Research article

Assigning taxonomy and traits to DNA sequences of river diatoms in a region with limited taxonomic knowledge using the updated and annotated reference library Diat.barcode

¹ Instituto de Limnología “Dr. Raúl A. Ringuelet” ILPLA CONICET-UNLP, Bv. 120 y 62 n 1437, La Plata, Buenos Aires, Argentina
² UMR CARRTEL, INRAE, Université Savoie-Mont Blanc, 75bis av. de Corzent − CS 50511, 74203 Thonon les Bains cedex, France
³ MAPIEM, Université de Toulon, Toulon, France
⁴ Department of Environmental Chemistry, Eawag: Swiss Federal Institute of Aquatic Science and Technology, Überlandstr. 133, CH-8600 Dübendorf, Switzerland
⁵ MicPhyc, 88 chemin Manouilh, Ilet à Vidot 97433 Salazie, La Réunion
⁶ Swedish University of Agricultural Sciences, Department of Aquatic Sciences and Assessment, PO Box 7050, SE- 750 07 Uppsala, Sweden
⁷ Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland. Eawag, Swiss Federal Institute of Aquatic Science and Technology, Department of Aquatic Ecology, Überlandstrasse 133, CH-8600 Dübendorf, Switzerland
⁸ Bowburn Consultancy, 11 Monteigne Drive, Bowburn, Durham DH6 5QB, UK and School of Geography, University of Nottingham, Nottingham NG7 2RD
⁹ Department of Ecology, Faculty of Science, Charles University, Viničná 7, Prague 2, CZ-12844, Czech Republic
¹⁰ Royal Botanic Garden Edinburgh, 20A Inverleith Row, Edinburgh EH3 5LR, Scotland, UK
¹¹ Center for Marine Research, Ruder Boskovic Institute, Giordano Paliaga 5, 52210 Rovinj, Croatia
¹² IRTA, Marine and Continental Waters, Ctra Poble Nou km 5.5, La Ràpita, Catalonia, Spain
¹³ SCIMABIO Interface, 5 Rue des Quatre Ventes, 74200 Thonon-les-Bains
¹⁴ University of Belgrade, Institute of Chemistry, Technology and Metallurgy, National Institute of the Republic of Serbia, Njegoseva 12, 11000 Belgrade, Serbia
¹⁵ Luxembourg Institute of Science and Technology (LIST), Environmental Sensing and Modelling unit, Biodiversity Monitoring and Assessment group, 41 rue du Brill, L-4422 Belvaux, Luxembourg
¹⁶ Botanic Garden and Botanical Museum, Freie Universität Berlin, Königin-Luise-Str. 6-8, 14195 Berlin, Germany
¹⁷ Biodiversity and Palaeobiology Group, Agharkar Research Institute, Pune, 411004, India. Department of Botany, Savitribai Phule Pune University, Pune, Maharashtra - 411007, India

^* Corresponding author: mercedesnicolosi@ilpla.edu.ar

Received: 11 July 2025
Accepted: 13 October 2025

Abstract

We present a new version of a barcoding reference library dedicated to diatoms, Diat.barcode v12, with newly published sequences, annotated with ecological, and biological traits (size class, life forms, ecological guilds, etc) and curated by a college of experts. Diat.barcode incorporates rbcL data on all diatoms, though freshwater taxa are better represented. We used this library in two different areas, one where the taxonomic coverage of the library was good (mainland France) and another where it was poor (French Guyana) with about 320 diatom samples collected for river monitoring across both regions. We show that a direct bioinformatic assignment of environmental sequences to traits (ecological guilds, habitats, morphology) has great potential in French Guyana where species knowledge is poor and therefore the proportion of assigned environmental sequences is much lower (12.8%) than trait assignation (30%). We used co-correspondence analyses to show that, unlike mainland France where all species and trait assignation datasets were significantly correlated, in French Guyana only 7 out of 13 trait categories showed a significant correlation. This indicates a significant loss of ecological information through species assignment in French Guyana. Consequently, directly assigning environmental sequences to traits can be useful and provide more ecological information in regions with poor taxonomic knowledge because of the many rbcL sequences without taxonomic assignations.