Copepod-associated microbial metacommunities reflect spatial gradients in the epipelagic ocean

Sampling was conducted in the framework of the French program PERLE (Pelagic Ecosystem Response to Dense Water Formation in the Levant Experiment, https://doi.org/10.17600/18001980). Physical and chemical variables were recorded in the epipelagic zone (0-200 m) at 46 stations distributed in the Mediterranean Sea during the PERLE-4 cruise, onboard the R/V L’Atalante between March 28 and April 26, 2021. Rosette sampler with a sampling system of 24 Niskin bottles and a CTD SeaBirdTM 911plus underwater unit equipped with pressure, temperature, conductivity, oxygen, and chlorophyll fluorescence sensors was deployed in the 46 stations. Seawater samples were collected to analyze dissolved inorganic nutrients (phosphate and nitrate + nitrite) and microbial communities (500 ml of seawater was collected from 5 depths for DNA analysis).  Vertical hauls with WP2 nets (200 μm mesh size Hydro-Bios, Germany) were deployed at 16 stations in the epipelagic zone (0-200 m) to collect mesozooplankton.  The collected samples were sieved through a 1000 µm mesh and freshly sorted onboard.  Adult individuals of calanoid Clausocalanus copepods and cyclopoid Farranula and Oncaea copepods were manually picked and identified under a stereomicroscope. Farranula and Oncaea individuals were collected at the 16 sampled stations, and Clausocalanus at eight stations. Five replicates of five individuals per taxon (whole organism) were collected for DNA extraction.