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Combining multi-marker metabarcoding and digital holography to describe eukaryotic plankton across the Newfoundland Shelf

The planktonic diversity throughout the oceans is vital to ecosystem functioning and linked to environmental change. Plankton monitoring tools have advanced considerably with high-throughput in-situ digital cameras and genomic sequencing, opening new challenges for high-frequency observations of com...

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Autores principales: MacNeil, Liam, Desai, Dhwani K., Costa, Maycira, LaRoche, Julie
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group UK 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9338326/
https://www.ncbi.nlm.nih.gov/pubmed/35906469
http://dx.doi.org/10.1038/s41598-022-17313-w
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author MacNeil, Liam
Desai, Dhwani K.
Costa, Maycira
LaRoche, Julie
author_facet MacNeil, Liam
Desai, Dhwani K.
Costa, Maycira
LaRoche, Julie
author_sort MacNeil, Liam
collection PubMed
description The planktonic diversity throughout the oceans is vital to ecosystem functioning and linked to environmental change. Plankton monitoring tools have advanced considerably with high-throughput in-situ digital cameras and genomic sequencing, opening new challenges for high-frequency observations of community composition, structure, and species discovery. Here, we combine multi-marker metabarcoding based on nuclear 18S (V4) and plastidial 16S (V4–V5) rRNA gene amplicons with a digital in-line holographic microscope to provide a synoptic diversity survey of eukaryotic plankton along the Newfoundland Shelf (Canada) during the winter transition phase of the North Atlantic bloom phenomenon. Metabarcoding revealed a rich eukaryotic diversity unidentifiable in the imaging samples, confirming the presence of ecologically important saprophytic protists which were unclassifiable in matching images, and detecting important groups unobserved or taxonomically unresolved during similar sequencing campaigns in the Northwest Atlantic Ocean. In turn, imaging analysis provided quantitative observations of widely prevalent plankton from every trophic level. Despite contrasting plankton compositions portrayed by each sampling method, both capture broad spatial differences between the northern and southern sectors of the Newfoundland Shelf and suggest complementary estimations of important features in eukaryotic assemblages. Future tasks will involve standardizing digital imaging and metabarcoding for wider use and consistent, comparable ocean observations.
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spelling pubmed-93383262022-07-31 Combining multi-marker metabarcoding and digital holography to describe eukaryotic plankton across the Newfoundland Shelf MacNeil, Liam Desai, Dhwani K. Costa, Maycira LaRoche, Julie Sci Rep Article The planktonic diversity throughout the oceans is vital to ecosystem functioning and linked to environmental change. Plankton monitoring tools have advanced considerably with high-throughput in-situ digital cameras and genomic sequencing, opening new challenges for high-frequency observations of community composition, structure, and species discovery. Here, we combine multi-marker metabarcoding based on nuclear 18S (V4) and plastidial 16S (V4–V5) rRNA gene amplicons with a digital in-line holographic microscope to provide a synoptic diversity survey of eukaryotic plankton along the Newfoundland Shelf (Canada) during the winter transition phase of the North Atlantic bloom phenomenon. Metabarcoding revealed a rich eukaryotic diversity unidentifiable in the imaging samples, confirming the presence of ecologically important saprophytic protists which were unclassifiable in matching images, and detecting important groups unobserved or taxonomically unresolved during similar sequencing campaigns in the Northwest Atlantic Ocean. In turn, imaging analysis provided quantitative observations of widely prevalent plankton from every trophic level. Despite contrasting plankton compositions portrayed by each sampling method, both capture broad spatial differences between the northern and southern sectors of the Newfoundland Shelf and suggest complementary estimations of important features in eukaryotic assemblages. Future tasks will involve standardizing digital imaging and metabarcoding for wider use and consistent, comparable ocean observations. Nature Publishing Group UK 2022-07-29 /pmc/articles/PMC9338326/ /pubmed/35906469 http://dx.doi.org/10.1038/s41598-022-17313-w Text en © The Author(s) 2022, corrected publication 2022 https://creativecommons.org/licenses/by/4.0/Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) .
spellingShingle Article
MacNeil, Liam
Desai, Dhwani K.
Costa, Maycira
LaRoche, Julie
Combining multi-marker metabarcoding and digital holography to describe eukaryotic plankton across the Newfoundland Shelf
title Combining multi-marker metabarcoding and digital holography to describe eukaryotic plankton across the Newfoundland Shelf
title_full Combining multi-marker metabarcoding and digital holography to describe eukaryotic plankton across the Newfoundland Shelf
title_fullStr Combining multi-marker metabarcoding and digital holography to describe eukaryotic plankton across the Newfoundland Shelf
title_full_unstemmed Combining multi-marker metabarcoding and digital holography to describe eukaryotic plankton across the Newfoundland Shelf
title_short Combining multi-marker metabarcoding and digital holography to describe eukaryotic plankton across the Newfoundland Shelf
title_sort combining multi-marker metabarcoding and digital holography to describe eukaryotic plankton across the newfoundland shelf
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9338326/
https://www.ncbi.nlm.nih.gov/pubmed/35906469
http://dx.doi.org/10.1038/s41598-022-17313-w
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