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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. [ABSTRACT FROM AUTHOR]

This paper is a practical contribution to two important debates raised by the implementation of marine ecosystem based management: (i) which ecosystem data can be provided by a fisheries survey optimised for ecosystem monitoring; and (ii) how to combine/select potential indicators to derive useful information on marine ecosystem status and dynamics? A suite of 143 potential indicators, including spatial indices, representing small pelagic fish and their biotic and abiotic environments are presented. Indicators were routinely derived from the PELGAS integrated ecosystem survey conducted in spring in the Bay of Biscay (BoB). The general patterns over time in this suite of 5–16 years, non-stationary time series are characterised using a methodology based on min–max autocorrelation factors (MAF), to select the most continuous indicators within, and across, several ecosystem components: hydrology, phytoplankton, mesozooplankton, small pelagic fish and megafauna. Potential interactions between selected indicators and external forcing variables, including climate and fishing, were assessed. The results confirm the importance of river discharges, bottom temperature, chlorophyll-a and mesozooplankton biomass in the dynamics of the BoB pelagic ecosystem. Small pelagic fish species appear to have followed distinct trajectories during the last 15 years. A marked decrease in anchovy and sardine mean weights at ages 1 and 2 over the last 15 years was highlighted; potentially caused by density-dependent competition. The quasi-absence of significant correlation between selected survey indicators and climate and fishing pressure proxies suggests a moderate exploitation rate of small pelagic fish resources, and confirms the so far limited effects of large-scale climate forcing on the BoB pelagic ecosystem. Perspectives for the assessment of marine ecosystem status on the basis of suites of indicators derived from integrated ecosystem surveys are discussed. [ABSTRACT FROM AUTHOR]

The Pélagiques Gascogne (PELGAS) integrated survey has been developed by a multidisciplinary team of Ifremer and La Rochelle University scientists since 2000, joined by commercial fishermen in 2007. Its initial focus was to assess the biomass and predict the recruitment success of anchovy in the Bay of Biscay in spring. Taking advantage of the space and versatility of R/V Thalassa II, sampling has been progressively extended to other ecosystem components. PELGAS therefore further developed the second objective of monitoring and studying the dynamic and diverse Biscay pelagic ecosystem in springtime. The PELGAS survey model has allowed for the establishment of a long-term time-series of spatially-explicit data of the Bay of Biscay pelagic ecosystem since the year 2000. Main sampled components of the targeted ecosystem are: hydrology, phytoplankton, mesozooplankton, fish and megafauna. The survey now provides two main ecosystem products: standard raster maps of ecosystem parameters, and a time series dataset of indicators of the Bay of Biscay pelagic ecosystem state. They are used to inform fish stock and ecosystem-based management, and support ecosystem research. The present paper introduces the PELGAS survey, as a practical example of an integrated, vessel-based, ecosystem survey. The evolution of the PELGAS scientific team and sampling protocols are presented and analysed, to outline factors crucial to the success of the survey. Data and results derived from PELGAS are reviewed, to exemplify scientific questions that can be tackled by integrated ecosystem survey data. Advantages and challenges of the survey are discussed and put into the context of marine ecosystem surveys in the European Marine Strategy Framework Directive and the Common Fisheries Policy. [ABSTRACT FROM AUTHOR]

Mapping habitats of species communities helps to inform on the ecological processes which drive their distribution. This information is critical to identify suitable areas for spatial management, aimed at preserving biodiversity, ecosystem functions or essential habitats. While demersal fish have been extensively studied at the community scale, small pelagic fish have mainly been characterised at the population scale. This paper presents a community-based approach on the biodiversity of small pelagic fish, with the aim to: (i) define small pelagic fish communities, (ii) characterise their spatial and interannual dynamics, and (iii) assess their habitats. We present a Multiple Factor Analysis (MFA)-based method that characterises the spatio-temporal variability in a series of multivariate maps. The main components of variability in these maps are identified to define “characteristic areas” displaying contrasting conditions in both MFA ordination and geographical spaces. Characteristic habitats of fish communities were defined by the correlation between the main components of variability from MFAs applied to maps containing fish information on one hand, and on hydrographic variables on the other hand. The analysis of the long term PELGAS survey series of fish biomass and hydrological indices maps resulted in the characterisation of mesoscale latitudinal gradients and coarse to mesoscale onshore-offshore gradients in both fish and hydrology datasets. A community with anchovy ( E. encrasicolus ) and chub mackerel ( S. colias ) as indicator species was consistently distributed in southeast Biscay. This area was associated with higher bottom temperatures, which likely affected the fish community through physiological processes. A second community with small clupeiforms as indicator species was found in coastal spawning habitats. These habitats were typically characterised by low salinity, a probable proxy for high productivity and good feeding grounds for those species. Mapping the habitats of small pelagic fish communities may inform marine spatial management, aimed at preserving biodiversity, ecosystem structure and function. In addition, it may help in achieving maximum sustainable yields of these commercially important species, and contribute to achieving and maintaining good environmental status of shelf seas ecosystems. [ABSTRACT FROM AUTHOR]

Measuring fish target strength (TS) in the wild is challenging because: (i) TS varies versus physical (orientation relative to the incident sound wave, size, and depth) and physiological fish attributes (maturity and condition), (ii) the target species and its aforementioned attributes are difficult to assess in near real time, and (iii) in the case of packed fish schools, accepted echoes may originate from multiple unresolved targets. We propose a method for controlled TS measurements of densely packed small pelagic fish during daytime, based on the joint use of a Remotely Operated Towed Vehicle, “EROC”, with a pelagic trawl fitted with a codend opening system, “ENROL”. EROC, equipped with a 70- kHz split-beam echosounder (Simrad EK60) and a low-light black and white camera, can be moved inside the fishing trawl. Pelagic fish are funnelled into the open trawl and their TS is measured in the middle of the net, where small groups actively swim towards the trawl mouth. The swimming behaviour allows for near-dorsal TS to be measured, minimizing the large effect of incidence angle on TS variability. The EROC camera, located near the open codend, provides optical identification of the species. This method was used to measure the TS of European Anchovy, Engraulis encrasicolus in the Bay of Biscay during 2014. The mean, near dorsal TS was -43.3 dB, for a mean fork length of 12.5 cm. This value is compared to published values of clupeiforms mean TS obtained for a range of natural incidence angles and discussed in the light of TS modelling results obtained for E. encrasicolus. [ABSTRACT FROM AUTHOR]

Petitgas, P., Doray, M., Massé, J., and Grellier, P. 2011. Spatially explicit estimation of fish length histograms, with application to anchovy habitats in the Bay of Biscay. – ICES Journal of Marine Science, 68: 2086–2095.Fish length frequency histograms from research surveys are of prime importance for identifying habitats of different life stages, as well as for stock assessment. However, no method has thus far been available for mapping these histograms as spatially varying curves. Here, a procedure is applied to map spatially connected curves, and detail is given on how it can be applied to map the length frequency histograms. At each sample location, a fish length frequency histogram is given as a vector of non-independent values. The histogram is first modelled as a polynomial expansion on the basis of orthogonal polynomials. Then, the polynomial coefficients are mapped by co-kriging, after fitting a model of co-regionalization. The length frequency map is finally derived by linearly combining maps of polynomial coefficients. An estimation variance associated with the map is also derived. Maps of anchovy length distributions are produced by applying the method to midwater trawl length data from the PELGAS acoustic surveys in the Bay of Biscay. This novel approach extends the application of kriging techniques to curves or functions, opening new perspectives for mapping more complex information than just the values of fish density. [ABSTRACT FROM PUBLISHER]

Doray, M., Mahévas, S., and Trenkel, V. M. 2010. Estimating gear efficiency in a combined acoustic and trawl survey, with reference to the spatial distribution of demersal fish. – ICES Journal of Marine Science, 67: 668–676.Few analyses have been performed to estimate the efficiency of trawls targeting demersal fish using the ratio of catches and acoustic densities. In summer 2006, acoustic and fishing data were collected simultaneously over 3 d by three fishing vessels equipped with identical pelagic trawls in the Bay of Biscay. Variography identified moderate spatial autocorrelation in the acoustic backscatter at a mean scale of 3 km, a scale slightly smaller than the mean haul length (3.5 km), indicating that fish horizontal availability did not influence trawl efficiency. Acoustic backscattering densities expressed as nautical area scattering coefficients (NASCs) recorded in the trawled layer were compared with equivalent NASC (ENASC) values calculated from the species composition in the trawl, fish-length structure, and available relationships between target strength and fish length. Estimates of trawl efficiency for hake-dominated trawls were computed as the slopes of the relationships ENASC = 0.008 NASC and ENASC = 0.18 NASC0.31 for trawls made by day and night, respectively. For the whole demersal community, the relationships were ENASC = 0.022 NASC and ENASC = 0.17 NASC0.33 for trawls made by day and night, respectively. [ABSTRACT FROM PUBLISHER]

Doray, M., Petitgas, P., Nelson, L., Mahévas, S., Josse, E., and Reynal, L. 2009. The influence of the environment on the variability of monthly tuna biomass around a moored, fish-aggregating device. – ICES Journal of Marine Science, 66: 1410–1416.Fish-aggregating devices (FADs) are increasingly used worldwide to enhance tuna catches. Meanwhile, ecosystem-based management of this fishery is constrained by a paucity of information regarding the interaction of FAD-associated tuna aggregations with their local environment. This paper reports the results of a nine-month study around a FAD moored near Martinique Island, aimed at assessing the effects of the local environment on the variability of monthly estimates of proximate tuna biomass. Dual-frequency, active acoustics provided high-resolution quantitative data on the pelagic community around the FAD, from fish to micronekton forage. Geostatistics were used to compute biomass estimates of the tuna aggregation comprising most of the FAD-associated fish biomass, with a sampling error of 27%. Environmental variability was summarized by a small set of principal components (PCs) derived from profiles of temperature, salinity, and dissolved oxygen vs. depth; and maps of chlorophyll a derived from remotely sensed, sea surface colour. A generalized linear model was used to relate tuna biomass to environmental PCs and revealed a positive correlation between tuna abundance and: (i) a micronekton layer sensed at 38 kHz and potentially consisting of preferred prey at ∼180-m depth; and (ii) low subsurface salinity (60–80 m). These favourable environmental conditions may be related to the presence of North Brazilian Current eddies that migrating tuna follow when not temporally associated with the FADs. [ABSTRACT FROM PUBLISHER]

From April 2003 to April 2004 monthly sea surveys were conducted around 2 fish aggregating devices (FADs) moored at 2000 and 2500 m depth in Martinique (Lesser Antilles). The use of a dual frequency splitbeam echosounder combined with an underwater camera and fishing methods allowed assessment of average space and time distribution of pelagic fish aggregated beneath the FADs, as well as identification of their overall size and species composition. At daytime, 4 fish aggregations were identified at each FAD, representing 4 distinct types: i) an aggregation of small juvenile tuna (mean fork length, FL: 30 cm) observed very close to the surface in 25% of daytime periods; ii) a small surface aggregation dominated by carangids, Caranx crysos, present in 65% of daytime periods; iii) a large subsurface aggregation observed during all daytime periods: this aggregation appeared to be primarily comprised of 58 cm FL blackfin tuna (Thunnus atlanticus), mixed with yellowfin (Thunnus albacares) and skipjack (Katsuwonus pelamis) tunas of the same size; and iv) sub-surface scattered large predators (mainly blue marlin, Makaira nigricans) present in 10% of daytime periods. A smaller sub-surface aggregation comprised of medium tuna mixed with "extranatants" (fishes which remain within 10 to 50 m of a FAD) was observed in 75% of night-time periods, whereas unidentified scattered fishes were detected from 70 to 400 m depth. The low daytime vulnerability of medium sub-surface tunas to applied line techniques leads us to assume that their feeding motivation was low during daytime. These tunas could preferentially feed on mesopelagic organisms during night-time and transition periods around Martinican moored FADs. Local fishermen mainly targeted the large scattered predators using very small tunas as living bait. The sub-surface tuna aggregation hence appeared to be currently unexploited by local fisheries, though it represented the large majority of the pelagic biomass around the moored FADs. [ABSTRACT FROM AUTHOR]

Abstract: Sea cruises were conducted for 57 days over 16 months to characterise pelagic fish aggregations around two moored fish aggregating devices (FADs) in Martinique (Lesser Antilles). Echosounder surveys run in a star pattern were used in conjunction with obliquely beamed sonar observations. An echo-integration-by-shoal algorithm was implemented to isolate pelagic fish shoals from sound scattering layers and to compute mean morphometric, positional and density parameters. Tree regressions were used to select and classify pelagic fish target strengths (TS), with reference to their spatial and temporal characteristics. The main type of pelagic fish aggregation was a large sub-surface aggregation. It was observed during all daytime periods within a radius of 400m of the FAD. A smaller type of aggregation was observed closer to the surface and to the FAD in 65% of daytime periods. Large scattered fish were observed in 16% of daytime periods. At night, a medium-sized aggregation was detected in the sub-surface in 75% of night-time periods. The sizes of the fish inside the aggregations (determined from TS values) were lower in the small near-surface aggregation than in the large sub-surface aggregation. Mean packing densities of sub-surface medium fish and near-surface small fish aggregations (determined from TS and shoal acoustic density) were respectively 0.2 and 1.3 fish per m3. The acoustic methodology and results are discussed with reference to the characteristics and performance of the echosounder and to the spatial structure of pelagic fish aggregations around moored FADs in Martinique. [Copyright &y& Elsevier]

This paper presents two metazoan zooplankton datasets obtained by imaging samples collected on the Bay of Biscay continental shelf in spring during the PELGAS (PELagique GAScogne) integrated surveys over the 2004–2019 period. The samples were collected at night with a 200 µm mesh-size WP2 net fitted with a Hydrobios (back-run stop) mechanical flowmeter and hauled vertically from the sea floor to the surface, with the maximum depth set at 100 m when the bathymetry was deeper than this. The first dataset originates from samples collected from 2004 to 2016 and 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 and imaged onboard the R/V Thalassa with the ZooCAM and is composed of 702 111 imaged and measured objects. The imaged objects are composed of zooplankton individuals, zooplankton pieces, non-living particles and imaging artefacts ranging from 300 µm to 3.39 mm in equivalent spherical diameter which were individually imaged, measured and identified. Each imaged object is geolocated and associated with a station, a survey, a year and other metadata. Each object is described by a set of morphological and grey-level-based features (8 bit encoding, 0 = black, 255 = white), including size, that were automatically extracted from 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, which was followed by expert validation or correction. The objects were sorted into 172 taxonomic and morphological groups. Each dataset features a table combining metadata and data at individual-object granularity from which one can easily derive quantitative population and community 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 in combination for ecological studies, as the two instruments are interoperable, or they can be used as training sets for ZooScan and ZooCAM users. The data presented here are available at the SEANOE dataportal: 10.17882/94052 (ZooScan dataset, Grandremy et al., 2023c) and 10.17882/94040 (ZooCAM dataset, Grandremy et al., 2023d). [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Fishery annual surveys are shifting towards integrated ecosystem surveys. However, monitoring the whole ecosystem once a year entails special attention to the interpretation of observations, because they only represent a snapshot in the seasonal dynamics of the environment, of a species, or any dynamic process of interest. The dependency of this snapshot to the timing, but also to the duration, of the survey with respect to this seasonal dynamics needs to be considered. Fish stock assessment is only little impacted by the observed timing within a given season, whereas warming, stratification, plankton bloom occurrence, or fish fecundity, are processes rapidly changing especially in spring. Firstly, from independent satellite data, we described the seasonal and interannual Sea Surface Temperature (SST) variability in the Bay of Biscay in spring around the annual PELGAS surveys. Our results revealed that the in-situ surface temperature snapshot from a given survey may be strongly misleading on the existing spatial pattern, blurring the latitudinal temperature gradient, with potential impact in e.g. species habitat modelling. Secondly, based on these survey-independent SST data, we proposed a methodology to position annual surveys in the environment spring schedule. Our temporal indicator is based on a degree-day metric, computed as the cumulated temperature from the previous winter date with minimum annual temperature. The annual degree-day is then compared to the climatology of the degree-day metric to correct the actual date of survey to an environment date. The methodology was spatialised to take into account both latitudinal shift in phasing of seasonality, and rapidly changing conditions in the environment during the survey itself. Finally, we tested the methodology to refine the description of anchovy and sardine spawning phenology, as well as spawning spatial distribution for particular years such as hot year 2003. More generally, this is an example of how synoptic, independent data from operational oceanography, as a background history of the environment dynamics, can be used to improve the interpretation of biological observations in marine ecosystems. [ABSTRACT FROM AUTHOR]

Mahévas, S., Trenkel, V. M., Doray, M., and Peyronnet, A. 2011. Hake catchability by the French trawler fleet in the Bay of Biscay: estimating technical and biological components. – ICES Journal of Marine Science, 68: 107–118. Several factors affect trawl catchability: (i) gear and vessel technical characteristics, (ii) anthropogenic factors, and (iii) biological factors. The objectives of this study were to assess the relative contribution of each factor to variations in hake (Merluccius merluccius) landings by the French trawler fleet operating on the shelf of the northern Bay of Biscay (ICES Subdivision VIIIa). Using generalized linear models, the impact of technical and anthropogenic factors was evaluated using landings per unit effort (lpue) obtained from logbooks. Variations in hake lpue were explained primarily by anthropogenic factors. For studying the biological components of catchability, the results of a scientific trawl survey in July 2006 involving three similar trawlers of the French trawler fleet were used. Daytime accessibility to large hake was lower than at night, and about zero for small hake (<19 cm). Estimates of spatial variation made using generalized linear mixed models showed a patchy fine-scale spatial distribution, but a random larger-scale distribution of hake over the area surveyed. [ABSTRACT FROM PUBLISHER]

Universal kriging was used to model the spatio-temporal variability in the acoustic density of tuna aggregations recorded during star echosounding surveys around moored fish aggregating devices (FADs) in Martinique (Lesser Antilles). The large-scale deterministic drift in the tuna spatial distribution was modeled using an advection–diffusion equation applied to animal grouping. Residuals from the drift were modeled as a random component with small-scale spatial correlation. An estimation variance formula was derived from this deterministic–statistical mixed model to assess the mean precision of density estimates of daytime tuna aggregation. The mean relative error obtained with our star design for daytime surveys was 24%. The methodology was applied to estimate daily maxima of tuna biomass around moored FADs during four monthly sea cruises. The daily peak of tuna biomass aggregated around moored FADs was 9 t on average (standard deviation = 4). Estimation variances for different survey designs were compared for optimizing sampling strategy. [ABSTRACT FROM AUTHOR]

Conservation has moved from species-centered to ecosystem-based approaches: the Marine Strategy Framework Directive requires the maintenance or restoration of ‘Good Environmental Status’ of all European marine waters. Monitoring biodiversity at the scale of whole ecosystems is salient, but challenging owing to the large spatial scale involved and the large spatio-temporal heterogeneity of marine ecosystems. We capitalized on the integrated ecosystemic PELGAS survey carried out in spring in the Bay of Biscay to document patterns of change in marine megafauna relative abundance at the community level over more than a decade (2004–2016). The relative abundance of the twenty-three most frequently sighted species (6 cetaceans and 17 seabirds) was estimated by distance sampling, and averaged over the study period and area. Temporal changes were investigated with a Dynamic Factor Analysis. This exploratory analysis suggested that approximately one third of all species showed an increase, another third a decrease, and the last third no overall change in relative abundance. The relative abundance of offshore species, including that of all studied cetaceans, slightly increased in spring between 2004 and 2016. Further investigations will correlate the uncovered changes at the marine megafauna community level with concommittent biological and oceanographic processes that are routinely monitored on the PELGAS integrated ecosystemic surveys. [ABSTRACT FROM AUTHOR]

Integrated marine survey series such as PELGAS provide comprehensive geo-referenced data over large sea areas in major ecosystem components with defined biological resolution and spatio-temporal sampling scale. These data enable to develop product at different levels of biological organization and spatial scale that are useful for ecosystem integrated assessments. Using the PELGAS integrated data series, we applied a generic procedure made of several steps to identify and map ecologically coherent ecosystem spatial units in the Bay of Biscay. First, the data were interpolated on a common spatial grid and organized as a time series of matrices containing at each time the variables as columns and the grid cell values as rows. The multi-table analysis method known as Multi-Factor Analysis (MFA) was then applied on the series of matrices, thus separating in the analysis the spatial from the temporal variability. Grouping the spatial grid cells based on their relative positions in the MFA space resulted in mapping ecosystem spatial entities based on common spatial patterns across ecosystem components. The result of the analysis is a map of ecosystem seascapes that are consistent over the years together with a map of their inter-annual variability. The ecosystem sub-units were in agreement with sub-regional production systems in the Bay of Biscay. This study thus highlights the possibility to characterize and monitor ecosystem spatial structure and develop indicators thereof for their use in ecosystem assessments. Also, it highlights the importance of identifying spatial limits of production systems for ecosystem description, assessment and management. [ABSTRACT FROM AUTHOR]

• Taxonomically and spatially–resolved zooplankton dataset over 16 years in spring. • Time–consistent zooplankton composition spatial structure with multi–table analysis. • Explanation of zooplankton spatial patterns with gradients in the pelagic ecosystem. • Zooplankton spatial pattern underpinned by taxonomic composition and size structure. • River plumes, temperature gradients and pelagic fish correlated zooplankton pattern. As mesozooplankton is the preferential prey of small pelagic fish (SPF), environmentally–driven mesozooplankton dynamics can have critical effects on SPF population dynamics. Despite previous studies on SPF habitats' dynamics, hydrological landscapes and mesozooplankton dynamics in the Bay of Biscay (BoB), knowledge gaps persist at the BoB regional–scale pelagic ecology and in particular about the mesozooplankton assemblages and their long–term space–time patterns. Here, we present 16 years of spring mesozooplankton assemblage interannual spatial dynamics over the BoB continental shelf and we describe the correlations between the mesozooplankton space–time patterns and those in hydrology, primary producers and SPF. We gathered data originating from the PELGAS surveys (2004–2019) and remote sensing products. Mesozooplankton samples were collected with a 200–µm mesh size WP2 net vertically towed from 100 m depth (or 5 m above the sea floor) to the surface. They were analysed with imaging and deep-learning tools and the biomass in 24 coarse taxonomic groups was calculated. Automated procedures for spatial gridding and missing data imputation enable the generation of yearly maps time series with the same spatial resolution across the pelagic ecosystem components and years. These comprehensive multivariate datasets were analysed with a multi–table method known as Multiple Factor Analyses to depict time–consistent spatial patterns in each ecosystem component and the temporal variability around them. Finally, the main time–consistent spatial patterns in the hydrology, primary producers and SPF ecosystem components were used as predictors in generalized linear models, to explain those in the mesozooplankton. Mesoscale coastal-offshore and north–south gradients were the main patterns observed in each of the pelagic ecosystem components studied. The spatial patterns in the mesozooplankton assemblage were stable, without any significant changes detected in the taxonomic composition nor its spatial structure over the studied period. Small copepods, gelatinous and meroplanktonic organisms characterised coastal areas. Euchaetidae and meroplanktonic crustaceans' larvae displayed higher biomass in the northern part of the BoB while Metridinidae, Cladocera, Appendicularia and Echinodermata had higher biomass in the southern part. Surface and bottom water temperature, salinity–related parameters, water column stratification and SPF biomasses were the variables that best explained the observed space–time patterns in the mesozooplankton communities. [ABSTRACT FROM AUTHOR]

• The decreasing trend in size continues for European anchovy and sardine. • We modeled the impact of temperature and zooplankton on growth variability. • Most of the variability in size was explained by regional environments. • Trends in the modeled environment were not sufficient to explain the decrease in size. • We further explored the effect of a potential decrease in food quality. Small pelagic fish have shown a general decrease in size and body condition over the past two decades in several European regional seas. Although the underlying processes are still not well understood, recent studies point to a bottom-up control. In order to better understand how the environment impacts the main individual life history traits, which themselves control the dynamic of the population, we developed a comparative approach between two species, European anchovy and sardine, and across three regions of the Northeast Atlantic and Mediterranean Sea: the English Channel in the north, to the Bay of Biscay and the Gulf of Lion in the south. We developed a bioenergetic modeling framework based on the Dynamic Energy Budget theory (DEB). Our DEB models were forced using two different representations of the lower trophic levels, POLCOMS-ERSEM and SEAPODYM models. Our models were calibrated for the Bay of Biscay and then projected on to the other regions, over the early 2000s (period with bigger fish) and the early 2010s (period with smaller fish). The environment alone, temperature and zooplankton, explained a significant part of the observed regional differences in growth. However, the temporal trends simulated by the lower trophic levels models, when transcribed through bioenergetics, could not explain the strong decrease in length and weight that occurred in the Bay of Biscay (-30 % in weight for anchovy and −20 % for sardine) and in the Gulf of Lion (-30 % for anchovy and −50 % for sardine). Through a scenario approach, we estimated that a decrease in zooplankton quality could be a significant driver of the observed decrease in size both in the Bay of Biscay and in the Gulf of Lion (decrease in assimilable energy of 4 to 5 % and 15 to 17 % in the Bay of Biscay and the Gulf of Lion, respectively). For such a decrease in size, a zooplankton biomass of the same quality should have been reduced by between 17 and 31 % in the Bay of Biscay over a 10- to 15-year period, while no biologically realistic estimations were obtained for the Gulf of Lion. The validity of these proposed changes in biomass and quality is discussed in context of alternative explanations. [ABSTRACT FROM AUTHOR]

This paper provides an overview of the progress Ifremer has made recently in fisheries acoustics and the study of small pelagic fish by: i) pushing observation frontiers using a range of platforms including an autonomous underwater vehicle, AUV, ii) developing measuring instruments and methods and iii) studying fish distributions. Presently, information from several frequencies of single-beam echosounders is routinely collected together with data from the ME70 multibeam echosounder. For onboard data acquisition control the HERMES software was developed. The new MOVIES 3D software includes modules for simultaneous realistic 3D visualisation and post-processing such as bottom detection, school extraction and calculation of descriptors and integration of all acoustic data. Several data analysis methods are being developed and some initial results are presented. Finally, results on the spatial distribution of small pelagic fish schools in the Bay of Biscay illustrate the role that acoustics can play, and are already playing, in the implementation of an ecosystem approach to fisheries. [ABSTRACT FROM AUTHOR]