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1. Toward a global reference database of COI barcodes for marine zooplankton

   https://doi.org/10.1007/s00227-021-03887-y  

   Bucklin, Ann; Peijnenburg, Katja T. C. A.; Kosobokova, Ksenia N.; O’Brien, Todd D.; Blanco-Bercial, Leocadio; Cornils, Astrid; Falkenhaug, Tone; Hopcroft, Russell R.; Hosia, Aino; Laakmann, Silke; et al (May 2021, Marine Biology)

   Abstract 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. 

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2. On the sensitivity of plankton ecosystem models to the formulation of zooplankton grazing

   https://doi.org/10.1371/journal.pone.0252033  

   Chenillat, Fanny; Rivière, Pascal; Ohman, Mark D. (May 2021, PLOS ONE)

   Gorokhova, Elena (Ed.)

   Model representations of plankton structure and dynamics have consequences for a broad spectrum of ocean processes. Here we focus on the representation of zooplankton and their grazing dynamics in such models. It remains unclear whether phytoplankton community composition, growth rates, and spatial patterns in plankton ecosystem models are especially sensitive to the specific means of representing zooplankton grazing. We conduct a series of numerical experiments that explicitly address this question. We focus our study on the form of the functional response to changes in prey density, including the formulation of a grazing refuge. We use a contemporary biogeochemical model based on continuum size-structured organization, including phytoplankton diversity, coupled to a physical model of the California Current System. This region is of particular interest because it exhibits strong spatial gradients. We find that small changes in grazing refuge formulation across a range of plausible functional forms drive fundamental differences in spatial patterns of plankton concentrations, species richness, pathways of grazing fluxes, and underlying seasonal cycles. An explicit grazing refuge, with refuge prey concentration dependent on grazers’ body size, using allometric scaling, is likely to provide more coherent plankton ecosystem dynamics compared to classic formulations or size-independent threshold refugia. We recommend that future plankton ecosystem models pay particular attention to the grazing formulation and implement a threshold refuge incorporating size-dependence, and we call for a new suite of experimental grazing studies. 

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3. Genomic evidence for global ocean plankton biogeography shaped by large-scale current systems

   https://doi.org/10.7554/eLife.78129  

   Richter, Daniel J; Watteaux, Romain; Vannier, Thomas; Leconte, Jade; Frémont, Paul; Reygondeau, Gabriel; Maillet, Nicolas; Henry, Nicolas; Benoit, Gaëtan; Da Silva, Ophélie; et al (August 2022, eLife)

   Oceans are brimming with life invisible to our eyes, a myriad of species of bacteria, viruses and other microscopic organisms essential for the health of the planet. These ‘marine plankton’ are unable to swim against currents and should therefore be constantly on the move, yet previous studies have suggested that distinct species of plankton may in fact inhabit different oceanic regions. However, proving this theory has been challenging; collecting plankton is logistically difficult, and it is often impossible to distinguish between species simply by examining them under a microscope. However, within the last decade, a research schooner called Tara has travelled the globe to gather thousands of plankton samples. At the same time, advances in genomics have made it possible to identify species based only on fragments of their DNA sequence. To understand the hidden geography of plankton communities in Earth’s oceans, Richter et al. pored over DNA from the Tara Oceans expedition. This revealed that, despite being unable to resist the flow of water, various planktonic species which live close to the surface manage to occupy distinct, stable provinces shaped by currents. Different sizes of plankton are distributed in different sized provinces, with the smallest organisms tending to inhabit the smallest areas. Comparing DNA similarities and speeds of currents at the ocean surface revealed how these might stretch and mix plankton communities. Plankton play a critical role in the health of the ocean and the chemical cycles of planet Earth. These results could allow deeper investigation by marine modellers, ecologists, and evolutionary biologists. Meanwhile, work is already underway to investigate how climate change might impact this hidden geography. 

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4. Revealing zooplankton diversity in the midnight zone

   https://doi.org/10.3389/fmars.2023.1252535  

   González, Carolina E.; Blanco-Bercial, Leocadio; Escribano, Rubén; Fernández-Urruzola, Igor; Rivera, Reinaldo; Ulloa, Osvaldo (December 2023, Frontiers in Marine Science)

   Sergio Stefanni (Ed.)

   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 bySubeucalanus 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. 

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5. Population Genomics of Marine Zooplankton

   https://doi.org/10.1007/13836_2017_9  

   Bucklin, A; DiVito, K; Smolina, I; Choquet, M; Questel, JM; Hoarau, G; O’Neill, RJ (January 2018, Population Genomics)

   The exceptionally large population size and cosmopolitan biogeographic distribution that distinguish many – but not all – marine zooplankton species generate similarly exceptional patterns of population genetic and genomic diversity and structure. The phylogenetic diversity of zooplankton has slowed the application of population genomic approaches, due to lack of genomic resources for closelyrelated species and diversity of genomic architecture, including highly-replicated genomes of many crustaceans. Use of numerous genomic markers, especially single nucleotide polymorphisms (SNPs), is transforming our ability to analyze population genetics and connectivity of marine zooplankton, and providing new understanding and different answers than earlier analyses, which typically used mitochondrial DNA and microsatellite markers. Population genomic approaches have confirmed that, despite high dispersal potential, many zooplankton species exhibit genetic structuring among geographic populations, especially at large ocean-basin scales, and have revealed patterns and pathways of population connectivity that do not always track ocean circulation. Genomic and transcriptomic resources are critically needed to allow further examination of micro-evolution and local adaptation, including identification of genes that show evidence of selection. These new tools will also enable further examination of the significance of small-scale genetic heterogeneity of marine zooplankton, to discriminate genetic “noise” in large and patchy populations from local adaptation to environmental conditions and change. 

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