Project

Marine ecosystems and organisms under anthropogenic pressure in Okinawa, Japan

Goal: Within Japan and globally, there is now a great need to focus on environmental assessment of marine ecosystems. There is a clear need for scientific and neutral evaluation of the state of the marine ecosystems of Okinawa Main Island, particularly on the east coast, which has been potentially impacted by landfills and industrial development. We will evaluate impacted and pristine marine ecosystems and their organisms on the bays of the east coast of Okinawa. Expected results will show increased environmental degradation in conjunction with coastal development such as landfill and artificial beaches. Still, some coastal development may not heavily impact marine ecosystems. Results will suggest potential methods to both minimize future impacts via conservation or reconciliatory/rehabilitation methods.

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James Davis Reimer
added 2 research items
The coral reefs of the Coral Triangle and nearby marine regions are the most biodiverse marine ecosystems in the world, providing ecosystem services to hundreds of millions of people. However, like coral reefs in other regions, these ecosystems are in decline due to a myriad of anthropogenically-induced stressors. To mitigate this decline, active coral reef restoration efforts have been increasing worldwide, including in this region. An important end-goal of coral reef restoration is the conservation of functional biodiversity of not only zooxanthellate scleractinian corals, but of all associated coral reef organisms. In this literature review, we collected papers from the Web of Science (1995-2021) focused specifically on coral reef restoration from six countries and regions around the Coral Triangle (Japan, Taiwan, mainland China, Philippines, Malaysia, Indonesia) to examine how much coral reef restoration research has been performed in each area, when it was performed, what methodologies were used, what organisms were targeted, and whether any assessment of biodiversity was included. Our results show great disparity in the research efforts of each area, with the Philippines clearly leading research in the region with almost half of the literature examined, followed by Japan and Indonesia, with nascent efforts in mainland China, Taiwan, and Malaysia. Overall, for the region, research appears to be increasing with time. Research in most areas was concentrated in one or two locations, and almost exclusively focused only on corals. Only approximately 38% of papers mentioned biodiversity in any manner, and only 14% included organisms other than scleractinian corals in their results. It is clear from this review that extensive research and data gaps exist regarding coral reef restoration in the western Pacific and Coral Triangle, particularly from the viewpoint of biodiversity. It is hoped that research can address these gaps before coral reef ecosystems in the region decline even further. Keywords: coral reef ecosystems, knowledge gaps, East Asia, South-East Asia, Indo-Pacific.
Tropicalization is rapidly restructuring subtropical marine communities. A key driver for tropicalization is changes in herbivory pressure that are linked with degrading ecosystem stability. Consequently, subtropical algal beds are being displaced by climate-mediated colonisation of coral communities. This process is thought to be aided by the elevated herbivory resulting from tropicalization, but the relative contribution to herbivory by different taxa is not fully understood. Evaluating herbivory pressure and its effect on coral cover and rugosity across a subtropical latitudinal gradient will help predict how these processes may change with further tropicalization and ocean warming. Herbivory pressure exerted by fishes and urchins across this subtropical latitudinal gradient remains unquantified. Using in-situ feeding observations, we quantify fish and urchin herbivory pressure at seven sites across non-accreting coral communities, and warmer accreting coral reefs in southern Japan. We then relate herbivory pressure to respective fish and urchin community structure and coral cover and rugosity. Urchin herbivory is greater on non-accreting coral communities than on true coral accreting reefs; a result which is reversed for fish herbivory. Overall, herbivory pressure is greater on accreting coral reefs than on coral non-accreting communities , but is dependent on reef characteristics as community structures differ more strongly among reefs than between regions. These factors are linked to coral cover and rugosity that differ between reefs, but not between climatic regions, further emphasising the influence of local factors on the benthic cover and the associated fish and urchin community, and thus herbivory pressure. Our findings provide a foundation for understanding how non-accreting coral communities may respond to ongoing tropicalization, given the fish and invertebrate herbivores they host.
James Davis Reimer
added a research item
The Indo-Pacific zooxanthellate scleractinian coral genus Montipora is the host of many coral diseases. Among these are cyanobacterial Black Band Disease (BBD) and Skeletal Growth Anomalies (GAs), but in general data on both diseases are lacking from many regions of the Indo-Pacific, including from Okinawa, southern Japan. In this study, we collected annual prevalence data of Black Band Disease (BBD) and Skeletal Growth Anomalies (GAs) affecting the encrusting form of genus Montipora within the shallow reefs of the subtropical Sesoko Island (off the central west coast of Okinawajima Island) from summer to autumn for four years (2017 to 2020). In 2020 Monti-pora percent coverage and colony count were also assessed. Generalized Linear Models (GLM) were used to understand the spatial and temporal variation of both BBD and GAs in the nearshore (NE) and reef edge (RE) sites, which revealed higher probability of BBD occurrence in RE sites. BBD prevalence was significantly higher in 2017 in some sites than all other years with site S12 having significant higher probability during all four surveyed years. In terms of GAs, certain sites in 2020 had higher probability of occurrence than during the other years. While the general trend of GAs increased from 2017 to 2020, it was observed to be non-fatal to colonies. In both diseases, the interaction between sites and years was significant. We also observed certain BBD-infected colonies escaping complete mortality. BBD progression rates were monitored in 2020 at site S4, and progression was related to seawater temperatures and was suppressed during periods of heavy rain and large strong typhoons. Our results suggest that higher BBD progression rates are linked with high sea water temperatures (SST > bleaching threshold SST) and higher light levels (> 1400 µmol m −2 s −1), indicating the need for further controlled laboratory experiments. The current research will help form the basis for continued future research into these diseases and their causes in Okinawa and the Indo-Pacific Ocean.
James Davis Reimer
added a research item
Offshore Onna Village, Okinawa Island, Japan, there is a large and densely covered coral assemblage of free-living mushroom corals (Scleractinia: Fungiidae) on a reef slope at depths from 20 m to 32 m, covering an area of approximately 350 × 40 m 2. From previous research, it is known that migration distances of mushroom corals may depend on coral shapes, coral sizes, substrate, and bottom inclination. However, until now there have been no published examples of regular Fungiidae movement and behavior from typhoon-exposed coastlines, such as those in the western Pacific Ocean. Our surveys across three years offshore Onna Village show that mushroom corals always move in down-slope direction from shallow to deeper reef zones. The results indicated that mushroom corals migrated faster in autumn than in other seasons, and that oval-elongate fungiids, and particularly those with a smooth underside, migrated more quickly than species with other shapes. Surprisingly, we observed a negative relationship between the presence of typhoons and migration rates. We also observed active migration by fungiid individuals to escape situations in which they were threatened to become overgrown by Acropora corals, or when they needed to escape from burial underneath coral debris.
James Davis Reimer
added a research item
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<0.01). In addition, there were significant positive correlations between epibionts and pigmentation response. It may be possible that pink and purple coloration are fundamentally different phenomena, although the physiological mechanisms of purple coloration have not been clarified.
James Davis Reimer
added a research item
Sea pen species of the genus Calibelemnon are important components of soft bottom communities. Here, we formally describe Calibelemnon hinoenma sp. nov. from shallow waters in Amami Oshima, Kagoshima in the Ryukyu Islands, via molecular and morphological observations and analyses. This species can be distinguished from its congeners by the presence of paired autozooids, siphonozooids aligned irregularly in one to three rows at the side of the rachis between polyps, and the red-brown rufous color of the oral disks. Phylogenetically, the new species is located in an Anthoptilum-Umbellula-Calibelemnon clade. Ancestral state reconstruction analyses suggest that Calibelemnon species may have undergone at least two habitat changes, from shallow to deep waters, followed by a return to shallow waters. In the Ryukyu Islands, there have been many recent discoveries of unique marine species, with this sea pen species being the latest.
James Davis Reimer
added a research item
• Anemonefish and host anemones are distributed in the shallow waters of coral reefs, and thus their existence may be affected by coastal development. The Ryukyu Archipelago includes the Okinawa and Sakishima Islands; the former has experienced extensive land reclamation and drainage in coastal areas while the latter still mostly contains natural coasts. To consider the layout of protected areas needed to conserve diversity of host anemones and anemonefish in the Ryukyu Archipelago, the community structure and coexistence mechanisms of anemones and anemonefish were compared between Okinawa and Sakishima Islands. • Six species of anemonefish and seven species of host anemone are distributed in both islands. Among 15 species‐pair interactions observed in six species of anemonefish in the Sakishima Islands, 14 were explained by the niche differentiation hypothesis and only one interaction was explained by the cohabitation hypothesis. In the Okinawa Islands, 13 interactions were explained by the niche differentiation hypothesis, one by the cohabitation hypothesis and one by the lottery hypothesis. • For both host anemones and anemonefish, β‐diversity in the Okinawa Islands was lower and had a more nested structure than that of the Sakishima Islands. β‐Diversity and its nestedness did not differ between the two regions excluding study sites adjacent to coastlines, suggesting that differences in the coastal environment affected the diversity of anemones and anemonefish in the Ryukyu Archipelago. • These results suggested that there is an urgent need to prioritize the conservation of reef edges, where species diversity is relatively higher than directly next to the terrestrial coastline in Okinawa Island. In the Sakishima Islands, where many natural coasts remain, a wider area from directly next to the coast out to the reef edge needs to be comprehensively protected to increase β‐diversity.
James Davis Reimer
added a research item
Global climate change is leading to damage and loss of coral reef ecosystems. On subtropical Okinawa Island in southwestern Japan, the prefectural government is working on coral reef restoration by outplanting coral colonies from family Acroporidae back to reefs after initially farming colonies inside protected nurseries. In order to establish a baseline for future comparisons, in this study we documented the current status of reefs undergoing outplanting at Okinawa Island, and nearby locations where no human manipulation has occurred. We examined three sites on the coast of Onna Village on the west coast of the island; each site included an outplanted and control location. We used (1) coral rubble sampling to measure and compare abundance and diversity of rubble cryptofauna; and (2) coral reef monitoring using Line Intercept Transects to track live coral coverage. Results showed that rubble shape had a positive correlation with the numbers of animals found within rubble themselves and may therefore constitute a reliable abundance predictor. Each outplanted location did not show differences with the corresponding control location in terms of rubble cryptofauna abundance, but outplanted locations had significantly lower coral coverage. Overall, differences between sites (Maeganeku1, Maeganeku2 and Manza, each including both outplanted and control locations) were significant, for both rubble cryptofauna and coral coverage. We recommend (1) to outplant colonies from more stress-resistant genera in place of Acropora, and (2) to conduct regular surveys to monitor the situation closely. With a lack of baseline data preceding impacts, rigorous monitoring over time can highlight trends towards increases or decreases in evaluated variables, allowing to obtain a clearer idea of the effects of transplants and on the trajectory of impacts due to climate change and local stressors. Finally, we also recommend (3) to establish conservation and sustainable practices that could aid the ongoing restoration efforts such as installing anchoring buoys to reduce impacts from anchoring, which could reduce coral mortality of both outplanted and native coral colonies.
James Davis Reimer
added a research item
Global warming is leading to range shifts of marine species, threatening the structure and functioning of ecological communities and human populations that rely on them. The largest changes are seen in biogeographic transition zones, such as subtropical reef communities, where species range shifts are already causing substantial community reorganisation. This causes functional changes in communities over subtropical latitudes, though a baseline functional understanding remains elusive for many taxa. One key marine taxon are molluscs, which provide many ecosystem services, are important prey for fishes and are also fisheries targets themselves, but remain largely unstudied. Here, we examine the trait composition, functional diversity, and functional redundancy of mollusc assemblages along the tropical-to-temperate transition in Japan (25° to 35° Northern latitude). Specifically, we use a trait database of 88 mollusc species from 31 subtropical reefs along the Pacific coast of Japan to show that trait composition of mollusc assemblages changes continuously along the latitudinal gradient. We discover that functional diversity of mollusc assemblages decreases with increasing latitude, a pattern associated with declines in functional dispersion. Moreover, we find a clear distinction between tropical and subtropical mollusc assemblages, with substrate-attached, suspension feeding bivalves more abundant in the tropics and free-living gastropod grazers more prevalent at higher latitudes. Our trait-based evidence in this study shows a contraction and almost complete shift in the functioning of marine mollusc assemblages at biogeographic transition zones and our trait database facilitates further study. Our findings provide evidence of the changing taxonomic and functional composition of extant mollusc communities with latitude, pointing to potential pertinent changes and tropicalisation of these communities with rapid ocean warming.
James Davis Reimer
added a research item
Loss of biodiversity from lower to upper trophic levels reduces overall productivity and stability of coastal ecosystems in our oceans, but rarely are these changes documented across both time and space. the characterisation of environmental DNA (eDNA) from sediment and seawater using metabarcoding offers a powerful molecular lens to observe marine biota and provides a series of 'snapshots' across a broad spectrum of eukaryotic organisms. Using these next-generation tools and downstream analytical innovations including machine learning sequence assignment algorithms and co-occurrence network analyses, we examined how anthropogenic pressures may have impacted marine biodiversity on subtropical coral reefs in Okinawa, Japan. Based on 18S ribosomal RNA, but not ITS2 sequence data due to inconsistent amplification for this marker, as well as proxies for anthropogenic disturbance, we show that eukaryotic richness at the family level significantly increases with medium and high levels of disturbance. This change in richness coincides with compositional changes, a decrease in connectedness among taxa, an increase in fragmentation of taxon co-occurrence networks, and a shift in indicator taxa. Taken together, these findings demonstrate the ability of eDNA to act as a barometer of disturbance and provide an exemplar of how biotic networks and coral reefs may be impacted by anthropogenic activities.
James Davis Reimer
added a research item
Shallow water coral reefs are the most diverse marine ecosystems, but there is an immense gap in knowledge when it comes to understanding the diversity of the vast majority of marine biota in these ecosystems. This is especially true when it comes to understudied small and cryptic coral reef taxa in understudied ecosystems, such as mesophotic coral reef ecosystems (MCEs). MCEs were reported in Japan almost fifty years ago, although only in recent years has there been an increase in research concerning the diversity of these reefs. In this study we describe the first stoloniferous octocoral from MCEs, Hadaka nudidomus gen. nov. et sp. nov., from Iriomote and Okinawa Islands in the southern Ryukyus Islands. The species is zooxanthellate; both specimens host Cladocopium LaJeunesse & H.J.Jeong, 2018 (formerly Symbiodinium 'Clade C') and were collected from depths of ~33 to 40 m. Additionally, H. nudidomus gen. nov. et sp. nov. is both sclerite-free and lacks free pinnules, and both of these characteristics are typically diagnostic for octocorals. The discovery and morphology of H. nudidomus gen. nov. et sp. nov. indicate that we still know very little about stoloniferous octocoral diversity in MCEs, their genetic relationships with shallower reef species, and octocoral-symbiont associations. Continued research on these subjects will improve our understanding of octocoral diversity in both shallow and deeper reefs.
James Davis Reimer
added a research item
Okinawa is the largest and most populated island of the Ryukyu Archipelago in southern Japan and is renowned for its natural resources and beauty. Similar as to what has been happening in the rest of the country, Okinawa Island has been affected by an increasing amount of development and construction work. The trend has been particularly acute after reversion to Japanese sovereignty in 1972, following 27 years of postwar American administration. A coastline once characterized by extended sandy beaches surrounded by coral reefs now includes tracts delimited by seawalls, revetments, and other human-made hardening structures. Additionally, part of coastal Okinawa Island was obtained by land-filling shallow ocean areas (land reclamation). Nevertheless, the current extension of the artificial coastline, as well as the level of fragmentation of the natural coastline are unclear, due to the lack of both published studies and easily accessible and updated datasets. The aims of this research were to quantify the extension of coastline alterations in Okinawa Island, including the amount of land-filling performed over the last 41 years, and to describe the coastlines that have been altered the most as well as those that are still relatively pristine. The analyses were performed using a reference map of Okinawa Island based on GIS vector data extracted from the OpenStreetMap (OSM) coastline dataset (average node distance for Okinawa Island = 24 m), in addition to satellite and aerial photography from multiple providers. We measured 431.8 km of altered coastline, equal to about 63% of the total length of coastline in Okinawa Island. Habitat fragmentation is also an issue as the remaining natural coastline was broken into 239 distinct tracts (mean length = 1.05 km). Finally, 21.03 km 2 of the island's surface were of land reclaimed over the last 41 years. The west coast has been altered the most, while the east coast is in relatively more natural conditions, particularly the northern part, which has the largest amount of uninterrupted natural coastline. Given the importance of the ecosystem services that coastal and marine ecosystems provide to local populations of subtropical islands, including significant economic income from tourism, conservation of remaining natural coastlines should be given high priority.
James Davis Reimer
added a research item
Okinawa is the largest and most populated island of the Ryukyu Archipelago in southern Japan and is renowned for its natural resources and beauty. Similar as to what has been happening in the rest of the country, Okinawa Island has been affected by an increasing amount of development and construction work. The trend has been particularly acute after reversion to Japanese sovereignty in 1972, following 27 years of post-war American administration. A coastline once characterized by extended sandy beaches surrounded by coral reefs now includes vast portions delimited by seawalls, revetments, and other human-made hardening structures. Additionally, a significant part of coastal Okinawa Island is now constituted by artificially reclaimed land. Nevertheless, the degree of severity of the current situation is unclear, due to the lack of both published studies and easily accessible and updated datasets. The aims of this study were to quantify the extension of coastline alterations in Okinawa Island, including the amount of land-filling performed over the last 51 years, and to describe the coastlines that have been altered the most as well as those that are still relatively pristine. Our analyses were performed using a reference map of Okinawa Island based on GIS vector data extracted from the OpenStreetMap (OSM) coastline dataset, in addition to satellite and aerial photography from multiple providers. We measured 431.8 km of altered coastline, equal to about 63% of the total length of coastline in Okinawa Island. Habitat fragmentation is also an issue as the remaining natural coastline was broken into 239 distinct tracts (mean length = 1.05 km). Finally, 21.03 km ² of the island’s surface were of land reclaimed over the last 51 years. The west coast has been altered the most, while the east coast is in relatively more natural condition, particularly the northern part, which has the largest amount of uninterrupted natural coastline. Given the importance of ecosystem services that coastal and marine ecosystems provide to local populations of subtropical islands, including significant economic income from tourism, conservation of remaining natural coastlines should be given high priority.
James Davis Reimer
added a research item
1. 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. 2. 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. 3. 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. 4. 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. 5. 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.
James Davis Reimer
added a research item
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.
James Davis Reimer
added an update
We have a new paper out providing baseline data for Okinawa Prefecture's coral restoration project. Free download link here (active for another 49 days):
 
Giovanni Diego Masucci
added a research item
Coral reefs in the Ryukyu Islands, southern Japan, have been undergoing degradation for at least five decades. Recently, the archipelago has been hit by bleaching events for two consecutive years (summers of 2016–2017). Shallow coral communities have been reported as especially affected. In this study, using underwater transects, we assessed the status of shallow coral reef communities in Kume Island, at seven distinct locations in Shimajiri Bay, following reports from local fishermen and divers of heavy bleaching across the bay. Our data and analyses revealed that the benthic environment in the bay has algae as the main component, with an average coral cover of only 7.2%. Branching coral colonies, which used to be the most common morphology in Kume Island reefs, accounted for just 7.6% of the total coral cover. Notably, the genus Acropora was almost completely absent from our transects, although its recent presence was confirmed by dead colonies making up 4.12% of total transect coverage, suggesting that restoration efforts focused on this genus might be possible in the future. In order for these to be successful, however, a better understanding of the environmental situation at Kume Island is required, including the effects of human activities on coral reef communities.
James Davis Reimer
added 6 research items
The species diversity of anemonefish in tropical regions has been explained by the niche differentiation hypothesis or cohabitation hypothesis. However, anemonefish community structure has seldom been investigated in high-latitude areas. To understand the mechanism underlying species diversity of anemonefish in the northern limits of their distribution and to compare with previous results from tropical and other areas, we investigated the community structure of anemonefish around the western coast of Okinawa-jima Island, Japan. Seven species of host anemones and six species of anemonefish were distributed across the 12 study sites. The diversity index of anemonefish and the host anemone varied among sites; anemonefish diversity increased with diversity of host anemones, which was associated with the ratio of sandy areas and distance from shore. The density of each species of anemonefish increased with the density of the primary host anemone, which suggests that niche differentiation may be occurring. However, results of two species of host anemone (Stichodactyla mertensii, Heteractis magnifica) associated each with two species of anemonefish did not support the niche differentiation hypothesis. Forty-seven percent of S. mertensii were shared by Amphiprion clarkii and A. sandaracinos simultaneously, supporting the cohabitation hypothesis. Amphiprion ocellaris and A. perideraion used the same host H. magnifica, but never shared a host simultaneously. Moreover, anemone size and water depth did not differ between the two anemonefish species, suggesting the possibility of the lottery model. In subtropical Okinawa, 86.7% of species interactions supported the niche differentiation hypothesis, 6.7% supported the cohabitation hypothesis, and 6.7% supported the lottery hypothesis. The mechanisms of coexistence of anemonefish in subtropical regions include not only niche differentiation and cohabitation but also the lottery hypothesis, which has not been reported in tropical regions.
Coral reefs are increasingly subject to erosion, pollutants and sediment-rich run offs due to deforestation, and intensive agriculture and urbanization. In Okinawa, Japan, reefs have been degrading dramatically over the last 50 years, mostly due to direct human pressure, aggravated by global change. Artificial barriers such as seawalls are known to lead to beach narrowing or loss, and to exacerbate erosion by increasing the intensity of longshore currents and preventing the exchange of sand between dunes and beaches, leading the offshore profile to become steeper and impacting species whose life cycles are fully or partially linked to the shoreline. Conversely, there have been reports of seawalls contributing to increased coral growth by providing hard substrate and protection. Overall, seawalls’ effects on tropical reef ecosystems are still mostly unknown or misunderstood. Regardless, seawalls, most commonly made in Japan by “tetrapod” blocks, have been deployed throughout the coasts of Okinawa Island, and 55% of the current coastline is artificially reinforced. In this study, we assessed the current environmental situation of the coast in front of Ogimi Village, in the north-west of Okinawa Island, by assessing the abundance of corals growing on the tetrapod seawall, and by comparing the area affected by the wall, both in front and behind, with a natural control location immediately next to it, at similar depths and distances from the shoreline. In order to compare the two locations, we analyzed the benthic community, depth profiles, sediment composition, and water energy levels. Our surveys revealed that the benthic community was heavily affected by the presence of the blocks, leading to the complete absence of living corals in front and behind the seawall, as opposed to the natural control area, where high coral cover was recorded. The seawall itself featured a coral cover of less than 1%. Depth was affected by the presence of the seawall with reductions both in front and behind the blocks, due to the accumulation of broken coral rubble and sediment. Granulometric analyses highlighted the presence of finer sediment behind the wall, indicative of low levels of water energy. Conversely, the area immediately in front of the wall was characterized by coarser sediment grains, typical of environments affected by a stronger water energy. The control area featured a sediment composition intermediate between the two situations measured in front and behind the seawall. To experimentally confirm the presence of different levels of water energy, spheres made in plaster were fixed to the seafloor and differences in weight and diameter were measured after a period of three days. The plaster balls placed in front of the seawall showed significantly higher levels of erosion compared to those at the control site, while the opposite was measured for the experimental units placed behind the blocks. Overall, our experiment and observations demonstrate that tetrapod seawalls affect the physical environment of a coastline and its benthic community, with dramatic negative consequences for coral survival. Given the abundance of these constructions on the island, more research is urgently needed, and the massive deployment of seawalls, which has increasingly affected Okinawa since 1972, should be reconsidered.
Given predicted increases in urbanization in tropical and subtropical regions, understanding the processes shaping urban coral reefs may be essential for anticipating future conservation challenges. We used a case study approach to identify unifying patterns of urban coral reefs and clarify the effects of urbanization on hard coral assemblages. Data were compiled from 11 cities throughout East and Southeast Asia, with particular focus on Singapore, Jakarta, Hong Kong, and Naha (Okinawa). Our review highlights several key characteristics of urban coral reefs, including “reef compression” (a decline in bathymetric range with increasing turbidity and decreasing water clarity over time and relative to shore), dominance by domed coral growth forms and low reef complexity, variable city-specific inshore-offshore gradients, early declines in coral cover with recent fluctuating periods of acute impacts and rapid recovery, and colonization of urban infrastructure by hard corals. We present hypotheses for urban reef community dynamics and discuss potential of ecological engineering for corals in urban areas.
James Davis Reimer
added a research item
Background Effective biodiversity monitoring is fundamental in tracking changes in ecosystems as it relates to commercial, recreational, and conservation interests. Current approaches to survey coral reef ecosystems center on the use of indicator species and repeat surveying at specific sites. However, such approaches are often limited by the narrow snapshot of total marine biodiversity that they describe and are thus hindered in their ability to contribute to holistic ecosystem-based monitoring. In tandem, environmental DNA (eDNA) and next-generation sequencing metabarcoding methods provide a new opportunity to rapidly assess the presence of a broad spectrum of eukaryotic organisms within our oceans, ranging from microbes to macrofauna. Methods We here investigate the potential for rapid universal metabarcoding surveys (RUMS) of eDNA in sediment samples to provide snapshots of eukaryotic subtropical biodiversity along a depth gradient at two coral reefs in Okinawa, Japan based on 18S rRNA. Results Using 18S rRNA metabarcoding, we found that there were significant separations in eukaryotic community assemblages (at the family level) detected in sediments when compared across different depths ranging from 10 to 40 m ( p = 0.001). Significant depth zonation was observed across operational taxonomic units assigned to the class Demospongiae (sponges), the most diverse class (contributing 81% of species) within the phylum Porifera; the oldest metazoan phylum on the planet. However, zonation was not observed across the class Anthozoa (i.e., anemones, stony corals, soft corals, and octocorals), suggesting that the former may serve as a better source of indicator species based on sampling over fine spatial scales and using this universal assay. Furthermore, despite their abundance on the examined coral reefs, we did not detect any octocoral DNA, which may be due to low cellular shedding rates, assay sensitivities, or primer biases. Discussion Overall, our pilot study demonstrates the importance of exploring depth effects in eDNA and suggest that RUMS may be applied to provide a baseline of information on eukaryotic marine taxa at coastal sites of economic and conservation importance.
James Davis Reimer
added 2 research items
In Japan, the subtropical Ryukyu Archipelago (RYS; also known as the Nansei Islands) with its coral reefs has 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 scientific literature in the Web of Science (WoS; 1995-2017) on six selected representative taxa spanning from 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 the clear need to study ‘understudied’ taxa in ‘understudied sub-regions’ (Tokara, Miyako, Yakutane, Amami Oshima), and to study ‘understudied areas’ of some sub-regions away from marine research stations. Second, we compared the numbers of scientific papers on eight ecological topics for the RYS with numbers from selected major coral reef regions of the world; the Caribbean (CAB), Great Barrier Reef (GBR), and the Red Sea (RES). Not unexpectedly, 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 CAB, RES, and GBR (4.6 to 8.4 times). As the RYS are considered to contain among the most critically endangered coral reef biodiversity in the world due to high levels of both endemism and anthropogenic threats, much work is urgently needed to address the areas of relative research weakness identified in this study.
In Japan, the subtropical Ryukyu Archipelago (RYS; also known as the Nansei Islands) with its coral reefs has 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 scientific literature in the Web of Science (WoS; 1995-2017) on six selected representative taxa spanning from 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 the clear need to study ‘understudied’ taxa in ‘understudied sub-regions’ (Tokara, Miyako, Yakutane, Amami Oshima), and to study ‘understudied areas’ of some sub-regions away from marine research stations. Second, we compared the numbers of scientific papers on eight ecological topics for the RYS with numbers from selected major coral reef regions of the world; the Caribbean (CAB), Great Barrier Reef (GBR), and the Red Sea (RES). Not unexpectedly, 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 CAB, RES, and GBR (4.6 to 8.4 times). As the RYS are considered to contain among the most critically endangered coral reef biodiversity in the world due to high levels of both endemism and anthropogenic threats, much work is urgently needed to address the areas of relative research weakness identified in this study.
James Davis Reimer
added an update
Our new work examining anemonefish diversity in the Ryukyus is out - while this work is not directly related with our project, it provides a base from which our next work - more related to human impacts and conservation - will emerge from.
 
James Davis Reimer
added an update
A massive review paper including information from Okinawa is now available freely online (and on ResearchGate).
Urban coral reefs: Degradation and resilience of hard coral assemblages in coastal cities of East and Southeast Asia. Heery et al. 2018 Marine Pollution Bulletin.
 
James Davis Reimer
added a research item
In Japan, the subtropical Ryukyu Archipelago (RYS; also known as the Nansei Islands) with its coral reefs has 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 scientific literature in the Web of Science (WoS; 1995-2017) on six selected representative taxa spanning from 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 the clear need to study ‘understudied’ taxa in ‘understudied sub-regions’ (Tokara, Miyako, Yakutane, Amami Oshima), and to study ‘understudied areas’ of some sub-regions away from marine research stations. Second, we compared the numbers of scientific papers on eight ecological topics for the RYS with numbers from selected major coral reef regions of the world; the Caribbean (CAB), Great Barrier Reef (GBR), and the Red Sea (RES). Not unexpectedly, 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 CAB, RES, and GBR (4.6 to 8.4 times). As the RYS are considered to contain among the most critically endangered coral reef biodiversity in the world due to high levels of both endemism and anthropogenic threats, much work is urgently needed to address the areas of relative research weakness identified in this study.
James Davis Reimer
added a research item
193 words) Environmental DNA (eDNA) metabarcoding has great potential in assessing comparative total biodiversity, and facilitating robust comparisons across a wide variety of sites and taxa. In particular, eDNA combined with next-generation sequencing can help address the huge critical data gaps in our understanding of marine biodiversity, especially in regions with high levels of understudied diversity such as the coral reefs of the Indo-Pacific region. Within this region, Okinawa is known for its high levels of marine biodiversity and endemicity, and also for the threats shallow coral reef ecosystems face from a variety of stressors including local-scale coastal development and over-exploitation to global scale threats such as climate change. In this study, we generated eDNA metabarcoding sequences from sediment and seawater samples from various reefs in Okinawa, Japan. At the same time, we developed a simple methodology to assess the relative health of these reefs based on anthropogenic and natural stressors. We discuss our eDNA results in comparison to coral reef health, identify potential bioindicator taxa, and explore the relative biodiversity of coral reef communities across sites. Our results indicate that taxa asides from the corals (Scleractinia) can provide robust information on coral reef health. Short description (120 characters): Utilization of eDNA metabarcoding to assess general health of wide range of coral reefs in Okinawa.
James Davis Reimer
added an update
At long last, the follow up to our 2015 Mar Poll Bull paper is out. This new paper investigates microbial communities and chemodiversity at the same sites on both sides of the Kaichu-Doro causeway... Check out the new paper!
Soliman et al. 2017 Frontiers in Microbiology
 
James Davis Reimer
added an update
Interviewed yesterday in a local newspaper about the potential effects of landfill and placement of 220 large concrete blocks in a pristine coral bay. Obviously there is a lot of work to do here.
 
James Davis Reimer
added 7 research items
The recently described aragonite calcium-carbonate skeleton forming octocoral species Nanipora kamurai (Cnidaria: Anthozoa: Octocorallia: Helioporacea) is known from only one locality in Okinawa, Japan. This locality, Ama Beach on Zamami Island, is a shallow (1 to 1.5 m) sandy reef moat popular with recreational swimmers and snorkelers during summer months. Additionally, the species has been reported to be rare at this site, although no concrete survey data existed. This study quantitatively examined the rarity of N. kamurai at this site via examining all rocks and rubbles within a transect survey (n=6) of 2400m2. Our results show that N. kamurai is indeed low in number, with only 8 colonies found over the entire survey area. Of coral rubble and rocks examined, only slightly more than 1% of rocks had N. kamurai colonies (8/739 rocks), for a density of 0.003 colonies per m2. As this species is known from only this location and additionally low in abundance, local management to ensure the designated recreational swimming area at Ama Beach does not overlap with the colonies’ direct habitat should be undertaken until additional populations at other locations can be confirmed.
Preliminary phylogenetic analyses of specimens of a leucothoid amphipod, Leucothoe vulgaris, collected from sponges, ascidians, and coral rubble from Okinawa, Japan, were completed using mitochondrial COI and nuclear 18S ribosomal DNA sequences. Analyses of sequences from 83 specimens demonstrate that populations of L. vulgaris likely entail at least two cryptic species, which are reciprocally monophyletic and reproductively isolated. These two potentially cryptic species live in sympatry but are apparently morphologically identical, suggesting a geographically driven divergence process and secondary contact. Within each clade, two major subclades corresponding to the east and west coast of Okinawa Island were present, with divergence times of approximately 1.61–1.83 mya. This last result suggests a role of Pleistocene sea level changes in the current patterns of intra-specific genetic structure and highlights the need for a more comprehensive sampling of L. vulgaris throughout the Indo-west Pacific. © The Trustees of the Natural History Museum, London 2015. All Rights Reserved.
Understanding genetic connectivity is fundamental for ecosystem-based management of marine resources. Here we investigate the metapopulation structure of the edible sea cucumber Holothuria edulis Lesson, 1830 across Okinawa Island, Japan. This species is of economic and ecological importance and is distributed from the Red Sea to Hawai‘i. We examined sequence variation in fragments of mitochondrial cytochrome oxidase subunit I (COI) and 16S ribosomal RNA (16S), and nuclear histone (H3) at six locations across Okinawa Island. We found higher haplotype diversity for mtDNA (COI: Hd = 0.69 and 16S: Hd = 0.67) and higher heterozygosity of nDNA (H3: H E = 0.39) in populations from the west coast of Okinawa compared to individuals from populations on the east coast (COI: Hd = 0.40; 16S: Hd = 0.21; H3: H E = 0.14). Overall population structure was significant (AMOVA results for COI: Φ ST = 0.49, P < 0.0001; 16S: Φ ST = 0.34, P < 0.0001; H3: Φ ST = 0.12, P < 0.0001). One population in the east, Uruma, showed elevated pairwise Φ ST values in comparisons with all other sites and a marked reduction of genetic diversity (COI: Hd = 0.25 and 16S: Hd = 0.24), possibly as a consequence of a shift to a more dominant asexual reproduction mode. Recent reports have indicated that coastal development in this area influences many marine organisms, and ecosystem degradation in this location could cause the observed decrease of genetic diversity and isolation of H. edulis in Uruma. Our study should provide valuable data to help with the urgently needed management of sea cucumber populations in Okinawa, and indicates particular attention needs to be paid to vulnerable locations.
James Davis Reimer
added a project goal
Within Japan and globally, there is now a great need to focus on environmental assessment of marine ecosystems. There is a clear need for scientific and neutral evaluation of the state of the marine ecosystems of Okinawa Main Island, particularly on the east coast, which has been potentially impacted by landfills and industrial development. We will evaluate impacted and pristine marine ecosystems and their organisms on the bays of the east coast of Okinawa. Expected results will show increased environmental degradation in conjunction with coastal development such as landfill and artificial beaches. Still, some coastal development may not heavily impact marine ecosystems. Results will suggest potential methods to both minimize future impacts via conservation or reconciliatory/rehabilitation methods.
 
James Davis Reimer
added a research item
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 ( 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.