Data_Sheet_1_Comparison of Two 16S rRNA Primers (V3–V4 and V4–V5) for Studies of Arctic Microbial Communities.PDF
Microbial communities of the Arctic Ocean are poorly characterized in comparison to other aquatic environments as to their horizontal, vertical, and temporal turnover. Yet, recent studies showed that the Arctic marine ecosystem harbors unique microbial community members that are adapted to harsh env...
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ftfrontimediafig:oai:figshare.com:article/14036954 2023-05-15T14:37:36+02:00 Data_Sheet_1_Comparison of Two 16S rRNA Primers (V3–V4 and V4–V5) for Studies of Arctic Microbial Communities.PDF Eduard Fadeev Magda G. Cardozo-Mino Josephine Z. Rapp Christina Bienhold Ian Salter Verena Salman-Carvalho Massimiliano Molari Halina E. Tegetmeyer Pier Luigi Buttigieg Antje Boetius 2021-02-16T04:16:36Z https://doi.org/10.3389/fmicb.2021.637526.s001 https://figshare.com/articles/dataset/Data_Sheet_1_Comparison_of_Two_16S_rRNA_Primers_V3_V4_and_V4_V5_for_Studies_of_Arctic_Microbial_Communities_PDF/14036954 unknown doi:10.3389/fmicb.2021.637526.s001 https://figshare.com/articles/dataset/Data_Sheet_1_Comparison_of_Two_16S_rRNA_Primers_V3_V4_and_V4_V5_for_Studies_of_Arctic_Microbial_Communities_PDF/14036954 CC BY 4.0 CC-BY Microbiology Microbial Genetics Microbial Ecology Mycology microbial communities amplicon sequencing method comparison universal primers Arctic Ocean molecular observatory Dataset 2021 ftfrontimediafig https://doi.org/10.3389/fmicb.2021.637526.s001 2021-02-17T23:57:55Z Microbial communities of the Arctic Ocean are poorly characterized in comparison to other aquatic environments as to their horizontal, vertical, and temporal turnover. Yet, recent studies showed that the Arctic marine ecosystem harbors unique microbial community members that are adapted to harsh environmental conditions, such as near-freezing temperatures and extreme seasonality. The gene for the small ribosomal subunit (16S rRNA) is commonly used to study the taxonomic composition of microbial communities in their natural environment. Several primer sets for this marker gene have been extensively tested across various sample sets, but these typically originated from low-latitude environments. An explicit evaluation of primer-set performances in representing the microbial communities of the Arctic Ocean is currently lacking. To select a suitable primer set for studying microbiomes of various Arctic marine habitats (sea ice, surface water, marine snow, deep ocean basin, and deep-sea sediment), we have conducted a performance comparison between two widely used primer sets, targeting different hypervariable regions of the 16S rRNA gene (V3–V4 and V4–V5). We observed that both primer sets were highly similar in representing the total microbial community composition down to genus rank, which was also confirmed independently by subgroup-specific catalyzed reporter deposition-fluorescence in situ hybridization (CARD-FISH) counts. Each primer set revealed higher internal diversity within certain bacterial taxonomic groups (e.g., the class Bacteroidia by V3–V4, and the phylum Planctomycetes by V4–V5). However, the V4–V5 primer set provides concurrent coverage of the archaeal domain, a relevant component comprising 10–20% of the community in Arctic deep waters and the sediment. Although both primer sets perform similarly, we suggest the use of the V4–V5 primer set for the integration of both bacterial and archaeal community dynamics in the Arctic marine environment. Dataset Arctic Arctic Ocean Sea ice Frontiers: Figshare Arctic Arctic Ocean |
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Open Polar |
collection |
Frontiers: Figshare |
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ftfrontimediafig |
language |
unknown |
topic |
Microbiology Microbial Genetics Microbial Ecology Mycology microbial communities amplicon sequencing method comparison universal primers Arctic Ocean molecular observatory |
spellingShingle |
Microbiology Microbial Genetics Microbial Ecology Mycology microbial communities amplicon sequencing method comparison universal primers Arctic Ocean molecular observatory Eduard Fadeev Magda G. Cardozo-Mino Josephine Z. Rapp Christina Bienhold Ian Salter Verena Salman-Carvalho Massimiliano Molari Halina E. Tegetmeyer Pier Luigi Buttigieg Antje Boetius Data_Sheet_1_Comparison of Two 16S rRNA Primers (V3–V4 and V4–V5) for Studies of Arctic Microbial Communities.PDF |
topic_facet |
Microbiology Microbial Genetics Microbial Ecology Mycology microbial communities amplicon sequencing method comparison universal primers Arctic Ocean molecular observatory |
description |
Microbial communities of the Arctic Ocean are poorly characterized in comparison to other aquatic environments as to their horizontal, vertical, and temporal turnover. Yet, recent studies showed that the Arctic marine ecosystem harbors unique microbial community members that are adapted to harsh environmental conditions, such as near-freezing temperatures and extreme seasonality. The gene for the small ribosomal subunit (16S rRNA) is commonly used to study the taxonomic composition of microbial communities in their natural environment. Several primer sets for this marker gene have been extensively tested across various sample sets, but these typically originated from low-latitude environments. An explicit evaluation of primer-set performances in representing the microbial communities of the Arctic Ocean is currently lacking. To select a suitable primer set for studying microbiomes of various Arctic marine habitats (sea ice, surface water, marine snow, deep ocean basin, and deep-sea sediment), we have conducted a performance comparison between two widely used primer sets, targeting different hypervariable regions of the 16S rRNA gene (V3–V4 and V4–V5). We observed that both primer sets were highly similar in representing the total microbial community composition down to genus rank, which was also confirmed independently by subgroup-specific catalyzed reporter deposition-fluorescence in situ hybridization (CARD-FISH) counts. Each primer set revealed higher internal diversity within certain bacterial taxonomic groups (e.g., the class Bacteroidia by V3–V4, and the phylum Planctomycetes by V4–V5). However, the V4–V5 primer set provides concurrent coverage of the archaeal domain, a relevant component comprising 10–20% of the community in Arctic deep waters and the sediment. Although both primer sets perform similarly, we suggest the use of the V4–V5 primer set for the integration of both bacterial and archaeal community dynamics in the Arctic marine environment. |
format |
Dataset |
author |
Eduard Fadeev Magda G. Cardozo-Mino Josephine Z. Rapp Christina Bienhold Ian Salter Verena Salman-Carvalho Massimiliano Molari Halina E. Tegetmeyer Pier Luigi Buttigieg Antje Boetius |
author_facet |
Eduard Fadeev Magda G. Cardozo-Mino Josephine Z. Rapp Christina Bienhold Ian Salter Verena Salman-Carvalho Massimiliano Molari Halina E. Tegetmeyer Pier Luigi Buttigieg Antje Boetius |
author_sort |
Eduard Fadeev |
title |
Data_Sheet_1_Comparison of Two 16S rRNA Primers (V3–V4 and V4–V5) for Studies of Arctic Microbial Communities.PDF |
title_short |
Data_Sheet_1_Comparison of Two 16S rRNA Primers (V3–V4 and V4–V5) for Studies of Arctic Microbial Communities.PDF |
title_full |
Data_Sheet_1_Comparison of Two 16S rRNA Primers (V3–V4 and V4–V5) for Studies of Arctic Microbial Communities.PDF |
title_fullStr |
Data_Sheet_1_Comparison of Two 16S rRNA Primers (V3–V4 and V4–V5) for Studies of Arctic Microbial Communities.PDF |
title_full_unstemmed |
Data_Sheet_1_Comparison of Two 16S rRNA Primers (V3–V4 and V4–V5) for Studies of Arctic Microbial Communities.PDF |
title_sort |
data_sheet_1_comparison of two 16s rrna primers (v3–v4 and v4–v5) for studies of arctic microbial communities.pdf |
publishDate |
2021 |
url |
https://doi.org/10.3389/fmicb.2021.637526.s001 https://figshare.com/articles/dataset/Data_Sheet_1_Comparison_of_Two_16S_rRNA_Primers_V3_V4_and_V4_V5_for_Studies_of_Arctic_Microbial_Communities_PDF/14036954 |
geographic |
Arctic Arctic Ocean |
geographic_facet |
Arctic Arctic Ocean |
genre |
Arctic Arctic Ocean Sea ice |
genre_facet |
Arctic Arctic Ocean Sea ice |
op_relation |
doi:10.3389/fmicb.2021.637526.s001 https://figshare.com/articles/dataset/Data_Sheet_1_Comparison_of_Two_16S_rRNA_Primers_V3_V4_and_V4_V5_for_Studies_of_Arctic_Microbial_Communities_PDF/14036954 |
op_rights |
CC BY 4.0 |
op_rightsnorm |
CC-BY |
op_doi |
https://doi.org/10.3389/fmicb.2021.637526.s001 |
_version_ |
1766309830233948160 |