Transforming the eukaryotic tree of life through isolation, characterisation, and phylogenetics of novel free-living protists

Abstract

The overwhelming majority of eukaryotic diversity is microbial and protistan. Major new groups are discovered nearly every year up to this day. I established several dozen cultures of heterotrophic protists comprised of two kinds of `unknowns': 1. Incertae sedis organisms previously described using morphological approaches but devoid of sequence data and difficult to place in the tree of eukaryotes based on their current taxonomy alone; and 2. Previously unattested morphotypes. Particularly productive were samples from anaerobic, hypersaline, and alkaline environments, and combinations thereof---in those environments, eukaryote predators of other protists comprised a generous portion of hitherto uncharacterised diversity. I used light microscopy to carefully characterise their cell morphology and life histories, and, for some taxa, electron microscopy was used to examine their fine structure. Using ribosomal DNA sequencing, I obtained molecular data for 39 isolates for phylogenetic analyses. Among them were considerable contributions to the diversity of breviates, metamonads, and novel rhizarian lineages among Filosa and Endomyxa. The phylogenetic position of several of these isolates remained unresolved by ribosomal DNA phylogenies; thus, two of these taxa---the gliding marine cell Meteora sporadica and 'Protist X', an anaerobic flagellate that preys upon other microbial eukaryotes---were then subject to transcriptome sequencing and multigene phylogenomic analyses. Surprisingly, these analyses revealed that Meteora sporadica and 'Protist X' form a robust clade with the deep-branching Hemimastigophora. This hints at the existence of a new biologically diverse supergroup in the eukaryotic Tree of Life. Finally, a survey of available molecular environmental sequence data found that about half of the novel taxa have been virtually undetected by environmental methods to date. Altogether, this emphasises the importance of cultivation not only for downstream research, but in the exploration of biodiversity itself.