Image_1_Influence of 16S rRNA Hypervariable Region on Estimates of Bacterial Diversity and Community Composition in Seawater and Marine Sediment.TIFF
To assess the influence of 16S ribosomal RNA (rRNA) tag choice on estimates of microbial diversity and/or community composition in seawater and marine sediment, we examined bacterial diversity and community composition from a site in the Central North Atlantic and a site in the Equatorial Pacific. F...
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ftfrontimediafig:oai:figshare.com:article/8874584 2023-05-15T17:35:10+02:00 Image_1_Influence of 16S rRNA Hypervariable Region on Estimates of Bacterial Diversity and Community Composition in Seawater and Marine Sediment.TIFF Zak Kerrigan John B. Kirkpatrick Steven D’Hondt 2019-07-16T07:25:34Z https://doi.org/10.3389/fmicb.2019.01640.s001 https://figshare.com/articles/Image_1_Influence_of_16S_rRNA_Hypervariable_Region_on_Estimates_of_Bacterial_Diversity_and_Community_Composition_in_Seawater_and_Marine_Sediment_TIFF/8874584 unknown doi:10.3389/fmicb.2019.01640.s001 https://figshare.com/articles/Image_1_Influence_of_16S_rRNA_Hypervariable_Region_on_Estimates_of_Bacterial_Diversity_and_Community_Composition_in_Seawater_and_Marine_Sediment_TIFF/8874584 CC BY 4.0 CC-BY Microbiology Microbial Genetics Microbial Ecology Mycology deep life deep biosphere marine sediment marine water column tag sequencing bacteria C-DEBI Image Figure 2019 ftfrontimediafig https://doi.org/10.3389/fmicb.2019.01640.s001 2019-07-17T23:01:37Z To assess the influence of 16S ribosomal RNA (rRNA) tag choice on estimates of microbial diversity and/or community composition in seawater and marine sediment, we examined bacterial diversity and community composition from a site in the Central North Atlantic and a site in the Equatorial Pacific. For each site, we analyzed samples from four zones in the water column, a seafloor sediment sample, and two subseafloor sediment horizons (with stratigraphic ages of 1.5 and 5.5 million years old). We amplified both the V4 and V6 hypervariable regions of the 16S rRNA gene and clustered the sequences into operational taxonomic units (OTUs) of 97% similarity to analyze for diversity and community composition. OTU richness is much higher with the V6 tag than with the V4 tag, and subsequently OTU-level community composition is quite different between the two tags. Vertical patterns of relative diversity are broadly the same for both tags, with maximum taxonomic richness in seafloor sediment and lowest richness in subseafloor sediment at both geographic locations. Genetic dissimilarity between sample locations is also broadly the same for both tags. Community composition is very similar for both tags at the class level, but very different at the level of 97% similar OTUs. Class-level diversity and community composition of water-column samples are very similar at each water depth between the Atlantic and Pacific. However, sediment communities differ greatly from the Atlantic site to the Pacific site. Finally, for relative patterns of diversity and class-level community composition, deep sequencing and shallow sequencing provide similar results. Still Image North Atlantic Frontiers: Figshare Pacific |
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Frontiers: Figshare |
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ftfrontimediafig |
language |
unknown |
topic |
Microbiology Microbial Genetics Microbial Ecology Mycology deep life deep biosphere marine sediment marine water column tag sequencing bacteria C-DEBI |
spellingShingle |
Microbiology Microbial Genetics Microbial Ecology Mycology deep life deep biosphere marine sediment marine water column tag sequencing bacteria C-DEBI Zak Kerrigan John B. Kirkpatrick Steven D’Hondt Image_1_Influence of 16S rRNA Hypervariable Region on Estimates of Bacterial Diversity and Community Composition in Seawater and Marine Sediment.TIFF |
topic_facet |
Microbiology Microbial Genetics Microbial Ecology Mycology deep life deep biosphere marine sediment marine water column tag sequencing bacteria C-DEBI |
description |
To assess the influence of 16S ribosomal RNA (rRNA) tag choice on estimates of microbial diversity and/or community composition in seawater and marine sediment, we examined bacterial diversity and community composition from a site in the Central North Atlantic and a site in the Equatorial Pacific. For each site, we analyzed samples from four zones in the water column, a seafloor sediment sample, and two subseafloor sediment horizons (with stratigraphic ages of 1.5 and 5.5 million years old). We amplified both the V4 and V6 hypervariable regions of the 16S rRNA gene and clustered the sequences into operational taxonomic units (OTUs) of 97% similarity to analyze for diversity and community composition. OTU richness is much higher with the V6 tag than with the V4 tag, and subsequently OTU-level community composition is quite different between the two tags. Vertical patterns of relative diversity are broadly the same for both tags, with maximum taxonomic richness in seafloor sediment and lowest richness in subseafloor sediment at both geographic locations. Genetic dissimilarity between sample locations is also broadly the same for both tags. Community composition is very similar for both tags at the class level, but very different at the level of 97% similar OTUs. Class-level diversity and community composition of water-column samples are very similar at each water depth between the Atlantic and Pacific. However, sediment communities differ greatly from the Atlantic site to the Pacific site. Finally, for relative patterns of diversity and class-level community composition, deep sequencing and shallow sequencing provide similar results. |
format |
Still Image |
author |
Zak Kerrigan John B. Kirkpatrick Steven D’Hondt |
author_facet |
Zak Kerrigan John B. Kirkpatrick Steven D’Hondt |
author_sort |
Zak Kerrigan |
title |
Image_1_Influence of 16S rRNA Hypervariable Region on Estimates of Bacterial Diversity and Community Composition in Seawater and Marine Sediment.TIFF |
title_short |
Image_1_Influence of 16S rRNA Hypervariable Region on Estimates of Bacterial Diversity and Community Composition in Seawater and Marine Sediment.TIFF |
title_full |
Image_1_Influence of 16S rRNA Hypervariable Region on Estimates of Bacterial Diversity and Community Composition in Seawater and Marine Sediment.TIFF |
title_fullStr |
Image_1_Influence of 16S rRNA Hypervariable Region on Estimates of Bacterial Diversity and Community Composition in Seawater and Marine Sediment.TIFF |
title_full_unstemmed |
Image_1_Influence of 16S rRNA Hypervariable Region on Estimates of Bacterial Diversity and Community Composition in Seawater and Marine Sediment.TIFF |
title_sort |
image_1_influence of 16s rrna hypervariable region on estimates of bacterial diversity and community composition in seawater and marine sediment.tiff |
publishDate |
2019 |
url |
https://doi.org/10.3389/fmicb.2019.01640.s001 https://figshare.com/articles/Image_1_Influence_of_16S_rRNA_Hypervariable_Region_on_Estimates_of_Bacterial_Diversity_and_Community_Composition_in_Seawater_and_Marine_Sediment_TIFF/8874584 |
geographic |
Pacific |
geographic_facet |
Pacific |
genre |
North Atlantic |
genre_facet |
North Atlantic |
op_relation |
doi:10.3389/fmicb.2019.01640.s001 https://figshare.com/articles/Image_1_Influence_of_16S_rRNA_Hypervariable_Region_on_Estimates_of_Bacterial_Diversity_and_Community_Composition_in_Seawater_and_Marine_Sediment_TIFF/8874584 |
op_rights |
CC BY 4.0 |
op_rightsnorm |
CC-BY |
op_doi |
https://doi.org/10.3389/fmicb.2019.01640.s001 |
_version_ |
1766134235974860800 |