title: Taxonomy-free molecular diatom index for high-throughput eDNA biomonitoring.
abstract: Current biodiversity assessment and biomonitoring are largely based on the morphological identification of selected bioindicator taxa. Recently, several attempts have been made to use eDNA metabarcoding as an alternative tool. However, until now, most applied metabarcoding studies have been based on the taxonomic assignment of sequences that provides reference to morphospecies ecology. Usually, only a small portion of metabarcoding data can be used due to a limited reference database and a lack of phylogenetic resolution. Here, we investigate the possibility to overcome these limitations using a taxonomy-free approach that allows the computing of a molecular index directly from eDNA data without any reference to morphotaxonomy. As a case study, we use the benthic diatoms index, commonly used for monitoring the biological quality of rivers and streams. We analysed 87 epilithic samples from Swiss rivers, the ecological status of which was established based on the microscopic identification of diatom species. We compared the diatom index derived from eDNA data obtained with or without taxonomic assignment. Our taxonomy-free approach yields promising results by providing a correct assessment for 77% of examined sites. The main advantage of this method is that almost 95% of OTUs could be used for index calculation, compared to 35% in the case of the taxonomic assignment approach. Its main limitations are under-sampling and the need to calibrate the index based on the microscopic assessment of diatoms communities. However, once calibrated, the taxonomy-free molecular index can be easily standardized and applied in routine biomonitoring, as a complementary tool allowing fast and cost-effective assessment of the biological quality of watercourses.
authors.affiliation: Department of Genetics and Evolution, University of Geneva, boulevard d'Yvoy 4, 1205, Geneva, Switzerland.
authors.forename: Laure
authors.identifier: http://orcid.org/0000-0002-8592-3079
authors.initials: L
authors.lastname: Apothéloz-Perret-Gentil
authors.affiliation: Water Ecology Service, Department of Territorial Management, Canton of Geneva, avenue de Sainte-Clotilde 23, 1211, Geneva, Switzerland.
authors.forename: Arielle
authors.initials: A
authors.lastname: Cordonier
authors.affiliation: PhycoEco, Rue des XXII-Cantons 39, 2300, La Chaux-de-Fonds, Switzerland.
authors.forename: François
authors.initials: F
authors.lastname: Straub
authors.affiliation: PhycoEco, Rue des XXII-Cantons 39, 2300, La Chaux-de-Fonds, Switzerland.
authors.forename: Jennifer
authors.initials: J
authors.lastname: Iseli
authors.affiliation: IRCAM, UMR 9912, Université Pierre et Marie Curie, place Igor Stravinsky 1, 75004, Paris, France.
authors.forename: Philippe
authors.initials: P
authors.lastname: Esling
authors.affiliation: Department of Genetics and Evolution, University of Geneva, boulevard d'Yvoy 4, 1205, Geneva, Switzerland.
authors.forename: Jan
authors.initials: J
authors.lastname: Pawlowski
mesh_terms: D044822:Biodiversity; D058893:DNA Barcoding, Taxonomic / Q000379:methods*; D017377:Diatoms / Q000145:classification / Q000235:genetics*; D056186:Metagenomics / Q000379:methods*; D045483:Rivers / Q000382:microbiology; D013557:Switzerland
keywords: bioindication; environmental DNA; metabarcoding; water quality