The aim of this study was to investigate the composition of an acoustic scattering layer in the North Sea that is particularly strong at 38 kHz. A full definition of the biological composition of the layer, along with its acoustic properties, would allow for it to be confidently removed from data collected during acoustic fish surveys, where it presents a potential source of bias. The layer, traditionally and informally referred to as consisting of zooplankton, appears similar to others observed internationally. The methodology utilised in this study consisted of biological and acoustic sampling, followed by application of forward and inverse acoustic modelling techniques. Acoustic data was collected at 38, 120 and 200 kHz in July 2003, with the addition of 18 kHz in July 2004. Net samples were collected in layers of relatively strong 38 kHz acoustic scattering using a U-tow vehicle (2003) and a MIKT net (2004). Acoustic data were scrutinised to determine actual backscattering, expressed as mean volume backscattering strength (MVBS) (dB). This observed MVBS (MVBSobs) was compared with backscattering predicted by applying the forward problem solution (MVBSpred) to sampled animal densities in order to determine whether those animals were responsible for the enhanced 38 kHz scattering. In most instances, MVBSobs > MVBSpred, more pronounced at 38 kHz. It was found that MVBSpred approached MVBSobs more closely with MIKT than with U-tow samples, but that the 38 kHz mismatch was present in both. Inversion of candidate acoustic models predicted gas-bearing scatterers, which are strong at 38 kHz, as most likely to be responsible for this. Potential sources of inconsistencies between MVBSpred and MVBSobs were identified. The presented forward and inverse solutions infer that although the layer often contains large numbers of common zooplankton types, such as copepods and euphausiids, these are not the dominant acoustic scatterer at 38 kHz. Rather, there remains an unidentified, probably gas-bearing scatterer that contributes significantly to observed scattering levels at this frequency. This study identifies and considerably narrows the list of candidates that are most likely to be responsible for enhanced 38 kHz scattering in the North Sea layer, and recommendations are made for potential future studies.

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.

This thesis presents the first description of the geographic and depth distributions of pelagic decapod shrimps in the area located around the Deepwater Horizon oil spill, based on the NOAA (National Oceanic and Atmospheric Administration) NRDA (National Resource Damage Assessment) trawl samples collected from April – June, 2011. This information is important in ecosystem models investigating trophic effects of the spill because pelagic decapod shrimp are consumed by a variety of organisms occupying higher trophic levels. One of the most abundant and diverse groups of decapods is the Family Oplophoridae. Their roles in pelagic food webs in the Gulf of Mexico (GOM) and other deep-sea ecosystems makes them ideal candidates for study; however, only a limited amount of research has been conducted on their distribution and reproductive biology. In the northeastern GOM, all previous studies have been conducted at Standard Station in the eastern Gulf (27°N, 86°W) (Hopkins and Lancraft, 1984; Hopkins et al., 1989; Hopkins and Gartner, 1992; Hopkins et al., 1994). The current study is unique because 1) it provides data from regions of the Gulf where oplophorids have never been studied, 2) allows for comparisons of distributions and abundances of oplophorid species in both the mesopelagic and bathypelagic zones by using a continuous data set, and 3) compares assemblages from two distinct bathymetric environments in the northeastern GOM: continental slope (200-1000 m bottom depth) and offshore (>1000 m). As the study site also encompasses the region most strongly impacted by the Deepwater Horizon oil spill, these data represent the first quantification of any component of the decapod crustacean assemblage in this location after the oil spill, and will be used for comparison with data obtained during future DEEPEND Consortium (Deep Pelagic Nekton Dynamics of the Gulf of Mexico) cruises to monitor changes, or lack thereof, in the assemblage after exposure to Deepwater Horizon oil and dispersants in the water column.

This thesis presents: 1) the first statistically rigorous support for the longstanding hypothesis that state of satiation modifies diel vertical migration patterns of deep-sea micronektonic crustaceans and fishes; and, 2) the first assessment of microplastic ingestion by deep-pelagic micronekton in the Gulf of Mexico and Straits of Florida. Deep-sea pelagic crustaceans and fishes significantly contribute to abundance and biomass of pelagic ecosystems, are frequently consumed by commercially valuable fishery species, and serve to transport both nutrients and pollutants between shallow and deep waters. The results presented herein will be valuable for assessing risk associated with potential biomagnification of plastic through consumption or indirect consumption of deep-sea biota. Moreover, these data demonstrate that the extent of feeding at depth by non-migratory taxa as well as non-migrating individuals of migratory taxa is substantial. Feeding at depth is usually excluded from biogeochemical models, and these data demonstrate that this is an important factor that must be included to obtain more precise estimates of active nutrient flux by micronekton.

The vertical and horizontal distributions of Euphausiacea in the northern Gulf of Mexico, including the location of the Deepwater Horizon oil spill, were analyzed from 340 trawl samples collected between April-June, 2011. This study is the first comprehensive survey of euphausiid distributions from depths deeper than 1000 m in the Gulf of Mexico and included stratified sampling from five discrete depth ranges (0-200 m, 200-600 m, 600-1000 m, 1000-1200 m, and 1200-1500 m). In addition, this study encompasses the region heavily impacted by the Deepwater Horizon oil spill. Data presented here could potentially be used in ecosystem models investigating trophic effects of the spill because euphausiids are the preferred prey of a variety of higher trophic organisms. Lastly, these data represent the first quantification of euphausiid assemblages in this location after the Deepwater Horizon event and can serve as a basis of comparison against which to monitor recovery of the euphausiid assemblage after exposure to Deepwater Horizon hydrocarbons and dispersant in the water column.

The larger pelagic crustacean fauna of the Gully submarine canyon is described for the first time, based on three annual summer surveys. The larger Crustacea are a significant part of the Gully fauna, and are dominated by cold temperate species, in particular the northern krill Meganyctiphanes norvegica and the decapod Sergestes arcticus. In all, at least 69 species were collected from the surface to bathypelagic depths, with seventeen being new Canadian records. With the exception of M. norvegica, inter-annual variation in the dominant species was minor. The species assemblage varied primarily with depth surveyed and diel cycle, and not year. Comparing the larger pelagic crustaceans in the Gully and over the adjacent continental slope showed that overall species number, biomass, and abundance were all greater in the canyon, the biomass of S. arcticus particularly showing a positive “Gully effect”.

Pour comprendre le fonctionnement d'un écosystème, il est essentiel de comprendre l'organisation du réseau trophique associé. Dans les eaux océaniques du sud-ouest de l'océan Indien (10-60°S, 35-90°E), si la répartition de la production primaire et la distribution des prédateurs supérieurs sont bien connues, un manque de connaissance demeure en ce qui concerne la distribution des différents organismes composant l'échelon trophique intermédiaire et ce, malgré leur importance écologique (pompe biologique et rôle trophique clé) et potentiellement économique (ambitions de pêche dans un futur proche). Pour combler ce manque, ce travail de thèse s'est concentré sur les distributions horizontale et verticale et la composition des organismes micronectoniques de cette région. La distribution du micronecton a donc été étudiée à méso- et large-échelle à partir d'enregistrements acoustiques (38 kHz). En termes de distribution verticale, une structuration en trois couches principales a été mise en évidence ; l'intensité et l'épaisseur de ces couches variant selon la période du jour (migrations nycthémérales) et les conditions océaniques (tourbillons océaniques à méso-échelle et fronts océaniques à large-échelle). En ce qui concerne la distribution horizontale, le sud-ouest de l'océan Indien a été caractérisé par des eaux (10 – 800 m) plus riches aux latitudes subtropicales, en été comme en hiver. Mais chaque type d'organisme ayant ses propres caractéristiques écologiques, il était important de pouvoir décrire les distributions propres à chaque groupe biologique composant ce micronecton. Une approche acoustique bifréquence (38 et 120 kHz) a permis de distinguer les crustacés micronectoniques des petits poissons mésopélagiques contenant une vessie natatoire gazeuse dans les eaux est de Kerguelen. En termes de distribution horizontale et de densité globale estimée, les crustacés micronectoniques dominaient les eaux océaniques à l'est de Kerguelen. Sur la verticale, deux types de structuration ont été mis en évidence : une structure agrégative et une structure en couches. Les crustacés micronectoniques ont été caractérisés par une structuration en couches, de jour comme de nuit, alors que les autres organismes sondés (les poissons ayant une vessie natatoire gazeuse notamment) présentaient une structuration mixte composée d'agrégats et de couches le jour et composée uniquement de couches la nuit. En résumé, l'approche acoustique utilisée dans ce travail a permis de décrire la distribution et la composition des organismes micronectoniques et fournit une base descriptive essentielle sur le micronecton du sud-ouest de l'océan Indien. / To understand the functioning of an ecosystem, it is essential to understand the organization of its associated food web. While the distribution of primary production and top predators in the Southwest Indian Ocean's oceanic waters (10-60 ° S, 35-90 ° E) are well known, a lack of knowledge remains regarding the distribution of mid-trophic level organisms, despite their ecological (biological pump and key trophic role) and potentially economic (commercial fisheries in the near future) importance. To fill this gap, this work focused on the horizontal and vertical distribution and composition of micronektonic communities in this region. Micronekton comprises relatively small organisms (1 to 20 cm long) able to swim freely without being unduly affected by currents. Micronekton distributions have been studied at meso- and large-scale using acoustic recordings (38 kHz). A vertical structure in three layers has been identified ; the intensity and thickness of these layers vary depending on the considered time period (diel migration) and ocean conditions (meso-scale oceanic eddies and large-scale oceanic fronts). Horizontaly, the Southwestern Indian Ocean harbours the richest waters (10-800 m) in subtropical latitudes in summer and winter times. Since every organism has its own ecological characteristics, it was important to separatly describe the distribution of biological groups composing micronekton. A bi-frequency acoustic approach (38 and 120 kHz) allowed the distinction of micronektonic crustaceans from small mesopelagic gas-filled swimbladder fish in waters east of Kerguelen where micronektonic crustaceans where dominant in terms of overall acoustic density. Two distinct types of vertical structure were highlighted : an aggregative and a layer structure. Micronektonic crustaceans were characterized by layering, day and night, while other organisms (gas-filled swimbladder fish in particular) exhibited structure mixing aggregates and layers during the day, but only composed of layers during the night. In summary, the acoustic approach used in this work helped to describe the distribution and composition of micronektonic organisms and provides an essential knowledge base on the micronekton of the southwest Indian Ocean.