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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2022
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Online Access: | https://oceanrep.geomar.de/id/eprint/56802/ https://oceanrep.geomar.de/id/eprint/56802/1/MacNeil_Scientific_Rep_2022.pdf https://oceanrep.geomar.de/id/eprint/56802/7/s41598-022-20894-1.pdf https://doi.org/10.1038/s41598-022-17313-w |
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ftoceanrep:oai:oceanrep.geomar.de:56802 2024-02-11T10:05:56+01:00 Combining multi-marker metabarcoding and digital holography to describe eukaryotic plankton across the Newfoundland Shelf MacNeil, Liam Desai, Dhwani K. Costa, Maycira LaRoche, Julie 2022-07-29 text https://oceanrep.geomar.de/id/eprint/56802/ https://oceanrep.geomar.de/id/eprint/56802/1/MacNeil_Scientific_Rep_2022.pdf https://oceanrep.geomar.de/id/eprint/56802/7/s41598-022-20894-1.pdf https://doi.org/10.1038/s41598-022-17313-w en eng https://oceanrep.geomar.de/id/eprint/56802/1/MacNeil_Scientific_Rep_2022.pdf https://oceanrep.geomar.de/id/eprint/56802/7/s41598-022-20894-1.pdf MacNeil, L. , Desai, D. K., Costa, M. and LaRoche, J. (2022) Combining multi-marker metabarcoding and digital holography to describe eukaryotic plankton across the Newfoundland Shelf. Open Access Scientific Reports, 12 (1). Art.Nr. 13078. DOI 10.1038/s41598-022-17313-w <https://doi.org/10.1038/s41598-022-17313-w>. doi:10.1038/s41598-022-17313-w cc_by_4.0 info:eu-repo/semantics/openAccess Article PeerReviewed 2022 ftoceanrep https://doi.org/10.1038/s41598-022-17313-w 2024-01-15T00:25:40Z 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. Article in Journal/Newspaper Newfoundland North Atlantic Northwest Atlantic OceanRep (GEOMAR Helmholtz Centre für Ocean Research Kiel) Canada Scientific Reports 12 1 |
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Open Polar |
collection |
OceanRep (GEOMAR Helmholtz Centre für Ocean Research Kiel) |
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ftoceanrep |
language |
English |
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. |
format |
Article in Journal/Newspaper |
author |
MacNeil, Liam Desai, Dhwani K. Costa, Maycira LaRoche, Julie |
spellingShingle |
MacNeil, Liam Desai, Dhwani K. Costa, Maycira LaRoche, Julie Combining multi-marker metabarcoding and digital holography to describe eukaryotic plankton across the Newfoundland Shelf |
author_facet |
MacNeil, Liam Desai, Dhwani K. Costa, Maycira LaRoche, Julie |
author_sort |
MacNeil, Liam |
title |
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_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_sort |
combining multi-marker metabarcoding and digital holography to describe eukaryotic plankton across the newfoundland shelf |
publishDate |
2022 |
url |
https://oceanrep.geomar.de/id/eprint/56802/ https://oceanrep.geomar.de/id/eprint/56802/1/MacNeil_Scientific_Rep_2022.pdf https://oceanrep.geomar.de/id/eprint/56802/7/s41598-022-20894-1.pdf https://doi.org/10.1038/s41598-022-17313-w |
geographic |
Canada |
geographic_facet |
Canada |
genre |
Newfoundland North Atlantic Northwest Atlantic |
genre_facet |
Newfoundland North Atlantic Northwest Atlantic |
op_relation |
https://oceanrep.geomar.de/id/eprint/56802/1/MacNeil_Scientific_Rep_2022.pdf https://oceanrep.geomar.de/id/eprint/56802/7/s41598-022-20894-1.pdf MacNeil, L. , Desai, D. K., Costa, M. and LaRoche, J. (2022) Combining multi-marker metabarcoding and digital holography to describe eukaryotic plankton across the Newfoundland Shelf. Open Access Scientific Reports, 12 (1). Art.Nr. 13078. DOI 10.1038/s41598-022-17313-w <https://doi.org/10.1038/s41598-022-17313-w>. doi:10.1038/s41598-022-17313-w |
op_rights |
cc_by_4.0 info:eu-repo/semantics/openAccess |
op_doi |
https://doi.org/10.1038/s41598-022-17313-w |
container_title |
Scientific Reports |
container_volume |
12 |
container_issue |
1 |
_version_ |
1790603283887292416 |