Authors: Miguel A Martinez, Clara María Hereu, María Clara Arteaga, Sylvia P A Jiménez-Rosenberg, Sharon Z Herzka, Anaid Saavedra-Flores, Javier Robles-Flores, Ricardo Gomez-Reyes, Paola Gabriela Batta-Lona, Jaime Gasca-Pineda, Clara E Galindo-Sánchez

Zooplankton is a key component in marine ecosystem health assessment. Here, we present a taxonomically comprehensive description of the zooplankton community (0–200 m) based on metabarcoding of the V9 hypervariable region of the 18S rRNA gene of 47 samples collected in the Gulf of Mexico (GoM) during summer 2015. Fourteen phyla were identified Arthropoda were dominant, with Calanidae, Metridinidae, and Euphausiidae as the most conspicuous families. Other abundant phyla were Cnidaria (Hydrozoa), Chordata (Tunicata), and Chaetognatha. The V9-18S sequence data were clustered into 1888 Operational Taxonomic Units (OTUs), of which 39 were cosmopolitan and belonging to various phyla, suggesting the presence of a core community with high local diversity throughout the GoM. Evaluation of metabarcoding sequences abundance showed overall positive correlations with morphologically quantified abundances except for specific groups. Cluster analysis of OTU distributions indicated two primary biographically distinctive groups of stations: one restricted to the Bay of Campeche, while the other occurred in the Central-West GoM, similar to previous descriptions of regional variation of the GoM based on environmental variables. Together these results provide a foundation for broad-scale zooplankton molecular biodiversity assessments in the southern GoM allowing evaluation of the effects of environmental changes on zooplankton communities.