18S & COI mesozooplankton metabarcoding - California Current Ecosystem 0-200m
Metabarcoding dataset of zooplankton communities from the California Current Ecosystem, generated to examine cross-shore diversity patterns and to calibrate PCR amplification bias. Zooplankton were collected with 202 um Bongo nets (0-200 m), size-fractionated (0.2-0.5 mm, 0.5-1 mm, 1-2 mm), and analyzed in parallel with Zooscan imaging for biomass and size structure. DNA was extracted from each size fraction and amplified using Leray COI primers (jgLCO1490 and jgHCO2198) and Zhang 18S-V4 primers (Uni18S and Uni18SR ). Amplicons were sequenced on an Illumina MiSeq and processed into amplicon sequence variants (ASVs) with DADA2, and taxonomy was assigned against the MetaZooGene database supplemented with CCE voucher specimens and BLAST. Samples span an upwelling-to-offshore gradient, enabling analysis of zooplankton diversity, size structure, and environmental relationships. In parallel, variable PCR cycle experiments were conducted on the mixed-community samples to quantify amplification efficiencies using a Bayesian multinomial logistic-normal model (fido package in R). Attempts to correct for PCR bias and improve quantitative interpretation of metabarcoding-based abundance estimates were made through comparison to Zooscan biomass.