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Marine Life Science & Technology May 2024Species of the ciliate genera and are found as endocommensals of terrestrial and freshwater mollusks, respectively. So far, there have been few studies of these genera...
Findings on three endocommensal scuticociliates (Protista, Ciliophora) from freshwater mollusks, including their morphology and molecular phylogeny with descriptions of two new species.
UNLABELLED
Species of the ciliate genera and are found as endocommensals of terrestrial and freshwater mollusks, respectively. So far, there have been few studies of these genera and morphological data for most members are often incomplete. In the present work, two new species, sp. nov. and sp. nov., and a known species, , were isolated from hosts in Lake Weishan Wetland, China. Taxonomic studies indicate that sp. nov. can be recognized mainly by the combination of about 60 somatic kineties on both ventral and dorsal sides and the presence of caudal cilia. sp. nov. differs from congeners in its body shape and size, having a glabrous area on the posterior right side, and having fewer somatic kineties. In addition, differences in their ITS2 (Internally Transcribed Spacer 2) secondary structures support the discrimination of the two new species from their highly similar congeners. An improved diagnosis for the poorly known species, is also provided. Phylogenetic analyses reveal that members of the genus belong to a fully supported clade that is sister to a large, poorly supported clade consisting of Hemispeiridae, Ancistridae, and several lineages of the nonmonophyletic Cyclidiidae. The clade also includes JQ956552, a possible misidentification. Sequences of the two new species cluster with other congeners in a fully supported clade that is unrelated to either the 'typical' thigmotrichs or to pleuronematids, thus conflicting with the traditional classification, and may represent an orphan scuticociliate lineage.
SUPPLEMENTARY INFORMATION
The online version contains supplementary material available at 10.1007/s42995-024-00230-4.
PubMed: 38827127
DOI: 10.1007/s42995-024-00230-4 -
Animals : An Open Access Journal From... Mar 2024We have conducted a 10-year-long coprological study of the animals housed in two zoological institutions (ZooAquarium and Faunia, Madrid, Spain) to assess the parasite...
We have conducted a 10-year-long coprological study of the animals housed in two zoological institutions (ZooAquarium and Faunia, Madrid, Spain) to assess the parasite biodiversity, prevalence, and their relation with host class, diet, and enclosure type (soil type and level of isolation from wild fauna). A total of 4476 faecal samples from 132 mammal species and 951 samples from 86 avian species were examined. The results indicated that only 12.8% of avian species had parasites at least once during the study period, whereas 62.1% of mammal species tested positive. Predominantly, protists (, flagellates, and ciliates) and nematodes (mainly ) were identified in the findings. Carnivorous species were primarily infected by nematodes, while herbivorous and omnivorous species were mainly infected by protists. The number of infected herbivorous and omnivorous species was significantly greater than carnivorous species. Differences were observed based on soil type (artificial, natural, mixed) and isolation level (isolated/accessible), but these differences were not statistically significant. Several parasites ( spp., spp., , spp.) could potentially be transmitted between humans and some mammals and birds. Regular animal analyses and a personnel health program in the institutions would minimise transmission risks between zoo animals, wildlife, and humans.
PubMed: 38473198
DOI: 10.3390/ani14050813 -
Journal of Chemical Information and... Feb 2024L-tryptophan (l-Trp), a vital amino acid for the survival of various organisms, is synthesized by the enzyme tryptophan synthase (TS) in organisms such as eubacteria,...
L-tryptophan (l-Trp), a vital amino acid for the survival of various organisms, is synthesized by the enzyme tryptophan synthase (TS) in organisms such as eubacteria, archaebacteria, protista, fungi, and plantae. TS, a pyridoxal 5'-phosphate (PLP)-dependent enzyme, comprises α and β subunits that typically form an αβ tetramer. The enzyme's activity is regulated by the conformational switching of its α and β subunits between the open (T state) and closed (R state) conformations. Many microorganisms rely on TS for growth and replication, making the enzyme and the l-Trp biosynthetic pathway potential drug targets. For instance, , bacteria, , , bacteria, and parasitic protozoa depend on l-Trp synthesis. Antibiotic-resistant strains have emerged, underscoring the need for novel drugs targeting the l-Trp biosynthetic pathway, especially for salmonella-related infections. A single amino acid mutation can significantly impact enzyme function, affecting stability, conformational dynamics, and active or allosteric sites. These changes influence interactions, catalytic activity, and protein-ligand/protein-protein interactions. This study focuses on the impact of mutating the βGln114 residue on the catalytic and allosteric sites of TS. Extensive molecular dynamics simulations were conducted on E(PLP), E(AEX), E(A-A), and E(C) forms of TS using the WT, βQ114A, and βQ114N versions. The results show that both the βQ114A and βQ114N mutations increase protein backbone root mean square deviation fluctuations, destabilizing all TS forms. Conformational and hydrogen bond analyses suggest the significance of βGln114 drifting away from cofactor/intermediates and forming hydrogen bonds with water molecules necessary for l-Trp biosynthesis. The βQ114A mutation creates a gap between βAla114 and cofactor/intermediates, hindering hydrogen bond formation due to short side chains and disrupting β-sites. Conversely, the βQ114N mutation positions βAsn114 closer to cofactor/intermediates, forming hydrogen bonds with O3 of cofactors/intermediates and nearby water molecules, potentially disrupting the l-Trp biosynthetic mechanism.
Topics: Humans; Tryptophan Synthase; Catalytic Domain; Molecular Dynamics Simulation; Cryptosporidiosis; Salmonella typhimurium; Cryptosporidium; Protein Conformation; Amino Acids; Mutation; Water; Kinetics
PubMed: 38291608
DOI: 10.1021/acs.jcim.3c01966 -
Environmental Science and Pollution... Jan 2024Microplastics (MPs), due to their micro size, which overlaps with the typical food size of various aquatic organisms, can be ingested and move up the food chain,...
Microplastics (MPs), due to their micro size, which overlaps with the typical food size of various aquatic organisms, can be ingested and move up the food chain, accumulating in the bodies of organisms at higher trophic levels. Few studies have focused on the uptake of MPs by ciliates, which are an important element of the microbial cycle. Three different ciliate species were used in this study: Blepharisma japonicum, Euplotes sp., and Spirostomum teres, as well as polystyrene beads with diameters of 1 and 2 µm at two concentrations (10 and 10 beads × mL). The results of the experiments showed that MPs have a variable, species-specific effect on the population growth rate of ciliates, which is directly dependent on their concentration in the environment (P < 0.01). It was also observed that the number of MPs ingested changed over time depending on their concentration and size. On average, the highest number of ingested MPs (883.11 ± 521.47) was recorded at 60 min of exposure to a low concentration of small beads in B. japonicum. The lowest number of beads was ingested after 5 min of exposure to a low concentration of large beads in the same species. The rate of MP uptake by the ciliate species was significantly dependent on their concentration, exposure time, and size (P < 0.001). The highest clearance rate was observed in the fifth minute of the experiment in the environment with the lowest MP concentration.
Topics: Microplastics; Plastics; Population Growth; Polystyrenes; Ciliophora; Water Pollutants, Chemical
PubMed: 38157169
DOI: 10.1007/s11356-023-31635-w -
Frontiers in Microbiology 2023Ciliates serve as excellent indicators for water quality monitoring. However, their utilization is hindered by various taxonomic confusions. The ciliate genus Bory de...
Ciliates serve as excellent indicators for water quality monitoring. However, their utilization is hindered by various taxonomic confusions. The ciliate genus Bory de Saint-Vincent, 1824 is commonly found in different aquatic habitats, but its taxonomy has been sparsely investigated using state-of-the-art methods. This study investigated two new species from Nanhui Wetland, Shanghai, China, using living observation, protargol staining, and molecular phylogeny methods. sp. nov. is 180-340 × 20-25 μm in size and possesses 12-16 somatic kineties, 1 terminal contractile vacuole, 2 macronuclear nodules, and 2 types of rod-shaped extrusomes. sp. nov. is distinguished from its congeners by its cell size of 210-400 × 25-35 μm, 14-17 somatic kineties, 1 terminal contractile vacuole, 1 macronucleus, and 2 types of rod-shaped extrusomes. Phylogenetic analyses based on SSU rRNA gene sequences indicate that Lacrymariidae is monophyletic but is not. Additionally, a brief review of the genus is provided in this study. We suggest that Alekperov, 1984, Kahl, 1930, and Burkovsky, 1970 be removed from the genus and propose nov. comb. and nov. comb. for the latter two. ZooBank registration: Present work: urn:lsid:zoobank.org:pub:CDFB1EBD-80BD-4533-B391-CEE89F62EDC4 sp. nov.: urn:lsid:zoobank.org:act:417E7C2D-DAEC-4711-90BB-64AB3CD2F7D5 sp. nov.: urn:lsid:zoobank.org:act:8778D6B0-1F2E-473C-BE19-3F685391A40D.
PubMed: 38029185
DOI: 10.3389/fmicb.2023.1259653 -
European Journal of Protistology Oct 2023Erniella Foissner, 1987 is a poorly known genus with its available information limited solely to morphological characteristics. In this study, the type species E....
Morphological, ontogenetic, and phylogenetic research of a poorly known non-dorsomarginalian ciliate: Erniella filiformis Foissner, 1987 (Protista, Ciliophora, Hypotrichia).
Erniella Foissner, 1987 is a poorly known genus with its available information limited solely to morphological characteristics. In this study, the type species E. filiformis, isolated from highly saline water in China, was investigated for morphology, morphogenesis, and phylogeny based on small subunit ribosomal DNA sequences. The main characteristic events during morphogenesis in Erniella filiformis are as follows: (1) in the proter, only the posterior part of the parental adoral zone is renewed and undulating membranes anlage is formed from the dedifferentiation of the old structure; (2) the oral primordium is formed intrakinetally in the opisthe; (3) frontoventral-transverse cirral anlagen II-IV develop in the primary mode, anlage V develops intrakinetally in the proter; and (4) the right frontoventral row is formed by a single anlage. The phylogenetic analyses indicate that Erniella forms a monophyletic group with Bistichella, Keronopsis, Lamtostyla, Orthoamphisiella, Parabistichella, Paraholosticha, and Uroleptoides.
Topics: Phylogeny; DNA, Ribosomal; China; Morphogenesis; Ciliophora; Hypotrichida
PubMed: 37925832
DOI: 10.1016/j.ejop.2023.126031 -
Nonlinear Dynamics, Psychology, and... Oct 2023In a recent article, we presented evidence demonstrating the existence of hidden y-stories within the genomes of humans and canines. These stories were found not only in...
In a recent article, we presented evidence demonstrating the existence of hidden y-stories within the genomes of humans and canines. These stories were found not only in the non-protein-coding regions but also within the genetic regions and the sequence of exons. Consequently, we are now exploring whether these discoveries are unique to humans and dogs or if they are more widely distributed throughout the cellular world. To approach this question, we embarked on an investigation of the genomes of various species across Whittaker's five kingdoms, namely Animalia, Plantae, Fungi, Protista, and Monera. Through online resources, we obtained and analysed whole-genome sequences of one avian species, one fish species, one reptile species, and one invertebrate species within the Animalia kingdom. Furthermore, we examined the genomes of one plant species, one fungus species, one protozoan species, and two bacterial species. Employing the same methods as in our prior studies, our findings in this study align with our proto knowledge hypothesis, suggesting that all living cells possess a repository of hidden y-information which determines the cellular design, sustains its overall functionality, and governs its performance and behaviour throughout its lifespan until death. We briefly explain life as a bio-linguistic phenomenon and future projects.
Topics: Humans; Animals; Dogs; Eukaryota; Plants; Fungi; Genome; Bacteria
PubMed: 37818598
DOI: No ID Found -
Scientific Data Oct 2023Calcite shells of planktic foraminifera (Protista, Rhizaria) constitute a large portion of deep-sea sediments. The shells are constructed by sequential addition of...
Calcite shells of planktic foraminifera (Protista, Rhizaria) constitute a large portion of deep-sea sediments. The shells are constructed by sequential addition of partly overlapping chambers with diverse shapes, resulting in complex shell architectures, which are genetically fixed and diagnostic at the species level. The characterisation of the complete architecture requires three-dimensional imaging of the shell, including the partially or entirely covered juvenile chambers. Here we provide reconstructed x-ray micro computed tomography image stacks of 179 specimens of extant planktic foraminifera collected from plankton tows, sediment traps and surface sediments. The specimens have fully resolved and curated taxonomy and represent 43 of the currently recognised 48 holoplanktic species and subspecies. The image stacks form a basis for further applications, such as the characterisation of the architectural morphospace of the extant taxa, allowing studies of species functional ecology, calcification intensity and reconstructions of phylogenetic relationships.
Topics: Ecology; Foraminifera; Phylogeny; X-Ray Microtomography
PubMed: 37798341
DOI: 10.1038/s41597-023-02498-0 -
Molecular Phylogenetics and Evolution Dec 2023The huge variety of species and worldwide distribution of ciliated protists in class Spirotrichea continue to make it one of the most complicated and confused groups in...
Three closely-related subclasses Phacodiniidia Small & Lynn, 1985, Protohypotrichia Shi et al., 1999, and Euplotia Jankowski, 1979 (Protista, Ciliophora): A new contribution to their phylogeny with reconsiderations on the evolutionary hypotheses.
The huge variety of species and worldwide distribution of ciliated protists in class Spirotrichea continue to make it one of the most complicated and confused groups in Ciliophora, despite significant research interest in the unique molecular genetics of these organisms. In this study, the morphological and molecular information were integrated, and it is inferred from a new perspective for the evolutionary relationship among Phacodiniidia, Protohypotrichia, Hypotrichia and Euplotia. Our results indicate that Kiitricha and Caryotricha, two members in Protohypotrichia, may represent two parallel branches of evolution; Euplotidae and Aspidiscidae represent the most recently diverged taxa within Euplotida, followed by Certesiidae, Gastrocirrhidae, and Uronychidae. Further, representative morphological characters (e.g. fronto-ventral-transverse cirral anlagen, undulating membranes, marginal cirri and caudal cirri) were stochastically mapped on phylogenies to speculate evolutionary path and morphological characters of the evolutionary transition node groups were assumed.
Topics: Phylogeny; Ciliophora
PubMed: 37778530
DOI: 10.1016/j.ympev.2023.107936 -
Molecular Phylogenetics and Evolution Nov 2023Marine planktonic ciliates are largely oligotrichs and choreotrichs, which are two subclasses of the class Spirotrichea. The current phylogenetic assignments of...
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.
Topics: Humans; Phylogeny; Ciliophora; DNA, Ribosomal; RNA; RNA, Ribosomal
PubMed: 37648182
DOI: 10.1016/j.ympev.2023.107911