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The Colpodea form a major clade of ciliates that are often found in environmental DNA sequencing studies. They are united by similar somatic ciliature, but differentiated by complex oral structures. Although there are four well supported colpodean subclades, there is disagreement in molecular phylogenetic inferences about their branching order. Using available nuclear SSU-rRNA sequences, we evaluated if the bursariomorphids or the platyophryids are sister to the remaining colpodeans. We inferred the "platyophryids-early" topologies using different alignment and masking methods, but constrained analyses could not reject the "bursariomorphids-early" topology. Both bursariomorphids and platyophryids clades have a similar number of nucleotide positions shared with the outgroup, and both are interconnected with the outgroup in phylogenetic networks. Based on these discordant results, it is hard to determine which clade branched off first, although the "platyophryids-early topology" is also supported by mitochondrial SSU-rRNA data. We also offer different reference alignments that can be used to phylogenetically place short- and long-read data from environmental DNA sequencing studies, and we propose some tentative evolutionary and ecological interpretations of those placements., (Copyright © 2020 Elsevier GmbH. All rights reserved.)

During the last decade, high-throughput metabarcoding became routine for analyzing protistan diversity and distributions in nature. Amid a multitude of exciting findings, scientists have also identified and addressed technical and biological limitations, although problems still exist for inference of meaningful taxonomic and ecological knowledge based on short DNA sequences. Given the extensive use of this approach, it is critical to settle our understanding on its strengths and weaknesses and to synthesize up-to-date methodological and conceptual trends. This article summarizes key scientific and technical findings, and identifies current and future directions in protist research that uses metabarcoding., (© 2020 International Society of Protistologists.)

This revision of the classification of eukaryotes follows that of Adl et al., 2012 [J. Euk. Microbiol. 59(5)] and retains an emphasis on protists. Changes since have improved the resolution of many nodes in phylogenetic analyses. For some clades even families are being clearly resolved. As we had predicted, environmental sampling in the intervening years has massively increased the genetic information at hand. Consequently, we have discovered novel clades, exciting new genera and uncovered a massive species level diversity beyond the morphological species descriptions. Several clades known from environmental samples only have now found their home. Sampling soils, deeper marine waters and the deep sea will continue to fill us with surprises. The main changes in this revision are the confirmation that eukaryotes form at least two domains, the loss of monophyly in the Excavata, robust support for the Haptista and Cryptista. We provide suggested primer sets for DNA sequences from environmental samples that are effective for each clade. We have provided a guide to trophic functional guilds in an appendix, to facilitate the interpretation of environmental samples, and a standardized taxonomic guide for East Asian users., (© 2019 International Society of Protistologists.)

Some protists with microsporidian-like cell biological characters, including Mitosporidium, Paramicrosporidium, and Nucleophaga, have SSU rRNA gene sequences that are much less divergent than canonical Microsporidia. We analysed the phylogenetic placement and environmental diversity of microsporidian-like lineages that group near the base of the fungal radiation and show that they group in a clade with metchnikovellids and canonical microsporidians, to the exclusion of the clade including Rozella, in line with what is currently known of their morphology and cell biology. These results show that the phylogenetic scope of Microsporidia has been greatly underestimated. We propose that much of the lineage diversity previously thought to be cryptomycotan/rozellid is actually microsporidian, offering new insights into the evolution of the highly specialized parasitism of canonical Microsporidia. This insight has important implications for our understanding of opisthokont evolution and ecology, and is important for accurate interpretation of environmental diversity. Our analyses also demonstrate that many opisthosporidian (aphelid+rozellid+microsporidian) SSU V4 OTUs from Neotropical forest soils group with the short-branching Microsporidia, consistent with the abundance of their protist and arthropod hosts in soils. This novel diversity of Microsporidia provides a unique opportunity to investigate the evolutionary origins of a highly specialized clade of major animal parasites., (© 2018 The Authors Journal of Eukaryotic Microbiology published by Wiley Periodicals, Inc. on behalf of International Society of Protistologists.)

Species in the genera Hexasterias and Halodinium have been recorded over the last decades as acritarchs in palynological and/or plankton studies. In paleoenvironmental studies, these resting stages are often interpreted as indicators of freshwater input. The biological affinity of these genera has never been definitely established. Here, a new species, Halodinium verrucatum sp. nov., is described and molecular evidence (single specimen SSU and LSU rDNA sequencing) reveals that both this new species and Hexasterias problematica, collected from sediment samples in the Skagerrak and Baltic Sea, are resting stages of prorodontid ciliates. Additionally, infrared spectroscopic analysis (micro-FTIR) of Hexasterias problematica and Halodinium spp. specimens indicates a carbohydrate-based composition of the cyst wall with evidence for nitrogen-containing functional groups. A similar composition is recorded for tintinnid loricae, which further supports the placement of Hexasterias and Halodinium as ciliate cysts, and the composition is consistent with the heterotrophic nature of ciliates. The morphologically similar species Radiosperma corbiferum has a comparable composition, suggesting a similar ciliate affinity and indicating the utility of micro-FTIR in understanding acritarch affinity. Hexasterias problematica typically occurs in coastal waters from temperate to arctic regions. Halodinium verrucatum sp. nov. is observed in temperate estuarine sediments in the northern hemisphere., (Copyright © 2018 Elsevier GmbH. All rights reserved.)

Background: Biological communities are normally composed of a few abundant and many rare species. This pattern is particularly prominent in microbial communities, in which most constituent taxa are usually extremely rare. Although abundant and rare subcommunities may present intrinsic characteristics that could be crucial for understanding community dynamics and ecosystem functioning, microbiologists normally do not differentiate between them. Here, we investigate abundant and rare subcommunities of marine microbial eukaryotes, a crucial group of organisms that remains among the least-explored biodiversity components of the biosphere. We surveyed surface waters of six separate coastal locations in Europe, independently considering the picoplankton, nanoplankton, and microplankton/mesoplankton organismal size fractions., Results: Deep Illumina sequencing of the 18S rRNA indicated that the abundant regional community was mostly structured by organismal size fraction, whereas the rare regional community was mainly structured by geographic origin. However, some abundant and rare taxa presented similar biogeography, pointing to spatiotemporal structure in the rare microeukaryote biosphere. Abundant and rare subcommunities presented regular proportions across samples, indicating similar species-abundance distributions despite taxonomic compositional variation. Several taxa were abundant in one location and rare in other locations, suggesting large oscillations in abundance. The substantial amount of metabolically active lineages found in the rare biosphere suggests that this subcommunity constitutes a diversity reservoir that can respond rapidly to environmental change., Conclusions: We propose that marine planktonic microeukaryote assemblages incorporate dynamic and metabolically active abundant and rare subcommunities, with contrasting structuring patterns but fairly regular proportions, across space and time., (Copyright © 2014 Elsevier Ltd. All rights reserved.)

Using 11 new SSU-rDNA sequences, we analyze relationships within the class Colpodea, especially of some uncommon taxa, such as Kalometopia duplicata, Cyrtolophosis minor, and Jaroschia sumptuosa. The sequences do not change the basic structure of the molecular Colpodea tree, i.e., all belong to one of the four molecular clades recognized by Foissner et al. (2011): Colpodida, Cyrtolophosidida, Bursariomorphida, and Platyophryida. The addition of three Colpoda sequences strengthens the observation that species of this genus are distributed over the whole molecular Colpodea tree. Very likely, this is caused by a fast radiation of Colpoda, several species of which then evolved independently, forming new genera and families. Cyrtolophosis minor, which belongs to the molecular Pseudocyrtolophosis clade, is referred to a new genus, Apocyrtolophosis nov. gen., characterized by a comparably large, deltoid oral opening, an unciliated posterior region, and the absence of an oblique kinety in the left oral polykinetid. Bryometopus triquetrus does not erase the paraphyly of its genus. Platyophrya vorax, P. spumacola, and P. bromelicola form a highly supported clade in the order Platyophryida. Platyophryides and Ottowphrya are close genetically but differ in the silverline pattern (colpodid vs. platyophryid)., (Copyright © 2013 Elsevier GmbH. All rights reserved.)

The Haptoria are free-living predatory ciliates living in terrestrial and aquatic habitats all around the world. They belong to a highly diverse class, Litostomatea, whose morphological and molecular classifications harmonize poorly since both approaches produce rather different frameworks. In the present study, we analyzed the genealogy of the litostomateans, including eight new haptorian 18S rRNA gene sequences. Apart from traditional tree-building methods, we also applied phylogenetic networks, split spectrum analysis and quartet likelihood mapping to assess the information content of alignments. These analyses show that: (1) there are several strongly supported monophyletic litostomatean lineages--Rhynchostomatia, Trichostomatia, Haptorida, Lacrymariida, Pleurostomatida, and Didiniida; (2) the Rhynchostomatia are the best candidates for a basal litostomatean group; (3) sister relationship of the Trichostomatia and Haptoria is very likely, which well corroborates the traditional morphology-based classifications; (4) molecular phylogeny of the order Spathidiida is only poorly resolved very likely due to one or several rapid radiation events or due to the incomplete lineage sorting at the rRNA locus; and (5) the basal position of the genera Chaenea and Trachelotractus in molecular trees and phylogenetic networks is very likely a result of class III long-branch effects., (Copyright © 2013 Elsevier GmbH. All rights reserved.)

Our understanding of the evolution of oral structures within the Colpodida is confounded by the low number of morphological characters that can be used in constructing hypotheses, and by the low taxon and character sampling in molecular phylogenetic analyses designed to assess these hypotheses. Here we increase character sampling by sequencing the mitochondrial SSU-rDNA locus for three isolates of the Marynidae sensu lato. We show that the inferred mitochondrial and nuclear SSU-rDNA trees, as well as concatenated and constrained analyses, are congruent in not recovering a monophyletic Marynidae. However, due to low node support, the trees are indifferent to whether the morphological characters used to unite the Marynidae are the result of retention of ancestral states or convergence. In light of this indifference and an increased amount of nuclear and mitochondrial SSU-rDNA data, alternative hypotheses of oral evolution in the Colpodida are presented., (Copyright © 2012 Elsevier GmbH. All rights reserved.)

Although euplotida ciliates are widely used as model organisms in multiple fields of biology, details of their phylogenetic relationships remain unresolved despite a rich history of investigation with small subunit (SSU) rDNA sequences and other characters. Here, six genera in Diophrys-like complex and three other euplotid genera are sampled for SSU-rDNA, ITS1-5.8S-ITS2 and LSU-rDNA, and their phylogenies were inferred with unconstrained and constrained analyses. In general, the concatenated analyses infer more reliable, less ambiguous phylogenies with higher node support values. The following conclusions can be made: (1) four well-supported clades are consistently detected in the family Uronychiidae, forming into two subgroups, which challenge the traditional arrangement based on morphological similarities; (2) the subfamily Diophryinae is paraphyletic; (3) the monophyly of Paradiophrys and the establishment of Apodiophrys and Diophryopsis is fully supported by concatenated data; (4) Apodiophrys and Paradiophrys form independent lineages, at the subfamily level, from other Diophrys-like genera; and (5) the highly specialized Pseudodiophrys nests within Diophrys., (Copyright © 2012 Elsevier Inc. All rights reserved.)

Using nine new taxa and statistical inferences based on morphological and molecular data, we analyze the evolution within the class Colpodea. The molecular and cladistic analyses show four well-supported clades: platyophryids, bursariomorphids, cyrtolophosidids, and colpodids. There is a widespread occurrence of homoplasies, affecting even conspicuous morphological characteristics, e.g. the inclusion of the micronucleus in the perinuclear space of the macronucleus. The most distinct changes in the morphological classification are the lack of a basal divergence into two subclasses and the split of the cyrtolophosidids into two main clades, differing mainly by the presence vs. absence of an oral cavity. The most complex clade is that of the colpodids. We partially reconcile the morphological and molecular data using evolutionary systematics, providing a scenario in which the colpodids evolved from a Bardeliella-like ancestor and the genus Colpoda performed an intense adaptive radiation, giving rise to three main clades: Colpodina n. subord., Grossglockneriina, and Bryophryina. Three new taxa are established: Colpodina n. subord., Tillinidae n. fam., and Ottowphryidae n. fam. Colpodean evolution and classification are far from being understood because sequences are lacking for most species and half of their diversity is possibly undescribed., (© 2011 The Author(s). Journal of Eukaryotic Microbiology © 2011 International Society of Protistologists.)

Taxon sampling for molecular phylogenetic inferences of microbial eukaryotes is limited because of the difficulties in finding specific taxa and culturing them. By contrast, unidentified sequences are easily collected during environmental diversity surveys. Here taxon sampling within prorodontid ciliates is increased using identified cultured isolates, and complemented with unidentified environmental sequences, with the nuclear small subunit rDNA locus. With identified cultured isolates there is support for the morphologically-circumscribed Colepidae. Increasing taxon sampling with unidentified environmental sequences is shown to change both topology and node support in clades that have low sampling for identified cultured isolates. This approach to increasing taxon sampling using unidentified environmental sequences can be used in other ciliate clades in which there is also low taxon sampling., (Copyright © 2010 Elsevier Inc. All rights reserved.)

The ciliate family Cyrtolophosididae Stokes, 1888 contains species that are poorly known from both the morphological and molecular perspectives. To further our understanding of this family, one species, Aristerostoma marinum Kahl, 1931, was redescribed. Cells in our population had a mean in vivo size of 15x8 microm. There were six rows of somatic kineties, as well as six dorsal kinetids belonging to sparsely ciliated somatic kineties. The oral apparatus comprised a bipartite paroral membrane and four adoral organelles. The optimal ecological tolerances for pH and O2 matched those of the environment in which the specimens were collected, but were different for salinity and temperature. To further test the phylogenetic placement of the family Cyrtolophosididae with increased taxon sampling, the small subunit rDNA of three morphospecies was characterized: A. marinum, Aristerostoma sp. ATCC 50986 and Pseudocyrtolophopsis alpestris. Unconstrained and constrained molecular analyses supported the non-monophyly of the order Cyrtolophosidida. The family Cyrtolophosididae fell out separately from the rest of its order. Haplotypes from previous environmental studies were also placed in a phylogenetic context within the class Colpodea.