Marine spatial planning to solve increasing conflicts at sea: A framework for prioritizing offshore windfarms and marine protected areas.

Direct and indirect anthropogenic pressures on biodiversity and ecosystems are expected to lower the provided ecosystem services (ES) in the near future. To limit these impacts, protected areas will be implemented as part of the Post-2020 Global Biodiversity Framework. Simultaneously, as an answer to climate change, renewable energies are being rapidly developed on a worldwide scale, leading to a significant increase in space use in the coming decades. Sharing space is an increasingly complex task, especially because of the high rate of emergence of such competitors for space. In fisheries-dominated socio-ecosystems, acceptability of offshore windfarms (OWFs) and marine protected areas (MPAs) is usually very low, partly due to an underrepresentation of fisheries in spatial plans and poor attention to equity in the spatial distribution of restrictive areas. Here we developed a framework with a marine spatial planning case study in the Bay of Biscay represented by the socio-ecosystem of the Grande Vasière, a mid-shelf mud belt spanning over 21,000 km2. We collected biological, environmental, and anthropogenic data to model the distribution of 62 bentho-demersal species, 7 regulating ES layers related to nutrient cycling, life cycle maintenance and food web functioning, as well as provisioning ES of 18 commercial species and 82 fisheries subdivisions. We used these spatial layers and a prioritization algorithm to explore siting scenarios of OWFs and two types of MPAs (benthic and total protection), aimed at conserving species, regulating and provisioning ES, while also ensuring that fisheries are equitably impacted. We demonstrate that equitable scenarios are not necessarily costlier and provide alternative spatial prioritizations. We emphasize the importance of exploring multiple targets with a Shiny app to visualize results and stimulate dialogue among stakeholders and policymakers. Overall, we show how our flexible, inclusive framework with particular attention to equity could be an ideal discussion tool to improve management practices.

EcoDiet: A hierarchical Bayesian model to combine stomach, biotracer, and literature data into diet matrix estimation.

Although quantifying trophic interactions is a critical path to understanding and forecasting ecosystem functioning, fitting trophic models to field data remains challenging. It requires flexible statistical tools to combine different sources of information from the literature and fieldwork samples. We present EcoDiet, a hierarchical Bayesian modeling framework to simultaneously estimate food-web topology and diet composition of all consumers in the food web, by combining (1) a priori knowledge from the literature on both food-web topology and diet proportions; (2) stomach content analyses, with frequencies of prey occurrence used as the primary source of data to update the prior knowledge on the topological food-web structure; (3) and biotracers data through a mixing model (MM). Inferences are derived in a Bayesian probabilistic rationale that provides a formal way to incorporate prior information and quantifies uncertainty around both the topological structure of the food web and the dietary proportions. EcoDiet was implemented as an open-source R package, providing a user-friendly interface to execute the model, as well as examples and guidelines to familiarize with its use. We used simulated data to demonstrate the benefits of EcoDiet and how the framework can improve inferences on diet matrix by comparison with classical network MM. We applied EcoDiet to the Celtic Sea ecosystem, and showed how combining multiple data types within an integrated approach provides a more robust and holistic picture of the food-web topology and diet matrices than the literature or classical MM approach alone. EcoDiet has the potential to become a reference method for building diet matrices as a preliminary step of ecosystem modeling and to improve our understanding of prey-predator interactions.

Biomass of slow life history species increases as local bottom trawl effort decreases in the Celtic sea.

Due to its selective removal, fishing pressure has long influenced the dynamics of species based on their life history traits. Sensitivity to fishing increases along a "fast-to-slow" gradient of life history strategies, and the "slow" species (large, long-lived, late-maturing, giving birth to few large offspring) require the most time to recover from fishing. In the North East Atlantic, after having reached extreme levels, fishing pressure has decreased since the 1980's due to management measures such as total allowable catch (TAC) or area closure. An effect on the distribution of species as well as a potential recovery could be expected. However, temporal patterns of life history strategies are rarely linked to management measures. In addition, a larger emphasis is often put on exploited or emblematic sensitive species but rarely on assembly processes at the ecosystem scale (both commercial and non-commercial species). Based on a 17-year time series of 101 taxa (fishes, elasmobranchs, bivalves, cephalopods and crustaceans), we observed a negative relationship between the biomass of taxa sensitive to fishing and bottom trawling pressure, as well as an increase in their total biomass in the Celtic Sea. Over the whole area, stochasticity appeared as the dominant assembly process. Deterministic assembly processes were at play in the centre of the area where significant overdispersion (caused by the presence of both slow and fast taxa) were observed. The absence of sensitive taxa from the rest of the Celtic Sea appeared to be caused mainly by a historical effect of environmental filtering when fishing was high. At the local scale, we related the decrease in fishing pressure to the increase in biomass of five of the most sensitive taxa. This local decrease in fishing pressure, resulting from the implementation of an area closure, highlights the positive effect of such management measures in less than two decades.

Environment outweighs the effects of fishing in regulating demersal community structure in an exploited marine ecosystem.

Global climate change has already caused bottom temperatures of coastal marine ecosystems to increase worldwide. These ecosystems face many pressures, of which fishing is one of the most important. While consequences of global warming on commercial species are studied extensively, the importance of the increase in bottom temperature and of variation in fishing effort is more rarely considered together in these exploited ecosystems. Using a 17 year time series from an international bottom trawl survey, we investigated covariations of an entire demersal ecosystem (101 taxa) with the environment in the Celtic Sea. Our results showed that over the past two decades, biotic communities in the Celtic Sea were likely controlled more by environmental variables than fisheries, probably due to its long history of exploitation. At the scale of the entire zone, relations between taxa and the environment remained stable over the years, but at a local scale, in the center of the Celtic Sea, dynamics were probably driven by interannual variation in temperature. Fishing was an important factor structuring species assemblages at the beginning of the time series (2000) but decreased in importance after 2009. This was most likely caused by a change in spatial distribution of fishing effort, following a change in targeted taxa from nephrops to deeper water anglerfish that did not covary with fishing effort. Increasing bottom temperatures could induce additional changes in the coming years, notably in the cold-water commercial species cod, hake, nephrops, and American plaice. We showed that analyzing covariation is an effective way to screen a large number of taxa and highlight those that may be most susceptible to future simultaneous increases in temperature and changes in exploitation pattern by fisheries. This information can be particularly relevant for ecosystem assessments.

From discard ban to exemption: How can gear technology help reduce catches of undersized Nephrops and hake in the Bay of Biscay trawling fleet?

On January 1st, 2016, the French mixed Nephrops and hake fishery of the Grande Vasière, an area located in the Bay of Biscay, fell under the discard ban implemented as part of the new European Common Fisheries Policy. The fleet records historically high levels of discard despite numerous gear selectivity studies. Together with high discards survival, new technological solutions to minimize catches of undersized individuals could justify local exemptions from the discard ban. Our study focuses on the effects of two selective devices, a square mesh cylinder (SMC) and a grid, on the escapement of undersized individuals and discard reduction. Relative catch probability of the modified gear compared with the traditional gear was modelled using the catch comparison method. Potential losses from the commercial fraction of the catch were taken into account to assess their influence on the economic viability of fishing with the modified gears. The two devices had similar effects on undersized Nephrops escapement and on discard reduction, with median values of 26.5% and 23.6% for the SMC and of 30.4% and 21.4% for the grid, respectively. Only the grid was efficient for undersized hake, recording median values of escapement and discard reduction equal to 25.0% and 20.6%, respectively. Some loss from the commercial fraction of the catch was to be expected with both devices, which could be compensated for in the long term by the contribution of undersized individuals to the stock biomass. Our results support the use of selective gears technology as part of an integrated framework including control and management measures to mitigate the effect of the discard ban both for fishers and for the ecosystem. Further work is needed to quantify the effect of additional escapement from the gear on stock dynamics.

Survival of European plaice discarded from coastal otter trawl fisheries in the English Channel.

Species that have a high likelihood of surviving the discarding process have become great concern since the European Union reformed the Common Fisheries Policy and enacted a landing obligation prohibiting the discarding any individuals of species under quota. Among species presenting an elevated survival potential, plaice (Pleuronectes platessa) is one of the most discarded in the coastal otter trawl fishery in the English Channel. The objective of this study is to provide the most reliable estimates of plaice survival after release in commercial conditions, and to identify the factors that influence survival rates. A captivity experiment was conducted in January-February in the English fishery to assess the survival of discarded plaice as a function of a semi-quantitative index of fish vitality, which has been demonstrated to be a good proxy of fish survival in comparable fishing and environmental conditions. This study examined the potential of this index to estimate discard survival in three trials from the English and French fisheries and at three different seasons. The vitality index was then used to analyse the influence of several factors (fishing practices, environmental conditions and fish biological characteristics) on the discard survival. The survival rates for plaice were accurately estimated at 62.8% in January-February, 66.6% in November and 45.2% in July. While these rates remained substantial whatever the fishing, environmental or fish biological conditions, the time fish spent on the deck, the bottom and air temperatures, the tow depth and the fish length had a significant influence on plaice survival. In practice, plaice survival could be enhanced by releasing the fish early during catch sorting and avoiding exposure to extreme air temperatures.

Assessment of sustainable baits for passive fishing gears through automatic fish behavior recognition.

Low-impact fishing gear, such as fish pots, could help reduce human's impact on coastal marine ecosystems in fisheries but catch rates remain low and the harvest of resources used for baiting increases their environmental cost. Using black seabreams (Spondyliosoma cantharus) as target species in the Bay of Biscay, we developed and assessed the efficiency of biodegradable biopolymer-based baits (hereafter bio-baits) made of cockles (Cerastoderma edule) and different biopolymer concentrations. Through a suite of deep and machine learning models, we automatized both the tracking and behavior classification of seabreams based on quantitative metrics describing fish motion. The models were used to predict the interest behavior of seabream towards the bait over 127 h of video. All behavior predictions categorized as interested to the bait were validated, highlighting that bio-baits have a much weaker attractive power than natural bait yet with higher activity after 4 h once natural baits have been consumed. We also show that even with imperfect tracking models, fine behavioral information can be robustly extracted from video footage through classical machine learning methods, dramatically lifting the constraints related to monitoring fish behavior. This work therefore offers new perspectives both for the improvement of bio-baits and automatic fish behavior recognition.

Is it worthy to use environmental DNA instead of scientific trawling or video survey to monitor taxa in soft-bottom habitats?

Non-extractive techniques such as video analysis are increasingly used by scientists to study marine communities instead of extractive methods such as trawling. Currently, environmental DNA (eDNA) analysis is seen as a revolutionary tool to study taxonomic diversity. We aimed to determine which method is the most appropriate to describe fish and commercial invertebrate diversity comparing bottom trawl hauls, video transects and seawater eDNA. Our results reveal that video detected the lowest number of taxa and trawling the highest. eDNA analysis is powerful to describe marine bony fish communities, but some taxa of importance for the ecosystem such as elasmobranchs, crustaceans or molluscs are poorly detected. This may be due to several factors such as marker specificity, incomplete reference gene databases or low DNA release in the environment. For now, the various methods provide different information and none is exhaustive enough to be used alone for biodiversity characterisation.

Gadiform species display dietary shifts in the Celtic Sea.

Global changes, through their impacts on ecosystem trophic structures, are behind regime shifts and cascading effects, and could result in the reorganization of whole ecosystems. The Celtic Sea is a temperate sea at risk of the above because of the interplay between climate change and fisheries. This sea has only displayed slight changes in species diversity between the late 20th century and the present day. However, this apparent stability in species diversity could be hiding structural transformations, including the rearrangement of trophic relationships. Historical stomach content database offers the opportunity to investigate changes in ecosystem trophic structure. Based on such database, this study explored shifts in the feeding habits of gadiform species in the Celtic Sea in the 1980s, 1990s, and 2010s. To this end, it examined dietary generalism and composition for four top predator fish species. During the target period, generalists maintained their diets, while specialists adopted more generalist diets. There were also decreases in frequencies of occurrence of certain fishes within the diets of gadiform species. These recent changes in trophic structure organization have likely been caused by the influence of global changes on both top-down and bottom-up processes that occurred in the Celtic Sea.

Boreal and Lusitanian species display trophic niche variation in temperate waters.

Climate change has non-linear impacts on species distributions and abundance that have cascading effects on ecosystem structure and function. Among them are shifts in trophic interactions within communities. Sites found at the interface between two or more biogeographical regions, where species with diverse thermal preferenda are assembled, are areas of strong interest to study the impact of climate change on communities' interactions. This study examined variation in trophic structure in the Celtic Sea, a temperate environment that hosts a mixture of cold-affiliated Boreal species and warm-affiliated Lusitanian species. Using carbon and nitrogen stable isotope ratios, trophic niche area, width, and position were investigated for 10 abundant and commercially important demersal fish species across space and time. In general, the niches of Boreal species appear to be contracting while those of Lusitanian species expand, although there are some fluctuations among species. These results provide evidence that trophic niches can undergo rapid modifications over short time periods (study duration: 2014-2021) and that this process may be conditioned by species thermal preferenda. Boreal species displayed spatial variation in trophic niche width and seem to be facing increased competition with Lusitanian species for food resources. These findings underscore the need to utilize indicators related to species trophic ecology to track the ecosystem alterations induced by climate change. Such indicators could reveal that the vulnerability of temperate ecosystems is currently being underestimated.

Assessing without harvesting: Pros and cons of environmental DNA sampling and image analysis for marine biodiversity evaluation.

Marine stock assessments or biodiversity monitoring studies, which historically relied on extractive techniques (e.g., trawl or grab surveys), are being progressively replaced by non-extractive approaches. For instance, species abundance indices can be calculated using data obtained from high-definition underwater cameras that enable to identify taxa at low taxonomical level. In biodiversity studies, environmental DNA (eDNA) has proven to be a useful tool for characterising fish species richness. However, several marine phyla remain poorly represented in reference gene databases or release limited amounts of DNA, restricting their detection. The absence of amplification of some invertebrate taxa might also reflect primer bias. We here explore and compare the performance of eDNA and image data in describing the marine communities of several sites in the Bay of Biscay. This was achieved by deploying a remotely operated vehicle to both record images and collect seawater samples. A total of 88 taxa were identified from the eDNA samples and 121 taxa from the images. For both methods, the best characterised phylum was Chordata, with 29 and 27 Actinopterygii species detected using image versus eDNA, respectively. Neither Bryozoa nor Cnidaria was detected in the eDNA samples while the phyla were easily identifiable by imagery. Similarly, Asteroidea (Echinodermata) and Cephalopoda (Mollusca) were scarcely detected in the eDNA samples but present on the images, while Annelida were mostly identified by eDNA (18 taxa vs 7 taxa from imagery). The complementary community descriptions we highlight from these two methods therefore advocate for using both eDNA and imagery in tandem in order to capture the macroscopic biodiversity of bentho-demersal marine communities.

TrophicCS: Spatialized trophic data of the Celtic Sea continental shelf food web.

Understanding the dynamics of species interactions for food (prey-predator, competition for resources) and the functioning of trophic networks (dependence on trophic pathways, food chain flows, etc.) has become a thriving ecological research field in recent decades. This empirical knowledge is then used to develop population and ecosystem modeling approaches to support ecosystem-based management. The TrophicCS data set offers spatialized trophic information on a large spatial scale (the entire Celtic Sea continental shelf and upper slope) for a wide range of species. It combines ingested prey (gut content analysis) and a more integrated indicator of food sources (stable isotope analysis). A total of 1337 samples of large epifaunal invertebrates (bivalve mollusks and decapod crustaceans), zooplankton, fish, and cephalopods, corresponding to 111 taxa (94% determined at the species level), were collected and analyzed for stable isotope analysis of their carbon and nitrogen content. Samples were collected between 2014 and 2016, mostly during the month of November and between 57 and 516 m depth. Sample size varied between taxa (from 1 to 52), with 98 taxa having at least three samples. The gut contents of 1027 fish belonging to 10 commercially important species: black anglerfish (Lophius budegassa), white anglerfish (Lophius piscatorius), blue whiting (Micromesistius poutassou), cod (Gadus morhua), haddock (Melanogrammus aeglefinus), hake (Merluccius merluccius), megrim (Lepidorhombus whiffiagonis), plaice (Pleuronectes platessa), sole (Solea solea), and whiting (Merlangius merlangus) were analyzed. Sampling occurred in November 2014 and 2015. The gut content data set contains the occurrence of prey in gut, identified to the lowest taxonomic level possible. No prey were assigned for 274 empty gut contents. To consider potential ontogenetic diet changes, a large size range was sampled for each species. The TrophicCS data set was used to improve understanding of trophic relationships and ecosystem functioning in the Celtic Sea. Data are released under a CC-BY-NC-SA license, and please cite this paper when reusing the data.

Assessing the diet and trophic level of marine fauna in a fishing ground subject to discarding activity using stable isotopes.

Discarding practices have become a source of concern for the perennation of marine resources, prompting efforts of discard reduction around the globe. However, little is known about the fate of discards in marine environments. Discarding may provide food for various marine consumers, potentially affecting food web structure and stability. Yet, quantifying reliance upon discards is difficult because identity and frequency of discards may change according to multiple factors, and most previously used diet assessment techniques do not allow to assume consistency of feeding strategies over time. One currently untested hypothesis is that significant contribution of discards over time should reflect in increased trophic level (TL) of marine fauna, particularly in low TL consumers. Here, we explored this hypothesis by modeling the TL and assimilated diet of consumers living in fishing grounds subject to important discarding activity using stable isotope analysis. We found indications that benthic invertebrates and Chondrichthyes may depict a higher than expected TL, while other fish tend to depict similar to lower TL compared to global averages from the literature. Based on prior knowledge of discard consumption in the same area, stable isotope mixing models congruently revealed that discards may represent substantial portions of the assimilated diet of most benthic invertebrate macrofauna, cephalopods and Chondrichthyes. We highlight limitations and challenges of currently used diet assessment techniques to study discard consumption and stress that understanding their reintegration in marine food webs is crucial in the context of an ecosystem approach to fisheries management and to better understand the functioning of marine ecosystems subject to fishing.

The low impact of fish traps on the seabed makes it an eco-friendly fishing technique.

Besides understanding the effects of fishing on harvested fish stocks, effects on non-target species, habitats and seafloor integrity also need to be considered. Static fishing gears have often been mentioned as a lower impact fishing alternative to towed gears, although studies examining their actual impact on the seafloor are scarce. In this study, we aimed to describe fish trap movements on the seafloor related to soaking time and trap retrieval. Impacts on the seafloor of lightweight rectangular traps and heavier circular traps were compared. We used 3D video cameras to estimate sweeping motion on the seabed and penetration into the sediment during soaking time. The area and distance swept by each type of trap during retrieval was determined by a camera set up facing the sea bottom. The potential rotation of the traps around the mainline was assessed using an Acoustic Doppler Current Profiler. Results showed that no penetration and almost no movements could be detected during soaking time for either lightweight or heavy commercial traps, even for high tidal coefficient (maximum 6 cm). No rotation could be observed when the tide turned. The swept area covered by a trap during retrieval was low (maximum 2.04 m2) compared to towed fishing gear and other static gear.

Contribution of anadromous fish to the diet of European catfish in a large river system.

Many anadromous fish species, when migrating from the sea to spawn in fresh waters, can potentially be a valuable prey for larger predatory fish, thereby efficiently linking these two ecosystems. Here, we assess the contribution of anadromous fish to the diet of European catfish (Silurus glanis) in a large river system (Garonne, southwestern France) using stable isotope analysis and allis shad (Alosa alosa) as an example of anadromous fish. Allis shad caught in the Garonne had a very distinct marine delta(13)C value, over 8 per thousand higher after lipid extraction compared to the mean delta(13)C value of all other potential freshwater prey fish. The delta(13)C values of European catfish varied considerably between these two extremes and some individuals were clearly specializing on freshwater prey, whereas others specialized on anadromous fish. The mean contribution of anadromous fish to the entire European catfish population was estimated to be between 53% and 65%, depending on the fractionation factor used for delta(13)C.

Using a trait-based approach to understand the efficiency of a selective device in a multispecific fishery.

Improving the selectivity of a fishing gear is one technical management measure to significantly reduce by-catch of non-commercial species or undersized individuals. The efficiency of selective device is mainly estimated by comparing species composition, the biomass and length spectrum of caught individuals and escapees while the functional traits of species are rarely accounted for. Using an innovative technical device to reduce catches of undersized individuals in a multispecific bottom trawl fishery in the Bay of Biscay, namely a T90 mesh cylinder, we measured functional traits on both caught and escaped individuals of 18 species. Using a Principal Component Analysis and K-means partitioning, we clustered species into 6 groups illustrating 6 different locomotion strategies. We identified functional traits related to body size, visual ability and locomotion, differing between caught individuals and escapees using Linear Mixed-effects Models. As expected, escapees were smaller on average but also tended to be more streamlined, with a high position of the eyes and fin features characteristic of manoeuvrability and propulsion. Here, we present how a trait-based approach can shed light on the biological characteristics influencing the efficiency of selective devices.

A global perspective on the trophic geography of sharks.

Sharks are a diverse group of mobile predators that forage across varied spatial scales and have the potential to influence food web dynamics. The ecological consequences of recent declines in shark biomass may extend across broader geographic ranges if shark taxa display common behavioural traits. By tracking the original site of photosynthetic fixation of carbon atoms that were ultimately assimilated into muscle tissues of 5,394 sharks from 114 species, we identify globally consistent biogeographic traits in trophic interactions between sharks found in different habitats. We show that populations of shelf-dwelling sharks derive a substantial proportion of their carbon from regional pelagic sources, but contain individuals that forage within additional isotopically diverse local food webs, such as those supported by terrestrial plant sources, benthic production and macrophytes. In contrast, oceanic sharks seem to use carbon derived from between 30° and 50° of latitude. Global-scale compilations of stable isotope data combined with biogeochemical modelling generate hypotheses regarding animal behaviours that can be tested with other methodological approaches.

Trophic ecology of the pikeperch (Sander lucioperca) in its introduced areas: a stable isotope approach in southwestern France.

During the last decades, non-native predatory fish species have been largely introduced in European lakes and rivers, calling for detailed information on the trophic ecology of co-existing native and non-native predators. The present study describes the trophic ecology of the introduced pikeperch (Sander lucioperca) in two southwestern French rivers, using stable isotope analysis. Pikeperch could be categorized as a top-predator, and had a significantly higher trophic position (TP, mean+/-SE=4.2+/-0.1) compared to other predatory fish such as the native pike (Esox lucius, TP=3.7+/-0.1) and the introduced European catfish (Silurus glanis, TP=3.8+/-0.1). Most studies of resource use in freshwaters consider predatory fish as ecologically equivalent; however, this study showed that the pikeperch occupied a higher trophic niche compared to other predatory species in the Lot and Tarn rivers (Garonne River basin). This apparent specialization may thus have consequences upon interspecific relationships within the predatory guild and upon the functional organization of biological communities.