title: Long-term dynamics in microbial eukaryotes communities: a palaeolimnological view based on sedimentary DNA.
abstract: Assessing the extent to which changes in lacustrine biodiversity are affected by anthropogenic or climatic forces requires extensive palaeolimnological data. We used high-throughput sequencing to generate time-series data encompassing over 2200 years of microbial eukaryotes (protists and Fungi) diversity changes from the sedimentary DNA record of two lakes (Lake Bourget in French Alps and Lake Igaliku in Greenland). From 176 samples, we sequenced a large diversity of microbial eukaryotes, with a total 16 386 operational taxonomic units distributed within 50 phylogenetic groups. Thus, microbial groups, such as Chlorophyta, Dinophyceae, Haptophyceae and Ciliophora, that were not previously considered in lacustrine sediment record analyses appeared to be potential biological markers of trophic status changes. Our data suggest that shifts in relative abundance of extant species, including shifts between rare and abundant taxa, drive ecosystem responses to local and global environmental changes. Community structure shift events were concomitant with major climate variations (more particularly in Lake Igaliku). However, this study shows that the impacts of climatic fluctuations may be overpassed by the high-magnitude eutrophication impacts, as observed in the eutrophicated Lake Bourget. Overall, our data show that DNA preserved in sediment constitutes a precious archive of information on past biodiversity changes.
authors.affiliation: CARRTEL, INRA, Université de Savoie Mont Blanc, 74200, Thonon-les-bains, France.
authors.forename: Eric
authors.initials: E
authors.lastname: Capo
authors.affiliation: Université Clermont Auvergne, Laboratoire "Microorganismes: Génome et Environnement", Université Blaise Pascal, BP 10448, F-63000, Clermont-Ferrand, France.|CNRS, UMR 6023, LMGE, Campus Universitaire des Cézeaux 63171, Aubière, France.
authors.forename: Didier
authors.initials: D
authors.lastname: Debroas
authors.affiliation: CNRS, UMR 5204 EDYTEM, Université Savoie Mont Blanc, 5 Boulevard de la mer Caspienne, 73376 Le Bourget du Lac Cedex, France.
authors.forename: Fabien
authors.initials: F
authors.lastname: Arnaud
authors.affiliation: Laboratoire Chrono-Environnement, UMR 6249 CNRS, Université de Bourgogne Franche-Comté, 16 Route de Gray, 25000 Besançon, France.
authors.forename: Typhaine
authors.initials: T
authors.lastname: Guillemot
authors.affiliation: Laboratoire Chrono-Environnement, UMR 6249 CNRS, Université de Bourgogne Franche-Comté, 16 Route de Gray, 25000 Besançon, France.
authors.forename: Vincent
authors.initials: V
authors.lastname: Bichet
authors.affiliation: Laboratoire Chrono-Environnement, UMR 6249 CNRS, Université de Bourgogne Franche-Comté, 16 Route de Gray, 25000 Besançon, France.
authors.forename: Laurent
authors.initials: L
authors.lastname: Millet
authors.affiliation: Laboratoire Chrono-Environnement, UMR 6249 CNRS, Université de Bourgogne Franche-Comté, 16 Route de Gray, 25000 Besançon, France.
authors.forename: Emilie
authors.initials: E
authors.lastname: Gauthier
authors.affiliation: Laboratoire Chrono-Environnement, UMR 6249 CNRS, Université de Bourgogne Franche-Comté, 16 Route de Gray, 25000 Besançon, France.
authors.forename: Charly
authors.initials: C
authors.lastname: Massa
authors.affiliation: CNRS, UMR 5204 EDYTEM, Université Savoie Mont Blanc, 5 Boulevard de la mer Caspienne, 73376 Le Bourget du Lac Cedex, France.
authors.forename: Anne-Lise
authors.initials: AL
authors.lastname: Develle
authors.affiliation: CNRS, UMR 5204 EDYTEM, Université Savoie Mont Blanc, 5 Boulevard de la mer Caspienne, 73376 Le Bourget du Lac Cedex, France.
authors.forename: Cécile
authors.initials: C
authors.lastname: Pignol
authors.affiliation: Department of Genetics and Evolution, University of Geneva, 4 Boulevard d'Yvoy, 1205 Geneva, Switzerland.
authors.forename: Franck
authors.initials: F
authors.lastname: Lejzerowicz
authors.affiliation: CARRTEL, INRA, Université de Savoie Mont Blanc, 74200, Thonon-les-bains, France.
authors.forename: Isabelle
authors.initials: I
authors.lastname: Domaizon
mesh_terms: D044822:Biodiversity; D002980:Climate; D017753:Ecosystem; D056890:Eukaryota / Q000145:classification; D005068:Eutrophication; D005602:France; D005658:Fungi / Q000145:classification; D019015:Geologic Sediments; D006116:Greenland; D060106:Lakes; D010802:Phylogeny; D011157:Population Dynamics; D014871:Water Microbiology
keywords: 
  eDNA
  ; climate change; eutrophication; lake; protists