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Zooplankton diel vertical migration (DVM) is a globally ubiquitous phenomenon and a critical component of the ocean's biological pump. During DVM, zooplankton metabolism leads to carbon and nutrient export to mesopelagic depths, where carbon can be sequestered for decades to millennia, while also introducing labile, energy-rich food sources to midwater ecosystems. Three pervasive metabolic pathways allow zooplankton to sequester carbon: fecal pellet egestion, dissolved organic matter excretion, and respiration. Additionally, there are several less well-parameterized sources of DVM transport associated with growth, feeding, reproduction, and mortality. These processes are challenging to measure in situ and difficult to extrapolate from laboratory experiments, making them some of the most poorly constrained factors in assessments and models of the biological pump. In this review, we evaluate and compare observational and modeling approaches to estimate zooplankton DVM and the resulting active carbon flux, highlighting major discrepancies and proposing directions for future research. 

ABSTRACT DNA metabarcoding of zooplankton biodiversity is used increasingly for monitoring global ocean ecosystems, requiring comparable data from different research laboratories and ocean regions. The MetaZooGene Intercalibration Experiment (MZG‐ICE) was designed to examine1 and analyse patterns of variation of DNA sequence data resulting from multi‐gene metabarcoding of 10 zooplankton samples carried out by 10 research groups affiliated with the Scientific Committee for Ocean Research (SCOR). Aliquots of DNA extracted from the 10 zooplankton samples were distributed to MZG‐ICE groups for metabarcoding of four gene regions: V1‐V2, V4 and V9 of nuclear 18S rRNA and mitochondrial COI. Molecular protocols and procedures were recommended; substitutions were allowed as necessary. Resulting data were uploaded to a common repository for centralised statistics and bioinformatics. Based on proportional sequence numbers for abundant phyla, overall patterns of variation were consistent across many—but not all—MZG‐ICE groups. V9 showed highest similarity, followed (in order) by V4, V1‐V2, and COI. Outlier data were hypothesised to result from the use of different PCR protocols and sequencing platforms, and possible contamination. MZG‐ICE results indicated that DNA metabarcoding data from different laboratories and research groups can provide reliable, accurate and valid descriptions of biodiversity of zooplankton throughout the ocean. Recommendations included: pre‐screening QA/QC of raw data, detailed records for laboratory protocols, reagents, and instrumentation, and centralised bioinformatics and multivariate statistics. In the absence of universal agreement on standardised protocols or best practices, intercalibration is the best way forward toward validation of DNA metabarcoding of zooplankton diversity for global ocean monitoring.