Coral Reef Habitats Research Articles

Reef Cover, a coral reef classification for global habitat mapping from remote sensing

Coral reef management and conservation stand to benefit from improved high-resolution global mapping. Yet classifications underpinning large-scale reef mapping to date are typically poorly defined, not shared or region-specific, limiting end-users’ ability to interpret outputs. Here we present Reef Cover, a coral reef geomorphic zone classification, developed to support both producers and end-users of global-scale coral reef habitat maps, in a transparent and version-based framework. Scalable classes were created by focusing on attributes that can be observed remotely, but whose membership rules also reflect deep knowledge of reef form and functioning. Bridging the divide between earth observation data and geo-ecological knowledge of reefs, Reef Cover maximises the trade-off between applicability at global scales, and relevance and accuracy at local scales. Two case studies demonstrate application of the Reef Cover classification scheme and its scientific and conservation benefits: 1) detailed mapping of the Cairns Management Region of the Great Barrier Reef to support management and 2) mapping of the Caroline and Mariana Island chains in the Pacific for conservation purposes.

Green morays (Gymnothorax funebris) have sedentary ways in mangrove bays, but also ontogenetic forays to reef enclaves

Surprisingly, little is known about basic life history of the largest moray eel species in the Caribbean region, the green moray eel (Gymnothorax funebris). Sixteen eels were captured from the mangrove fringe in multiple bays on St. Croix, USVI, implanted with coded acoustic transmitters, and their movements were tracked for up to 11 months using an array of 37 stationary acoustic receivers. They exhibited high site fidelity in the bays during their residence, using the same general parts of individual bays and did not switch bays except for one individual. There was no relationship between eel size (mean TL = 83 cm, range = 54–126 cm) and home range size (mean area of 95% KUD = 5.8 ha ± 0.7 SE). Most individuals were more frequently detected at night than during the day suggesting greater nocturnal activity. Several of the larger eels (mean TL = 93 cm ± 5.9 SE) showed clear and permanent emigration tracks out of the mangrove estuary to coral reef habitats offshore. For some individuals, these habitat shifts were preceded by exploratory movements away from the eel’s typical home range the night before emigration. All final emigration events took place nocturnally, happened during a single night, and occurred during months from December to May. Mean emigration speed was 3.4 km/h. This study is the first documentation of an ontogenetic habitat shift in moray eels, as well as the first determination of home range size for this species and their site fidelity in mangrove habitats.

Habitat type and complexity drive fish assemblages in a tropical seascape.

Inshore marine seascapes support a diversity of interconnected habitats and are an important focus for biodiversity conservation. This study examines the importance of habitat attributes to fish assemblages across a mosaic of inshore habitats: coral reefs, rocky reefs, macroalgae beds and sand/rubble beds. Fishes and benthic habitats were surveyed at 34 sites around continental islands of the central Great Barrier Reef using baited remote underwater video stations (BRUVS). Species richness was influenced foremost by habitat type and also by structural complexity within habitat types. The most speciose assemblages occurred in coral and rocky reef habitats with high structural complexity, provided by the presence of coral bommies/overhangs, boulders and rock crevices. Nonetheless, macroalgae and sand/rubble beds also supported unique species, and therefore contributed to the overall richness of fish assemblages in the seascape. Most trophic groups had positive associations with complexity, which was the most important predictor for abundance of piscivorous fishes and mobile planktivores. There was significant differentiation of fish assemblages among habitats, with the notable exception of coral and rocky reefs. Species assemblages overlapped substantially between coral and rocky reefs, which had 60% common species, despite coral cover being lower on rocky reefs. This suggests that, for many species, rocky and coral substrates can provide equivalent habitat structure, emphasizing the importance of complexity in providing habitat refuges, and highlighting the contribution of rocky reefs to habitat provision within tropical seascapes. The results of this study support an emerging recognition of the collective value of habitat mosaics in inshore marine ecosystems.

An updated inventory of sea slugs from Koh Tao, Thailand, with notes on their ecology and a dramatic biodiversity increase for Thai waters.

Improved access to field survey infrastructure throughout South-East Asia has allowed for a greater intensity of biodiversity surveys than ever before. The rocky bottoms and coral reef habitats across the region have been shown to support some of the highest sea slug biodiversity on the planet, with ever increasing records. During the past ten years, intensive SCUBA surveys have been carried out at Koh Tao, in the Gulf of Thailand, which have yielded remarkable findings in sea slug biology and ecology. In this work a brief history of sea slug biodiversity research from Thailand is covered and a complete inventory of sea slugs from Koh Tao, Gulf of Thailand is provided. This inventory is based on surveys from 2012 to 2020, with previously unreported findings since 2016. Habitat specificity and species-specific ecology are reported where available with a focused comparison of coral reef habitats and deeper soft-sediment habitats. The findings contribute 90 new species records for Thai waters (92 for the Gulf of Thailand) and report a remarkable consistency in the proportional diversity found to be exclusive to one habitat type or another. Additionally, taxonomic remarks are provided for species documented from Koh Tao that have not been discussed in past literature from Thailand, and a summary of previous records in the Indo-West Pacific is given.

3D assessment of a coral reef at Lalo Atoll reveals varying responses of habitat metrics following a catastrophic hurricane

Extreme disturbances such as hurricanes can cause reductions in coral cover and three-dimensional (3D) structural complexity of coral reefs. We examined changes in structural complexity utilizing 3D reconstruction of a coral-reef site before and after Hurricane Walaka passed through Lalo of the Northwestern Hawaiian Islands. This event resulted in complete destruction of the coral-reef habitat, with dramatic changes in benthic cover from pre-hurricane tabulate coral to post-hurricane rubble. Rugosity and mean slope decreased after the hurricane, while structural complexity, captured by vector ruggedness measure (VRM), showed resolution-specific responses. This metric captured the structural complexity of rubble at a high raster resolution of 1 cm and that of tabulate coral at lower resolutions, resulting in decreases in mean VRM values at 2- and 4-cm resolutions but an increase at 1-cm resolution. Variability in profile and planform curvature was reduced after the hurricane due to a disappearance of extreme curvature values created by the tabulate coral after the hurricane. This study highlights the varying responses of habitat complexity metrics to the complete destruction of a coral reef and provides us with insights into how choices of habitat complexity metrics can affect quantitative assessments of 3D habitat structure.

Will the High Biodiversity of Eels in the Coral Triangle be Affected by Climate Change?

The Indonesian Seas are at the center of the Coral Triangle, which has the highest marine biodiversity in the world, and the region is under threat from climate change. Freshwater habitats in the region have a high number of anguillid eels compared to other regions of the world, but it is more difficult to capture marine eels to assess their biodiversity. Catches of leptocephali from 5 internationally collaborative surveys for eel larvae (leptocephali) in the Coral Triangle have collected about 126-169 species of larvae, which indicates that the Coral Triangle region likely has the highest marine eel biodiversity in the world based on comparisons to similar larval surveys in the Indian, Pacific, and Atlantic oceans (29-107 species). These marine eel species inhabit a wide range of benthic and pelagic habitats, but how they might be affected by climate changes such as ocean warming has not been considered. Anguillid eels in the Coral Triangle region could be affected mainly by changes in rainfall patterns that could affect their freshwater growth stage or their reproductive maturation patterns and migration. Effects on marine eels would depend on the types of habitats where they live, with the least impacts occurring for deep benthic or pelagic species. Marine eels that live in shallow habitats would be most affected if warming seas and coral bleaching reduce the types of prey species they depend on. Based on their possible association with coral reef habitats, eels of the families Muraenidae and Chlopsidae appear to the most likely types of eels to be impacted by changes in community structure resulting from coral bleaching. All leptocephali species live in the ocean surface layer where they feed on marine snow, so warmer ocean temperatures might reduce the amount or quality of marine snow that is available, resulting in lower larval survival rates. Further studies on eel biodiversity and habitat use will provide more insight into the possible loss of endemic species in the Coral Triangle due to climate change, but presently it is unclear how many species of eels may be directly affected by climate change.

Establishing optimal broodstock sex ratios for the royal gramma (Gramma loreto) in small scale system aquaculture

The royal gramma (Gramma loreto) is vulnerable to anthropogenic impact in its coral reef habitats, and is deemed an “indicator” species of pollution. It is also heavily fished for the aquarium trade, being among the top 1% of imported marine aquarium fish species into the U.S. The objective of this study was to establish optimal sex ratios of broodstock groups for aquaculture as an alternative to wild capture, while balancing territorial aggression. Three two-month breeding trials were carried out in six 23 L aquaria stocked with one male and one, two, or three females. During the trials, each aquarium was filmed weekly for one hour at first light to record courtship, nest use, and aversive behaviors. Behaviors were quantified with JWatcher software and analyzed in repeated measures ANOVAs. Results suggest that in small aquaria, a sex ratio of one male to two females may be optimal for spawning because courtship and nest use behaviors are optimized while aversive behaviors are moderated. Past efforts to aquaculture the species have typically been conducted at broodstock sex ratios of 1:1. These results offer the potential to increase productivity of commercial aquaculture of the species.

Hide ‘n seq: Direct versus indirect metabarcoding of coral reef cryptic communities

AbstractEcological patterns in biodiversity are primarily based on conspicuous organisms. Few methods are used to survey the taxonomically rich cryptobiome, which is made up of inhabitants from within microhabitats. One way that cryptic marine biodiversity can be non‐invasively surveyed is by analyzing environmental DNA (eDNA) present in seawater. Using coral reefs as a model system, here we compare estimates of cryptic diversity among community biomass and eDNA metabarcoding sampling methods with a broad eukaryotic marker (COI). First, contributions to eDNA were investigated across cryptobiomes through a comparison of community metabarcoded biomass from standardized autonomous reef monitoring structures (ARMS) to eDNA acquired from seawater in which individual ARMS were soaked. Second, we compared these results to those from eDNA samples taken from within reef crevices and the ambient water column. Metabarcoding of community biomass from ARMS and eDNA from the two types of water samples revealed significantly different communities of cryptic coral reef habitat with little overlap between methods. Taxa that were unique to metabarcoding of ARMS biomass were predominantly from chitinous and calcifying groups (polychaetes, palaemonid shrimp, mollusks, brittle stars, and red algae), which suggests that these taxa are underrepresented in eDNA surveys. Other than the corals themselves, sponges and red algae were significant drivers of reef crevice community differences, while ambient seawater samples detected mostly planktonic organisms and reef fishes. Our data indicate that both eDNA and ARMS provide incomplete accounting of cryptic diversity. Direct sampling of biomass is best suited for building taxonomies and improving databases, whereas eDNA methods offer rapid insights into the composition of cryptobiomes. Because each method likely captures different taxa, multiple targeted assays can be used to provide the greatest estimates of metazoan and macroalgal richness.

Spatial analysis of geophysical and environmental factors characterize distinct coral reef habitats around Sri Lanka; implications for management

Spatial distribution patterns of coral reefs are maintained by a magnitude of chemical, physical and biological factors. Being a small continental island in the Indian Ocean, the extent of coral reef habitats around Sri Lanka has been limited and patchy showing unique, regional distribution patterns owing to these factors. However, the available data on these factors are sparse and outdated hindering proper management implications of these coral reefs. Here, we use remote sensing data on coral reefs in providing a framework to formulate hypotheses about the ecological processes governing these spatial and temporal patterns of coral reef distribution around the country. The results explained that the coral reef habitats around Sri Lanka are mostly shaped by the variation in nutrient levels (phosphate, nitrate and silicate), annual variance in sea surface salinity, mean current velocity and bathymetric shape. The study identified four unique coral reef areas around the island owing to variations of these factors; east coast reefs, south coast reefs, west coast reefs and north/northwestern reefs around Jaffna peninsula and Gulf of Mannar. The predicted Maximum entropy distribution models for the coral reef habitats of Sri Lanka revealed a significant amount of coral reef cover around the island (~2739 km2) which might deplete by ~4% in another 30 years due to changes in these factors. The highest amount of loss will be in the west coast (~17.76%) and least amount of loss will be in the east coast (~5.54%). The current research aids in understanding the reef ecology around Sri Lanka and provides implications for marine ecosystem management and conservation planning.

Microhabitats of sharknose goby (Elacatinus evelynae) cleaning stations and their links with cleaning behaviour

Coral reefs are renowned for the complexity of their habitat structures and their resulting ability to host more species per unit area than any another marine ecosystem. Dedicated cleaner fish, which acquire all their food resources through client interactions, rely on both the habitat structures (by using topological cleaning stations) and the wide diversity of fish species available on coral reefs, to function. As a result of natural and anthropogenic threats, coral reef habitat structures and their complexity are being lost—despite this threat it is unclear how important reef geometry is to key ecological interactions, like cleaning. Using an established Caribbean reef study site, three-dimensional constructions of discrete coral heads were used to investigate how fine-scale structural complexity traits (structural complexity—measured by rugosity and vector dispersion—height, volume, surface area, percentage live coral cover and refuge availability) relate to cleaner occupancy, abundance and their cleaning interactions with clients. Coral height was a particularly important trait for cleaning, correlating with both the occurrence of cleaning stations on a reef, and with increased cleaning durations and reduced cleaning frequencies/rates. Cleaning stations were also more structurally complex than non-cleaning coral heads, and the increased availability of uneven surfaces (creating cracks and crevices) and refuge availability linked with increased cleaning durations/rates. By understanding habitat features important to cleaner fish on a typical Caribbean fringing reef, we can gain a better understanding of how important reef geometry might be for governing the occurrence and dynamics of such mutualisms.

The performance of coral nursery with rope tree techniques in the moderate sea current environment: Morotai pilot project

Acknowledged as the famous destination for shark diving tourism, Morotai waters poses increasing coral reef degradation risk in recent years. Coral restoration program is needed to battle the decreasing coral cover in this waters. Instead of garnering the fragment directly from healthy coral reef habitat, which is potentially damaging the healthy coral reef, a coral nursery can be proposed as an alternative method to maintain the pristine environment of coral reef habitat in Morotai waters with future coral restoration programs. Coral rope tree nursery has proven to be effective at achieving growth speed compared to other coral nursery methods as well as high performance to withstand moderate current risk. Performance of a pilot project of coral tree rope nursery in Morotai waters has been studied for more than five months and it shows as promising method for future massive nursery.

Helminth Communities of Anisotremus virginicus (Perciformes: Haemulidae) In Veracruz, Mexico.

A helminthological analysis was performed on 91 specimens of the porkfish, Anisotremus virginicus (Linnaeus) (Haemulidae), captured in coral reef habitats of the Parque Nacional Sistema Arrecifal Veracruzano (PNSAV) (Veracruz Reef System National Park), in Veracruz, Mexico. A total of 22 helminth taxa were recorded: 9 digeneans, 6 monogeneans, 1 cestode, 4 nematodes, and 2 acanthocephalans. From the 22 taxa, 11 are new host records and 7 are new geographic records. The highest prevalence was found for Monorchis latus Manter, 1942 (69%), and Mexicana anisotremumCezar, Paschoal and Luque, 2012 (68%), and the highest mean intensity was found for M. anisotremum (19.6), M. latus (18.9), and Dollfusentis chandleri Golvan, 1969 (10.8). Other important values were the component community richness (S = 22), diversity (Shannon index H' = 1.6), and infracommunity level (S = 3.1 ± 1.4; Brillouin index, H = 0.52 ± 0.3), which were similar to those found in other marine fish at the same study site. Our result represents a significant range extension for several helminth taxa. The parasite communities of A. virginicus rank among the richer parasite communities of neotropical marine fishes. In addition, the results reveal the PNSAV is a diverse area for the parasite assemblage of neotropical reef marine fishes, particularly of haemulids but also for other fish families.

Responses of benthic habitat and fish to severe tropical cyclone Winston in Fiji

Tropical cyclones can dramatically reduce coral cover, coral diversity and structural complexity, which can all cause flow-on effects to fish communities. In 2016, Fiji sustained extensive damage from one of the most severe cyclones recorded in the southern hemisphere (Category 5 cyclone Winston). We assessed the impacts of cyclone Winston on the coral reef habitat and fish assemblages in Kubulau and Levuka districts in Fiji. Wave modelling showed that cyclone-generated waves were substantially larger and persisted longer in Levuka than Kubulau. Damage to live corals was spatially variable and highest in Levuka, with the extent of damage highly correlated to the exposure, height and duration of waves at each site. We recorded increases in macroalgae directly after the cyclone and increases in encrusting coralline algae two years after the cyclone. We did not detect many changes in the fish assemblage caused by cyclone Winston. Obligate corallivores, and species within this group, Chaetodon baronessa and Labrichthys unilineatus, were the only fish to show a decline post-cyclone, most likely caused by declines in coral cover. We found that the modelling of cyclone wave dynamics (wave height, duration and exposure) explained the variation and damage to live corals better than proximity to the cyclone path, providing a useful tool to predict cyclone damage. Future climate models predict that more cyclones will reach the highest intensities. Understanding the impact this will have on vulnerable coastal communities that are dependent on marine resources and are protected from wave energy by reefs is essential for effective mitigation and adaptive management plans.

The trophic structure of fish in seaweed farms, and adjacent seagrass and coral habitats in Zanzibar, Tanzania

Coral reefs, seagrasses and seaweed farms (Eucheuma denticulatum) are characteristic habitats in many parts of the coast of Zanzibar, Tanzania. However, information on trophic interactions, movements of fish, and variation in fish diet specialization between these habitats are scarce. The present study determined the trophic structure and the variation in diet composition of fish caught in (floating) seaweed farms, and in adjacent seagrass and coral reef habitats in Pongwe, Zanzibar. Fish were caught using traditional basket traps (dema) and gut contents of 392 fish were analyzed. A one-way Analysis of Similarities (ANOSIM) showed that there was a significant difference in the composition of prey items eaten by invertivores in different habitats (Global R = 0.109, p = 0.002.). There was no significant difference in the composition of prey items eaten by herbivores, invertivore-piscivores and omnivores (p > 0.05), likely due to movement of fish between these habitats for foraging. There was no significant difference in the relative proportion of trophic groups between the habitats (p > 0.05) except for herbivores (p < 0.05). Floating seaweed farms attract invertebrates and smaller fish, thus providing feeding grounds for predatory fish, and should be considered as ecologically important habitats as are coral reefs and seagrass beds.

Biodiversity of macroinvertebrate in artificial substrate from several habitats at Ponelo Island, Gorontalo

Ponelo Island is located at the North Gorontalo District, Province Gorontalo, with a position close to the Wallace line. The impact of the position makes Ponelo Island having high biodiversity, such as macroinvertebrates. This study aimed to compare the biodiversity of macroinvertebrates living in artificial substrates form anthropogenic, seagrass, mangrove, and coral reefs habitat at Ponelo Island, Gorontalo. This study was conducted from August to October 2019 in four different habitats at Ponelo Island. The specimens were identified at the Laboratory of Micro Biology, Department of Aquatic Resources Management, IPB University. The data were analyzed by calculating the diversity index, evenness index, dominance index, similarity analysis among habitats, and ANOVA test. The macroinvertebrate samples from all stations were found in 58 species, consisting of phylum Annelids, Crustaceans, and Molluscs. The diversity value of macroinvertebrate in seagrass and coral reef habitats is higher and vice versa the association level is lower than in other habitats. Acetes sp., Clypeomorus bifasciata, and Sesarma sp. were obtained in all locations. The placement of the artificial substrate had no significant effect on the density of macroinvertebrates in all habitats.

New record of Sphenopid Zoanthid species Palythoa tuberculosa (Esper, 1805) from Gulf of Mannar, India

Coral reefs provide a suitable habitat for many marine flora and fauna. Zoanthid is one of the most common inhabitants in coral reef habitats. A sub-massive colony of Sphenopid Zoanthid species Palythoa tuberculosa belonging to the order Zoantharia was documented for the first time from Gulf of Mannar (GoM) during an intensive coral reef monitoring survey conducted in Manoli, Manoliputti and Shingle Island. Photographic evidence of the colony along with its morphological characteristics are described in the present study.

MONITORING CHANGES IN CORAL REEF HABITAT COVER ON BERALAS PASIR ISLAND USING SPOT 4 AND SPOT 7 IMAGERY FROM 2011 AND 2018

Beralas Pasir is part of the Regional Marine Conservation Area (KKLD), which was established by the Bintan Regency Government with Bintan Regent Decree No. 261 / VIII / 2007. Water tourism activities undertaken by tourists on the island have had an impact on the condition of the coral reefs, as have other factors, such as bauxite, granite and land sand mining activities around the island. This research aims to determine changes in the coral reef habitat cover and the condition of the coral reefs around Beralas Pasir Island with a remote sensing function, using SPOT 4 imagery acquired on June 1, 2011 and SPOT 7 imagery from April 5, 2020. Data collection of environmental parameters related to the coral reefs was also made. The image processing used the Lyzenga algorithm to simplify the image classification process. The percentage of coral live cover around the island ranges from 26% -53%; this has experienced a significant change, from 67,560 hectares in 2011 to 38,338 hectares in 2018, a total decrease in the area of 29,222 hectares. Some of the natural factors found in the research which have caused damage to the reefs were Drupella snails, the abundance of Caulerpa racemosaalgae, and sea urchins. The majority of the coral reef types consist of Non-Acropora: Coral Massive, Coral, Coral Foliose, Coral Encrusting, Acropora: Acropora Tabulate, Acropora Encrusting, and Acropora Digitate

Spatial ecology of hawksbill sea turtles (Eretmochelys imbricata) in foraging habitats of the Gulf of California, Mexico

Understanding movement patterns and habitat preferences of endangered species during their most vulnerable life stages is a key step to developing effective conservation strategies that prevent extinctions. Hawksbills (Eretmochelys imbricata) are among the most-imperiled sea turtles and are generally thought to associate with very specific coral and rocky reef habitats. However, in the Eastern Pacific, hawksbills have also been found to have a strong association with mangrove estuaries. Eastern Pacific hawksbills constitute one of the most endangered sea turtle populations globally, and the Gulf of California, Mexico, was recently identified as a potentially important foraging region. Here we analyzed movement patterns of 12 individuals equipped with Argos-linked GPS transmitters. We calculated home ranges using kernel density estimations and found that hawksbills were highly restricted in their movements, spending months to years in areas ranging from 0.05 to 17 km2. Mean sizes of 50% and 95% kernel utilization distributions were 0.72 km2 and 3.8 km2, respectively. Also, 85.6% of hawksbill locations were associated within, or in close proximity to, mangrove estuaries, further highlighting the importance of these fragile ecosystems for hawksbill conservation. The fine-scale resident behavior of hawksbill turtles in foraging grounds presents a unique conservation opportunity while also underscoring the need to identify these sites and work with local communities to protect them.

Benthic and coral reef community field data for Heron Reef, Southern Great Barrier Reef, Australia, 2002\u20132018

This paper describes benthic coral reef community composition point-based field data sets derived from georeferenced photoquadrats using machine learning. Annually over a 17 year period (2002–2018), data were collected using downward-looking photoquadrats that capture an approximately 1 m2 footprint along 100 m–1500 m transect surveys distributed along the reef slope and across the reef flat of Heron Reef (28 km2), Southern Great Barrier Reef, Australia. Benthic community composition for the photoquadrats was automatically interpreted through deep learning, following initial manual calibration of the algorithm. The resulting data sets support understanding of coral reef biology, ecology, mapping and dynamics. Similar methods to derive the benthic data have been published for seagrass habitats, however here we have adapted the methods for application to coral reef habitats, with the integration of automatic photoquadrat analysis. The approach presented is globally applicable for various submerged and benthic community ecological applications, and provides the basis for further studies at this site, regional to global comparative studies, and for the design of similar monitoring programs elsewhere.

Large scale study of benthic communities in Eastern Indonesia’s reef systems

Broad-scale studies and regional comparisons of Indonesia’s coral reefs are critical given the relative lack of information about these large, diverse, and threatened ecosystems. Most studies on reef benthic composition and distribution have largely focused on rather short transects spanning relatively small areas. Here, we quantify the shallow large-scale spatial distribution of benthic communities in four locations in Eastern Indonesia, i.e. the Spermonde Archipelago in South Sulawesi, and Ambon, Halmahera and Lucipara in Maluku Islands. Shallow coral reef ecosystems (0.5-2 m depth) were assessed using a georeferenced photoquadrat survey method that can cover larger proportions of reefs, as well as benthic assemblages in deeper reefs (∼8 m depth) recorded with photoquadrats. A total of 27.8 km of shallow and 4.8 km of deeper reef ecosystem transects were surveyed in this study. We found that reef benthic communities at the study locations were mainly characterized by low to moderate cover of live hard corals and relatively high cover of dead corals or abiotic components. Ninety percent of the surveyed reefs at both depths exhibited < 50% cover of live hard corals, whereas 88% of shallow and 78% of deeper reef sites consisted of > 25% dead corals or abiotic components. A combination of georeferenced photoquadrats and CoralNet machine learning rapidly identified benthic composition across a large area, which is useful for mapping or other large-scale applications. This information can support decision-makers for better management of resources and marine spatial planning, crucial for an archipelagic state with tens of thousands of islands such as Indonesia. Our broad-scale reef surveying, focusing on under-studied areas of Indonesia, can contribute to this effort, as well as others seeking to better map coral reef habitats, as an important foundation for their conservation amidst growing threats.