Coral Reef Research Articles

Delineation of outbreak stages of the coral-killing sponge Terpios hoshinota

Outbreaks of the cyanobacteriosponge Terpios hoshinota are one of the many issues contributing to coral reef decline in the Indo-Pacific. This species occasionally undergoes local outbreaks, becoming an aggressive space competitor and overgrowing and killing zooxanthellate corals. Large outbreaks have been observed in Taiwan and the Ryukyu Islands in southern Japan. Many questions regarding the characteristics and chronology of T. hoshinota outbreaks remain unsolved. Therefore, the aim of this research was to identify outbreak stages at an outbreak site (Ogimi) on the west coast of northern Okinawa Island, Japan. We developed a novel approach to understand the chronology of outbreaks. Distinct outbreak stages were defined based on observations, in which Terpios: 1) starts overgrowing coral colonies, 2) covers a whole coral colony, 3) in the case of branching corals, causes the coral colony to collapse, and 4) the sponge is eventually overgrown by other organisms including turf algae and other sponges. Analyses were done based on photographic transects and the relative proportions of each stage were calculated. Results showed Ogimi is likely in final outbreak stages as overgrown Terpios had the highest share of all stages (57.9% and 44.9% at two outbreak sites), while smaller patches of Terpios, marking the starting point of the successional process, made up less than 1.5% of all observations. We suggest collecting such stage information during Terpios monitoring as it can allow identification of outbreaks at early stages, and potentially identify global patterns.

EDGARDO D. GOMEZ: Vignettes of an Eminent Marine Scientist and Institution Builder

Dr. Edgardo D. Gomez is recognized for his significant pioneering contributions to invertebrate biology and ecology, giant clam culture and restoration, coral reef assessment and conservation, and in the strengthening of marine science education and research. He established the Marine Science Institute and developed it from a small university center to a world-recognized institution in marine sciences. Dr. Gomez is also known for his advocacy of indigenous trees.

Metabolic complexities and heterogeneity in quorum sensing signaling molecules in bacteria isolated from black band disease in a Caribbean coral

Coral diseases contribute to the worldwide loss of coral reefs, with the Black Band Disease (BBD) being a prominent example. BBD is an infectious condition with lesions with a pigmented mat composed of cyanobacteria, sulphate-reducing, sulphide-oxidizing, and heterotrophic bacteria. We compared the heterotrophic bacterial communities of healthy and BBD-affected colonies of the Caribbean coral Orbicella faveolata using culture-dependent and -independent techniques. Twenty and 23 bacterial isolates were identified from healthy and diseased tissues, respectively, which differed in their capacities to metabolize carbohydrates and citrate, either anaerobically or aerobically. They also differed in their quorum-sensing (QS) activity, as QS signaling molecules were found exclusively, and QS-inhibition was found primarily, in isolates from diseased tissues. Screening of bacterial diversity by 16SrDNA metabarcoding showed that members of the bacterial genera Muricauda and Maritimimonas were dominant in healthy tissues whereas members of the cyanobacterial genus Roseofilum were dominant in diseased tissues. These results suggest that bacterial dysbiosis can be linked with altered bacterial communication, likely leading to diachrony and imbalance that may participate in the progression of BBD. Investigating physiological traits and QS-based communication offers insights into the onset and progression of coral infections, paving the way for novel strategies to mitigate their impact.

Replayed reef sounds induce settlement of Favia fragum coral larvae in aquaria and field environmentsa).

Acoustic cues of healthy reefs are known to support critical settlement behaviors for one reef-building coral, but acoustic responses have not been demonstrated in additional species. Settlement of Favia fragum larvae in response to replayed coral reef soundscapes were observed by exposing larvae in aquaria and reef settings to playback sound treatments for 24-72 h. Settlement increased under 24 h sound treatments in both experiments. The results add to growing knowledge that acoustically mediated settlement may be widespread among stony corals with species-specific attributes, suggesting sound could be one tool employed to rehabilitate and build resilience within imperiled reef communities.

Suva Urban Reefs: An ecological history of the coral reefs of the Greater Suva Urban Area, Fiji

Suva Urban Reefs: An ecological history of the coral reefs of the Greater Suva Urban Area, Fiji

Chatting behind the reef: Fish bioacoustic diversity of tropical back-reefs in Fiji, South Pacific.

Back-reef habitats are important and fragile transition zones acting as nurseries for many coral reef fishes. In this framework, Passive Acoustic Monitoring (PAM) can be an important tool to evaluate the diversity and dynamics of sonic fish community. Here, we investigated the diversity, spatial and diel dynamics of fish sounds in back-reef habitats at Makogai Island in Fiji, South Pacific. Synchronized underwater recorders were deployed in 4 bays collecting data for about 4 days. The abundance of 12 different sub-categories of fish sounds were quantified. Signals were acoustically characterized and the level of discrimination between the sub-categories was evaluated by Discrimination Function Analysis. Generalized Additive Models showed that the abundance of signals was related to the bay and the hour. Moreover, the Shannon Diversity and Equitability Indices were calculated using acoustic and visual census data to describe fish biodiversity of each bay. The two bays with greater biodiversity based on visual census also showed a greater acoustic diversity at dawn and night. Our results highlight the importance of PAM to reveal the diversity of fish community in back-reef habitats, providing a baseline to understand future changes in these crucial environments.

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.

Mechanism Analysis of Strengthening the Coral Reef Sand Foundation by Dynamic Compaction Method Based on Discrete Element Theory

Mechanism Analysis of Strengthening the Coral Reef Sand Foundation by Dynamic Compaction Method Based on Discrete Element Theory

ANALYSING THE POTENTIAL OF CORAL REEF ECOSYSTEMS FOLLOWING THE COVID-19 PANDEMIC IN BONDALEM, BULELENG, BALI

Coastal and marine areas have considerable biological resource potential, because they are supported by three main ecosystems, namely mangrove ecosystems, seagrass beds and coral reefs. Coral reefs are one of the coastal ecosystems that contribute greatly to coastal areas. But behind the great potential, it is also very vulnerable to damage, both caused by nature and human activities on land and in sea waters. As an effort to maintain the existence of these ecosystems, ecosystem monitoring is needed to find out how much potential is still available in the coastal area. The purpose of this study was to determine and provide information related to the potential and condition of coral reefs in Bondalem Village. This research used descriptive quantitative method with purposive sampling technique. The data taken is primary data that includes observations of coral reefs based on the form of growth (lifeform). Coral reef data collection was carried out using the UPT (Underwater Photo Transect, Underwater Photo Transect) method. The results obtained, coral reefs at the observation station have a total of 18 lifeforms. The percentage of coral cover obtained at a depth of 3 meters has a coral cover ranging from 35.34%, while at a depth of 10 meters the result of coral cover is 26.30% (medium category). The coral reef ecosystem uniformity index ranges from 0.96 - 0.97 (high). The diversity index of coral reef ecosystems in Bondalem Village ranged from 1.25 which is included in the relatively medium category (1<H'<3). The dominance index of coral reef ecosystem in Bondalem Village ranged from 0.064 - 0.066 (low).

Coral reefs of Pakistan: a comprehensive review of anthropogenic threats, climate change, and conservation status

The coral reefs along Pakistan’s coastline are of ecological and economic significance. However, they are increasingly threatened by anthropogenic threats and climate change. These vulnerable ecosystems are declining due to various factors such as sedimentation, climate change, overfishing, destructive fishing practices, marine pollution, and tourism development. We found that 29%, 24%, 26%, 16% and 18% of the studies exceeding, marine pollution, overfishing/destructive fishing, coastal tourism, climate change and sedimentation, respectively; thus, indicating inadequate water quality status in part of Pakistan coastal water. These influences lead to several negative impacts, such as jeopardized coral health, decline in biodiversity, and the simplification of reef structures. In response to these threats, conservation efforts are imperative. This literature review provides an in-depth analysis of anthropogenic threats, climate change and the conservation of coral reefs in Pakistan. This review provides suggestions on how the country could better conserve its coral reef ecosystem. These include (1) initiatives such as establishing marine protected areas (MPAs), (2) encouraging sustainable fishing practices and reducing pollution, (3) developing the country as an ecotourism destination and implementing climate change adaptation measures, and (4) community engagement through awareness campaigns and fostering collaboration among, governmental organizations, non-governmental organizations (NGOs) and scientists. These comprehensive conservation policies address human-caused and other challenges, safeguarding their ecological, economic, and cultural relevance for future generations.

Analysis on Coral Bleaching (Soft/Hard Coral) and Coral Ecosystem Restoration Strategies—Linkage to Sustainable Industries and Economic Valuation†

Among marine ecosystems, coral reefs play crucial roles in terms of ecological functions such as biodiversity protection and coastal protection and have significant economic value, estimated at approximately 2.7 trillion USD per year. However, the current state of coral reefs is alarming, with more than 93% of coral ecosystems being damaged primarily by human activity and climate change. In line with UN Sustainable Development Goals 13 and 14, this research aims to analyze coral bleaching in soft corals in Korea and coral reefs in Malaysia through field surveys and interviews to assess their current conditions. This study also explores strategies for the restoration of coral ecosystems, utilizing economic valuation methods such as the Toolkit for Ecosystem Service Site-Based Assessment (TESSA). Despite the limitations of applying a landscape-focused methodology to the marine environment and the lack of available data, this study emphasizes the importance of sustainable tourism and collaborative educational curricula involving governmental research institutes, universities, NGOs, and divers. These efforts are inspired by interactions with the Borneo Marine Research Institute (BMRI) at Sabah University and the Reef Check Center in Malaysia.

Untargeted Metabolomics Approach for the Discovery of Salinity-Related Alkaloids in a Stony Coral-Derived Fungus Aspergillus terreus

As a part of the important species that form coral reef ecosystems, stony corals have become a potential source of pharmacologically active lead compounds for an increasing number of compounds with novel chemical structures and strong biological activity. In this study, the secondary metabolites and biological activities are reported for Aspergillus terreus C21-1, an epiphytic fungus acquired from Porites pukoensis collected from Xuwen Coral Reef Nature Reserve, China. This strain was cultured in potato dextrose broth (PDB) media and rice media with different salinities based on the OSMAC strategy. The mycelial morphology and high-performance thin layer chromatographic (HPTLC) fingerprints of the fermentation extracts together with bioautography were recorded. Furthermore, an untargeted metabolomics study was performed using principal component analysis (PCA), orthogonal projection to latent structure discriminant analysis (O-PLSDA), and feature-based molecular networking (FBMN) to analyze their secondary metabolite variations. The comprehensive results revealed that the metabolite expression in A. terreus C21-1 differed significantly between liquid and solid media. The metabolites produced in liquid medium were more diverse but less numerous compared to those in solid medium. Meanwhile, the mycelial morphology underwent significant changes with increasing salinity under PDB cultivation conditions, especially in PDB with 10% salinity. Untargeted metabolomics revealed significant differences between PDB with 10% salinity and other media, as well as between liquid and solid media. FBMN analysis indicated that alkaloids, which might be produced under high salt stress, contributed largely to the differences. The biological activities results showed that six groups of crude extracts exhibited acetylcholinesterase (AChE) inhibitory activities, along with 1,1-diphenyl-2-picrylhydrazyl (DPPH) free radical scavenging and antibacterial activities. The results of this study showed that the increase in salinity favored the production of unique alkaloid compounds by A. terreus C21-1.

Comparing modeled predictions of coral reef diversity along a latitudinal gradient in Mozambique

IntroductionPredictive models based on environmental proxy data are being used to predict biodiversity on large and even global scales. Yet, some of the underlying assumptions about the relationship between proxy variables and predictions require investigations and testing the consequences of using model alternatives, data sources, variables choices, and scales, extent, and overlap among the predictions. Mozambican coral reefs provide a good case study to test these assumptions given the paucity of field data, its long coastline, and transitions from tropical to temperate environments.MethodsThree modelling formulations and 5 specific models were made using satellite and shipboard measurements and extensive fish and corals field data to test their performance in predicting numbers of fish species and coral taxa from field data. Model predictions were mapped for the 1180 ~6.25 km2 Mozambican coral reef cells. Predictions were made and mapped 1) based on ~1000 field sites in the Western Indian Ocean (WIO) faunal province model, 2) using environmental variable selected in the WIO model (WIOMOD) but trained only with Mozambican field data (<113 sites), and 3) using only Mozambican environmental and field data and standard variable redundancy and selection procedures.Results and discussionTraining and testing cross validation of models indicated modest predictive ability (R2~0.42-0.56%) and reasonable transferability. Consequently, there was unexplained variation likely due to small-scale environmental variability finer than the mapped cell scale. Differences between model predictions were caused by different variable rankings and response relationship. For example, the Mozambique-only model predicted more fish but fewer coral taxa, a larger role of water quality and sediments, habitats, and temperature variation, and a lesser role of human influence than the WIOMOD. Therefore, differences between models indicate that large scale models (i.e. provincial or global) can contribute to understanding gross patterns but miss important local environmental and human drivers in transitional environments. Nevertheless, 79% of the fish and 88% of coral taxa cell-level predictions of taxonomic diversity had standardized coefficients of variations of <10%.

Community-Based Management: Marine Tourism Development for Ecological and Economic Sustainability

This study analyzes community-based management approaches in the Kapoposang Marine Nature Tourism Park (TWAL) as a model for sustainable tourism development. The research examines how local community involvement in managing marine tourism areas enhances economic, social, and ecological sustainability. Using a mixed-method approach, the study combines qualitative and quantitative data, including interviews with stakeholders, direct observations, and surveys of local residents and tourists. Findings reveal that participatory approaches significantly enhance the effectiveness of marine ecosystem management, particularly in coral reef conservation, while also contributing to increased local income. However, challenges remain, particularly in infrastructure development, which limits tourism growth and local benefits. The study suggests strategies for maximizing Kapoposang's tourism potential through inclusive community engagement, addressing infrastructure gaps, and promoting sustainable practices. These insights offer valuable guidance for policymakers aiming to foster sustainable marine tourism and community empowerment in protected marine areas, providing a replicable model for similar regions seeking balanced development.

Coastal Chronicles: Journey into the World of Coastal Systems

Coastal systems are complex and dynamic settings where the atmosphere, sea, and land combine to create a variety of landscapes, including coral reefs, beaches, and estuaries. These areas contribute to global sustainability initiatives delineated in the United Nations Sustainable Development Goals (SDGs), sustain biodiversity, and play crucial ecological and economic roles. For sustainable management and protection of coastal environments, it is imperative to possess an understanding of the physical attributes, biological constituents, and mechanisms that dictate their dynamics. The natural processes of tides, waves, and currents impact the geomorphology of coastal systems, resulting in the formation of features including dunes, beaches, estuaries, and deltas. Coastal vegetation that stabilizes sediments and supports a variety of habitats, like seagrasses, mangroves, and salt marshes, further enriches these landscapes. Fish, crabs, mollusks, and birds are among the coastal fauna that flourish in these habitats and add to the diversity of coastal life. However, human activities that accelerate natural processes like erosion, accretion, and sea-level riseuch as industrialization, pollution, and climate change pose an increasing threat to coastal systems. Thus, it is essential to use sustainable management techniques that strike a balance between development objectives and conservation initiatives. Coastal ecosystems must be protected and enhanced through the implementation of policies like Integrated Coastal Zone Management (ICZM), habitat restoration, and Marine Protected Areas (MPAs). A combination of mitigation and adaptation strategies, such as building coastal fortifications and promoting nature-based solutions, are also necessary for climate change adaption. We can ensure the resilience and vitality of coastal systems for present and future generations, as well as their sustained ecological and economic significance in the global environment, by tackling these intricate concerns cooperatively and comprehensively.

Evaluation of carbon dioxide partial pressure and air-sea fluxes in the Sea of Marmara

The increasing impact of global warming has made it crucial to monitor greenhouse gases (GHG). Carbon dioxide (CO2) is especially important due to its significant increase. Oceans and seas play a vital role in absorbing excess CO2 from the atmosphere, but they are facing challenges such as ocean acidification and damage to coral reefs. Therefore, it's essential to thoroughly understand climate change and its human-caused effects and to take necessary precautions or improve existing measures. In this direction, in seawater, determining alkalinity is crucial for monitoring CO2, along with other physical and chemical parameters, in order to help set carbon budgets and reduce environmental pressures. For this purpose, in this study in the Sea of Marmara, alkalinity and CO2 measurements were conducted for the first time at stations CG2, CG3, MD26, and MD24. The CO2 partial pressure (pCO2) values ranged from 95 to 165 µatm at the surface of all stations, and total alkalinity values ranged from 1.075 to 1.46 mmol kg-1 at specified depths. Based on these measurements, flux values were calculated between −1.10 and −5.39 mmol m2 day-1, indicating that the Sea of Marmara acted as a net CO2 sink.

Community Structure of Fishes the Association with Seagrasses at Bama Beach, Baluran National Park, Situbondo, East Java

Seagrass bed has an important role for biota in waters. The existence of fish in seagrass is influenced by other ecosystems close to seagrass, such as mangroves and coral reefs. This study focuses on fish associated with seagrass in Bama Beach. The data include seagrass coverage and the number of fish for the Diversity, Uniformity, and Dominance. The study was carried out on March 15 to 20, 2018 using the Underwater Visual Census. Results show that seagrass cover was highest in seagrass stations near mangroves (62,66%), while at stations near coral reefs was 37,66. The composition of fish associated with seagrass near mangroves was 361 individuals, while near reefs was 1.454 individuals. The values of diversity, uniformity, and dominance of fish associated with seagrass near mangroves are 2,62; 0,88; and 0,09 respectively while those associated with coral reefs have values of 2,93; 0,85; and 0,06. Family Aulostomidae was dominant in the morning at the station near mangroves, and in the afternoon was dominated by Apogonidae. At the station near coral reefs, the Family Pomacentridae was dominant both in the morning and afternoon. The seagrass conditions in this study are in the healthy category with quite diverse fishes. The level of fish diversity in seagrass was influenced by habitats associated with seagrasses than seagrass cover levels. The condition of Bama Beach as a conservation area is quite good, but the activity of tourists around the coastline must be monitored to maintain the environment.

The role of mesoscale-driven connectivity patterns in coral recovery around Moorea and Tahiti, French Polynesia

Coral reefs are declining due to anthropogenic warming. Nonetheless, some have recovered quickly from repeated bleaching events. Coral recovery depends on adaptation capabilities, fishing pressure, overall number of stressors, reef conditions before the event, and degree of connectivity. Coral reefs that are connected to many others can receive viable larvae and regain coverage faster. Around Moorea and Tahiti, within the Society Islands of French Polynesia, coral cover has regained its previous levels rapidly, despite several mass bleaching events over the past three decades. Here it is explored whether the connectivity with distant reefs may support such recovery by modeling the transport of coral larvae around the islands over 28 years. Ocean currents enable connectivity with the Tuamotu Islands, ~ 250 km to the northeast, that act as sources to Moorea and Tahiti for pelagic larval durations of three weeks or longer. The circulation around Moorea and Tahiti is very dynamic; mesoscale eddies can also halt the connectivity with the Tuamotu Islands and sporadically transport larvae from reefs to the west and southeast instead. With many undisturbed coral reefs within a 300 km radius and strong mesoscale variability, a dynamic, long-range connectivity may explain the recovery of reefs around Moorea and Tahiti.

Climate adaptive loci revealed by seascape genomics correlate with phenotypic variation in heat tolerance of the coral Acropora millepora

One of the main challenges in coral reef conservation and restoration is the identification of coral populations resilient under global warming. Seascape genomics is a powerful tool to uncover genetic markers potentially involved in heat tolerance among large populations without prior information on phenotypes. Here, we aimed to provide first insights on the role of candidate heat associated loci identified using seascape genomics in driving the phenotypic response of Acropora millepora from New Caledonia to thermal stress. We subjected 7 colonies to a long-term ex-situ heat stress assay (4 °C above the maximum monthly mean) and investigated their physiological response along with their Symbiodiniaceae communities and genotypes. Despite sharing similar thermal histories and associated symbionts, these conspecific individuals differed greatly in their tolerance to heat stress. More importantly, the clustering of individuals based on their genotype at heat-associated loci matched the phenotypic variation in heat tolerance. Colonies that sustained on average lower mortality, higher Symbiodiniaceae/chlorophyll concentrations and photosynthetic efficiency under prolonged heat stress were also the closest based on their genotypes, although the low sample size prevented testing loci predictive accuracy. Together these preliminary results support the relevance of coupling seascape genomics and long-term heat stress experiments in the future, to evaluate the effect size of candidate heat associated loci and pave the way for genomic predictive models of corals heat tolerance.

An advanced early warning technology for coral bleaching crisis based on the electrochemical biosensing of coral-symbiotic zooxanthellae eDNA

The symbiotic zooxanthellae in corals are extremely sensitive to the marine environment, and corals bleach rapidly when the symbiotic zooxanthellae are detached from their coral hosts. Currently, ecological monitoring techniques face many problems in coral health assessment, especially coral reef destruction during sampling. In this paper, an electrochemical eDNA biosensor based on ECM/MoS2 nanocomposites constructed with specific DNA probes was developed to detect the environmental DNA of free zooxanthellae at a low limit of detection (LOD = 0.223 pM) and limit of quantification (LOQ = 0.743 pM) under the experimentally optimized conditions, demonstrating excellent specificity and steadiness. Over and above, the electrochemical response of the biosensor to zooxanthellae DNA was significantly higher than that of other interferent targets, proving its high selectivity. On this basis, the dependability and precision of the biosensor were further verified by comparing the biosensor with ddPCR (P > 0.05, RSD < 5 %). Hence, this electrochemical biosensor can dynamically monitor community changes in zooxanthellae without destroying coral reefs and may serve as a non-invasive method for early warning of coral reef crises. The technique can also be upgraded with portable capabilities in future studies to provide greater convenience in the field analysis of coral bleaching.