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Abstract Metabarcoding of zooplankton communities is becoming more common, but molecular results must be interpreted carefully and validated with morphology-based analyses, where possible. To evaluate our metabarcoding approach within the California Current Ecosystem, we tested whether physical subsampling and PCR replication affects observed community composition; whether community composition resolved by metabarcoding is comparable to morphological analyses by digital imaging; and whether pH neutralization of ethanol with ammonium hydroxide affects molecular diversity. We found that (1) PCR replication was important to accurately resolve alpha diversity and that physical subsampling can decrease sensitivity to rare taxa; (2) there were significant correlations between relative read abundance and proportions of carbon biomass for most taxonomic groups analyzed, but such relationships showed better agreement for the more dominant taxonomic groups; and (3) ammonium hydroxide in ethanol had no effect on molecular diversity. Together, these results indicate that with appropriate replication, paired metabarcoding and morphological analyses can characterize zooplankton community structure and biomass, and that metabarcoding methods are to some extent indicative of relative community composition when absolute measures of abundance or biomass are not available. 

In subtropical oceans phytoplankton carbon: phosphorus (C : P) ratios are high, and these ratios are predicted to increase further with rising ocean temperatures and stratification. Prey stoichiometry may pose a problem for copepod zooplankton nauplii, which have high phosphorus demands due to rapid growth. We hypothesised that nauplii meet this demand by consuming bacteria. Naupliar bacterial and phytoplankton carbon and phosphorus ingestion, assimilation and incorporation were traced using³³P and¹⁴C radioisotopes. Bacterial carbon was incorporated four times less efficiently into biomass than phytoplankton carbon. In contrast, bacterial and phytoplankton phosphorus were incorporated at similar efficiencies, and bacteria could meet a substantial amount of naupliar phosphorus requirements. As parts of the ocean become more oligotrophic, bacteria could help sustain naupliar growth and survival under suboptimal stoichiometric conditions. Thus, nauplii may be a shortcut for phosphorus from the microbial loop to the classical food web.

 

Although metazoan animals in the mesopelagic zone play critical roles in deep pelagic food webs and in the attenuation of carbon in midwaters, the diversity of these assemblages is not fully known. A metabarcoding survey of mesozooplankton diversity across the epipelagic, mesopelagic and upper bathypelagic zones (0–1500 m) in the North Pacific Subtropical Gyre revealed far higher estimates of species richness than expected given prior morphology‐based studies in the region (4,024OTUs, 10‐fold increase), despite conservative bioinformatic processing. Operational taxonomic unit (OTU) richness of the full assemblage peaked at lower epipelagic–upper mesopelagic depths (100–300 m), with slight shoaling of maximal richness at night due to diel vertical migration, in contrast to expectations of a deep mesopelagic diversity maximum as reported for several plankton groups in early systematic and zoogeographic studies. Four distinct depth‐stratified species assemblages were identified, with faunal transitions occurring at 100 m, 300 m and 500 m. Highest diversity occurred in the smallest zooplankton size fractions (0.2–0.5 mm), which had significantly lower %OTUs classified due to poor representation in reference databases, suggesting a deep reservoir of poorly understood diversity in the smallest metazoan animals. A diverse meroplankton assemblage also was detected (350OTUs), including larvae of both shallow and deep living benthic species. Our results provide some of the first insights into the hidden diversity present in zooplankton assemblages in midwaters, and a molecular reappraisal of vertical gradients in species richness, depth distributions and community composition for the full zooplankton assemblage across the epipelagic, mesopelagic and upper bathypelagic zones.