Small Subunit Ribosomal Gene Sequences Research Articles

Morphology, Morphogenesis and Molecular Phylogeny of Two Freshwater Ciliates (Alveolata, Ciliophora), with Description of Pseudosincirra binaria sp. nov. and Redefinition of Pseudosincirra and Perisincirra

Ciliated microeukaryotes are insufficiently investigated despite their ubiquity and ecological significance. The morphology and morphogenesis of a new Stichotrichida species, Pseudosincirra binaria sp. nov., and the known Perisincirra paucicirrata Foissner et al., 2002, are here studied using live observations and protargol staining methods. The new species is characterized by having one buccal, one parabuccal and three frontal cirri, one frontoventral row extending to the posterior half of the cell, three left and two right marginal rows and three dorsal kineties with the left kinety conspicuously bipartite, along with one caudal cirrus at the rear end of each kinety. During morphogenesis, there exist five frontal-ventral cirral anlagen with anlagen IV and V forming a frontoventral row in the proter, and four cirral anlagen with only anlage IV generating a frontoventral row in the opisthe. The anlagen for marginal rows and dorsal kineties develop intrakinetally. The new population of Perisincirra paucicirrata corresponds well with other isolates regarding morphology and cell development. Phylogenetic analyses based on small subunit ribosomal gene sequence data revealed that both Perisincirra and Pseudosincirra are deeply clustered in the clade consisting of species from the genera Deviata and Heterodeviata, supporting the placement of both genera into the family Deviatidae Foissner, 2016.

Prevalence and Genetic Diversity of a Microsporidian Parasite in the Black Imported Fire Ant and Its Social Parasitic Ant (Formicidae: Myrmicinae: Solenopsis) in Buenos Aires Province, Argentina.

Microsporidia are natural pathogens of arthropods and have been used as biological control against insect pests. In the United States, efforts to control the invasive Red Imported Fire Ant, Solenopsis invicta, and Black Imported Fire Ant, Solenopsis richteri, have included the use of the microsporidium, Kneallhazia solenopsae. However, there is limited information about the genetic differences among the microsporidian variants found in S. invicta and in S. richteri. In this study, we assessed the prevalence and genetic diversity of K. solenopsae in native populations of S. richteri in Argentina (South America). Additionally, we examined the social parasitic ant, Solenopsis daguerrei, which is found in some S. richteri nests, for the presence of this microsporidium. The survey of 219 S. richteri nests revealed K. solenopsae infections in all five sites analyzed, with 28 colonies (12.8%) positive for the microsporidium. Among the 180 S. daguerrei individuals collected, seven ants (3.9%) from three sites tested positive for K. solenopsae. Phylogenetic analyses of the microsporidian variants present in S. richteri and S. daguerrei based on partial small subunit ribosomal gene sequences (SSU rRNA) showed that both ant species shared the same variant, which is different from the ones found in S. invicta. Further studies are needed to determine the pathogenicity of genetically different K. solenopsae variants among Solenopsis species.

Morphology, morphogenesis and molecular phylogeny of a new marine ciliate, Trichototaxis marina n. sp. (Ciliophora, Urostylida)

The live morphology, infraciliature and morphogenesis of a new urostylid ciliate, Trichototaxis marina n. sp., collected from coastal water in Qingdao, China, were studied based on the observations of live and silver stained specimens. The new species is characterised as follows: body very flexible and contractile, slight to brick-reddish in colour due to irregularly-shaped, brick-red pigments; ca. 70 adoral membranelles; about 17 frontal cirri arranged in a bicorona; average 67 midventral pairs, the right base of each pair being conspicuously larger than the left base; five to seven transverse cirri; constantly two frontoterminal, one buccal and two pretransverse ventral cirri; two or three left marginal rows; right and innermost left marginal rows with 56–92 and 66–106 cirri, respectively; six bipolar dorsal kineties; more than 100 macronuclear nodules. The characteristic morphogenetic feature in T. marina is the development of the left marginal rows, that is, only one left marginal row is newly built the other one or two being retained from the parental cell. Phylogenetic analyses based on small subunit ribosomal gene sequence data reveal a close relationship of T. marina with members of family Pseudokeronopsidae.

Biology of a new xenoma-forming gonadotropic microsporidium in the invasive blotchfin dragonet Callionymus filamentosus.

A gonadotropic microsporidian parasite, Obruspora papernae gen. et sp. nov. (Microsporidia: Enterocytozoonidae), is described from Callionymus filamentosus (Teleostei: Callionymidae) in the Mediterranean Sea. The host, a Red Sea invasive species which entered the Mediterranean through the Suez Canal, was first collected in the Levant Basin in 1953, whereas its parasite went unobserved until 2008. Analysis of partial small subunit ribosomal gene sequences (SSU rDNA) placed the new species within the Nucleospora, Desmozoon, and Paranucleospora clade, and as it differs from each of them, it is assigned to a new genus. The development of the parasite is described, and the biological mechanisms underlying this parasite-host system are analyzed. Prevalence of infection approached 80% in female samples throughout most of the year. Males showed no signs of infection, but parasite rDNA was detected in male internal organs. The parasite-induced xenomas progressively occupied and eventually replaced much of the ovary, in some cases producing effective castration. Despite high levels of parasite infection, current trawl fishery statistics indicate that the abundance of Mediterranean populations of the host remains high. The parasite impact on the host population dynamics is unclear. Possible effects of the new microsporidian parasite on the reproductive effort of C. filamentosus and the potential role of another parasite, the ectoparasitic copepod Lernanthropus callionymicola, as an additional host in the life cycle of O. papernae, require further investigation.

Molecular profiling and identification of methanogenic archaeal species from rabbit caecum

During a comparison of 16S rDNA PCR-denaturant gradient gel electrophoresis (DGGE) profiles of methanogenic archaea from rumen fluid, rabbit caecum and pig feces, a unique band common to all rabbit caecum samples was observed. DGGE profiling also showed that the methanogen community from the New Zealand White adult rabbits is different and less complex than the methanogen communities from the rumen and pig feces. Small subunit ribosomal gene sequences of methanogenic archaea were subsequently retrieved from the constructed rabbit caecum 16S rDNA gene library. Results of the phylogenetic analysis indicated that rabbit caecum is inhabited by members of the genus Methanobrevibacter and is possibly one-species dominated, because all the retrieved sequences exhibited similarity values of 99% or higher. This species may well be a novel species of the genus Methanobrevibacter. It belongs to a distinct phylogenetic group containing Methanobrevibacter woesei, Methanobrevibacter thaueri and Methanobrevibacter gottschalkii strains isolated from animal feces, and Methanobrevibacter smithii from the predominating methanogen population of the human large bowel.

Phylogenetic Position of the Green FlagellateMesostigma virideBased on α‐Tubulin and β‐Tubulin Gene Sequences

The green alga Mesostigma viride has attracted considerable recent attention as a model system useful for understanding the evolutionary origin of the Viridiplantae (all green algae plus embryophytes) or the Streptophyta (charophycean algae plus embryophytes). Mesostigma’s utility for such studies depends on its phylogenetic position, which has been controversial. Phylogenetic analyses based on organellar genes have given conflicting results; some support a hypothesis that Mesostigma represents the first branch of the Viridiplantae, whereas others support an alternative hypothesis that it occupies a basal position within Streptophyta. Nuclear‐encoded actin and small subunit ribosomal gene sequences also mark Mesostigma as a basal lineage in Streptophyta. We tested these two alternative hypotheses by analyses of nuclear‐encoded α‐ and β‐tubulin sequences. We obtained new α‐ and β‐tubulin gene sequences from M. viride as well as from the charophycean Coleochaete scutata and the green flagellates Pterosperma cristatum, Nephroselmis rotunda, and Mantoniella squamata, each representing a major clade within Prasinophyceae, in order to increase the taxon richness of the databases. We employed Bayesian and maximum likelihood procedures and paid particular attention to codon position effects on the phylogenetic analysis. On balance, our results support the hypothesis that M. viride is a basal streptophyte.

ABUNDANCE OF A NOVEL DINOFLAGELLATE PHYLOTYPE IN THE ROSS SEA, ANTARCTICA1

The biodiversity of protistan assemblages present in microhabitats of the Ross Sea, Antarctica, was examined using molecular biological methods to obtain a greater understanding of the genetic diversity present. Sequencing of 18S clone libraries indicated genetically diverse collections of organisms in the water column, ice, and meltwater layer (slush), but a single small subunit ribosomal DNA (srDNA) sequence type dominated clone libraries (>30%) from seawater and slush samples taken within the ice pack of this ecosystem. The BLAST searches indicated that this dominant clone was derived from a dinoflagellate, and that it shared sequence similarity (97.6%–98.3%) with both Karenia and Karlodinium species. Phylogenetic analyses based on small subunit ribosomal gene sequences supported its placement as a sister group to these taxa, and suggested that it represented a novel genus. The dinoflagellate was successfully recovered in culture, and morphological analyses have shown that it contains chloroplasts, is gymnodinoid, appears not to have thecal plates, and has an apical groove and sulcal structure that confirm its placement as a relative of the Karenia/Karlodinium group. The abundance of this phylotype in natural samples was confirmed by quantitative PCR analyses of water and slush communities, and suggests that this dinoflagellate can be a major constituent of the protistan assemblages of some Antarctic microhabitats of the Ross Sea.

Comparative morphology and molecular phylogeny of aplanochytrids (Labyrinthulomycota)

Aplanochytrids comprise one of three major subgroups within the Labyrinthulomycota. We have surveyed the diversity of aplanochytrids and have discovered that most isolates are difficult to identify to species because of character plasticity and ambiguity. Ten isolates were studied using molecular phylogenies based on small subunit ribosomal gene sequences (SSU rDNA) and morphological characters derived from light microscopy, SEM and TEM (e.g., colony size, colony shape, colony pattern, agar penetration, cell shape, cell surface patterns, cell inclusion characteristics and ectoplasmic net morphology). Of these isolates, we could positively identify two of them to species, namely Aplanochytrium yorkensis (Perkins, 1973) Leander and Porter, 2000 and A. minuta (Watson and Raper, 1957) Leander and Porter, 2000. We used standardized conditions for growing aplanochytrid isolates in order to minimize environmentally induced phenotypic plasticity in our comparative studies of morphology. By mapping the morphological characters listed above onto a conservative phylogenetic topology derived from SSU rDNA sequences, we were able to identify several synapomorphies (e.g., gross colony characteristics and cell surface patterns) that serve as valuable taxonomic characters for the identification of species and specific clades of aplanochytrids.

Retortamonad flagellates are closely related to diplomonads--implications for the history of mitochondrial function in eukaryote evolution.

We present the first molecular phylogenetic examination of the evolutionary position of retortamonads, a group of mitochondrion-lacking flagellates usually found as commensals of the intestinal tracts of vertebrates. Our phylogenies include small subunit ribosomal gene sequences from six retortamonad isolates-four from mammals and two from amphibians. All six sequences were highly similar (95%-99%), with those from mammals being almost identical to each other. All phylogenetic methods utilized unequivocally placed retortamonads with another amitochondriate group, the diplomonads. Surprisingly, all methods weakly supported a position for retortamonads cladistically within diplomonads, as the sister group to Giardia. This position would conflict with a single origin and uniform retention of the doubled-cell organization displayed by most diplomonads, but not by retortamonads. Diplomonad monophyly was not rejected by Shimodaira-Hasegawa, Kishino-Hasegawa, and expected likelihood weights methods but was marginally rejected by parametric bootstrapping. Analyses with additional phylogenetic markers are needed to test this controversial branching order within the retortamonad + diplomonad clade. Nevertheless, the robust phylogenetic association between diplomonads and retortamonads suggests that they share an amitochondriate ancestor. Because strong evidence indicates that diplomonads have secondarily lost their mitochondria (rather than being ancestrally amitochondriate), our results imply that retortamonads are also secondarily amitochondriate. Of the various groups of eukaryotes originally suggested to be primitively amitochondriate under the archezoa hypothesis, all have now been found to have physical or genetic mitochondrial relics (or both) or form a robust clade with an organism with such a relic.

A simple test: evaluating explanations for the relative simplicity of the Edwardsiidae (Cnidaria: Anthozoa).

Many members of the cnidarian subclass Zoantharia (sea anemones, corals, and their allies) pass through a larval stage with eight complete mesenteries and without posterior musculature. This larva is usually transient, developing into an adult with 12 or more mesenteries. The adults of one family of sea anemones, the Edwardsiidae, bear the larval number and arrangement of mesenteries and lack the pedal disc seen in other sea anemones. The morphology of the Edwardsiidae has been interpreted in a number of ways: (1) the Edwardsiidae are the most basal extant zoantharian, having diverged before the evolution of additional mesenteries and basal musculature; (2) they are relatively advanced sea anemones that have secondarily simplified because they burrow in sand or mud rather than attaching to a hard substrate; or (3) edwardsiids are derived anemones that have retained a juvenile morphology through paedomorphosis. Phylogenetic analyses of small subunit ribosomal gene sequences reveal that the Edwardsiidae are derived zoantharians, nested within sea anemones. None of the proposed explanations fully explain the edwardsiid's body plan; edwardsiid anatomy is a mosaic of retained primitive and derived features. The results of the present study provide insight into zoantharian phylogeny and illustrate how phylogenetic tests can be used to study the evolution of cnidarian body plans.

Hyperamoeba isolated from human feces: Description and phylogenetic affinity

Summary The morphology and phylogenetic affinity of Hyperamoeba isolated from human feces is described. During its life cycle, it switches reversibly from flagellate to aflagellated amoebae and is capable of forming cysts. It grows aerobically. Under anaerobic conditions it persists but does not replicate. The amoeboflagellate has a single nucleus with a distinct nucleolus. Its mitochondria possess tubular cristae and a central electron dense body, similar to that of plasmodial slime molds. A single contractile vacuole is evident. The flagellate has one detectable anterior flagellum but two basal bodies are visible at the ultrastructure level. The flagellar apparatus is very similar to that found in some Eumycetozoa, especially the myxogastrids. The uninucleate cyst has a bi-layered endocyst and a membranous, irregular shaped, faintly laminated ectocyst that harbors bacterial inclusions. Phylogenetic reconstructions based on nuclear small subunit ribosomal gene sequence comparisons show that Hyperamoeba is closely related to the plasmodial slime mold Physarum polycephalum. These protists share a most recent common ancestry that excludes all other taxa in the database. This phylogenetic relationship is supported by detailed similarities in both mitochondrial and flagellar apparatus ultrastructure.

Do Galeate-Ascospore Members of the Cephaloascaceae, Endomycetaceae and Ophiostomataceae Share a Common Phylogeny?

Using partial small subunit ribosomal gene sequences we show that yeast-like genera that produce galeate (hat-shaped) ascospores and similar-spored members of the Ophiostomatales do not form a monophyletic group. Based on distance and parsimony methods Cephaloascus fragrans and Endomyces decipiens failed to form a monophyletic grouping with species of Ceratocystis sensu stricto and Ophiostoma. Instead these yeast species clustered with Saccharomyces cerevisiae, Kluyveromyces lactis, and Torulaspora delbrueckii in >9% of both the distance and parsimony majority-rule consensus trees generated using the statistical method of bootstrapping. Therefore galeate ascospores appear to be an example of convergent evolution in fungi and by itself this trait should not be considered as an indicator of evolutionary relatedness.

Do Galeate-Ascospore Members of the Cephaloascaceae, Endomycetaceae and Ophiostomataceae Share a Common Phylogeny?

Using partial small subunit ribosomal gene sequences we show that yeast-like genera that produce galeate (hat-shaped) ascospores and similar-spored members of the Ophiostomatales do not form a monophyletic group. Based on distance and parsimony methods Cephaloascusfragrans and Endomyces decipiens failed to form a monophyletic grouping with species of Ceratocystis sensu stricto and Ophiostoma. Instead these yeast species clustered with Saccharomyces cerevisiae, Kluyveromyces lactis, and Torulaspora delbrueckii in >99% of both the distance and parsimony majority-rule consensus trees generated using the statistical method of bootstrapping. Therefore galeate ascospores appear to be an example of convergent evolution in fungi and by itself this trait should not be considered as an indicator of evolutionary relatedness.