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The Benguela Upwelling System (BUS) is one of the world’s most productive ecosystems, supporting globally relevant pelagic fisheries. BUS marine community can change as a function of nutrients and omega-3 long chain polyunsaturated fatty acids (hereafter, omega-3) availability. Phytoplankton growth is supported by upwelled nitrate, a new source of nitrogen (N), or by recycled N forms such as ammonium. Preferential assimilation of one N form over another may lead to differences in omega-3 production between high and low food-quality species. This study evaluates how upwelling and the N source(s) used by phytoplankton influence omega-3 production. Sampling was conducted in the BUS at an anchor station sampled daily for 10 consecutive days. An upwelling event on days 5-6-7 supplied high concentrations of nutrients to surface waters, while pre- and post- upwelling the water column was well-stratified with low nutrient concentrations. Omega-3 and phytoplankton concentrations declined to ⁓zero during the upwelling event. Nanoplankton (2.7-10µm) were responsible for most of the productivity (30-95%) and relied on nitrate for their growth. Omega-3 concentrations at the surface reached peaks of 215.5 and 175.3µgL-1 pre- and post-upwelling, which were up to 10-times higher than previous measurements from the BUS. Pre-upwelling, non-diatom trophic markers were dominant, with a rapid switch (over just two days) to diatom trophic markers post-upwelling. This study defines the key role of upwelling in promoting phytoplankton omega-3 production, which is tightly coupled to the introduction of new-N during upwelling. The high concentrations of omega-3 reported suggest that global omega-3 production is largely underestimated.

The Benguela Upwelling System (BUS) is one of the world’s most productive ecosystems, supporting globally‐relevant fisheries. The BUS marine community is modulated by the availability of nutrients and omega‐3 long chain polyunsaturated fatty acid (hereafter, LC omega‐3). Phytoplankton growth in the BUS can be supported by upwelled nitrate, a new nitrogen (N) source to the surface, or by recycled N such as ammonium. Preferential assimilation of one N source over another may yield differences in LC omega‐3 production between high and low food‐quality species. To evaluate how upwelling and the N source(s) consumed by phytoplankton influence LC omega‐3 production, we sampled a BUS anchor station daily for 10 days. Upwelling on days 5‐7 supplied high concentrations of nutrients to the surface, while pre‐ and post‐upwelling, surface waters were stratified and nutrient concentrations were low. LC omega‐3 and phytoplankton concentrations were near‐zero during upwelling, and elevated pre‐ and post‐upwelling. Throughout our sampling, nanoplankton (2.7‐10µm) dominated primary production (30‐95%), relying mainly on nitrate to support their growth. Surface LC omega‐3 concentrations reached peaks of 215 and 175 µgL‐1 pre‐ and post‐upwelling, up to 10‐times higher than previous measurements from the BUS (<5 µgL‐1). Pre‐upwelling, non‐diatom trophic markers (18:1n‐9,18:4n‐3,18:5n‐3) were dominant, with a switch over just two days to diatom trophic markers post‐upwelling (16:1n‐7,16:2n‐4,16:2n‐7,16:3n‐4,16:4n‐1). This study reveals the key role of upwelling in promoting phytoplankton LC omega‐3 production, which is tightly coupled to the supply of new nitrate. Additionally, the high observed LC omega‐3 concentrations suggest that global LC omega‐3 production is underestimated.

Small pelagic fishes such as sardine and anchovy are among the richest species in essential fatty acids that are eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA), whose bioavailability may depend on its esterification to polar or neutral lipids. The EPA and DHA quantities in neutral and polar lipids were compared in sardine (from the English Channel) and anchovy (from the Bay of Biscay) fillets, and in red and white muscle separately. Sardine fillets had the highest EPA+DHA content (760±670 vs 370±510 mg/100 g in anchovy fillets), mainly because of their largest proportion of lipid-rich red muscle and its relatively high lipid content. However, DHA esterified to polar lipids was higher in anchovy than in sardine fillet (270±60 vs 230±30 mg/100 g). EPA+DHA content were higher in red than white muscle for both species. This study highlights the nutritional interest of red muscle to provide essential dietary fatty acids to consumers, and the necessity to consider its importance in nutrition studies.

Studying adverse effects of chemical pressure on aquatic ecosystems needs a comprehensive knowledge of bioaccumulation mechanisms of pollutants in biota to predict internal concentrations, especially for Persistent Organic Pollutants (POPs). However, the large variability of responses in measured POP concentrations requires explicit consideration of both individual variability and environmental influences. Dynamic Energy Budget (DEB) theory provides a rigorous and generic conceptual framework for tackling these questions in a relevant mechanistic way. In the present study, parameterisation and calibration of previous DEB models for Solea solea were revisited in order to accurately represent the full life cycle with an original emphasis on larval stage, metamorphosis, reproduction rules and sexual differences. We first improved calibration thanks to the use of the estimation procedure developed by the DEB network coupled with a broad compilation of data from literature. Then, we validated this set of parameter estimates on independent datasets of i) individual monitoring of larval growth in controlled food conditions from a novel experiment, and ii) juvenile and adult growth, and female fecundity, from a natural population. Finally, we combined the DEB model developed in the present paper with we used a simple toxicokinetic (TK) model from literature. This TK model was also combined to a previous DEB model and was used to reproduce the mean trajectories of a growth and contamination dataset. We applied the same TK model with our DEB model considering inter-individual variability in food availability. This application highlighted the need to accurately consider inter-individual variability in ingestion to correctly estimate growth and contamination variability. The present work is the first step in the development of a mechanistic TK model that will be used in a companion paper for investigations of juvenile sole sensitivity to warming, nursery quality and prey contam

The amount of potentially toxic chemicals in a fish depends on various environmental factors, such as temperature and feeding ecology, which can be affected by Global Changes (GC). The main objective of the present work was to study the relative influence of temperature, food quality and food availability on the growth and contamination of juveniles of common sole (Solea solea), a marine flatfish species known to be a relevant indicator of the nursery quality. It focuses on two Persistent Organic Pollutants (CB153 and L-PFOS) of legacy and emerging concern, respectively. To achieve this, we used a toxicokinetic (TK) model in which toxicant flows are mechanistically predicted using a bioenergetic model based on the Dynamic Energy Budget (DEB) theory. This modelling framework was applied to juvenile sole from the Gironde estuary (SW France) and allows accounting for the influence of environmental conditions on fish biological processes involved in toxicant fluxes. To compare their respective influence on model predictions of age, length, and contamination at puberty, we included in a global sensitivity analysis: (1) environmental variability gathered from literature for this particular estuary and (2) TK parameters (i.e. assimilation efficiency AE and elimination rate ) variability and uncertainty gathered from literature about each contaminant but for different fish species and experimental conditions. Then, model predictions were confronted to fish contamination measurements from the Gironde Estuary with different combinations of TK parameter values from literature. Results highlighted a key role of diet composition on fish contamination and growth while water temperature only affected growth. It stressed the need to focus on GC impact on benthic communities and their consequences on juvenile fish diet for future work on GC scenarios. Furthermore, for both chemical, the range of variability of TK parameters from experiments led to underestimated fish contaminations.

The black-lipped pearl oyster (Pinctada margaritifera) is extensively farmed in French Polynesia to produce black pearls. For a sustainable management of marine resources, studying interactions between organisms and environment, and the associated factors and processes that will impact their life cycle and thus modulate population dynamics is a major research priority. Here, we describe black-lipped pearl oyster energy acquisition and use, and its control by temperature and food concentration within the Dynamic Energy Budget (DEB) theory framework. The model parametrization was based on literature data and a specific laboratory experiment. Model validation was carried out thanks to historical in-situ datasets and a dedicated field survey. Three theoretical environmental scenarios were built to investigate the response of the pearl oyster to environmental variations. We successfully modeled a wide range of life-stage-specific traits and processes, especially the delayed acceleration of growth after settlement. Applying the model on field data collected at three different culture sites required only one free-fitted parameter, the half saturation coefficient Xk, which controls how ingestion depends on food density. Xk integrates all variations linked to the trophic environment. Analysis of the kinetics of energy fluxes under theoretical environmental scenarios suggests that temperature variations induce seasonality of reproduction in a species thought to spawn opportunistically throughout the whole year. The major influence of food concentration fluctuations on growth rate and reproductive effort is highlighted. The model showed the lower performances associated with recovery time between food-rich and starvation periods. The implications of these findings in the context of black pearl farming in a changing environment are discussed.

Hypoxia is a decrease in dissolved oxygen that causes physiological disturbances in marine fishes and invertebrates, including reduced mobility, growth rate and reproductive success, altered phenology and increased vulnerability to diseases. Under pressure from global changes such as warming or eutrophication, ocean and coastal ecosystems worldwide are becoming less oxygenated. In order to better understand the consequences of hypoxia on marine systems, there is a need for predicting hypoxia-induced changes from individual organisms to populations. By combining the effect of several stressors on species metabolic performances and life-history traits across their full life-cycle, the Dynamic Energy Budget (DEB) theory offers a suitable framework for studying the consequences of hypoxia on marine organisms and to envision an upscaling of these effects at population level through individual-based modelling approaches. Here, we propose a set of stylized biological facts which give a broad generalization of the effects of hypoxia on metabolic functions based on empirical findings. We used these stylized facts to derive assumptions on how to incorporate the effects of hypoxia on marine organisms in the framework of the DEB theory. We then validate some of these assumptions on marine species for which experimental datasets under hypoxic conditions and DEB parameters were available. We discuss the main issues that need to be dealt with, such as the various time-scales, ontogenic responses and multi-stressor effects which appear now as important targets of investigation for studying the effect of hypoxia on marine organisms.

The present study aimed to improve understanding of the environmental conditions influencing the reproductive cycle of the great scallop Pecten maximus in two locations in Brittany (France). We also evaluated potential consequences of future climate change for reproductive success in each site. We simulated reproductive traits (spawning occurrences and synchronicity among individuals) of P. maximus, using an existing Dynamic Energy Budget (DEB) model. To validate and test the model, we used biological and environmental datasets available for the Bay of Brest (West Brittany, France) between 1998 and 2003. We also applied the scallop DEB model in the Bay of Saint-Brieuc (North Brittany, France) for the same period (1998–2003) to compare the reproductive cycle in different environmental conditions. In order to accurately model the P. maximus reproductive cycle we improved the scallop DEB model in two ways: through (1) energy acquisition, by incorporating microphytobenthos as a new food source; and (2) the reproductive process, by adding a new state variable dedicated to the gamete production. Finally, we explored the effects of two contrasting IPCC climate scenarios (RCP2.6 and RCP8.5) on the reproductive cycle of P. maximus in these two areas at the 2100 horizon. In the Bay of Brest, the simulated reproductive cycle was in agreement with field observations. The model reproduced three main spawning events every year (between May and September) and asynchronicity in the timing of spawning between individuals. In the Bay of Saint-Brieuc, only two summer spawning events (in July and August) were simulated, with a higher synchronicity between individuals. Environmental conditions (temperature and food sources) were sufficient to explain this well-known geographic difference in the reproductive strategy of P. maximus. Regarding the forecasting approach, the model showed that, under a warm scenario (RCP8.5), autumnal spawning would be enhanced at the 2100 horizon with an inc

Low concentrations of oxygen determine marine species distribution and abundance along the Peruvian coast with consequences for human activity such as fishing and aquaculture. In order to assess bioenergetic consequences of oxygen limitation on the Peruvian scallop Argopecten purpuratus, we first developed a Dynamic Energy Budget (DEB) model of growth and reproduction calibrated on field experimental datasets. Then, we included oxygen availability as an additional forcing variable using a simple rule based on the ability of the scallop to regulate oxygen consumption. The resulting model was tested using growth/reproduction monitoring and simultaneous high frequency environmental records in Paracas Bay (Peru) at two different depths: suspended in the water column and on the sea bottom. Simulations indicated that scallops' growth and reproduction was not food-limited. The negative observed effects of hypoxia on growth and reproduction could be explained by a decrease in both assimilation and reserve mobilization. However, hypoxic conditions in summer were not sufficient to explain the observed losses in somatic tissue weights and the disruption of reproduction. The latter two patterns were better simulated when assuming increased somatic maintenance costs due to the presence of H2S during milky turquoise water discolouration events observed during summer.

Identifying the drivers that control the reproductive success of a population is vital to forecasting the consequences of climate change in terms of distribution shift and population dynamics. In the present study, we aimed to improve our understanding of the environmental conditions that allowed the colonization of the Pacific oyster, Crassostrea gigas, in the Bay of Brest since its introduction in the 1960s. We also aimed to evaluate the potential consequences of future climate change on its reproductive success and further expansion. Three reproductive traits were defined to study the success of the reproduction: the spawning occurrence, synchronicity among individuals and individual fecundity. We simulated these traits by applying an individual-based modeling approach using a Dynamic Energy Budget (DEB) model. First, the model was calibrated for C. gigas in the Bay of Brest using a 6-year monitoring dataset (2009–2014). Second, we reconstructed past temperature conditions since 1960 in order to run the model backwards (hindcasting analysis) and identified the emergence of conditions that favored increasing reproductive success. Third, we explored the regional consequences of two contrasting IPCC climate scenarios (RCP2.6 and RCP8.5) on the reproductive success of this species in the bay for the 2100 horizon (forecasting analysis). In both analyses, since phytoplankton concentration variations were, at that point, unknown in the past and unpredicted in the future, we made an initial assumption that our six years of observed phytoplankton concentrations were informative enough to represent “past and future possibilities” of phytoplankton dynamics in the Bay of Brest. Therefore, temperature is the variable that we modified under each forecasting and hindcasting runs. The hindcasting simulations showed that the spawning events increased after 1995, which agrees with the observations made on C. gigas colonization. The forecasting simulations showed that under the war

Like many marine species around the globe, several stocks of Atlantic cod (Gadus morhua) live in increasingly hypoxic waters. In the Gulf of Saint Lawrence (GSL) in Canada, the deep channels traversing the semi-enclosed sea exhibit year-round hypoxia, identified as one of the limiting factor for the recovery of GSL cod in its northern part. While many individuals in the northern GSL are known to venture in deeper, warmer, and more hypoxic waters of the Gulf channels, those in the southern GSL live in a shallower, colder, and more oxygenated environment. In this study, we use the modeling framework of the Dynamic Energy Budget (DEB) theory to disentangle the effects of hypoxia, temperature and food on the life-history traits of these two populations of cod in the GSL. Following recent advances by Thomas et al. (submitted, this issue) on the mechanisms for the effects of hypoxia within the context of DEB theory, we implemented a correction of ingestion depending on dissolved oxygen (DO) saturation. We successfully developed and validated a set of parameters for a GSL Atlantic cod DEB model. Using simulations of historical growth trajectories from 1990 until 2004 estimated from data collected through fisheries research surveys, we found that temperature explained about half (48%) of the difference in length and 59% of the difference in mass between the two populations. The remaining proportion was attributed to exposure to hypoxia and food input. We also used our model to explore scenarios of duration, frequency, and intensity of hypoxia on cod's life-history traits, which showed that decreasing DO linearly reduces growth and reproduction while young cod seem to avoid impairing conditions resulting in limiting effects on developmental stages.

The Peruvian scallop (Argopecten purpuratus) is the second main contributor to the total catch of mollusks in Peru, after jumbo squid. There are two main scallop banks populations in northern Peru: Lobos de Tierra Island (LTI) and Sechura Bay (SB). Despite a continuous, intense relocation of seeds from LTI, the natural bank population still persists there. To understand this, we studied larval connectivity between LTI and SB using the first invertebrate larval transport biophysical model developed in the region. Larval local retention were 2.4% and 1.57% on average at LTI and SB respectively, while larval transport from SB to LTI was 0.02% on average and 0.07% in the opposite direction. Both larval retention and larval transport increased with spawning depth and were highest in austral summer. Two main larval transport paths from SB to LTI were identified, resulting from a combination of horizontal mesoscale circulation patterns and vertical flows. Potential management implications for these natural banks are discussed.

Dynamic Energy Budget (DEB) theory constitutes a coherent set of universal biological processes that have been used as building blocks for modeling biological systems over the last 40 years in many applied disciplines. In the context of extracting parameters for DEB models from data, we discuss the methodology of fitting multiple models, which share parameters, to multiple data sets in a single parameter estimation. This problem is not specific to DEB models, and is (or should be) really general in biology. We discovered that a lot of estimation problems that we suffered from in the past originated from the use of a loss function that was not symmetric in the role of data and predictions. We here propose two much better symmetric candidates, that proved to work well in practice. We illustrate estimation problems and their solutions with a Monte-Carlo case study for increasing amount of scatter, which decreased the amount of information in the data about one or more parameter values. We here validate the method using a set of models with known parameters and different scatter structures. We compare the loss functions on the basis of convergence, point and interval estimates. We also discuss the use of pseudo-data, i.e. realistic values for parameters that we treat as data from which predictions can differ. These pseudo-data are used to avoid that a good fit results in parameter values that make no biological sense. We discuss our new method for estimating confidence intervals and present a list of concrete recommendations for parameter estimation. We conclude that the proposed method performs very well in recovering parameter values of a set of models, applied to a set of data. This is consistent with our large-scale applications in practice.