Search

The worldwide decline of coral reefs necessitates targeting management solutions that can sustain reefs and the livelihoods of the people who depend on them. However, little is known about the context in which different reef management tools can help to achieve multiple social and ecological goals. Because of nonlinearities in the likelihood of achieving combined fisheries, ecological function, and biodiversity goals along a gradient of human pressure, relatively small changes in the context in which management is implemented could have substantial impacts on whether these goals are likely to be met. Critically, management can provide substantial conservation benefits to most reefs for fisheries and ecological function, but not biodiversity goals, given their degraded state and the levels of human pressure they face.

The productivity of most marine ecosystems is limited by the availability of dissolved nitrogen (N) and phosphorus (P). Nutrient recycling is therefore a key process for ecosystem functioning. Fish recycle nutrients through the excretion of ammonia and phosphate and can influence the abundance and community structure of primary producers such as phytoplankton. However, the effect of fish on other plankton compartments, and whether all fish species have similar effects, is largely unknown. We used a tank experiment to test how 2 Mediterranean fish species, gilthead seabream Sparus aurata and golden mullet Chelon auratus, with distinctly different N and P excretion rates, can affect the abundance and community structure of 3 plankton compartments: phytoplankton, bacterioplankton, and microzooplankton. We found that the nutrients released by seabream (whose excreta had an N:P molar ratio greater than the Redfield ratio of 16:1) induced a substantial increase in the abundance of all plankton compartments. In addition, with seabream, the relative abundance of diatoms in the phytoplankton communities increased. However, no significant change was observed with mullet, which had a low excreta N:P molar ratio, suggesting that the growth of microbial plankton was limited by the availability of N. Our results demonstrate that nutrient excretion by fish affects the microbial food web through a species-specific bottom-up effect on the total abundance and community structure of the phytoplankton, bacterioplankton, and microzooplankton communities.

The effects of environmental change on biodiversity are still poorly understood. In particular, the consequences of shifts in species composition for marine ecosystem function are largely unknown. Here we assess the loss of functional diversity, i.e. the range of species biological traits, in benthic marine communities exposed to ocean acidification (OA) by using natural CO2 vent systems. We found that functional richness is greatly reduced with acidification, and that functional loss is more pronounced than the corresponding decrease in taxonomic diversity. In acidified conditions, most organisms accounted for a few functional entities (i.e. unique combination of functional traits), resulting in low functional redundancy. These results suggest that functional richness is not buffered by functional redundancy under OA, even in highly diverse assemblages, such as rocky benthic communities.

Agricultural land use is a primary driver of environmental impacts on streams. However, the causal processes that shape these impacts operate through multiple pathways and at several spatial scales. This complexity undermines the development of more effective management approaches, and illustrates the need for more in-depth studies to assess the mechanisms that determine changes in stream biodiversity. Here we present results of the most comprehensive multi-scale assessment of the biological condition of streams in the Amazon to date, examining functional responses of fish assemblages to land use. We sampled fish assemblages from two large human-modified regions, and characterized stream conditions by physical habitat attributes and key landscape-change variables, including density of road crossings (i.e. riverscape fragmentation), deforestation, and agricultural intensification. Fish species were functionally characterized using ecomorphological traits describing feeding, locomotion, and habitat preferences, and these traits were used to derive indices that quantitatively describe the functional structure of the assemblages. Using structural equation modeling, we disentangled multiple drivers operating at different spatial scales, identifying causal pathways that significantly affect stream condition and the structure of the fish assemblages. Deforestation at catchment and riparian network scales altered the channel morphology and the stream bottom structure, changing the functional identity of assemblages. Local deforestation reduced the functional evenness of assemblages (i.e. increased dominance of specific trait combinations) mediated by expansion of aquatic vegetation cover. Riverscape fragmentation reduced functional richness, evenness and divergence, suggesting a trend toward functional homogenization and a reduced range of ecological niches within assemblages following the loss of regional connectivity. These results underscore the often-unrecognized import

Background: The surface of marine animals is covered by abundant and diversified microbial communities, which have major roles for the health of their host While such microbiomes have been deeply examined in marine invertebrates such as corals and sponges, the microbiomes living on marine vertebrates have received less attention. Specifically, the diversity of these microbiomes, their variability among species, and their drivers are still mostly unknown, especially among the fish species living on coral reefs that contribute to key ecosystem services while they are increasingly affected by human activities. Here, we investigated these knowledge gaps analyzing the skin microbiome of 138 fish individuals belonging to 44 coral reef fish species living in the same area. Results: Prokaryotic communities living on the skin of coral reef fishes are highly diverse, with on average more than 600 OTUs per fish, and differ from planktonic microbes. Skin microbiomes varied between fish individual and species, and interspecific differences were slightly coupled to the phylogenetic affiliation of the host and its ecological traits. Conclusions: These results highlight that coral reef biodiversity is greater than previously appreciated, since the high diversity of macro-organisms supports a highly diversified microbial community. This suggest that beyond the loss of coral reefs-associated macroscopic species, anthropic activities on coral reefs could also lead to a loss of still unexplored host-associated microbial diversity, which urgently needs to be assessed.

Sustainably managing natural resources under climate change requires understanding how species distribution shifts can impact ecosystem structure and functioning. While numerous studies have documented changes in species’ distributions and abundances in response to warming, the consequences for the functional structure of ecosystems (i.e., composition of species’ functional traits) have received less attention. Here, using thirty years of fish monitoring, we show that two connected North Atlantic ecosystems (E. English Channel and S. North Sea) underwent a rapid shift in functional structure triggered by a climate oscillation to a prevailing warm-phase in the late-1990s. Using time-lag-based causality analyses, we found that rapid warming drove pelagic fishes with r-selected life history traits (e.g., low age and size at maturity, small offspring, low trophic level) to shift abruptly northward from one ecosystem to the other, causing an inversion in functional structure between the two connected ecosystems. While we observed only a one-year time-lag between the climate oscillation and the functional shift, indicating rapid responses to a changing environment, historical overfishing likely rendered these ecosystems susceptible to climatic stress, and declining fishing in the North Sea may have exacerbated the shift. This shift likely had major consequences for ecosystem functioning due to potential changes in biomass turnover, nutrient cycling, and benthic-pelagic coupling. Under ongoing warming, climate oscillations and extreme warming events may increase in frequency and severity, which could trigger functional shifts with profound consequences for ecosystem functioning and services.

Identifying and counting fish individuals on photos and videos is a crucial task to cost-effectively monitor marine biodiversity, yet it remains difficult and time-consuming. In this paper, we present a method to assist the identification of fish species on underwater images, and we compare our model performances to human ability in terms of speed and accuracy. We first tested the performance of a convolutional neural network (CNN) trained with different photographic databases while accounting for different post-processing decision rules to identify 20 fish species. Finally, we compared the performance of species identification of our best CNN model with that of humans on a test database of 1197 fish images representing nine species. The best CNN was the one trained with 900,000 images including (i) whole fish bodies, (ii) partial fish bodies and (iii) the environment (e.g. reef bottom or water). The rate of correct identification was 94.9%, greater than the rate of correct identification by humans (89.3%). The CNN was also able to identify fish individuals partially hidden behind corals or behind other fish and was more effective than humans to identify fish on smallest or blurry images while humans were better to identify fish individuals in unusual positions (e.g. twisted body). On average, each identification by our best CNN using a common hardware took 0.06 s. Deep Learning methods can thus perform efficient fish identification on underwater images and offer promises to build-up new video-based protocols for monitoring fish biodiversity cheaply and effectively.

Trail-based ecology has been developed for decades lo infer ecosystem responses to stressors based on the functional structure of communities, yet its value in species-poor systems is largely unknown. Here, we used an extensive clataset in a Spanish region highly prone to non-native fish invasions (15 catchments, N 389 sites) to assess for the first time how species-poor communities respond to large-scale environmental gradients using a taxonomic and functional trait-based approach in riverine fish. We examined total species richness and three functional trait-based indices available when many sites have <= 3 species (specialization, FSpe; onginaliy, FOri and entropy, FEnt). We assessed the responses of these taxonomic and functional indices along gradients of altitude, water pollution, physical habitat degradation and non-native fish biomass. Whilst species richness was relatively sensitive to spatial effects, functional diversity indices were responsive across natural and anthropogenic gradients. All four diversity measures declined with altitude but this decline was modulated by physical habitat degradation (richness, FSpe and FEnt) and the non-native total fish biomass ratio (FSpe and FOri) in ways that varied between indices. Furthermore, FSpe and FOri were significantly correlated with Total Nitrogen. Non-native fish were a major component of the taxonomic and functional structure of fish communities, raising concerns about potential misdiagnosis between invaded and environmentally-degraded river reaches. Such misdiagnosis was evident in a regional fish index widely used in official monitoring programs. We recommend the application of FSpe and FOri to extensive clatasets from monitoring programs in order to generate valuable cross-system information about the impacts of non-native species and habitat degradation, even in species-poor systems. Scoring non-native species apart from habitat degradation in the indices used to determine ecosystem health is essentia

The aesthetic value of landscapes contributes to human well-being. However, studies which have investigated the link between biodiversity and ecosystem services have not taken aesthetic value into account. In this study we evaluated how the aesthetics of coralligenous reefs, a key marine ecosystem in the Mediterranean, is perceived by the general public and how aesthetic preferences are related to biodiversity facets (taxonomic, phylogenetic and functional diversities). We performed both biodiversity measures and online-surveys of aesthetic perception on photographic quadrats sampled along the French Mediterranean coast. Our results show that species richness and functional richness have a significant positive effect on aesthetic value. Most of the ecological literature, exploring the relationship between biodiversity and ecosystem functioning and service has focused so far on 'economical' aspects of biodiversity (provision or regulation). Our results illustrate that cultural facets, such as 'beauty', should also be central in our motivations to preserve ecological diversity.

High species richness is thought to support the delivery of multiple ecosystem functions and services under changing environments. Yet, some species might performunique functional roles while others are redundant. Thus, the benefits of high species richness in maintaining ecosystem functioning are uncertain if functions have little redundancy, potentially leading to high vulnerability of functions. We studied the natural propensity of assemblages to be functionally buffered against loss prior to fishing activities, using functional trait combinations, in coral reef fish assemblages across unfished wilderness areas of the Indo-Pacific: Chagos Archipelago, New Caledonia and French Polynesia. Fish functional diversity in these wilderness areas is highly vulnerable to fishing, explained by species-and abundance-based redundancy packed into a small combination of traits, leaving most other trait combinations (60%) sensitive to fishing, with no redundancy. Functional vulnerability peaks for mobile and sedentary top predators, and large species in general. Functional vulnerability decreases for certain functional entities in New Caledonia, where overall functional redundancy was higher. Uncovering these baseline patterns of functional vulnerability can offer early warning signals of the damaging effects from fishing, and may serve as baselines to guide precautionary and even proactive conservation actions.

In this paper, we present two supervised machine learning methods to automatically detect and recognize coral reef fishes in underwater HD videos. The first method relies on a traditional two-step approach: extraction of HOG features and use of a SVM classifier. The second method is based on Deep Learning. We compare the results of the two methods on real data and discuss their strengths and weaknesses.

Viruses inhabiting the surface mucus layer of scleractinian corals have received little ecological attention so far. Yet they have recently been shown to be highly abundant and could even play a pivotal role in coral health. A fundamental aspect that remains unresolved is whether their abundance and diversity change with the trophic state of their environment. The present study examined the variability in the abundance of viral and bacterial epibionts on 13 coral species collected from 2 different sites in the Ha Long Bay, Vietnam: one station heavily affected by anthropogenic activity (Cat Ba Island) and one protected offshore station (Long Chau Island). In general, viral abundance was significantly higher in coral mucus (mean = 10.6 +/- 2.0 x 10(7) virus-like particles ml(-1)) than in the surrounding water (5.2 +/- 1.3 x 10(7) virus-like particles ml(-1)). Concomitantly, the abundance and community diversity (inferred from phylogenetic and morphological analyses) of their mucosal bacterial hosts strongly differed from their planktonic counterparts. Surprisingly, despite large differences in water quality and nutrient concentrations between Cat Ba and Long Chau, there were no significant differences in the concentrations of epibiotic viruses and bacteria measured in the only 2 coral species (i.e. Pavona decussata and Lobophyllia flabelliformis) that were common at both sites. The ability of corals to shed bacteria to compensate for their fast growth in nutrient-rich mucus is questioned here.

Animal-associated microbiotas form complex communities, which are suspected to play crucial functions for their host fitness. However, the biodiversity of these communities, including their differences between host species and individuals, has been scarcely studied, especially in case of skin-associated communities. In addition, the intraindividual variability (i.e. between body parts) has never been assessed to date. The objective of this study was to characterize skin bacterial communities of two teleostean fish species, namely the European seabass (Dicentrarchus labrax) and gilthead seabream (Sparus aurata), using a high-throughput DNA sequencing method. In order to focus on intrinsic factors of host-associated bacterial community variability, individuals of the two species were raised in controlled conditions. Bacterial diversity was assessed using a set of four complementary indices, describing the taxonomic and phylogenetic facets of biodiversity and their respective composition (based on presence/absence data) and structure (based on species relative abundances) components. Variability of bacterial diversity was quantified at the interspecific, interindividual and intraindividual scales. We demonstrated that fish surfaces host highly diverse bacterial communities, whose composition was very different from that of surrounding bacterioplankton. This high total biodiversity of skin-associated communities was supported by the important variability, between host species, individuals and the different body parts (dorsal, anal, pectoral and caudal fins).