Medinger, Ralph; Nolte, Viola; Panday, Ram Vinay; Jost, Steffen Oliver; Ottenwälder, Birgit; Schlötterer, Christian; Boenigk, Jens:
Diversity in a hidden world : potential and limitation of next-generation sequencing for surveys of molecular diversity of eukaryotic microorganisms
2010
In: Molecular Ecology, Jg. 19 (2010), Heft Supplement s1, S. 32 - 40
Artikel/Aufsatz in Zeitschrift / Fach: Biologie
Fakultät für Biologie » Allgemeine Botanik
Titel:
Diversity in a hidden world : potential and limitation of next-generation sequencing for surveys of molecular diversity of eukaryotic microorganisms
Autor(in):
Medinger, Ralph; Nolte, Viola; Panday, Ram Vinay; Jost, Steffen Oliver im Online-Personal- und -Vorlesungsverzeichnis LSF anzeigen; Ottenwälder, Birgit; Schlötterer, Christian; Boenigk, Jens im Online-Personal- und -Vorlesungsverzeichnis LSF anzeigen
Erscheinungsjahr:
2010
Erschienen in:
Molecular Ecology, Jg. 19 (2010), Heft Supplement s1, S. 32 - 40
ISSN:
DOI:
Link URL:

Abstract:

With the delivery of millions of sequence reads in a single experiment, next-generation sequencing (NGS) is currently revolutionizing surveys of microorganism diversity. In particular, when applied to Eukaryotes, we are still lacking a rigorous comparison of morphological and NGS-based diversity estimates. In this report, we studied the diversity and the seasonal community turnover of alveolates (Ciliophora and Dinophyceae) in an oligotrophic freshwater lake by SSU amplicon sequencing with NGS as well as by classical morphological analysis. We complemented the morphological analysis by single-cell PCR followed by Sanger sequencing to provide an unambiguous link to the NGS data. We show that NGS and morphological analyses generally capture frequency shifts of abundant taxa over our seasonal samples. The observed incongruencies are probably largely due to rDNA copy number variation among taxa and heterogeneity in the efficiency of cell lysis. Overall, NGS-based amplicon sequencing was superior in detecting rare species. We propose that in the absence of other nuclear markers less susceptible to copy number variation, rDNA-based diversity studies need to be adjusted for confounding effects of copy number variation.