title: Is Planktonic Diversity Well Recorded in Sedimentary DNA? Toward the Reconstruction of Past Protistan Diversity.
abstract: Studies based on the coupling of a paleolimnological approach and molecular tools (e.g., sequencing of sedimentary DNA) present a promising opportunity to obtain long-term data on past lacustrine biodiversity. However, certain validations are still required, such as the evaluation of DNA preservation in sediments for various planktonic taxa that do not leave any morphological diagnostic features. In this study, we focused on the diversity of planktonic unicellular eukaryotes and verified the presence of their DNA in sediment archives. We compared the molecular inventories (high-throughput sequencing of 18S ribosomal DNA) obtained from monitoring the water column with those obtained for DNA archived in the first 30 cm of sediment. Seventy-one percent of taxonomic units found in the water samples were detected in sediment samples, including pigmented taxa, such as Chlorophyta, Dinophyceae, and Chrysophyceae, phagotrophic taxa, such as Ciliophora, parasitic taxa, such as Apicomplexa and Chytridiomycota, and saprotrophs, such as Cryptomycota. Parallel analysis of 18S ribosomal RNA (rRNA) transcripts revealed the presence of living eukaryotic taxa only in the top 2 cm of sediment; although some limits exist in using RNA/DNA ratio as indicator of microbial activity, these results suggested that the sedimentary DNA mostly represented DNA from past and inactive communities. Only the diversity of a few groups, such as Cryptophyta and Haptophyta, seemed to be poorly preserved in sediments. Our overall results showed that the application of sequencing techniques to sedimentary DNA could be used to reconstruct past diversity for numerous planktonic eukaryotic groups.
authors.affiliation: INRA, UMR 42 CARRTEL, 74203, Thonon-les-bains Cedex, France.|Université Savoie Mont Blanc, UMR 42 CARRTEL, 73379, Le Bourget du Lac, France.
authors.forename: Eric
authors.initials: E
authors.lastname: Capo
authors.affiliation: Clermont Université, Université Blaise Pascal, CNRS, UMR 6023 LMGE, 63171, Aubière, France.
authors.forename: Didier
authors.initials: D
authors.lastname: Debroas
authors.affiliation: CNRS, UMR 5204 EDYTEM, Université Savoie Mont Blanc, 73379, Le Bourget du Lac Cedex, France.
authors.forename: Fabien
authors.initials: F
authors.lastname: Arnaud
authors.affiliation: INRA, UMR 42 CARRTEL, 74203, Thonon-les-bains Cedex, France. isabelle.domaizon@thonon.inra.fr.
authors.forename: Isabelle
authors.initials: I
authors.lastname: Domaizon
mesh_terms: D044822:Biodiversity; D004275:DNA, Ribosomal / Q000235:genetics; D056890:Eukaryota / Q000145:classification* / Q000235:genetics*; D005658:Fungi / Q000145:classification / Q000235:genetics; D019015:Geologic Sediments / Q000382:microbiology* / Q000469:parasitology*; D060106:Lakes / Q000382:microbiology / Q000469:parasitology; D010802:Phylogeny; D010933:Plankton / Q000145:classification* / Q000235:genetics*; D012337:RNA, Ribosomal, 18S / Q000235:genetics; D017422:Sequence Analysis, DNA
chemical_list: D004275:DNA, Ribosomal; D012337:RNA, Ribosomal, 18S
keywords: 454 sequencing; Paleolimnology; Plankton; Protists; Sedimentary DNA