Application of Dual Metabarcoding Platforms for the Meso- and Macrozooplankton Taxa in the Ross Sea
Meso- and macrozooplankton play crucial roles in the trophic web and the biological carbon pump in the ocean by transferring energy from lower to higher trophic levels and vertically exporting carbon from the surface to the deep ocean and seabed. In this study, zooplankton community structures in th...
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2022
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Online Access: | https://doi.org/10.3390/genes13050922 https://doaj.org/article/f7f35d31256f4bbdb087f944b27c7d0f |
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ftdoajarticles:oai:doaj.org/article:f7f35d31256f4bbdb087f944b27c7d0f 2023-05-15T13:36:40+02:00 Application of Dual Metabarcoding Platforms for the Meso- and Macrozooplankton Taxa in the Ross Sea Ji-Hyun Lee Hyoung Sul La Jeong-Hoon Kim Wuju Son Hyun Park Young-Mog Kim Hyun-Woo Kim 2022-05-01T00:00:00Z https://doi.org/10.3390/genes13050922 https://doaj.org/article/f7f35d31256f4bbdb087f944b27c7d0f EN eng MDPI AG https://www.mdpi.com/2073-4425/13/5/922 https://doaj.org/toc/2073-4425 doi:10.3390/genes13050922 2073-4425 https://doaj.org/article/f7f35d31256f4bbdb087f944b27c7d0f Genes, Vol 13, Iss 922, p 922 (2022) Ross Sea metabarcoding zooplankton next-generation sequencing antarctica Genetics QH426-470 article 2022 ftdoajarticles https://doi.org/10.3390/genes13050922 2022-12-30T23:52:29Z Meso- and macrozooplankton play crucial roles in the trophic web and the biological carbon pump in the ocean by transferring energy from lower to higher trophic levels and vertically exporting carbon from the surface to the deep ocean and seabed. In this study, zooplankton community structures in the Ross Sea, Antarctica, were analyzed using metabarcoding methods. Both regular barcode (RB) (using a PacBio Sequel system) and mini barcode (MB) (using the Illumina MiSeq platform) methods were utilized. As the result of a combination of the two bioinformatic pipelines used in the RB, 55 reliable haplotypes were obtained from the pooled zooplankton net samples, whereas 183 amplicon sequence variants (ASVs) were isolated from the MB metabarcoding analyses of 14 individual stations. Among these, 39 (70.9%) and 125 (90.6%) showed higher than 99% sequence identity to the database, indicating that there were sufficient reference sequences to employ metabarcoding analysis—except for several taxa, including small-sized copepods, cnidarians, and pneumodermatids. A high degree of shared taxa showed that both metabarcoding analyses were feasible for use in the analysis of zooplankton assemblages in the Ross Sea. However, RB would be more useful for the construction of a reference database due to its relatively high cost, whereas MB would be more economic for ecological surveys due to its relatively low cost (albeit, only if reference sequences were well documented using RB). Zooplankton assemblages were highly diverse in each sample site, presumably due to the narrow covered volumes of the vertical net-towed samples from polynyas in the Ross Sea. As metabarcoding data accumulate, we will gain better insights into zooplankton communities and their ecological implications in the Ross Sea. Article in Journal/Newspaper Antarc* Antarctica Ross Sea Copepods Directory of Open Access Journals: DOAJ Articles Ross Sea Genes 13 5 922 |
institution |
Open Polar |
collection |
Directory of Open Access Journals: DOAJ Articles |
op_collection_id |
ftdoajarticles |
language |
English |
topic |
Ross Sea metabarcoding zooplankton next-generation sequencing antarctica Genetics QH426-470 |
spellingShingle |
Ross Sea metabarcoding zooplankton next-generation sequencing antarctica Genetics QH426-470 Ji-Hyun Lee Hyoung Sul La Jeong-Hoon Kim Wuju Son Hyun Park Young-Mog Kim Hyun-Woo Kim Application of Dual Metabarcoding Platforms for the Meso- and Macrozooplankton Taxa in the Ross Sea |
topic_facet |
Ross Sea metabarcoding zooplankton next-generation sequencing antarctica Genetics QH426-470 |
description |
Meso- and macrozooplankton play crucial roles in the trophic web and the biological carbon pump in the ocean by transferring energy from lower to higher trophic levels and vertically exporting carbon from the surface to the deep ocean and seabed. In this study, zooplankton community structures in the Ross Sea, Antarctica, were analyzed using metabarcoding methods. Both regular barcode (RB) (using a PacBio Sequel system) and mini barcode (MB) (using the Illumina MiSeq platform) methods were utilized. As the result of a combination of the two bioinformatic pipelines used in the RB, 55 reliable haplotypes were obtained from the pooled zooplankton net samples, whereas 183 amplicon sequence variants (ASVs) were isolated from the MB metabarcoding analyses of 14 individual stations. Among these, 39 (70.9%) and 125 (90.6%) showed higher than 99% sequence identity to the database, indicating that there were sufficient reference sequences to employ metabarcoding analysis—except for several taxa, including small-sized copepods, cnidarians, and pneumodermatids. A high degree of shared taxa showed that both metabarcoding analyses were feasible for use in the analysis of zooplankton assemblages in the Ross Sea. However, RB would be more useful for the construction of a reference database due to its relatively high cost, whereas MB would be more economic for ecological surveys due to its relatively low cost (albeit, only if reference sequences were well documented using RB). Zooplankton assemblages were highly diverse in each sample site, presumably due to the narrow covered volumes of the vertical net-towed samples from polynyas in the Ross Sea. As metabarcoding data accumulate, we will gain better insights into zooplankton communities and their ecological implications in the Ross Sea. |
format |
Article in Journal/Newspaper |
author |
Ji-Hyun Lee Hyoung Sul La Jeong-Hoon Kim Wuju Son Hyun Park Young-Mog Kim Hyun-Woo Kim |
author_facet |
Ji-Hyun Lee Hyoung Sul La Jeong-Hoon Kim Wuju Son Hyun Park Young-Mog Kim Hyun-Woo Kim |
author_sort |
Ji-Hyun Lee |
title |
Application of Dual Metabarcoding Platforms for the Meso- and Macrozooplankton Taxa in the Ross Sea |
title_short |
Application of Dual Metabarcoding Platforms for the Meso- and Macrozooplankton Taxa in the Ross Sea |
title_full |
Application of Dual Metabarcoding Platforms for the Meso- and Macrozooplankton Taxa in the Ross Sea |
title_fullStr |
Application of Dual Metabarcoding Platforms for the Meso- and Macrozooplankton Taxa in the Ross Sea |
title_full_unstemmed |
Application of Dual Metabarcoding Platforms for the Meso- and Macrozooplankton Taxa in the Ross Sea |
title_sort |
application of dual metabarcoding platforms for the meso- and macrozooplankton taxa in the ross sea |
publisher |
MDPI AG |
publishDate |
2022 |
url |
https://doi.org/10.3390/genes13050922 https://doaj.org/article/f7f35d31256f4bbdb087f944b27c7d0f |
geographic |
Ross Sea |
geographic_facet |
Ross Sea |
genre |
Antarc* Antarctica Ross Sea Copepods |
genre_facet |
Antarc* Antarctica Ross Sea Copepods |
op_source |
Genes, Vol 13, Iss 922, p 922 (2022) |
op_relation |
https://www.mdpi.com/2073-4425/13/5/922 https://doaj.org/toc/2073-4425 doi:10.3390/genes13050922 2073-4425 https://doaj.org/article/f7f35d31256f4bbdb087f944b27c7d0f |
op_doi |
https://doi.org/10.3390/genes13050922 |
container_title |
Genes |
container_volume |
13 |
container_issue |
5 |
container_start_page |
922 |
_version_ |
1766082311862878208 |