Progress in studies on the diversity and distribution of planktonic ciliates (Protista, Ciliophora) in the South China Sea

Genomic insights into the cellular specialization of predation in raptorial protists

BACKGROUND

Predation is a fundamental mechanism for organisms to acquire energy, and various species have evolved diverse tools to enhance their hunting abilities. Among protozoan predators, raptorial Haptorian ciliates are particularly fascinating as they possess offensive extrusomes known as toxicysts, which are rapidly discharged upon prey contact. However, our understanding of the genetic processes and specific toxins involved in toxicyst formation and discharge is still limited.

RESULTS

In this study, we investigated the predation strategies and subcellular structures of seven Haptoria ciliate species and obtained their genome sequences using single-cell sequencing technology. Comparative genomic analysis revealed distinct gene duplications related to membrane transport proteins and hydrolytic enzymes in Haptoria, which play a crucial role in the production and discharge of toxicysts. Transcriptomic analysis further confirmed the abundant expression of genes related to membrane transporters and cellular toxins in Haptoria compared to Trichostomatia. Notably, polyketide synthases (PKS) and L-amino acid oxidases (LAAO) were identified as potentially toxin genes that underwent extensive duplication events in Haptoria.

CONCLUSIONS

Our results shed light on the evolutionary and genomic adaptations of Haptorian ciliates for their predation strategies in evolution and provide insights into their toxic mechanisms.

Description of Holostichides (Extraholostichides) eastensis tianjinensis subgen. nov. subspec. nov. (Ciliophora, Hypotricha) from northern China

The morphology and morphogenesis of a new urostylid, Holostichides (Extraholostichides) eastensis tianjinensis subgen. nov. subspec. nov. were analyzed. The new subspecies differs from the nominotypical subspecies H. (Extraholostichides) eastensis eastensis Wang et al., 2022 by the relatively long frontoterminal row (about 60% vs. 30% of body length), colorless cortical granules (vs. dark brown), two (vs. one) parabuccal cirri, and usually an extra cirrus behind the first midventral pair (vs. lacking). Based on the difference in the frontal ciliature, we split Holostichides into two subgenera: H. (Extraholostichides) subgen. nov. (type species Holostichides eastensis Wang et al., 2022; with a short cirral row behind the middle frontal cirrus) and H. (Holostichides) Foissner, 1987 (type species Holostichides chardezi Foissner, 1987; lacking this short row). The main morphogenetic characters of the new subspecies are very similar to those of H. (Extraholostichides) eastensis eastensis except for some minor differences. Phylogenetic analyses based on SSU rDNA sequences indicate that H. (Extraholostichides) subgen. nov. is monophyletic and nested within the monophyletic genus Holostichides, which is sister to Eschaneustyla lugeri.

Cellular interactions and evolutionary origins of endosymbiotic relationships with ciliates

As unicellular predators, ciliates engage in close associations with diverse microbes, laying the foundation for the establishment of endosymbiosis. Originally heterotrophic, ciliates demonstrate the ability to acquire phototrophy by phagocytizing unicellular algae or by sequestering algal plastids. This adaptation enables them to gain photosynthate and develop resistance to unfavorable environmental conditions. The integration of acquired phototrophy with intrinsic phagotrophy results in a trophic mode known as mixotrophy. Additionally, ciliates can harbor thousands of bacteria in various intracellular regions, including the cytoplasm and nucleus, exhibiting species specificity. Under prolonged and specific selective pressure within hosts, bacterial endosymbionts evolve unique lifestyles and undergo particular reductions in metabolic activities. Investigating the research advancements in various endosymbiotic cases within ciliates will contribute to elucidate patterns in cellular interaction and unravel the evolutionary origins of complex traits.

New evidence of consistency between phylogeny and morphology for two taxa in ciliated protists, the subclasses Oligotrichia and Choreotrichia (Protista, Ciliophora)

Marine planktonic ciliates are largely oligotrichs and choreotrichs, which are two subclasses of the class Spirotrichea. The current phylogenetic assignments of oligotrichs and choreotrichs are inconsistent with previous results based on morphological features, probably hindered by the limited information from a single gene locus. Here we provide 53 new sequences from small subunit ribosomal RNA (SSU rDNA), ITS1-5.8S rDNA-ITS2, and large subunit ribosomal RNA (LSU rDNA) gene loci in 25 oligotrich and choreotrich species. We also predict RNA secondary structures for the ITS2 regions in 55 species, 48 species of which are reported for the first time. Based on these novel data, we make a more comprehensive phylogenetic reconstruction, revealing consistency between morphological taxonomy and an updated phylogenetic system for oligotrichs and choreotrichs. With the addition of data from ciliature patterns and genes, the phylogenetic analysis of the subclass Oligotrichia suggests three evolutionary trajectories, among which: 1) Novistrombidium asserts an ancestral ciliary pattern in Oligotrichia; 2) the subgenera division of Novistrombidium and Parallelostrombidium are fully supported; 3) the three families (Tontoniidae, Pelagostrombidiidae and Cyrtostrombidiidae) all evolved from the most diverse family Strombidiidae, which explains why strombidiids consistently form polyphyletic clades. In the subclass Choreotrichia, Strombidinopsis likely possesses an ancestral position to other choreotrichs, and both phylogenetic analysis and RNA secondary structure prediction support the hypothesis that tintinnids may have evolved from Strombidinopsis. The results presented here offer an updated hypothesis for the evolutionary history of oligotrichs and choreotrichs based on new evidence obtained by expanding sampling of molecular information across multiple gene loci.

Taxonomy and molecular phylogeny of pleurostomatid ciliates from China with a description of two new species

Ciliates in the order Pleurostomatida are found free-living in many habitats including within biofilms, but some (e.g. Pseudoamphileptus spp.) are ectocommensal on various hosts. Due to issues involving overall undersampling, the exact diversity and molecular phylogeny of this group remain largely underexplored. To combat this deficiency, detailed investigations were undertaken in northern China. As a result of these studies, we provide the morphological descriptions of two new species. Pseudoamphileptus apomacrostoma sp. nov., a new ectocommensal species, is characterized by the broadly oval cell shape, numerous scattered contractile vacuoles, and unique densely bounded extrusomes; Amphileptus qingdaoensis sp. nov., a marine form, is characterized by possessing oblong extrusomes with a conical anterior end, a single contractile vacuole and 5-7 left and 18-23 right kineties. In addition, a new population of Amphileptus orientalis Zhang et al., 2022, a freshwater representative, was documented and an improved diagnosis is provided. The phylogenetic analyses based on the SSU rDNA sequences imply that the genus Pseudoamphileptus is monophyletic whereas the genus Amphileptus is paraphyletic. The new molecular sequences presented here further support the establishment of two new species.

Doublets of the unicellular organism Euplotes vannus (Alveolata, Ciliophora, Euplotida): the morphogenetic patterns of the ciliary and nuclear apparatuses associated with cell division

Ciliated protists are one of the most diverse and highly differentiated group among unicellular organisms. Doublets occur in ciliates when two cells fuse into a single individual. Doublets contain two major cellular components (either cell in a doublet) and have traditionally been considered as developmental anomalies. Nevertheless, doublets can divide or even conjugate effectively, which may represent dispersal forms of the life stages. In addition, morphogenesis, as an important process in the life cycle, will provide important insights into the complex differentiation mechanism and various physiological phenomena. However, morphogenetic studies focusing on doublets of ciliates are very limited, which has become an obstacle to understand their complete life history. Here we isolated a doublet strain from the marine species Euplotes vannus (Müller, 1786) Diesing, 1850 and investigated its morphogenetic events during asexual reproduction. Our results indicate that: (1) the opisthe's oral primordium develops de novo beneath the cortex; (2) the frontoventral and transverse cirral anlagen, cirrus I/1, and marginal anlagen in both dividers develop de novo separately; (3) the dorsal kinety anlagen, the three rightmost ones of which produce three caudal cirri for the proter, occur within the parental structures in the mid-body region; (4) the opisthe acquires two caudal cirri, one from the end of each two rightmost kineties; and (5) there are two macronuclei and one micronucleus in the doublet and they divide amitotically and mitotically, respectively. Finally, we speculate that this special differentiation may be an adaptive form to adverse environments.

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.

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 widely reported but poorly studied ciliate family Folliculinidae (Protozoa, Ciliophora, Heterotrichea): a revision with notes on its taxonomy, morphology and phylogenetic relationships

Ciliates of the heterotrich family Folliculinidae are widespread in various habitats and are distinguished by their transparent loricae of various shapes, conspicuous peristomial lobes, and dimorphic life cycles. They usually attach firmly to the surface of substrates, feed on bacteria and microalgae, and play a significant role in energy flow and material cycling in the microbial food web. However, little is known regarding their biodiversity and systematics. In this work, we establish the terminology of the family Folliculinidae and select six crucial features for genus recognition. Based on previous studies, we revise the classification of Folliculinidae, supply improved diagnoses for each of the 33 folliculinid genera, and provide a key to their identification. Moreover, phylogenetic analyses based on small subunit ribosomal DNA (SSU rDNA) sequences revealed that the family is monophyletic and comprises two subclades (subclades I II) which can be identified by the flexibility of their peristomial lobes and the sculpturing of their necks. Furthermore, we investigate the evolutionary relationships of folliculinids using the six chosen generic features.

Supplementary Information

The online version contains supplementary material available at 10.1007/s42995-022-00152-z.

Effect of Environmental Heterogeneity and Trophic Status in Sampling Strategy on Estimation of Small-Scale Regional Biodiversity of Microorganisms

Microorganisms are diverse and play key roles in lake ecosystems, therefore, a robust estimation of their biodiversity and community structure is crucial for determining their ecological roles in lakes. Conventionally, molecular surveys of microorganisms in lakes are primarily based on equidistant sampling. However, this sampling strategy overlooks the effects of environmental heterogeneity and trophic status in lake ecosystems, which might result in inaccurate biodiversity assessments of microorganisms. Here, we conducted equidistant sampling from 10 sites in two regions with different trophic status within East Lake (Wuhan, China), to verify the reliability of this sampling strategy and assess the influence of environmental heterogeneity and trophic status on this strategy. Rarefaction curves showed that the species richness of microbial communities in the region of the lake with higher eutrophication failed to reach saturation compared with that in lower trophic status. The microbial compositions of samples from the region with higher trophic status differed significantly (P < 0.05) from those in the region with lower trophic status. The result of this pattern may be explained by complex adaptations of lake microorganisms in high eutrophication regions with environmental conditions, where community differentiation can be viewed as adaptations to these environmental selection forces. Therefore, when conducting surveys of microbial biodiversity in a heterogeneous environment, investigators should incorporate intensive sampling to assess the variability in microbial distribution in response to a range of factors in the local microenvironment.

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.

Community assembly and co-occurrence network complexity of pelagic ciliates in response to environmental heterogeneity affected by sea ice melting in the Ross Sea, Antarctica

In the Southern Ocean, the living environment of organisms has changed due to the dramatic increase in melting sea ice and the loss of glaciers, which have consequently caused substantial changes in biodiversity. Samples of pelagic ciliates from 13 sites were collected as bioindicators to demonstrate the relationship between spatial distribution patterns and environmental heterogeneity affected by sea ice melting and to reveal the community assembly mechanisms in the Ross Sea. Univariate analyses and multivariate analyses were effective tools demonstrating clear spatial patterns and providing a sufficient explanation to interpret strong correlations between pelagic ciliate communities and environmental variations, especially the distribution pattern of nutrients and Chl a. Moreover, environmental heterogeneity might affect the co-occurrence network complexity of ciliate communities. Furthermore, our results also indicated that stochastic processes play a significant role in the community assembly of pelagic ciliates. This study examined the controlling mechanisms of environmental heterogeneity affected by sea ice melting on pelagic ciliate communities and provided explanations for the community assembly of pelagic ciliates in polar marine ecosystems.

Study on Analysis of Several Molecular Identification Methods for Ciliates of Colpodea (Protista, Ciliophora)

The application of molecular techniques to accurately identify protozoan species can correct previous misidentifications based on traditional morphological identification. Colpodea ciliates have many toxicological and cytological applications, but their subtle morphological differences and small body size hinder species delineation. Herein, we used Cox I and β-tubulin genes, alongside fluorescence in situ hybridization (FISH), to evaluate each method in delineating Colpodea species. For this analysis, Colpoda harbinensis n. sp., C. reniformis, two populations of C. inflata, Colpoda compare grandis, and five populations of Paracolpoda steinii, from the soil in northeastern China, were used. We determined that (1) the Cox I gene was more suitable than the β-tubulin gene as a molecular marker for defining intra- and interspecific level relationships of Colpoda. (2) FISH probes designed for Colpoda sp., C. inflata, Colpoda compare grandis, and Paracolpoda steinii, provided rapid interspecific differentiation of Colpodea species. (3) Colpoda harbinensis n. sp. was established and mainly characterized by its size in vivo (approximately $80\times 60\mu \text{m}$ ), a reniform body in outline, one macronucleus, its spherical shape, a sometimes nonexistent micronucleus, 11–15 somatic kineties, and five or six postoral kineties. In conclusion, combining oligonucleotide probes, DNA barcoding, and morphology for the first time, we have greatly improved the delineation of Colpodea and confirmed that Cox I gene was a promising DNA barcoding marker for species of Colpodea, and FISH could provide useful morphological information as complementing traditional techniques such as silver carbonate.

Diversity Patterns of Protists Are Highly Affected by Methods Disentangling Biological Variants: A Case Study in Oligotrich (s.l.) Ciliates

Protists are a dominant group in marine microplankton communities and play important roles in energy flux and nutrient cycling in marine ecosystems. Environmental sequences produced by high-throughput sequencing (HTS) methods are increasingly used for inferring the diversity and distribution patterns of protists. However, studies testing whether methods disentangling biological variants affect the diversity and distribution patterns of protists using field samples are insufficient. Oligotrich (s.l.) ciliates are one group of the abundant and dominant planktonic protists in coastal waters and open oceans. Using oligotrich (s.l.) ciliates in field samples as an example, the present study indicates that DADA2 performs better than SWARM, UNOISE, UPARSE, and UCLUST for inferring diversity patterns of oligotrich (s.l.) ciliates in the Pearl River Estuary and surrounding regions. UPARSE and UNOISE might underestimate species richness. SWARM might not be suitable for the resolution of alpha diversity owing to its rigorous clustering and sensitivity to sequence variations. UCLUST with 99% clustering threshold overestimates species richness, and the beta diversity pattern inferred by DADA2 is more reasonable than that of the other methods. Additionally, salinity is shown to be one of the key factors responsible for variations in the community distribution of ciliates, but infrequent marine-freshwater transitions occurred during evolutionary terms of this group.

Redescription of Bakuella (Bakuella) marina Agamaliev and Alekperov, 1976 (Protozoa, Hypotrichia), With Notes on Its Morphology, Morphogenesis, and Molecular Phylogeny

Because the original description of Bakuella (Bakuella) marina, type of the genus, is only based on protargol-impregnated specimens, one of the important living features, namely, the presence/absence of cortical granules, remains unknown so far. In the present work, a detailed investigation of a Chinese population of B. (Bakuella) marina is carried out using the integrated approaches, and the live morphology, ontogenesis, and molecular information of B. (Bakuella) marina are presented for the first time. The infraciliature of this population corresponds perfectly with that of the original description. The in vivo observation indicates that B. (Bakuella) marina possesses colorless cortical granules. The most prominent morphogenetic feature of B. (Bakuella) marina is that the parental adoral zone of membranelles is completely replaced by the newly formed one of the proters. Molecular phylogenetic analysis based on a small subunit ribosomal gene (SSU rDNA) shows that five Bakuella species are clustered with the species from other six Urostylid genera, namely, Anteholosticha, Apobakuella, Diaxonella, Holosticha, Neobakuella, and Urostyla. The monophyletic probabilities of the family Bakuellidae, genus Bakuella, subgenus B. (Bakuella), and subgenus B. (Pseudobakuella) are rejected by the approximately unbiased test. This study further shows that the family Bakuellidae, genus Bakuella, and subgenus B. (Bakuella) are all nonmonophyletic groups. In order to establish a reasonable classification system, information on molecular and morphogenesis of more Bakuellids and its related species is urgently needed.

A Case Study of the Morphological and Molecular Variation within a Ciliate Genus: Taxonomic Descriptions of Three Dysteria Species (Ciliophora, Cyrtophoria), with the Establishment of a New Species

Three Dysteria species, D. crassipes Claparède & Lachmann, 1859; D. brasiliensis Faria et al., 1922; and D. paracrassipes n. sp., were collected from subtropical coastal waters of the East China Sea, near Ningbo, China. The three species were studied based on their living morphology, infraciliature, and molecular data. The new species D. paracrassipes n. sp. is very similar to D. crassipes in most morphological features except the preoral kinety, which is double-rowed in the new species (vs. single-rowed in D. crassipes). The difference in the small ribosomal subunit sequences (SSU rDNA) between these two species is 56 bases, supporting the establishment of the new species. The Ningbo population of D. crassipes is highly similar in morphology to other known populations. Nevertheless, the SSU rDNA sequences of these populations are very different, indicating high genetic diversity and potentially cryptic species. Dysteria brasiliensis is cosmopolitan with many described populations worldwide and four deposited SSU rDNA sequences. The present work supplies morphological and molecular information from five subtropical populations of D. brasiliensis that bear identical molecular sequences but show significant morphological differences. The findings of this study provide an opportunity to improve understanding of the morphological and genetic diversity of ciliates.

Taxonomy and systematics of a new pleurostomatid ciliate, Pseudolitonotus spirelis gen. et sp. n. (Protozoa, Ciliophora, Haptoria)

Recent studies have revealed a high diversity of pleurostomatid ciliates in brackish habitats. Here, a novel species, Pseudolitonotus spirelis gen. et sp. n., isolated from a mangrove wetland of southern China, was investigated based on living observation, protargol staining, and molecular analyses. The new genus Pseudolitonotus gen. n. is characterized by the last left somatic kinety (LKn) being shortened and none of the right somatic kineties extending to the anterior end of the cell, thus distinguishing it from all known pleurostomatid genera. The type species, Pseudolitonotus spirelis sp. n., is characterized by the possession of two macronuclear nodules, 11-15 right and 7-9 left kineties, a single contractile vacuole subterminally located, extrusomes evenly spaced along the entire ventral margin and some forming an "apical group", two types of cortical granules, and the bottom of the oral slit invariably being twisted. Litonotus gracilis (Pan et al. Eur J Protistol 51:494-506, 2015) is believed to be another member of this new genus as its LKn and right somatic kineties are all shortened. Hence, a new combination, Pseudolitonotus gracilis (Pan et al., 2015) comb. n., is suggested and its diagnosis is improved. Molecular phylogenetic analyses based on SSU rDNA sequence data reveal that Pseudolitonotus gen. n. is monophyletic and groups with Apolitonotus (Pan et al. J Eukaryot Microbiol 67:252-262, 2020) of the family Protolitonotidae (Wu et al. Zool Scr 46:245-253, 2017). However, the familial assignment of this new genus is uncertain based on current data.

Morphology, Life Cycle, and SSU rDNA-based Phylogeny of Two Folliculinid Ciliates (Ciliophora, Heterotrichea, Folliculinidae) Collected from Subtropical Coastal Wetlands of China

Most ciliates of the heterotrich family Folliculinidae are flagship periphytic species. They are characterized by their transparent lorica, conspicuous peristomial lobes, and dimorphic life cycle. However, the understanding of their biodiversity and systematics is relatively poor. In the present study, we investigate the morphology and phylogenetic affinities of Ampullofolliculina lageniformis Hadži, 1951 and Metafolliculina producta (Wright, 1859) Dons, 1934, collected from subtropical coastal wetlands in China. An integrative approach combining investigations of their morphology, life cycle and ecology was used. Phylogenetic analyses based on small subunit ribosomal DNA (SSU rDNA) sequences showed that: all folliculinid genera form a monophyletic clade; the two genera with flexible peristomial lobes, Metafolliculina and Eufolliculina, are closely related; the other three genera with inflexible peristomial lobes, Ampullofolliculina, Diafolliculina and Folliculina, group together.

Chromosome organization and gene expansion in the highly fragmented genome of the ciliate Strombidium stylifer

Chromosomes are well-organized carriers of genetic information in eukaryotes and are usually quite long, carrying hundreds and thousands of genes. Intriguingly, a clade of single-celled ciliates, Spirotrichea, feature nanochromosomes-also called "gene-sized chromosomes". These chromosomes predominantly carry only one gene, flanked by short telomere sequences. However, the organization and copy number variation of the chromosomes in these highly fragmented genomes remain unexplored in many groups of Spirotrichea, including the marine Strombidium. Using deep genome sequencing, we assembled the macronuclear genome of Strombidium stylifer into more than 18,000 nanochromosomes (~2.4 Kb long on average). Our results show that S. stylifer occupies an intermediate position during the evolutionary history of Strombidium lineage and experienced significant expansions in several gene families related to guanyl ribonucleotide binding. Based on the nucleotide distribution bias analysis and conserved motifs search in non-genic regions, we found that the subtelomeric regions have a conserved adenine-thymine (AT)-rich sequence motif. We also found that the copy number of nanochromosomes lacks precise regulation. This work sheds light on the unique features of chromosome structure in eukaryotes with highly fragmented genomes and reveals that a rather specialized evolutionary strategy at the genomic level has resulted in great diversity within the ciliated lineages.

Overview of the Diversity, Phylogeny and Biogeography of Strombidiid Oligotrich Ciliates (Protista, Ciliophora), With a Brief Revision and a Key to the Known Genera

Strombidiids are common free-living ciliates that have colonized coastal and open oceanic waters across the world. In recent years, numerous new taxa and gene sequences of strombidiids have been reported, revealing a large diversity of both their morphologic and genetic features. Here, we compare the taxonomic characters of all genera in the family Strombidiidae, provide a key to their identification, and investigate their molecular phylogeny. In addition, we analyze their regional distribution based on faunal data accumulated in China and attempt to infer their global distribution based on SSU rRNA gene sequence data. The current work revises the systematics of strombidiids based on morphologic, phylogenetic, and biogeographic evidence and provides a genus-level review of marine strombidiids.

Taxonomy and SSU rDNA-Based Phylogeny of Two Heterotrich Ciliates (Ciliophora, Heterotrichea) Collected From Subtropical Wetlands of China, Including the Description of a New Species, Linostomella pseudovorticella n. sp

The Heterotrichea Stein, 1859 are a group of ciliated protists (single-celled eukaryotes) that occur in a wide variety of aquatic habitat where they play important roles in the flow of nutrients and energy within the microbial food web. Many species are model organisms for research in cytology and regenerative biology. In the present study, the morphology and phylogeny of two heterotrich ciliates, namely, Linostomella pseudovorticella n. sp. and Peritromus kahli Villeneuve-Brachon, 1940, collected from subtropical wetlands of China, were investigated using morphological and molecular methods. L. pseudovorticella n. sp. differs from its only known congener, Linostomella vorticella Ehrenberg, 1833 Aescht in Foissner et al., 1999, by having more ciliary rows (48-67, mean about 56 vs. 26-51, mean about 42) and its small-subunit (SSU) rDNA sequence, which shows a 15-bp divergence. Although P. kahli has been reported several times in recent decades, its infraciliature has yet to be described. A redescription and improved diagnosis of this species based on a combination of previous and present data are here supplied. Phylogenetic analyses based on SSU rDNA sequences revealed that the genus Linostomella is positioned within Condylostomatidae, and Peritromidae is sister to Climacostomidae with relatively low support, and the family Spirostomidae is the root branch of the class Heterotrichea.

Distribution Patterns of Ciliate Diversity in the South China Sea

Ciliates are abundant microplankton that are widely distributed in the ocean. In this paper, the distribution patterns of ciliate diversity in the South China Sea (SCS) were analyzed by compiling community data from previous publications. Based on morphological identification, a total of 592 ciliate species have been recorded in the SCS. The ciliate communities in intertidal, neritic and oceanic water areas were compared in terms of taxonomy, motility and feeding habit composition, respectively. Significant community variation was revealed among the three areas, but the difference between the intertidal area and the other two areas was more significant than that between neritic and oceanic areas. The distributions of ciliates within each of the three areas were also analyzed. In the intertidal water, the community was not significantly different among sites but did differ among habitat types. In neritic and oceanic areas, the spatial variation of communities among different sites was clearly observed. Comparison of communities by taxonomic and ecological traits (motility and feeding habit) indicated that these traits similarly revealed the geographical pattern of ciliates on a large scale in the SCS, but to distinguish the community variation on a local scale, taxonomic traits has higher resolution than ecological traits. In addition, we assessed the relative influences of environmental and spatial factors on assembly of ciliate communities in the SCS and found that environmental selection is the major process structuring the taxonomic composition in intertidal water, while spatial processes played significant roles in influencing the taxonomic composition in neritic and oceanic water. Among ecological traits, environmental selection had the most important impact on distributions.

High salinity gradients and intermediate spatial scales shaped similar biogeographical and co-occurrence patterns of microeukaryotes in a tropical freshwater-saltwater ecosystem

Microeukaryotes play key ecological roles in the microbial web of aquatic ecosystems. However, large knowledge gaps urgently need to be filled regarding the biogeography with associated shaping mechanisms and co-occurrence patterns of microeukaryotes under freshwater-saltwater gradients, especially true in tropical regions. Here, we investigated microeukaryotes of six mixed freshwater-saltwater regions in the Pearl River Estuary and surrounding coasts in southern China, with salinity ranging 0.1-32.0% and distances spanned up to 500 km, using molecular ecological methods. Results indicate that the biogeography of abundant and rare microeukaryotic communities was similar, both their co-occurrence patterns and biogeographical patterns were driven by deterministic and stochastic processes. The environmental factors with higher selective pressure than dispersal limitation meant that the role of deterministic process in structuring communities was more significant than that of stochastic process, and salinity played important role in structuring both microeukaryotic communities and networks. The abundant communities had stronger influence on entire microeukaryotic communities and seemed to be more sensitive to environmental changes than their rare counterparts, while rare ones had stronger interspecific relationships. Finally, the geographic scale and environmental gradients of study regions should firstly be clarified in future research on the ecological processes of microeukaryotes before conclusions are drawn.

Integrative taxonomy and molecular phylogeny of three poorly known tintinnine ciliates, with the establishment of a new genus (Protista; Ciliophora; Oligotrichea)

BACKGROUND

The taxonomic classification of the suborder Tintinnina Kofoid & Campbell, 1929, a species-rich group of planktonic ciliated protistans with a characteristic lorica, has long been ambiguous largely due to the lack of cytological and molecular data for most species. Tintinnopsis is the largest, most widespread, and most taxonomically complex genus within this group with about 170 species occurring in nearshore waters. Previous molecular phylogenetic studies have revealed that Tintinnopsis is polyphyletic.

RESULTS

Here we document the live morphology, infraciliature, gene sequences, and habitat characteristics of three poorly known tintinnine species, viz. Tintinnopsis karajacensis Brandt, 1896, Tintinnopsis gracilis Kofoid & Campbell, 1929, and Tintinnopsis tocantinensis Kofoid & Campbell, 1929, isolated from the coastal waters of China. Based on a unique cytological feature (i.e., an elongated ciliary tuft with densely arranged kinetids) in the former two species, Antetintinnopsis gen. nov. is erected with Antetintinnopsis hemispiralis (Yin, 1956) comb. nov. (original combination: Tintinnopsis hemispiralis Yin, 1956) designated as the type species. Moreover, A. karajacensis (Brandt, 1896) comb. nov. (original combination: Tintinnopsis karajacensis Brandt, 1896) and A. gracilis (Kofoid & Campbell, 1929) comb. nov. (original combination: Tintinnopsis gracilis Kofoid & Campbell, 1929) are placed in a highly supported clade that branches separately from Tintinnopsis clades in phylogenetic trees based on SSU rDNA and LSU rDNA sequence data, thus supporting the establishment of the new genus. One other species is assigned to Antetintinnopsis gen. nov., namely A. subacuta (Jörgensen, 1899) comb. nov. (original combination Tintinnopsis subacuta Jörgensen, 1899).

CONCLUSIONS

The findings of the phylogenetic analyses support the assertion that cytological characters are taxonomically informative for tintinnines. This study also contributes to the broadening of our understanding of the tintinnine biodiversity and evolution.

Morphology and molecular phylogeny of a new brackish pleurostomatid ciliate, Loxophyllum paludosum sp. n. (Ciliophora, Litostomatea, Haptoria), from a mangrove wetland in China

A new ciliate species of the genus Loxophyllum Dujardin, 1841, Loxophyllum paludosum sp. n., is described from a mangrove wetland near Daya Bay in Guangdong Province, southern China, based on morphological and molecular analyses. The new species can be distinguished from its congeners by a combination of the following characters: (1) 12-14 right kineties and 4-6 left kineties; (2) two macronuclear nodules and one micronucleus; (3) a single contractile vacuole located terminally; (4) extrusomes bar-shaped, evenly spaced along entire ventral margin, and clustered to form 5-7 warts along dorsal margin; and (5) presence of three ridges on the left side of cell. The new species is divergent from its congeners from 0.4% to 6.7% (5-104 nucleotide sites) based on the small subunit (SSU) rRNA gene sequence data. The validity of the new species is also supported by molecular phylogenetic trees inferred from SSU rRNA gene sequences.