Centre de Recherches Insulaires et Observatoire de l'Environnement

Greening roofs or walls to cool down city areas during summer, to capture storm water, to abate pollution, and to increase human well-being while enhancing biodiversity: nature-based solutions (NBS) refer to the sustainable management and use of nature for tackling societal challenges. Building on and comple- menting traditional biodiversity conservation and management strategies, NBS integrate science, policy, and practice and create biodiversity benefits in terms of diverse, well-managed ecosystems.

BACKGROUND: Coral bleaching events vary in severity, however, to date, the hierarchy of susceptibility to bleaching among coral taxa has been consistent over a broad geographic range and among bleaching episodes. Here we examine the extent of spatial and temporal variation in thermal tolerance among scleractinian coral taxa and between locations during the 2010 thermally induced, large-scale bleaching event in South East Asia. METHODOLOGY/PRINCIPAL FINDINGS: Surveys to estimate the bleaching and mortality indices of coral genera were carried out at three locations with contrasting thermal and bleaching histories. Despite the magnitude of thermal stress being similar among locations in 2010, there was a remarkable contrast in the patterns of bleaching susceptibility. Comparisons of bleaching susceptibility within coral taxa and among locations revealed no significant differences between locations with similar thermal histories, but significant differences between locations with contrasting thermal histories (Friedman = 34.97; p<0.001). Bleaching was much less severe at locations that bleached during 1998, that had greater historical temperature variability and lower rates of warming. Remarkably, Acropora and Pocillopora, taxa that are typically highly susceptible, although among the most susceptible in Pulau Weh (Sumatra, Indonesia) where respectively, 94% and 87% of colonies died, were among the least susceptible in Singapore, where only 5% and 12% of colonies died. CONCLUSIONS/SIGNIFICANCE: The pattern of susceptibility among coral genera documented here is unprecedented. A parsimonious explanation for these results is that coral populations that bleached during the last major warming event in 1998 have adapted and/or acclimatised to thermal stress. These data also lend support to the hypothesis that corals in regions subject to more variable temperature regimes are more resistant to thermal stress than those in less variable environments.

Networks of no-take marine protected areas (MPAs) have been widely advocated for the conservation of marine biodiversity. But for MPA networks to be successful in protecting marine populations, individual MPAs must be self-sustaining or adequately connected to other MPAs via dispersal. For marine species with a dispersive larval stage, populations within MPAs require either the return of settlement-stage larvae to their natal reserve or connectivity among reserves at the spatial scales at which MPA networks are implemented. To date, larvae have not been tracked when dispersing from one MPA to another, and the relative magnitude of local retention and connectivity among MPAs remains unknown. Here we use DNA parentage analysis to provide the first direct estimates of connectivity of a marine fish, the orange clownfish (Amphiprion percula), in a proposed network of marine reserves in Kimbe Bay, Papua New Guinea. Approximately 40% of A. percula larvae settling into anemones in an island MPA at 2 different times were derived from parents resident in the reserve. We also located juveniles spawned by Kimbe Island residents that had dispersed as far as 35 km to other proposed MPAs, the longest distance that marine larvae have been directly tracked. These dispersers accounted for up to 10% of the recruitment in the adjacent MPAs. Our findings suggest that MPA networks can function to sustain resident populations both by local replenishment and through larval dispersal from other reserves. More generally, DNA parentage analysis provides a direct method for measuring larval dispersal for other marine organisms.

Abstract Increasingly frequent severe coral bleaching is among the greatest threats to coral reefs posed by climate change. Global climate models (GCMs) project great spatial variation in the timing of annual severe bleaching (ASB) conditions; a point at which reefs are certain to change and recovery will be limited. However, previous model-resolution projections (~1 × 1°) are too coarse to inform conservation planning. To meet the need for higher-resolution projections, we generated statistically downscaled projections (4-km resolution) for all coral reefs; these projections reveal high local-scale variation in ASB. Timing of ASB varies &gt;10 years in 71 of the 87 countries and territories with &gt; 500 km 2 of reef area. Emissions scenario RCP4.5 represents lower emissions mid-century than will eventuate if pledges made following the 2015 Paris Climate Change Conference (COP21) become reality. These pledges do little to provide reefs with more time to adapt and acclimate prior to severe bleaching conditions occurring annually. RCP4.5 adds 11 years to the global average ASB timing when compared to RCP8.5; however, &gt;75% of reefs still experience ASB before 2070 under RCP4.5. Coral reef futures clearly vary greatly among and within countries, indicating the projections warrant consideration in most reef areas during conservation and management planning.

This paper addresses the following question: how does one relate the biological and behavioral characteristics of animals to habitat characteristics of the locations at which they are found? Ecologists often assemble data on species composition at different localities, habitat descriptions of these localities, and biological or behavioral traits of the species. These data tables are usually analyzed two by two: species composition against habitat characteristics, or against behavioral data, using such methods as canonical analysis. We propose a solution to the problem of estimating the parameters describing the relationship between habitat characteristics and biology or behavior, and of testing the statistical significance of these parameters; this problem is referred to as the fourth-corner problem, from its matrix formulation. In other words, the fourth-corner method offers a way of analyzing the relationships between the supplementary variables associated with the rows and columns of a binary (presence or absence) data table. The test case that motivated this study concerns a coral reef fish assemblage (280 species). Biological and behavioral characteristics of the species were used as supplementary variables for the rows, and characteristics of the environment for the columns. Parameters of the association between habitat characteristics (distance from beach, water depth, and substrate variables) and biological and behavioral traits of the species (feeding habits, ecological niche categories, size classes, egg types, activity rhythms) were estimated and tested for significance using permutations. Permutations can be performed in different ways, corresponding to different ecological hypotheses. Results were compared to predictions made independently by reef fish ecologists, in order to assess the method as well as the pertinence of the variables subjected to the analysis. The new method is shown to be applicable to a wide class of ecological problems.

Managing coral reefs for resilience to climate change is a popular concept but has been difficult to implement because the empirical scientific evidence has either not been evaluated or is sometimes unsupportive of theory, which leads to uncertainty when considering methods and identifying priority reefs. We asked experts and reviewed the scientific literature for guidance on the multiple physical and biological factors that affect the ability of coral reefs to resist and recover from climate disturbance. Eleven key factors to inform decisions based on scaling scientific evidence and the achievability of quantifying the factors were identified. Factors important to resistance and recovery, which are important components of resilience, were not strongly related, and should be assessed independently. The abundance of resistant (heat-tolerant) coral species and past temperature variability were perceived to provide the greatest resistance to climate change, while coral recruitment rates, and macroalgae abundance were most influential in the recovery process. Based on the 11 key factors, we tested an evidence-based framework for climate change resilience in an Indonesian marine protected area. The results suggest our evidence-weighted framework improved upon existing un-weighted methods in terms of characterizing resilience and distinguishing priority sites. The evaluation supports the concept that, despite high ecological complexity, relatively few strong variables can be important in influencing ecosystem dynamics. This is the first rigorous assessment of factors promoting coral reef resilience based on their perceived importance, empirical evidence, and feasibility of measurement. There were few differences between scientists' perceptions of factor importance and the scientific evidence found in journal publications but more before and after impact studies will be required to fully test the validity of all the factors. The methods here will increase the feasibility and defensibility of including key resilience metrics in evaluations of coral reefs, as well as reduce costs. Adaptation, marine protected areas, priority setting, resistance, recovery.

Fish mucus layers are the main surface of exchange between fish and the environment, and they possess important biological and ecological functions. Fish mucus research is increasing rapidly, along with the development of high-throughput techniques, which allow the simultaneous study of numerous genes and molecules, enabling a deeper understanding of the fish mucus composition and its functions. Fish mucus plays a major role against fish infections, and research has mostly focused on the study of fish mucus bioactive molecules (e.g., antimicrobial peptides and immune-related molecules) and associated microbiota due to their potential in aquaculture and human medicine. However, external fish mucus surfaces also play important roles in social relationships between conspecifics (fish shoaling, spawning synchronisation, suitable habitat finding, or alarm signals) and in interspecific interactions such as prey-predator relationships, parasite–host interactions, and symbiosis. This article reviews the biological and ecological roles of external (gills and skin) fish mucus, discussing its importance in fish protection against pathogens and in intra and interspecific interactions. We also discuss the advances that “omics” sciences are bringing into the fish mucus research and their importance in studying the fish mucus composition and functions.

With broad distributions, diadromous fishes can be exposed to multiple threats at different stages of development. For the primarily catadromous eels of the family Anguillidae, there is growing international concern for the population abundance and escapement trends of some of these species and yet incomplete knowledge of their remarkable life-histories hampers management and conservation. Anguillids experience a suite of pressures that include habitat loss/modification, migration barriers, pollution, parasitism, exploitation, and fluctuating oceanic conditions that likely have synergistic and regionally variable impacts, even within species. In beginning to redress this rather fragmented picture, we evaluated the extinction risk of these species using the IUCN Red List of Threatened Species Categories and Criteria to infer population-wide trends from catch and monitoring data. Here we consolidate and build upon these species assessments by presenting an overview of the current state of global eel data and conservation, categorising the knowledge gaps and geographic regions where resources are needed and discussing future recommendations to improve our understanding of anguillids. We find stark disparity between the quality and length of data available to assess population trends and conservation priorities in temperate and tropical anguillids. Of the 13 species assessed, four were listed as ‘Threatened’ (Vulnerable, Endangered or Critically Endangered); four were Near Threatened, three were Data Deficient and two were deemed Least Concern. Comparing with other diadromous species, we examine the multiple threats that impact eels during their different life-history stages, highlighting the challenges of applying the Red List Categories and Criteria to geographically-expansive, catadromous and panmictic groups of species.

Overfishing and habitat destruction due to local and global threats are undermining fisheries, biodiversity, and the long-term sustainability of tropical marine ecosystems worldwide, including in the Coral Triangle. Well-designed and effectively managed marine reserve networks can reduce local threats, and contribute to achieving multiple objectives regarding fisheries management, biodiversity conservation and adaptation to changes in climate and ocean chemistry. Previous studies provided advice regarding ecological guidelines for designing marine reserves to achieve one or two of these objectives. While there are many similarities in these guidelines, there are key differences that provide conflicting advice. Thus, there is a need to provide integrated guidelines for practitioners who wish to design marine reserves to achieve all three objectives simultaneously. Scientific advances regarding fish connectivity and recovery rates, and climate and ocean change vulnerability, also necessitate refining advice for marine reserve design. Here we review ecological considerations for marine reserve design, and provide guidelines to achieve all three objectives simultaneously regarding: habitat representation; risk spreading; protecting critical, special and unique areas; reserve size, spacing, location, and duration; protecting climate resilient areas; and minimizing and avoiding threats. In addition to applying ecological guidelines, reserves must be designed to address social and governance considerations, and be integrated within broader fisheries and coastal management regimes.

Environmental plastic pollution is a major ecological and societal concern today. Over the past decade, a broad range of laboratory and experimental studies have complemented field observations in the hope of achieving a better understanding of the fate and impact of micro- and/or nanoplastics (MP/NP) on diverse organisms (e.g., birds, fish, and mammals). However, plastic pollution remains challenging to monitor in the environment and to control under laboratory conditions, and plastic particles are often naturally or experimentally co-contaminated with diverse chemical pollutants. Therefore, our understanding of the effects of virgin MP/NP in freshwater and marine fish is still limited. Here, we performed a systematic review of the most up-to-date literature on the effects of virgin MP/NP on fish under laboratory conditions. A total of 782 biological endpoints investigated in 46 studies were extracted. Among these endpoints, 32% were significantly affected by exposure to virgin MP/NP. More effects were observed for smaller plastic particles (i.e., size ≤20 μm), affecting fish behavioral and neurological functions, intestinal permeability, metabolism, and intestinal microbiome diversity. In addition, we propose suggestions for new research directions to lead toward innovative, robust, and scientifically sound experiments in this field. This review of experimental studies reveals that the toxicity of virgin MP/NP on fish should be more systematically evaluated using rigorous laboratory-based methods and aims toward a better understanding of the underlying mechanisms of this toxicity to fish.

Abstract Symbiosis between dinoflagellates of the genus Symbiodinium and reef-building corals forms the trophic foundation of the world’s coral reef ecosystems. Here we present the first draft genome of Symbiodinium goreaui (Clade C, type C1: 1.03 Gbp), one of the most ubiquitous endosymbionts associated with corals, and an improved draft genome of Symbiodinium kawagutii (Clade F, strain CS-156: 1.05 Gbp) to further elucidate genomic signatures of this symbiosis. Comparative analysis of four available Symbiodinium genomes against other dinoflagellate genomes led to the identification of 2460 nuclear gene families (containing 5% of Symbiodinium genes) that show evidence of positive selection, including genes involved in photosynthesis, transmembrane ion transport, synthesis and modification of amino acids and glycoproteins, and stress response. Further, we identify extensive sets of genes for meiosis and response to light stress. These draft genomes provide a foundational resource for advancing our understanding of Symbiodinium biology and the coral-algal symbiosis.

Coral reefs and the services they provide are seriously threatened by ocean acidification and climate change impacts like coral bleaching. Here, we present updated global projections for these key threats to coral reefs based on ensembles of IPCC AR5 climate models using the new Representative Concentration Pathway (RCP) experiments. For all tropical reef locations, we project absolute and percentage changes in aragonite saturation state (Ωarag) for the period between 2006 and the onset of annual severe bleaching (thermal stress >8 degree heating weeks); a point at which it is difficult to believe reefs can persist as we know them. Severe annual bleaching is projected to start 10-15 years later at high-latitude reefs than for reefs in low latitudes under RCP8.5. In these 10-15 years, Ωarag keeps declining and thus any benefits for high-latitude reefs of later onset of annual bleaching may be negated by the effects of acidification. There are no long-term refugia from the effects of both acidification and bleaching. Of all reef locations, 90% are projected to experience severe bleaching annually by 2055. Furthermore, 5% declines in calcification are projected for all reef locations by 2034 under RCP8.5, assuming a 15% decline in calcification per unit of Ωarag. Drastic emissions cuts, such as those represented by RCP6.0, result in an average year for the onset of annual severe bleaching that is ~20 years later (2062 vs. 2044). However, global emissions are tracking above the current worst-case scenario devised by the scientific community, as has happened in previous generations of emission scenarios. The projections here for conditions on coral reefs are dire, but provide the most up-to-date assessment of what the changing climate and ocean acidification mean for the persistence of coral reefs.

Ocean Sampling Day was initiated by the EU-funded Micro B3 (Marine Microbial Biodiversity, Bioinformatics, Biotechnology) project to obtain a snapshot of the marine microbial biodiversity and function of the world's oceans. It is a simultaneous global mega-sequencing campaign aiming to generate the largest standardized microbial data set in a single day. This will be achievable only through the coordinated efforts of an Ocean Sampling Day Consortium, supportive partnerships and networks between sites. This commentary outlines the establishment, function and aims of the Consortium and describes our vision for a sustainable study of marine microbial communities and their embedded functional traits.

BACKGROUND: Climate-induced coral bleaching poses a major threat to coral reef ecosystems, mostly because of the sensitivities of key habitat-forming corals to increasing temperature. However, susceptibility to bleaching varies greatly among coral genera and there are likely to be major changes in the relative abundance of different corals, even if the wholesale loss of corals does not occur for several decades. Here we document variation in bleaching susceptibility among key genera of reef-building corals in Moorea, French Polynesia, and compare bleaching incidence during mass-bleaching events documented in 1991, 1994, 2002 and 2007. METHODOLOGY/PRINCIPAL FINDINGS: This study compared the proportion of colonies that bleached for four major genera of reef-building corals (Acropora, Montipora, Pocillopora and Porites), during each of four well-documented bleaching events from 1991 to 2007. Acropora and Montipora consistently bleached in far greater proportions (up to 98%) than Pocillopora and Porites. However, there was an apparent and sustained decline in the proportion of colonies that bleached during successive bleaching events, especially for Acropora and Montipora. In 2007, only 77% of Acropora colonies bleached compared with 98% in 1991. Temporal variation in the proportion of coral colonies bleached may be attributable to differences in environmental conditions among years. Alternately, the sustained declines in bleaching incidence among highly susceptible corals may be indicative of acclimation or adaptation. CONCLUSIONS/SIGNIFICANCE: Coral genera that are highly susceptible to coral bleaching, and especially Acropora and Montipora, exhibit temporal declines in their susceptibility to thermal anomalies at Moorea, French Polynesia. One possible explanation for these findings is that gradual removal of highly susceptible genotypes (through selective mortality of individuals, populations, and/or species) is producing a coral assemblage that is more resistant to sustained and ongoing ocean warming.

Events occurring early in life history can have profound effects on the structure of populations and communities. In particular, susceptibility to predation is often highest early in life, and can greatly influence community structure. To better understand these events in reef-forming coral communities, we investigated how spatial variation in recruitment and early post-settlement predation influenced the spatial structure of a coral assemblage. Over a 5 yr period, we compared recruitment of corals and abundance of juveniles and adults at a combination of 3 locations and 3 depths in French Polynesia. We then measured mortality of recruits (< 3 mo old) and juveniles (about 1 to 4 yr old), and abundance of potential predators. Results demonstrate the crucial role of events occurring in the first weeks of the benthic stage. The abundance of scraping herbivorous parrotfishes explained substantial spatial variation in the mortality of recruits, but not juveniles, revealing a likely effect of incidental removal by grazing. Conversely, abundance of coral-feeding butterflyfishes explained substantial spatial variation in the mortality of juveniles. These findings underscore the importance of incidental mortality from grazing and specialized corallivory on coral populations. Moreover, these processes can play a key role in determining spatial patterns in coral assemblage structure.

Abstract Aim In the Indo‐Pacific, the mass of islands of the Indonesian archipelago constitute a major biogeographical barrier (the Indo‐Pacific Barrier, IPB) separating the Pacific and Indian oceans. Evidence for other, more localized barriers include high rates of endemism at the Marquesas and other isolated peripheral islands in the Pacific. Here we use mitochondrial‐sequence comparisons to evaluate the efficacy of biogeographical barriers on populations of the snappers Lutjanus kasmira and Lutjanus fulvus across their natural ranges. Location Pacific and Indian oceans. Methods Mitochondrial cytochrome b sequence data were obtained from 370 individuals of L. kasmira and 203 individuals of L. fulvus collected from across each species’ range. Allele frequency data for two nuclear introns were collected from L. kasmira . Phylogenetic and population‐level analyses were used to determine patterns of population structure in these species and to identify barriers to dispersal. Results Lutjanus kasmira lacks genetic structure across the IPB and throughout 12,000 km of its central Indo‐Pacific range. In contrast, L. fulvus demonstrates high levels of population structure at all geographical scales. In both species, highly significant population structure results primarily from the phylogenetic distinctiveness of their Marquesas Islands populations ( L. kasmira , d = 0.50–0.53%; L. fulvus , d = 0.87–1.50%). Coalescence analyses of the L. kasmira data indicate that populations at opposite ends of its range (western Indian Ocean and the Marquesas) are the oldest. Coalescence analyses for L. fulvus are less robust but also indicate colonization from the Indian to the Pacific Ocean. Main conclusions The IPB does not act as a biogeographical barrier to L. kasmira , and, in L. fulvus , its effects are no stronger than isolating mechanisms elsewhere. Both species demonstrate a strong genetic break at the Marquesas. Population divergence and high endemism in that archipelago may be a product of geographical isolation enhanced by oceanographic currents that limit gene flow to and from those islands, and adaptation to unusual ecological conditions. Lutjanus kasmira shows evidence of Pleistocene population expansion throughout the Indo‐central Pacific that originated in the western Indian Ocean rather than the Marquesas, further demonstrating a strong barrier at the latter location.

In November and December 1991, gross production and respiration were respectively 640.2-753 and 590.4-641.5 mmol (O2 or CO2)m-2d-1 (7.7-9.0 and 7.1-7.7 g C m-2d-1) and the reef displayed a slightly negative excess (=net) production. The contribution of planktonic primary production to reef metabolism was negligible (0.15% of total gross production). Net calcification was positive both during the day and at night; its daily value was 243 mmol CaCO3m-2d-1 (24.3 g CaCO3m-2d-1). Reef metabolism decreased seawater total CO2 by 433.3 mmol m-2d-1. The air-sea CO2 fluxes were close to zero in the ocean but displayed a strong daily pattern at the reef front and the back reef. Fluxes were positive (CO2 evasion) at night, decreased as irradiance increased and were negative during the day (CO2 invasion). Integration of the fluxes measured during a 24 h experiment at the back reef showed that the reef was a source of CO2 to the atmosphere (1.5 mmol m-2d-1).

Understanding the mechanisms responsible for stability and persistence of ecosystems is one of the greatest challenges in ecology. Robert May showed that, contrary to intuition, complex randomly built ecosystems are less likely to be stable than simpler ones. Few attempts have been tried to test May's prediction empirically, and we still ignore what is the actual complexity-stability relationship in natural ecosystems. Here we perform a stability analysis of 116 quantitative food webs sampled worldwide. We find that classic descriptors of complexity (species richness, connectance and interaction strength) are not associated with stability in empirical food webs. Further analysis reveals that a correlation between the effects of predators on prey and those of prey on predators, combined with a high frequency of weak interactions, stabilize food web dynamics relative to the random expectation. We conclude that empirical food webs have several non-random properties contributing to the absence of a complexity-stability relationship.

We studied the genetic diversity of a coral reef fish species to investigate the origin of the differentiation. A total of 727 Acanthurus triostegus collected from 15 locations throughout the Pacific were analyzed for 20 polymorphic loci. The genetic structure showed limited internal disequilibrium within each population; 3.7% of the loci showed significant Hardy-Weinberg disequilibrium, mostly associated with Adh*, and we subsequently removed this locus from further analysis of geographic pattern. The genetic structure of A. triostegus throughout the tropical Pacific Ocean revealed a strong geographic pattern. Overall, there was significant population differentiation (multilocus F(ST) = 0.199), which was geographically structured according to bootstraps of neighbor-joining analysis on Nei's unbiased genetic distances and AMOVA analysis. The genetic structure revealed five geographic groups in the Pacific Ocean: western Pacific (Guam, Philippines, Palau, and Great Barrier Reef); central Pacific (Solomons, New Caledonia, and Fiji); and three groups made up of the eastern populations, namely Hawaiian Archipelago (north), Marquesas (equatorial), and southern French Polynesia (south) that incorporates Clipperton Island located in the northeastern Pacific. In addition, heterozygosity values were found to be geographically structured with higher values grouped within Polynesian and Clipperton populations, which exhibited lower population size. Finally, the genetic differentiation (F(ST)) was significantly correlated with geographic distance when populations from the Hawaiian and Marquesas archipelagos were separated from all the other locations. These results show that patterns of differentiation vary within the same species according to the spatial scale, with one group probably issued from vicariance, whereas the other followed a pattern of isolation by distance. The geographic pattern for A. triostegus emphasizes the diversity of the evolutionary processes that lead to the present genetic structure with some being more influential in certain areas or according to a particular spatial scale.

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