Fottea

Fottea 2018, 18(1):37-54 | DOI: 10.5507/fot.2017.013

The potential of High-Throughput Sequencing (HTS) of natural samples as a source of primary taxonomic information for reference libraries of diatom barcodes

Frédéric Rimet^1,2*, Nelida Abarca³, Agnès Bouchez^1,2, Wolf-Henning Kusber³, Regine Jahn³, Maria Kahlert⁴, François Keck⁴, Martyn G. Kelly⁵, David. G. Mann⁶, André Piuz⁷, Rosa Trobajo⁸, Kalman Tapolczai^1,2, Valentin Vasselon^1,2, Jonas Zimmermann³

¹ INRA - UMR Carrtel, FR-74200 Thonon-les-Bains, France; ^* Corresponding author e-mail: frederic.rimet@inra.fr

² Université Savoie Mont Blanc, UMR, 73000 Carrtel Chambéry, France

³ Botanischer Garten und Botanisches Museum Berlin-Dahlem, Freie Universität Berlin, Königin-Luise-Str. 6-8, 14195 Berlin, Germany

⁴ Swedish University of Agricultural Sciences, Department of Aquatic Sciences and Assessment, PO Box 7050, SE- 750 07 Uppsala, Sweden

⁵ Bowburn Consultancy, 11 Monteigne Drive, Bowburn, Durham DH6 5QB, UK

⁶ Royal Botanic Garden Edinburgh, Edinburgh, EH3 5LR, Scotland, UK

⁷ Muséum d'Histoire Naturelle, Route de Malagnou 1, Case postale 6434, CH-1211 Genève 6, Switzerland

⁸ Aquatic Ecosystems, Institute for Food and Agricultural Research and Technology (IRTA), Crta de Poble Nou Km 5.5, Sant Carles de la Ràpita, Catalonia, Spain

Diatoms are used routinely to assess pollution level in rivers and lakes. Current methods are based on identification by light microscopy, which is laborious. An alternative is to identify species based on short DNA fragments and High-Throughput Sequencing (HTS). However a potential limitation is the incomplete coverage of species in reference barcode libraries. Usually these libraries are compiled by isolating cells, before culturing and sequencing them, which is tedious and often unsuccessful. Here we propose the use of rbcL sequences from environmental samples analysed by HTS. We set several criteria to ensure good sequence quality and correspondence with the target species observed in microscopy: the sequence needed to be abundant in the sample, and with no insertions nor deletions or stop codon, phylogenetic neighbour taxa had to correspond to neighbour taxonomic taxa expected from morphological observations. Four species from tropical rivers are given as examples, including one that is new to science.

Keywords: algae, Bacillariophyta, biomonitoring, data traceability, DNA barcoding, eDNA, ecosystem assessment, metabarcoding, pollution, Water Framework Directive

Received: January 26, 2017; Accepted: April 11, 2017; Prepublished online: February 27, 2018; Published: March 31, 2018Show citation