Overview of freshwater microbial eukaryotes diversity: a first analysis of publicly available metabarcoding data.
Although they are widespread, diverse and involved in biogeochemical cycles, microbial eukaryotes attract less attention than their prokaryotic counterparts in environmental microbiology. In this study, we used publicly available 18S barcoding data to define biases that may limit such analyses and to gain an overview of the planktonic microbial eukaryotic diversity in freshwater ecosystems. The richness of the microbial eukaryotes was estimated to 100 798 operational taxonomic units (OTUs) delineating 1267 clusters or phylogenetic units (PUs, i.e. monophyletic groups of OTUs that are phylogenetically close). By summing the richness found in aquatic environments, we can predict the microbial eukaryotic richness to be around 200 000-250 000 species. The molecular diversity of protists in freshwater environments is generally higher than that of the morphospecies and cultivated species catalogued in public databases. Amoebozoa, Viridiplantae, Ichthyosporea, and Cryptophyta are the most phylogenetically diverse taxa, and characterisation of these groups is still needed. A network analysis showed that Fungi, Stramenopiles and Viridiplantae play central role in lake ecosystems. Finally, this work provides guidance for compiling metabarcoding data and identifies missing data that should be obtained to increase our knowledge on microbial eukaryote diversity.
Université Clermont Auvergne, CNRS, Laboratoire: Microorganismes: Génome et Environnement, F-63000 Clermont-Ferrand, France.
Didier
D
Debroas
INRA, UMR 42 Centre Alpin de Recherche sur les Réseaux Trophiques et Ecosystèmes Limniques, F-74200 Thonon Les Bains, France.
Isabelle
I
Domaizon
INRA, UMR BIOEMCO, Site de l'ENS, 46 rue d'Ulm, 75005 Paris, France.
Jean-Francois
JF
Humbert
Unité d'Ecologie, Systématique et Evolution, CNRS UMR 8079, Université Paris-Sud, 91405 Orsay, France.
Ludwig
L
Jardillier
Université Clermont Auvergne, CNRS, Laboratoire: Microorganismes: Génome et Environnement, F-63000 Clermont-Ferrand, France.
Cécile
C
Lepère
Université Clermont Auvergne, CNRS, Laboratoire: Microorganismes: Génome et Environnement, F-63000 Clermont-Ferrand, France.
Anne
A
Oudart
Université Clermont Auvergne, CNRS, Laboratoire: Microorganismes: Génome et Environnement, F-63000 Clermont-Ferrand, France.
Najwa
N
Taïb
D044785:Cryptophyta / Q000145:classification; D017753:Ecosystem; D056890:Eukaryota / Q000145:classification*; D005658:Fungi / Q000145:classification; D060106:Lakes / Q000382:microbiology; D010802:Phylogeny; D010933:Plankton / Q000145:classification*; D058009:Stramenopiles / Q000145:classification
bioinformatics; freshwater; metabarcoding; microbial eukaryotes