title: Protist metabarcoding and environmental biomonitoring: Time for change.
abstract: High-throughput amplicon sequencing of environmental DNA and/or RNA proved to be a powerful tool to describe protist diversity. This new approach called also the metabarcoding has totally transformed our view of protist diversity, revealing a large number of novel lineages and expanding the range of protist phylogenetic diversity at almost every taxonomic level. However, until now the objectives of the vast majority of metabarcoding studies were purely academic. Practical applications of protist metabarcoding are surprisingly scarce, despite the fact that several groups of protists are commonly used as bioindicators of environmental impacts in freshwater or marine ecosystems. Here, we are reviewing studies that examine the ecological applications of metabarcoding for two groups of well-known protist bioindicators: diatoms and foraminifera. The results of these studies show that despite some biological and technical biases, molecular data quite faithfully reflect the morphology-based biotic indices and provide a similar assessment of ecosystem status. In view of these results, protist metabarcoding appears as a rapid and accurate tool for the evaluation of the quality of aquatic ecosystems. Hence, we plead for integration of protist metabarcoding in future biomonitoring projects as a complement of traditional methods and a source of new biosensors for environmental impact assessment.
authors.affiliation: Department of Genetics and Evolution, University of Geneva, 1211 Geneva, Switzerland. Electronic address: jan.pawlowski@unige.ch.
authors.forename: J
authors.initials: J
authors.lastname: Pawlowski
authors.affiliation: Department of Genetics and Evolution, University of Geneva, 1211 Geneva, Switzerland.
authors.forename: F
authors.initials: F
authors.lastname: Lejzerowicz
authors.affiliation: Department of Genetics and Evolution, University of Geneva, 1211 Geneva, Switzerland.
authors.forename: L
authors.initials: L
authors.lastname: Apotheloz-Perret-Gentil
authors.affiliation: ID-Gene Ecodiagnostics Ltd., 1228 Plan-les-Ouates, Switzerland.
authors.forename: J
authors.initials: J
authors.lastname: Visco
authors.affiliation: Department of Genetics and Evolution, University of Geneva, 1211 Geneva, Switzerland; IRCAM, UMR 9912, Université Pierre et Marie Curie, Paris, France.
authors.forename: P
authors.initials: P
authors.lastname: Esling
mesh_terms: D058893:DNA Barcoding, Taxonomic; D017377:Diatoms / Q000235:genetics; D004784:Environmental Monitoring / Q000379:methods*; D056890:Eukaryota / Q000145:classification* / Q000235:genetics*; D056908:Foraminifera / Q000235:genetics
keywords: Bioindicators; Diatoms; Environmental DNA; Foraminifera; Metabarcoding; Microbial eukaryotes