Machine-Learning-Based Proteomic Predictive Modeling with Thermally-Challenged Caribbean Reef Corals

Coral health is currently diagnosed retroactively; colonies are deemed “stressed” upon succumbing to bleaching or disease. Ideally, health inferences would instead be made on a pre-death timescale that would enable, for instance, environmental mitigation that could promote coral resilience. To this end, diverse Caribbean coral (Orbicella faveolata) genotypes of varying resilience to high temperatures along the Florida Reef Tract were exposed herein to elevated temperatures in the laboratory, and a proteomic analysis was taken with a subset of 20 samples via iTRAQ labeling followed by nano-liquid chromatography + mass spectrometry; 46 host coral and 40 Symbiodiniaceae dinoflagellate proteins passed all stringent quality control criteria, and the partial proteomes of biopsies of (1) healthy controls, (2) sub-lethally stressed samples, and (3) actively bleaching corals differed significantly from one another. The proteomic data were then used to train predictive models of coral colony bleaching susceptibility, and both generalized regression and machine-learning-based neural networks were capable of accurately forecasting the bleaching susceptibility of coral samples based on their protein signatures. Successful future testing of the predictive power of these models in situ could establish the capacity to proactively monitor coral health.

The coral reef health at surrounding blue swimming crab fishery sites in Mandangin Island, East Java, Indonesia

Blue swimming crab fishery activities very often do not put into account the environmental condition. Coral reef, as one of the blue swimming crab habitats, can be affected by these activities. This study aims to determine the effect of blue swimming crab fisheries on coral health in Mandangin Island, East Java, Indonesia. Data collection points are determined based on the results of interviews by participatory mapping. Water quality data includes visibility, temperature, salinity, pH, DO, current velocity. Collecting coral reef data were using Line Intercept Transect (LIT), while for reef fish Underwater Visual Census (UVC) were used. The coral health index was determined based on the relevance between benthic components and fish components. The average of Mandangin Island’s water quality is in accordance with the quality standards of the Indonesian Minister of Environment Decree No.51 of 2004. Hard coral cover and fish biomass are classified as low, but the value of resilience is high. The coral reef health index value on Mandangin Island is 3.

Coral diseases of mushroom coral (Fungiidae) in Pari Island, Kepulauan Seribu, Jakarta

Coral disease is one of the causes of the decline in the condition of coral reef ecosystems. This study aims to measure coral health based on the abundance and prevalence of coral health categories. The research was conducted in the Pari Island Cluster, Seribu Islands at four stations. The Belt Transect method with 2 × 100 meters was used to calculate coral health and a 30 m Line Intercept Transect (LIT) with three replications to determine substrate cover. The condition of coral reefs can be categorized as moderate to good based on this percentage value. The study results found five genera from the Fungiidae, namely Fungia, Ctenactis, Herpolitha, Heliofungia, and Sandalolitha. The most commonly found genus is the genus Fungia. The health condition of Fungiidae corals in Pari Island is divided into two categories, namely 35% healthy and 65% unhealthy, consisting of changes in tissue color - white (coral bleaching), changes in tissue color - not white (yellow band disease), and compromised health (damage by sedimentation). Yellow band disease is only found in the genus ˆ and is not found in other genera.

DIVE SITE ATTRACTIVENESS INDEX (DSAI) AS AN INNOVATION IN SCUBA DIVING TOURISM: A CASE OF PERHENTIAN ISLANDS

Dive sites which are home to various forms of marine life, unique structures and corals have become the main attraction for scuba divers. Divers normally choose the most attractive diving sites by visiting dive centers or getting referrals from other divers. However, there is problem in conventional subjective judgments where no standard measures have been considered. As a result, the judgments on dive site attractiveness may satisfy some divers but not others. To avoid these uncertainties, this research innovatively developed the world’s first index model for the attractiveness a dive site. Eight factors have been carefully selected, namely visibility, current stability, uniqueness of underwater scenery, coral health, the immensity of the coral reef, diversity and density of marine life. Then, these identified factors were ranked and assessed by using an Analytical Hierarchy Process (AHP) and Evidential Reasoning (ER). Finally, all dive sites are indexed so it can be compared with others for better decision-making. To test the applicability of this proposed model, 22 dive sites in Perhentian Island were successfully assessed, indexed, and mapped. Terumbu Tiga (T3), Sail Rock and Tokong Laut were indexed as the top three dive sites in Perhentian Islands. The results also showed that the most profound factor that determined the attractiveness of a dive site was the diversity of its marine life followed by the diversity of its coral species, and the uniqueness of its underwater scenery. Practically, this model can be applied and widely used for indexing all dive sites in the world based on decision-makers’ preferences. It is expected that this index model will benefit divers, dive centers, marine parks, and related agencies by providing a new information that can be used in marine tourism.

Microbiome restructuring: dominant coral bacterium Endozoicomonas species display differential adaptive capabilities to environmental changes

Bacteria in the coral microbiome play a crucial role in determining coral health and fitness, and the coral host often restructures its microbiome composition in response to external factors. An important but often neglected factor determining this microbiome restructuring is the capacity of microbiome members to adapt to a new environment. To address this issue, we examined how the microbiome structure of Acropora muricata corals changed over 9 months following a reciprocal transplant experiment. Using a combination of metabarcoding, genomics, and comparative genomics approaches, we found that coral colonies separated by a small distance harbored different dominant Endozoicomonas related phylotypes belonging to two different species, including a novel species, Candidatus Endozoicomonas penghunesis 4G, whose chromosome level (complete) genome was also sequenced in this study. Furthermore, the two dominant Endozoicomonas species showed varied adaptation capabilities when coral colonies were transplanted in a new environment. The differential adaptation capabilities of dominant members of the microbiome can a) provide distinct advantages to coral hosts when subjected to changing environmental conditions and b) have positive implications for future reefs.

Analysis of composition and abundance of viral communities associated with coral \(\textit{Acropora formosa}\)

Coral reefs harbor the extraordinary biodiversity and not only provide livelihoods for coastal communities but also play a crucial role in economic development generally. Unfortunately, they are in decline in Vietnam and around the world because mass coral bleaching events have become more common worldwide. However, little is discovered, about viruses that infect corals and their symbionts. Herein, we present metagenomic analyses of the viral communities in coral mucus associated with healthy and bleached coral Acropora formosa which was collected at Con Dao Island, Vietnam. Interestingly, the number of viral species in bleached specimens are higher than those in healthy status. Viruses similar to those that infect humans and some marine animals also appeared in the coral viral assemblage. The results indicated that the proportion of shared viruses were quite small, and represented extremely abundance. Among the phage identified, vibriophage and cyanophage were only presented in healthy and bleached coral, respectively. Therefore, coral-associated viruses could prospectively infect all constituents of the holobiont - coral, microalgal and microbial. Thus, we expect viruses to be illustrated prominently in the preservation and breakdown of coral health.

Asymmetric physiological response of a reef-building coral to pulsed versus continuous addition of inorganic nutrients

Coral reefs, especially those located near-shore, are increasingly exposed to anthropogenic, eutrophic conditions that are often chronic. Yet, corals under unperturbed conditions may frequently receive natural and usually temporary nutrient supplementation through biological sources such as fishes. We compared physiological parameters indicative of long- and short-term coral health (day and night calcification, fragment surface area, productivity, energy reserves, and tissue stoichiometry) under continuous and temporary nutrient enrichment. The symbiotic coral Acropora intermedia was grown for 7 weeks under continuously elevated (press) levels of ammonium (14 µmol L−1) and phosphate (10 µmol L−1) as separate and combined treatments, to discern the individual and interactive nutrient effects. Another treatment exposed A. intermedia twice-daily to an ammonium and phosphate pulse of the same concentrations as the press treatments to simulate natural biotic supplementation. Press exposure to elevated ammonium or phosphate produced mixed effects on physiological responses, with little interaction between the nutrients in the combined treatment. Overall, corals under press exposure transitioned resources away from calcification. However, exposure to nutrient pulses often enhanced physiological responses. Our findings indicate that while continuous nutrient enrichment may pose a threat to coral health, episodic nutrient pulses that resemble natural nutrient supplementation may significantly benefit coral health and physiology.