Molecular phylogeny of a new gonostomatid ciliate revealing a discrepancy between interphasic and cell divisional patterns (Ciliophora, Hypotricha)

Morphology and molecular phylogeny of two hypotrichous ciliates (Ciliophora, Spirotrichea) from South Korea, including Hemiurosomoida koreana n. sp

The living morphology, infraciliature, and molecular phylogeny of a new soil ciliate, Hemiurosomoida koreana n. sp., discovered in a sample collected from a mountain in the northeast of South Korea, were investigated. The new species possesses the characteristics of the genus Hemiurosomoida, i.e., a reduced number of frontal-ventral-transverse cirri, three dorsal kineties of which kineties 1 and 2 each bears a caudal cirrus, and a single dorsomarginal kinety. It is distinguishable from congeners and other similar species by at least one distinct qualitative or quantitative character including the body size, the presence and arrangement of cortical granules, the number of adoral membranelles, marginal cirri, and dorsal dikinetids, or by the arrangement of transverse cirri. Phylogenetic analyses based on 18S rRNA gene sequences also support the assignment of the new species to the non-monophyletic genus Hemiurosomoida. In addition, the living morphology, infraciliature, and the 18S rRNA gene sequence of a Korean population of Nothoholosticha flava were studied.

Integrative data of a novel ciliate (Alveolata, Ciliophora) propose the establishment of Heterodeviata nantongensis nov. sp

BACKGROUND

As unicellular eukaryotes, ciliates are an indispensable component of micro-ecosystems that play the role of intermediate nutrition link between bacteria or algae and meiofauna. Recent faunistic studies have revealed many new taxa of hypotrich ciliates, indicating their diversity is greater than previously thought. Here we document an undescribed form isolated from an artificial brackish water pond in East China. Examination of its morphology, ontogenesis and molecular phylogeny suggests that it represents a new species.

RESULTS

The morphology and morphogenesis of the new brackish-water deviatid ciliate, Heterodeviata nantongensis nov. sp., isolated from Nantong, China, were investigated using live observations and protargol staining. The diagnostic traits of the new species include three frontal cirri, one buccal cirrus, one or two parabuccal cirri, an inconspicuous frontoventral cirral row of four to six frontoventral cirri derived from two anlagen, three left and two right marginal rows, two dorsal kineties, dorsal kinety 1 with 9-14 dikinetids and dorsal kinety 2 with only two dikinetids, and one to three caudal cirri at the rear end of dorsal kinety 1. Its main morphogenetic features are: (i) the old oral apparatus is completely inherited by the proter except undulating membranes, which are reorganized in situ; (ii) anlagen for marginal rows and the left dorsal kinety develop intrakinetally in both proter and opisthe; (iii) dorsal kinety 2 is generated dorsomarginally; (iv) five cirral anlagen are formed in both proter and opisthe; (v) in the proter, anlagen I and II very likely originate from the parental undulating membranes and the buccal cirrus, respectively, anlage III from anterior parabuccal cirrus, anlage IV originates from the parental frontoventral cirri and anlage V from the innermost parental right marginal row; and (vi) anlagen I-IV of the opisthe are all generated from oral primordium, anlage V from the innermost parental right marginal row. Phylogenetic analyses based on SSU rRNA gene sequence data were performed to determine the systematic position of the new taxon.

CONCLUSIONS

The study on the morphology, and ontogenesis of a new brackish-water taxon increases the overall knowledge about the biodiversity of this ciliate group. It also adds to the genetic data available and further provides a reliable reference for environmental monitoring and resource investigations.

Morphology, morphogenesis and molecular phylogeny of a novel saline soil ciliate, Urosoma quadrinucleatum n. sp. (Ciliophora, Hypotrichia)

The morphology and morphogenesis of a new saline soil hypotrichous ciliate, Urosoma quadrinucleatum n. sp., collected from northwestern China, were studied based on live observations and protargol stained specimens. The new species is characterized as follows: size in vivo 90-130 × 20-30 μm; body outline elongate-elliptical with both ends broadly rounded; four macronuclear nodules; cortical granules present; paroral in front of endoral; usually 16 frontal-ventral-transverse cirri. Urosoma quadrinucleatum n. sp. has almost the same morphogenetic characteristics as its congeners U. gigantea and U. salmastra, and differs from other three congeners whose morphogenesis is known in the formation of the frontal-ventral-transverse cirral anlagen as well as the development of marginal and dorsal kineties anlagen. The sequence differences among U. quadrinucleatum n. sp. and other Urosoma species further support the validity of the present organism as novel species. Further, U. quadrinucleatum n. sp. clusters with U. salmastra in the phylogenetic analyses based on small subunit ribosomal RNA gene (SSU rDNA) sequence data.

Ontogenesis and systematic position of a new hypotrichous ciliate, Chaetospira sinica sp. nov., with an improved diagnosis of the poorly defined family Chaetospiridae Jankowski, 1985 (Protozoa, Ciliophora, Hypotrichia)

Ciliates are unique single-celled organisms that play important roles in ecological, environmental, evolutionary, and ontogenetic research. In the present study, phylogenetic analyses based on 18S rRNA gene sequence data reveal that Chaetospira sinica sp. nov. clusters with Stichotricha aculeata with strong to full support (97% ML, 1.00 BI), but is not closely related to members of Spirofilidae Gelei, 1929 to which Chaetospira and Stichotricha have previously been assigned. Phylogenetic analyses, together with morphological and morphogenetic data from Chaetospira sinica sp. nov., support the validity of family Chaetospiridae Jankowski, 1985. Chaetospira and Stichotricha are here assigned to the family Chaetospiridae, the improved diagnosis of which is as follows: non-dorsomarginalian Hypotrichia with flask-shaped body; oral region extending along narrow anterior neck region; lorica usually present; two ventral and two marginal cirral rows, all distinctly spiraled or obliquely curved; pretransverse and transverse cirri absent. The basic morphogenetic features in C. sinica sp. nov. can be summarized as: (1) the oral primordium for the opisthe develops de novo and the parental adoral zone is completely retained by the proter; (2) all ventral cirral anlagen and marginal anlagen developed intrakinetally; (3) three dorsal kineties anlagen formed intrakinetally in each daughter cell; and (4) macronuclear nodules fuse into a single mass. Exconjugant cells were also isolated and their morphologic and molecular data are provided.

Hypotrichidium tisiae (Gelei, 1929) Gelei, 1954: a unique hypotrichid ciliate having a highly specialized developmental pattern during binary division

In sharp contrast to their pelagic relatives, the oligotrichs, the overwhelming majority of hypotrich ciliates inhabit the benthos. Only a few species, including those of the genus Hypotrichidium Ilowaisky, 1921, have adapted to a planktonic lifestyle. The ontogenetic mode of the highly differentiated ciliate, Hypotrichidium tisiae (Gelei, 1929) Gelei, 1954, is unknown. In this study, the interphase morphology and the ontogenetic process of this species are investigated. Accordingly, the previously unidentified ciliary pattern of Hypotrichidium is redefined. The main morphogenetic features are as follows: (1) The parental adoral zone of membranelles is inherited completely by the proter and the oral primordium of the opisthe arises in a deep pouch. (2) Five frontoventral cirral anlagen (FVA) are formed: FVA I contributes to the single frontal cirrus, FVA II-IV generate three frontoventral cirral rows, FVA V migrates and forms postoral ventral cirri. (3) All marginal cirral row anlagen develop de novo: each of the two left anlagen forms a single cirral row, while the single right anlage fragments into anterior and posterior parts. (4) Two dorsal kinety anlagen occur de novo, with the right one fragmenting to form kineties 2 and 3. (5) Two long caudal cirral rows are formed at the ends of dorsal kineties 1 and 3. On the basis of the morphogenetic features and phylogenetic analyses, the assignment of Hypotrichidium to the family Spirofilidae Gelei, 1929 within Postoralida is supported. The establishment of separate families for the slender "tubicolous" spirofilids and the highly helical spirofilids is also validated.

Supplementary Information

The online version contains supplementary material available at 10.1007/s42995-022-00148-9.

Biodiversity of freshwater ciliates (Protista, Ciliophora) in the Lake Weishan Wetland, China: the state of the art

Ciliates are core components of the structure of and function of aquatic microbial food webs. They play an essential role in the energy flow and material circulation within aquatic ecosystems. However, studies on the taxonomy and biodiversity of freshwater ciliates, especially those in wetlands in China are limited. To address this issue, a project to investigate the freshwater ciliates of the Lake Weishan Wetland, Shandong Province, commenced in 2019. Here, we summarize our findings to date on the diversity of ciliates. A total of 187 ciliate species have been found, 94 of which are identified to species-level, 87 to genus-level, and six to family-level. These species show a high morphological diversity and represent five classes, i.e., Heterotrichea, Litostomatea, Prostomatea, Oligohymenophorea, and Spirotrichea. The largest number of species documented are oligohymenophoreans. A comprehensive database of these ciliates, including morphological data, gene sequences, microscope slide specimens and a DNA bank, has been established. In the present study, we provide an annotated checklist of retrieved ciliates as well as information on the sequences of published species. Most of these species are recorded in China for the first time and more than 20% are tentatively identified as new to science. Additionally, an investigation of environmental DNA revealed that the ciliate species diversity in Lake Weishan Wetland is higher than previously supposed.

Supplementary Information

The online version contains supplementary material available at 10.1007/s42995-022-00154-x.

The taxonomy and molecular phylogeny of two epibiotic colonial peritrich ciliates (Ciliophora, Peritrichia)

Two colonial sessilid peritrichs, Epistylis qingdaoensis n. sp. and Carchesium cyclopidarum Nenninger, 1948, were isolated from a marine crustacean and a freshwater mayfly, respectively. Morphological characters for each species were revealed by in vivo observations and silver staining methods. Epistylis qingdaoensis n. sp. is characterized by the apperance of the colony which is up to 250 μm high and usually contains fewer than eight zooids, the single-layered peristomial lip, the conspicuously conical peristomial disc, and the structure of infundibular polykinety 3 which comprises three isometric ciliary rows. Carchesium cyclopidarum is recognized by the colony height of about 600 μm, the small zooid size of 35-50 × 20-30 μm, and the low number of silverlines. Phylogenetic analyses based on small subunit ribosomal DNA sequences were performed to reveal their evolutionary relationships. Surprisingly, neither species clustered with its congeners. Epistylis qingdaoensis n. sp. nested within a clade of Zoothamnium species that was sister to a clade comprising core Epistylis species and several Zoothamnium species. Carchesium cyclopidarum nested within a clade comprising solitary peritrichs and was distantly related to the type species of Carchesium, C. polypinum. These findings imply for the first time that Carchesium is non-monophyletic.

Insights into the phylogeny of the family Deviatidae (Protozoa, Ciliophora, Hypotrichia) based on multi-gene, morphological and ontogenetic information, with the establishment of a new species Deviata multilineae n. sp

Hitherto, the phylogeny of ciliated protists, an important group of model organisms in many fields, has been mainly based on a single marker gene (SSU rDNA, nuclear small subunit ribosomal RNA gene). However, there is increasing evidence showing this is insufficient to provide robust phylogenies and has resulted in confusing systematics in many ciliates groups. Among these, the phylogenies within family Deviatidae (Spirotrichea, Hypotrichia) are ambiguous due to the dependence on SSU rDNA and undersampling. Here, we provide eight new sequences and conduct phylogenetic analyses based on both multi-gene and single-gene to clarify evolutionary relationships among all deviatids for which gene sequence are available. The results reveal that: (1) the monophyly of Deviatidae is well-supported by both single-gene and concatenated data; (2) the presence of fine cirri and relatively wide spacing of these cirri within all rows are plesiomorphies of Deviatidae; (3) Pseudosincirra longicirrata is closely related to Deviata rositae, which is supported by their shared possession of dorsomarginal kineties; (4) phylogenetic analyses and approximately unbiased test based on multi-gene support a close relationship among taxa lacking dorsomarginal kineties (D. parabacilliformis, D. multilineae nov. spec., D. abbrevescens, D. brasiliensis and Perisincirra paucicirrata); (5) Deviatidae shows a close relationship with Dorsomarginalia and Strongylidium-Hemiamphisiella-Pseudouroleptus assemblage, suggesting the presence/absence of dorsomarginal kineties is phylogenetically informative in this family and presence of them may be a plesiomorphy. Based on the morphological, morphogenetic and phylogenetic data, the evolutionary relationships within Deviatidae are hypothesized, and a new ciliate, Deviata multilineae nov. spec., collected from China, is investigated.

Phylogeny of a new ciliate family Clampidae fam. nov. (Protista: Ciliophora), with notes on morphology and morphogenesis

Hypotrichs comprise a highly differentiated and diversified group of ciliates with an evolutionary history characterized by an exceptional number of convergences and reversions. A new hypotrich ciliate from a freshwater fishpond is investigated based on morphological, morphogenetic and molecular data. The phylogenetic analyses reveal that the new species is closely related to Simplicitergida despite the absence of zigzag-patterned midventral cirral pairs, a common feature of simplicitergids. The phylogenetic position of this atypical simplicitergid species is strongly supported by the conserved features of dorsal ciliature and nuclear apparatus, which are probably more informative than cirral patterns for higher-rank classification. The close phylogenetic relationships among those Simplicitergida with varied cirral patterns could be explained by evolutionary convergences and reversions. The new species is recognized mainly by three frontoventral rows, several short midventral rows, two long midventral rows and the absence of zigzag-patterned midventral cirral pairs. Based on comprehensive phylogenetic analyses, together with detailed morphological and morphogenetic comparisons, a new family, Clampidae fam. nov., is proposed for the new genus and species, Clampia sinica gen. et sp. nov. In addition, an emended diagnosis of the morphologically similar family Epiclintidae is provided.

Deciphering phylogenetic relationships in class Karyorelictea (Protista, Ciliophora) based on updated multi-gene information with establishment of a new order Wilbertomorphida n. ord

The class Karyorelictea, a unique assemblage of ciliates, is a key group in deciphering ciliate evolution history. However, the systematic relationships among members of this class remain poorly understood. Here we newly obtained eight small subunit (SSU) rDNA, 24 large subunit (LSU) rDNA, and 25 ITS1-5.8S-ITS2 sequences (covering 25 species, 10 genera and 4 out of 6 families) to analyze the phylogenetic relationships within Karyorelictea. Our results indicate that: (1) considering its unique morphology and early branching position in the SSU rDNA-based tree, the family Wilbertomorphidae represents a new taxon at order level, hence the new order Wilbertomorphida n. ord. is established; (2) all five families with available molecular information are monophyletic, as expected, and the orders Loxodida and Protostomatida show a closer relationship than with Protoheterotrichida; (3) in Trachelocercidae, the compound circumoral kineties is believed to be a plesiomorphic feature while the single circumoral kinety is synapomorphic; and (4) the freshwater genus Loxodes could be derived from the marine Remanella and both share most morphological features. Taken together, these muti-gene analyses provide further insights into the phylogeny of the diverse clades in Karyorelictea.

Redescription, Morphogenesis, and Molecular Phylogeny of Pseudosincirra longicirrata nov. comb., With Establishment of a New Genus Pseudosincirra nov. gen. (Ciliophora, Hypotrichia)

The morphology and morphogenesis of Pseudosincirra longicirrata nov. gen. and nov. comb., isolated from southern China, were investigated with living observation and protargol staining. Our population is similar to the original population in living characteristics and ciliary patterns. The main determinable morphogenetic features of P. longicirrata nov. comb. are the presence of five frontoventral-transverse cirral anlagen (FVT-anlagen) and a dorsomarginal kinety anlage. According to the origin of FVT-anlagen IV and V in proter, it can be determined that P. longicirrata nov. comb. possesses two frontoventral rows and one right marginal row. Hence, a new genus, Pseudosincirra nov. gen., is proposed, and the diagnosis of P. longicirrata nov. comb. is improved. The new genus is diagnosed as follows: adoral zone of membranelles and undulating membranes is in a Gonostomum pattern; there are three enlarged frontal cirri, one buccal cirrus, and one parabuccal cirrus; postperistomial cirrus and transverse cirri are lacking; there are two more or less long frontoventral rows and one right and two or more left marginal rows; cirri within all rows very widely spaced; dorsal kinety pattern is of Urosomoida type, that is, three dorsal kineties and one dorsomarginal kinety; and caudal cirri are present. Phylogenetic analyses based on the small subunit ribosomal (SSU rDNA) sequence data indicate that P. longicirrata nov. comb. clusters with Deviata and Perisincirra. It is considered that Pseudosincirra nov. gen. and Perisincirra paucicirrata should be assigned to the family Deviatidae; fine cirri, and cirri within all rows being relatively widely spaced, should be considered as plesiomorphies of Deviatidae; and Deviatidae is closely related to Dorsomarginalia or Strongylidium-Hemiamphisiella-Pseudouroleptus.