Coral Reef Ecology Research Articles

MPA-FishMApp – A Citizen Science App That Simplifies Monitoring of Coral Reef Fish Density and Biomass in Marine Protected Areas

Monitoring changes in fish density and biomass inside marine protected areas (MPAs) through fish visual census (FVC) can determine if MPAs are achieving their goal of promoting fish population recovery. Simplified FVC methods have been developed for citizen scientists to enable them to monitor fish populations in MPAs. However, MPA monitoring programs led by local stakeholders remain rare and difficult to sustain due to technical barriers related to FVC data management. Here, we describe and evaluate a novel online app called MPA-FishMApp, which we developed to help stakeholders of MPAs that protect coral reefs in the Philippines efficiently store, analyze, and visualize FVC data. MPA-FishMApp is coupled to a simplified FVC method wherein the observer records only 21 reef fish species groups during surveys. The app provides a simple data entry interface, cloud storage, and algorithms to estimate fish density and biomass. Spatial and temporal trends in fish density and biomass can be instantaneously visualized in the app based on relative importance to fisheries. Field testing suggested that the MPA-FishMApp methodology (simplified FVC and app) is sensitive enough to detect qualitative patterns showing differences in density and biomass that may develop between MPAs and fished sites, especially in fishes that are highly important to fisheries. However, users must have sufficient training and experience in simplified FVC to produce reliable data. MPA-FishMApp may help reverse the lack of monitoring in MPAs across the Philippines and offers an accessible, transparent, and auditable venue for collaboration between citizen scientists and professional scientists.

Digitizing the coral reef: Machine learning of underwater spectral images enables dense taxonomic mapping of benthic habitats

Abstract Coral reefs are the most biodiverse marine ecosystems, and host a wide range of taxonomic diversity in a complex spatial community structure. Existing coral reef survey methods struggle to accurately capture the taxonomic detail within the complex spatial structure of benthic communities. We propose a workflow to leverage underwater hyperspectral image transects and two machine learning algorithms to produce dense habitat maps of 1150 m2 of reefs across the Curaçao coastline. Our multi‐method workflow labelled all 500+ million pixels with one of 43 classes at taxonomic family, genus or species level for corals, algae, sponges, or to substrate labels such as sediment, turf algae and cyanobacterial mats. With low annotation effort (only 2% of pixels) and no external data, our workflow enables accurate (Fbeta of 87%) survey‐scale mapping, with unprecedented thematic detail and with fine spatial resolution (2.5 cm/pixel). Our assessments of the composition and configuration of the benthic communities of 23 image transects showed high consistency. Digitizing the reef habitat and community structure enables validation and novel analysis of pattern and scale in coral reef ecology. Our dense habitat maps reveal the inadequacies of point sampling methods to accurately describe reef benthic communities.

Deciphering the disturbance mechanism of BaP on the symbiosis of Montipora digitata via 4D-Proteomics approach

The coral holobiont is mainly composed of coral polyps, zooxanthellae, and coral symbiotic microorganisms, which form the basis of coral reef ecosystems. In recent years, the severe degradation of coral reefs caused by climate warming and environmental pollution has aroused widespread concern. Benzo(a)pyrene (BaP) is a widely distributed pollutant in the environment. However, the underlying mechanisms of coral symbiosis destruction due to the stress of BaP are not well understood. In this study, diaPASEF proteomics and 16S rRNA amplicon pyrosequencing technology were used to reveal the effects of 50 μg/L BaP on Montipora digitate. Data analysis was performed from the perspective of the main symbionts of M. digitata (coral polyps, zooxanthellae, and coral symbiotic microorganisms). The results showed that BaP impaired cellular antioxidant capacity by disrupting the GSH/GSSG cycle, and sustained stress causes severe impairment of energy metabolism and protein degradation in coral polyps. In zooxanthellae, BaP downregulated the protein expression of SOD2 and mtHSP70, which then resulted in oxidative free radical accumulation and apoptosis. For coral symbiotic microorganisms, BaP altered the community structure of microorganisms and decreased immunity. Coral symbiotic microorganisms adapted to the stress of BaP by adjusting energy metabolism and enhancing extracellular electron transfer. BaP adversely affected the three main symbionts of M. digitata via different mechanisms. Decreased antioxidant capacity is a common cause of damages to coral polyps and zooxanthellae, whereas coral symbiotic microorganisms are able to appropriately adapt to oxidative stress. This study assessed the effects of BaP on corals from a symbiotic perspective, which is more comprehensive and reliable. At the same time, data from the study supports new directions for coral research and coral reef protection.

ANALYSIS OF PHOTOCHEMICAL PROFILE AND ENDOSYMBION BIOMASS OF CORAL Symbiodinium sp

Coral reefs are important ecosystems with the highest species diversity on earth. Besides its high ecological and economic value, it turns out that coral reefs are facing global climate change. One of the environmental factors affected by the effects of global climate change is the penetration of sunlight that reaches the earth's surface. Symbiodinium as a coral endosymbiont turns out to have an adaptation pattern that is correlated with environmental conditions, especially light. The research focused on the interaction between solar radiation and Symbiodinium and its biochemical profiles, which have an important meaning for coral reef ecology and its recovery when affected by excessive light. In addition, it opens up opportunities for the use of light as a triggering factor for the production of certain biochemical compounds in cells. The micro-habitat conditions in the laboratory are made in such a way that it can provide penetration of light intensity that is at the optimal or extreme threshold for Symbiodinium. The measured light intensity is expected to trigger the process of cellular adaptation and the production of certain biochemical compounds in cells. The results are expected to show that light has a significant effect on changes in the content of biochemical compounds in Symbiodinium biomass. The increase in light intensity is expected to guide cells to increase the concentration of lipids and intracellular fibers.

Long-term ecological monitoring of reefs on Hawai’i Island (2003-2020): Characterization of a common cryptic crust, Ramicrusta hawaiiensis (Peyssonneliales, Rhodophyta)

The recently described crustose calcifying red algal species Ramicrusta hawaiiensis, known only from mesophotic depths off Lehua Island, west of Kaua’i Island, was found in shallow benthic reef habitats (3-18 m deep) along the western coast of Hawai’i Island. Molecular and microscopy techniques were used for genetic confirmation and for detailed morphological and anatomical examination. Two independent benthic cover survey datasets collected from west Hawai’i Island were used to investigate temporal and geographic distribution of Ramicrusta. In both datasets, we report Ramicrusta at approximately 60% of the sites surveyed. Benthic cover for this alga varies among sites and among years and its presence in west Hawai’i is evident since at least 2003. These findings help to document Hawaiian coral reef ecosystem change and benthic community composition reshuffling. This study also emphasizes the critical importance of taxonomy and proper identification of macroalgal species to understand the potential for phase-shifts of dominant taxa in coral reef ecosystems after environmental disturbances and fluctuations in abiotic factors. In the last decade, members of the red algal order Peyssonneliales have increased in abundance and overgrown other benthic species in reef ecosystems in the Caribbean and tropical Pacific. The novel aspect of finding abundant Ramicrusta in much shallower water than originally described, the decadal presence of Ramicrusta, and its potential for competition with other benthic organisms make this research valuable to coral reef ecology and justify further investigation of Ramicrusta ecology and biology in the Hawaiian Islands and globally.

Effects of immersion and navigation agency in virtual environments on emotions and behavioral intentions

We present a study investigating the question whether and how people’s intention to change their environmental behavior depends on the degrees of immersion and freedom of navigation when they experience a deteriorating virtual coral reef. We built the virtual reef on top of a biologically sound model of the ecology of coral reefs, which allowed us to simulate the realistic decay of reefs under adverse environmental factors. During their experience, participants witnessed those changes while they also explored the virtual environment. In a two-factorial experiment (N = 224), we investigated the effects of different degrees of immersion and different levels of navigation freedom on emotions, the feeling of presence, and participants’ intention to change their environmental behavior. The results of our analyses show that immersion and navigation have a significant effect on the participants’ emotions of sadness and the feeling of helplessness. In addition, we found a significant effect, mediated by the participants’ emotions, on the intention to change their behavior. The most striking result is, perhaps, that the highest level of immersion combined with the highest level of navigation did not lead to the highest intentions to change behavior. Overall, our results show that it is possible to raise awareness of environmental threats using virtual reality; it also seems possible to change people’s behavior regarding these threats. However, it seems that the VR experience must be carefully designed to achieve these effects: a simple combination of all affordances offered by VR technology might potentially decrease the desired effects.

Wide-Area Three-Dimensional Imaging of Mesophotic Coral Reefs Using a Low-Cost AUV

Abstract Surveys and monitoring are essential to study the biology and ecology of coral reefs in order to understand the reasons behind reef demise and recovery. However, mesophotic coral ecosystems (MCEs) remain largely unknown compared to their shallow counterparts because it is difficult to observe the seafloor below 30 m depths. Here, we propose a seafloor observation method using a low-cost autonomous underwater vehicle (AUV). This method was developed to allow many people to easily perform underwater observations of MCEs, and is also applicable to general seafloor surveys, such as underwater artificial structures, hydrothermal vent fields, etc. The method possesses three important attributes to achieve effective surveys. First, it can be applied in highly rugged terrains and enables the AUV to track omnidirectional surfaces at high speed (Max. ~1 m/s). Second, it can produce a reliable three-dimensional (3D) image of the seafloor based on a depth sensor. Third, it can be used to estimate the flow velocity field. The proposed method was tested by using the AUV HATTORI-2, which is a lightweight, one-man portable AUV equipped with commercial off-the-shelf sensors. Our study area is the Sekisei Lagoon in the South Ryukyus, which represents the largest coral reef complex in Japan. The method enabled us not only to obtain a wide and high-definition 3D image of mesophotic coral reefs that captures detailed characteristics of marine habitats but also to acquire environmental data, such as flow velocity field and seawater temperature, spatially and temporally aligned with the 3D image.

A social-ecological engagement with reef passages in New Caledonia: Connectors between coastal and oceanic spaces and species

Healthy and protected coral reefs help island systems in the tropics thrive and survive. Reef passages link the open ocean to lagoon and coastal areas in these ecosystems and are home to an exceptionally diverse and abundant marine life, hosting emblematic species and fish spawning aggregations. Their multiple benefits for the islands and their peoples (e.g., for transport, fishing, socio-cultural aspects) remain yet understudied. Drawing from qualitative interviews with fishers, scuba divers, and surfers along the coast of Grande Terre in New Caledonia, this study highlights the multi-faceted importance of these keystone places. It shows that reef passages are locally deemed ‘communication zones’ between coastal and oceanic spaces and species, and have significant un(der)explored ecological and socio-cultural roles. Understanding and protecting these ecological and cultural keystone places will strengthen both the reef ecosystems and the people dependent on them.

Evolutionarily Ancient Caspase-9 Sensitizes Immune Effector Coelomocytes to Cadmium-Induced Cell Death in the Sea Cucumber, Holothuria leucospilota.

Heavy-metal pollution has increasingly jeopardized the habitats of marine organisms including the sea cucumber, a seafloor scavenger vital to seawater bio-decontamination, ocean de-acidification and coral-reef protection. Normal physiology including immune functions of sea cucumbers is toxicologically modulated by marine metal pollutants such as cadmium (Cd). The processes underpinning Cd’s toxic effects on immune systems in the sea cucumber, Holothuria leucospilota, are still poorly understood. To this end, we cloned and characterized a full-length caspase-9 (Hl-CASP9) cDNA in the sea cucumber, Holothuria leucospilota. Hl-CASP9 mRNA levels evolved dynamically during embryonic development. Coelomocytes, a type of phagocytic immune effectors central to H. leucospilota immunity, were found to express Hl-CASP9 mRNA most abundantly. Hl-CASP9 protein structurally resembles caspases-2 and -9 in both invertebrate and vertebrate species, comprising a CARD domain and a CASc domain. Remarkably, Hl-CASP9 was transcriptionally sensitive to abiotic oxidative stress inducers including hydrogen peroxide (H2O2), nitric oxide (•NO) and cadmium (Cd), but insensitive to immunostimulants including lipopolysaccharide (LPS), and poly(I:C). Overexpression of Hl-CASP9 augmented mitochondria-dependent apoptosis in HEK293T cells, while knock-down of Hl-CASP9 blunted Cd-induced coelomocyte apoptosis in vivo. Overall, we illustrate that an evolutionarily ancient caspase-9-dependent pathway exists to sensitize coelomocytes to premature cell death precipitated by heavy metal pollutants, with important implications for negative modulation of organismal immune response in marine invertebrates.

Prevalence and extent of coral diseases in shallow and mesophotic reefs of the Southwestern Atlantic

Coral reef ecology has advanced in many fields, but disease patterns across depth gradients remain unclear. By comparing the prevalence and extent of bleaching and diseases in 160 colonies of Siderastrea stellata between shallow and mesophotic reefs, we observed that prevalence was high (75%) regardless of depth, but the extent was about two times greater in mesophotic than shallow reefs (14.4% vs. 6.6% of colony area, respectively). Across the shallow reefs, where S. stellata co-occurred with Montastraea cavernosa, M. cavernosa showed lower prevalence (27% of 30 colonies) and extent (1.8% of colony area) compared to S. stellata. Besides bleaching, five coral diseases afflicted S. stellata and two affected M. cavernosa. Because diseases are spread over the entire gradient of depth, any attempt of managing the diseases should consider both shallow and deep reefs to be effective.

International Symposium on New Frontiers in Reef Coral Biotechnology (5 May 2022, Taiwan)

Given the global threats towards coral reefs, this conference’s central theme, “Reef coral biotechnology”, is particularly timely. Our goal is to promote communication and dialogue in this field among marine researchers within and outside of Taiwan, and we have invited experts in the fields of coral reef ecology, physiology, conservation, and biotechnology to discuss their recent findings with a cadre of both local and foreign scientists, as well as students (undergraduate, Master’s, and Ph.D. students). We envision that these presentations will segue into discussions and collaborations that stimulate innovation in reef coral biotechnology, and particularly in the development of tools and approaches that improve the odds of conserving coral reefs and biopreserving reef corals.

Pengenalan Ekosistem Terumbu Karang Terhadap Amgpm Cabang Elim 1 – Amahusu Ambon

The coral reef ecosystem in Amahusu village has been damaged, resulting in reduced production of fisheries and other animal products. This damage is continuously caused by natural and unnatural factors, so that it can disrupt the economy of fishing communities who depend on marine products for their daily lives. The purpose of this activity is to equip the Maluku Protestant Church Youth Troops (AMGPM) Nusaniwe sub- district, the basics of coral conservation through coral reef restoration activities. Coral transplantation is a method of restoring the condition of coral reefs to restore and restore the natural ecosystem of coral reefs. The methods include: introduction of coral transplantation, preparation and process of coral transplantation. The introduction of coral biota is the most basic thing that the public must know in order to understand the potential and role of corals in the coral reef ecosystem. In addition, the community is gradually being taught how to use the correct transplant method, hopefully in the future they will be independent and able to do it themselves. Coral transplantation is one method of coral reef restoration in Amahusu Village. This presentation is a deep understanding of the community that with significant assistance they are expected to be independent in protecting coral reefs.

Coral and it's symbionts responses to the typical global marine pollutant BaP by 4D-Proteomics approach

The symbiosis of corals, zooxanthellae, and microbes is the foundation of the coral reef ecosystem. In addition to global warming, marine pollutants are another important factor causing the breakdown of coral symbiosis. Benzo(a)pyrene (BaP) is a globally widespread marine environmental pollutant that poses a severe threat to marine ecosystems. However, responses of coral symbionts to global marine pollutant stress remain unclear. In this study, we selected Acropora formosa as the target coral to explore its response to 50 μg L−1 BaP stress using diaPASEF proteomics and 16s rRNA microbiome analysis. The results showed that: 1) the coral symbionts were sensitive to BaP stress; 2) the photosynthetic system of zooxanthellae was crucial for the balance of symbiotic relationships; 3) the destruction of the photosynthetic system induced a zooxanthellae hypoxic stress response; 4) corals adapted to BaP stress by promoting non-essential protein degradation and changing energy metabolism strategies; 5) symbiotic bacteria showed strong adaptability to BaP. This study not only fills the gap in understanding the response mechanism of coral symbionts under BaP stress, but also provides fundamental data for coral reef protection strategies.

Limiting motorboat noise on coral reefs boosts fish reproductive success

Anthropogenic noise impacts are pervasive across taxa, ecosystems and the world. Here, we experimentally test the hypothesis that protecting vulnerable habitats from noise pollution can improve animal reproductive success. Using a season-long field manipulation with an established model system on the Great Barrier Reef, we demonstrate that limiting motorboat activity on reefs leads to the survival of more fish offspring compared to reefs experiencing busy motorboat traffic. A complementary laboratory experiment isolated the importance of noise and, in combination with the field study, showed that the enhanced reproductive success on protected reefs is likely due to improvements in parental care and offspring length. Our results suggest noise mitigation could have benefits that carry through to the population-level by increasing adult reproductive output and offspring growth, thus helping to protect coral reefs from human impacts and presenting a valuable opportunity for enhancing ecosystem resilience.

Evidence that Indo-Pacific bottlenose dolphins self-medicate with invertebrates in coral reefs

SummaryIndo-Pacific bottlenose dolphins (Tursiops aduncus) have been observed queueing up in natural environments to rub particular body parts against selected corals (Rumphella aggregata, Sarcophyton sp.) and sponges (Ircinia sp.) in the Egyptian Northern Red Sea. It was hypothesized that the presence of bioactive metabolites accounts for this selective rubbing behavior. The three invertebrates preferentially accessed by the dolphins, collected and analyzed by hyphenated high-performance thin-layer chromatography contained seventeen active metabolites, providing evidence of potential self-medication. Repeated rubbing allows these active metabolites to come into contact with the skin of the dolphins, which in turn could help them achieve skin homeostasis and be useful for prophylaxis or auxiliary treatment against microbial infections. This interdisciplinary research in behavior, separation science, and effect-directed analysis highlighted the importance of particular invertebrates in coral reefs, the urgent need to protect coral reefs for dolphins and other species, and calls for further vertebrate-invertebrate interaction studies.

Influence of Climate Change On Marine Species and Its Solutions

Marine species are the major components of living organisms on the Earth that have dominated nearly 90 percent of the habitat of Earth. Climate changes have changed the distribution of the marine species among the world and causing extinctions and eventually greatly impacts the whole marine ecosystem. This paper is going to discuss the impacts of climate change on marine species and what humans could do to protect the marine species under the change of the climate. This paper first introduces the global background about the climate change and how does it affects marine species. Then evaluates the whole systems to three smaller parts: fish industry, coral reefs and seagrass. The protection of coral reef and seagrass habitats are necessary to maintain the marine ecosystem. Finally the paper proposals several solutions to minimize the impacts of climate change on marine species. The advanced technology, government support and volunteer works would be essential to save the marine species from the undergoing life threatening situation. From now on, humans should stand together to protect our common habitat and save other species who share the Earth with humans. This paper is important because it evaluates the recent conditions of marine species under the climate change and it explores the potential solutions to solve the ongoing issues.

Deliberating coral reef protection – Cultural Theory tested

Cultural Theory has been tested in various ways and across different topics. This study sought to extend the literature on Cultural Theory’s prediction that different cultural biases emerge in every social interaction by applying a structured observation method to the local level but complex issue of coral reef protection in Sulawesi of Indonesia. Three deliberative approaches, Musyawarah, focus group discussions, and planning cells, were selected to encourage public discussions. Different statements on how to protect coral reefs emerged from the discussions, reflecting different cultural biases. However, this study was unable to confirm Cultural Theory’s hypothesis that four opposing cultural biases emerge within every social interaction: only hierarchical, egalitarian, and individualistic biases were strongly evident in the study; fatalism was not. In response, this paper recommends that further research replicate and improve the study’s methods.

A biological condition gradient for coral reefs in the US Caribbean Territories: Part I. Coral narrative rules

As coral reef condition and sustainability continue to decline worldwide, losses of critical habitat and their ecosystem services have generated an urgency to understand and communicate reef response to management actions, environmental contamination, and natural disasters. Increasingly, coral reef protection and restoration programs emphasize the need for robust assessment tools for protecting high-quality waters and establishing conservation goals. Of equal importance is the need to communicate assessment results to stakeholders, beneficiaries, and the public so that environmental consequences of decisions are understood. The Biological Condition (BCG) model provides a structure to evaluate the condition of a coral reef in increments of change along a gradient of human disturbance. Communication of incremental change, regardless of direction, is important for decision makers and the public to better understand what is gained or lost depending on what actions are taken. We developed a narrative (qualitative) Biological Condition Gradient (BCG) from the consensus of a diverse expert panel to provide a framework for coral reefs in US Caribbean Territories. The model uses narrative descriptions of biological attributes for benthic organisms to evaluate reefs relative to undisturbed or minimally disturbed conditions. Using expert elicitation, narrative decision rules were proposed and deliberated to discriminate among six levels of change along a gradient of increasing anthropogenic stress. Narrative rules for each of the BCG levels are presented to facilitate the evaluation of benthic communities in coral reefs and provide specific narrative features to detect changes in coral reef condition and biological integrity. The BCG model can be used in the absence of numeric, or quantitative metrics, to evaluate actions that may encroach on coral reef ecosystems, manage endangered species habitat, and develop and implement management plans for marine protected areas, watersheds, and coastal zones. The narrative BCG model is a defensible model and communication tool that translates scientific results so the nontechnical person can understand and support both regulatory and non-regulatory water quality and natural resource programs.

Law enforcement over illegal fishing to protect coral reefs during the Covid-19 pandemic in Buton

The purpose of this study was to determine the role and obstacles faced by Fishery Civil Servant Investigators (FCSI) in the prevention and handling of Fisheries Crimes in the Buton Regency. With empirical legal methods, research data were obtained from direct interviews, showing that in 2018 there were two cases of destructive fishing using the fish bombing method, three cases in 2019, namely one case of fish bombing and two cases of exploitation of protected marine habitats, while in 2020 and 2021, there were two cases of fish bombing each. The results showed that Fisheries FCSI’s role constitutes prevention and prosecution for fisheries crime involving the destruction of ships that do not have permits for fishing vessels with sizes above 5 GT, exploitation of protected fish habitats, and fishing vessels failing to demonstrate proper seaworthiness. Fisheries crime cases that occur are fishing practices that involve the destruction of fish resources and aquatic habitats such as fish bombing, fish anesthesia, and the use of cyanide poison. Law enforcement during the covid-19 pandemic over these cases is carried out online at the witness examination stage or at a stage that involves the investigation of the suspect through a video conference interview. Provided that there is a Summoning Letter, based on Article 112 of the Criminal Procedure Code, the obstacles experienced by the Fisheries FCSI are influenced by internal factors in the form of lack of quality and quantity of supervision facilities and infrastructure, human resources, budget, and poor handling of evidence. Meanwhile, external factors involve the lack of public awareness to prevent the occurrence of fisheries crime, the lack of supporting facilities and infrastructure for the Supervisory Community Group, and weak coordination between law enforcement institutions.

Genetic Diversity and Structure of Tropical Porites lutea Populations Highlight Their High Adaptive Potential to Environmental Changes in the South China Sea

Global climate change and anthropogenic disturbance have significantly degraded biodiversity in coral reef ecosystems. The genetic potential and adaptability of corals are key factors used to predict the fate of global coral reefs under climate change. In this study, we used eight microsatellite loci to study the patterns of reproduction, genetic diversity, and genetic structure of 302 Porites lutea samples across 13° latitudes in the South China Sea (8.8644°N–22.6117°N). The results indicated that P. lutea reproduces largely via sexual reproduction on scales of 5 m and greater and has abundant gene diversity. Additionally, the tropical populations harbored high genetic diversity (based on alleles, effective number of alleles, gene diversity, and heterozygosity). In contrast, genetic diversity was lower in subtropical coral populations. Genetic variation values and pairwise FST revealed that tropical and subtropical populations had significantly different genetic structures. Finally, the Mantel tests showed that the genetic differentiation and genetic variation of P. lutea were strongly correlated with sea surface temperature and slightly correlated with geographical distance. These results indicated that tropical P. lutea populations have high genetic potential and adaptability because of their sexual reproduction and genetic diversity, giving them a greater capacity to cope with climate change. Subtropical coral populations showed lower genetic diversity and, thus, relatively poor genetic resilience in response to low average sea surface temperature and human activities. Our study provides a theoretical basis for the protection and restoration of coral reefs.