DNA metabarcoding and morphological analysis - Assessment of zooplankton biodiversity in transitional waters

Schroeder, Anna; Stanković, D; Pallavicini, Alberto; Gionechetti, Fabrizia; Pansera, Marco; Camatti, Elisa

doi:10.1016/j.marenvres.2020.104946

Cited by 41 publications

(36 citation statements)

References 87 publications

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“…However, our metabarcoding results suggested slightly higher species richness. It is not uncommon to detect higher richness of taxa through metabarcoding as demonstrated in many other studies, for example for benthic macroinvertebrates , for zooplankton (Schroeder et al, 2020) and for phytoplankton (Zimmermann et al, 2015).…”

Section: Comparison Of Molecular and Morphological Analysessupporting

confidence: 58%

High‐throughput identification of non‐marine Ostracoda from the Tibetan Plateau: Evaluating the success of various primers on sedimentary DNA samples

et al. 2021

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Section: Comparison Of Molecular and Morphological Analysessupporting

confidence: 58%

High‐throughput identification of non‐marine Ostracoda from the Tibetan Plateau: Evaluating the success of various primers on sedimentary DNA samples

et al. 2021

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“…The present study is one of only a few studies combining metabarcoding and morphological identification to study the seasonal variability of a zooplankton community with relatively high temporal resolution (Gran-Stadniczeñko et al, 2019;Schroeder et al, 2020). This approach enabled us to describe the seasonal variability of the zooplankton community in Ramfjord with high quantitative and taxonomical accuracy, while at the same time also linking the detected changes to environmental variables.…”

Section: Discussionmentioning

confidence: 99%

Seasonal Variability in the Zooplankton Community Structure in a Sub-Arctic Fjord as Revealed by Morphological and Molecular Approaches

et al. 2021

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Phyto- and zooplankton in Arctic and sub-Arctic seas show very strong seasonal changes in diversity and biomass. Here we document the seasonal variability in the mesozooplankton community structure in a sub-Arctic fjord in Northern Norway based on monthly sampling between November 2018 and February 2020. We combined traditional morphological zooplankton identification with DNA metabarcoding of a 313 base pair fragment of the COI gene. This approach allowed us to provide the most detailed mesozooplankton species list known for this region across an entire year, including both holo- and meroplankton. The zooplankton community was dominated by small copepods throughout the sampling period both in terms of abundance and relative sequence counts. However, meroplankton was the most diverse group, especially within the phylum polychaeta. We identified four distinct periods based on the seasonal analysis of the zooplankton community composition. The pre-spring bloom period (February–March) was characterized by low abundance and biomass of zooplankton. The spring bloom (April) was characterized by the presence of Calanus young stages, cirripedia and krill eggs. The spring-summer period (May–August) was characterized by a succession of meroplankton and a relatively high abundance of copepods of the genus Calanus spp. Finally, the autumn-winter period (September–December) was characterized by a high copepod diversity and a peak in abundance of small copepods (e.g., Oithona similis, Acartia longiremis, Pseudocalanus acuspes, Pseudocalanus elongatus, Pseudocalanus moultoni, Pseudocalanus minutus). During this period, we also observed an influx of boreal warm-water species which were notably absent during the rest of the year. Both the traditional community analysis and metabarcoding were highly complementary and with a few exceptions showed similar trends in the seasonal changes of the zooplankton community structure.

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“…The Cnidaria and Ctenophora are taxonomic groups that, as a whole, are often missed or ignored by routine plankton surveys using nets and morphological identification, and utilizing molecular methods could provide increased data on their diversity and distributions (Hosia et al 2017;Leduc et al 2019;Schroeder et al 2020). Molecular methods can also improve our understanding of the trophic role of gelatinous zooplankton.…”

Section: Priorities For Dna Barcoding and Metabarcodingmentioning

confidence: 99%

Toward a global reference database of COI barcodes for marine zooplankton

et al. 2021

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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.

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DNA metabarcoding and morphological analysis - Assessment of zooplankton biodiversity in transitional waters

Cited by 41 publications

References 87 publications

High‐throughput identification of non‐marine Ostracoda from the Tibetan Plateau: Evaluating the success of various primers on sedimentary DNA samples

High‐throughput identification of non‐marine Ostracoda from the Tibetan Plateau: Evaluating the success of various primers on sedimentary DNA samples

Seasonal Variability in the Zooplankton Community Structure in a Sub-Arctic Fjord as Revealed by Morphological and Molecular Approaches

Toward a global reference database of COI barcodes for marine zooplankton

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