The Northwestern Mediterranean Sea stands as a critical region, experiencing pronounced environmental shifts due to climate variability and significant human pressures. Understanding these changes necessitates robust, multidisciplinary observation. The Mediterranean Ocean Observing System for the Environment (MOOSE) program embodies this necessity, integrating physical, chemical, and biological data across diverse temporal and spatial scales. This study leverages MOOSE’s extensive data to provide a holistic assessment of planktonic communities, employing advanced techniques like environmental genomics and high-resolution imaging. By examining all plankton size fractions and depths, researchers gain a comprehensive view, revealing how these foundational organisms respond to dynamic oceanographic conditions. The findings underscore that plankton assemblages are fundamentally shaped by organism size and water column depth, with the surface and deep chlorophyll maximum layers exhibiting particularly high biodiversity in the 0.2–3 µm and 3–180 µm fractions.
Further analysis reveals distinct community compositions across different size classes. Metazoans, notably Arthropoda, dominate fractions larger than 64 µm, indicative of larger zooplankton. In contrast, microbial communities sampled via Niskin bottles are primarily comprised of protists, including Syndiniales and Rhizaria. Temporal variations were most pronounced in the Niskin bottle samples, particularly for diatoms and dinoflagellates, suggesting a sensitivity of these phytoplankton groups to short-term environmental fluctuations. Plankton tow samples, however, demonstrated less temporal variability, highlighting that different sampling methods capture distinct aspects of plankton dynamics. Physical clustering of sampling stations clearly delineates cross-shelf and basin-scale gradients, which, at a fine taxonomic resolution, align closely with observed community structures for smaller plankton. This indicates that spatial structuring is a significant driver of plankton distribution.
The integration of environmental genomics with high-resolution imaging proves invaluable, enhancing the characterization of key taxa such as Copepoda and Rhizaria. While imaging provides quantitative data on abundance and morphology, environmental genomics captures cryptic and morphologically indistinct taxa, especially crucial for microbial plankton. This synergy demonstrates the complementary strengths of molecular and imaging approaches, offering a more complete picture of plankton biodiversity. Ultimately, this research emphasizes that depth, size, and taxonomic resolution are paramount dimensions for deciphering community structure over time. The MOOSE program’s success in ecosystem-scale monitoring provides an essential foundation for future assessments of biogeochemical processes and how marine ecosystems will respond to ongoing climate change and human-induced alterations in the vital Mediterranean Sea.