Key Expoitable Results (KERs)

Thesis

This paper presents the quantitative imaging datasets collected during the Tara Pacific expedition (2016–2018) carried out on the schooner Tara. The datasets cover a wide range of plankton sizes, from microphytoplankton (> 20 µm in size) to mesozooplankton (a few centimetres in size), and non-living particles such as plastic and detrital particles. It consists of surface samples collected across the North Atlantic and the North and South Pacific Ocean from open-ocean stations (a total of 357 samples) and from stations located in coastal waters, lagoons or reefs of 32 Pacific islands (a total of 228 samples). As this expedition involved long distances and long sailing times, we designed two sampling systems to collect plankton while sailing at speeds of up to 9 knots. To sample microplankton, surface water was pumped aboard using a customised pumping system and filtered through a 20 µm mesh size plankton net (hereafter referred to as the deck net – DN). A high-speed net (HSN; 330 µm mesh size) was developed to sample the mesoplankton. In addition, a manta net (330 µm) was also used, when possible, to collect mesoplankton and plastics simultaneously. We could not deploy these nets at the reef and lagoon stations of islands. Instead, two bongo nets (20 µm) attached to an underwater scooter were used to sample microplankton. In addition to describing and presenting the datasets, the complementary aim of this paper is to investigate and quantify the potential sampling biases associated with these two high-speed sampling systems and the different net types, in order to improve further ecological interpretations. Regarding the imaging techniques, microplankton (20–200 µm) from the DN and bongo net were imaged directly aboard Tara using a FlowCam instrument (Fluid Imaging Technologies), whereas mesoplankton (>200 µm) from the HSN and manta net were analysed in the laboratory with a ZooScan system (back on land). Organisms and other particles were taxonomically and morphologically classified using the automatic sorting tools of the EcoTaxa web application; following this, validation or correction was carried out by taxonomic experts. For microplankton smaller than 45 µm, a subsample of 30 % of the annotations was 100 % visually validated by experts. More than 300 different taxonomic and morphological groups were identified. The datasets include the metadata and the raw data from which morphological traits such as size (equivalent spherical diameter) and biovolume were calculated for each particle as well as a number of quantitative descriptors of the surface plankton communities. These descriptors include abundance, biovolumes, the Shannon diversity index and normalised biovolume size spectrum, allowing the study of their structures (e.g. taxonomic, functional, size and trophic structures) according to a wide range of environmental parameters at the basin scale.

Microbial competition for scarce resources shapes biodiversity patterns and ecosystem function across global biomes, yet quantifying this process from genomic data has remained elusive. Here, we introduce CaCo, a scalable metric that transforms metagenomic carbohydrate-active enzyme profiles into precise measures of niche overlap and competition potential (Resource Partitioning Score, RPS). Analyzing 14,691 high-quality metagenome-assembled genomes spanning Ocean, freshwater, soil, and human gut microbiomes, we reveal a striking macroecological pattern: Niche overlap increases from partitioned specialists in oligotrophic oceans to overlapping generalists in carbon-rich environments, including the human gut. This gradient aligns with classic niche theory, as phylogenetic signals indicate that closely related taxa may compete most intensely. Multitiered validation, spanning BIOLOG phenotypes, synthetic cocultures, and interaction gradients, confirms CaCo’s predictive power and captures competitive exclusion. CaCo bridges genomic potential and ecological reality, providing niche-breadth metrics and enabling testable predictions of how resource availability shapes microbial competition and community structure.

Master's Thesis

Marine species are increasingly threatened by extreme and compound events, as warming, deoxygenation, and acidification unfold. Yet, the surface and especially the subsurface distribution and evolution of such compound events remain poorly understood. We present the current and projected distributions of compound marine heatwave (MHW), low oxygen (LOX), and high acidity (OAX) events throughout the water column, using observation-based data from 2004 to 2019 and large ensemble Earth system model simulations from 1890 to 2100. Our findings reveal that compound MHW-OAX and OAX-LOX events are prevalent in the low to mid latitudes at the ocean surface. At 200 and 600 m, MHW-OAX and MHW-LOX events are frequent in the high latitudes and parts of the tropics, while OAX-LOX events occur globally. Subsurface compound events are often associated with vertical displacements of water masses, with the climatological vertical gradients of ecosystem stressors typically explaining their occurrence patterns. Projections show a strong rise in compound event frequency over the historical period and under continued global warming, primarily driven by shifts in mean oceanic conditions. The portion of the top 2,000 m affected by extreme or compound events rises from 20 to 98 under 2°C of global warming in a high emissions scenario using a preindustrial baseline, and to 30 using a shifting-mean baseline. However, physical and biogeochemical changes may also lead to regional decreases in subsurface events, highlighting complexities in how warming, deoxygenation, and acidification unfold in the ocean interior. Increasing compound event frequency poses a major threat to marine ecosystems, potentially disrupting food webs and biodiversity.

The contribution of the ocean biological carbon pump to the export of organic carbon at depth has predominantly been assessed by considering sinking particulate matter and vertically migrating organisms. Despite growing recognition of the importance of dynamical pathways that export carbon through upper-ocean mixing and advection, observation-based estimates of their global impact are still lacking. Here, we quantify the values and uncertainties of the export driven by the physical injection pump (PIP) and its interannual variability by leveraging a 4D data-driven time series (1997-2018) of particulate organic carbon concentration (POC) and ocean circulation, as well as 3D fields of climatological dissolved organic carbon (DOC). Vertical diffusion dominates our POC export estimates, but remains the most uncertain process. Assuming maximal diffusivity estimates that are consistent with observations, POC and DOC export amount to 0.37 Pg C yr−1 and 0.48 Pg C yr−1, respectively. The contribution from entrainment and advection is strongly modulated by the POC annual cycle, revealing the critical coupling between biological production and upper-layer mixing in driving the net annual export. Observed interannual signals correlate with a linear combination of El Niño–Southern Oscillation and Southern Annular Mode indices, suggesting that the PIP is connected to intermediate- and mode-water formation dynamics in the Southern Ocean.