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Characterization of species diversity of zooplankton is key to understanding, assessing, and predicting the function and future of pelagic ecosystems throughout the global ocean. The marine zooplankton assemblage, including only metazoans, is highly diverse and taxonomically complex, with an estimated ~28,000 species of 41 major taxonomic groups. This review provides a comprehensive summary of DNA sequences for the barcode region of mitochondrial cytochrome oxidase I (COI) for identified specimens. The foundation of this summary is the MetaZooGene Barcode Atlas and Database (MZGdb), a new open-access data and metadata portal that is linked to NCBI GenBank and BOLD data repositories. The MZGdb provides enhanced quality control and tools for assembling COI reference sequence databases that are specific to selected taxonomic groups and/or ocean regions, with associated metadata (e.g., collection georeferencing, verification of species identification, molecular protocols), and tools for statistical analysis, mapping, and visualization. To date, over 150,000 COI sequences for ~ 5600 described species of marine metazoan plankton (including holo- and meroplankton) are available via the MZGdb portal. This review uses the MZGdb as a resource for summaries of COI barcode data and metadata for important taxonomic groups of marine zooplankton and selected regions, including the North Atlantic, Arctic, North Pacific, and Southern Oceans. The MZGdb is designed to provide a foundation for analysis of species diversity of marine zooplankton based on DNA barcoding and metabarcoding for assessment of marine ecosystems and rapid detection of the impacts of climate change.

Due to historical under‐sampling of the deep ocean, the distributional ranges of mesopelagic zooplankton are not well documented, leading to uncertainty about the mechanisms that shape midwater zooplankton community composition. Using a combination of DNA metabarcoding (18S‐V4 and mtCOI) and trait‐based analysis, we characterized zooplankton diversity and community composition in the upper 1000 m of the northeast Pacific Ocean. We tested whether the North Pacific Transition Zone is a biogeographic boundary region for mesopelagic zooplankton. We also tested whether zooplankton taxa occupying different vertical habitats and exhibiting different ecological traits differed in the ranges of temperature, Chl‐a, and dissolved oxygen conditions inhabited. The depth of the maximum taxonomic richness deepened with increasing latitude in the North Pacific. Community similarity in the mesopelagic zone also increased in comparison with the epipelagic zone, and no evidence was found for a biogeographic boundary between previously delineated mesopelagic biogeochemical provinces. Epipelagic zooplankton exhibited broader temperature and Chl‐a ranges than mesopelagic taxa. Within the epipelagic, taxa with broader temperature and Chl‐a ranges also had broader distributional ranges. However, mesopelagic taxa were distributed across wider dissolved oxygen ranges, and within the mesopelagic, only oxygen ranges covaried with distributional ranges. Environmental and distributional ranges also varied among traits, both for epipelagic taxa and mesopelagic taxa. The strongest differences in both environmental and distributional ranges were observed for taxa with or without diel vertical migration behavior. Our results suggest that species traits can influence the differential effects of physical dispersal and environmental selection in shaping biogeographic distributions. The mechanisms shaping midwater zooplankton community composition are uncertain. We used a strong environmental gradient across the North Pacific Transition Zone to test the effects of temperature, Chl‐a, and dissolved oxygen concentrations on epipelagic and mesopelagic species distributions. We found broader species distributions and greater community similarity at mesopelagic depths. Variability in environmental ranges suggests that species traits can affect the relative contributions of physical dispersal and environmental selection to biogeographic distributions.

The diversity and specific composition of zooplankton communities have a direct effect on the ecosystem services (e.g. carbon export) and structure of ocean food webs. In areas where diversity is high, a detailed characterization of the whole community can represent a hurdle that prevents a complete understanding of those processes and interactions. One such region is the Sargasso Sea, where zooplankton diversity is among the highest in the world oceans. As a consequence, at the Bermuda Atlantic Time-series Study location, most research has focused on zooplankton biomass or on particular groups. To provide new insight into the total community composition at the BATS site, in this study the zooplankton community is investigated by means of metabarcoding of the 18S V9 hypervariable region. Day and night samples from a full year (2015) show the signature of diel vertical migration, driven by those groups with a higher representation in the metabarcoding reads. Seasonal ordination was detected after square-root transformation and, similarly to temperate regions, four seasons could be differentiated based on community composition (post-spring bloom, summer stratification, fall mixing event and winter mixing), with no correspondence with the zooplankton biomass patterns. This community ordination showed correlation with the measured vertical flux, highlighting the need of understanding community regimes, even in theoretically stable regions such as the oligotrophic ocean, to advance in our understanding of zooplankton-mediated processes

Corrigendum on: González CE, Blanco-Bercial L, Escribano R, Fernández-Urruzola I, Rivera R and Ulloa O (2023) Revealing zooplankton diversity in the midnight zone. Front. Mar. Sci. 10:1252535. doi: 10.3389/fmars.2023.1252535 In the published article, there was an error in the Funding statement. The text says: \"The author(s) declare financial support was received for the research, authorship, and/or publication of this article. The ship time for FS Sonne was provided by the BMBF (Germany).\" The correct Funding statement appears below.The ship time for FS Sonne was provided by the BMBF (Germany). The molecular analyses were funded by the Chilean Agency for Research and Development (ANID-FONDECYT 3220468 research project) and Millennium Science Initiative Project (grant ICN12_019-IMO). MOCNESS was provided by FONDEQUIP grant EQM 140029. SCOR WG157 was funded by the U.S. National Science Foundation (OCE-1840868). L.B.B. was partially supported by the US National Science Foundation under Grant OCE-1948162 and I.F.U. under the ANID-FONDECYT 11221079 Research Project.The authors apologize for this error and state that this does not change the scientific conclusions of the article in any way. The original article has been updated.

For the first time, the phylogenetic relationships between representatives of all 10 copepod orders have been investigated using 28S and 18S rRNA, Histone H3 protein and COI mtDNA. The monophyly of Copepoda (including Platycopioida Fosshagen, 1985) is demonstrated for the first time using molecular data. Maxillopoda is rejected, as it is a polyphyletic group. The monophyly of the major subgroups of Copepoda, including Progymnoplea Lang, 1948 (=Platycopioida); Neocopepoda Huys and Boxshall, 1991; Gymnoplea Giesbrecht, 1892 (=Calanoida Sars, 1903); and Podoplea Giesbrecht, 1892, are supported in this study. Seven copepod orders are monophyletic, including Platycopioida, Calanoida, Misophrioida Gurney, 1933; Monstrilloida Sars, 1901; Siphonostomatoida Burmeister, 1834; Gelyelloida Huys, 1988; and Mormonilloida Boxshall, 1979. Misophrioida (=Propodoplea Lang, 1948) is the most basal Podoplean order. The order Cyclopoida Burmeister, 1835, is paraphyletic and now encompasses Poecilostomatoida Thorell, 1859, as a sister to the family Schminkepinellidae Martinez Arbizu, 2006. Within Harpacticoida Sars, 1903, both sections, Polyarthra Lang, 1948, and Oligoarthra Lang, 1948, are monophyletic, but not sister groups. The order Canuelloida is proposed while maintaining the order Harpacticoida s. str . (Oligoarthra). Cyclopoida, Harpacticoida and Cyclopinidae are redefined, while Canuelloida ordo. nov ., Smirnovipinidae fam. nov . and Cyclopicinidae fam. nov are proposed as new taxa.

Krill are vital as food for many marine animals but also impacted by global warming. To learn how they and other zooplankton may adapt to a warmer world we studied local adaptation in the widespread Northern krill ( Meganyctiphanes norvegica ). We assemble and characterize its large genome and compare genome-scale variation among 74 specimens from the colder Atlantic Ocean and warmer Mediterranean Sea. The 19 Gb genome likely evolved through proliferation of retrotransposons, now targeted for inactivation by extensive DNA methylation, and contains many duplicated genes associated with molting and vision. Analysis of 760 million SNPs indicates extensive homogenizing gene-flow among populations. Nevertheless, we detect signatures of adaptive divergence across hundreds of genes, implicated in photoreception, circadian regulation, reproduction and thermal tolerance, indicating polygenic adaptation to light and temperature. The top gene candidate for ecological adaptation was nrf-6 , a lipid transporter with a Mediterranean variant that may contribute to early spring reproduction. Such variation could become increasingly important for fitness in Atlantic stocks. Our study underscores the widespread but uneven distribution of adaptive variation, necessitating characterization of genetic variation among natural zooplankton populations to understand their adaptive potential, predict risks and support ocean conservation in the face of climate change. Marine life depends on zooplankton like krill, but it’s uncertain how these species will respond to a warming ocean. This study of genome variation in the Northern krill uncovered many gene variants that could be crucial for environmental adaptation and support stock assessment under climate change.

Editor's Note: this Article has been retracted; the Retraction Note is available at https://www.nature.com/articles/s41598-020-72330-x.Editor's Note: this Article has been retracted; the Retraction Note is available at https://www.nature.com/articles/s41598-020-72330-x.

Protists represent the majority of the eukaryotic diversity in the oceans. They have different functions in the marine food web, playing essential roles in the biogeochemical cycles. While the available data is rich in horizontal and temporal coverage, little is known on their vertical structuring, particularly below the photic zone. The present study applies V4 18S rDNA metabarcoding to samples collected over three years in conjunction with the BATS time-series to assess marine protist communities in the epipelagic and mesopelagic zones (0-1000 m). The protist community showed a dynamic seasonality in the epipelagic, responding to hydrographic yearly cycles. Mixotrophic lineages dominated throughout the year. However, autotrophs bloomed during the rapid transition between the winter mixing and the stratified summer, and heterotrophs had their peak at the end of summer, when the base of the thermocline reaches its deepest depth. Below the photic zone, the community, dominated by Rhizaria, is depth-stratified and relatively constant throughout the year, although they followed local hydrographic and biological features such as the oxygen minimum zone. The results suggest a dynamic partitioning of the water column, where the niche vertical position for each community changes throughout the year in the epipelagic, likely depending on nutrient availability, the mixed layer depth, and other hydrographic features. At depth, the protist community closely tracked mesoscale events (eddies), where the communities followed the hydrographic uplift, raising the deeper communities for hundreds of meters, and compressing the communities above.

Tetragoniceps bermudensis sp. nov. (Copepoda, Harpacticoida, Tetragonicipitidae) is described based on an ovigerous female collected from Roadside Cave, a tidally influenced anchialine cavern in Bermuda. The new taxon represents the 16 th recorded species of Tetragoniceps Brady, 1880. It can be distinguished from congeneric species by the length:width ratio of the caudal rami (approximately 10 times longer than wide), its cephalothorax with a smooth dorsal surface, and the diagnostic setal formula of its pereiopods 1–5. Tetragoniceps bermudensis sp. nov. is the first record of Tetragoniceps from Bermuda and the first known anchialine species in the genus globally. Based on our description of the new species, we provide a revised key to the species of Tetragoniceps . In addition, we include an updated table of salient morphological characters for the females of the genus, providing grounds for a preliminary analysis of the phylogenetic relationships of its constituent species.

Zooplankton diversity in the deep “midnight zone” (>1000 m), where sunlight does not reach, remains largely unknown. Uncovering such diversity has been challenging because of the major difficulties in sampling deep pelagic fauna and identifying many (unknown) species that belong to these complex swimmer assemblages. In this study, we evaluated zooplankton diversity using two taxonomic marker genes: mitochondrial cytochrome oxidase subunit 1 (COI) and nuclear 18S ribosomal RNA (18S). We collected samples from plankton net tows, ranging from the surface to a depth of 5000 m above the Atacama Trench in the Southeast Pacific. Our study aimed to assess the zooplankton diversity among layers from the upper 1000 m to the ultra-deep abyssopelagic zone to test the hypothesis of decreasing diversity with depth resulting from limited carbon sources. The results showed unique, highly vertically structured communities within the five depth strata sampled, with maximal species richness observed in the upper bathypelagic layer (1000–2000 m). The high species richness of zooplankton (>750 OTUS) at these depths was higher than that found in the upper 1000 m. The vertical diversity trend exhibited a pattern similar to the well-known vertical pattern described for the benthic system. However, a large part of this diversity was either unknown (>50%) or could not be assigned to any known species in current genetic diversity databases. DNA analysis showed that the Calanoid copepods, mostly represented by Subeucalanus monachus , the Euphausiacea, Euphausia mucronata , and the halocypridade, Paraconchoecia dasyophthalma , dominated the community. Water column temperature, dissolved oxygen, particulate carbon, and nitrogen appeared to be related to the observed vertical diversity pattern. Our findings revealed rich and little-known zooplankton diversity in the deep sea, emphasizing the importance of further exploration of this ecosystem to conserve and protect its unique biota.