazing, whereas those of the east station alternated between top-down and bottom-up control, with mesozooplankton being the major grazers. Overall, the trophic transfer efficiency from nutrients to mesozooplankton in the eutrophic west station was less efficient than in the east station, but this was mostly because a poor use of inorganic nutrients by phytoplankton rather than an inefficient trophic transfer of carbon. Some hypotheses explaining this result are discussed. [ABSTRACT FROM AUTHOR]

Coral bleaching events have been predicted to occur more frequently in the coming decades with global warming. The susceptibility of corals to bleaching during thermal stress episodes is dependent on many factors and an understanding of these underlying drivers is crucial for conservation management. In 2013, a mild bleaching episode ensued in response to elevated sea temperature on the sediment-burdened reefs in Singapore. Surveys of seven sites highlighted variable bleaching susceptibility among coral genera–Pachyseris and Podabacia were the most impacted (31% of colonies of both genera bleached). The most susceptible genera such as Acropora and Pocillopora, which were expected to bleach, did not. Susceptibility varied between less than 6% and more than 11% of the corals bleached, at four and three sites respectively. Analysis of four of the most bleached genera revealed that a statistical model that included a combination of the factors (genus, colony size and site) provided a better explanation of the observed bleaching patterns than any single factor alone. This underscored the complexity in predicting the coral susceptibility to future thermal stress events and the importance of monitoring coral bleaching episodes to facilitate more effective management of coral reefs under climate change. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]