Soil Ciliate Research Articles

First Record of Four Soil Ciliates from Korea

First Record of Four Soil Ciliates from Korea

Two Gonostomatid Ciliates from the Soil of Lombardia, Italy; including Note on the Soil Mapping Project.

Two gonostomatid ciliates, Gonostomum paronense n. sp. and G. strenuum, isolated from the soil sample of paddy field, Lombardia, Italy, were investigated using live observation and protargol impregnation. Gonostomum paronense n. sp. is mainly characterized by a tailed body, frontoventral cirri arranged in pairs, and presence of pretransverse and transverse cirri. Morphologically and morphometrically, the new species is similar to Gonostomum namibiense in having a tailed body and frontoventral cirral pairs; however, it differs mainly in the number of frontoventral cirral pairs (seven vs. three). Phylogenetic analyses based on the SSU rDNA sequences show that the new species is more closely related to G. namibiense than to G. strenuum, supporting the morphological classification based on the cirral pattern and the tailed body. However, due to the poor nodal support and absence of gene sequence of the type species Gonostomum, a more robust phylogeny of this group still remains unresolved. The biometric data of the Italian population of Gonostomum strenuum overlap with those from other known populations. Both species were collected from the industrial area of Parona, in the framework of the "Soil Mapping, Lombardia" project in which, for the first time in Italy, soil ciliates were used as bioindicators of soil quality.

Unveiling the species-rank abundance distribution by generalizing the Good-Turing sample coverage theory.

Based on a sample of individuals, we focus on inferring the vector of species relative abundance of an entire assemblage and propose a novel estimator of the complete species-rank abundance distribution (RAD). Nearly all previous estimators of the RAD use the conventional "plug-in" estimator Pi (sample relative abundance) of the true relative abundance pi of species i. Because most biodiversity samples are incomplete, the plug-in estimators are applied only to the subset of species that are detected in the sample. Using the concept of sample coverage and its generalization, we propose a new statistical framework to estimate the complete RAD by separately adjusting the sample relative abundances for the set of species detected in the sample and estimating the relative abundances for the set of species undetected in the sample but inferred to be present in the assemblage. We first show that P, is a positively biased estimator of pi for species detected in the sample, and that the degree of bias increases with increasing relative rarity of each species. We next derive a method to adjust the sample relative abundance to reduce the positive bias inherent in j. The adjustment method provides a nonparametric resolution to the longstanding challenge of characterizing the relationship between the true relative abundance in the entire assemblage and the observed relative abundance in a sample. Finally, we propose a method to estimate the true relative abundances of the undetected species based on a lower bound of the number of undetected species. We then combine the adjusted RAD for the detected species and the estimated RAD for the undetected species to obtain the complete RAD estimator. Simulation results show that the proposed RAD curve can unveil the true RAD and is more accurate than the empirical RAD. We also extend our method to incidence data. Our formulas and estimators are illustrated using empirical data sets from surveys of forest spiders (for abundance data) and soil ciliates (for incidence data). The proposed RAD estimator is also applicable to estimating various diversity measures and should be widely useful to analyses of biodiversity and community structure.

Ciliates from ancient permafrost: Assessment of cold resistance of the resting cysts

There is evidence that resting cysts of soil ciliates and numerous taxa of other protists can survive in permafrost for thousands of years at subzero temperatures; however, our knowledge about mechanisms of long term cryobiosis remains incomplete. In order to better understand the means by which ancient cysts survive, we investigated resistance to cyclical supercooling stress of resting cysts of the soil ciliate Colpoda steinii (Colpodida, Ciliophora). Three clonal strains were used for comparison, isolated from Siberian tundra soil, ancient Holocene (5–7,000 y) and late Pleistocene (32–35,000 y) permafrost sediments. To determine the viability of the ancient and contemporary ciliate cysts we improved and validated a cultivation-independent method of vital fluorescent staining with a combination of two nucleic acid binding dyes, acridine orange and propidium iodide. The viability of Colpoda steinii cysts during low-temperature experiments was measured using both the proposed vital fluorescent staining method and standard germination test. Our results indicate that the dual-fluorescence technique is a more accurate, rapid, and efficient method for estimating cyst viability. We found that cysts of ancient ciliates display lower tolerance to the impact of cyclical cold compared to cysts of contemporary ciliates from Siberian permafrost affected soils.

Protist-facilitated particle transport using emulated soil micromodels.

Microbial processes in the subsurface can be visualized directly using micromodels to emulate pore-scale geometries. Here, emulated soil micromodels were used to measure transport of fluorescent beads in the presence and absence of the soil ciliate Colpoda sp. under quiescent conditions. Beads alone or beads with protists were delivered to the input wells of replicate micromodels that contained three 20 mm(2) channels emulating a sandy loam microstructure. Bead abundance in microstructured channels was measured by direct counts of tiled confocal micrographs. For channels with protists, average bead abundances were approximately 320, 560, 710, 830, and 790 mm(-2) after 1, 2, 3, 5, and 10 days, respectively, versus 0, 0, 0.3, 7.8, and 45 mm(-2) without protists. Spatial and temporal patterns of bead abundance indicate that protist-facilitated transport is not a diffusive-type process but rather a function of more complex protist behaviors, including particle uptake and egestion and motility in a microstructured habitat. Protist-facilitated transport may enhance particle mixing in the soil subsurface and could someday be used for targeted delivery of nanoparticles, encapsulated chemicals, or bacteria for remediation and agriculture applications.

SEASONAL DYNAMICS OF SOIL CILIATES OF SAMUR-YALAMA NATIONAL PARK

The article describes the seasonal dynamics, as well as a comparison of the species composition and structural analysis of communities of soil ciliates. Methods . Assembled with standard collection points soil samples delivered to the laboratory for further processing. Comparison of species composition of soil ciliates two different sites was carried out by Czekanowski-Sorensen, and to analyze the community structure of soil ciliates are normally used in environmental studies-dominance indices Simpson, Margalef species diversity. Results .Studies have shown that the species composition and abundance of soil ciliates individual species consistently changing seasons of the year. In general it can be noted that the total number of seasonal dynamics of soil ciliates is a bimodal curve with peaks in spring and autumn and minima in winter and summer. Main conclusions. Species composition and the total number of soil ciliates in the territory of the Samur-Yalama National Park varies both qualitatively and quantitatively depending on the time of year. Some regularities in the change of species of soil ciliates in forest soils Samur - Yalama National Park. Studies have shown the presence of certain seasonal faunal assemblages in communities of soil ciliates. The qualitative and quantitative distribution of ciliates pedobiontov affect environmental factors (both abiotic and biotic) causing microzonation distribution of these free-celled animals within a few centimeters.

Morphology, morphogenesis and molecular phylogeny of a soil ciliate, Pseudouroleptus caudatus caudatus Hemberger, 1985 (Ciliophora, Hypotricha), from Lhalu Wetland, Tibet

Pseudouroleptus caudatus caudatus Hemberger, 1985, a soil ciliate isolated from Tibet, was studied in vivo and after protargol impregnation. The Tibetan population is mainly characterized by: elongate body with narrowly rounded anterior end and tapered posterior end; length of buccal area relative to body length ca. 20–25%; cortical granules colourless, round, densely distributed throughout sub-pellicular layer of cell; one parabuccal cirrus; post-peristomial cirrus lacking in 75% of specimens analyzed; left and right ventral rows commence at same level; four dorsal kineties; 3–6 inconspicuous caudal cirri; two macronuclear nodules; 2–7 micronuclei; contractile vacuole located at about 33% of body length near left margin. Morphogenesis is characterized by: (1) parental adoral zone of membranelles retained completely; (2) anterior segments of streaks VI and IV and the whole of streak V form the anterior, middle, posterior segments of the mixed row, respectively; (3) right ventral row originates de novo in both daughter cells; (4) marginal rows develop intrakinetally; (5) dorsal kinety anlage 3 develops de novo in the proter and intrakinetally in the opisthe; and (6) the two macronuclear nodules fuse into a single mass which then divides. Molecular phylogenies corroborate the morphological identification and support the close relationship between Pseudouroleptus and Strongylidium.

Morphology and molecular phylogeny of Pseudouroleptus jejuensis nov. spec., a new soil ciliate (Ciliophora, Spirotrichea) from South Korea

A new soil ciliate, Pseudouroleptus jejuensis, was discovered from Jeju Island, South Korea and described based on live observation, protargol impregnation, and SSU rRNA gene sequence analyses. Pseudouroleptus jejuensis differs from other congeneric species mainly by number of dorsal kineties (5 vs. 4). Based on our observation of late dividers, we confirm that the dorsal kinety anlage 3 forms 3 kineties (i.e., dorsal kineties 3–5), and the dorsal kinety anlagen 1–3 form 3–5/1–2/0 caudal cirri, respectively. Our gene trees support the assignment of this new species in Pseudouroleptus to full supporting values.

Morphological and molecular characterization of Parafurgasonia zhangi spec. nov. and Chilodonella acuta Kahl, 1931 (Protozoa, Ciliophora), from a soil habitat of Saudi Arabia.

The morphology and infraciliature of two soil ciliates, Parafurgasonia zhangi spec. nov. and Chilodonella acuta Kahl, 1931, collected from Saudi Arabia, were investigated by observations of both living cells and specimens after standard staining methods. P. zhangi differs from its congeners by the combination of the following features: excretory pore quite near posterior end of paroral membrane, 16 or 17 somatic kineties with about 11 kinetids in each one on dorsal side, paroral membrane gently curved and composed of about 15 dikinetids, and hypostomial organelle composed of four or five files of kinetids with four monokinetids each. The diagnosis of Chilodonella acuta was renewed to include characteristics revealed by the silver impregnation method: cells in vivo measuring 33-45) × 18-26) µm, dorsal hump and tail-like podite present, two contractile vacuoles, seven left and five right kineties, 9-11 nematodesmal rods, and dorsal brush containing about 11 basal bodies. Phylogenetic analyses based on small-subunit rRNA gene sequences showed that P. zhangi was closer to species of the Colpodidiidae rather than the Furgasoniidae represented by Furgasonia blochmanni, and Chilodonella acuta clustered with its congener Chilodonella uncinata but was a well-outlined species of the genus.

Spatio‐temporal Variations in the Molecular Diversity of Microeukaryotes in Particular Ciliates in Soil of the Yellow River Delta, China

The Yellow River delta in China is one of the most active regions of land-ocean interaction. It has suffered serious salinization due to drying-up of the Yellow River, rising sea level, and seashore erosion, and thus represents a special and extreme environment. We evaluated the microeukaryotic molecular diversity and its response to change of seasons and environmental variables, in particular salinity in the soil of the Yellow River delta, by denaturing gradient gel electrophoresis (DGGE) and gene sequencing. The sequencing of the microeukaryotic DGGE bands revealed the presence of diverse groups dominated by protists in particular ciliates. We further recovered a high diversity of marine and soil ciliates inhabiting in coastal soil using the ciliate-specific DGGE. The neighbor-joining tree indicated that the ciliate 18S rDNA sequences from high-salinity soil were affiliated to Colpodea, Spirotrichea, Litostomatea, and Oligohymenophorea, while all the sequences unique to the low-salinity soil were affiliated to Colpodea. Statistical analysis indicated that the microeukaryotic molecular diversity was significantly different among sites, while statistically indistinguishable among seasons. Soil salinity might be the main factor regulating the distribution of microeukaryotes in the soil from the Yellow River delta.

Hypotrichous ciliates (Protozoa: Ciliophora) from a temporary pond in Argentina, with redescription of Apoamphisiella hymenophora (Stokes, 1886) Berger, 1999.

Hypotrichous ciliates collected in the plankton and soil samples from a temporary pond in Buenos Aires province, Argentina, were characterized after live observations and protargol impregnation. Apoamphisiella hymenophora (Stokes) Berger is redescribed and the neotype material deposited. Apoamphisiella hymenophora differs from its congeners in having 2 macronuclear nodules, 1 contractile vacuole with anterior and posterior collecting canals, the absence of cortical granules, 2 cirri behind the rightmost frontal cirrus, 1 postoral cirrus, 6 dorsal rows of dikinetids along with scattered dikinetids on the right body margin, and 3-9 caudal cirri arranged in groups at the ends of dorsal rows 1, 2, and 4. Rigidohymena candens, R. quadrinucleata, Histriculus histrio, Gastrostyla steinii, and Pseudouroleptus caudatus are new for the Argentine microfauna. Since especially the soil ciliates have been almost unexplored in South America, the results from the present investigation describe and contribute to the knowledge of the diversity of these microorganisms within this geographical region.

Ultrastructural observations on the resting cyst of the soil ciliate, Territricha stramenticola and the freshwater ciliate, Urostyla grandis

The ultrastructure of non-dividing cells and resting cysts of soil ciliate Territricha stramenticola and freshwater ciliate Urostyla grandis were observed using scanning and transmission electron microscopy. The results show that the resting cell of T. stramenticola shared many similarities with that of U. grandis. Inside the cytoplasm of both resting cysts, there existed organelles such as mitochondria and autophagic vacuoles. The resting cyst of the freshwater ciliate U. grandis is spherical or ellipsoid in shape, but its cyst wall is composed of three layers: the ectocyst, the endocyst and the granular layer. However, the cyst wall of T. stramenticola was quite different from U. grandis. The cyst wall of T. stramenticola was composed of the ectocyst and the endocyst; the former was made up of small regular rectangular units tightly packed together like that of beehive, while the latter was an irregular layer of varied thickness between the ectocyst and the pellicle. Such cyst wall, quite unlike those of other freshwater ciliates, might help the cyst keep the moisture inside, thus playing an important role in tiding the resting cells over the unfavorably dryer conditions and in maintaining its existence under extreme circumstances. Those suggested that T. stramenticola would take form of another kind of kinetosome-resorbing cyst. The results of this study would help reveal how soil ciliate T. stramenticola adapt to their environment and structural differences under certain conditions. Key words: Territricha stramenticola, Urostyla grandis, cyst wall, resting cyst, ultrastructure

Morphology and morphogenesis of a soil ciliate, Rigidohymena candens (Kahl, 1932) Berger, 2011 (Ciliophora, Hypotricha, Oxytrichidae), with notes on its molecular phylogeny based on small-subunit rDNA sequence data

The morphology and morphogenesis of the stylonychine hypotrich Rigidohymena candens (Kahl, 1932) Berger, 2011, isolated from garden soil in Qingdao, China, were investigated using live observation and protargol impregnation methods. The Qingdao isolate possesses all diagnostic morphological characters of R. candens. The main events during binary fission are as follows: (i) the proter retains the parental adoral zone of membranelles entirely, whereas the old undulating membranes dedifferentiate into an anlage that gives rise to the leftmost frontal cirrus and the new undulating membranes of the proter; (ii) five streaks of fronto-ventral-transverse cirral anlagen are segmented in the pattern 3 : 3 : 3 : 4 : 4 from left to right, which form two frontal, four frontoventral, one buccal, five ventral and five transverse cirri, respectively; (iii) dorsal morphogenesis is in the typical Oxytricha pattern; (iv) three caudal cirri are formed, one at the posterior end of each of dorsal kineties 1, 2 and 4; and (v) the postoral ventral cirrus V/3 is not involved in primordia formation. The morphological and morphogenetic observations and phylogenetic analyses based on the small-subunit rDNA sequence data support the validity of Rigidohymena Berger, 2011 and its systematic position in the subfamily Stylonychinae.

Morphology and morphometry of Bresslauides pratensis n. sp., a new soil ciliate (Ciliophora, Colpodea) from Turkey

A new colpodid ciliate, Bresslauides pratensis n. sp., was discovered in soil from a meadow field in Turkey. Its morphology was investigated using live observation, protargol impregnation, silver nitrate impregnation, and scanning electron microscopy. The new species differs from the congeners by the following combination of features: the cell size in vivo is about 135–180μm×130–160μm; the body has an almost circular outline with a conspicuous bulge on the ventral side; the somatic cilia are arranged in about 105 densely spaced, sigmoidal kineties; a diagonal groove extends to the left cell side, terminating in a pronounced postoral sack; one almost globular macronucleus and usually two globular micronuclei; the oral structures occupy almost the anterior half of the cell and comprise a distally elongated right polykinetid and a crescentic left oral polykinetid, both restricted to the vestibulum; on average 12 vestibular, 31 postoral, and 55 left oral kineties. Based on the morphological data, it was concluded that B. pratensis is a well-outlined and distinctive member of the genus Bresslauides. Additionally, the most recent molecular data on the order Colpodida and genera Colpoda, Bresslaua, and Bresslauides are briefly discussed.

Application of the Ludox-QPS method for estimating ciliate diversity in soil and comparison with direct count and DNA fingerprinting

Soil ciliates have advantages in monitoring soil quality after pollution and disturbance. However the potential is limited by the shortcoming of integrating quantitative and qualitative techniques. Here we utilized the Ludox-Quantitative Protargol Stain (Ludox-QPS) method which was originally developed for marine sediment to assess ciliate diversity in soil. The method was tested with three soil samples and compared with a ciliate-specific Denaturing Gradient Gel Electrophoresis (DGGE) and direct count method. The Ludox-QPS method obtained significantly higher number of ciliates with higher taxonomic resolution than the direct count, and revealed higher diversity than the DGGE as well as subsequent gene sequencing. Besides, we evaluated the effects of 2% glutaraldehyde fixative and the QPS preparation on cell size of one species from each of the three dominant ciliate assemblages in soil: colpodids, hypotrichs and haptorids. The experiment indicates a biovolume conversion factor of ∼0.69 for soil ciliates treated with the Ludox-QPS method. The Ludox-QPS method fulfills the enumeration of soil ciliates with good taxonomic resolution and thus promotes the utilization of ciliates in the bioassessment of soil environments.

Allelopathy of diterpenoids on three species of soil ciliates

Allelopathy of diterpenoids extracted from plants of the genus Robdosia on three common species of soil ciliates, Colpoda inflata, Colpoda cucullus and Euplotes muscicola, was studied by acute toxicity test, sub-lethal effect test and morphological observation. Acute toxicity test showed that there was remarkable toxicity of the diterpenoids on the individuals of the three soil ciliate species, and there was close correlation between toxicity and concentration of the diterpenoids. 12 h-LC 50 values of the diterpenoids on the individuals of C. inflata, C. cucullus and E. muscicola were 161.40 mg L −1, 94.80 mg L −1 and 83.70 mg L −1 respectively, and 24 h-LC 50 values were 114.90 mg L −1, 92.30 mg L −1and 65.80 mg L −1 separately. Sub-lethal effect test of soil ciliates suggested that there existed significant inhibition of the diterpenoids on population growth of the three ciliates with dose-dependant relationships, population density and growth rate of the test group was obviously lower than that of the control group. Morphological observation indicated that diterpenoids affected the body shapes of the three ciliates and made them shorter and thicker, and the higher the concentration of diterpenoids, the greater the affection. The results are of great significance for understanding the functions of ciliates and their relationships to other organisms, and for the application of allelopathy in biological pest control in the soil ecosystems.

First Record of Five Soil Ciliates (Ciliophora, Hypotricha) from Saudi Arabia

First Record of Five Soil Ciliates (Ciliophora, Hypotricha) from Saudi Arabia

Response of the soil ciliate community to ecological restoration in Huajialing, Dingxi, Gansu

To obtain a better understanding of the responses of soil ciliate communities to ecological restoration, a quarterly survey of the soil ciliate community and seasonal dynamics across five sampling sites of artificial spruce forest was undertaken. A contrast sampling site of wild grassland was used and live observation ciliates and the three level ten-fold dilution method was used in Huajialing, Dingxi, Gansu. A total of 127 species were identified, belonging to three classes, nine orders, 34 families and 50 genera. Results show that the species distribution had obvious differences across the sampling sites, the community structure of soil tended to be complicated and species comparability decreased gradually with the number of restoration years, and abundance, species richness and species diversity index showed an upward trend. The dominant groups of soil ciliates changed during ecological restoration. Colpodida was the dominant group in sampling site I and site II, whereas Hypotrichida was the dominant group in the late recovery sampling sites. This study shows that the dynamics of the soil ciliate community better respond to soil condition changes in the ecological restoration process. Although the soil ciliate community can be used to evaluate the effect of ecological restoration of terrestrial ecosystems, plenty of further systematic research to establish an effective and feasible evaluation index system is required.

Community Structure and Biodiversity of Soil Ciliates at Dongzhaigang Mangrove Forest in Hainan Island, China

The distribution of soil ciliates in three different habitats within a typical mangrove forest in Dongzhaigang, Hainan, China was investigated. The abundance, biodiversity, and community similarity of ciliates in fresh and air-dried soil with different, physical/chemical properties were analyzed. Three Classes, 11 Orders, 34 Genera, and 70 species of ciliates were found with the first dominant group being Hypotrichida. Ciliate biodiversities followed Site B < Site A < Site C in both fresh and dried samples. Ciliate abundance was positively correlated with soil moisture, salinity, organic matter (OM), total nitrogen (TN), total phosphorus (TP), and sulfate (SO42−), but negatively with pH and total potassium (TK). Site A and Site B and Site B and Site C showed the highest similarity in fresh and dried samples, respectively. The ubiquitous characteristics of ciliate distribution suggested their important role in food webs and nutrient cycling. The presence of Colpodida was linked with mangrove plants.

Application of the denaturing gradient gel electrophoresis (DGGE) technique as an efficient diagnostic tool for ciliate communities in soil

Ciliates (or Ciliophora) are ubiquitous organisms which can be widely used as bioindicators in ecosystems exposed to anthropogenic and industrial influences. The evaluation of the environmental impact on soil ciliate communities with methods relying on morphology-based identification may be hampered by the large number of samples usually required for a statistically supported, reliable conclusion. Cultivation-independent molecular-biological diagnostic tools are a promising alternative to greatly simplify and accelerate such studies. In this present work a ciliate-specific fingerprint method based on the amplification of a phylogenetic marker gene (i.e. the 18S ribosomal RNA gene) with subsequent analysis by denaturing gradient gel electrophoresis (DGGE) was developed and used to monitor community shifts in a polycyclic aromatic hydrocarbon (PAH) polluted soil. The semi-nested approach generated ciliate-specific amplification products from all soil samples and allowed to distinguish community profiles from a PAH-polluted and a non-polluted control soil. Subsequent sequence analysis of excised bands provided evidence that polluted soil samples are dominated by organisms belonging to the class Colpodea. The general DGGE approach presented in this study might thus in principle serve as a fast and reproducible diagnostic tool, complementing and facilitating future ecological and ecotoxicological monitoring of ciliates in polluted habitats.