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Fig. 5 in Morphological and Morphogenetic Redescriptions and SSU rRNA Gene-based Phylogeny of the Poorly-known Species Euplotes amieti Dragesco, 1970 (Ciliophora, Euplotida)
Fig. 5. Phylogenetic tree based on SSU rRNA gene sequences, showing the position of Euplotes amieti (arrow) by Maximum Likelihood (ML) and Bayesian inference (BI). Numbers near branches denote ML bootstrap value/BI posterior probability value. '–' indicates topologies that differ between the ML and BI phylogenies. Fully supported (100%/1.00) branches are marked with solid circles. All branches are drawn to scale. The scale bar corresponds to 5 substitutions per 100 nucleotide positions. GenBank accession numbers are given for each species. Systematic classification is mainly according to Lynn (2008). Euplotid clades I–VI were designated according to Yi et al. (2009).
Fig. 1. Euplotes amieti Dragesco, 1970 in Morphological and Morphogenetic Redescriptions and SSU rRNA Gene-based Phylogeny of the Poorly-known Species Euplotes amieti Dragesco, 1970 (Ciliophora, Euplotida)
Fig. 1. Euplotes amieti Dragesco, 1970 in vivo (A), after protargol (B–D) and silver nitrate (E, F) impregnation. (A) Ventral view of a representative cell. Arrows indicate caudal cirri. (B) Different shapes of macronucleus. (C, D) Ventral (C) and dorsal (D) view, showing the infraciliature and nuclear apparatus. Arrow shows the sigmoidal adoral zone. (E, F) Silverline system on ventral (E) and dorsal side (F). Arrow shows the sigmoidal adoral zone. AZM, adoral zone of membranelles; CC, caudal cirri; CVP, contractile vacuole pore; FVC, frontoventral cirri; MC, marginal cirri; PM, paroral membrane; TC, transverse cirri. Scale bars: 100 μm.
Fig. 4 in Morphological and Morphogenetic Redescriptions and SSU rRNA Gene-based Phylogeny of the Poorly-known Species Euplotes amieti Dragesco, 1970 (Ciliophora, Euplotida)
Fig. 4. Photomicrographs of Euplotes amieti during morphogenesis after protargol impregnation. (A) Ventral view of a middle divider showing the migration of cirri and the division of the macronucleus. (B, C) Ventral view of an early divider demonstrating two sets of frontal-ventral-transverse cirral streaks (arrowheads) and the oral primordium in opisthe (arrow). (D) To show new cirri derived from the frontal-ventral-transverse cirral anlagen. (E) Ventral view, arrows point to the paroral membrane (PM) in the proter and the development of the PM-anlage in the opisthe; arrowhead indicates the frontal cirrus I/1 in the opisthe formed de novo. (F) Ventral view, indicating the marginal anlagen of the proter (arrow) and the opisthe (arrowhead). (G) Arrowheads showing the dorsal kinety anlage of an early divider. (H) Portion of the ventral view, showing the marginal cirri in the proter (arrow) and the opisthe (arrowhead). (I) Dorsal view, arrowheads indicating the development of the dorsal kinety anlage. (J) Portion of the dorsal view, to show the newly formed caudal cirri in the proter (arrowheads). Scale bars: 100 μm.
Fig. 3 in Morphological and Morphogenetic Redescriptions and SSU rRNA Gene-based Phylogeny of the Poorly-known Species Euplotes amieti Dragesco, 1970 (Ciliophora, Euplotida)
Fig. 3. Morphogenesis of Euplotes amieti after protargol impregnation. (A, B) Ventral (A) and dorsal (B) view of the same specimen at an early stage to show the five frontal-ventral-transverse cirral streaks and oral primordium within which membranelles are forming (arrow). (C, D) Ventral (C) and dorsal (D) view of the same specimen at a middle stage to show the completion of the cirral formation, the differen- tiation of caudal cirri at posterior ends of the two rightmost dorsal anlagen (arrowheads), the de novo formation of the new marginal cirri and the frontal cirrus I/1 in both proter and opisthe (arrows). (E, F) Ventral (E) and dorsal (F) view, showing the migration of newly formed cirri and the development of dorsal kineties, arrowheads show the marginal cirri. (G, H) Ventral (G) and dorsal (H) side of the same divider at a late stage showing infraciliature and nuclear apparatus. Scale bars: A–D = 100 μm; E–H = 150 μm.
SSU rRNA Gene Analysis of the Environmental and Biological Influences on Carbonate Precipitation within Hot Spring Microbial Mats in Little Hot Creek, CA
<p>R Markdown notebook and all data required to recreate the 16S rRNA Gene analysis figures found in Wilmeth et. al (In Submission), including mapping files, BIOM files, and R markdown notebook. </p>
FIGURE 3 in Morphology and SSU rRNA gene sequence of the new brackish water ciliate, Anteholosticha pseudomonilata n. sp. (Ciliophora, Hypotrichida, Holostichidae) from Korea
FIGURE 3. The alignment of variable sites for SSU rRNA gene sequences of Anteholosticha pseudomonilata n. sp. and five congeners. Nucleotide position number is marked at the top of each aligned line. Missing sites are indicate by gaps (–) and the sites matched with A. pseudomonilata are represented with dots.
FIGURE 2 in Morphology and SSU rRNA gene sequence of the new brackish water ciliate, Anteholosticha pseudomonilata n. sp. (Ciliophora, Hypotrichida, Holostichidae) from Korea
FIGURE 2. Photomicrographs of Anteholosticha pseudomonilata n. sp. from live cells (A–E), and after protargol staining (F– H). (A, B) Ventral view of typical individuals. (C) Partial of dorsal view, to show the distribution of cortical granules (arrowheads) and dorsal bristles (arrows). (D) Ventral view showing macronuclear nodules (arrows) and micronuclei (arrowheads). (E) Posterior body, arrows mark the inclusions within cytoplasm. (F) Ventral view of the holotype specimen (the same individual as illustrated in 1D, E and 2G, H), arrow denotes anterior end of left marginal row. (G) Ventral view of mid-posterior portion, arrows and arrowheads show micronuclei and macronuclear nodules, respectively. (H) Anterior portion of ventral side, showing the buccal cirrus (arrow), frontoterminal cirri (arrowheads), and the right frontal cirrus (double-arrowheads). Scale bars = 50 µm.
FIGURE 1. Anteholosticha pseudomonilata n in Morphology and SSU rRNA gene sequence of the new brackish water ciliate, Anteholosticha pseudomonilata n. sp. (Ciliophora, Hypotrichida, Holostichidae) from Korea
FIGURE 1. Anteholosticha pseudomonilata n. sp. from live cells (A–C), and after protargol impregnation (D, E). (A) Ventral view of a typical individual. (B) Ventral view, arrows indicate the inclusions within cytoplasm at both cell ends. (C) Noting arrangement of cortical granules (arrows). (D, E) Ventral and dorsal views of the holotype specimen, showing the general infraciliature. Arrow in D marks the posterior end of the midventral complex. Arrowheads in E depict the "extra" dikinetids ahead of the right marginal row. AZM = adoral zone of membranelles; BC = buccal cirrus; EM = endoral membrane; FC = frontal cirri; FTC = frontoterminal cirri; LMR = left marginal row; Ma = macronuclei; Mi = micronuclei; MP = midventral pairs; PM = paroral membrane; PTC = pretransverse ventral cirri; RMR = right marginal row; TC = transverse cirri; 1-4 = dorsal kineties. Scale bars in (A) = 40 µm; in (D, E) = 30 µm.
FIGURE 2 in The morphology and SSU rRNA gene sequence analysis of a poorly-known brackish water ciliate, Pinacocoleps tesselatus (Kahl, 1930) (Ciliophora, Colepidae) from Hangzhou Bay, China
FIGURE 2. Photomicrographs of Pinacocoleps tesselatus (Kahl, 1930) from live cells (A–G), after silver carbonate impregnation (H, J), and after protargol impregnation (I). (A) Lateral view of a typical individual. (B) Anterior secondary plate. (C) Anterior main plate. (D) Posterior main plate. (E) Posterior secondary plate. (F) A squashed specimen showing the arrangement of plates. (G) Posterior view, arrows mark the posterior spines. (H) Lateral view, arrows denote the oral basket, arrowheads mark the extrusomes. (I) Anterior view, showing the oral structure, arrows indicate the adoral organelles. (J) Lateral view, showing the ciliary pattern. Scale bars (in A, J) = 30 μm; in (B–H) = 10 μm.
FIGURE 1 in The morphology and SSU rRNA gene sequence analysis of a poorly-known brackish water ciliate, Pinacocoleps tesselatus (Kahl, 1930) (Ciliophora, Colepidae) from Hangzhou Bay, China
FIGURE 1. Morphology and infraciliature of Pinacocoleps tesselatus (Kahl, 1930) Foissner et al. 2008 (A–E), P. similis (Kahl, 1933) Chen et al. 2010 (F, G), P. heteracanthus (Noland, 1937) Chen et al. 2010 (H), P. arenarius (Bock, 1952) Chen et al. 2010 (I), P. spiralis (Noland, 1937) Chen et al. 2010 (J), P. i n c u r v u s (Ehrenberg, 1833) Foissner et al. 2008 (K), and P. pulcher (Spiegel, 1926) Foissner et al. 2008 (L). (A) Lateral view of typical individual. (B) One row of plates. The circumoral plate is omitted. (C) Ciliary pattern at apical end of body. (D) Ciliary pattern of P. t e s s e l a t u s. (E) P. tesselatus (Kahl, 1930) (from Kahl 1930). (F) P. similis (Kahl, 1933) (from Chen et al. 2010). (G) P. similis (Kahl, 1933) (from Borror 1972). (H) P. heteracanthus (Noland, 1937) (from Noland 1937). (I) P. arenarius (Bock, 1952) (from Bock 1952). (J) P. spiralis (Noland, 1937) (from Noland 1937). (K) P. i n c u r v u s (Ehrenberg, 1933) (from Kahl 1930). (L) P. pulcher (Spiegel, 1926) (from Kahl 1930). AO = adoral organelle; AS = anterior spine; CC = caudal cilium; CK = circumoral kinety; Ma = macronucleus; Mi = micronucleus; PC = perioral ciliature; PS = posterior spine; SK = somatic kinety. Scale bars = 30 μm.
FIGURE 3 in The morphology and SSU rRNA gene sequence analysis of a poorly-known brackish water ciliate, Pinacocoleps tesselatus (Kahl, 1930) (Ciliophora, Colepidae) from Hangzhou Bay, China
FIGURE 3. Maximum likelihood (ML) phylogenetic tree based on the small subunit (SSU) rDNA of Pinacocoleps tesselatus and other colepids. Numbers at branching points show bootstrap values of 1,000 replicates for ML tree and posterior probability for Bayesian (BI) tree, respectively. Fully supported (100%/1.00) branches are marked with solid circles. The scale bar corresponds to 10 substitutions per 100 nucleotide positions. Taxonomic classification mainly follows Lynn (2008). GenBank numbers follow species names.
FIGURE 7. Bayesian phylogenetic tree inferred from SSU rRNA gene sequences. Posterior probabilities greater than 50 in Description of Trischistoma abharensis n. sp. (Nematoda: Trischistomatidae) and first record of Tripylella intermedia (Bütschli, 1873) Brzeski & Winiszewska-Ślipinska, 1993 (Nematoda: Tripylidae) from Iran
FIGURE 7. Bayesian phylogenetic tree inferred from SSU rRNA gene sequences. Posterior probabilities greater than 50% are given on appropriate clades. Nematode species, GenBank accession numbers, and locations are listed for each taxon if known. The accession no. AY284737 was originally deposited in GenBank as Paratripyla sp., but it was used as Tripylella sp. by van Megen et. al. (2009).
FIGURE 5 in Phylogenetic positions of four hypotrichous ciliates (Protista, Ciliophora) based on SSU rRNA gene, with notes on their morphological characters
FIGURE 5. Maximum likelihood (ML) phylogenetic tree based on SSU rRNA sequences showing the position of Rigidohymena inquieta, Pattersoniella vitiphila, Notohymena australis and Cyrtohymena (Cyrtohymenides) australis (in bold). Numbers at nodes are the bootstrap values from ML and the posterior probabilities from BI. Accession numbers are provided after species names. Asterisks at nodes indicate disagreement between the two methods. Arrows indicate the first included sequences. Bar, 1 substitution 100nt positions. Urostyla grandis and Anteholosticha multistilata are the outgroup taxa.
FIGURE 3 in Phylogenetic positions of four hypotrichous ciliates (Protista, Ciliophora) based on SSU rRNA gene, with notes on their morphological characters
FIGURE 3. Notohymena australis from life (A–E) and after staining with protargol (F, G). A, B. Ventral (A) and dorsal (B) view of typical individual, showing the cortical granules that arranged in rows on dorsal side (arrowheads in B). C, E. Details of cortical granules on dorsal side, showing the different clusters (arrowheads). D. Lateral view of cortical granules (arrowheads). F. Anterior part of ventral infraciliature, arrowhead depicts the curve at the anterior end of paroral membrane. G. Ventral view of infraciliature, arrowhead refers to the multiple caudal cirri. Scale bars = 40 Μm.
FIGURE 2 in Phylogenetic positions of four hypotrichous ciliates (Protista, Ciliophora) based on SSU rRNA gene, with notes on their morphological characters
FIGURE 2. Photomicrographs of Pattersoniella vitiphila in vivo (A–D) and after staining with protargol (E–G). A, B. Ventral view of two cells, showing the cirri on ventral side (A) and the contractile vacuole (B, arrow); C. Details of membranelles and their basal fibers (arrows); D. Frontal cirri and their well-developed associated basal fibers; E. Details of oral structure, showing the basal fibers of cirri; F. Dorsal kinetids and associated fibers; G. Ventral infraciliature. Scale bars: A, B = 180 Μm, G = 75 Μm.
FIGURE 1 in Phylogenetic positions of four hypotrichous ciliates (Protista, Ciliophora) based on SSU rRNA gene, with notes on their morphological characters
FIGURE 1. Rigidohymena inquieta from life (A, F–K) and after staining with protargol (D, E, L). A. Ventral view of living cells; B, C, L. Ventral (B, L) and dorsal (C) view of infraciliature; D, E. Ventral and dorsal view during later stage of reorganization; F, G. Ventral view of two typical individuals, arrow in G marks the contractile vacuole; G. Showing the crystals in cytoplasm; H. Showing the membranelles of adoral zone (arrowhead) and the transverse cirri (arrow); I. Details of oral structure, arrowhead marks the anteriorly curved Cyrtohymena-like paroral membrane; J. The collar part of adoral zone of membrane; K. Cyst; FC, frontal cirri; LMR, left marginal row; Ma, macronuclei; Mi, micronuclei; PM, paroral membrane; RMR, right marginal row; VC, ventral cirri; TC, transverse cirri. Scale bars = 50 Μm.
FIGURE 4 in Phylogenetic positions of four hypotrichous ciliates (Protista, Ciliophora) based on SSU rRNA gene, with notes on their morphological characters
FIGURE 4. Cyrtohymena (Cyrtohymenides) australis from life (A–D) and after staining with protargol (E–G). A, B. Two typical individuals, showing the body shape and colour. C. Cortical granules on dorsal side, arrows mark the cortical granules that scattered in pellicle. D. Cyst. E. The three anlagen for dorsal kineties of proter (arrowheads). F, G. Four dorsomarginal anlagen of proter (arrowhead, F) and opisthe (arrowhead, G) in the same specimen as in E. Scale bars = 100 Μm (A, B), 30 Μm (D).
FIGURE 1 in Analysis of primary structure loops from Hairpins 35 and 48 of the Nematoda SSU rRNA gene provides further evidence that the genera Tripylina Brzeski, 1963, Trischistoma Cobb, 1913 and Rhabdolaimus de Man, 1880 are members of Enoplida
FIGURE 1. Localisation of synapomorphic molecular traits in 18S r RNA genes of Enoplida. A. Fragments of alignments of aligned gene sequences corresponding to SSU rRNA regions of hairpins 35 and 48. Presumed synapomorphies of Trichistoma, Tripylina and other Enoplida are marked and given a dark background. B. Secondary structures of Hairpin 35 of Loricera foveata. C. Secondary structures of Hairpin 35 of Trischistoma and Tripylina. Arrowed, 1280 A → G substitution. D. Secondary structures of Hairpin 48 of Loricea foveata. E. Secondary structures of Hairpin 48 of Trischistoma and Tripylina. Arrowed: 1820 G → Y substitution.
Fig. 2 in Morphological and Morphogenetic Redescriptions and SSU rRNA Gene-based Phylogeny of the Poorly-known Species Euplotes amieti Dragesco, 1970 (Ciliophora, Euplotida)
Fig. 2. Photomicrographs of Euplotes amieti Dragesco, 1970 in vivo (A–H), after protargol (I–K) and silver nitrate (L, M) impregnation. (A) Ventral view of a representative individual. Arrow points to the contractile vacuole. (B, C) Different body shapes. (D) Lateral view showing flattened body. (E) Posterior part of an individual, arrowheads show the caudal cirri and arrows indicate the left marginal cirri. (F) Numerous irregular ellipsoid to oval granules (possibly mitochondria) extremely densely packed beneath dorsal and ventral pellicle. (G) Detailed view, arrows point to the basal positions of dorsal cilia. (H) Showing the endoplasm and the typical 3-shaped macronucleus. (I) Individual with three caudal cirri (arrowheads). (J, K) Ventral (J) and dorsal (K) view of the same specimen, showing the infraciliature and nuclear apparatus. (L, M) Portion of dorsal (L) and ventral (M) silverline system. Arrow indicates the position of contractile vacuole pore. Scale bars: 100 μm.
Data from: Phylogenetic affiliation of SSU rRNA genes generated by massively parallel sequencing: new insights into the freshwater protist diversity
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