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Hydrobiologia

, Volume 807, Issue 1, pp 37–51 | Cite as

Metabarcoding of lake benthic diatoms: from structure assemblages to ecological assessment

  • S. F. Rivera
  • V. Vasselon
  • S. Jacquet
  • A. Bouchez
  • D. Ariztegui
  • F. Rimet
Primary Research Paper

Abstract

Benthic diatoms are relevant indicators of the ecological status of the littoral zone of lakes. Their use as bio-indicators is based on their morphological identification at species level using microscopy which is time consuming, requires taxonomic expertise, and is consequently expensive. To overcome these limitations, a molecular approach for diatom identification has been tested with success in rivers. DNA metabarcoding enables species identification from a standardized DNA barcode and high-throughput sequencing (HTS), using DNA reference library. The suitability of the morphological and molecular approaches to assess the diatom community structure and the ecological status of the littoral zone of the largest deep lake in France (Lake Bourget) was compared. 66 sites were sampled in August 2015 along the shoreline, all around the lake. The composition of diatom assemblages was similar with both morphological and molecular approaches, and diatom assemblages were structured by the same environmental factors. However, the ecological status of Lake Bourget differed significantly among approaches since floristic inventories to species level also differed significantly. The main source of this difference was the incompleteness of the DNA reference library. Nevertheless, in a near future, when this constraint will be solved, the use of DNA metabarcoding for biomonitoring purposes seems promising.

Keywords

Algae Benthic biomonitoring Eutrophication High-throughput sequencing Lake Bourget Pollution 

Notes

Acknowledgements

The data presented herein is part of a master thesis in environmental sciences presented at the University of Geneva by the first author. The first author is in debt to the Simon I. Patiño Foundation for awarding the scholarship to undertake a Master in Environmental Sciences at the University of Geneva. We thank Lea Féret and Victor Frossard for the sample collection. We also thank the CISALB (Comité Intersyndical pour l’Assainissement du Lac du Bourget) for financing part of the study. The authors also acknowledge the European COST network DNAqua-Net (CA15219) as a fruitful scientific discussion space on molecular approaches for biomonitoring.

Supplementary material

10750_2017_3381_MOESM1_ESM.docx (13 kb)
Supplementary material 1 (DOCX 12 kb) Supplementary data 1. Results of the assessment of the ecological status of the littoral zone of Lake Bourget according to the three diatom indices: IPS, EPI-L and S
10750_2017_3381_MOESM2_ESM.docx (51 kb)
Supplementary material 2 (DOCX 50 kb) Supplementary data 2. Comparison between diatom taxa detected with the morphological (LM) and the molecular approach (Metabarcoding)

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Copyright information

© Springer International Publishing AG 2017

Authors and Affiliations

  • S. F. Rivera
    • 1
  • V. Vasselon
    • 2
  • S. Jacquet
    • 2
  • A. Bouchez
    • 2
  • D. Ariztegui
    • 3
  • F. Rimet
    • 2
  1. 1.Institute for Environmental SciencesUniversity of GenevaGenevaSwitzerland
  2. 2.CARRTEL, INRAUniversité de Savoie Mont BlancThonon les bains CedexFrance
  3. 3.Section of Earth & Environmental SciencesUniversity of GenevaGenevaSwitzerland

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