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Environmental rRNA inventories miss over half of protistan diversity
BACKGROUND: The main tool to discover novel microbial eukaryotes is the rRNA approach. This approach has important biases, including PCR discrimination against certain rRNA gene species, which makes molecular inventories skewed relative to the source communities. The degree of this bias has not been...
Autores principales: | , , , , , |
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Formato: | Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2008
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2625359/ https://www.ncbi.nlm.nih.gov/pubmed/19087295 http://dx.doi.org/10.1186/1471-2180-8-222 |
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author | Jeon, Sunok Bunge, John Leslin, Chesley Stoeck, Thorsten Hong, Sunhee Epstein, Slava S |
author_facet | Jeon, Sunok Bunge, John Leslin, Chesley Stoeck, Thorsten Hong, Sunhee Epstein, Slava S |
author_sort | Jeon, Sunok |
collection | PubMed |
description | BACKGROUND: The main tool to discover novel microbial eukaryotes is the rRNA approach. This approach has important biases, including PCR discrimination against certain rRNA gene species, which makes molecular inventories skewed relative to the source communities. The degree of this bias has not been quantified, and it remains unclear whether species missed from clone libraries could be recovered by increasing sequencing efforts, or whether they cannot be detected in principle. Here we attempt to discriminate between these possibilities by statistically analysing four protistan inventories obtained using different general eukaryotic PCR primers. RESULTS: We show that each PCR primer set-specific clone library is not a sample from the community diversity but rather from a fraction of this diversity. Therefore, even sequencing such clone libraries to saturation would only recover that fraction, which, according to the parametric models, varies between 17 ± 4% to 49 ± 10%, depending on the set of primers. The pooled data is thus qualitatively richer than individual libraries, even if normalized to the same sequencing effort. CONCLUSION: The use of a single pair of primers leads to significant underestimation of the true community richness at all levels of taxonomic hierarchy. The majority of available protistan rRNA gene surveys likely sampled less than half of the target diversity, and might have completely missed the rest. The use of multiple PCR primers reduces this bias but does not necessarily eliminate it. |
format | Text |
id | pubmed-2625359 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2008 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-26253592009-01-14 Environmental rRNA inventories miss over half of protistan diversity Jeon, Sunok Bunge, John Leslin, Chesley Stoeck, Thorsten Hong, Sunhee Epstein, Slava S BMC Microbiol Research Article BACKGROUND: The main tool to discover novel microbial eukaryotes is the rRNA approach. This approach has important biases, including PCR discrimination against certain rRNA gene species, which makes molecular inventories skewed relative to the source communities. The degree of this bias has not been quantified, and it remains unclear whether species missed from clone libraries could be recovered by increasing sequencing efforts, or whether they cannot be detected in principle. Here we attempt to discriminate between these possibilities by statistically analysing four protistan inventories obtained using different general eukaryotic PCR primers. RESULTS: We show that each PCR primer set-specific clone library is not a sample from the community diversity but rather from a fraction of this diversity. Therefore, even sequencing such clone libraries to saturation would only recover that fraction, which, according to the parametric models, varies between 17 ± 4% to 49 ± 10%, depending on the set of primers. The pooled data is thus qualitatively richer than individual libraries, even if normalized to the same sequencing effort. CONCLUSION: The use of a single pair of primers leads to significant underestimation of the true community richness at all levels of taxonomic hierarchy. The majority of available protistan rRNA gene surveys likely sampled less than half of the target diversity, and might have completely missed the rest. The use of multiple PCR primers reduces this bias but does not necessarily eliminate it. BioMed Central 2008-12-16 /pmc/articles/PMC2625359/ /pubmed/19087295 http://dx.doi.org/10.1186/1471-2180-8-222 Text en Copyright © 2008 Jeon et al; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( (http://creativecommons.org/licenses/by/2.0) ), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Research Article Jeon, Sunok Bunge, John Leslin, Chesley Stoeck, Thorsten Hong, Sunhee Epstein, Slava S Environmental rRNA inventories miss over half of protistan diversity |
title | Environmental rRNA inventories miss over half of protistan diversity |
title_full | Environmental rRNA inventories miss over half of protistan diversity |
title_fullStr | Environmental rRNA inventories miss over half of protistan diversity |
title_full_unstemmed | Environmental rRNA inventories miss over half of protistan diversity |
title_short | Environmental rRNA inventories miss over half of protistan diversity |
title_sort | environmental rrna inventories miss over half of protistan diversity |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2625359/ https://www.ncbi.nlm.nih.gov/pubmed/19087295 http://dx.doi.org/10.1186/1471-2180-8-222 |
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