Coral reef classification using drone screening in Teluk Segadas, Pulau Pangkor

Recent studies suggest a future increase in sponge bioerosion as an outcome of coral reef decline around the world. However, the factors that shape boring sponge assemblages in coral reefs are not currently well understood. This work presents the results of a 17‐month assessment of the presence and species richness of boring sponges in fragments collected from living corals, dead coral reef matrix and coral rubble from Punta de Mita and Isabel Island, two coral reefs from the central coast of the Mexican Pacific Ocean. Both localities have a high cover of dead corals generated by past El Niño Southern Oscillation events, but Punta de Mita was also highly exposed to anthropogenic impacts. Additionally, environmental factors (water transparency, water movement, temperature, sediment deposition, SST, and chlorophyll concentration) were assessed to test the hypothesis that environmental conditions which are potentially harmful for corals can enhance sponge bioerosion. Isabel Island and Punta de Mita showed a similar species richness (13 and 11 species, respectively) but boring sponge presence in both live and dead corals was higher at Isabel Island (57.6%) than at Punta de Mita (35.7%). The same result was obtained when each type of substrate was analysed separately: dead coral reef matrix (81.3% versus 55.5%), coral rubble (47.7% versus 20.0%) and living corals (43.7% versus 31.7%). A principal components analysis showed a higher environmental heterogeneity at Punta de Mita, as well as important environmental differences between Punta de Mita and Isabel Island, due to sediment deposition (2.0 versus 0.2 kg·m−2·d−1) and water movement (24.5% versus 20.5% plaster dissolution day−1), that were also negatively correlated with boring sponge presence (r = −0.7). By analysing the boring sponge assemblage, we found that environmental settings, together with habitat availability (i.e., dead coral substrate) differentiated assemblage structure at both localities. Major structural differences were largely due to species such as Cliona vermifera, Cliona tropicalis and Aka cryptica. In conclusion, factors such as habitat availability favored the presence of boring sponges but some environmental factors such as abrasion resulting from moving sediment acted restrictively, and exerted a major role in structuring boring sponge assemblages in the Mexican Pacific.

Coral reefs are known to undergo phase shift in to macro-algae and reefs have lost the capacity to remain in or return to a coral-dominated state. This shift will not only affect corals, but the others heavily depend on heterogeneous habitat afforded by corals. Sallitivu in Panichchankerni, Eastern province, is a small island (41328 m2). The Island is surrounded by a ring of coral reef with an elevated breaking reef crest, seaward slope and centred shallow lagoon (<1.2m at high tide). The shore is entirely a thick layer of washed coral rubbles. The archived aerial photographs confirmed these coral rubbles present only after 2004 tsunami.Underwater visual census were carried out within the reef lagoon and three sites in reef slope using 30 m long belt transect. In addition to diversity of corals and algae, percentages of live, dead and bleached coral cover were recorded. The reef lagoon is shallow (10-60 cm) and much of the reef crest is exposed at low tide. Within the reef lagoon, the live coral cover was <5%. Around 15% was observed recently bleached, 12% were overgrown by algae; Padina sp, Halimeda sp, Sargassum sp, Caulerpa recemosa and Dictyota sp, and the rest was dead corals smothered by sediments. The seaward slope with high wave action was mostly smothered dead corals with live corals <3%. Coral colonies were represented by Acroporidae (branching and table corals)-Acropora cytherea, A. divaricata, A. formosa, A. gemmifera, A. grandis, A. hemprichii, A. hyacinthus, A. latistella, Acropora sp., A. nobilis, and A. robusta; (Foliaceous)-Montipora aequituberculata and M. hispida; Faviidae (sub massive and encrusting)-Favites halicora, Favites spinosa, Leptastrea purpurea and Platygyra daedalea; Pocilloporidae (Lace/cauliflower) -Pocillopora damicornis; Poritidae (Massive/submassive)-Porites evermanni, P. paliformis, and P. rus. Live corals observed were immature. Southern end of the reef slope had emerging corals among unstable coral rubbles. It is assumed that the degradation was started post-tsunami and continued due to natural stresses. The recovery of corals may hindered by macro-algal growth and resulting accumulation of sediments, smothering due to less wave action within reef lagoon and resulting recruitment and settlement failure. Recent bleaching would be due to exposure to direct sunlight during the change of tides and low sea level. Increasing oxygen level due to algal blooms would also prone for bleaching. Avoiding such undesirable phase shifts from coral dominance to algae and reverse them when occur, requires an urgent reform of scientific approaches to understand the processes causing the degradation. A better understanding on why some reefs rapidly degrade and others do not is critical. Most reef conservation efforts are directed toward reserve implementation, but new approaches are needed to sustain ecosystem function since demarcation of a marine reserve alone would not benefit in improving reef resilience.Keywords: Phase-shift, Coral reefs, Macro-algae, Bleaching, Sallitive Island

Biodiversity of terrestrial and marine ecosystems, including coral reefs, is dominated by small, often cryptic, invertebrate taxa that play important roles in ecosystem structure and functioning. While cryptofauna community structure is determined by strong small‐scale microhabitat associations, the extent to which ecological and environmental factors shape these communities are largely unknown, as is the relative importance of particular microhabitats in supporting reef trophodynamics from the bottom up.The goal of this study was to address these knowledge gaps, provided coral reefs are increasingly exposed to multiple disturbances and environmental gradients that influence habitat complexity, condition and ecosystem functioning.We compared the density, biomass, size range, phylogenetic diversity and functional roles of motile cryptofauna in Palau, Western Micronesia, among four coral‐derived microhabitats representing various states of degradation (live coral [Acropora and Pocillopora], dead coral and coral rubble) from reefs along a gradient of effluent exposure.In total, 122 families across ten phyla were identified, dominated by the Arthropoda (Crustacea) and Mollusca. Cryptofauna biomass was greatest in live Pocillopora, while coral rubble contained the greatest density and diversity. Size ranges were broader in live corals than both dead coral and rubble. From a bottom‐up perspective, effluent exposure had mixed effects on cryptic communities including a decline in total biomass in rubble. From a top‐down perspective, cryptofauna were generally unaffected by predator biomass.Our data show that, as coral reef ecosystems continue to decline in response to more frequent and severe disturbances, habitats other than live coral may become increasingly important in supporting coral reef biodiversity and food webs.

Crustaceans are an important component of coral reef ecosystems, occupying a broad range of microhabitats, but achieving the greatest biomass in dead coral and coral rubble. These 2 microhabitats are therefore hypothesised to be focal foraging locations for crustacean-feeding fishes. The present study investigated the relationship between foraging in wrasses (Labridae), a major group of crustacean predators, and 5 major microhabitats on a coral reef: live coral, dead coral, coral rubble, sand and the epilithic algal matrix (EAM). Although the greatest biomass of crustaceans typically occurs in dead coral and coral rubble, crustacean-feeding wrasses displayed positive selection for a more diverse range of microhabitats. In contrast, sand and live coral were not positively selected by any taxa. The relationships between crustacean predators and their prey appear to be more complicated than previously assumed, and may be mediated by habitat structure, preferred prey, predation risk and behavioural and morphological adaptations.

Natural and anthropogenic disturbances are leading to changes in the nature of many habitats globally, and the magnitude and frequency of these perturbations are predicted to increase under climate change. Globally coral reefs are one of the most vulnerable ecosystems to climate change. Fishes often show relatively rapid declines in abundance when corals become stressed and die, but the processes responsible are largely unknown. This study explored the mechanism by which coral bleaching may influence the levels and selective nature of mortality on a juvenile damselfish, Pomacentrus amboinensis, which associates with hard coral. Recently settled fish had a low propensity to migrate small distances (40 cm) between habitat patches, even when densities were elevated to their natural maximum. Intraspecific interactions and space use differ among three habitats: live hard coral, bleached coral and dead algal-covered coral. Large fish pushed smaller fish further from the shelter of bleached and dead coral thereby exposing smaller fish to higher mortality than experienced on healthy coral. Small recruits suffered higher mortality than large recruits on bleached and dead coral. Mortality was not size selective on live coral. Survival was 3 times as high on live coral as on either bleached or dead coral. Subtle behavioural interactions between fish and their habitats influence the fundamental link between life history stages, the distribution of phenotypic traits in the local population and potentially the evolution of life history strategies.

Increasing sediment onto coral reefs has been identified as a major source of habitat degradation, and yet little is known about how it affects reef fishes. In this study, we tested the hypothesis that sediment-enriched water impairs the ability of larval damselfish to find suitable settlement sites. At three different experimental concentrations of suspended sediment (45, 90, and 180 mg l−1), pre-settlement individuals of two species (Pomacentrus amboinensis and P. moluccensis) were not able to select their preferred habitat. In a clear water environment (no suspended sediment), both species exhibit a strong preference for live coral over partially dead and dead coral, choosing live coral 70 and 80% of the time, respectively. However, when exposed to suspended sediment, no habitat choice was observed, with individuals of both species settling on live coral, partially dead, and dead coral, at the same frequency. To determine a potential mechanism underlying these results, we tested chemosensory discrimination in sediment-enriched water. We demonstrated that sediment disrupts the ability of this species to respond to chemical cues from different substrata. That is, individuals of P. moluccensis prefer live coral to dead coral in clear water, but in sediment-enriched water, chemical cues from live and dead coral were not distinguished. These results suggest that increasing suspended sediment in coral reef environments may reduce settlement success or survival of coral reef fishes. A sediment-induced disruption of habitat choice may compound the effects of habitat loss on coral reefs.

Coral reefs are important because of their high biodiversity and their key role in the tropical marine biosphere. Furthermore, coral reefs are very valuable as a socioeconomic resource as they make important contributions to the gross domestic product of many countries. Thus, it is very important to monitor dynamic spatial distributions of coral reefs and related habitats dominated by coral rubble, dead coral, and bleached corals. Despite these natural and socio-economic advantages, many factors are threatening coral reefs. The study site was selected in Spermonde archipelago, South Sulawesi, Indonesia because this area is included in the Coral Triangle, recognized as the epicenter of coral diversity and a priority for conservation. Images of Landsat MSS, Landsat TM, Landsat ETM, Landsat ETM+, and Landsat 8 data were used to examine changes in the coral reefs of Suranti Island in the Spermonde Archipelago during forty one years from 1972 to 2013. The image processing includes gap fills, atmospheric corrections, geometric corrections, image composites, water column corrections, unsupervised classifications, and reclassifications. Fill Gap processing was done on Landsat ETM+ SLC-off. Subsequently, a multi-component change detection procedure was applied to define changes. Shallow water bottom types classification was divided into live coral, rubble and sand habitats, dead coral with algae, rubble, and sand. Preliminary results showed significant changes during the period 1972–2013 as well as changes in coral reefs, likely explained partly by destructive fishing practices.

Coral reefs are often called the 'rainforests of the sea' because they are among the most diverse and complex of all ecosystems. Coral reefs play a vital role in the coastal and marine ecosystem. The Philippines has the second largest coral reef area in Southeast Asia which is estimated to be about 26,000 square kilometres. It lies within the Coral Triangle or the Indo-Malayan Triangle, a centre of marine biodiversity. However, reefs today are facing a wide and serious threats. Most of the coral reefs in the world are potentially endangered, mainly because of the unsustainable human exploitation exacerbated by global climate change. Mapping of coral reefs provides information to support the protection, conservation and monitoring of this vulnerable benthic habitat. However, typical maps derived using remote sensing data only includes classification of benthic communities due to the high level of complexity and spatial heterogeneity of the coral reef environment. Thus, there is a need to examine the reflectance properties or the spectral response of the different bottom types to serve as a reference for the characterization of the features. This study was conducted to identify spectral characteristics of various reef components by determining the wavelength bands in discriminating coral reef types which can aid in a high-resolution mapping of features. It also proposed a standardized methodology for field measurements of the different coastal habitats using a portable spectrometer in various sites of the Philippines. Spectral measurements of the different coral reefs were taken using the OceanOptics spectrometer unit with wavelength range of 200-1100 nanometres. The acquired spectral curves were divided into the following classes: live corals, dead corals, sand, dead coral with algae, coral rubbles, and bleached corals. Twenty-five in-situ spectral measurements for each sample were averaged and smoothed using the Savitzky-Golay algorithm. This method fits a least square polynomial curve in smoothing the data and is a function of filter size for the calculation of the curve equation, and the degree of polynomial to be used. After the smoothing process, the spectral properties of the measured benthic feature were evaluated using derivative analysis. This calculates the n-derivatives of the reflectance curves to identify the optimal wavelengths for spectral discrimination. Results showed that there are differences in the optical characteristics among the coral reef types which could be used to improve the accuracy of classification and an efficient aid in mapping corals in the country.

Coral reefs are undergoing rapid changes as living corals give way to dead coral on which other benthic organisms grow. This decline in live coral could influence habitat availability for fish parasites with benthic life stages. Gnathiid isopod larvae live in the substratum and are common blood-feeding parasites of reef fishes. We examined substrate associations and preferences of a common Caribbean gnathiid, Gnathia marleyi. Emergence traps set over predominantly live coral substrata captured significantly fewer gnathiids than traps set over dead coral substrata. In laboratory experiments, gnathiids preferred dead coral and sponge and tended to avoid contact with live coral. When live gnathiids were added to containers with dead or live coral, significantly fewer were recovered from the latter after 24 h. Our data therefore suggest that live coral is not suitable microhabitat for parasitic gnathiid isopods and that a decrease in live coral cover increases available habitat for gnathiids.

Macroalgae are an important and diverse component of tropical inshore reefs, providing a range of ecological and functional services. Most of the research emphasis has focused on the negative effects of increased macroalgae on coral reefs to the growth and persistence of corals and fishes. However, on undisturbed reefs, macroalgal beds provide important habitats for newly settled fishes, many of which have ontogenetic changes to coral reefs and replenish adult populations that help control macroalgal growth. The few studies that have investigated macroalgal associations of juvenile fishes have treated macroalgae as a single entity. In doing so, any associations of fishes with taxonomic or functional groups cannot be discerned. The objective of this thesis was to undertake observational and experimental studies to investigate the patterns and mechanisms of habitat selection and preferences in algal-associated juvenile fishes on coastal reefs. In Chapter 2, I investigated the availability, use and selectivity of microhabitats on the reef flat of an inshore reef by recently settled coral reef fishes. Fish and benthic communities were quantified along three 50m transects at each of six reef flat sites along the leeward side of Orpheus Island, an inshore island on the central Great Barrier Reef (GBR). Benthic communities were quantified using the point-intercept method, recording the benthos directly underneath the transect every 0.5m. Recently settled fish were surveyed within a 2m belt along each transect. All recently settled fishes were identified to species, and the microhabitat they were associated with was recorded. A total of 22 species of recently settled fish were recorded across all transects, with the majority of the species being herbivorous as adults. Examination of the microhabitat preferences of the six most abundant species revealed that the two herbivorous rabbitfish species, Siganus lineatus and S. canaliculatus, appeared to associate with large fleshy macroalgae (namely Padina and Sargassum). In contrast, three herbivorous damselfishes, Pomacentrus wardi, P. adelus and P. chrysurus, and the invertebrate feeding cardinalfish Apogon cookii showed no apparent selection for any of the microhabitats examined. These findings suggest that macroalgae are important habitats for some newly settled coral reef fishes, and the availability and composition of macroalgae may shape juvenile populations. Both habitat selection at settlement and/or post-settlement processes may contribute to the establishment of these patterns. The objective of Chapter 3 was to investigate the specific habitat and olfactory preferences of two rabbitfishes (S. lineatus and S. canaliculatus) and two herbivorous damselfishes (P. wardi and P. adelus) at settlement. Naive settlement-stage fishes were collected in light traps and used in a series of aquarium-based settlement choice experiments in which an individual larva was introduced into the centre of a 500L aquarium and allowed to choose among four habitat options. The fishes were released overnight and their associations with the four habitats recorded the following morning. Four separate habitat-choice experiments were conducted, each with four different substratum options: (1) benthic habitats (live coral, dead coral, macroalgae, coral rubble), (2) macroalgal species (Sargassum, Padina, Galaxaura, coral rubble), (3) macroalgal density (8, 4, 1, 0 Sargassum thalli) and (4) macroalgal height (30, 20, 10, 0cm Sargassum). In addition, the role of olfaction was investigated using a 2 channel-choice flume chamber, pairing a benthic substrate water cue to the off-reef control cue (1 km from the nearest reef). The aquarium trials showed that both rabbitfish species preferred macroalgae in experiment 1 and the highest density Sargassum patch in experiment 3. The two rabbitfishes also differed in their habitat preferences as only S. canaliculatus preferred Sargassum in experiment 2 and S. lineatus preferred the tallest Sargassum patch in experiment 4. In contrast, neither damselfish species displayed any preferences among the habitats present. The olfactory trials revealed significant but weak attractions to various chemical cues from benthic microhabitats, however, these varied among species and are unlikely to be biologically significant. It is apparent that juvenile rabbitfishes have strong innate preferences for macroalgae at settlement, however, species-specific preferences for macroalgal species and habitat features may affect the distribution of juveniles on the reef. In summary, macroalgae appear to provide important settlement and juvenile habitats for at least the two rabbitfishes species examined herein, and given the prevalence of juvenile fishes in this habitat, it is likely that such preferences may be more widespread. It is unclear why these early life stages are using macroalgae, but they may be associated with the provision of refugia from predation, or enhanced food supply as these fishes transition from a carnivorous to herbivorous diet. Interestingly, many studies have focused on the role of herbivorous rabbitfishes in removing macroalgae from coral reefs, yet the results of this thesis highlight that these same fishes are dependent on macroalgae at a critical life stage. Clearly, further investigations are required to elucidate the importance of macroalgae to reef fishes at settlement, and potentially other life stages.

ABSTRACTCoral reef fishes face unprecedented threats, as extensive habitat degradation compromises their ecological functions by modifying assemblage structure. It remains unknown how resistant reef fishes are to widespread losses in coral cover, and most studies tend to focus on adults, overlooking the important role of recruits. This study employed taxonomic and trait‐based approaches to investigate how live and dead branching corals influence reef fish assemblages across life stages. Over 1 year, we monitored recruitment and the migration of post‐recruits (juveniles and adults) on manually constructed 1 m2 patches of live and dead branching corals in a degraded reef. Recruit assemblages, composed mainly of two trophic groups, exhibited similar abundance and richness in the complex structures of dead and live coral patches, compared to flat control patches. Conversely, post‐recruit fishes were more abundant, species‐rich, and functionally diverse in live coral patches, encompassing several trophic groups and displaying a dominance shift between mobile and sedentary species. Our findings reveal that while dead coral structures can serve as temporary shelters for mobile recruits, live corals are essential for supporting long‐term biodiversity and diverse functional traits. This study underscores the complementary roles of both live and dead corals in promoting reef fish recovery and highlights the value of integrative strategies for reef ecosystem restoration.

The present study aimed to investigate the spatial structure of fish communities at juvenile and adult stages on coral reefs at Kudaka Island (Ryukyu Archipelago, Japan) and to relate spatial patterns in the structure of the fish communities to gradients in environmental variables. Diurnal visual censuses allowed us to record 2,602 juveniles belonging to 60 species and 1,543 adults belonging to 53 species from October to December 2005. The distribution of species highlighted that the juvenile community was organised into three distinct assemblages, rather than exhibiting gradual change in community structure along the cross-reef gradient. Correlations between spatial patterns of juvenile community and environmental variables revealed that the most significant factors explaining variation in community structure were coral rubble and coral slab. In contrast, the adult community was organised into one assemblage, and the most significant variation factors in community structure were depth, live coral in massive form, live coral in branched form, dead coral and sand. Overall, the present study showed that most juvenile and adult coral reef fish at Kudaka Island exhibited striking patterns in their distribution and depth and some biological factors (e.g., abundance of live coral, dead coral and coral rubble) might exert considerable influence on the distribution of fishes.

Bioerosion of Live Massive Corals and Branching Coral Rubble on Indonesian Coral Reefs

Coral reefs is are an important community in coastal and marine ecosystems. Currently, they are under high environmental pressures and suffer damages from human activities and increased sea surface temperature, narrowing the live coral cover. This study aimed to assess the mapping accuracy of the live and dead coral covers using PlanetScope satellite images around Mandangin Island, Madura, Indonesia. Minimum Noise Fraction (MNF) was applied to the bands corrected for the effect of energy attenuation by the water column using the Depth Invariant Bottom Index method, and Random Forest (RF) algorithm was used for mapping. The classification results showed five classes of benthic habitat 2021, namely live coral, dead coral, rubble, seagrass, and sand. Using the confusion matrix, it was found that the live and dead coral cover models had 72.5% accuracy. The mean live coral and dead coral covers were 18.87% and 36.40%, respectively.

Coral reefs are declining worldwide as a result of many anthropogenic disturbances. This trend is alarming because coral reefs are hotspots of marine biodiversity and considered the ‘rainforests of the sea. As in the rainforest, much of the diversity on a coral reef is cryptic, remaining hidden among the cracks and crevices of structural taxa. Although the cryptofauna make up the majority of a reef’s metazoan biodiversity, we know little about their basic ecology or how these communities respond to reef degradation. Emerging research shows that the species richness of the motile cryptofauna is higher among dead (framework) vs. live coral substrates and, surprisingly, increases within successively more eroded reef framework structures, ultimately reaching a maximum in dead coral rubble. Consequently, the paradigm that abundant live coral is the apex of reef diversity needs to be clarified. This provides guarded optimism amidst alarming reports of declines in live coral cover and the impending doom of coral reefs, as motile cryptic biodiversity should persist independent of live coral cover. Granted, the maintenance of this high species richness is contingent on the presence of reef rubble, which will eventually be lost due to physical, chemical, and biological erosion if not replenished by live coral calcification and mortality. The trophic potential of a reef, as inferred from the abundance of cryptic organisms, is highest on live coral. Among dead framework substrates, however, the density of cryptofauna reaches a peak at intermediate levels of degradation. In summary, the response of the motile cryptofauna, and thus a large fraction of the reef’s biodiversity, to reef degradation is more complex and nuanced than currently thought; such that species richness may be less sensitive than overall trophic function.