Overview of freshwater microbial eukaryotes diversity: a first analysis of publicly available metabarcoding data

Abstract

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.

Tracking a century of changes in microbial eukaryotic diversity in lakes driven by nutrient enrichment and climate warming

“…Two groups generally dominate lacustrine microbial eukaryotes: Alveolata, which are mainly represented by Dinophyceae and Ciliophora and Fungi, which are mainly represented by Dikarya, Chytridiomycota and Cryptomycota. Stramenopiles, Viridiplantae and Rhizaria are three other dominant groups within these assemblages, with Chrysophyceae, Chlorophyta and Cercozoa being typical representatives of these three groups, respectively (Taib et al ., ; Capo et al ., ; Debroas et al ., ; Kammerlander et al ., ; Oikonomou et al ., ; Filker et al ., ). These conserved patterns tend to support the idea that sedimentary DNA does not give a distorted view of eukaryotic assemblages.…”

Dynamics of Bacterial Community Diversity and Structure in the Terminal Reservoir of the South-To-North Water Diversion Project in China

“…The next-generation sequencing technology has immensely contributed to the global increase in microbial diversity and ecology studies employing samples from different environments, for example, water, soil and extreme environments [11][12][13]. In this study, we applied the next-generation sequencing technology named Illumina HiSeq sequencing to detect bacteria diversity in the reservoir.…”

Novel Diversity of Deeply Branching Holomycota and Unicellular Holozoans Revealed by Metabarcoding in Middle Paraná River, Argentina

“…However, there is an increasing number of studies that show that some "marine" lineages are also present in freshwater ecosystems, although in lower abundances (Alverson et al, 2007;Bråte et al, 2010;Simon et al, 2013Simon et al, , 2014Debroas et al, 2017).…”

“…Some of these studies found novel eukaryotic clades, and showed the presence of some putatively marine-exclusive lineages in those freshwater environments. However, fewer molecular biodiversity surveys have been conducted in rivers (Berney et al, 2004;Thomas et al, 2012;Debroas et al, 2017).…”