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Marine community datasets are key to the effective management and conservation of marine ecosystems, including coral reefs, which are increasingly threatened by a myriad of stressors. Although community information exists for many comparatively well-studied taxa, other common groups remain to be examined for even such basic information. In this study, we report on the zoantharian communities (Cnidaria: Anthozoa: Hexacorallia: Zoantharia) on the reefs of Bonaire in the southern Caribbean, and compare current results from 30, 20, 10, and 5 m depths to recent similar surveys from nearby Curaçao. The surveys revealed a total of 17 zoantharian species and epibiotic associations on the reefs of Bonaire. Additionally, results showed that while zoantharian assemblages around Bonaire at shallow 5 and 10 m depths, dominated by Palythoa spp., were similar to those found on Curaçao, diversity and numbers of zoantharians were higher at 20 and 30 m due to more abundant epibiotic Parazoanthidae species associated with sponges. Differences in assemblage structure were seen in deeper 20 and 30 m depths between the two islands, implying that conservation of deeper reef slopes, or along depth gradients, may need to be independently considered and addressed for each location. Analyses with environmental parameters on the Bonaire dataset indicate the potential importance of coral reef rugosity and physical structure in shaping these zoantharian communities, aspects that should be focused on in more detail in future research.

The diversity of symbiotic dinoflagellate Symbiodiniaceae hosted by anthozoans is known to be driven by the environment where the hosts are found. This study examined how environmental variations (Palythoa tuberculosa. We monitored the dominant Symbiodiniaceae lineages within tagged P. tuberculosa colonies near the Hija River mouth and adjacent coastal reefs at Mizugama, Okinawa, Japan, between July 2016 and April 2018. Seven sites were chosen based on depth and distance from the river mouth, with 5 tagged colonies at each site. Water parameters of tidal pools (TPs) at the river mouth, especially temperature, were significantly different from other sites. Surprisingly, P. tuberculosa colonies at TPs were more resilient to bleaching during summers compared to colonies at other shallow sites. We observed different Cladocopium psbAncr lineages hosted by the tagged P. tuberculosa, with TPs colonies usually hosting one Cladocopium lineage (designated as lineage 4). Colonies from the deep sites and other shallow sites hosted mostly Cladocopium lineages 1 (generalist) and 2 (riverine specialist). Throughout the study period, the shallow colonies (included TPs) recorded higher rates of switching dominant Cladocopium lineages (mostly to lineage 1), whereas most deep colonies did not switch their dominant Cladocopium lineages. Our results show that Cladocopium lineage 1, previously reported as a generalist lineage in terms of environmental parameters, could also be an opportunist lineage during periods of host stress. Our study confirms that Cladocopium lineage flexibility likely helps the resilience of P. tuberculosa in such variable environments.

Ocean warming is increasing the incidence, scale, and severity of global-scale coral bleaching and mortality, culminating in the third global coral bleaching event that occurred during record marine heatwaves of 2014-2017. While local effects of these events have been widely reported, the global implications remain unknown. Analysis of 15,066 reef surveys during 2014-2017 revealed that 80% of surveyed reefs experienced significant coral bleaching and 35% experienced significant coral mortality. The global extent of significant coral bleaching and mortality was assessed by extrapolating results from reef surveys using comprehensive remote-sensing data of regional heat stress. This model predicted that 51% of the world’s coral reefs suffered significant bleaching and 15% significant mortality, surpassing damage from any prior global bleaching event. These observations demonstrate that global warming’s widespread damage to coral reefs is accelerating and underscores the threat anthropogenic climate change poses for the irreversible transformation of these essential ecosystems.

1. Coral growth rate is one of the common measurements used as an indicator of coral reef health. The traditional approach is by directly measuring the linear extension rate. Yet, this method is a one-dimensional measurement where it underestimated actual coral growth due to coral morphotypes. Therefore, a multidimensional measurement would provide a better understanding on coral dynamic growth. Moreover, current practices are either invasive or needs a sample to be sacrificed therefore unfeasible for repeated sampling. This study aims to evaluate the accuracy of 3D-photogrammetry by comparing with standardised stainless steel gauge blocks of known dimensions. Also, aluminium foil wrap methods were compared with 3D photogrammetry to examine coral surface area of different morphotypes. 2. To explore the application of 3D-photogrammetry, 10 coral nubbins (approximately 3cm) of Acropora digitifera were taken from Pulau Bidong and transported back to the mesocosm system. Three different approaches were tested, they are (1) Photo-geometry linear extension (LE) rate using ImageJ software, (2) buoyant weight (BW), and (3) surface area (SA) estimation via 3D-photogrammetry modelling using Agisoft Photoscan software. Coral growth rates were measured every 14 days. 3. The coral growth was significantly reduced at week-8 as showed by the reduction in LE rate and BW values, while SA values increased exponentially. This was believed due to energy shift to form thin calcified layer at the base of the nubbins for stabilisation. 4. This finding suggests corals prioritise in establishment of a base for stability over linear growth after the asexual fragmentation. 3D photogrammetry allows a better understanding of corals’ life history strategy by recreating fairly accurate estimates of real objects (irregular coral) without sacrificing and removing it from water. In conclusion, this method further contributes to understanding coral performances after it is transplanted and for future in-situ long term coral monitoring purposes.

Sea surface temperatures (SST) and chlorophyll a concentrations (Chl a) in the southern Red Sea have wide variations based on distance from the coast. To understand how these variations can affect the diversity of symbionts hosted by reef-associated organisms, we conducted a study in the central and southern Red Sea to examine the diversity of Symbiodiniaceae hosted by the zooxanthellate zoantharian Palythoa tuberculosa at different distances from the coast: offshore (FBO), midshelf (FBM) and inshore (FBI) of Farasan Banks, and inshore at Thuwal (TI). Genomic DNA was extracted from 198 specimens, followed by amplification of the ribosomal DNA internal transcribed spacer 2 (ITS-2) and noncoding region of the chloroplast plastid minicircle (psbAncr). Durusdinium and six lineages of Cladocopium (Pt-1-a, Pt-1-b, Pt-1-c, Pt-1-d, Pt-3-a, Pt-3-b) were identified based on sequences of the two marker regions. Changes in composition of Symbiodiniaceae lineages were observed from FBI (high SST, high Chl a) to FBO (low SST, low Chl a). Molecular variance analyses showed that distance from coast was the most likely predictor of differences in Cladocopium lineages. Multinomial logistic regression analysis showed a transition among different Cladocopium lineages as SST increased. One Cladocopium lineage, Pt-1-b, demonstrated higher prevalences at high SSTs and increased in prevalences at the same rate as thermotolerant Durusdinium. Additionally, Cladocopium lineage Pt-3-a had a high affinity to low Chl a concentrations. This study demonstrates that environmental variations in SSTs and Chl a concentrations are significant predictors for the diversity of dominant Symbiodiniaceae within individual host P. tuberculosa colonies. We theorize that flexibility with different lineages of Symbiodiniaceae allows generalist P. tuberculosa to live across a wide range of environments in the southern Red Sea.

The seas of Southeast Asia are home to some of the world’s most diverse ecosystems and resources that support the livelihoods and wellbeing of millions of people. Climate change will bring temperature changes, acidification and other environmental change, with uncertain consequences for human and natural systems in the region. We present the first regional-scale projections of change in the marine environment up to the end of 21st century. A coupled physical-biogeochemical model with a resolution of 0.1° (approximately 11 km) was used to create projections of future environmental conditions under two greenhouse gas scenarios, RCP4.5 and RCP8.5. These show a sea that is warming by 1.1–2.9°C through the 21st century, with surface pH falling by up to 0.02 and dissolved oxygen decreasing by 5 to 13 mmol m− 3. Changes for different parts of the region, including four sensitive coastal sites, are presented. The changes reach all parts of the water column and many places are projected to experience conditions well outside the range seen at the start of the century. Altered species distribution and damage to coral reefs resulting from this environmental change would have consequences for biodiversity, for the livelihoods of small-scale fishers and for the food security of coastal communities across the region. Projections of this type are a key tool for communities planning how they will adapt to the challenge of climate change.

Giant clams provide and support valuable functions to coral reefs, as well as represent a sustainable resource for traditional fisheries throughout the Indo‐Pacific region. The Ryukyu Archipelago (southern Japan) is known to be the northern latitudinal limits of giant clam distribution, but there is only limited information in the literature regarding species diversity, status, and distribution in this region. In this study, we report findings from a rapid survey in 2016, the first of its kind for the Ryukyu Islands, to determine species distribution and abundance of giant clams (tridacnines) around Okinawa‐jima Island. Results indicate the presence of four species with an overall density of 5.03 per 100 m², from most to least abundant: Tridacna crocea, Tridacna maxima, Tridacna squamosa, and Tridacna noae. The previously reported species Tridacna gigas and Hippopus hippopus were both absent from the surveys. The densities and distributions of tridacnines varied among species and sites, which are likely attributable to efforts in replenishing and protecting stocks of selected species. The most abundant species, T. crocea, is an important fishery species in Okinawa, and has been widely cultured and restocked to augment depleted populations. In comparison, restocking efforts for less popular species, such as T. squamosa, have been limited, and their current sizes and numbers suggest recruitment constraints. Given the importance of the giant clam fishery in this region and the current declines of various species (except T. crocea), further regulations should focus on the protection of larger and mature clams that function as broodstock necessary to maintain spawning and natural recruitment.

Symbiodiniaceae diversity in hosts is known to change with the environment and particularly with temperature and light intensity. However, higher levels of pCO2, as could be expected under future ocean acidification scenarios, have been documented to show little to no effect in influencing the diversity of Symbiodiniaceae in hosts in previous studies. In this study, we examined hypervariable psbAncr sequences to identify the Cladocopium (former Symbiodinium ‘Clade C’) diversity within the zooxanthellate zoantharian Palythoa tuberculosa at an acidified reef in southern Japan. Palythoa tuberculosa were collected from a reef at the volcanic island of Iwotorishima in southern Japan; specimens from a high pCO2 site and from a nearby control (normal pCO2) site (Inoue et al. in Nat Clim Change 3:683–687, 2013). We observed a statistically significant reduction in Cladocopium diversity at the high pCO2 site with only one Cladocopium lineage present, compared to at the control site with two lineages present. Our results demonstrate that higher pCO2 can potentially negatively influence the diversity of host Symbiodiniaceae within anthozoan hosts, an important implication in the face of ongoing ocean acidification and climate change.

Despite much research on zoantharians, little work has been done on the abundance of these animals in depths greater than 5 m. In this study, we examined the abundance of zoantharian species and th...

Parasitic sacculinids Sacculina beauforti infection is prevalent in the orange mud crab Scylla olivacea population in Marudu Bay, Sabah. Being a commercially important species and of high-value to the aquaculture and fisheries sector, this infestation on S. olivacea is alarming. Discriminant ratios were calculated based on the measurements of carapace width, abdomen width, gonopod length and pleopod length. A stepwise discriminant analysis was conducted and two discriminant functions were proposed for identifying infected males and females from the normal S. olivacea population. Only applicable in male, Function 1 incorporates five ratios and correctly classified 93.7% of individuals. Function 2 uses two ratios to identify infected females and has a success rate of 100%. When tested with the ratios of normal S. olivacea from other populations, Function 1 achieved 89–98% whereas Function 2 achieved 100% of re-classification success. These functions may serve as a fast, simple, inexpensive and non-invasive tool for identifying infected crabs rapidly when other methods such as molecular approach and direct identification based on the presence of externa are not applicable. The availability of this tool will aid in the control of S. beauforti infection by preventing them from being spread to other S. olivacea populations and/or aquaculture farms.

In enhancing coral reef management, identifying the key threats that influence the coral reefs ecosystem needs accurate information on the current knowledge of coral health status and coral communities. This study attempts to update such information by evaluating the data of coral assessment on the reef areas in the southern part of the South China Sea (SCS); the Labuan Marine Park (LMP), Pulau Tioman Marine Park (PTMP), Pulau Kapas Marine Park (PKMP), Pulau Bidong (PB) and Pulau Perhentian Marine Park (PPMP). The Coral Video Transect (CVT) technique was utilised to examine the biotic [live coral (C), algae (ALG) and other invertebrates (OT)] and abiotic [(dead coral (DC), sand, silt and rock (SR)] composition, coral health status and coral communities. The variation of biotic and abiotic components was significantly influenced by ‘Area’ and ‘Tourism Development’, which implied that the reefs were influenced by proximity from the mainland and varying human-induced stressors within the site in the survey area. Lower C composition and high cover of ALG, DC and SR can be associated with the decreasing proximity of the reef ‘Area’ to the mainland and the criteria of ‘Tourism Development’. ‘Areas’ close to the mainland such as PKMP and LMP was mainly dominated by abiotic components. High ALG composition was found in PPMP and some sites in LMP, indicating the high commercial use in the ‘Area’ have induced the algae colonisation. The reefs nearby the mainland and intense human activities consequently resulting in coral health status with some sites rated as ‘poor’ condition. PTMP and PB recorded the highest C composition, suggesting distance from the mainland as a factor to PTMP while low human intervention is an attributable factor to PB. No ‘poor’ sites were found in PTMP and PB, implying that both areas face minimal impact from the local stressors. The coral communities among the areas were dominated by three types of communities; Acropora-Porites-Montipora (LMP), Acropora-Porites (PTMP, PKMP and PPMP) and Acropora-Porites-Fungia (PB), suggesting linkages to the environmental stressor. Conclusively, apart from filling in the information gaps on the current status of the coral reefs, the findings underline the urgent need for systematic Marine Spatial Planning design and adoption to accurately mitigate threats against a more resilient coral reef health in Malaysia.

Zooxanthellate zoantharians of the genera Zoanthus and Palythoa are increasingly being studied in baseline work such as confirming distributions and long-term monitoring studies in shallow subtropical and tropical waters. There is some evidence that suggests that these genera increase in abundance as an ecological ‘phase shift’ response to ecological degradation. However, such studies have been limited to a few regions, including the Greater Caribbean, Brazil, and Japan, with little work performed in the waters of Southeast Asia and the central Indo-Pacific (CIP). We investigated changes in zoantharian cover within coral reef benthic communities around Terengganu, Malaysia, between July 2013 and September 2014, utilizing the Coral Video Transect method to survey the benthic communities of nine coral reefs. Zoantharian abundance was observed to be inversely proportionate to other major benthic groups (algae, dead corals, hard corals). Overall, zoantharians thrived in reefs with lower biological diversity of reef-building corals. Additionally, at one site (Pasir Akar) we documented a very sudden and large increase of zoantharian cover over two months from March to May 2014. This increase occurred after the reef was heavily damaged during monsoon season. Our results demonstrate that zoantharians are an understudied yet common major component of reefs in Southeast Asia, and that large changes in their abundance can occur very rapidly. Further research investigating longer-term trends of zoantharian abundance in Southeast Asia and the CIP are needed to ascertain if dramatic increases are part of a ‘normal’ recovery process or represent phase shifts in the benthic community structure of coral reefs.

Subtropical Okinawa Island is known for its high marine biodiversity, yet relatively little work has been performed on examining the impacts of coastal development on its marine ecosystems. In this study, we examined three sandy disturbed beaches (including two artificial beaches) on three different sides of the island (artificial Ginowan Tropical Beach on the west coast, artificial Azama San-san Beach on the east coast, public Odo John Man Beach on the south coast) to investigate if differences exist in the environment and crustacean biota between paired disturbed and natural beaches. We conducted seasonal surveys ( n = 4 surveys) by placing quadrats at three paired locations (artificial/disturbed and natural beaches at each location, to collect and record the diversity of infaunal crustacean (isopods and amphipods) taxa. Amphipods and isopods are basal parts of the food chain and therefore many marine creatures’ diets contain them directly or indirectly, and they have been used in many studies as bioindicators. As well, environmental parameters including sand grain size, water temperature, and seawater quality (salinity, dissolved oxygen content, particulate organic matter, turbidity, conductivity, pH, phosphate, nitrite, nitrate, ammonium levels) were obtained from each site during each survey. The results showed that while water nutrients, sand composition, and water quality were very similar between paired disturbed and natural beaches, disturbed beaches had significantly less biodiversity. These results show that despite no obvious effects on water nutrients or quality, disturbed and artificial beaches influence the infaunal crustacean biodiversity/community in the classic manner of a disturbance. Furthermore, our results indicate that amphipods may be better indicators of disturbance compared to isopods, as the numbers of isopods were too low to be used in statistically robust analyses. With increasing tourism and corresponding development of artificial beaches in Okinawa Island, it is clear more research needs to be done on this subject.

Porites is a major reef building coral genus within coral reef ecosystems, and massive Porites are known to be comparatively resistant to changes in water temperature and pH, and to other environmental disturbances. Pink pigmentation response has often been reported in massive Porites. In this study, around Okinawa, Japan, we not observed only pink but also purple pigmentation response on massive Porites. As there have been few ecological studies investigating the prevalence of these pigmentation responses, we examined their frequency on massive Porites around Okinawajima Island, and attempted to clarify what factors potentially affect pigmentation responses More than 30 Porites colonies at each of 17 sites were examined between February to April 2015. On the basis of images, pigmentation response patterns, pigmentation response occurrence levels, and the presence of epibionts, algae, and other species of coral, were also recorded for each colony. The prevalence of pink coloration was 42% higher than purple coloration. At two sites (Odo and Oujima) the prevalence and levels of pigmentation response were approximately half than at all other sites (SIMPROF, p

Marine biodiversity and derived ecosystem services are critical to the healthy functioning of marine ecosystems, and to human economic and societal well-being. Thus, an understanding of marine biodiversity in different ecosystems is necessary for their conservation and management. Coral reefs in particular are noted for their high levels of biodiversity, and among the world’s coral reefs, the subtropical Ryukyu Islands (RYS; also known as the Nansei Islands) in Japan have been shown to harbor very high levels of marine biodiversity. This study provides an overview of the state of marine biodiversity research in the RYS. First, we examined the amount of English language scientific literature in the Web of Science (WoS; 1995–2017) on six selected representative taxa spanning protists to vertebrates across six geographic sub-regions in the RYS. Our results show clear taxonomic and sub-region bias, with research on Pisces, Cnidaria, and Crustacea to be much more common than on Dinoflagellata, Echinodermata, and Mollusca. Such research was more commonly conducted in sub-regions with larger human populations (Okinawa, Yaeyama). Additional analyses with the Ocean Biogeographic Information System (OBIS) records show that within sub-regions, records are concentrated in areas directly around marine research stations and institutes (if present), further showing geographical bias within sub-regions. While not surprising, the results indicate a need to address ‘understudied’ taxa in ‘understudied sub-regions’ (Tokara, Miyako, Yakutane, Amami Oshima), particularly sub-regions away from marine research stations. Second, we compared the numbers of English language scientific papers on eight ecological topics for the RYS with numbers from selected major coral reef regions of the world; the Caribbean (CAR), Great Barrier Reef (GBR), and the Red Sea (RES). As expected, the numbers for all topics in the RYS were well below numbers from all other regions, yet within this disparity, research in the RYS on ‘marine protected areas’ and ‘herbivory’ was an order of magnitude lower than numbers in other regions. Additionally, while manuscript numbers on the RYS have increased from 1995 to 2016, the rate of increase (4.0 times) was seen to be lower than those in the CAR, RES, and GBR (4.6–8.4 times). Coral reefs in the RYS feature high levels of both endemism and anthropogenic threats, and subsequently they contain a concentration of some of the world’s most critically endangered marine species. To protect these threatened species and coral reef ecosystems, more data are needed to fill the research gaps identified in this study.

Variety in video sampling protocol for coral reef survey worldwide has prompted this study to create an optimized protocol for Coral Video Transect (CVT) technique for coral reef survey in Malaysia. The effect of different vertical distance of the camera above the substrate during video recording, number of frames and points analyzed as well as time spent during field and analysis were examined to determine an optimal protocol for CVT technique at different coral reef conditions in Malaysia’s water. Video recording taken at 0.5 m camera distance was selected as optimize vertical distance above the substrate as it can identify more benthic categories than 1.0 m with lesser time taken as well as frames extracted than 0.2 m. Respectively, 80% of total frames extracted from 20 m transect and analyzed with 50 points per frames were chosen as an optimized sample size for its ability to precisely estimate percent cover and accurately identify benthic categories. This optimized protocol was then compared with Line Intercept Transect (LIT) method. No clear difference in estimating percentage cover of major benthic categories between CVT and LIT method, but CVT recorded a significantly higher number of benthic categories with lesser time spent during field survey as compared to LIT method. This implied that the optimize CVT method can precisely estimate percent cover and accurately identify benthic categories in coral communities and are thus more suitable for scientific research and management purposes than LIT method. Other advantages of using this technique are by providing a permanent data that can be reassessed later on, lesser field time and wider survey area. Overall, this study showed that CVT technique is an acceptable alternative method of coral reef survey in Malaysia.