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Declining water quality is one of the main reasons of coral reef degradation in the Thousand Islands off the megacity Jakarta, Indonesia. Shifts in benthic community composition to higher soft coral abundances have been reported for many degraded reefs throughout the Indo-Pacific. However, it is not clear to what extent soft coral abundance and physiology are influenced by water quality. In this study, live benthic cover and water quality (i.e. dissolved inorganic nutrients (DIN), turbidity (NTU), and sedimentation) were assessed at three sites (< 20 km north of Jakarta) in Jakarta Bay (JB) and five sites along the outer Thousand Islands (20-60 km north of Jakarta). This was supplemented by measurements of photosynthetic yield and, for the first time, respiratory electron transport system (ETS) activity of two dominant soft coral genera, Sarcophyton spp. and Nephthea spp. Findings revealed highly eutrophic water conditions in JB compared to the outer Thousand Islands, with 44% higher DIN load (7.65 μM/L), 67% higher NTU (1.49 NTU) and 47% higher sedimentation rate (30.4 g m -2 d -1 ). Soft corals were the dominant type of coral cover within the bay (2.4% hard and 12.8% soft coral cover) compared to the outer Thousand Islands (28.3% hard and 6.9% soft coral cover). Soft coral abundances, photosynthetic yield, and ETS activity were highly correlated with key water quality parameters, particularly DIN and sedimentation rates. The findings suggest water quality controls the relative abundance and physiology of dominant soft corals in JB and may thus contribute to phase shifts from hard to soft coral dominance, highlighting the need to better manage water quality in order to prevent or reverse phase shifts., Competing Interests: The authors declare that they have no competing interests.

Ongoing declines in the structure and function of the world’s coral reefs require novel approaches to sustain these ecosystems and the millions of people who depend on them3. A presently unexplored approach that draws on theory and practice in human health and rural development is to systematically identify and learn from the ‘outliers’—places where ecosystems are substantially better (‘bright spots’) or worse (‘dark spots’) than expected, given the environmental conditions and socioeconomic drivers they are exposed to. Here we compile data from more than 2,500 reefs worldwide and develop a Bayesian hierarchical model to generate expectations of how standing stocks of reef fish biomass are related to 18 socioeconomic drivers and environmental conditions. We identify 15 bright spots and 35 dark spots among our global survey of coral reefs, defined as sites that have biomass levels more than two standard deviations from expectations. Importantly, bright spots are not simply comprised of remote areas with low fishing pressure; they include localities where human populations and use of ecosystem resources is high, potentially providing insights into how communities have successfully confronted strong drivers of change. Conversely, dark spots are not necessarily the sites with the lowest absolute biomass and even include some remote, uninhabited locations often considered near pristine6. We surveyed local experts about social, institutional, and environmental conditions at these sites to reveal that bright spots are characterized by strong sociocultural institutions such as customary taboos and marine tenure, high levels of local engagement in management, high dependence on marine resources, and beneficial environmental conditions such as deep-water refuges. Alternatively, dark spots are characterized by intensive capture and storage technology and a recent history of environmental shocks. Our results suggest that investments in strengthening fisheries governance, particularly aspects such as participation and property rights, could facilitate innovative conservation actions that help communities defy expectations of global reef degradation.

Changes in the coral reef complex can affect predator-prey relationships, resource availability and niche utilisation in the associated fish community, which may be reflected in decreased stability of the functional traits present in a community. This is because particular traits may be favoured by a changing environment, or by habitat degradation. Furthermore, other traits can be selected against because degradation can relax the association between fishes and benthic habitat. We characterised six important ecological traits for fish species occurring at seven sites across a disturbed coral reef archipelago in Indonesia, where reefs have been exposed to eutrophication and destructive fishing practices for decades. Functional diversity was assessed using two complementary indices (FRic and RaoQ) and correlated to important environmental factors (live coral cover and rugosity, representing local reef health, and distance from shore, representing a cross-shelf environmental gradient). Indices were examined for both a change in their mean, as well as temporal (short-term; hours) and spatial (cross-shelf) variability, to assess whether fish-habitat association became relaxed along with habitat degradation. Furthermore, variability in individual traits was examined to identify the traits that are most affected by habitat change. Increases in the general reef health indicators, live coral cover and rugosity (correlated with distance from the mainland), were associated with decreases in the variability of functional diversity and with community-level changes in the abundance of several traits (notably home range size, maximum length, microalgae, detritus and small invertebrate feeding and reproductive turnover). A decrease in coral cover increased variability of RaoQ while rugosity and distance both inversely affected variability of FRic; however, averages for these indices did not reveal patterns associated with the environment. These results suggest that increased degradation of coral reefs is associated with increased variability in fish community functional composition resulting from selective impacts on specific traits, thereby affecting the functional response of these communities to increasing perturbations.

Worldwide, coral reefs are challenged by multiple stressors due to growing urbanization, industrialization and coastal development. Coral reefs along the Thousand Islands off Jakarta, one of the largest megacities worldwide, have degraded dramatically over recent decades. The shift and decline in coral cover and composition has been extensively studied with a focus on large-scale gradients (i.e. regional drivers), however special focus on local drivers in shaping spatial community composition is still lacking. Here, the spatial impact of anthropogenic stressors on local and regional scales on coral reefs north of Jakarta was investigated. Results indicate that the direct impact of Jakarta is mainly restricted to inshore reefs, separating reefs in Jakarta Bay from reefs along the Thousand Islands further north. A spatial patchwork of differentially degraded reefs is present along the islands as a result of localized anthropogenic effects rather than regional gradients. Pollution is the main anthropogenic stressor, with over 80% of variation in benthic community composition driven by sedimentation rate, NO2, PO4 and Chlorophyll a. Thus, the spatial structure of reefs is directly related to intense anthropogenic pressure from local as well as regional sources. Therefore, improved spatial management that accounts for both local and regional stressors is needed for effective marine conservation.

Coral reef ecosystems fringing the coastline of Dahab (South Sinai, Egypt) have experienced increasing anthropogenic disturbance as an emergent international tourism destination. Previous reports covering tourism-related impacts on coastal environments, particularly mechanical damage and destructive fishing, have highlighted the vital necessity for regular ecosystem monitoring of coral reefs near Dahab. However, a continuous scientific monitoring programme of permanent survey sites has not been established to date. Thus, this study conducted in situ monitoring surveys to investigate spatio-temporal variability of benthic reef communities and selected reef-associated herbivores along with reef health indicator organisms by revisiting three of the locally most frequented dive sites during expeditions in March 2010, September 2011 and February 2013. In addition, inorganic nutrient concentrations in reef-surrounding waters were determined to evaluate bottom-up effects of key environmental parameters on benthic reef community shifts in relation to grazer-induced top-down control. Findings revealed that from 2010 to 2013, live hard coral cover declined significantly by 12 % at the current-sheltered site Three Pools (TP), while showing negative trends for the Blue Hole (BH) and Lighthouse (LH) sites. Hard coral cover decline was significantly and highly correlated to a substantial increase in turf algae cover (up to 57 % at TP) at all sites, replacing hard corals as dominant benthic space occupiers in 2013. These changes were correlated to ambient phosphate and ammonium concentrations that exhibited highest values (0.64 ± 0.07 μmol PO4 (3-) l(-1), 1.05 ± 0.07 μmol NH4 (+) l(-1)) at the degraded site TP. While macroalgae appeared to respond to both bottom-up and top-down factors, change in turf algae was consistent with expected indications for bottom-up control. Temporal variability measured in herbivorous reef fish stocks reflected seasonal impacts by local fisheries, with concomitant changes in macroalgal cover. These findings represent the first record of rapid, localised change in benthic reef communities near Dahab, consistent with indications for bottom-up controlled early-stage phase shifts, underlining the necessity for efficient regional wastewater management for coastal facilities.

Difficulties in scaling up theoretical and experimental results have raised controversy over the consequences of biodiversity loss for the functioning of natural ecosystems. Using a global survey of reef fish assemblages, we show that in contrast to previous theoretical and experimental studies, ecosystem functioning (as measured by standing biomass) scales in a non-saturating manner with biodiversity (as measured by species and functional richness) in this ecosystem. Our field study also shows a significant and negative interaction between human population density and biodiversity on ecosystem functioning (i.e., for the same human density there were larger reductions in standing biomass at more diverse reefs). Human effects were found to be related to fishing, coastal development, and land use stressors, and currently affect over 75% of the world's coral reefs. Our results indicate that the consequences of biodiversity loss in coral reefs have been considerably underestimated based on existing knowledge and that reef fish assemblages, particularly the most diverse, are greatly vulnerable to the expansion and intensity of anthropogenic stressors in coastal areas., Competing Interests: The authors have declared that no competing interests exist.

The Malayan term trepang describes a variety of edible holothurians commonly known as sea cucumbers. Although found in temperate and tropical marine waters all over the world, the centre of species diversity and abundance are the shallow coastal waters of Island Southeast Asia. For at least 300 years, trepang has been a highly priced commodity in the Chinese market. Originally, its fishing and trade was a specialized business, centred on the town of Makassar in South Sulawesi (Indonesia). The rise of trepang fishing in the 17(th) century added valuable export merchandize to the rich shallow seas surrounding the islands of Southeast Asia. This enabled local communities to become part of large trading networks and greatly supported their economic development. In this article, we follow Makassan trepang fishing and trading from its beginning until the industrialization of the fishery and worldwide depletion of sea cucumbers in the 20(th) century. Thereby, we identify a number of characteristics which trepang fishing shares with the exploitation of other marine resources, including (1) a strong influence of international markets, (2) the role of patron-client relationships which heavily influence the resource selection, and (3) the roving-bandit-syndrome, where fishermen exploit local stocks of valuable resources until they are depleted, and then move to another area. We suggest that understanding the similarities and differences between historical and recent exploitation of marine resources is an important step towards effective management solutions.