Tropidoatractidae fam. nov., a Deep Branching Lineage of Metopida (Armophorea, Ciliophora) Found in Diverse Habitats and Possessing Prokaryotic Symbionts

Reductitherus cryptostomus n. gen., n. sp. (Ciliophora: Armophorea: Clevelandellida), a remarkable new nyctotherid from an Australian cockroach, Parapanesthia gigantea (Blaberidae: Panesthiinae)

Ciliates of the family Nyctotheridae (Armophorea: Clevelandellida) are frequent intestinal symbionts of various invertebrates and some poikilotherm vertebrates. Depending on the classification scheme, there are between 15 and 18 recognized genera of Nyctotheridae, the majority of which exhibit a rather uniform morphology. They have round to ellipsoidal cells with an adoral zone of membranelles that begins anteriorly in an adoral groove and continues posteriorly into the buccal cavity where it extends deep into the cell in the peristomial funnel. The taxonomy of the Nyctotheridae is primarily based on the number and location of kinetal sutures. The only known divergence from the relatively conservative nyctortherid body plan are the bizarre symbionts of Panesthiinae cockroaches, ciliates of the family Clevelandellidae, which forms a clade nested within the Nyctotheridae genus Nyctotherus. In this study we report another ciliate that diverges morphologically from the canonical Nyctotheridae body plan, and which is also found in Panesthiinae hosts. The novel ciliate Reductitherus cryptostomus n. gen., n. sp. differs from the rest of Nyctotheridae by absence of the anterior adoral groove, a shortened adoral zone completely enclosed in a notably small buccal cavity, and two strongly reduced kinetal sutures, one left anterodorsal and the other right posterodorsal.

Bit by bit toward the diversity of metopids: Description of the genus Pidimetopus n. gen. (Ciliophora: Armophorea)

While metopids (Armophorea: Metopida) represent the most species-rich group of free-living anaerobic ciliates thriving in hypoxic environments, our understanding of their true diversity remains incomplete. Most metopid species are still characterized only morphologically. Particularly, the so-called IAC clade (named in the past after some of the taxa included, Idiometopus, Atopospira, and Clevelandellida), comprising free-living members as well as the endosymbiotic ones (order Clevelandellida), is in serious need of revision. In our study, we establish a new free-living genus in the IAC clade, Pidimetopus n. gen., with descriptions of two new species, P. nanus n. sp., and P. permonicus n. sp., using up-to-date molecular and morphologic methods. The genus is characterized by small cells (up to 75 μm long), not more than 10 adoral membranelles and eight somatic kineties, and usually, four long caudal cilia that can stiffen. In addition to morphologic and molecular characterizations, we also conducted a statistical morphotype analysis of the polymorphic species P. nanus n. sp. We discuss the relevance of the earlier morphologically described species Metopus minor as a putative collective taxon for several small metopids less than 50 μm long.

Redescription and molecular phylogeny of the freshwater metopid, Castula strelkowi (Jankowski, 1964) from the Czech Republic and synonymization of Pileometopus with Castula

The relationships of the mainly free living, obligately anaerobic ciliated protists belonging to order Metopida continue to be clarified and now comprise three families: Metopidae, Tropidoatractidae, and Apometopidae. The most species-rich genus of the Metopidae, Metopus has undergone considerable subdivision into new genera in recent years as more taxa are characterized by modern morphologic and molecular methods. The genus, Castula, was established to accommodate setae-bearing species previously assigned to Metopus: C. setosa and C. fusca, and one new species, C. flexibilis. Another new species, C. specialis, has been added since. Here we redescribe another species previously included in Metopus, using morphologic and molecular methods, and transfer it to Castula as C. strelkowi n. comb. (original combination Metopus strelkowi). We also reassess the monotypic genus, Pileometopus, which nests within the strongly supported Castula clade in 18S rRNA gene trees and conclude that it represents a morphologically divergent species of Castula.

Morphology, morphogenesis, and molecular characterization of Castula specialis sp. nov. (Ciliophora, Armophorea, Metopida)

The morphology, morphogenesis, and molecular phylogeny of a new metopid ciliate, Castula specialis sp. nov., comprising three strains from geographically distant (China, Mexico, Czech Republic) anoxic freshwater habitats, were studied based on microscopic observation of live and protargol-stained specimens as well as SSU rRNA gene sequence data. The new species is characterized as follows: size in vivo 105-220 × 25-70 μm, body oblong to elongated ellipsoidal and asymmetrical; preoral dome distinctly projecting beyond the body; 32-46 adoral membranelles; 31-52 somatic kineties; and 4-7 setae. This study brings the first morphogenetic investigation of a member of the genus Castula. The morphogenesis of the type population (China) of the new species proceeds as in Metopus spp. comprising drastic changes in body shape and a pleurotelokinetal stomatogenesis; however, the main difference is the origin of the opisthe's paroral membrane that derives from all perizonal rows and some adjacent dome kineties. Phylogenetically, the genus Castula is paraphyletic.

Single cell transcriptomics reveals UAR codon reassignment in Palmarella salina (Metopida, Armophorea) and confirms Armophorida belongs to APM clade

Anaerobes have emerged in several major lineages of ciliates, but the number of independent transitions to anaerobiosis among ciliates is unknown. The APM clade (Armophorea, Muranotrichea, Parablepharismea) represents the largest clade of obligate anaerobes among ciliates and contains free-living marine and freshwater representatives as well as gut endobionts of animals. The evolution of APM group has only recently started getting attention, and our knowledge on its phylogeny and genetics is still limited to a fraction of taxa. While ciliates portray a wide array of alternatives to the standard genetic code across numerous classes, the APM ciliates were considered to be the largest group using exclusively standard nuclear genetic code. In this study, we present a pan-ciliate phylogenomic analysis with emphasis on the APM clade, bringing the first phylogenomic analysis of the family Tropidoatractidae (Armophorea) and confirming the position of Armophorida within Armophorea. We include five newly sequenced single cell transcriptomes from marine, freshwater, and endobiotic APM ciliates - Palmarella salina, Anteclevelandella constricta, Nyctotherus sp., Caenomorpha medusula, and Thigmothrix strigosa. We report the first discovery of an alternative nuclear genetic code among APM ciliates, used by Palmarella salina (Tropidoatractidae, Armophorea), but not by its close relative, Tropidoatractus sp., and provide a comparative analysis of stop codon identity and frequency indicating the precedency to the UAG codon loss/reassignment over the UAA codon reassignment in the specific ancestor of Palmarella. Comparative genomic and proteomic studies of this group may help explain the constraints that underlie UAR stop-to-sense reassignment, the most frequent type of alternative nuclear genetic code, not only in ciliates, but eukaryotes in general.

Morphogenesis of an anaerobic ciliate Heterometopus palaeformis (Kahl, 1927) Foissner, 2016 (Ciliophora, Armophorea) with notes on its morphological and molecular characterization

The morphology, morphogenesis, and molecular phylogeny of Heterometopus palaeformis (Kahl, 1927) Foissner, 2016 were studied using microscopical observations on live and protargol-stained specimens as well SSU rRNA gene sequencing. The morphogenetic data for the genus are presented for the first time. Compared to other metopids, the morphogenesis of H. palaeformis is distinct since its (1) perizonal stripe rows 4 and 5 are involved in the formation of the opisthe's adoral polykinetids; (2) perizonal stripe rows 3-5 and two adjacent preoral dome kineties contribute to most of the opisthe's paroral membrane while perizonal stripe rows 1 and 2 contribute very little; (3) four kinety rows are formed to the left of the opisthe's adoral zone of polykinetids. The Chinese population resembles the original and neotype populations well in terms of general morphology - characterized by a life size of 55-120 × 10-20 μm, an elongate ellipsoidal body with a hardly spiralized flat preoral dome, about 18 somatic kineties and 20 adoral polykinetids. The SSU rDNA sequence of the present population exhibits a disparity of 1.33%-2.22% divergence from sequences of other populations. Nevertheless, phylogenetic analysis reveals that populations of H. palaeformis form a separate, stable cluster within the paraphyletic Metopidae clade.

Methanogenic symbionts of anaerobic ciliates are host and habitat specific

The association between anaerobic ciliates and methanogenic archaea has been recognized for over a century. Nevertheless, knowledge of these associations is limited to a few ciliate species, and so the identification of patterns of host-symbiont specificity has been largely speculative. In this study, we integrated microscopy and genetic identification to survey the methanogenic symbionts of 32 free-living anaerobic ciliate species, mainly from the order Metopida. Based on Sanger and Illumina sequencing of the 16S rRNA gene, our results show that a single methanogenic symbiont population, belonging to Methanobacterium, Methanoregula, or Methanocorpusculum, is dominant in each host strain. Moreover, the host's taxonomy (genus and above) and environment (i.e. endobiotic, marine/brackish, or freshwater) are linked with the methanogen identity at the genus level, demonstrating a strong specificity and fidelity in the association. We also established cultures containing artificially co-occurring anaerobic ciliate species harboring different methanogenic symbionts. This revealed that the host-methanogen relationship is stable over short timescales in cultures without evidence of methanogenic symbiont exchanges, although our intraspecific survey indicated that metopids also tend to replace their methanogens over longer evolutionary timescales. Therefore, anaerobic ciliates have adapted a mixed transmission mode to maintain and replace their methanogenic symbionts, allowing them to thrive in oxygen-depleted environments.

Comprehensive phylogenomic analyses reveal that order Armophorida is most closely related to class Armophorea (Protista, Ciliophora)

Ciliate species within the class Armophorea are widely distributed in various anaerobic environments, hence they are of great interest to researchers studying evolution and adaptation of eukaryotes to extreme habitats. However, phylogenetic relationships within the class remain largely elusive, most especially assignment of the order Armophorida and classification within the family Metopidae. In this study, we newly sequenced transcriptomes and the SSU rDNA of five armophorean species, Sulfonecta cf. uniserialis (order Armophorida), Nyctotheroides sp. (order Clevelandellida), and Metopus major, M. paraes, and Brachonella contorta (order Metopida). Comprehensive phylogenomic analyses revealed that Armophorea was most closely related to Muranotrichea and Parablepharismea. Our results indicate that the order Armophorida either belongs to Armophorea or represents a new class within APM (Armophorea-Parablepharismea-Muranotrichea). Analyses combining ecological niches and molecular trees showed that APM species might descend from an anaerobic free-living ciliate species. Existing molecular phylogenomic/phylogenetic and morphological evidence indicate that the family Metopidae is non-monophyletic and should be further classified with inclusion of additional lines of evidences. Our results provide new insights into the long-debated relationships within Armophorea.

Morphology and phylogenetic position of three anaerobic ciliates from the classes Odontostomatea and Muranotrichea (Ciliophora)

The diversity of the classes Odontostomatea and Muranotrichea, which contain solely obligate anaerobes, is poorly understood. We studied two populations of Mylestoma sp., one of Saprodinium dentatum (Odontostomatea), two of Muranothrix felix sp. nov., and one of Muranothrix sp. (Muranotrichea) employing live observation, protargol impregnation, scanning electron microscopy, and 18S rRNA gene sequencing. Conspecificity of Mylestoma sp., described here, with a previously described species of this genus cannot be excluded since no species have been studied with modern methods. Phylogenetically, the genus Mylestoma is closely related to the odontostomatid Discomorphella pedroeneasi, although the phylogenetic position of class Odontostomatea itself remains unresolved. The newly described muranotrichean species, Muranothrix felix sp. nov., is morphologically similar to M. gubernata but can be distinguished by its fewer macronuclear nodules and fewer adoral membranelles; moreover, it is clearly distinguished from M. gubernata by its 18S rRNA gene sequence. Another population, designated here as Muranothrix sp., most likely represents a separate species.

Phylogeny of the anaerobic ciliate genus Sonderia (Protista: Ciliophora: Plagiopylea), including the description of three novel species and a brief revision of the genus

Anaerobic protists in general, and ciliates in particular, are important components of anoxic or hypoxic environments, however, their diversity remains underestimated. Sonderia is a poorly studied genus that is distributed worldwide and is commonly found in anaerobic environments. In the present study, the taxonomy and phylogeny of three new species, namely Sonderia aposinuata sp. nov., Sonderia paramacrochilus sp. nov. and Sonderia steini sp. nov., collected from China, were investigated based on microscopic observations and SSU rRNA gene sequencing methods. Sonderia aposinuata sp. nov. is diagnosed mainly by having a relatively large body size, a crescent-shaped oral opening, numerous slender extrusomes, one suture on the ventral side and two on the dorsal side, and a buccal cavity that occupies the anterior third of the cell. Sonderia paramacrochilus sp. nov. closely resembles S. macrochilus but differs mainly by its oral opening being located closer to the anterior cell margin and its spindle-shaped extrusomes. Sonderia steini sp. nov. is a freshwater species that can be recognized by its shallow buccal cavity, sparsely distributed rod-shaped extrusomes, and having 68-79 monokinetidal somatic kineties that form sutures on both sides of the body. Phylogenetic analyses based on small subunit ribosomal RNA (SSU rRNA) gene sequence data support the monophyly of the family Sonderiidae, however, Sonderia is paraphyletic. The genus Sonderia is briefly revised and a key to the identification of species belonging to this genus is supplied.

Diversity and Phylogenetic Position of Bothrostoma Stokes, 1887 (Ciliophora: Metopida), with Description of Four New Species

Bothrostoma is a genus of anaerobic ciliates in family Metopidae comprising four species, all described based solely on the morphology of living and fixed cells. Unlike other metopids, cells of Bothrostoma are not twisted anteriorly, have a flattened preoral dome, a very prominent sail-like paroral membrane, and an adoral zone of distinctive, very narrow, curved membranelles confined to a wide, non-spiraling peristome on the ventral side. We examined 20 populations of Bothrostoma from hypoxic freshwater sediments. We provide morphological characterization and 18S rRNA gene sequences of four new species, namely B. bimicronucleatum sp. nov., B. boreale sp. nov., B. kovalyovi sp. nov., and B. robustum sp. nov., as well as B. undulans (type species), B. nasutum, and B. ovale comb. nov. (original combination Metopus undulans var. ovalis Kahl, 1932). Except for B. nasutum, Bothrostoma species show low genetic variability among geographically distant populations. Intraspecific phenotypic variability might be driven by environmental conditions. In phylogenetic analyses, Bothrostoma is not closely related to Metopus sensu stricto and forms a moderately supported clade with Planometopus, here referred to as BoPl clade. The anterior axial torsion of the body, typical of other Metopidae, appears to have been lost in the last common ancestor of the BoPl clade.

Anaerobic Ciliates as a Model Group for Studying Symbioses in Oxygen-depleted Environments

Anaerobiosis has independently evolved in multiple lineages of ciliates, allowing them to colonize a variety of anoxic and oxygen-depleted habitats. Anaerobic ciliates commonly form symbiotic relationships with various prokaryotes, including methanogenic archaea and members of several bacterial groups. The hypothesized functions of these ecto- and endosymbionts include the symbiont utilizing the ciliate's fermentative end-products to increase host's anaerobic metabolic efficiency, or the symbiont directly providing the host with energy by denitrification or photosynthesis. The host, in turn, may protect the symbiont from competition, the environment, and predation. Despite rapid advances in sampling, molecular, and microscopy methods, as well as the associated broadening of the known diversity of anaerobic ciliates, many aspects of these ciliate symbioses, including host-specificity and co-evolution, remain largely unexplored. Nevertheless, with the number of comparative genomic and transcriptomic analyses targeting anaerobic ciliates and their symbionts on the rise, insights into the nature of these symbioses and the evolution of the ciliate transition to obligate anaerobiosis continue to deepen. This review summarizes the current body of knowledge regarding the complex nature of symbioses in anaerobic ciliates, the diversity of these symbionts, their role in the evolution of ciliate anaerobiosis and their significance in ecosystem-level processes.

Morphology and phylogeny of two anaerobic freshwater ciliates: Brachonella comma sp. nov. and the widely-distributed but little-known caenomorphid, Ludio parvulus Penard, 1922

Hypoxic, sulfidic freshwater sediments typically support a diffuse consortium of distinctive ciliated protists, including caenomorphids, metopids, and odontostomatids among others. A recent resurgence of interest in these important members of sapropelic food webs has resulted in the description of many new species and an effort, still in its infancy, to characterize them from a morphologic, molecular, and metabolic standpoint and to determine their phylogenetic relationships. Their seemingly invariable association with prokaryotic endosymbionts and, less commonly, ectosymbionts, has become a focus for many researchers. In this report, based on morphologic and molecular data we describe a Brachonella species (Ciliophora, Metopida) new to science and analyze its phylogeny. We also provide a morphologic and molecular characterization of the smallest representative of the Caenomorphidae Poche, 1913, Ludio parvulus Penard, 1922. The phylogenetic analysis confirms the inclusion of this species in the Caenomorphidae.

Ciliate SSU-rDNA reference alignments and trees for phylogenetic placements of metabarcoding data

Although ciliates are one of the most dominant microbial eukaryotic groups in many environments, there is a lack of updated global ciliate alignments and reference trees that can be used for phylogenetic placement methods to analyze environmental metabarcoding data. Here we fill this gap by providing reference alignments and trees for those ciliates taxa with available SSU-rDNA sequences derived from identified species. Each alignment contains 478 ciliate and six outgroup taxa, and they were made using different masking strategies for alignment positions (unmasked, masked and masked except the hypervariable V4 region). We constrained the monophyly of the major ciliate groups based on the recently updated classification of protists and based on phylogenomic data. Taxa of uncertain phylogenetic position were kept unconstrained, except for Mesodinium species that we constrained to form a clade with the Litostomatea. These ciliate reference alignments and trees can be used to perform taxonomic assignments of metabarcoding data, discover novel ciliate clades, estimate species richness, and overlay measured ecological parameters onto the phylogenetic placements.

Usefulness of a 3D-printing air sampler for capturing live airborne bacteria and exploring the environmental factors that can influence bacterial dynamics

We created a handmade 3D-printed air sampler to effectively collect live airborne bacteria, and determined which environmental factors influenced the bacteria. Bacterial colony forming units (CFUs) in the air samples (n=37) were monitored by recording the environmental changes occurring over time, then determining the presence/absence of correlations among such changes. The bacterial CFUs changed sharply and were significantly correlated with the DNA concentrations, indicating that the captured bacteria made up most of the airborne bacteria. Spearman's rank correlation analysis revealed significant correlations between the bacterial CFU values and some environmental factors (humidity, wind speed, insolation, and 24-h rainfall). Similarly the significant associations of CFU with humidity and wind speed were also found by multiple regression analysis with box-cox transformation. Among our panel of airborne bacteria (952 strains), 70 strains were identified as soil-derived Bacillus via the production of Escherichia coli- and Staphylococcus aureus-growth inhibiting antibiotics and by 16S rDNA typing. Soil-derived protozoa were also isolated from the air samples. We conclude that the airborne bacteria mainly derived from soil can alter in number according to environmental changes. Our sampler, which was created by easy-to-customize 3D printing, is a useful device for understanding the dynamics of live airborne bacteria.

Morphology and molecular phylogeny of the anaerobic freshwater ciliate Urostomides spinosus nov. spec. (Ciliophora, Armophorea, Metopida) from China

The morphology and molecular phylogeny of a new metopid ciliate, Urostomides spinosus nov. spec., discovered in a freshwater ditch in Qingdao, China, were investigated using live observation, morphometry and protargol staining as well as molecular phylogenetic methods. Diagnostic features of the new species include a broadly obpyriform body carrying three posterior spines, eight somatic kineties, five preoral dome kineties with specialized row 3, adoral zone composed of about 28 membranelles, making a 270° turn around body axis. Phylogenetic analyses of the SSU rDNA sequence revealed that the genus Urostomides is monophyletic, but its interspecific relationships remained unresolved. Moreover, a closer relationship of the new species with the morphologically similar Urostomides campanula was not supported by the molecular data.

Two Anaerobic Ciliates (Ciliophora, Armophorea) from China: Morphology and SSU rDNA Sequence, with Report of a New Species, Metopus paravestitus nov. spec

The morphology and phylogeny of two metopid ciliates, collected from anaerobic habitats in China, were investigated using live observation, protargol staining method, and SSU rDNA sequencing. The new species Metopus paravestitus nov. spec. can be distinguished by a combination of the following features: oblong cell with densely arranged ectobiotic prokaryotes perpendicular to cell surface, filiform intracytoplasmic structures packed in the anterior portion of the cell. Our work also demonstrates the wide geographical distribution of Metopus es (Müller, 1776) Lauterborn, 1916. The order Metopida is consistently depicted as a paraphylum in SSU rDNA phylogeny. Metopus paravestitus nov. spec. is closely related to its marine congeners than to freshwater forms. The present study confirms once again the non-monophyly of the genus Metopus and genus Metopidae.

Description of Three New Genera of Metopidae (Metopida, Ciliophora): Pileometopus gen. nov., Castula gen. nov., and Longitaenia gen. nov., with Notes on the Phylogeny and Cryptic Diversity of Metopid Ciliates

We report the discovery of three new species of freshwater metopid ciliates, Pileometopus lynni gen. et sp. nov., Castula flexibilis gen. et sp. nov., and Longitaenia australis gen. et sp. nov. Based on morphologic features and the 18S rRNA gene phylogeny, we transfer two known species of Metopus to the new genus Castula, as C. fusca (Kahl, 1927) comb. nov. and C. setosa (Kahl, 1927) comb. nov. and another known species is herein transferred to the new genus Longitaenia, as L. gibba (Kahl, 1927) comb. nov. Pileometopus is characterized by a turbinate body shape, a dorsal field of densely spaced dikinetids, a bipartite paroral membrane, and long caudal cilia. A distinctive morphologic feature of Castula species is long setae arising over the posterior third of the body (as opposed to a terminal tuft). Longitaenia spp. are characterized by an equatorial cytostome and long perizonal ciliary stripe relative to the cell length. Based on phylogenetic analyses of 18S rRNA gene sequences, we identify and briefly discuss strongly supported clades and intraspecific genetic polymorphism within the order Metopida.

Genomics of New Ciliate Lineages Provides Insight into the Evolution of Obligate Anaerobiosis

Oxygen plays a crucial role in energetic metabolism of most eukaryotes. Yet adaptations to low-oxygen concentrations leading to anaerobiosis have independently arisen in many eukaryotic lineages, resulting in a broad spectrum of reduced and modified mitochondrion-related organelles (MROs). In this study, we present the discovery of two new class-level lineages of free-living marine anaerobic ciliates, Muranotrichea, cl. nov. and Parablepharismea, cl. nov., that, together with the class Armophorea, form a major clade of obligate anaerobes (APM ciliates) within the Spirotrichea, Armophorea, and Litostomatea (SAL) group. To deepen our understanding of the evolution of anaerobiosis in ciliates, we predicted the mitochondrial metabolism of cultured representatives from all three classes in the APM clade by using transcriptomic and metagenomic data and performed phylogenomic analyses to assess their evolutionary relationships. The predicted mitochondrial metabolism of representatives from the APM ciliates reveals functional adaptations of metabolic pathways that were present in their last common ancestor and likely led to the successful colonization and diversification of the group in various anoxic environments. Furthermore, we discuss the possible relationship of Parablepharismea to the uncultured deep-sea class Cariacotrichea on the basis of single-gene analyses. Like most anaerobic ciliates, all studied species of the APM clade host symbionts, which we propose to be a significant accelerating factor in the transitions to an obligately anaerobic lifestyle. Our results provide an insight into the evolutionary mechanisms of early transitions to anaerobiosis and shed light on fine-scale adaptations in MROs over a relatively short evolutionary time frame.