Over the years, coral reefs in the South China Sea have degraded and faced severe threats from rapid development, coral bleaching, and Crown-of-Thorns Starfish (COTS) outbreak. There is limited knowledge relating to the effects of anthropogenic disturbances and natural events on the coral reefs of Pulau Layang-Layang. This study aims to assess reef cover changes by utilizing Landsat satellite images spanning from 1989 to 2022. Using the object-based image analysis method, this study classified the reef cover into three categories: coral, rock and rubble, and sand. The supervised classification had an overall accuracy of 86.41-87.38 % and Tau's coefficients of 0.80-0.81. The results showed island development and construction of artificial bird sanctuary have led to an increase in coral cover. Furthermore, it was illustrated that the impact of COTS outbreaks in 2010 and 2020 differed significantly, with the latter showing no signs of recovery. Our study underscores the importance of timely intervention to mitigate the spread of COTS. This study provides insights into the resilience and vulnerability of these ecosystems in the face of various stressors.
Vibrio coralliilyticus, a prominent pathogenic bacteria, is known to cause tissue damage in the coral Pocillopora damicornis and is attracted towards the coral via chemotaxis. However, the potential of V. coralliilyticus to infect most of the other coral hosts via chemotaxis is unknown. In this study, we used capillary assays to quantify the chemotactic response of V. coralliilyticus to the mucus of four tank-cultivated coral species (Cataphyllia jardine, Mussidae sp., Nemenzophyllia turbida, and Euphyllia ancora), and mucus from three wild coral species (Acropora sp., Porites sp., and Montipora sp.). The bacteria showed a positive chemotactic response to each coral mucus tested, with the highest response recorded to the mucus of Acropora sp. and the lowest response to the mucus of Montipora sp. A microfluidic chip was then used to assess the chemotactic preference of V. coralliilyticus to the mucus of the tank cultivated corals. Here too, the bacterium showed positive response, but with a slightly different ranking order. The strong chemotactic response of V. coralliilyticus towards the mucus tested could indicate a broader host range of V. coralliilyticus, and by extension, indicate a threat to weakened coral reefs worldwide.
Without drastic efforts to reduce carbon emissions and mitigate globalized stressors, tropical coral reefs are in jeopardy. Strategic conservation and management requires identification of the environmental and socioeconomic factors driving the persistence of scleractinian coral assemblages-the foundation species of coral reef ecosystems. Here, we compiled coral abundance data from 2,584 Indo-Pacific reefs to evaluate the influence of 21 climate, social and environmental drivers on the ecology of reef coral assemblages. Higher abundances of framework-building corals were typically associated with: weaker thermal disturbances and longer intervals for potential recovery; slower human population growth; reduced access by human settlements and markets; and less nearby agriculture. We therefore propose a framework of three management strategies (protect, recover or transform) by considering: (1) if reefs were above or below a proposed threshold of >10% cover of the coral taxa important for structural complexity and carbonate production; and (2) reef exposure to severe thermal stress during the 2014-2017 global coral bleaching event. Our findings can guide urgent management efforts for coral reefs, by identifying key threats across multiple scales and strategic policy priorities that might sustain a network of functioning reefs in the Indo-Pacific to avoid ecosystem collapse.
Eucheuma denticulatum or commonly known as "Spinosum", is an economically important red alga that naturally grows on coral reefs with moderately strong currents in tropical and sub-tropical areas. This species is the primary source of iota-carrageenan which has high demands in the food, pharmaceutical and manufacturing industries, and as such it has been widely cultivated. The increasing global demand for carrageenan has led to extensive commercial cultivation of carrageenophytes mainly in the tropics. The carrageenophyte seaweeds including E. denticulatum are indigenous to Sabah, Malaysia. To enrich the information on the genes involved in carrageenan biosynthesis, RNA sequencing has been performed and transcriptomic dataset has been generated using Illumina HiSeq™ 2000 sequencer. The raw data and transcriptomic data have been deposited in NCBI database with the accession number PRJNA477734. These data will provide valuable resources for functional genomics annotation and investigation of mechanisms underlying the regulations of genes in this algal species.
Biodiversity surveys are crucial for monitoring the status of threatened aquatic ecosystems, such as tropical estuaries and mangroves. Conventional monitoring methods are intrusive, time-consuming, substantially expensive, and often provide only rough estimates in complex habitats. An advanced monitoring approach, environmental DNA (eDNA) metabarcoding, is promising, although only few applications in tropical mangrove estuaries have been reported. In this study, we explore the advantages and limitations of an eDNA metabarcoding survey on the fish community of the Merbok Estuary (Peninsular Malaysia). COI and 12S eDNA metabarcoding assays collectively detected 178 species from 127 genera, 68 families, and 25 orders. Using this approach, significantly more species have been detected in the Merbok Estuary over the past decade (2010-2019) than in conventional surveys, including several species of conservation importance. However, we highlight three limitations: (1) in the absence of a comprehensive reference database the identities of several species are unresolved; (2) some of the previously documented specimen-based diversity was not captured by the current method, perhaps as a consequence of PCR primer specificity, and (3) the detection of non-resident species-stenohaline freshwater taxa (e.g., cyprinids, channids, osphronemids) and marine coral reef taxa (e.g., holocentrids, some syngnathids and sharks), not known to frequent estuaries, leading to the supposition that their DNA have drifted into the estuary through water movements. The community analysis revealed that fish diversity along the Merbok Estuary is not homogenous, with the upstream more diverse than further downstream. This could be due to the different landscapes or degree of anthropogenic influences along the estuary. In summary, we demonstrated the practicality of eDNA metabarcoding in assessing fish community and structure within a complex and rich tropical environment within a short sampling period. However, some limitations need to be considered and addressed to fully exploit the efficacy of this approach.
Marine mammal searches were opportunistically conducted during the East Coast Johor Scientific Expedition (ECJSE) on 21-30 May 2012, on a live-on-board (LOB) diving vessel, MV BLACK PEARL. The expedition was designed mainly to survey coral reef ecosystems and water quality. Daylight visual observations of the sea were undertaken during sailing and stopping/anchored from the most upper open-deck of the vessel. The survey resulted in two sightings of long-beaked common dolphins (Delphinus capensis), each at Pulau Aur and Pulau Tinggi. Both observations were brief (< 5 minutes) and were made when the vessel was anchored. Based on anecdotal evidences, skeletal remains and previous surveys, the vulnerable dugong, Indo-Pacific bottlenose, Indo-Pacific humpback, Irrawaddy and long-beaked common dolphins, the false killer and pygmy killer whales, and the baleen whales are known to occur in the East Coast Johor waters, at least occasionally. The low sighting rate with marine mammals during this survey is highly likely caused by the survey design and also may be due to the environmental conditions and ecological factors. Dedicated and periodical boat and aerial surveys for marine mammals need to be conducted to determine species diversity and to understand the seasonality, habitat use, and social interactions of the marine mammal populations in the area. The findings will be most useful for marine park and fisheries authorities to plan conservation management strategies for marine mammals and promote their conservation through eco-tourism activities.
Coral reefs in the northern region of the Straits of Malacca have a diverse group
of octocorals growing on its bed. The octocorals identified in this study are from islands
along the Straits. In this study, 23 specimens were identified, belonging to 4 sub-orders,
which have been subdivided into 8 families. From these 8 families, 15 different genera
have been identified. The identification process for this research was conducted based on
five important keys; the external form and colouration, polyps or colonial and fundamental
structure of colonies, monomorphic or dimorphic, the arrangement of polyps, and the
arrangement of sclerites.
Management of wild fisheries resources requires accurate knowledge on which species are being routinely exploited, but it can be hard to identify fishes to species level, especially in speciose fish groups where colour patterns vary with age. Snappers of the genus Lutjanus represent one such group, where fishes can be hard to identify and as a result fisheries statistics fail to capture species-level taxonomic information. This study employs traditional morphological and DNA barcoding approaches to identify adult and juvenile Lutjanus species harvested in Malaysian waters. Our results reveal a suite of species that differs markedly from those that have previously been considered important in the Malaysian wild-capture fishery and show that official fisheries statistics do not relate to exploitation at the species level. Furthermore, DNA barcoding uncovered two divergent groups of bigeye snapper ('Lutjanus lutjanus') distributed on either side of the Malay Peninsula, displaying a biogeographical pattern similar to distributions observed for many co-occurring reef-distributed fish groups. One of these bigeye snapper groups almost certainly represents an unrecognized species in need of taxonomic description. The study demonstrates the utility of DNA barcoding in uncovering overlooked diversity and for assessing species catch composition in a complicated but economically important taxonomic group.
Reef rubble representsthe broken components of the coraland reefstructure which could be in the form of dead,broken or other fragmented coral.The process to estimate the distribution of reef rubble is currently done manually and thus takesa long timeto completeand is laborious. This paper presentsan image-processing-basedmethod to estimate the distribution of reef rubbles in a coral reef environmentfrom a still image. The method is basically a series of image processing steps includingimage complement, image binarization, edgedetection, smoothing by Weiner filter and followed by erosion and dilation process.The experimentalresults showedthat the system wasable to roughly estimate the distribution of reef rubble.
At present, marine scientists employ manual method to estimate the components in coral reef environment,where Coral Point Count with Excel extensions (CPCe) software is used to determine the coral reef components and substrate coverage. This manual processis laboriousand time consuming,and needsexpertsto conduct the survey. In this paper, a prototype for estimating the distribution of sand cover in coral reef environment from still images by using colourextraction methods was introduced. The coloursegmentation called delta E was used to calculate the colourdifference between two coloursamples. Another method used wascolourthresholdby setting the range of sand colourpixels. Thesystem was developed by using a MATLAB software withimage processing toolbox. The developed system was semi-automatic computer-based system that can be used by researcherseven with little knowledge and experience to estimatethepercentage of sand coveragein coral reef still images.
Acropora is the most biologically diverse group of reef-building coral, and its richness peaks at the Indo-Malay-Philippine Archipelago, the centre of global coral reef biodiversity. In this paper, we describe the species richness of Acropora fauna of North Borneo, East Malaysia, based on review of literature and as corroborated by voucher specimens. Eighty-three species of Acropora are reported here; four species are literature based and 79 are supported by voucher specimens that were subsequently photographed. New records for North Borneo were recorded for 12 species, including Acropora suharsonoi Wallace 1994 that was previously thought to be confined to a few islands along Lombok Strait, Indonesia. The diversity of Acropora in North Borneo is comparable to that of Indonesia and the Philippines, despite the area's smaller reef areas. This further reinforces its inclusion as part the global hotspot of coral biodiversity.
Decommissioning of the offshore platform as an artificial reef, known as Rigs-to-Reefs (R2R), has become a sustainable approach for oil companies. The platform was reused to serve the underwater ecosystem as an artificial reef for a new marine ecosystem which helps to tackle food security issue. This paper presents the findings of the formulation of the reefing viability index to recognize an offshore region that can be used for R2R projects within the South China Sea. The combined effects of spatial data, numerical modelling, and geographic system (GIS) are proposed to study the relationship of spawning ground coral reefs, diversity, and planula larvae in the process of colonization to establish a map of the reef potential environment. Coral connectivity and spawning behaviour were studied to determine the possible source of coral seedling released during the spawning season, twice a year. A geographic reef viability index was established consisting of seven parameters which are coral larval density, pelagic larval length, sea currents, temperature, chlorophyll-a, depth, and substrate availability. The ocean hydrodynamic model was designed to resemble the pattern of larval scattering. By using the simulations and rankings, there were 95 (21%) sites which could probably be used for in situ reefing, whereas 358 (79%) sites were likely ideal for ex situ reefing. Validation of the viability index was carried out using media footage assessment of remotely operated vehicle (ROV).
A new species of Leptostraca, Nebalia terazakii sp. n. is described and figured. The species was sampled from the coral reefs of Pulau Payar Marine Park, Langkawi, Malaysia. There are 32 existing species of Nebalia but Nebalia terazakii sp. n. can be distinguished from the other known species of Nebalia by the following combination of characters: the rostrum is 1.89 times as long as wide and the eyes have no dorsal papilla or lobes. Article 4 of the antennular peduncle has one short thick distal spine. The proximal article of the endopod of maxilla 2 is shorter than the distal, a feature peculiar to Nebalia terazakii sp. n., the exopod of maxilla 2 is longer than article 1 of the endopod, the posterior dorsal borders of the pleonites 6 to 7 are provided with distally sharp denticles, anal plate with prominent lateral shoulder and finally, the terminal seta of the caudal rami is 1.17 times the length of the entire rami.
Coral reefs are rich in biodiversity and ecosystem services. However increase in degradation are still occurring at an alarming rate. In management of this ecosystem, determination of its spatial distribution is of importance. Satellite imageries can be used to map distribution extent using spectral characteristics which is a fundamental parameter in mapping. The aims of this study were to determine the spectral characteristics of corals and associated habitats and to map its spatial distribution using 2009 ALOS advanced visible and near infrared radiometer type 2 (AVNIR-2) satellite imagery. Results indicated that coral and habitats surrounding the area display variation in the spectral characteristics magnitude but displays similar spectral curve. Spectral characteristics from the corals and surrounding habitats were determined by presence of benthic microalgae and calcium carbonate. Maximum likelihood classification on the image produced five main classes. Spatial distribution of coral and associated habitats indicated five main zones which are sandy shore zone, sandy intertidal zone, seagrass zone, coral/submerged sandy zone and rocky zone. Distribution of live corals indicated coverage of 0.54 km2, sea grass (0.94 km2), sandy bottom (1.31 km2) and rocky shores (0.19 km2). The results of this study indicated that ALOS satellite data was able to determine variation in spectral characteristics of coral reefs and other habitats thus is capable of mapping the ecosystems spatial distribution.
Due to extremely high rates of evaporation and low precipitation in the Persian Gulf, discharges from desalination plants (DPs) can lead to ecological stresses by increasing water temperatures, salinities, and heavy metal concentrations, as well as decreasing dissolved oxygen levels. We discuss the potential ecological impacts of DPs on marine organisms and propose mitigating measures to reduce the problems induced by DPs discharges. The daily capacity of DPs in the Persian Gulf exceeds 11 million m3 per day, which is approximately half of global daily freshwater production; multistage flash distillation (MSF) is the dominant desalination process. Results from field and laboratory studies indicate that there are potentially serious and chronic threats to marine communities following exposure to DP discharges, especially within the zoobenthos, echinodermata, seagrasses, and coral reefs. DP discharges can lead to decreases in sensitive species, plankton abundance, hard substrate epifauna, and growth rates of seagrasses. However, the broad applicability of any one of these impacts is currently hard to scale because of the limited number of studies that have been conducted to assess the ecological impacts of DP discharge on Persian Gulf organisms. Even so, available data suggest that appropriately sited, designed, and operated DPs combined with current developments in impingement and entrainment reduction technology can mitigate many of the negative environmental impacts of DPs.
Body size influences many life-history traits, with small-bodied animals tending to have short life spans, high mortality and greater reproductive effort early in life. In this study, the authors investigated the life-history traits and reproductive strategies of three small-bodied coral reef gobies of the genus Trimma: Trimma benjamini, Trimma capostriatum and Trimma yanoi. The authors found all Trimma species studied attained a small body size of <25 mm, had a short life span of <140 days and experienced high estimated daily mortality of 3.0%-6.7%. Furthermore, the pelagic larval phase accounted for 25.3%-28.5% of the maximum life span, and maturation occurred between 74.1 and 82.1 days at 15.2-15.8 mm, leaving only 35%-43% of the total life span as a reproductively viable adult. All mature individuals had gonad structures consistent with bidirectional sex change, with bisexual gonads including both ovarian and testicular portions separated by a thin wall of connective tissue. In the female and male phases, only ovaries or testes were mature, whereas gonadal tissue of the non-active sex remained. One T. benjamini individual and one T. yanoi individual had ovarian and testicular tissue active simultaneously. The results of this study highlight the life-history challenges small CRFs face on their path to reproduction and reproductive strategies that could be beneficial in fishes with high and unpredictable mortality and short reproductive life spans.
Despite increasing threats to Tonga's coral reefs from stressors that are both local (e.g. overfishing and pollution) and global (e.g. climate change), there is yet to be a systematic assessment of the status of the country's coral reef ecosystem and reef fish fishery stocks. Here, we provide a national ecological assessment of Tonga's coral reefs and reef fish fishery using ecological survey data from 375 sites throughout Tonga's three main island groups (Ha'apai, Tongatapu and Vava'u), represented by seven key metrics of reef health and fish resource status. Boosted regression tree analysis was used to assess and describe the relative importance of 11 socio-environmental variables associated with these key metrics of reef condition. Mean live coral cover across Tonga was 18%, and showed a strong increase from north to south correlated with declining sea surface temperature, as well as with increasing distance from each provincial capital. Tongatapu, the southernmost island group, had 2.5 times greater coral cover than the northernmost group, Vava'u (24.9% and 10.4% respectively). Reef fish species richness and density were comparable throughout Tongatapu and the middle island group, Ha'apai (~35 species/transect and ~2500 fish/km2), but were significantly lower in Vava'u (~24 species/transect and ~1700 fish/km2). Spatial patterns in the reef fish assemblage were primarily influenced by habitat-associated variables (slope, structural complexity, and hard coral cover). The biomass of target reef fish was greatest in Ha'apai (~820 kg/ha) and lowest in Vava'u (~340 kg/ha), and was negatively associated with higher human influence and fishing activity. Overall mean reef fish biomass values suggest that Tonga's reef fish fishery can be classified as moderately to heavily exploited, with 64% of sites having less than 500 kg/ha. This study provides critical baseline ecological information for Tonga's coral reefs that will: (1) facilitate ongoing management and research; and (2) enable accurate reporting on conservation targets locally and internationally.
Marine litter is recognized as an increasing component of marine ecosystem pollution. In this baseline study, we document the magnitude, types, sources, and potential impacts of litter on six coral reefs in East Sabah. We applied a simplified classification of litter to extract abundance data from video transects. The average density was 10.7 items per 100 m2. Plastics represent 91% and the remaining 9% were metal, glass, and wood. Most (~70%) plastics are single-use items derived from dumping. Discarded fishing gear accounts for ~25%. Litter pollution increases closer to urban developments, with Sakar reef having higher densities (51 items per 100 m2), and higher Clean Coast Index (CCI = 10.2, dirty) and higher Plastic Abundance Index (PAI = 4.68) scores. This method could and should be readily integrated into ongoing monitoring programs to support assessments of the extent and magnitude of marine litter pollution on reefs worldwide.
Pulau Tioman is a famous tourist island off Peninsular Malaysia with beautiful coral reefs. This study aims to assess the health of the coral reefs surrounding Pulau Tioman based on the application of the Foraminifera in Reef Assessment and Monitoring Index (FI). Ten sampling sites around Pulau Tioman were studied with a total of 30 samples. Eight orders, 41 families, 80 genera, and 161 species of benthic foraminifera were identified. The agglutinated type of foraminifera constituted 2-8% of the total assemblages. Calcareous hyaline and porcelaneous groups represented 79% and 19% of the total assemblages, respectively. Symbiont-bearing taxa were the most common foraminifera. The results indicate that most of the sampling sites are conducive for coral reef growth with good recoverability from future stress to the ecosystem. However, several areas with higher coastal development and tourism have reduced water and sediment quality. Therefore, the limit on the number of visitors and tourists should be revised to enable coral growth and health. The FI values in this study showed a positive correlation with good water qualities and a negative correlation with organic matter enrichment. The FI is a good measure to assess the health of a coral reef and can be applied to other reef ecosystems around Malaysia.
Coral reefs in the Central Indo-Pacific region comprise some of the most diverse and yet threatened marine habitats. While reef monitoring has grown throughout the region in recent years, studies of coral reef benthic cover remain limited in spatial and temporal scales. Here, we analysed 24,365 reef surveys performed over 37 years at 1972 sites throughout East Asia by the Global Coral Reef Monitoring Network using Bayesian approaches. Our results show that overall coral cover at surveyed reefs has not declined as suggested in previous studies and compared to reef regions like the Caribbean. Concurrently, macroalgal cover has not increased, with no indications of phase shifts from coral to macroalgal dominance on reefs. Yet, models incorporating socio-economic and environmental variables reveal negative associations of coral cover with coastal urbanisation and sea surface temperature. The diversity of reef assemblages may have mitigated cover declines thus far, but climate change could threaten reef resilience. We recommend prioritisation of regionally coordinated, locally collaborative long-term studies for better contextualisation of monitoring data and analyses, which are essential for achieving reef conservation goals.