A morphogenetic survey on ciliate plankton from a mountain lake pinpoints the necessity of lineage-specific barcode markers in microbial ecology
Article first published online: 15 JUL 2013
© 2013 The Authors. Environmental Microbiology published by Society for Applied Microbiology and John Wiley & Sons Ltd.
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Thematic Issue: Protists
Volume 16, Issue 2, pages 430–444, February 2014
How to Cite
Stoeck, T., Breiner, H.-W., Filker, S., Ostermaier, V., Kammerlander, B. and Sonntag, B. (2014), A morphogenetic survey on ciliate plankton from a mountain lake pinpoints the necessity of lineage-specific barcode markers in microbial ecology. Environmental Microbiology, 16: 430–444. doi: 10.1111/1462-2920.12194
- Issue published online: 27 JAN 2014
- Article first published online: 15 JUL 2013
- Accepted manuscript online: 19 JUN 2013 06:38AM EST
- Manuscript Revised: 11 JUN 2013
- Manuscript Accepted: 11 JUN 2013
- Manuscript Received: 9 APR 2013
- Austrian Science Fund (FWF). Grant Numbers: P21013-B03, P16559-B06
- Deutsche Forschungsgemeinschaft (DFG). Grant Number: STO414/3-2
Analyses of high-throughput environmental sequencing data have become the ‘gold-standard’ to address fundamental questions of microbial diversity, ecology and biogeography. Findings that emerged from sequencing are, e.g. the discovery of the extensive ‘rare microbial biosphere’ and its potential function as a seed-bank. Even though applied since several years, results from high-throughput environmental sequencing have hardly been validated. We assessed how well pyrosequenced amplicons [the hypervariable eukaryotic V4 region of the small subunit ribosomal RNA (SSU rRNA) gene] reflected morphotype ciliate plankton. Moreover, we assessed if amplicon sequencing had the potential to detect the annual ciliate plankton stock. In both cases, we identified significant quantitative and qualitative differences. Our study makes evident that taxon abundance distributions inferred from amplicon data are highly biased and do not mirror actual morphotype abundances at all. Potential reasons included cell losses after fixation, cryptic morphotypes, resting stages, insufficient sequence data availability of morphologically described species and the unsatisfying resolution of the V4 SSU rRNA fragment for accurate taxonomic assignments. The latter two underline the necessity of barcoding initiatives for eukaryotic microbes to better and fully exploit environmental amplicon data sets, which then will also allow studying the potential of seed-bank taxa as a buffer for environmental changes.