Zooplankton community structure, diversity, and environmental context across the California Current Ecosystem based on dual-marker DNA metabarcoding (18S V4, COI) and paired Zooscan imaging during CCE-LTER Process Cruise P2107 (July–August 2021)

Zooplankton communities were sampled during the California Current Ecosystem Long-Term Ecological Research (CCE-LTER) Process Cruise P2107 (R/V Roger Revelle, July 21 – August 11 2021), spanning freshly upwelled to oligotrophic offshore waters. Oblique Bongo net tows (0.71 m diameter, 202 µm mesh) were collected to ~200 m depth, split quantitatively, size-fractionated (0.2-5 mm), and analyzed by paired morphological imaging (Zooscan) and dual-marker DNA metabarcoding targeting 18S V4 (Zhan et al. 2013) and COI (Leray et al. 2013). Environmental data (temperature, salinity, oxygen, fluorescence, nutrients,etc) were obtained from CTD casts and bottle samples. This dataset includes (1) raw read-count OTU tables for 18S and COI, (2) corresponding taxonomic assignments, and (3) environmental metadata matched by sample ID. These data provide high-resolution measurements of zooplankton community diversity, biomass proxies, and associated environmental gradients across the upwelling–offshore continuum of the California Current System.