This dataset complements previously published data (https://doi.org/10.1594/PANGAEA.950368). This dataset includes measured and calculated data over the epi-mesopelagic layer (0-800 m depth) of 26 stations with 13 of them inside or in the vicinity of a cyclonic eddy that formed off Mauritania along the 900 km zonal corridor between Mauritania and the Cabo Verde islands in the eastern Tropical North Atlantic during the M156 cruise on the RV Meteor from July 3rd to August 1st 2019. Heterotrophic bacteria, photosynthetic bacteria (Prochlorococcus and Synechococcus), and autotrophic pico and nanoplankton (<20 μm) abundances were measured by flow cytometry. Bacterial biomass production rates were measured through the incorporation of labelled leucine (3H) using the microcentrifuge method (Kirchman et al., 1985, https://doi.org/10.1128/aem.49.3.599-607.1985; Smith and Azam, 1992). Chlorophyll a was measured after Evans, C. A., O'Reily, J. E., and Thomas, J. P.: A handbook for measurement of Chl a and primary production, College Station, TX, Texas A and M University, ISBN:9780948277078, 0948277076, 1987.