Cited by 685Microbial Community Ecology and PhysiologyEnvironmental DNA in Biodiversity StudiesGenomics and Phylogenetic Studies

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Strengths and Limitations of 16S rRNA Gene Amplicon Sequencing in Revealing Temporal Microbial Community Dynamics

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Poretsky, Rachel, Rodriguez-R, Luis M., Luo, Chengwei, Tsementzi, Despina, Konstantinidis, Konstantinos T.·2014·PLoS ONE

DOI 10.1371/journal.pone.0093827PMC PMC3979728

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Abstract

This study explored the short-term planktonic microbial community structure and resilience in Lake Lanier (GA, USA) while simultaneously evaluating the technical aspects of identifying taxa via 16S rRNA gene amplicon and metagenomic sequence data. 16S rRNA gene amplicons generated from four temporally discrete samples were sequenced with 454 GS-FLX-Ti yielding ∼40,000 rRNA gene sequences from each sample and representing ∼300 observed OTUs. Replicates obtained from the same biological sample clustered together but several biases were observed, linked to either the PCR or sequencing-preparation steps. In comparisons with companion whole-community shotgun metagenome datasets, the estimated number of OTUs at each timepoint was concordant, but 1.5 times and ∼10 times as many phyla and genera, respectively, were identified in the metagenomes. Our analyses showed that the 16S rRNA gene captures broad shifts in community diversity over time, but with limited resolution and lower sensitivity compared to metagenomic data. We also identified OTUs that showed marked shifts in abundance over four close timepoints separated by perturbations and tracked these taxa in the metagenome vs. 16S rRNA amplicon data. A strong summer storm had less of an effect on community composition than did seasonal mixing, which revealed a distinct succession of organisms. This study provides insights into freshwater microbial communities and advances the approaches for assessing community diversity and dynamics in situ.

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Authors: Poretsky, R., Rodriguez-R, L. M., Luo, C., Tsementzi, D., & Konstantinidis, K. T.
Affiliations: Georgia Institute of Technology (US)
Corresponding author: Poretsky, Rachel
ORCID: Poretsky, Rachel
Luo, Chengwei
Tsementzi, Despina
Konstantinidis, Konstantinos T.
Venue: PLoS ONE
Publisher: Public Library of Science (PLoS)
Published: 2014-04-08
Volume: 9
Issue: 4
Pages: e93827
ISSN: 1932-6203 (ISSN-L)
DOI: 10.1371/journal.pone.0093827
PMC: PMC3979728
OpenAlex: W2019163239
Cited by: 684
References: 63
Citations by year: 2026: 50 · 2025: 70 · 2024: 45 · 2023: 78 · 2022: 71 · 2021: 83 · 2020: 69 · 2019: 67 · 2018: 62 · 2017: 37 · 2016: 29 · 2015: 20 · 2014: 2
FWCI: 25.43
Type: journal article
Language: en
Open access: gold
doi.org
Licence: cc-by
creativecommons.org/licenses/by/4.0/ (unspecified)
Locations: PLoS ONE (publishedVersion, cc-by)
Europe PMC (PubMed Central) (publishedVersion, other-oa)
PubMed Central (publishedVersion, cc-by)
PubMed (publishedVersion)
OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information) (submittedVersion)
DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
Funders: National Science Foundation (1241046)
U.S. Department of Energy (DESC0006662)
Emory University
Topics: Physical Sciences › Environmental Science › Ecology › Microbial Community Ecology and Physiology
Physical Sciences › Environmental Science › Ecology › Environmental DNA in Biodiversity Studies
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
Keywords: 16S rRNA gene amplicon sequencing, metagenomics, planktonic microbial communities, freshwater microbial communities, Lake Lanier, community resilience, sequencing bias, PCR bias, seasonal mixing, storm disturbance, microbial succession, community diversity
MeSH terms: Bacteria, Fresh Water, Plankton, RNA, Ribosomal, 16S, Metagenome, Metagenomics

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Strengths and Limitations of 16S rRNA Gene Amplicon Sequencing in Revealing Temporal Microbial Community Dynamics

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