Stephanoeca arndti spec. nov. – First cultivation success including molecular and autecological data from a freshwater acanthoecid choanoflagellate from Samoa

Morphological and molecular reinvestigation of acanthoecid species III. - Kalathoeca cupula (Leadbeater, 1972) gen. et comb. nov. (=Stephanoeca cupula (Leadbeater) Thomsen, 1988)

Based on a further re-examination of loricate choanoflagellate species with detailed morphological (SEM/TEM) and molecular data of the SSU and LSU rRNA, the present study aims to give new insights for Stephanoeca cupula. In contrast to the original allocation within the family of tectiform reproducing species, morphological and molecular data of S. cupula sensu Leadbeater, 1972 points towards an affiliation within the nudiform reproducing family. Based on these new data, we here erect the nudiform genus Kalathoeca with its type species K. cupula gen. et comb. nov. Our data challenges morphological species assignments, as K. cupula shares its morphological lorica characteristics with tectiform reproducing species of Stephanoeca sensu stricto. Kalathoeca cupula is an interesting candidate for further investigating and understanding the evolutionary relationship of tectiform and nudiform reproducing species. Stephanoeca cupula sensu Thomsen, 1988 has been morphologically re-examined based on the renewed understanding of the morphological variability associated with S. cupula sensu Leadbeater, 1972 (=K. cupula), allowing us now to distribute the different morphological forms investigated within K. cupula and Pseudostephanoeca quasicupula.

Significance of the Nudiform and Tectiform Modes of Silica Deposition, Lorica Assembly and Cell Division in Choanoflagellates as Exemplified by Stephanoeca diplocostata and Enibas spp

The deposition of silicified costal strips and lorica assembly in choanoflagellates is precisely linked to the cell cycle. A minority of species undergo nudiform division whereby a loricate cell divides to produce a naked daughter cell that deposits a set of costal strips and then assembles a lorica. Most species undergo tectiform division whereby a parent loricate cell produces a set of costal strips, divides and passes on the stored strips to a daughter cell that immediately assembles a lorica. Many phylogenetic analyses recover nudiform and tectiform species as sister-clades giving the impression that they are distinct evolutionary lineages. However, the tectiform species Stephanoeca diplocostata is capable of undergoing nudiform division and depositing costal strips and assembling a lorica with certain modifications in a nudiform manner. The recent discovery of a new genus, Enibas, comprising species with Stephanoeca-like loricae that undergo nudiform cell division and on phylogenetic analysis occur as a sister group to other nudiform species has drawn attention to whether there are also unique features in lorica construction. A range of Enibas loricae is illustrated and it appears that there are unique features which might be interpreted as being derived from a Stephanoeca-like ancestor.

Re-evaluating Loricate Choanoflagellate Phylogenetics: Molecular Evidence Points to the Paraphyly of Tectiform Species

Lorica-bearing choanoflagellates belong to the order Acanthoecida, a taxon which has been consistently recovered as monophyletic in molecular phylogenies. Based upon differences in lorica development and morphology, as well as the presence or absence of a motile dispersal stage, species are labelled as either nudiform or tectiform. Whilst Acanthoecida is robustly resolved in molecular phylogenies, the placement of the root of the clade is less certain with two different positions identified in past studies. One recovered root has been placed between the nudiform family Acanthoecidae and the tectiform family Stephanoecidae. An alternative root placement falls within the tectiform species, recovering the monophyletic Acanthoecidae nested within a paraphyletic Stephanoecidae. Presented here is a 14-gene phylogeny, based upon nucleotide and amino acid sequences, which strongly supports tectiform paraphyly. The horizontal transfer of a ribosomal protein gene, from a possible SAR donor, into a subset of acanthoecid species provides further, independent, support for this root placement. Differing patterns of codon usage bias across the choanoflagellates are proposed as the cause of artefactual phylogenetic signals that lead to the recovery of tectiform monophyly.

Evolution and Diversity of Semaphorins and Plexins in Choanoflagellates

Semaphorins and plexins are cell surface ligand/receptor proteins that affect cytoskeletal dynamics in metazoan cells. Interestingly, they are also present in Choanoflagellata, a class of unicellular heterotrophic flagellates that forms the phylogenetic sister group to Metazoa. Several members of choanoflagellates are capable of forming transient colonies, whereas others reside solitary inside exoskeletons; their molecular diversity is only beginning to emerge. Here, we surveyed genomics data from 22 choanoflagellate species and detected semaphorin/plexin pairs in 16 species. Choanoflagellate semaphorins (Sema-FN1) contain several domain features distinct from metazoan semaphorins, including an N-terminal Reeler domain that may facilitate dimer stabilization, an array of fibronectin type III domains, a variable serine/threonine-rich domain that is a potential site for O-linked glycosylation, and a SEA domain that can undergo autoproteolysis. In contrast, choanoflagellate plexins (Plexin-1) harbor a domain arrangement that is largely identical to metazoan plexins. Both Sema-FN1 and Plexin-1 also contain a short homologous motif near the C-terminus, likely associated with a shared function. Three-dimensional molecular models revealed a highly conserved structural architecture of choanoflagellate Plexin-1 as compared to metazoan plexins, including similar predicted conformational changes in a segment that is involved in the activation of the intracellular Ras-GAP domain. The absence of semaphorins and plexins in several choanoflagellate species did not appear to correlate with unicellular versus colonial lifestyle or ecological factors such as fresh versus salt water environment. Together, our findings support a conserved mechanism of semaphorin/plexin proteins in regulating cytoskeletal dynamics in unicellular and multicellular organisms.

The Hidden Diversity of Flagellated Protists in Soil

Protists are among the most diverse and abundant eukaryotes in soil. However, gaps between described and sequenced protist morphospecies still present a pending problem when surveying environmental samples for known species using molecular methods. The number of sequences in the molecular PR² database (∼130,000) is limited compared to the species richness expected (>1 million protist species) - limiting the recovery rate. This is important, since high throughput sequencing (HTS) methods are used to find associative patterns between functional traits, taxa and environmental parameters. We performed HTS to survey soil flagellates in 150 grasslands of central Europe, and tested the recovery rate of ten previously isolated and cultivated cercomonad species, among locally found diversity. We recovered sequences for reference soil flagellate species, but also a great number of their phylogenetically evaluated genetic variants, among rare and dominant taxa with presumably own biogeography. This was recorded among dominant (cercozoans, Sandona), rare (apusozoans) and a large hidden diversity of predominantly aquatic protists in soil (choanoflagellates, bicosoecids) often forming novel clades associated with uncultured environmental sequences. Evaluating the reads, instead of the OTUs that individual reads are usually clustered into, we discovered that much of this hidden diversity may be lost due to clustering.