Diversity and ecology of protists revealed by metabarcoding

Abstract

Protists are the dominant eukaryotes in the biosphere where they play key functional roles. While protists have been studied for over a century, it is the high-throughput sequencing of molecular markers from environmental samples -the approach of metabarcoding -that has revealed just how diverse, and abundant, these small organisms are. Metabarcoding is now routine to survey environmental diversity, so data have rapidly accumulated from a multitude of environments and at different sampling scales. This mass of data has provided unprecedented opportunities to study the taxonomic and functional diversity of protists, and how this diversity is organised in space and time. Here, we use metabarcoding as a common thread to discuss the state of knowledge in protist diversity research, from technical considerations of the approach to important insights gained on diversity patterns and the processes that might have structured this diversity. In addition to these insights, we conclude that metabarcoding is on the verge of an exciting added dimension thanks to the maturation of high-throughput long-read sequencing, so that a robust eco-evolutionary framework of protist diversity is within reach. ll

Size-Fractionated Microbiome Structure in Subarctic Rivers and a Coastal Plume Across DOC and Salinity Gradients

“…Microbial eukaryote richness was higher for the small fraction in the SAS and KWK rivers suggesting that smaller eukaryotes could potentially be favored in these CDOM-rich waters. All of these analyses are subject to the usual limitations of primer mismatches and amplicon biases (e.g., Burki et al, 2021 ; Vaulot et al, 2021 ).…”

Mitochondrial Cytochrome Oxidase Subunit 1: A Promising Molecular Marker for Species Identification in Foraminifera

“…Macher et al (2021b) recently discovered the first mitochondrial COI gene in Foraminifera. COI is a molecular marker commonly used in molecular research on animals (Hebert et al, 2003) and has been shown to be informative on other protists (Nassonova et al, 2010;Pawlowski et al, 2012;Burki et al, 2021). There are many advantages of using a coding region such as COI in addition to a non-coding region such as 18S.…”

metaPR2: a database of eukaryotic 18S rRNA metabarcodes with an emphasis on protists

“…This gene has the advantage of being universal and having well annotated reference databases such as Silva or PR 2 (Guillou et al 2013; Quast et al 2013) which allow, for many protist groups, a precise taxonomic assignation. Within the 18S rRNA gene, several variable regions have been used as barcodes, in particular the V4 region located near the middle of the gene and the shorter V9 region located at its 3’ end (Burki et al 2021; Pawlowski et al 2012). The V4 region in particular is currently most often used in recent studies (Lopes dos Santos et al 2021).…”