ZooSCAN images of zooplankton collected during BATS MOCNESS tows during R/V Atlantic Explorer cruises AE1614, AE1712, AE1830, and AE1819 in the vicinity of the Bermuda Atlantic Time-series Study from 2016 to 2018

Dataset: ZooSCAN Images BATS: M3 to M13ZooSCAN images from BATS MOCNESS tows during R/V Atlantic Explorer cruises AE1614, AE1712, AE1830, and AE1819 in the vicinity of the Bermuda Atlantic Time-series Study (BATS) in July of 2016, 2017, and 2018 as well as October 2018 (eight casts in total, 63 discrete nets). These data were published in Maas et al. (2021). For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/853440Simons Foundation (Simons) unknown SCOPE Simons, NSF Division of Ocean Sciences (NSF OCE) OCE-1829318, NSF Division of Ocean Sciences (NSF OCE) OCE-194816

Diel metabolic patterns in a migratory oceanic copepod

© The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Tarrant, A. M., McNamara-Bordewick, N., Blanco-Bercial, L., Miccoli, A., & Maas, A. E. Diel metabolic patterns in a migratory oceanic copepod. Journal of Experimental Marine Biology and Ecology, 545, (2021): 151643, https://doi.org/10.1016/j.jembe.2021.151643.Diel vertical migration of zooplankton profoundly impacts the transport of nutrients and carbon through the water column. Despite the acknowledged importance of this active flux to ocean biogeochemistry, these contributions remain poorly constrained, in part because daily variations in metabolic rates are not considered or are modeled as simple functions of temperature. To address this uncertainty, we sampled the subtropical copepod Pleuromamma xiphias at 4- to 7-h intervals throughout the daily migration and measured rates of oxygen consumption, ammonium excretion, fecal pellet production and metabolic enzyme activity. No significant patterns were detected in rates of oxygen consumption or ammonium excretion for freshly caught animals over the diel cycle. Fecal pellet production was highest during mid-night, consistent with several hours of feeding near the surface. Surface feeding resulted in fecal pellet production at depth in the morning, providing direct evidence that active flux of particulate organic carbon occurs in this region. Electron transport system activity was highest during the afternoon, contrary to our prediction of reduced daytime metabolism. Activity of both glutamate dehydrogenase and citrate synthase increased during early night, reflecting higher capacity for excretion and aerobic respiration, respectively. Overall, these results show that activities of metabolic enzymes vary during diel vertical migration. The surprising observation of elevated afternoon enzyme activity coupled with daytime fecal pellet and ammonium production suggests that additional characterization of the daytime activity of migratory zooplankton is warranted.This work was supported by the National Science Foundation [Grants OCE-1829318 to AEMand LBB, and OCE-1829378 to AMT]. Support for NM-B was provided by the Woods Hole Oceanographic Institution's Summer Student Fellows Program

Variations in copepod proteome and respiration rate in association with diel vertical migration and circadian cycle

Author Posting. © University of Chicago, 2018. This article is posted here by permission of University of Chicago for personal use, not for redistribution. The definitive version was published in Biological Bulletin 235 (2018): 30-42, doi:10.1086/699219.The diel vertical migration of zooplankton is a process during which individuals spend the night in surface waters and retreat to depth during the daytime, with substantial implications for carbon transport and the ecology of midwater ecosystems. The physiological consequences of this daily pattern have, however, been poorly studied beyond investigations of speed and the energetic cost of swimming. Many other processes are likely influenced, such as fuel use, energetic trade-offs, underlying diel (circadian) rhythms, and antioxidant responses. Using a new reference transcriptome, proteomic analyses were applied to compare the physiological state of a migratory copepod, Pleuromamma xiphias, immediately after arriving to the surface at night and six hours later. Oxygen consumption was monitored semi-continuously to explore underlying cyclical patterns in metabolic rate under dark-dark conditions. The proteomic analysis suggests a distinct shift in physiology that reflects migratory exertion and changes in metabolism. These proteomic analyses are supported by the respiration experiments, which show an underlying cycle in metabolic rate, with a peak at dawn. This project generates molecular tools (transcriptome and proteome) that will allow for more detailed understanding of the underlying physiological processes that influence and are influenced by diel vertical migration. Further, these studies suggest that P. xiphias is a tractable model for continuing investigations of circadian and diel vertical migration influences on plankton physiology. Previous studies did not account for this cyclic pattern of respiration and may therefore have unrepresented respiratory carbon fluxes from copepods by about 24%.Funding for ET-S was provided by a Training Grant from the National Institutes of Health (T32 HG00035), and proteomics work was supported in part by the University of Washington’s Proteomics Resource (UWPR95794). Funding was provided by Simon’s Foundation International as part of the BIOSSCOPE project.2019-08-1

Migratory zooplankton excreta and its influence on prokaryotic communities

© The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Maas, A. E., Liu, S., Bolanos, L. M., Widner, B., Parsons, R., Kujawinski, E. B., Blanco-Bercial, L., & Carlson, C. A. Migratory zooplankton excreta and its influence on prokaryotic communities. Frontiers in Marine Science, 7, (2020): 573268, doi:10.3389/fmars.2020.573268.Particulate organic matter (POM) (fecal pellets) from zooplankton has been demonstrated to be an important nutrient source for the pelagic prokaryotic community. Significantly less is known about the chemical composition of the dissolved organic matter (DOM) produced by these eukaryotes and its influence on pelagic ecosystem structure. Zooplankton migrators, which daily transport surface-derived compounds to depth, may act as important vectors of limiting nutrients for mesopelagic microbial communities. In this role, zooplankton may increase the DOM remineralization rate by heterotrophic prokaryotes through the creation of nutrient rich “hot spots” that could potentially increase niche diversity. To explore these interactions, we collected the migratory copepod Pleuromamma xiphias from the northwestern Sargasso Sea and sampled its excreta after 12–16 h of incubation. We measured bulk dissolved organic carbon (DOC), dissolved free amino acids (DFAA) via high performance liquid chromatography and dissolved targeted metabolites via quantitative mass spectrometry (UPLC-ESI-MSMS) to quantify organic zooplankton excreta production and characterize its composition. We observed production of labile DOM, including amino acids, vitamins, and nucleosides. Additionally, we harvested a portion of the excreta and subsequently used it as the growth medium for mesopelagic (200 m) bacterioplankton dilution cultures. In zooplankton excreta treatments we observed a four-fold increase in bacterioplankton cell densities that reached stationary growth phase after five days of dark incubation. Analyses of 16S rRNA gene amplicons suggested a shift from oligotrophs typical of open ocean and mesopelagic prokaryotic communities to more copiotrophic bacterial lineages in the presence of zooplankton excreta. These results support the hypothesis that zooplankton and prokaryotes are engaged in complex and indirect ecological interactions, broadening our understanding of the microbial loop.Funding for this research was provided by Simons Foundation International as part of the BIOS-SCOPE project to AM, LB-B, CC, and EK

Genome- and transcriptome-assisted development of nuclear insertion/deletion markers for Calanus species (Copepoda: Calanoida) identification

Submitted version (preprint).This is the pre-peer reviewed version of the following article: Smolina, I., Kollias, S., Poortvliet, M., Nielsen, T.G., Lindeque, P., Castellani, C., ... Hoarau, G.G. (2014). Genome- and transcriptome-assisted development of nuclear insertion/deletion markers for Calanus species (Copepoda: Calanoida) identification. Molecular Ecology Resources, 14(5), 1072-1079, which has been published in final form at http://dx.doi.org/10.1111/1755-0998.12241. This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Self-Archiving (http://olabout.wiley.com/WileyCDA/Section/id-820227.html)

Genome- and transcriptome-assisted development of nuclear insertion/deletion markers for Calanus species (Copepoda: Calanoida) identification

Submitted version (preprint).This is the pre-peer reviewed version of the following article: Smolina, I., Kollias, S., Poortvliet, M., Nielsen, T.G., Lindeque, P., Castellani, C., ... Hoarau, G.G. (2014). Genome- and transcriptome-assisted development of nuclear insertion/deletion markers for Calanus species (Copepoda: Calanoida) identification. Molecular Ecology Resources, 14(5), 1072-1079, which has been published in final form at http://dx.doi.org/10.1111/1755-0998.12241. This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Self-Archiving (http://olabout.wiley.com/WileyCDA/Section/id-820227.html)

Towards population genomics in non-model species with large genomes : a case study of the marine zooplankton Calanus finmarchicus

publishedVersio

Toward a global reference database of COI barcodes for marine zooplankton

© The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Bucklin, A., Peijnenburg, K. T. C. A., Kosobokova, K. N., O'Brien, T. D., Blanco-Bercial, L., Cornils, A., Falkenhaug, T., Hopcroft, R. R., Hosia, A., Laakmann, S., Li, C., Martell, L., Questel, J. M., Wall-Palmer, D., Wang, M., Wiebe, P. H., & Weydmann-Zwolicka, A. Toward a global reference database of COI barcodes for marine zooplankton. Marine Biology, 168(6), (2021): 78, https://doi.org/10.1007/s00227-021-03887-y.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.Funding sources for authors of the review paper are described here: Scientific Committee on Oceanic Research (SCOR), and a grant to SCOR from the U.S. National Science Foundation (OCE-1840868). Netherlands Organization for Scientific Research (NWO) Vidi Grant/Award Number: 016.161.351 to K.T.C.A.P. European Union Horizon 2020 research and innovation program under the Marie Sklodowska-Curie grant agreement No. 746186 (POSEIDoN) to D.W.P. The work of K.N.K. was performed in the framework of the state assignment of IO RAS (Theme No. 0128-2021-0007) and partially supported by Russian Foundation for Basic Research grants No. 18-05-60158 and No. 19-04-00955. The work of A.W.Z. was supported by a grant from HIDEA—Hidden diversity of the Arctic Ocean (No. 2017/27/B/NZ8/01056) from the National Science Centre, Poland, and a Fulbright Senior Award. The Norwegian Taxonomy Initiative of the Norwegian Biodiversity Information Centre provided funding for A.H. and L.M. (Project Nos. 70184233/HYPNO and 70184240/NORHYDRO), and for T.F. (Project Nos. 70184233/COPCLAD and 70184241/HYPCOP). The work of R.R.H. and J.M.Q. was supported by Census of Marine Life and NOAA Ocean Exploration and Research (NA05OAR4601079 and NA15OAR0110209). The work of S.L. was conducted at the Helmholtz Institute for Functional Marine Biodiversity at the University of Oldenburg (HIFMB). HIFMB is a collaboration between the Alfred-Wegener-Institute, Helmholtz-Center for Polar and Marine Research, and the Carl-von-Ossietzky University Oldenburg, initially funded by the Ministry for Science and Culture of Lower Saxony and the Volkswagen Foundation through the Niedersächsisches Vorab’ grant program (Grant No. ZN3285)

Reexamination of the species assignment of Diacavolinia pteropods using DNA barcoding

© The Author(s), 2013. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS ONE 8 (2013): e53889, doi:10.1371/journal.pone.0053889.Thecosome pteropods (Mollusca, Gastropoda) are an ecologically important, diverse, and ubiquitous group of holoplanktonic animals that are the focus of intense research interest due to their external aragonite shell and vulnerability to ocean acidification. Characterizing the response of these animals to low pH and other environmental stressors has been hampered by continued uncertainty in their taxonomic identification. An example of this confusion in species assignment is found in the genus Diacavolinia. All members of this genus were originally indentified as a single species, Cavolinia longirostris, but over the past fifty years the taxonomy has been revisited multiple times; currently the genus comprises 22 different species. This study examines five species of Diacavolinia, including four sampled in the Northeast Atlantic (78 individuals) and one from the Eastern tropical North Pacific (15 individuals). Diacavolina were identified to species based on morphological characteristics according to the current taxonomy, photographed, and then used to determine the sequence of the “DNA barcoding” region of the cytochrome c oxidase subunit I (COI). Specimens from the Atlantic, despite distinct differences in shell morphology, showed polyphyly and a genetic divergence of <3% (K2P distance) whereas the Pacific and Atlantic samples were more distant (~19%). Comparisons of Diacavolinia spp. with other Cavolinia spp. reveal larger distances (~24%). These results indicate that specimens from the Atlantic comprise a single monophyletic species and suggest possible species-level divergence between Atlantic and Pacific populations. The findings support the maintenance of Diacavolinia as a separate genus, yet emphasize the inadequacy of our current taxonomic understanding of pteropods. They highlight the need for accurate species identifications to support estimates of biodiversity, range extent and natural exposure of these planktonic calcifiers to environmental variability; furthermore, the apparent variation of the pteropods shell may have implications for our understanding of the species’ sensitivity to ocean acidification.This material is based upon work supported by the National Science Foundation under Grant Number OCE-0928801. AEM was funded through the WHOI Postdoctoral Scholarship. Support to LBB was provided by the College of Liberal Arts & Sciences, University of Connecticut; and by the Census of Marine Life/Alfred P. Sloan Foundation

Molecular Systematic of Three Species of Oithona (Copepoda, Cyclopoida) from the Atlantic Ocean: Comparative Analysis Using 28S rDNA

Species of Oithona (Copepoda, Cyclopoida) are highly abundant, ecologically important, and widely distributed throughout the world oceans. Although there are valid and detailed descriptions of the species, routine species identifications remain challenging due to their small size, subtle morphological diagnostic traits, and the description of geographic forms or varieties. This study examined three species of Oithona (O. similis, O. atlantica and O. nana) occurring in the Argentine sector of the South Atlantic Ocean based on DNA sequence variation of a 575 base-pair region of 28S rDNA, with comparative analysis of these species from other North and South Atlantic regions. DNA sequence variation clearly resolved and discriminated the species, and revealed low levels of intraspecific variation among North and South Atlantic populations of each species. The 28S rDNA region was thus shown to provide an accurate and reliable means of identifying the species throughout the sampled domain. Analysis of 28S rDNA variation for additional species collected throughout the global ocean will be useful to accurately characterize biogeographical distributions of the species and to examine phylogenetic relationships among them