Optimal design of ecosystem module

Within Task 5.3 “Regional Observing system simulation experiments and process modelling”; CLS is in charge of improving an ecosystem module for the ocean mid-trophic levels (i.e. micronekton) that utilizes multiple in-situ and satellite data as input to derive predictions for different trophic levels including fish [D5.5] and has the potential to be implemented into the routine services supported by a future IAOOS. With physical and biogeochemical variables becoming available in real-time, the real-time monitoring of marine resources relying on the development of ecosystem models is envisaged. Optimal design of acoustic sampling to calibrate the model parameters is investigated and the ecosystem module prepared for integration into the operational system in support of Task 8.7

KRILLPODYM: a mechanistic, spatially resolved model of Antarctic krill distribution and abundance

Robust prediction of population responses to changing environments requires the integration of factors controlling population dynamics with processes affecting distribution. This is true everywhere but especially in polar pelagic environments. Biological cycles for many polar species are synchronised to extreme seasonality, while their distributions may be influenced by both the prevailing oceanic circulation and sea-ice distribution. Antarctic krill (krill, Euphausia superba) is one such species exhibiting a complex life history that is finely tuned to the extreme seasonality of the Southern Ocean. Dependencies on the timing of optimal seasonal conditions have led to concerns over the effects of future climate on krill’s population status, particularly given the species’ important role within Southern Ocean ecosystems. Under a changing climate, established correlations between environment and species may breakdown. Developing the capacity for predicting krill responses to climate change therefore requires methods that can explicitly consider the interplay between life history, biological conditions, and transport. The Spatial Ecosystem And Population Dynamics Model (SEAPODYM) is one such framework that integrates population and general circulation modelling to simulate the spatial dynamics of key organisms. Here, we describe a modification to SEAPODYM, creating a novel model – KRILLPODYM – that generates spatially resolved estimates of krill biomass and demographics. This new model consists of three major components: (1) an age-structured population consisting of five key life stages, each with multiple age classes, which undergo age-dependent growth and mortality, (2) six key habitats that mediate the production of larvae and life stage survival, and (3) spatial dynamics driven by both the underlying circulation of ocean currents and advection of sea-ice. We present the first results of KRILLPODYM, using published deterministic functions of population processes and habitat suitability rules. Initialising from a non-informative uniform density across the Southern Ocean our model independently develops a circumpolar population distribution of krill that approximates observations. The model framework lends itself to applied experiments aimed at resolving key population parameters, life-stage specific habitat requirements, and dominant transport regimes, ultimately informing sustainable fishery management

Modeling marine zooplankton and micronekton

Le zooplancton et le micronecton sont les deux premiers échelons animaux de la chaine trophique marine. Bien que de tailles très différentes (200μm à 2mm pour le zooplancton, 2 à 20cm pour le micronecton), ces deux groupes d'espèces variées partagent un comportement singulier : les migrations nycthémérales. Ces migrations journalières entre la profondeur de jour et la surface de nuit induisent des flux de matière organique très importants entre les différentes profondeurs de l'océan. L'étude des cycles biogéochimiques océaniques a une grande importance pour l'étude du changement climatique. Cette étude est notamment conduite à travers le développement de modèles globaux de circulation océanique et de biogéochimie. La suite logique de ces développements est donc la modélisation du zooplancton et du micronecton. La gamme de modèles SEAPODYM modélise avec parcimonie la chaine trophique depuis le zooplancton jusqu'aux prédateurs supérieurs à l'aide de trois modèles. Cette thèse présente le modèle de biomasse de zooplancton SEAPODYM-LTL (pour lower trophic level, niveau trophique bas), ainsi qu'une analyse de sa sensibilité aux forçages. En effet, la particularité de ces modèles est leur forçage offline par des champs de courants, température et production primaire produits par d'autres modèles. Le modèle SEAPODYM-LTL est également comparé au modèle PISCES (NPZD), et présente des performances similaires à ce dernier dans le cas testé. Afin d'améliorer les prédictions du modèle SEAPODYM-MTL (mid-trophic level, i.e. le modèle de biomasse de micronecton), une méthodologie d'assimilation de données a été mise en place pour affiner la paramétrisation utilisée. Des données d'acoustique active (38kHz) sont donc utilisées pour enrichir le modèle. Cette méthodologie a été conçue autour d'un cas test présenté dans cette thèse. L'extension du jeu de données acoustiques assimilées au modèle a permis de mettre en évidence le besoin de mieux modéliser les profondeurs des couches verticales de SEAPODYM. Cela a été réalisé à l'aide du jeu de données acoustiques évoqué précédemment. Cette étude est également présentée dans cette thèse.Zooplankton and micronecton are the first marine trophic levels. Different by their size (200μm to 2mm for zooplankton, 2 to 20cm for micronekton), this two groups undergo diel vertical migration from depth by day to the surface during the night. These migrations create major organic matter fluxes between the deep ocean and the surface. Biogeochemical cycles are of great importance for climate change studies. These studies are conducted with ocean global circulation model and biogeochemical model. The way to go is develop low and mid-trophic level modelling approaches. SEAPODYM ensemble of models are three parsimonious model of biomass at diverse level of the trophic chain, from zooplankton to top predators. This thesis introduce the zooplankton biomass model SEAPODYM-LTL (lower trophic level) and a forcing fields sensitivity analysis. Indeed, these model are forced off line by currents, temperature and primary production fields produced by other models. SEAPODYM-LTL has also been compared to PISCES (NPZD) and both have similar performance score in this study. In order to improve SEAPODYM-MTL (mid trophic level) predictions, a data assimilation framework has been developed to find a better parameterisation. 38kHz active acoustic data have been used to improve the model. This methodology has been develop thanks to a test case that we present in this thesis. The gathered acoustic dataset permitted to show the need of a better definition of vertical layer depths. It has been developed using the acoustic dataset. The related study is presented in this thesis

Modélisation du zooplancton et du micronecton marins

Zooplankton and micronecton are the first marine trophic levels. Different by their size (200μm to 2mm for zooplankton, 2 to 20cm for micronekton), this two groups undergo diel vertical migration from depth by day to the surface during the night. These migrations create major organic matter fluxes between the deep ocean and the surface. Biogeochemical cycles are of great importance for climate change studies. These studies are conducted with ocean global circulation model and biogeochemical model. The way to go is develop low and mid-trophic level modelling approaches. SEAPODYM ensemble of models are three parsimonious model of biomass at diverse level of the trophic chain, from zooplankton to top predators. This thesis introduce the zooplankton biomass model SEAPODYM-LTL (lower trophic level) and a forcing fields sensitivity analysis. Indeed, these model are forced off line by currents, temperature and primary production fields produced by other models. SEAPODYM-LTL has also been compared to PISCES (NPZD) and both have similar performance score in this study. In order to improve SEAPODYM-MTL (mid trophic level) predictions, a data assimilation framework has been developed to find a better parameterisation. 38kHz active acoustic data have been used to improve the model. This methodology has been develop thanks to a test case that we present in this thesis. The gathered acoustic dataset permitted to show the need of a better definition of vertical layer depths. It has been developed using the acoustic dataset. The related study is presented in this thesis.Le zooplancton et le micronecton sont les deux premiers échelons animaux de la chaine trophique marine. Bien que de tailles très différentes (200μm à 2mm pour le zooplancton, 2 à 20cm pour le micronecton), ces deux groupes d'espèces variées partagent un comportement singulier : les migrations nycthémérales. Ces migrations journalières entre la profondeur de jour et la surface de nuit induisent des flux de matière organique très importants entre les différentes profondeurs de l'océan. L'étude des cycles biogéochimiques océaniques a une grande importance pour l'étude du changement climatique. Cette étude est notamment conduite à travers le développement de modèles globaux de circulation océanique et de biogéochimie. La suite logique de ces développements est donc la modélisation du zooplancton et du micronecton. La gamme de modèles SEAPODYM modélise avec parcimonie la chaine trophique depuis le zooplancton jusqu'aux prédateurs supérieurs à l'aide de trois modèles. Cette thèse présente le modèle de biomasse de zooplancton SEAPODYM-LTL (pour lower trophic level, niveau trophique bas), ainsi qu'une analyse de sa sensibilité aux forçages. En effet, la particularité de ces modèles est leur forçage offline par des champs de courants, température et production primaire produits par d'autres modèles. Le modèle SEAPODYM-LTL est également comparé au modèle PISCES (NPZD), et présente des performances similaires à ce dernier dans le cas testé. Afin d'améliorer les prédictions du modèle SEAPODYM-MTL (mid-trophic level, i.e. le modèle de biomasse de micronecton), une méthodologie d'assimilation de données a été mise en place pour affiner la paramétrisation utilisée. Des données d'acoustique active (38kHz) sont donc utilisées pour enrichir le modèle. Cette méthodologie a été conçue autour d'un cas test présenté dans cette thèse. L'extension du jeu de données acoustiques assimilées au modèle a permis de mettre en évidence le besoin de mieux modéliser les profondeurs des couches verticales de SEAPODYM. Cela a été réalisé à l'aide du jeu de données acoustiques évoqué précédemment. Cette étude est également présentée dans cette thèse

Influence of oceanic conditions in the energy transfer efficiency estimation of a micronekton model

Micronekton – small marine pelagic organisms mostly in the size range 1–10 cm – is a key component of the ocean ecosystem, as it constitutes the main source of forage for all larger predators. Moreover, the mesopelagic component of micronekton that undergoes Diel Vertical Migration (DVM) likely plays a key role in the transfer and storage of CO2 in the deep ocean: the so-called ‘biological pump’ mechanism. SEAPODYM-MTL is a spatially explicit dynamical model of micronekton. It simulates six functional groups of migrant and non-migrant micronekton, in the epipelagic and mesopelagic layers. Coefficients of energy transfer efficiency between primary production and each group are unknown. But they are essential as they control the predicted biomass. Since these coefficients are not directly measurable, a data assimilation method is used to estimate them. In this study, Observing System Simulation Experiments (OSSE) in the framework of twin experiments are used to test various observation networks at a global scale regarding energy transfer coefficients estimation. Observational networks show a variety of performances. It appears that environmental conditions are crucial to determine network efficiency. According to our study, ideal sampling areas are warm, non-dynamic and productive waters like the eastern side of tropical Oceans. These regions are found to reduce the error of estimated coefficients by 20 % compared to cold and dynamic sampling regions. The results are discussed in term of interactions between physical and biological processes

KauNet: improving reproducibility for wireless and mobile research

This paper presents the KauNet emulation system that provides pattern-based emulation. KauNet enables bit precise placement of bit-errors, exact and repeatable packet losses, delays and bandwidth variations. The design and performance of KauNet is discussed. An example is also provided of how it can be integrated in a specific emulation framework to enhance emulation for mobile and wireless systems

Emerging monitoring technologies to reduce illegal fishing activities at sea and prevent entry of fraudulent fish into markets

National and global priorities are increasingly focused on the concurrent marine fisheries challenges of food security, illegal fishing, and declining fisheries resources. Molecular genetics and electronic monitoring technologies can advance solutions to these challenges, particularly in fisheries surveillance and seafood traceability, and a growing number of studies continues to validate the utility of these tools. What is needed next is guidance to support their wider, more conventional adoption and implementation, either complementary to or in the absence of government policies. Here, we synthesize discussion held during the Borchard Foundation Colloquium held in July 2022 in Missillac, France on modernizing global fisheries with emerging technologies. Our aim is to provide perspectives to scientists, resource managers, and policy makers of emerging monitoring technologies, summarize the utility of these technologies in fisheries, and conclude with how the objective to modernize global marine fisheries is a prime opportunity to engage fresh talent in a new era of fisheries innovation

Modelled prey fields predict marine predator foraging success

Modelling marine predator foraging habitats is a widespread research approach for projecting species responses to a rapidly changing Southern Ocean. Yet a key remaining challenge is to understand how changing prey biomass within foraging habitats could affect predator foraging success. Quantifying this using observed prey information is challenging given a paucity of synoptic data. Here, we investigated whether prey biomass from a mechanistic model, could provide useful predictions of pre-breeding arrival body mass of macaroni penguins (Eudyptes chrysolophus) from Marion Island, a standard metric of predator foraging success, measured over a 20-year period. In testing this, we used a spatially iterative correlation approach between predicted prey biomass and observed penguin arrival body mass, allowing likely foraging areas to emerge in regions most frequently associated with significant correlations. We then considered whether the distribution of these emergent foraging areas is consistent with tracking-derived foraging distributions for this species and island. Our results indicated emergent foraging areas where prey biomass was most often correlated with arrival body mass were located within expected and observed foraging ranges. Further, variability in prey biomass, within these emergent foraging areas provided reasonable predictions of annual penguin arrival body mass and outperformed metrics of primary production within these foraging areas. Our findings demonstrate that mechanistic models can provide biologically meaningful representations of difficult-to-observe prey, and can predict predator foraging success. This work could improve understanding of predator responses in a changing habitat

The influence of oceanographic features on the foraging behavior of the olive ridley sea turtle Lepidochelys olivacea along the Guiana coast

International audienceThe circulation in the Western Equatorial Atlantic is characterized by a highly dynamic mesoscale activity that shapes the Guiana continental shelf. Olive ridley sea turtles (Lepidochelys olivacea) nesting in French Guiana cross this turbulent environment during their post-nesting migration. We studied how oceanographic and biological conditions drove the foraging behavior of 18 adult females, using satellite telemetry, remote sensing data (sea surface temperature, sea surface height, current velocity and euphotic depth), simulations of micronekton biomass (pelagic organisms) and in situ records (water temperature and salinity). The occurrence of foraging events throughout migration was located using Residence Time analysis, while an innovative proxy of the hunting time within a dive was used to identify and quantify foraging events during dives. Olive ridleys migrated northwestwards using the Guiana current and remained on the continental shelf at the edge of eddies formed by the North Brazil retroflection, an area characterized by low turbulence and high micronekton biomass. They performed mainly pelagic dives, hunting for an average 77% of their time. Hunting time within a dive increased with shallower euphotic depth and with lower water temperatures, and mean hunting depth increased with deeper thermocline.This is the first study to quantify foraging activity within dives in olive ridleys, and reveals the crucial role played by the thermocline on the foraging behavior of this carnivorous species. This study also provides novel and detailed data describing how turtles actively use oceanographic structures during post-nesting migration

Macrozooplankton and micronekton diversity and associated carbon vertical patterns and fluxes under distinct productive conditions around the Kerguelen Islands

International audienceMesopelagic communities are characterized by a large biomass of diverse macrozooplankton and micronekton (MM) performing diel vertical migration (DVM) connecting the surface to the deeper ocean and contributing to biogeochemical fluxes. In the Southern Ocean, a prominent High Nutrient Low Chlorophyll (HNLC) and low carbon export region, the contribution of MM to the vertical carbon flux of the biological pump remains largely unknown. Furthermore, few studies have investigated MM communities and vertical flux in naturally iron fertilized areas associated with shallow bathymetry. In this study, we assessed the MM community diversity, abundance and biomass in the Kerguelen Island region, including two stations in the HNLC region upstream of the islands, and two stations in naturally iron fertilized areas, one on the Plateau, and one downstream of the Plateau. The MM community was examined using a combination of trawl sampling and acoustic measurements at 18 and 38 kHz from the surface to 800 m. A conspicuous three-layer vertical system was observed in all areas - a shallow scattering layer, SSL, between 10 and 200 m; mid-depth scattering layer, MSL, between 200 and 500 m; deep scattering layer, DSL, between 500 and 800 m - but communities differing among stations. While salps (Salpa thompsoni) dominated the biomass at the productive Kerguelen Plateau and the downstream station, they were scarce in the HNLC upstream area. In addition, crustaceans (mainly Euphausia vallentini and Themisto gaudichaudii) were particularly abundant over the Plateau, representing a large, although varying, carbon stock in the 0–500 m water layer. Mesopelagic fish were prominent below 400 m where they formed permanent or migrant layers accounting for the main source of carbon biomass. Through these spatial and temporal sources of variability, complex patterns of the MM vertical distribution and associated carbon content were identified. The total carbon flux mediated by migratory myctophids at the four stations was quantified. While this flux was likely underestimated, this study identified the main components and mechanisms of active carbon export in the region and how they are modulated by complex topography and land mass effects