Redescription and SSU rRNA gene-based phylogeny of an anaerobic ciliate, Plagiopyla ovata Kahl, 1931 (Ciliophora, Plagiopylea).
01 Aug 2021-International Journal of Systematic and Evolutionary Microbiology (Int J Syst Evol Microbiol)-Vol. 71, Iss: 8
TL;DR: The morphology and molecular phylogeny of Plagiopyla ovata Kahl, 1931, a poorly known anaerobic ciliate, were investigated based on a population isolated from sand samples collected from the Yellow Sea coast at Qingdao, PR China.
Abstract: The morphology and molecular phylogeny of Plagiopyla ovata Kahl, 1931, a poorly known anaerobic ciliate, were investigated based on a population isolated from sand samples collected from the Yellow Sea coast at Qingdao, PR China. Details of the oral ciliature are documented for the first time to our knowledge and an improved species diagnosis is given. The small subunit ribosomal RNA (SSU rRNA) gene was newly sequenced and phylogenetic analyses revealed that P. ovata clusters within the monophyletic family Plagiopylidae. However, evolutionary relationships within both the family Plagiopylidae and the genus Plagiopyla remain obscure owing to undersampling, the lack of sequence data from known species and low nodal support or unstable topologies in gene trees. A key to the identification of the species of the genus Plagiopyla with validly published names is also supplied.
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TL;DR: Phylogenetic analyses confirmed that the Metopus is not monophyletic, and first revealed that all marine species of Metopus form a well-supported clade.
Abstract: Armophorean ciliates constitute an important component of microeukaryotic community in anaerobic or hypoxic environments. Yet, their diversity remains poorly known due to under-sampling or the scarcity of knowledge. In this study, three metopid ciliates, i.e., Metopus paraes sp. n., Metopus spiculatus sp. n., and Metopus parapellitus sp. n., collected from coastal sediments in Qingdao and Rizhao, China, were investigated using live observation, protargol staining, and molecular phylogenetic methods. M. paraes sp. n. can be distinguished by its long caudal cilia. M. spiculatus sp. n. resembles M. vestitus in many ways, but differs mainly in having a beak-like preoral dome end and a conspicuous tail. The most remarkable features of M. parapellitus sp. n. include an ovate body shape, caudal cilia located at the rear end and right posterior body, and an adoral zone that never extends onto the dorsal surface. Sequence divergences supported the species identification of these three species. Phylogenetic analyses confirmed that the Metopus is not monophyletic, and first revealed that all marine species of Metopus form a well-supported clade. The clustering of these marine forms with M. es (type species) is not rejected by the AU test, which infers that the marine clade represents the genus Metopus together with M. es.
2 citations
TL;DR: Wang et al. as discussed by the authors investigated two species, namely Trimyema claviforme Kahl, 1933 and Plagiopyla nasuta Stein, 1860, collected in China from marine and freshwater anaerobic sediments, respectively.
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TL;DR: The newest addition in MEGA5 is a collection of maximum likelihood (ML) analyses for inferring evolutionary trees, selecting best-fit substitution models, inferring ancestral states and sequences, and estimating evolutionary rates site-by-site.
Abstract: Comparative analysis of molecular sequence data is essential for reconstructing the evolutionary histories of species and inferring the nature and extent of selective forces shaping the evolution of genes and species. Here, we announce the release of Molecular Evolutionary Genetics Analysis version 5 (MEGA5), which is a user-friendly software for mining online databases, building sequence alignments and phylogenetic trees, and using methods of evolutionary bioinformatics in basic biology, biomedicine, and evolution. The newest addition in MEGA5 is a collection of maximum likelihood (ML) analyses for inferring evolutionary trees, selecting best-fit substitution models (nucleotide or amino acid), inferring ancestral states and sequences (along with probabilities), and estimating evolutionary rates site-by-site. In computer simulation analyses, ML tree inference algorithms in MEGA5 compared favorably with other software packages in terms of computational efficiency and the accuracy of the estimates of phylogenetic trees, substitution parameters, and rate variation among sites. The MEGA user interface has now been enhanced to be activity driven to make it easier for the use of both beginners and experienced scientists. This version of MEGA is intended for the Windows platform, and it has been configured for effective use on Mac OS X and Linux desktops. It is available free of charge from http://www.megasoftware.net.
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TL;DR: The program MODELTEST uses log likelihood scores to establish the model of DNA evolution that best fits the data.
Abstract: Summary: The program MODELTEST uses log likelihood scores to establish the model of DNA evolution that best fits the data. Availability: The MODELTEST package, including the source code and some documentation is available at http://bioag.byu.edu/zoology/crandall―lab/modeltest.html. Contact: dp47@email.byu.edu.
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TL;DR: The new version provides convergence diagnostics and allows multiple analyses to be run in parallel with convergence progress monitored on the fly, and provides more output options than previously, including samples of ancestral states, site rates, site dN/dS rations, branch rates, and node dates.
Abstract: Since its introduction in 2001, MrBayes has grown in popularity as a software package for Bayesian phylogenetic inference using Markov chain Monte Carlo (MCMC) methods. With this note, we announce the release of version 3.2, a major upgrade to the latest official release presented in 2003. The new version provides convergence diagnostics and allows multiple analyses to be run in parallel with convergence progress monitored on the fly. The introduction of new proposals and automatic optimization of tuning parameters has improved convergence for many problems. The new version also sports significantly faster likelihood calculations through streaming single-instruction-multiple-data extensions (SSE) and support of the BEAGLE library, allowing likelihood calculations to be delegated to graphics processing units (GPUs) on compatible hardware. Speedup factors range from around 2 with SSE code to more than 50 with BEAGLE for codon problems. Checkpointing across all models allows long runs to be completed even when an analysis is prematurely terminated. New models include relaxed clocks, dating, model averaging across time-reversible substitution models, and support for hard, negative, and partial (backbone) tree constraints. Inference of species trees from gene trees is supported by full incorporation of the Bayesian estimation of species trees (BEST) algorithms. Marginal model likelihoods for Bayes factor tests can be estimated accurately across the entire model space using the stepping stone method. The new version provides more output options than previously, including samples of ancestral states, site rates, site d(N)/d(S) rations, branch rates, and node dates. A wide range of statistics on tree parameters can also be output for visualization in FigTree and compatible software.
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TL;DR: It is demonstrated that the microfaunal communities can be correlated with the oxidation-reduction properties of sediments and with their mechanical composition and that the endproducts of anaerobic decomposition are of large trophic significance to the sediment ecosystem through the activity of cherno- and photoautotrophic bacteria.
Abstract: The paper describes the ecosystem constituted by marine sediments and their microfiora and fauna but with special emphasis on the ecology of ciliated protozoa. This description is based on quantitative studies of the vertical and horizontal distribution of the fauna, the physicochemical factors (O2, H2, S, Eh, pH, grain size, organic matter, salinity) and the microfiora, and on model experiments with artificial and natural sediments. Factors controlling the oxidation-reduction properties of sediments, the O2-uptake of reduced sediments and the respiration and photosynthesis of undisturbed sediments were studied. Among other things it is demonstrated that the microfaunal communities can be correlated with the oxidation-reduction properties of sediments and with their mechanical composition and that the endproducts of anaerobic decomposition (notably H2S) are of large trophic significance to the sediment ecosystem through the activity of cherno- and photoautotrophic bacteria. The energetic role of ...
565 citations
TL;DR: The ciliates are manipulated at all stages by means of micropipettes and fine needles, proceeding by the following steps: Fix the material in a small receptacle with Champy's fluid 1–3 minutes following with Da Fano's solution for several hours, and embed them in gelatin containing 0.05% sodium chloride.
Abstract: The ciliates are manipulated at all stages by means of micropipettes and fine needles, proceeding by the following steps: Fix the material in a small receptacle with Champy's fluid 1–3 minutes following with Da Fano's solution for several hours. Transfer the specimens to a slide, withdraw excess fluid and embed them in warm (35°–45°C.) gelatin containing 0.05% sodium chloride. Refrigerate in a moist chamber until the gelatin has set, and then immerse 10–20 minutes in 3% silver nitrate (aqueous) at 5–10°C. Wash with cold distilled water, submerge the preparation in cold water to a depth of several centimeters and expose to a strong light for 10–30 minutes. Silver is deposited on various pellicular structures which then appear black in the dehydrated and mounted specimens. Neatly revealed are the many longitudinal and transverse fibrils of the “silverline system”, basal granules of the cilia, bases of buccal ciliary organelles, contractile vacuole pores and the cytoproct. None of these structures, which tod...
313 citations