What Can Environmental Sequences Tell Us About the Distribution of Low‐Rank Taxa? The Case of Euplotes (Ciliophora, Spirotrichea), Including a Description of Euplotes enigma sp. nov.

Abstract

Environmental sequences have become a major source of information. High-throughput sequencing (HTS) surveys have been used to infer biogeographic patterns and distribution of broad taxa of protists. This approach is, however, more questionable for addressing low-rank (less inclusive) taxa such as species and genera, because of the increased chance of errors in identification due to blurry taxonomic boundaries, low sequence divergence, or sequencing errors. The specious ciliate genus Euplotes partially escapes these limitations. It is a ubiquitous, monophyletic taxon, clearly differentiated from related genera, and with a relatively well-developed internal systematics. It has also been the focus of several ecological studies. We present an update on Euplotes biogeography, taking into consideration for the first time environmental sequences, both traditional (Sanger) and HTS. We inferred a comprehensive small subunit rRNA gene phylogeny of the genus including a newly described marine species, Euplotes enigma, characterized by a unique question mark-shaped macronucleus. We then added available environmental sequences to the tree, mapping associated metadata. The resulting scenario conflicts on many accounts with previously held views, suggesting, for example, that a large diversity of anaerobic Euplotes species exist, and that marine representatives of mainly freshwater lineages (and vice-versa) might be more common than previously thought.

Two new species of Euplotes with cirrotype-9, Euplotes foissneri sp. nov. and Euplotes warreni sp. nov. (Ciliophora, Spirotrichea, Euplotida), from the coasts of Patagonia: implications from their distant, early and late branching in the Euplotes phylogenetic tree

“…However, statistical support is very weak. On the other hand, E. warreni does not cluster with any of the major clades—either with the six clades numbered I to VI from bottom to top [39, 40] or the five clades labelled A to E from top to bottom [18, 19]—that are generally recognized in the Euplotes phylogenetic tree. It represents a new, independent lineage that branches off immediately after the clade formed by E. petzi and E. sinicus Jiang et al ., 2010.…”

“…The remarkable species richness and the cosmopolitan distribution of Euplotes are supported by unceasing descriptions of species new to science. As many as eight novel taxa, E. bergeri Lian et al, 2020 [20], E. curdsi Syberg-Olsen et al, 2016 [23], E. domenicanus Živaljić et al, 2020 [18], E. enigma Boscaro a, After Curds [1]; b, after Schwartz et al [41]; c, after Lian et al [19]; d, after Valbonesi and Luporini [37].…”

“…The remarkable species richness and the cosmopolitan distribution of Euplotes are supported by unceasing descriptions of species new to science. As many as eight novel taxa, E. bergeri Lian et al ., 2020 [20], E. curdsi Syberg-Olsen et al ., 2016 [23], E. domenicanus Živaljić et al ., 2020 [18], E. enigma Boscaro et al ., 2019 [19], E. estuarinus Yan et al ., 2018 [43], E. shini Lian et al ., 2020 [20], E. weissei [20] and E. wuhanensis Lian et al ., 2019 [21], have been recognized in the past 3 or 4 years, and E. foissneri and E. warreni can now be added on this list. However, most old Euplotes descriptions remain merely typological and based on counts and measurements of individuals from temporary cultures raised from only few natural isolates.…”

Thiotrophic bacterial symbiont induces polyphenism in giant ciliate host Zoothamnium niveum

“…alternans also from geographically distant locations and considered morphologically identical 53 exhibit 96.7% sequence similarity 45 . This rather points to different species 51 when applying a threshold between 97 to 99% 51 or 99% sequence similarity 80 . Even more so, Z .…”

Morphology, ultrastructure, genomics, and phylogeny of Euplotes vanleeuwenhoeki sp. nov. and its ultra-reduced endosymbiont “Candidatus Pinguicoccus supinus” sp. nov.

“…As an example, some authors 69 even proposed to synonymise almost all species possessing ten FVC and a double dargyrome under the name of E. charon. Obviously, nowadays, this proposal is 50,67,70 and because of other morphological features characterizing some of the organisms (e.g. dorsal furrows/ridges, and body shape and proportions).…”