Le mésozooplancton marin désigne les animaux marins mesurant entre 0,2 et 20 mm ne pouvant lutter contre les courants, il soutient les pêcheries mondiales et joue un rôle clé dans la pompe à carbone biologique (PCB), en exportant du carbone organique vers l'intérieur de l'océan. Ce transfert repose notamment sur la production de particules (pelotes fécales, mues, carcasses) formant une partie de la neige marine qui sédimente. Les pelotes fécales en constituent la majeure partie. Par ailleurs, certaines espèces du mésozooplancton effectuent des migrations verticales, quotidiennes ou saisonnières, amplifiant l'intensité de la PCB. De récentes méthodes, telles que l'imagerie ou le métabarcoding, complètent les méthodes traditionnelles (filets à plancton et loupe binoculaire pour le mésozooplancton, pièges à sédiments pour les particules) et permettent d'aborder l'étude des écosystèmes à travers une approche par traits fonctionnels. Ce sont des caractéristiques individuelles mesurables influençant la valeur sélective des organismes (capacité à survivre, croître et se reproduire). Ils peuvent être associés à des fonctions écologiques à l'échelle de l'écosystème, telles que l'export de carbone. En complément, l'utilisation de modèles permet de réaliser des bilans à l'échelle de l'océan global, en se basant sur des informations (e.g., paramètres) obtenues depuis les données. Dans ce contexte, l'objectif de cette thèse est d'étudier le rôle du mésozooplancton et des particules qu'il produit dans l'export de carbone, en mobilisant diverses méthodes d'analyses. Dans le Chapitre 1, j'analyse des données d'imagerie et de métabarcoding issues d'échantillons de mésozooplancton collectés sur le site de Bermuda Atlantic Time-serie Study (BATS). J'identifie des groupes de taxons fortement corrélés (“modules”) constitués d'organismes plus ou moins transparents. Ces variations de transparence peuvent être attribuées à des fonctions physiologiques ou écologiques. Les modules apparaissent dans des dynamiques d'écosystème différentes (e.g., période productive, période oligotrophe) et leurs abondances relatives varient selon l'intensité de l'export de carbone. Un espace morphologique met en évidence la taille et la transparence comme traits influençant cet export. Dans le Chapitre 2, je m'intéresse à l'identification de pelotes fécales cylindriques, typiques de celles produites par le mésozooplancton arctique, parmi les particules non-vivantes imagées in situ dans la Baie de Baffin (Océan Arctique), en période de forte productivité, grâce à l'Underwater Vision Profiler. Les 50 771 particules identifiées par leur morphologie correspondent probablement à des pelotes produites par les grands copépodes Calanus hyperboreus, les amphipodes ou les euphausiacés, selon une comparaison avec des données de référence. Ce travail met en lumière la pertinence des approches d'imagerie in situ pour quantifier les flux de carbone associés à la production de pelotes fécales dans les écosystèmes productifs. Enfin, dans le Chapitre 3, je dresse un état des lieux du rôle des pelotes fécales dans l'export de carbone, à partir d'une méta-analyse rassemblant 197 articles scientifiques. Ainsi, l'abondance, la biomasse et la contribution des pelotes fécales dans les flux de carbone sont étroitement liées à la productivité des écosystèmes. La vitesse de sédimentation des pelotes fécales est fortement corrélée à leur morphologie mais semble être indépendante de la profondeur. Il est nécessaire de mieux caractériser les types de pelotes étudiés et de mesurer plusieurs variables sur un même échantillon pour mieux comprendre leur dynamique et proposer des valeurs de paramètres plus réalistes. Cette thèse ouvre des perspectives pour l'analyse croisée des données d'imagerie et de métabarcoding, notamment via les réseaux de co-occurrence, et propose une caractérisation des particules de neige marine impliquées dans l'export de carbone grâce à l'imagerie.

Abstract Faecal pellets of marine zooplankton play a key role in the biological carbon pump, i.e. all biologically mediated processes by which organic carbon produced by photosynthesis is stored in the ocean’s interior. Numerous factors (size and biomass of faecal pellets, composition and abundance of zooplankton, etc.) can affect the sinking rate of zooplankton faecal pellets and thus the efficiency of their export at depth. A number of quantitative studies of the role of zooplankton faecal pellets in the biological carbon pump have been conducted, focusing either on a region or a type of faecal pellets. These studies highlighted the large variability in the contribution of faecal pellets to carbon fluxes, ranging from 0% to 100%. Here, we used a meta-analysis approach to extract quantitative data on the size, biomass, and role of marine zooplankton faecal pellets in ocean carbon export from 197 scientific articles. Our study focused on the six most studied faecal pellet types (mixed, cylindrical, ellipsoidal, tabular, spherical, and drop-shaped). We showed that abundance and biomass fluxes of faecal pellets, as well as their contribution to particulate organic carbon fluxes, increased with ecosystem productivity, here approximated by surface chlorophyll-a concentration. Furthermore, the fluxes of marine zooplankton faecal pellets (both by abundance and biomass) were positively correlated, and the sampling location, rather than the type of faecal pellet, better explained this correlation. Additionally, sinking rates were strongly correlated with volume, length, and width of faecal pellets, for all faecal pellet types. Sinking rates did not vary with depth, although measurements become scarcer with depth. Our literature review highlights the crucial role of faecal pellets in the biological carbon pump and the need to study less known types of faecal pellets, such as ellipsoidal faecal pellets, and to measure multiple variables on the same samples. Finally, we recommend that modellers wishing to represent faecal pellets in global biogeochemical models choose a constant sinking rate with depth within the range of the quantitative values reported here.

Zooplankton play a crucial role in the biological carbon pump by producing sinking particles including sloppy feeding by-products, fecal pellets, molts and carcasses. However, quantifying their impact of these particles on the carbon cycle remains difficult. The contribution of fecal pellets to particulate organic carbon export is usually assessed using fecal pellets collected from sediment traps and laboratory studies. Here, we identified 50 771 fecal pellet-like particles distributed across three morphological clusters. These were extracted from 987 236 in situ images of non-living particles collected from Baffin Bay (Arctic Ocean) using the Underwater Vision Profiler (UVP). We associated which taxonomic groups produced the fecal pellets by comparing the UVP images with observations of fecal pellet morphology and length. Our results emphasize the feasibility of quantifying fecal pellets from in situ images and the importance of developing the resolution of imaging tools that would simultaneously identify smaller fecal pellet-like particles and capture images of large crustacean zooplankton. Using in situ images in identifying fecal pellets will facilitate a better understanding of their dynamics, a more accurate calculation of carbon fluxes, and the representation of fecal pellets in biogeochemical models.

Mesozooplankton is a very diverse group of small animals ranging in size from 0.2 to 20 mm not able to swim against ocean currents. It is a key component of pelagic ecosystems through its roles in the trophic networks and the biological carbon pump. Traditionally studied through microscopes, recent methods have been however developed to rapidly acquire large amounts of data (morphological, molecular) at the individual scale, making it possible to study mesozooplankton using a trait-based approach. Here, combining quantitative imaging with metabarcoding time-series data

Imaging is increasingly used to capture information on the marine environment thanks to the improvements in imaging equipment, devices for carrying cameras and data storage in recent years. In that context, biologists, geologists, computer specialists and end-users must gather to discuss the methods and procedures for optimising the quality and quantity of data collected from images. The 4 th Marine Imaging Workshop was organised from 3-6 October 2022 in Brest (France) in a hybrid mode. More than a hundred participants were welcomed in person and about 80 people attended the online sessions. The workshop was organised in a single plenary session of presentations followed by discussion sessions. These were based on dynamic polls and open questions that allowed recording of the imaging community’s current and future ideas. In addition, a whole day was dedicated to practical sessions on image analysis, data standardisation and communication tools. The format of this edition allowed the participation of a wider community, including lower-income countries, early career scientists, all working on laboratory, benthic and pelagic imaging. This article summarises the topics addressed during the workshop, particularly the outcomes of the discussion sessions for future reference and to make the workshop results available to the open public.

Mesozooplankton play an important role in pelagic ecosystems. Linking primary producers and higher trophic levels, they are also involved in the biological carbon pump through the production of particles sinking into the deep ocean. This carbon flux is amplified by the diel vertical migrations (DVM) of some mesozooplankton taxa. Recent methods, like quantitative imaging, produce an enormous quantity of data at the individual scale. Then, data can be used in a trait-based approach in order to better understand how an ecosystem works. Additionally, high throughput sequencing of environmental DNA permits the rapid identification of species at a community-level. Thus, metabarcoding can provide a complementary vision to the functional approach.In this study, we investigate variations of the morphological and taxonomic facets of mesozooplankton diversity, and link its realized and potential traits with environmental and/or ecosystem’s functioning changes.We analysed 69,950 individual images of mesozooplankton, obtained by the Zooscan, together with the 225 most abundant unique 18S V1V2 sequences, acquired by metabarcoding. Data were sampled monthly, during the day and at night, between March-2016 and May-2017, in the first 200 m of the water column at the Bermuda Atlantic Time-series Study. A morphological space was created based on 18 morphological descriptors from the entire set of images to identify the main morphological traits that vary in the mesozooplankton community.Our results showed that environment variations structured the taxonomic composition of mesozooplankton, but did not affect the overall morphology of the community. Three distinct communities were defined based on taxonomic composition, and succeeded one another throughout the study period. A co- occurrences network was built from metabarcoding data and 6 groups of taxa (or "modules") were identified. These were linked to changes in ecosystem’s functioning and/or in the community’s morphology. DVM importance was confirmed by the existence of a module with taxa preferentially sampled during the night, and by a darker opacity for migratory organisms that was linked to higher carbon export.