Coral Reef Research Articles

Improving Underwater Photogrammetric 3D Reconstruction Processing of Shipwreck Sites

Abstract. Applying image processing algorithms to enhance the clarity of underwater images can significantly assist in the visual interpretation of subsea environments. Taking advantage of techniques to maximise the information extracted from the captured input data to produce the highest quality output ensures a higher utilisation of the valuable recorded content which may have been collected at the high cost of a laborious diver survey or an expensive ROV (Remotely Operated Vehicle) expedition. Adopting photogrammetric 3D reconstruction processing in underwater imaging has enabled the creation of high-fidelity digital 3D models which have been used to map subsea infrastructure for maintenance and repair, coral reefs for ecological monitoring, and in the primary context of this article, shipwrecks sites for maritime archaeology and accident investigation. Alongside exploring algorithms to reduce the characteristic haze of underwater photography, this article illustrates the advantages of optimising the processes utilised at distinct stages of the photogrammetric 3D reconstruction workflow to improve the photorealism of the digital 3D models.

Unifying Coral Reef States Through Space and Time Reveals a Changing Ecosystem

ABSTRACTAimEcological state shifts that alter the structure and function of entire ecosystems are a concerning consequence of human impact. Yet, when, where and why discrete ecological states emerge remains difficult to predict and monitor, especially in high‐diversity systems. We sought to quantify state shifts and their drivers through space and time in the most ecologically complex marine ecosystem: tropical coral reefs.LocationWorldwide.Time Period1987–2019.Major Taxa StudiedCoral reef communities.MethodsUsing a global dataset of 3375 coral reef surveys, along with 13 time series datasets ranging between 1987 and 2019, we applied a novel double‐dichotomy approach to classify coral reefs into four simplified and discrete states based on the relative contributions of corals versus algae to benthic cover and small‐bodied versus large‐bodied fishes to fish standing stock. We then examined state shifts considering a range of spatial predictors and tested whether states have shifted directionally over time, and the nature of the most common transitions.ResultsWe show that geographic, environmental and anthropogenic context fundamentally shapes coral reef states at the local scale, which explains disparities among case studies, and stakes out critical baseline expectations for regional management efforts. We also reveal clear multi‐decadal state shifts on coral reefs: over time, systems dominated by reef‐building corals and small‐bodied, planktivorous fishes tend to have been replaced with reefs characterised by algae and larger‐bodied fishes.Main ConclusionsOur results suggest a previously unrecognised transition from systems that harness external subsidies through small‐bodied consumers associated with structurally complex live corals, to herbivore‐dominated systems with stronger bottom‐up dynamics. Overall, the partitioning of complex reef ecosystems into a small suite of discrete ecological states suggests that spatial context‐dependency, shifting baselines and changes in reef functioning are crucial considerations for coral reef management in the 21st century.

Risk assessments of microplastic exposure in bivalves living in the coral reefs of Vietnam

This study aimed to assess the presence of microplastics in bottom sediment and bivalve species, including Pinna bicolor, Atrina vexillum, Saccostrea sp., and Pinctada margaritifera, living in coral reefs on Vietnam's Southern coastal. The average microplastic abundance were 0.45 ± 0.13 items/g of wet soft tissue weight or 5.60 ± 1.49 items/individual in bivalve samples and 294 ± 43 items/kg dry weight of sediment samples. The fragment shape, size smaller than 100 μm, and polyethylene, polyamide, cellophane and polyethylene terephthalate were identified as the predominant constituents of the microplastics. The pollution load and potential ecological risk index of microplastics were at a minor level, whereas the polymer hazard index was at a high level. Overall, this study provides a basis for assessing the risks posed by microplastics in the marine ecosystems of Vietnam.

Differential spatio-temporal responses of Red Sea coral reef benthic communities to a mass bleaching event

Understanding how coral reefs respond to disturbances is fundamental to assessing their resistance and resilience, particularly in the context of climate change. Due to the escalating frequency and intensity of coral bleaching events, it is essential to evaluate spatio-temporal responses of coral reef communities to disentangle the mechanisms underlying ecological changes. Here, we used benthic data collected from 59 reefs in the Red Sea over five years (2014–2019), a period that encompasses the 2015/2016 mass bleaching event. Reefs were located within three different geographic regions with different environmental settings: north (Duba; Al Wajh), central (Jeddah; Thuwal), and south (Al Lith; Farasan Banks; Farasan Islands). Coral community responses were region-specific, with communities in the south being more promptly affected than those in the northern and central regions, with hard and soft coral cover dropping drastically in several reefs from around > 40% to < 5% two years after bleaching. Coral bleaching effects were particularly evident in the decrease of cover in branching corals. Overall, we documented a shift towards a dominance of macroalgae, turf algae, and crustose coralline algae (CCA). Using remote sensing data, we analyzed sea surface temperature (SST) regimes at the study sites to infer potential drivers of changes in benthic composition. Both SST and Degree Heating Weeks (DHW) only partially aligned with the responses of benthic communities, highlighting the need for more accurate predictors of coral bleaching in the Red Sea. In times of intense coastal development along Saudi Arabia’s Red Sea coast, our study provides crucial baseline information on developments in coral reef community composition, as well as to guide decision-making, namely restoration efforts.

A Circulation Study Based on the 2022 Sino–Vietnamese Joint Survey Data from the Beibu Gulf

This study analyzed the horizontal and vertical distribution characteristics of temperature and salinity in the central and eastern regions of the Beibu Gulf, based on conductivity measurements in summer 2022, temperature, and depth (CTD) measurement data from the Sino–Vietnamese cooperative project “Demonstration Study on Ecological Protection and Management in Typical Bays: Seasonal Survey of the Beibu Gulf”. Furthermore, the study utilized the computational results from the numerical Finite-Volume Coastal Ocean Model (FVCOM) to elucidate the intrinsic patterns that formed the temperature and salinity distribution characteristics in August 2022 from both thermodynamic and dynamic perspectives. The circulation in the Beibu Gulf drives external seawater to move northward from the bay mouth. During this movement, numerous upwelling areas are created by lateral Ekman transport. The formation of different scales of cyclonic and anticyclonic vortices and current convergence zones is influenced by topography, runoff, and the water flux from the Qiongzhou Strait, which are key factors in the formation of upwelling and downwelling. The surface circulation in August 2022 significantly differed from the 20-year average surface circulation, with an influx of 1.15 × 104 m3/s more water entering the Beibu Gulf compared to the multi-year average. The water flux from the Qiongzhou Strait is a critical factor affecting the circulation patterns in the Beibu Gulf. The northeastern waters of the Beibu Gulf are characterized by current convergence zones, where extensive upwelling occurs. The rich nutrient salts in these areas promote the reproduction and growth of phytoplankton and zooplankton, making this the most favorable ecological environment in the Beibu Gulf and serving as a natural reserve for fisheries, coral reefs, dugongs, and Bryde’s whales.

Coral diversity and abundance patterns at the West Coast of Sabah: a case study of Kota Kinabalu coral reefs

Coral diversity and abundance patterns at the West Coast of Sabah: a case study of Kota Kinabalu coral reefs

Comprehensive biodiversity assessment of flora and fauna along the Kedah coastline: Implications for conservation and sustainable management

Preserving the unique ecosystems of specific coastal areas is crucial for environmental health and the welfare of local communities. This study explores the rich biodiversity of flora and fauna along the Kedah state coastline, a 440 km stretch along the Strait of Malacca. Through meticulous site surveys and comprehensive data collection across multiple locations, followed by laboratory analyses, this research reveals a vibrant tapestry of life. The Kedah coastal area boasts a remarkable diversity, with 60 fish species identified, predominantly from the Carangidae (12 %) and Mugilidae (10 %) families. Additionally, five marine mammal species were documented, though turtles and terrapins were notably absent. The condition of coral reefs varied, with "fair" conditions observed at stations St-1 and St-2 (31.67 % and 35.67 % live coral, respectively), and "poor" conditions at St-3 (10.67 % live coral). High densities of phytoplankton, zooplankton, macrobenthos, and seaweed were recorded, whereas seagrass vegetation was absent. The study on Kedah’s coastal flora and fauna revealed a diverse range of species, including fish, marine mammals, corals, phytoplankton, zooplankton, macrobenthos, and seaweed. Coral reefs were found to be in varying conditions, with some needing restoration. The study recommends long-term monitoring, seasonal surveys, and focused research on key species. Habitat protection, community awareness, and sustainable practices are also emphasized to preserve the ecological balance of these marine environments. Moreover, the findings of this study provide a critical understanding of the Kedah coastal ecosystem and offer valuable insights for local authorities to develop effective conservation strategies. This research underscores the importance of preserving biodiversity to maintain ecological balance and support sustainable development in coastal regions.

Multiple negative impacts of marine plastic pollution on tropical coastal ecosystem services, and human health and well-being

There is limited empirical evidence showing the impacts of marine plastic pollution on ecosystem services or on human health and well-being in Global South countries. We aimed to estimate these impacts in the tropical archipelago of Indonesia, one of the top emitters of marine plastics globally, through an iterative Delphi survey, with an expert panel (n = 42) consisting of equal numbers of Indonesian scientists, policymakers, and practitioners. After two rounds of the survey, the analysis of interquartile ranges indicated that the experts reached a consensus in their predictions. The experts agreed that, over the next 10 years, plastics would be mainly accumulated in the coastal area of Java, the most densely populated island, and mostly in mangrove ecosystems. While all ecosystem services were harmed by plastic pollution, the most vulnerable services were food provisioning, genetic materials, nursery habitat, and recreation supplied by the highly vulnerable coastal ecosystems of, in descending order, mangrove, coral reef, seagrass, and sandy beach. These impacts on ecosystem services influenced different dimensions of human health and well-being and were dependent on the ecosystem types, as indicated in several statistically significant positive correlations (Spearman's rank), including those between the decline of mangrove ecosystem services and reduced household income, and between the decrease of coral reef ecosystem services and both deteriorating mental health and reduced household income. Overall, this study provides the first indication of Indonesian coastal ecosystems and ecosystem services to be prioritized for mitigation and monitoring efforts. The focus on impacts on human health and well-being also incentivizes ongoing efforts by policymakers, industry and commerce, the third sector, and the public in the country to address the contribution to global marine plastic pollution.

Vibrio cholerae: a fundamental model system for bacterial genetics and pathogenesis research.

Species of the Vibrio genus occupy diverse aquatic environments ranging from brackish water to warm equatorial seas to salty coastal regions. More than 80 species of Vibrio have been identified, many of them as pathogens of marine organisms, including fish, shellfish, and corals, causing disease and wreaking havoc on aquacultures and coral reefs. Moreover, many Vibrio species associate with and thrive on chitinous organisms abundant in the ocean. Among the many diverse Vibrio species, the most well-known and studied is Vibrio cholerae, discovered in the 19th century to cause cholera in humans when ingested. The V. cholerae field blossomed in the late 20th century, with studies broadly examining V. cholerae evolution as a human pathogen, natural competence, biofilm formation, and virulence mechanisms, including toxin biology and virulence gene regulation. This review discusses some of the historic discoveries of V. cholerae biology and ecology as one of the fundamental model systems of bacterial genetics and pathogenesis.

Prior heat stress increases pathogen susceptibility in the model cnidarian Exaiptasia diaphana

Anthropogenic climate change has significantly altered terrestrial and marine ecosystems globally, often in the form of climate-related events such as thermal anomalies and disease outbreaks. Although the isolated effects of these stressors have been well documented, a growing body of literature suggests that stressors often interact, resulting in complex effects on ecosystems. This includes coral reefs where sequential associations between heat stress and disease have had profound impacts. Here we used the model cnidarian Exaiptasia diaphana to investigate mechanisms linking prior heat stress to increased disease susceptibility. We examined anemone pathogen susceptibility and physiology (symbiosis, immunity, and energetics) following recovery from heat stress. We observed significantly increased pathogen susceptibility in anemones previously exposed to heat stress. Notably, prior heat stress reduced anemone energetic reserves (carbohydrate concentration), and activity of multiple immune components. Minimal effects of prior heat stress on symbiont density were observed. Together, results suggest changes in energetic availability might have the strongest effect on pathogen susceptibility and immunity following heat stress. The results presented here provide critical insight regarding the interplay between heat stress recovery and pathogen susceptibility in cnidarians and are an important first step towards understanding temporal associations between these stressors.

Calcification and growth of the reef coral Porites panamensis in a shallow hydrothermal field in the Gulf of California, Mexico

Calcification and growth of the reef coral Porites panamensis in a shallow hydrothermal field in the Gulf of California, Mexico

Distinct bacterial and eukaryotic communities reflect the specificity of different coral reefs in the South China Sea

The microbial composition of surrounding waters is crucial for the health of coral reefs and holds significant value for understanding the complexity and environmental adaptability of coral reef ecosystems. This study reveals the spatial heterogeneity and diversity characteristics of bacterial and eukaryotic communities in different coral reef regions of the South China Sea. Chao and Shannon indices showed significant differences (p < 0.05) in diversity of bacterial and eukaryotic communities across different coral reefs. PCoA (principal coordinate analysis) indicates significant differences in community composition among regions, highlighting the crucial role of coral reef environmental heterogeneity on microbial community. NST (normalized stochasticity ratio) analysis indicates that community assembly in coral reef areas is more influenced by ecological stochastic processes. Major bacterial groups include Proteobacteria, Cyanobacteria, and Bacteroidota, while dominant eukaryotic groups include Dinophyceae, Apicomplexa, Bacillariophyta, Florideophyceae, Mamiellophyceae, Syndiniales, Prasino-Clade-VII, and Ascomycota, each showing significant abundance differences across coral reef regions (p < 0.05). High abundance of Rhodobacterales and Flavobacteriales are detected in all coral reef waters. Correlation analysis indicates that temperature, pH, and salinity are important factors affecting the bacterial and eukaryotic communities. This study reveals the spatial heterogeneity of microbial communities in coral reef regions of South China Sea and underscores the significant impact of marine environmental heterogeneity on community structure.

Sea cucumbers and their symbiotic microbiome have evolved to feed on seabed sediments

Sea cucumbers are predominant deposit feeders in benthic ecosystems, providing protective benefits to coral reefs by reducing disease prevalence. However, how they receive sufficient nutrition from seabed sediments remains poorly understood. Here, we investigate Holothuria leucospilota, an ecologically significant tropical sea cucumber, to elucidate digestive mechanisms underlying marine deposit-feeding. Genomic analysis reveals intriguing evolutionary adaptation characterized by an expansion of digestive carbohydrase genes and a contraction of digestive protease genes, suggesting specialization in digesting microalgae. Developmentally, two pivotal dietary shifts, namely, from endogenous nutrition to planktonic feeding, and from planktonic feeding to deposit feeding, induce changes in digestive tract enzyme profiles, with adults mainly expressing carbohydrases and lipases. A nuanced symbiotic relationship exists between gut microbiota and the host, namely, specific resident bacteria supply crucial enzymes for food digestion, while other bacteria are digested and provide assimilable nutrients. Our study further identifies Holothuroidea lineage-specific lysozymes that are restrictedly expressed in the intestines to support bacterial digestion. Overall, this work advances our knowledge of the evolutionary innovations in the sea cucumber digestive system which enable them to efficiently utilize nutrients from seabed sediments and promote food recycling within marine ecosystems.

Spatial variability of sedimentary assemblages reflects variations in bioerosion pressure of adjacent coral reefs.

The composition of coral-reef sediments is highly variable across space and time, and differences in the life histories of the dominant calcifying organisms on reefs contribute to the heterogeneity of reef sediments. Previous studies have suggested that variations in coral-reef bioerosion can influence spatial and temporal variations of sedimentary assemblages: elevated erosion rates of dead coral skeletons can trigger a pulse of coral-derived sediments and cause a shift in the dominance of sedimentary grains from coralline algae, such as Halimeda, to coral. We assessed the variability of the sedimentary composition and bioerosion rates of reefs at different spatial scales to determine the association between these two variables. We surveyed the benthic assemblages on reefs exhibiting different ecological states and collected samples of the associated sediments. We calculated the carbonate budget for each site and compared their variability at different hierarchical levels to the variability of their respective sedimentary assemblages. At the scale of sites (1-10 km), Halimeda cover was a significant predictor of the relative abundance of Halimeda grains. Both the relative abundance of coral grains and reef bioerosion rates varied significantly at the scale of locality (tens to hundreds of km), with high abundances of coral grains in the sediments coinciding with high rates of bioerosion. The main drivers of bioerosion at our localities were parrotfish assemblages dominated by large size classes of excavating species such as Sparisoma viride. Reef sediments may reflect the gross degree of bioerosion pressure that reefs experience, and historical changes in bioerosion rates could potentially be assessed by examining the sediments across temporal scales.

Importance of tides and winds in influencing the nonstationary behaviour of coastal currents in offshore Singapore

Abstract. Coastal currents significantly impact port activities, coastal landform morphodynamics, and ecosystem functioning. It is therefore necessary to understand the physical characteristics and natural variability of these currents within coastal settings. Traditional methods, such as harmonic analysis, assume stationarity of tide-driven currents and may thus not be applicable to systems modulated by variable nontidal inputs and processes. Here we deployed eight tilt current meters in shallow (&lt; 5 m) coral reef environments in southern Singapore. Tilt current meters were positioned around the reefs at the main compass bearings to analyse the spatiotemporal variability of coastal currents in the frequency domain for 1 year (March 2018 to March 2019). Tidal motions were the primary mechanism of current flow on reefs and account for between 14 % and 45 % of total variance across all sites, with diurnal currents having either a similar or greater proportion of energy compared to semidiurnal currents. The relationship between currents and wind stress was then investigated across various frequencies. There is high correlation at low frequencies during the northeast monsoon, when the Madden–Julian Oscillation (MJO) is more active, thus generating currents that propagate either in phase or ahead of the MJO. At diurnal frequencies, the interaction between P1 and K1 results in a semi-annual cycle where currents are stronger during the monsoon seasons. This interaction could help to explain the seasonal variation in correlation as well as the K1 amplitude, the latter of which could be further enhanced by the diurnal wind stress. The phase relationship between currents and wind stress is highly complex due to the variable bathymetry and could only be partially accounted for by the orientation of the coastlines relative to that of the wind. Given the importance of wind, we thus require longer time-series datasets to examine the role of atmospheric phenomena at greater timescales to improve our understanding of the variability of coastal currents.

The effect of gamified e-learning on marine ecology education: insights from Iranian maritime students

This study aimed to evaluate the effectiveness of a gamified e-learning experience in marine ecology among Iranian maritime students. A pre-test/post-test design was adopted to achieve this purpose, focussing on the gamified experience itself rather than comparing it with traditional instructional approaches. The statistical population consisted of 15 undergraduate students at a maritime institute in Tehran, Iran, who were randomly selected. Reliability tests were conducted to collect data, and the test’s validity was approved by teachers and experts in the field of environmental education. Its reliability was determined to be 0.75 using the Kuder-Richardson methodology. Participants engaged in a gamified learning experience over a 2-week period. The study highlighted the post-test results and participants’ perceptions within the gamified learning environment. The results revealed that e-learning paired with gamification had a positive impact on students’ engagement and understanding of geographically remote ecological topics, including coral reefs, mangrove forests, seagrass beds and endemic species of the regions. These findings provide valuable insights for environmental teachers, learners, authorities and curriculum developers in maritime educational systems, emphasising the potential benefits of incorporating gamified learning experiences in educational curricula.

Thoraco-abdominal Aortic Bypass in a Patient with Coral Reef Aorta

Thoraco-abdominal Aortic Bypass in a Patient with Coral Reef Aorta

Hybridization and inbreeding affect the survival of a critically endangered coral

Coral reefs face escalating pressures leading to unprecedented declines in the populations of reef-building corals.1,2 Conservation genomic studies are critical in understanding and formulating interventions to reverse such declines but thus far have only focused on a handful of broadcast-spawning species in shallow waters.3,4 The recent International Union for Conservation of Nature (IUCN) reclassification of six different brooding corals as "critically endangered"5 indicates that such species are equally threatened. However, we lack a thorough understanding of the factors underlying their decline. Here, we comprehensively examine the genetic impacts of a severe population decline in the brooding coral Helioseris cucullata, once a major contributor to Caribbean reefs but now critically endangered.6,7,8 Genome-wide sequencing of colonies across five locations revealed the presence of two distinct species, indicating that the remaining population sizes are even smaller than previously estimated. Using an exhaustive, spatially explicit sampling approach (across a total of ∼2.5 hectares), we observed extremely low genetic diversity and identified how localized dispersal, excessive inbreeding, and prevalent asexual reproduction may contribute to an extinction vortex. However, we also found evidence for recent hybridization and introgression, providing an avenue for the reintroduction of genetic diversity into both lineages. With many brooding species now under threat, these results highlight the critical need to assess the genetic processes associated with their declines so that these can be harnessed or mitigated to deliver effective conservation outcomes.

Synergistic effects of waste coral powder and metakaolin in cement pastes: Hydration, pore structure, rheology, and strength

Coral reefs are abundant in waste coral powder, and how to utilize coral powder efficiently to construct far-sea projects has become a major focus of research and engineering field, which is conducive to the development of green economy. However, existing research lacks a comprehensive and systematic investigation of the cement-coral powder-metakaolin ternary system. In this study, the hydration and rheological behavior, micromechanical and mechanical properties, and pore structure evolution of the ternary system are systematically investigated to uncover the synergistic mechanism between metakaolin and coral powder. The results indicated that, based on hydration, rheology, and mechanical properties, the recommended proportions of cement, coral powder, and metakaolin are 75 %, 10 %, and 15 %, respectively. The combination of coral powder and metakaolin effectively promotes hydration. Furthermore, it accelerates the aluminate reaction, resulting in a stronger aluminate exothermic peak immediately. In addition, metakaolin reacts with coral powder to form carboaluminate, activating the activity of the coral powder, which in turn improves the mechanical properties and pore structure of the ternary system. Moreover, metakaolin undergoes a pozzolanic reaction with calcium hydroxide, which contributes to optimizing the pore structure of the ternary system and enhancing its mechanical properties. Additionally, coral powder promotes the conversion of monosulfate to carboaluminate while inhibiting the transformation of ettringite into monosulfate. The Herschel-Bulkley model accurately simulates the dynamic rheological behavior of the ternary system. This study is highly significant and practically valuable for transforming waste coral powder into a supplementary cementitious material for the construction of the far-sea projects, providing a scientific basis for future related studies.

Utilisation of macroalgal habitats by juvenile rabbitfishes on an inshore reef

AbstractMacroalgal beds are increasingly recognised as nursery habitats for coral reef fish; however, the extent to which they are used as a source of food and/or a refuge from predation remains largely unexplored. Here, we investigate the distribution, feeding behaviour, diet, and predation risk for juvenile rabbitfish in macroalgal habitats on Orpheus Island, Great Barrier Reef. Visual surveys revealed that juvenile and adult Siganus doliatus had different among-habitat distributions with juveniles being largely restricted to the reef flat and positively associated with macroalgal cover, while adults were abundant on the reef crest. Focal feeding observations show that within macroalgal habitats, juvenile S. doliatus targeted epiphytes on Sargassum (80% of bites), with relatively few bites taken on turfs or the Sargassum itself (27% and 8%, respectively). These observations were supported by stomach content analyses with filamentous algae being the dominant item in the stomach content of both small (&lt; 4 cm total length, TL; 58%) and large juvenile S. doliatus (&gt; 4 cm TL; 47%). The stomach content of juvenile S. doliatus, S. canaliculatus, and S. spinus collected from macroalgal habitats was similar, consisting primarily of filamentous algae and detritus. We found no relationship between the abundance of potential predators and juvenile rabbitfishes across the study sites. Collectively, our results suggest that juvenile rabbitfishes are using macroalgal habitats on this, and potentially other, inshore reefs as a food source and add to a growing body of literature highlighting the importance of these habitats for the early life stages of reef fish.