Integrating dimensions of biodiversity in choreotrichs and oligotrichs of marine plankton

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.

The hidden microbial ecosystem in the perennial ice from a Pyrenean ice cave

Over the last years, perennial ice deposits located within caves have awakened interest as places to study microbial communities since they represent unique cryospheric archives of climate change. Since the beginning of the twentieth century, the temperature has gradually increased, and it is estimated that by the end of this century the increase in average temperature could be around 4.0°C. In this context of global warming the ice deposits of the Pyrenean caves are undergoing a significant regression. Among this type of caves, that on the Cotiella Massif in the Southern Pyrenees is one of the southernmost studied in Europe. These types of caves house microbial communities which have so far been barely explored, and therefore their study is necessary. In this work, the microbial communities of the Pyrenean ice cave A294 were identified using metabarcoding techniques. In addition, research work was carried out to analyze how the age and composition of the ice affect the composition of the bacterial and microeukaryotic populations. Finally, the in vivo effect of climate change on the cellular machinery that allow microorganisms to live with increasing temperatures has been studied using proteomic techniques.

Morphological, Molecular, and Growth Characteristics of a Cryptic Species, Strombidium parasulcatum n. sp. (Alveolata: Ciliophora: Oligotrichida)

A new marine planktonic ciliate from Taiwan, Strombidium parasulcatum sp. n., is described based on live observations, protargol staining, and molecular data. Its morphological characters are similar to those of Strombidium sulcatum Claparède and Lachmann, 1859 sensu Song et al., 2000 but differ from S. sulcatum sensu Fauré-Fremiet, 1912 and sensu Fauré-Fremiet and Ganier, 1970 by several morphological characters. The 18S rRNA gene sequences of the two forms display 76 base pair differences (about 5%), indicating that they should be considered separate species. The highest observed specific growth rates of S. parasulcatum in culture were 1.79 day^–1 over 1 day and 1.52 day^–1 over 2 days, both starting at day 5. Bacteria appear to be an important food resource for the cultivation of this medium-sized oligotrich ciliate. This and other recent studies suggest that cryptic species may be common in the genus Strombidium, and an integrative approach including morphological, ecological, and molecular data should be used to address this question.

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.

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.

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

As an important component of microzooplankton, ciliates play a key role in matter cycling and energy flow in marine planktonic ecosystems. Studies of planktonic ciliate have been extensive in the South China Sea (SCS) over the last 20 years. Here, we summarize the recent progress on the diversity and distribution of this group in the SCS. This includes that in: (1) the waters covering the intertidal zone of the northern SCS, most studies have focused on taxonomy, with 71 species collected, identified, and described (with ~ 40% new species); (2) neritic waters distribution patterns have been examined at a regional scale, with ciliates displaying significant spatial variations and seasonal dynamics; (3) in oceanic waters, there has been a focus on ciliate distribution in north, centre, and south regions, where mesoscale physical processes play roles in controlling distributions, and noticeable vertical variations occur. More generally, some studies examine the influences of environment variables on ciliates, and indicate that chlorophyll a concentration is commonly positively correlated with ciliates abundance. In addition, some significant findings are summarized, the limitations of past studies are considered, and recommendations are made for future work on planktonic ciliates in SCS.

Symposium on Ciliates in Memory of Denis Lynn

Denis Lynn (1947-2018) was an outstanding protistologist, applying multiple techniques and data sources and thus pioneering an integrative approach in order to investigate ciliate biology. For example, he recognized the importance of the ultrastructure for inferring ciliate phylogeny, based on which he developed his widely accepted classification scheme for the phylum Ciliophora. In this paper, recent findings regarding the evolution and systematics of both peritrichs and the mainly marine planktonic oligotrichean spirotrichs are discussed and compared with the concepts and hypotheses formulated by Denis Lynn. Additionally, the state of knowledge concerning the diversity of ciliates in bromeliad phytotelmata and amitosis in ciliates is reviewed.

Morphology and Molecular Phylogeny of Two Freshwater Oligotrich Ciliates (Protozoa, Ciliophora, Oligotrichia), Pelagostrombidium fallax (Zacharias, 1895) Krainer, 1991 and Limnostrombidium viride (Stein, 1867) Krainer, 1995, with Brief Notes on Stomatogenesis

The morphology of two oligotrich ciliates, Pelagostrombidium fallax (Zacharias, 1895) Krainer, 1991 and Limnostrombidium viride (Stein, 1867) Krainer, 1995, collected from a freshwater pond in northern China, was studied based on live observation and protargol staining. Currently, undescribed features in the girdle kinety in P. fallax are (a) sparsely spaced single argyrophilic basal bodies in the shoulder region and (b) a U-shape formed below the buccal peristome. An improved diagnosis for P. fallax is supplied, based on previous and present morphological descriptions. In addition, certain ontogenetic stages of P. fallax are reported for the first time. During division, two new embryonic bodies are successively generated de novo, the first one goes to the proter, the second one to the opisthe; the new canal derives from the old canal. The morphology of L. viride is redescribed in detail; the Chinese population is highly consistent with populations in Europe. The SSU rRNA gene of P. fallax was sequenced for the first time. Phylogenetic analyses, based on SSU rRNA gene sequence data, reveal that P. fallax and L. viride cluster with Strombidium species while the result of an AU test did not reject the possibility of monophyly of the family Pelagostrombidiidae.

Taxonomy and phylogeny of two poorly studied genera of marine oligotrich ciliates including descriptions of two new species: Cyrtostrombidium paraboreale sp. n. and Apostrombidium orientale sp. n. (Ciliophora: Spirotrichea)

Although it is widely recognized that oligotrich ciliates are the dominant constituent of microzooplankton communities and perform key functions in energy flow and material cycling in marine microbial food webs, knowledge of their diversity is scant. In the present study, we investigate the oligotrich genera, Cyrtostrombidium and Apostrombidium, with emphasis on their morphology and evolutionary relationships. Three isolates were collected from coastal waters of northern and southern China including two new species, viz., Cyrtostrombidium paraboreale sp. n., Apostrombidium orientale sp. n., and Apostrombidium pseudokielum Xu et al., 2009. Cyrtostrombidium paraboreale sp. n. is characterized by possessing 64-98 cytopharyngeal rods and two macronuclear nodules. Apostrombidium orientale sp. n. is characterized by its somatic kinety consisting of five fragments including a horizontally orientated subterminal fragment and possessing conspicuously long dorsal cilia. Apostrombidium pseudokielum is redescribed based on the new population and a re-examination of the type material. Phylogenetic analyses were performed for the subclass Oligotrichia, incorporating SSU rRNA gene sequences of the three species investigated here. The results indicate that the genus Cyrtostrombidium is monophyletic with C. paraboreale sp. n. occupying the basal position. The genus Apostrombidium is not monophyletic as Varistrombidium kielum is nested within it.