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

Abstract

Protists, that is, microbial eukaryotes that are not plants, animals or fungi (Archibald et al., 2017), are one of the most dominant life forms on earth, comprising up to 80% of the total eukaryotic diversity in the environment (de Vargas et al., 2015;Mahé et al., 2017;Massana et al., 2015). Protists play key ecological roles and are involved in primary productivity, nutrient cycling and carbon sequestration. It is thus crucial to assess protist diversity and the factors that determine community composition in order to predict how protists will respond to environmental change (Cavicchioli et al., 2019). While protists have historically been more difficult to study due to their small size, the explosion of metabarcoding studies over the past 10 years has greatly expanded our knowledge of these organisms (Burki et al., 2021;Santoferrara et al., 2020).

Beyond the limits of the unassigned protist microbiome: inferring large-scale spatio-temporal patterns of Syndiniales marine parasites

“…They have been recently employed among prokaryotes for surveying the coding part of genomes and metagenomes [6] and taxonomy across extreme aquatic environments [12]. By exploring the biogeography of these sequences we can reveal core taxa shared across ecosystems [12,58]. Here we have explored both biogeographical and temporal patterns of protists at the species level without requiring a reference taxonomic match.…”

Fungal Diversity and Community Composition across Ecosystems

“…This gap becomes even more relevant in light of recent findings highlighting the critical importance of fungi not only in soils but also in aquatic ecosystems [9,10,[14][15][16][17]. To reduce this gap, here we used a recently published compilation of metabarcoding studies allowing for large-scale comparisons of eukaryotic microorganisms across ecosystems, which focuses on the V4 region of the 18S rRNA as ASVs [18]. We hypothesised to find different fungal diversities and community assemblages across systems, with higher diversities in soils than in aquatic environments.…”

Identifying Eukaryotes and Factors Influencing Their Biogeography in Drinking Water Metagenomes

“…130 Compared to prokaryotes and viruses, both the reference data and the option of tools available for eukaryotes are limited, further exacerbating the complexity of the reconstruction of their genomes. In addition, due to the wealth of data provided by marine expeditions, reference databases included in several tools are highly skewed toward marine taxa (e.g., Levy Karin and collaborators, 81 Vaulot and collaborators 131 ), potentially limiting and biasing the analyses performed on other environments. While new tools will improve the analysis of eukaryotes from mixed metagenomes, only focused sampling efforts are needed to overcome the compositional bias of current references and enable a clearer view of eukaryotes in DWDSs.…”