Protistan Diversity in Environmental Molecular Surveys

Abstract

Marine protists include a heterogeneous collection of phototrophic and heterotrophic unicells covering a wide cell size range and belonging to virtually all eukaryotic lineages. They have been identifi ed by microscopy, which allows a reasonable level of resolution for the larger specimens but is clearly insuffi cient for the smallest ones. Moreover, as occurs with their prokaryotic counterparts, a large majority of marine protists are uncultivable. Molecular tools have revolutionized fi eld studies of protists' diversity, allowing exhaustive species inventories especially when combined with high-throughput sequencing technologies. These surveys have shown that natural assemblages are very diverse, including novel phylogenetic lineages that had remained uncharacterized despite their evident ecological significance. The extent of diversity and novelty is largest within the assemblage of the smallest protists, the picoeukaryotes. The information gathered by sequencing phylogenetic marker genes has been combined with an array of complementary molecular methods such as fi ngerprinting tools to study diversity changes along spatial and temporal gradients, fl uorescence in situ hybridization (FISH) to put a face on the novel lineages and perform specifi c cell counts, and metagenomics to explore ecological adaptations on the basis of the genetic potential. This chapter presents an overview of the molecular approaches currently applied to gain knowledge on the diversity and function of protists in the environment.

Recent Reticulate Evolution in the Ecologically Dominant Lineage of Coccolithophores

“…A major limitation in the study of marine microbes is that a large fraction of their diversity has not been successfully cultured (Rappe and Giovannoni, 2003 ; Massana, 2015 ). This study, combined with the previous first successful isolation of G. muellerae (Bendif et al, 2015 ), shows that single-cell sorting using novel detection mechanisms to target specific functional groups can be highly successful at enhancing the cultured diversity of certain groups.…”

Vertical niche definition of test-bearing protists (Rhizaria) into the twilight zone revealed by in situ imaging

“…Over the last two decades, interest has been elevated in the role of unicellular eukaryotes 37 (i.e., protists) in marine global biogeochemical cycles (Worden et al 2015). Among the large 38 diversity of protists inhabiting the ocean (Massana 2015;Simpson et al 2017), the Rhizaria is a 39 diverse super-group of unicellular organisms, some of which have planktonic life styles (Burki 40 and Keeling 2014). A typical feature of many marine rhizarians is the formation of a mineral test 41 (or skeleton), whose chemical nature varies between taxa: Acantharia use strontium sulfate 42 (SrSO4), Polycystine radiolarians and Phaeodaria secrete opaline silica (SiO2 nH2O), and 43…”

A Hard Day's Night: Diel Shifts in Microbial Eukaryotic Activity in the North Pacific Subtropical Gyre

“…Additionally, recent tag-sequencing efforts that target cellular ribosomal RNA (rRNA) have provided an approach for determining the metabolically active members of the community by comparing rRNA-and rDNA-derived tag sequences. The latter are more likely to include dead, inactive cellular material (Blazewicz et al, 2013), while the former serve as a proxy for presumed transcriptional activity and the precursor for protein synthesis (Poulsen et al, 1993;Corinaldesi et al, 2011;Lejzerowicz et al, 2013;Egge et al, 2015;Massana, 2015).…”