Microbial Ecology

, Volume 70, Issue 4, pp 865–875 | Cite as

Is Planktonic Diversity Well Recorded in Sedimentary DNA? Toward the Reconstruction of Past Protistan Diversity

  • Eric Capo
  • Didier Debroas
  • Fabien Arnaud
  • Isabelle DomaizonEmail author
Microbiology of Aquatic Systems


Studies based on the coupling of a paleolimnological approach and molecular tools (e.g., sequencing of sedimentary DNA) present a promising opportunity to obtain long-term data on past lacustrine biodiversity. However, certain validations are still required, such as the evaluation of DNA preservation in sediments for various planktonic taxa that do not leave any morphological diagnostic features. In this study, we focused on the diversity of planktonic unicellular eukaryotes and verified the presence of their DNA in sediment archives. We compared the molecular inventories (high-throughput sequencing of 18S ribosomal DNA) obtained from monitoring the water column with those obtained for DNA archived in the first 30 cm of sediment. Seventy-one percent of taxonomic units found in the water samples were detected in sediment samples, including pigmented taxa, such as Chlorophyta, Dinophyceae, and Chrysophyceae, phagotrophic taxa, such as Ciliophora, parasitic taxa, such as Apicomplexa and Chytridiomycota, and saprotrophs, such as Cryptomycota. Parallel analysis of 18S ribosomal RNA (rRNA) transcripts revealed the presence of living eukaryotic taxa only in the top 2 cm of sediment; although some limits exist in using RNA/DNA ratio as indicator of microbial activity, these results suggested that the sedimentary DNA mostly represented DNA from past and inactive communities. Only the diversity of a few groups, such as Cryptophyta and Haptophyta, seemed to be poorly preserved in sediments. Our overall results showed that the application of sequencing techniques to sedimentary DNA could be used to reconstruct past diversity for numerous planktonic eukaryotic groups.


Paleolimnology Sedimentary DNA Protists Plankton 454 sequencing 



For financial support, we thank the EC2CO INSU program (France), who supported the program “REPLAY” and INRA EFPA, who supported the program “CADILAC.” We also benefited from the database on deep peri-alpine lakes observations (SOERE OLA; © SOERE OLA-IS, INRA Thonon-les-Bains, CISALB, Eco-Informatique ORE de l’INRA) and support from ALLENVI for DNA monitoring in lakes. For their technical help in the field, we thank the EDYTEM (CNRS) staff who participated in the sediment coring on Lake Bourget, and P Perney and G Paolini, who performed the water sampling on Lake Bourget. C. Chardon, L. Jacas and B. Leberre brought their technical support for molecular analyses. We thank the Région Rhône-Alpes for their financial support of the PhD thesis of E Capo. English language corrections were performed using the “English Language Editing” Elsevier service and American Manuscript Editors. We are grateful for the useful comments and suggestions from two anonymous reviewers.

Conflict of Interest

The authors declare no conflicts of interest.

Supplementary material

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Copyright information

© Springer Science+Business Media New York 2015

Authors and Affiliations

  • Eric Capo
    • 1
    • 2
  • Didier Debroas
    • 3
  • Fabien Arnaud
    • 4
  • Isabelle Domaizon
    • 1
    Email author
  1. 1.INRA, UMR 42 CARRTELThonon-les-bains CedexFrance
  2. 2.Université Savoie Mont Blanc, UMR 42 CARRTELLe Bourget du LacFrance
  3. 3.Clermont Université, Université Blaise Pascal, CNRS, UMR 6023 LMGEAubièreFrance
  4. 4.CNRS, UMR 5204 EDYTEMUniversité Savoie Mont BlancLe Bourget du Lac CedexFrance

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