Combining multi-marker metabarcoding and digital holography to describe eukaryotic plankton across the Newfoundland Shelf
Abstract 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 observatio...
| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
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Nature Portfolio
2022-07-01
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| Series: | Scientific Reports |
| Online Access: | https://doi.org/10.1038/s41598-022-17313-w |
| _version_ | 1828751952363651072 |
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| author | Liam MacNeil Dhwani K. Desai Maycira Costa Julie LaRoche |
| author_facet | Liam MacNeil Dhwani K. Desai Maycira Costa Julie LaRoche |
| author_sort | Liam MacNeil |
| collection | DOAJ |
| description | Abstract 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. |
| first_indexed | 2024-12-10T21:01:16Z |
| format | Article |
| id | doaj.art-eeec5c1f405e423d82a3172a537ee1d7 |
| institution | Directory Open Access Journal |
| issn | 2045-2322 |
| language | English |
| last_indexed | 2024-12-10T21:01:16Z |
| publishDate | 2022-07-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Scientific Reports |
| spelling | doaj.art-eeec5c1f405e423d82a3172a537ee1d72022-12-22T01:33:47ZengNature PortfolioScientific Reports2045-23222022-07-0112111110.1038/s41598-022-17313-wCombining multi-marker metabarcoding and digital holography to describe eukaryotic plankton across the Newfoundland ShelfLiam MacNeil0Dhwani K. Desai1Maycira Costa2Julie LaRoche3Biology Department, Dalhousie UniversityBiology Department, Dalhousie UniversityDepartment of Geography, University of VictoriaBiology Department, Dalhousie UniversityAbstract 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.https://doi.org/10.1038/s41598-022-17313-w |
| spellingShingle | Liam MacNeil Dhwani K. Desai Maycira Costa Julie LaRoche Combining multi-marker metabarcoding and digital holography to describe eukaryotic plankton across the Newfoundland Shelf Scientific Reports |
| 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 |
| url | https://doi.org/10.1038/s41598-022-17313-w |
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