AtlantECO-KER-AM-2

Master's Thesis

Microbial communities are essential to marine ecosystem functioning, yet much of their metabolic potential remains hidden within unassigned sequence space, the ocean’s functional dark matter. Analyzing 1,379 sunlit-ocean metagenomes, we developed a protein-centric framework that clusters 147 million predicted proteins into Operational Protein Units (OPUs), sequence-based groups encompassing both known and uncharacterized proteins. This approach captures the full breadth of microbial functional diversity, extending beyond genome- or pathway-centric views. Using machine learning on OPU profiles, we identified ten Ocean Microbiome Signatures (OMSs), functional groups that represent dominant metabolic strategies of marine microbial communities. Each OMS displays distinct spatial patterns, taxonomic composition, and functional repertoires. By integrating functional dark matter into ecosystem-level analyses, this protein-centric framework expands current models of the ocean microbiome. It uncovers fundamental principles linking protein repertoires to environmental structure, revealing how conserved ecological strategies underpin the potential metabolic architecture of the global ocean.

Interactions between mesoscale eddies and seamounts can strongly modify local circulation, influencing nutrient transport and planktonic communities. This study investigates the coupling between hydrodynamics features and zooplankton dynamics along the Vitória–Trindade Seamount Chain (VTC) in the southwestern Atlantic, using hydrographic (CTD) measurements and Underwater Vision Profiler (UVP5) observations collected along two transects: one crossing the VTC and a second located slightly south of the chain. Flow–topography interactions involving the Vitória Eddy (VE) and regional seamounts were found to modulate chlorophyll-a distributions and zooplankton abundance. Although classical seamount-induced upwelling was not detected, elevated chlorophyll-a concentrations within thermocline depths and downstream of Davis Bank indicate enhanced vertical mixing associated with flow–seamount interactions and eddy deformation. Rhizaria numerically dominated the zooplankton community, particularly within the euphotic zone and thermocline layers. Analysis of the normalized biovolume size spectrum (NBSS) revealed flatter slopes and higher intercepts near the shelf and in VE-influenced regions, indicating a greater contribution of large-bodied organisms and higher trophic transfer efficiency. In contrast, offshore and seamount-only stations exhibited steeper size spectra consistent with oligotrophic, energy-limited conditions. Particulate organic carbon (POC) fluxes were highest at stations influenced by the VE, reflecting the combined effects of lateral shelf inputs and particle retention driven by flow–topography interactions. Enhanced subsurface and seamount-associated POC fluxes further highlight the joint role of mesoscale eddies and seamounts in regulating carbon export along the VTC.