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This paper presents two metazoan zooplankton datasets obtained by imaging samples collected on the Bay of Biscay continental shelf in spring during the PELGAS integrated surveys, over the 2004–2019 period. The samples were collected at night, with a WP2 200 µm mesh size fitted with a Hydrobios (back-run stop) mechanical flowmeter, hauled vertically from the sea floor to the surface with a maximum depth set at 100 m when the bathymetry is deeper. The first dataset originates from samples collected from 2004 to 2016, imaged on land with the ZooScan and is composed of 1,153,507 imaged and measured objects. The second dataset originates from samples collected from 2016 to 2019, imaged on board the R/V Thalassa with the ZooCAM and is composed of 702,111 imaged and measured objects. The imaged objects is composed of zooplankton individuals, zooplankton pieces, non-living particles and imaging artefacts, ranging from 300 µm to 3.39 mm Equivalent Spherical Diameter, individually imaged, measured and identified. Each imaged object is geolocated, associated to a station, a survey, a year and other metadata. Each object is described by a set of morphological and grey level based features (8 bits encoding, 0 = black, 255 = white), including size, automatically extracted on each individual image. Each object was taxonomically identified using the web based application Ecotaxa with built-in, random forest and CNN based, semi-automatic sorting tools followed by expert validation or correction. The objects were sorted in 172 taxonomic and morphological groups. Each dataset features a table combining metadata and data, at the individual object granularity, from which one can easily derive quantitative population and communities descriptors such as abundances, mean sizes, biovolumes, biomasses, and size structure. Each object’s individual image is provided along with the data. These two datasets can be used combined together for ecological studies as the two instruments are interoper

Le projet Delmoges vise à produire de nouvelles connaissances écologiques et halieutiques, pour réduire les captures accidentelles de dauphins dans le golfe de Gascogne (GdG). Ce livrable présente les cartes produites par un modèle hiérarchique de la distribution saisonnière et interannuelle des principales proies des dauphins, les petits poissons pélagiques. Le modèle intègre 3 types de données : présence-absence et biomasse de poissons des campagnes scientifiques et présences de poissons par les données de pêche. Le modèle a fourni pour la première fois une description quantitative de la dynamique spatiale saisonnière de la sardine et des pêcheries associées. Les principales zones de distribution de la sardine étaient côtières, de l'embouchure de la Gironde au sud-ouest de la Bretagne. La sardine était en moyenne distribuée sur une plus large zone sous forme de petits agrégats au printemps. Elle semblait se concentrer dans ses zones de distribution principales en été et se disperser vers le large en automne, mais dans une moindre mesure qu’au printemps. Les pêcheries étaient concentrées dans les zones de distribution principale de la sardine à la côte, et étaient plus intenses en été, puis à l’automne et moins intenses au printemps. Après avoir intégré les données hivernales, l’application de notre modèle à l’anchois, et son couplage avec les distributions de dauphins communs devrait à terme permettre d'améliorer notre compréhension des interactions entre les petits poissons pélagiques et les dauphins et d’évaluer leur influence sur les captures accidentelles.

Depuis les années 1990, la France connaît régulièrement des épisodes de mortalités importantes de dauphins, qui entraînent des pics d’échouages sur le littoral Atlantique en hiver. Depuis 2016, les échouages de petits cétacés dans le golfe de Gascogne présentant des traces de capture, atteignent des niveaux inédits. Si les données scientifiques actuelles permettent d’évaluer globalement le risque induit par ces captures accidentelles pour la conservation de la population de dauphins communs, elles sont toutefois trop lacunaires pour comprendre les déterminants écosystémiques et halieutiques à l’origine de ces captures. La Rochelle Université-CNRS et l’Institut français de recherche pour l’exploitation de la mer (Ifremer) ont construit en concertation avec l’Office Français de la Biodiversité (OFB), les professionnels de la pêche et l’État, le projet Delmoges (Delphinus Mouvements Gestion). Il vise, dans un premier temps, à combler ces lacunes en allant chercher des nouvelles données sur les habitats des dauphins, sur leurs interactions trophiques dans l’écosystème et leurs interactions techniques avec les engins de pêche. Ensuite, le projet propose d’intégrer les connaissances sur l’ensemble du socio-écosystème pour envisager une diversité de scénarios de diminution des captures accidentelles incluant des solutions technologiques et, enfin, d’en évaluer les conséquences biologiques et socio-économiques. Ce rapport présente les différents aspects du projet et leurs avancées entre le 15 décembre 2022 et le 31 décembre 2023. On y retrouve les aspects scientifiques développés dans chacun des WPs, les comptes-rendus des réunions de COPILs et des comités de gouvernance, ainsi que le bilan des communications.

This document presents the results of the acoustic biomass estimation of small pelagic fish near sea surface in the Bay of Biscay in spring 2023, based on PELGAS survey data. Estimates were based on lateral echosounder data.

Acoustic and egg-based indices produced by the scientific surveys conducted in the Bay of Biscay (BoB) under the hauspices of the ICES Working Group ACEGG were compared since 2000, to identify potential bias. Potential effects on biomass estimates of changes in daily fecundity are discussed. A workplan was proposed to further investigate discrepancies between acoustic and egg-based biomass estimates.

La mer nous a toujours nourri-e-s. Nous avons longtemps cru qu’ils pouvaient pêcher ou récolter sans risque d’épuiser ses ressources. L’histoire et la biologie ont montré qu’il n’en était rien. La pêche est devenue l’activité humaine impactant le plus les océans. La mer nourrit, mais elle stocke aussi l’essentiel des gaz à effet de serre et le réchauffement produits par les activités humaines. Le dérèglement climatique d’origine humaine devrait devenir la pression principale sur les écosystèmes marins, s’ajoutant aux effets de la pêche, des autres pollutions, et de la destruction de zones sensibles. Dans ces conditions, la mer va-t-elle rester nourricière ? Tout dépend des actes que nous posons aujourd’hui. Afin d’éclairer nos choix, une démarche prospective a été menée dans le cadre du projet FORESEA 2050 de l’Ifremer. L’objectif était d’écrire des scénarios décrivant des futurs possibles pour la pêche et de l’aquaculture en France en 2050. Comme des balises sur une carte marine, ces scénarios aident à esquisser aujourd’hui les trajectoires les plus souhaitables pour demain. Comme dans l’océan, vous pouvez choisir d’en explorer les profondeurs, ou de rester en surface. La carte est entre vos mains. Faires en bon usage, et bonne exploration. Pour que la mer reste nourricière.

Characterizing the structure and functioning of marine ecosystems requires a deep understanding of the dynamics of its populations and the biotic interactions among them. To this end, we developed a mass-balanced food-web model of a regional sea in the Northeast Atlantic, the Bay of Biscay (BoB), considering one of the most important anthropogenic disturbance in the area, the fishing pressure. The food-web model was performed for the whole BoB region for the first time. The model represents the ecosystems in the early 2000s, encompassing 120433 km2 between 0 and 1000 m depth. The model was composed of 52 functional groups, ranging from primary producers to top predators, and considering both Spanish and French fishing fleets. Input data included biomass obtained locally from bottom trawl and acoustic surveys, data from stock assessment, official fishery statistics, published and unpublished data on stomach content analyses and the use of empirical equations to estimate consumption and production rates. Our results highlight the importance of the pelagic domain, since the main trophic flows are determined by the interaction between phytoplankton, zooplankton and forage fishes. The role of the detritivore pathway was also relevant due to the relatively high abundance of detritivores organisms and the large percentage of primary production flowing to the detritus. Forage fish have resulted to be a key compartment fostering the connectivity between the benthic and pelagic domains. Pelagic sharks, dolphins, anglerfish, large hake and large demersal fishes were identified as potential keystone functional groups in the BoB model. The results also showed an intense exploitation by fisheries in early 2000s. Different strategies between Spanish and French fleets were also found. French fleets were mainly focussed on low trophic level forage fish (e.g., sardine and anchovy) and had larger impacts on higher trophic levels, while Spanish fleets mostly focussed on higher trophic

Depuis les années 1990, la France connaît régulièrement des épisodes de mortalités importantes de dauphins, qui entraînent des pics d’échouages sur le littoral Atlantique en hiver. Depuis 2016, les échouages de petits cétacés dans le golfe de Gascogne présentant des traces de capture, atteignent des niveaux inédits. Si les données scientifiques actuelles permettent d’évaluer globalement le risque induit par ces captures accidentelles pour la conservation de la population de dauphins communs, elles sont toutefois trop lacunaires pour comprendre les déterminants écosystémiques et halieutiques à l’origine de ces captures. La Rochelle Université-CNRS et l’Institut français de recherche pour l’exploitation de la mer (Ifremer) ont construit en concertation avec l’Office Français de la Biodiversité (OFB), les professionnels de la pêche et l’État, le projet Delmoges (Delphinus Mouvements Gestion). Il vise, dans un premier temps, à combler ces lacunes en allant chercher des nouvelles données sur les habitats des dauphins, sur leurs interactions trophiques dans l’écosystème et leurs interactions techniques avec les engins de pêche. Ensuite, le projet propose d’intégrer les connaissances sur l’ensemble du socio-écosystème pour envisager une diversité de scénarios de diminution des captures accidentelles incluant des solutions technologiques et, enfin, d’en évaluer les conséquences biologiques et socio-économiques. Ce rapport présente les différents aspects du projet et leurs avancées depuis son lancement au 1er mars 2022. On y retrouve les aspects scientifiques développés dans chacun des WPs, le bilan annuel des communications, les comptes-rendus des réunions de COPILs et des comités de gouvernance.

Plusieurs analyses sont proposées dans ce cadre et en réponse à la saisine : 1) un bilan de l’effort de pêche des navires français en zone CIEM VIII aux engins sensibles aux captures accidentelles sur les périodes hivernales de 2019 à 2021 (entre le 1er décembre et le 31 mars), 2) une cartographie de l’effort de pêche aux engins sensibles sur ces mêmes périodes, 3) une analyse de l’évolution de l’activité halieutique française et étrangère entre 2010 et 2020 avec une attention particulière portée aux périodes hivernales et aux engins sensibles, 4) des premiers éléments sur la problématiques de l’estimation des métriques d’effort de pêche des engins sensibles en particulier des filets, 5) une actualisation de la typologie des navires pratiquant le filet dans la zone CIEM VIII durant les périodes hivernales étendue 2019 et 2020 (entre le 1er décembre et le 31 mai) et enfin 6) une analyse de l’évolution de l’abondance des espèces – proies des cétacés. Selon le niveau de précision disponible dans les données. Par exemple en l’absence de géolocalisation généralisée des navires de pêche, la cartographie des activités de pêche des navires français de moins de 12 mètre n’a pu être réalisée qu’au niveau des rectangles statistiques ICES, niveau insuffisant pour une bonne représentation de l’activité de pêche de ces navires.

This year the group changed its name to Working Group on Acoustic and Egg Surveys for small pelagic fish in NE Atlantic (WGACEGG). WGACEGG coordinates, assesses and quality controls acoustic and daily egg production (DEPM) surveys of several pelagic stocks in ICES areas 6-9. During three 2020 WGACEGG meetings, results of three DEPM surveys, three spring/summer acoustic surveys and all six autumn surveys were presented. Implications of the cancellation of three surveys (SAREVA and PELACUS (Spain)) and PELGAS (France) were also discussed, as were possible mitigations to minimize the effects on the relevant stock assessments. No concerns were raised about the surveys that took place. The results from the DEPM survey for sardine in 9a could not be provided until December, as COVID-19 had restricted laboratory access. WGACEGG also met with members of the Working Group on Southern Horse Mackerel, Anchovy, and Sardine (WGHANSA) to present the results from the 2020 Portuguese (PELAGO) acoustic survey in advance of the June assessment meeting. The working groups discussed the implications of PELAGO using a different vessel and of the earlier timing (compared to the timeseries) on the sardine and anchovy indices. The joint meeting also identified which surveys were at risk of being cancelled because of COVID-19 and discussed possible mitigations. Biomass estimates for both sardine and anchovy in division 9a were higher than observed in recent years as confirmed by both acoustic and DEPM surveys; DEPM derived Bay of Biscay anchovy spawning stock biomass was the highest on record although the number of recruits in the Bay of Biscay observed later in autumn did not reflect this increase. However, this was at least partly due to a northwards expansion into the English Channel where Bay of Biscay juveniles were found for the first time; sardine biomass in the Bay of Biscay from all available surveys suggested slightly lower values than the long-term average; in the English Channel

This study aims at estimating the anchovy biomass that was missed in the echosounder surface blind zone during the PELGAS survey, in an attempt to explain the relative difference between acoustic and DEPM biomass estimates in springtime 2019 in the Bay of Biscay. Acoustic data collected by a side-looking echosounder are analysed in order to estimate the negative bias introduced in acoustic biomass estimates by the acoustic blind zone. Corrected anchovy acoustic biomass estimates and maps are compared to DEPM ones, in an attempt to reconcile egg and acoustic estimates. Remaining discrepancies are discussed in the light of acoustic and egg biomass estimation assumptions. We showed that surface school biomass can be calculated while applying standard acoustic data analysis methodology to horizontal echosounder data, combined to broadband in-situ TS measurements. In spring 2019, the surface blind zone observation bias was not significant, as only 5% of the anchovy biomass was located in the 0-10m surface layer. The difference between acoustic and DEPM global biomass estimates observed in 2019 hence remains unexplained. Differences between acoustic biomass and egg counts maps were likely due to local differences in fecundity, probably caused, at least in the North Western area, by the presence of shallow schooling large anchovy displaying higher fecundity. This pilot study might pave the way to the routine combination of vertical and horizontal acoustic data to correct surface blind zone bias and improve small pelagic fish acoustic biomass estimates. DEPM and acoustic biomass estimates have to be calculated within post-stratification regions as homogeneous as possible, to reduce bias and improve estimate precision. The high spatial resolution of acoustic backscatter generally allows to delineate reasonibly homogeneous post-stratification regions. The coarser spatial resolution of the trawl hauls providing biological data used to calculate daily fecundity estimates in the

Understanding discrepancies in particular years between acoustic and Daily Egg Production Method (DEPM) estimates is essential to better understand potential bias impacting both estimates, and develop a weighting per year assessing the coherence between survey estimates, to input in stock assessment models. Several plans for collaborative work have been proposed within WGACEGG to compare acoustic and DEPM indices (WGACEGG 2013, 2015, 2016), until the inclusion of such comparative approach as a formal group ToR in 2017 (ICES, 2017). Different approaches have been adopted so far, including the comparison between two egg production estimates (DEPM BIOMAN; CUFES PELGAS) and one acoustic estimate (PELGAS), analysis of the sensitivity of each estimate to its parameters, and the comparison between egg and adult maps. We here provide some rationale on how to investigate differences between acoustic and egg indices.

Investigating the drivers of fish assemblage trophic structure is a critical question, in order to better understand ecosystem functioning, predict the effects of perturbations and implement integrated management of exploited marine ecosystems. Ecosystemic surveys enabled the determination of the trophic structure of the fish assemblages in three French marine ecosystems, namely the Eastern English Channel, the Bay of Biscay and the Gulf of Lions, through the simultaneous collection of qualitative (stable isotopes and energy content) and quantitative (biomass) data. In the Bay of Biscay and in the Gulf of Lions, pelagic primary production supported at least 80% of the fish biomass production, and explained the dominance of pelagic species, but with differences resulting from the different productivity. The lower productivity in the oligotrophic Gulf of Lions led to a lower total biomass, energy density as well as the predominance of zooplankton feeders. In contrast, fluxes in the Bay of Biscay were sufficient to support a higher biomass of pelagic piscivores, and of species with higher energy content. In the shallow Eastern English Channel, the respective contributions of pelagic and benthic sources were similar. Bentho-demersal species of higher trophic level dominated this assemblage, because of their ability to exploit both pathways. Results of the present study confirmed that fisheries-focused surveys can be used as efficient platforms to address questions about ecosystem functioning. Here it confirmed the expected differences between ecosystems and the importance of primary production and environment as drivers of fish assemblage structure and functioning. Future studies should nevertheless develop new methods to better assess the paramount role of low trophic level consumers.

he Working Group on Acoustic and Egg Surveys (WGACEGG) coordinates pelagic surveys for a number of stocks and provides monitoring for the two major sardine and anchovy stocks in ICES areas 6, 7, 8, and 9. The group evaluated small pelagic fish biomass indices derived from acoustic and Daily Egg Production Method (DEPM) surveys in ICES areas 6, 7, 8 and 9. These indices have been provided to the ICES Working Group on Southern Horse Mackerel, Anchovy and Sardine (WGHANSA), the Working Group on Widely Distributed Stocks (WGWIDE) and the Herring Assessment Working Group for the Area South of 62ºN (HAWG) stock assessment group, to serve as fishery-independent input for analytical assessment purposes. DEPM and acoustic indices were derived based on data collected using independent methods. Acoustic- and DEPM-derived biomass indices from quasi-synoptic surveys conducted in the Bay of Biscay in spring were compared, to assess the presence of potential bias and to improve the precision of fish stock biomass estimates. The DEPM-based anchovy biomass index was 22% higher than the acoustic index in 2019. Unusual concentrations of anchovy in Eastern Cantabrian Sea, an area not covered by the acoustic survey, and the presence near the sea surface of actively spawning individuals possibly under-sampled by acoustics in central Bay of Bay had been postulated as potential causes of this discrepancy. No significant difference was found between sardine biomass indices derived from DEPM and acoustics in 2019. The group has updated its database of standard gridded maps covering the European Atlantic area. This initiative continues to inform on the spatial dynamics of various parameters collected during the surveys coordinated under the auspices of the group (fish acoustic densities, anchovy and sardine egg abundance, surface temperature and salinity). Results of an analysis of the time series of gridded maps (anchovy and sardine acoustic density, surface salinity and temperature) showed

Sound scattering layers (SSLs) are observed over a broad range of spatio-temporal scales and geographical areas. SSLs represent a large biomass, likely involved in the biological carbon pump and the structure of marine trophic webs. Yet, the taxonomic composition remains largely unknown for many SSLs. To investigate the challenges of SSL sampling, we performed a survey in a small study area in the Northern Bay of Biscay (France) by combining broadband and narrowband acoustics, net sampling, imagery and video recordings. In order to identify organisms contributing to the observed SSLs, we compared measured frequency spectra to forward predicted spectra derived from biological data. Furthermore, to assess the confidence in SSL characterization, we evaluated uncertainties in modeling, acoustical and biological samplings. Here, we demonstrate for the first time that SSL backscattering intensity in the Bay of Biscay can be dominated in springtime by resonant gas bearing organisms below 100 kHz, namely siphonophores and juvenile fishes and by pteropods at higher frequencies. Thus, we demonstrate the importance of broadband acoustics combined to nets, imagery and video to characterize resonant backscatterers and mixed mesozooplankton assemblages.

L'objectif des Nation Unies pour le développement durable de l’Océan (ODD14) peut il se décliner dans le secteur de la pêche en France ? Et si oui comment ? La principale fonction de la pêche (et de l’aquaculture) françaises étant la fourniture de produits de la mer à des fins alimentaires, nous replaçons la pêche (et de l’aquaculture) françaises dans le contexte plus large de l’approvisionnement alimentaire du pays. Nous présentons le scénario prospectif Afterres2050, qui propose une trajectoire vers un approvisionnement alimentaire durable pour le France (et quelques voisins) en 2050. Afterres2050 est un scénario technique qui vise à satisfaire nos besoins, en alimentation, en énergie, et en matériaux à l’horizon 2050, dans le respect des écosystèmes, des contraintes territoriales et des objectifs de santé publique. La philosophie du scénario et ses principaux résultats sont présentés, avant de détailler la place des produits de la mer dans cette visions prospective. La trajectoire proposée est discutée au regard de la structuration actuelle de la filière et des enjeux alimentaires futurs liés aux produits de la mer et des pistes d’amélioration du volet aquatique du scénario Afterres2050 sont proposées. Le concept de développement durable de la pêche française est enfin discuté sous l’éclairage du scénario et dans le contexte de l’accélération du changement global.

In this tutorial, you will learn how to convert hydro-acoustic data in Simrad .raw format into HAC international format (McQuinn et al., 2005).

Prey and predator distributions influence one another. Understanding the scale and the orientation of predator-prey spatial correlations is crucial in foraging ecology. Growing evidence suggests that predator-prey interactions are more constrained by functional characteristics of both the predator and the prey. Unfortunately, in marine pelagic systems, the scale and orientation of spatial correlations between predators and prey have been only little explored from a functional point of view. We tested the existence of fine-scale association between predators and fish functional groups. Visual predator sightings and acoustic fish records were collected synchronously during oceanographic surveys from 2004 to 2014. Prey biomass was integrated by nautical miles and split into four size classes (<10 cm; 10-20 cm; 20-30 cm; >30 cm) and two depth layers (surface, deep). We computed the relative biomass by prey size and depth category from 0 to 12 nm around predator sightings to determine the predators' proximity to local prey biomass. Two cetaceans (common, bottlenose dolphins) and three seabirds (northern gannets, auks, northern fulmars) were studied. No association was found in fulmars, indicating they probably do not feed on considered fishes in the area. Gannets and auks were positively correlated with local prey biomass for sizes <20 cm at both depth layers. Significant negative relationships were found between common dolphins and prey size classes <20 cm at both depth layers, and between bottlenose dolphins and all size ranges at the deeper layer. Our results suggest that the fine-scale spatial overlap of predator and prey is influenced by their functional traits, and that prey exhibit predator avoidance behaviour in presence of swimming predators but not of flying ones.