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Primer selection impacts specific population abundances but not community dynamics in a monthly time‐series 16S rRNA gene amplicon analysis of coastal marine bacterioplankton
Primers targeting the 16S small subunit ribosomal RNA marker gene, used to characterize bacterial and archaeal communities, have recently been re‐evaluated for marine planktonic habitats. To investigate whether primer selection affects the ecological interpretation of bacterioplankton populations an...
Autores principales: | , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
John Wiley and Sons Inc.
2018
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6175402/ https://www.ncbi.nlm.nih.gov/pubmed/29521439 http://dx.doi.org/10.1111/1462-2920.14091 |
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author | Wear, Emma K. Wilbanks, Elizabeth G. Nelson, Craig E. Carlson, Craig A. |
author_facet | Wear, Emma K. Wilbanks, Elizabeth G. Nelson, Craig E. Carlson, Craig A. |
author_sort | Wear, Emma K. |
collection | PubMed |
description | Primers targeting the 16S small subunit ribosomal RNA marker gene, used to characterize bacterial and archaeal communities, have recently been re‐evaluated for marine planktonic habitats. To investigate whether primer selection affects the ecological interpretation of bacterioplankton populations and community dynamics, amplicon sequencing with four primer sets targeting several hypervariable regions of the 16S rRNA gene was conducted on both mock communities constructed from cloned 16S rRNA genes and a time‐series of DNA samples from the temperate coastal Santa Barbara Channel. Ecological interpretations of community structure (delineation of depth and seasonality, correlations with environmental factors) were similar across primer sets, while population dynamics varied. We observed substantial differences in relative abundances of taxa known to be poorly resolved by some primer sets, such as Thaumarchaeota and SAR11, and unexpected taxa including Roseobacter clades. Though the magnitude of relative abundances of common OTUs differed between primer sets, the relative abundances of the OTUs were nonetheless strongly correlated. We do not endorse one primer set but rather enumerate strengths and weaknesses to facilitate selection appropriate to a system or experimental goal. While 16S rRNA gene primer bias suggests caution in assessing quantitative population dynamics, community dynamics appear robust across studies using different primers. |
format | Online Article Text |
id | pubmed-6175402 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2018 |
publisher | John Wiley and Sons Inc. |
record_format | MEDLINE/PubMed |
spelling | pubmed-61754022018-10-19 Primer selection impacts specific population abundances but not community dynamics in a monthly time‐series 16S rRNA gene amplicon analysis of coastal marine bacterioplankton Wear, Emma K. Wilbanks, Elizabeth G. Nelson, Craig E. Carlson, Craig A. Environ Microbiol Research Articles Primers targeting the 16S small subunit ribosomal RNA marker gene, used to characterize bacterial and archaeal communities, have recently been re‐evaluated for marine planktonic habitats. To investigate whether primer selection affects the ecological interpretation of bacterioplankton populations and community dynamics, amplicon sequencing with four primer sets targeting several hypervariable regions of the 16S rRNA gene was conducted on both mock communities constructed from cloned 16S rRNA genes and a time‐series of DNA samples from the temperate coastal Santa Barbara Channel. Ecological interpretations of community structure (delineation of depth and seasonality, correlations with environmental factors) were similar across primer sets, while population dynamics varied. We observed substantial differences in relative abundances of taxa known to be poorly resolved by some primer sets, such as Thaumarchaeota and SAR11, and unexpected taxa including Roseobacter clades. Though the magnitude of relative abundances of common OTUs differed between primer sets, the relative abundances of the OTUs were nonetheless strongly correlated. We do not endorse one primer set but rather enumerate strengths and weaknesses to facilitate selection appropriate to a system or experimental goal. While 16S rRNA gene primer bias suggests caution in assessing quantitative population dynamics, community dynamics appear robust across studies using different primers. John Wiley and Sons Inc. 2018-04-06 2018-08 /pmc/articles/PMC6175402/ /pubmed/29521439 http://dx.doi.org/10.1111/1462-2920.14091 Text en © 2018 The Authors. Environmental Microbiology published by Society for Applied Microbiology and John Wiley & Sons Ltd. This is an open access article under the terms of the http://creativecommons.org/licenses/by-nc/4.0/ License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited and is not used for commercial purposes. |
spellingShingle | Research Articles Wear, Emma K. Wilbanks, Elizabeth G. Nelson, Craig E. Carlson, Craig A. Primer selection impacts specific population abundances but not community dynamics in a monthly time‐series 16S rRNA gene amplicon analysis of coastal marine bacterioplankton |
title | Primer selection impacts specific population abundances but not community dynamics in a monthly time‐series 16S rRNA gene amplicon analysis of coastal marine bacterioplankton |
title_full | Primer selection impacts specific population abundances but not community dynamics in a monthly time‐series 16S rRNA gene amplicon analysis of coastal marine bacterioplankton |
title_fullStr | Primer selection impacts specific population abundances but not community dynamics in a monthly time‐series 16S rRNA gene amplicon analysis of coastal marine bacterioplankton |
title_full_unstemmed | Primer selection impacts specific population abundances but not community dynamics in a monthly time‐series 16S rRNA gene amplicon analysis of coastal marine bacterioplankton |
title_short | Primer selection impacts specific population abundances but not community dynamics in a monthly time‐series 16S rRNA gene amplicon analysis of coastal marine bacterioplankton |
title_sort | primer selection impacts specific population abundances but not community dynamics in a monthly time‐series 16s rrna gene amplicon analysis of coastal marine bacterioplankton |
topic | Research Articles |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6175402/ https://www.ncbi.nlm.nih.gov/pubmed/29521439 http://dx.doi.org/10.1111/1462-2920.14091 |
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