scholarly journals Disentangling the Taxonomy of Rickettsiales and Description of Two Novel Symbionts (“Candidatus Bealeia paramacronuclearis” and “Candidatus Fokinia cryptica”) Sharing the Cytoplasm of the Ciliate Protist Paramecium biaurelia

2016 ◽  
Vol 82 (24) ◽  
pp. 7236-7247 ◽  
Author(s):  
Franziska Szokoli ◽  
Michele Castelli ◽  
Elena Sabaneyeva ◽  
Martina Schrallhammer ◽  
Sascha Krenek ◽  
...  
Keyword(s):  
Phylogenetic Analyses ◽  
Small Subunit ◽  
Sensu Stricto ◽  
The Other ◽  
Rrna Genes ◽  
Small Subunit Rrna ◽  
Taxonomic Assignment ◽  
Content Type ◽  
The Family ◽  
Critical Revision

ABSTRACTIn the past 10 years, the number of endosymbionts described within the bacterial orderRickettsialeshas constantly grown. Since 2006, 18 novelRickettsialesgenera inhabiting protists, such as ciliates and amoebae, have been described. In this work, we characterize two novel bacterial endosymbionts fromParameciumcollected near Bloomington, IN. Both endosymbiotic species inhabit the cytoplasm of the same host. The Gram-negative bacterium “CandidatusBealeia paramacronuclearis” occurs in clumps and is frequently associated with the host macronucleus. With its electron-dense cytoplasm and a distinct halo surrounding the cell, it is easily distinguishable from the second smaller symbiont, “CandidatusFokinia cryptica,” whose cytoplasm is electron lucid, lacks a halo, and is always surrounded by a symbiontophorous vacuole. For molecular characterization, the small-subunit rRNA genes were sequenced and used for taxonomic assignment as well as the design of species-specific oligonucleotide probes. Phylogenetic analyses revealed that “CandidatusBealeia paramacronuclearis” clusters with the so-called “basal”Rickettsiales, and “CandidatusFokinia cryptica” belongs to “CandidatusMidichloriaceae.” We obtained tree topologies showing a separation ofRickettsialesinto at least two groups: one represented by the familiesRickettsiaceae,Anaplasmataceae, and “CandidatusMidichloriaceae” (RAM clade), and the other represented by “basalRickettsiales,” including “CandidatusBealeia paramacronuclearis.” Therefore, and in accordance with recent publications, we propose to limit the orderRickettsialesto the RAM clade and to raise “basalRickettsiales” to an independent order,Holosporalesord. nov., insideAlphaproteobacteria, which presently includes four family-level clades. Additionally, we define the family “CandidatusHepatincolaceae” and redefine the familyHolosporaceae.IMPORTANCEIn this paper, we provide the characterization of two novel bacterial symbionts inhabiting the sameParameciumhost (Ciliophora, Alveolata). Both symbionts belong to “traditional”Rickettsiales, one representing a new species of the genus “CandidatusFokinia” (“CandidatusMidichloriaceae”), and the other representing a new genus of a “basal”Rickettsiales. According to newly characterized sequences and to a critical revision of recent literature, we propose a taxonomic reorganization of “traditional”Rickettsialesthat we split into two orders:Rickettsiales sensu strictoandHolosporalesord. nov. This work represents a critical revision, including new records of a group of symbionts frequently occurring in protists and whose biodiversity is still largely underestimated.

scholarly journals Specificity of Associations between Bacteria and the Coral Pocillopora meandrina during Early Development

2012 ◽  
Vol 78 (20) ◽  
pp. 7467-7475 ◽  
Author(s):  
Amy Apprill ◽  
Heather Q. Marlow ◽  
Mark Q. Martindale ◽  
Michael S. Rappé
Keyword(s):  
Small Subunit ◽  
Rrna Genes ◽  
Polymorphism Analysis ◽  
Roseobacter Clade ◽  
Small Subunit Rrna ◽  
Content Type ◽  
Sterile Seawater ◽  
Show Evidence ◽  
Coral Health

ABSTRACTRelationships between corals and specific bacterial associates are thought to play an important role in coral health. In this study, the specificity of bacteria associating with the coralPocillopora meandrinawas investigated by exposing coral embryos to various strains of cultured marine bacteria, sterile seawater, or raw seawater and examining the identity, density, and location of incorporated cells. The isolates utilized in this experiment included members of the Roseobacter and SAR11 clades of theAlphaproteobacteria, aPseudoalteromonasspecies of theGammaproteobacteria, and aSynechococcusspecies of theCyanobacteriaphylum. Based on terminal restriction fragment length polymorphism analysis of small-subunit rRNA genes, similarities in bacterial communities associated with 170-h-old planulae were observed regardless of treatment, suggesting that bacteria may have been externally associated from the outset of the experiment. Microscopic examination ofP. meandrinaplanulae by fluorescencein situhybridization with bacterial and Roseobacter clade-specific oligonucleotide probes revealed differences in the densities and locations of planulae-associated cells. Planulae exposed to either raw seawater or strains ofPseudoalteromonasand Roseobacter harbored the highest densities of internally associated cells, of which 20 to 100% belonged to the Roseobacter clade. Planulae exposed to sterile seawater or strains of the SAR11 clade andSynechococcusdid not show evidence of prominent bacterial associations. Additional analysis of the raw-seawater-exposed planulae via electron microscopy confirmed the presence of internally associated prokaryotic cells, as well as virus-like particles. These results suggest that the availability of specific microorganisms may be an important factor in the establishment of coral-bacterial relationships.

scholarly journals Description of Eurystomatella sinica n. gen., n. sp., with establishment of a new family Eurystomatellidae n. fam. (Protista, Ciliophora, Scuticociliatia) and analyses of its phylogeny inferred from sequences of the small-subunit rRNA gene

2010 ◽  
Vol 60 (2) ◽  
pp. 460-468 ◽  
Author(s):  
Miao Miao ◽  
Yangang Wang ◽  
Weibo Song ◽  
John C. Clamp ◽  
Khaled A. S. Al-Rasheid
Keyword(s):  
New Genus ◽  
Phylogenetic Analyses ◽  
Sister Group ◽  
Small Subunit ◽  
Rrna Gene ◽  
Small Subunit Rrna ◽  
New Family ◽  
Small Subunit Rrna Gene ◽  
The Family ◽  
Great Divergence

Recently, an undescribed marine ciliate was isolated from China. Investigation of its morphology and infraciliature revealed it as an undescribed species representing a new genus, Eurystomatella n. gen., the type of the new family Eurystomatellidae n. fam. The new family is defined by close-set, apically positioned oral membranelles and a dominant buccal field that is surrounded by an almost completely circular paroral membrane. The new genus is defined by having a small oral membranelle 1 (M1), bipartite M2 and well-developed M3, a body surface faintly sculptured with a silverline system in a quadrangular, reticulate pattern and a cytostome located at the anterior third of a large buccal field. The type species of the new genus, Eurystomatella sinica n. sp., is a morphologically unique form that is defined mainly by the combination of a conspicuously flattened body, several caudal cilia, extremely long cilia associated with the buccal apparatus and a contractile vacuole located subcaudally. According to phylogenetic analyses of small-subunit (SSU) rRNA gene sequences, Eurystomatella clusters with the genus Cyclidium, as a sister group to the family Pleuronematidae. The great divergence in both buccal and somatic ciliature between Eurystomatella and all other known scuticociliates supports the establishment of a new family for Eurystomatella.

Vairimorpha imperfecta n.sp., a microsporidian exhibiting an abortive octosporous sporogony in Plutella xylostella L. (Lepidoptera: Yponomeutidae)

Parasitology ◽  
1999 ◽  
Vol 119 (3) ◽  
pp. 273-286 ◽  
Author(s):  
E. U. CANNING ◽  
A. CURRY ◽  
S. CHENEY ◽  
N. J. LAFRANCHI-TRISTEM ◽  
M. A. HAQUE
Keyword(s):  
Plutella Xylostella ◽  
Phylogenetic Analyses ◽  
Diamondback Moth ◽  
Small Subunit ◽  
Rrna Genes ◽  
Direct Control ◽  
Small Subunit Rrna ◽  
Polar Tube ◽  
Cell Cytoplasm ◽  
Host Cell Cytoplasm

The microsporidian genus Nosema is characterized by development in direct control with host cell cytoplasm, diplokaryotic nuclei throughout development and disporous sporogony. The genus Vairimorpha exhibits the same features plus an octoporous sporogony producing uninucleate spores in a sporophorous vesicle. A microsporidium from diamondback moth, Plutella xylostella, falls between Nosema and Vairimorpha in that it initiates but fails to complete the octosporous sequence in this host. The name Vairimorpha imperfecta n.sp. is proposed. Merogony is mainly by formation of buds from multinucleate meronts, the buds remaining attached in chains. Diplokaryotic spores measure 4·3×2·0 μm (fresh) and have 15·5 coils of the polar tube in 1 rank. The octosporous sporogony is aborted owing to irregular formation of nuclear spindles, incomplete cytoplasmic fission and bizarre deposition of electron-dense episporontal secretions. Phylogenetic analyses of the sequences of the small subunit rRNA genes of V. imperfecta and of several Nosema and Vairimorpha spp. place V. imperfecta in a clade with Nosema spp. from Lepidoptera rather than in the clade containing the more typical species of Vairimorpha. It is suggested that the ancestors of the Vairimorpha/Nosema complex of species exhibited both disporous and octosporous sporogonies, as does the type species of Vairimorpha, Vairimorpha necatrix. It would follow that true Nosema spp. have lost the ability to express an octosporous sequence and that V. imperfecta is in the process of losing it. It is proposed that the genera Nosema and Vairimorpha be placed in the same family Nosematidae Labbé 1899, rather than in separate families and orders as at present.

Redescriptions of three trachelocercid ciliates (Protista, Ciliophora, Karyorelictea), with notes on their phylogeny based on small subunit rRNA gene sequences

2013 ◽  
Vol 63 (Pt_9) ◽  
pp. 3506-3514 ◽  
Author(s):  
Ying Yan ◽  
Yuan Xu ◽  
Zhenzhen Yi ◽  
Alan Warren
Keyword(s):  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Small Subunit ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Ssu Rrna ◽  
Small Subunit Rrna ◽  
Small Subunit Rrna Gene ◽  
Ssu Rrna Gene Sequence ◽  
First Time

Three trachelocercid ciliates, Kovalevaia sulcata (Kovaleva, 1966) Foissner, 1997, Trachelocerca sagitta (Müller, 1786) Ehrenberg, 1840 and Trachelocerca ditis (Wright, 1982) Foissner, 1996, isolated from two coastal habitats at Qingdao, China, were investigated using live observation and silver impregnation methods. Data on their infraciliature and morphology are supplied. The small subunit rRNA (SSU rRNA) genes of K. sulcata and Trachelocerca sagitta were sequenced for the first time. Phylogenetic analyses based on SSU rRNA gene sequence data indicate that both organisms, and the previously sequenced Trachelocerca ditis, are located within the trachelocercid assemblage and that K. sulcata is sister to an unidentified taxon forming a clade that is basal to the core trachelocercids.

Small-subunit rRNA gene sequences from representatives of selected families of the Gigartinales and Rhodymeniales (Rhodophyta). 1. Evidence for the Plocamiales ord.nov.

1994 ◽  
Vol 72 (9) ◽  
pp. 1250-1263 ◽  
Author(s):  
G. W. Saunders ◽  
G. T. Kraft
Keyword(s):  
Phylogenetic Analyses ◽  
Small Subunit ◽  
Rrna Gene ◽  
Small Subunit Rrna ◽  
Chain Reaction ◽  
Small Subunit Rrna Gene ◽  
New Information ◽  
The Family ◽  
Close Relationship ◽  
Polymerase Chain

Nucleotide sequences of the nuclear, small-subunit (SSU) ribosomal RNAs, as inferred from polymerase chain reaction (PCR)-amplified products, are presented for Areschougia congesta (Turner) J. Agardh (Solieriaceae), Dasyphloea insignis Montagne (Dumontiaceae), Sarcothalia crassifolia (C. Agardh) Edyvane & Womersley (Gigartinaceae), Nizymenia australis Sonder (Nizymeniaceae), Phacelocarpus peperocarpos (Poiret) Wynne, Ardré & Silva (Phacelocarpaceae), Plocamiocolax pulvinata Setchell, Plocamium angustum (J. Agardh) J.D. Hooker, Plocamium cartilagineum (Linnaeus) Dixon (Plocamiaceae), Rhodymenia linearis J. Agardh (Rhodymeniaceae), and Sphaerococcus coronopifolius Stackhouse (Sphaerococcaceae). Phylogenetic analyses of the SSU sequences between the Plocamiaceae and members of the Sphaerococcaceae, Phacelocarpaceae, and Nizymeniaceae, with which the Plocamiaceae has been associated historically, show SSU differences of between 87 and 105 nucleotides and do not indicate a close relationship. A review of anatomical knowledge of the Plocamiaceae and Pseudoanemoniaceae and new information on vegetative and tetrasporangial development in Plocamium and Plocamiocolax are presented to buttress a case for the Plocamiales ord.nov. Representatives of the Nizymeniaceae and Phacelocarpaceae differ from one another by only nine nucleotides, suggesting that these two taxa are very closely related and perhaps not distinct at the family rank. Key words: Gigartinales, PCR, phylogeny, Plocamiales ord.nov., Pseudoanemoniaceae, Rhodophyta, small-subunit rRNA, systematics.

scholarly journals Regulation of Plasmodium yoelii Oocyst Development by Strain- and Stage-Specific Small-Subunit rRNA

mBio ◽  
2015 ◽  
Vol 6 (2) ◽  
Author(s):  
Yanwei Qi ◽  
Feng Zhu ◽  
Richard T. Eastman ◽  
Young Fu ◽  
Martine Zilversmit ◽  
...  
Keyword(s):  
Developmental Stages ◽  
Small Subunit ◽  
Plasmodium Yoelii ◽  
Rrna Genes ◽  
Parasite Development ◽  
Rrna Gene ◽  
Small Subunit Rrna ◽  
Malaria Parasites ◽  
Content Type ◽  
Small Subunit Rrna Gene

ABSTRACT One unique feature of malaria parasites is the differential transcription of structurally distinct rRNA (rRNA) genes at different developmental stages: the A-type genes are transcribed mainly in asexual stages, whereas the S-type genes are expressed mostly in sexual or mosquito stages. Conclusive functional evidence of different rRNAs in regulating stage-specific parasite development, however, is still absent. Here we performed genetic crosses of Plasmodium yoelii parasites with one parent having an oocyst development defect (ODD) phenotype and another producing normal oocysts to identify the gene(s) contributing to the ODD. The parent with ODD—characterized as having small oocysts and lacking infective sporozoites—was obtained after introduction of a plasmid with a green fluorescent protein gene into the parasite genome and subsequent passages in mice. Quantitative trait locus analysis of genome-wide microsatellite genotypes of 48 progeny from the crosses linked an ~200-kb segment on chromosome 6 containing one of the S-type genes (D-type small subunit rRNA gene [D-ssu]) to the ODD. Fine mapping of the plasmid integration site, gene expression pattern, and gene knockout experiments demonstrated that disruption of the D-ssu gene caused the ODD phenotype. Interestingly, introduction of the D-ssu gene into the same parasite strain (self), but not into a different subspecies, significantly affected or completely ablated oocyst development, suggesting a stage- and subspecies (strain)-specific regulation of oocyst development by D-ssu. This study demonstrates that P. yoelii D-ssu is essential for normal oocyst and sporozoite development and that variation in the D-ssu sequence can have dramatic effects on parasite development. IMPORTANCE Malaria parasites are the only known organisms that express structurally distinct rRNA genes at different developmental stages. The differential expression of these genes suggests that they play unique roles during the complex life cycle of the parasites. Conclusive functional proof of different rRNAs in regulating parasite development, however, is still absent or controversial. Here we functionally demonstrate for the first time that a stage-specifically expressed D-type small-subunit rRNA gene (D-ssu) is essential for oocyst development of the malaria parasite Plasmodium yoelii in the mosquito. This study also shows that variations in D-ssu sequence and/or the timing of transcription may have profound effects on parasite oocyst development. The results show that in addition to protein translation, rRNAs of malaria parasites also regulate parasite development and differentiation in a strain-specific manner, which can be explored for controlling parasite transmission.

Morphology and molecular phylogeny of four Frontonia species from Turkey (Protista, Ciliophora)

Zootaxa ◽  
2019 ◽  
Vol 4609 (3) ◽  
pp. 548
Author(s):  
SIBEL KIZILDAG ◽  
ISMAIL YILDIZ
Keyword(s):  
Phylogenetic Trees ◽  
Turkish Population ◽  
Small Subunit ◽  
The Other ◽  
Aquatic Environments ◽  
Rrna Gene ◽  
Small Subunit Rrna ◽  
Small Subunit Rrna Gene ◽  
The Family ◽  
Systematic Relationships

In this study, Frontonia leucas, Frontonia acuminata, Frontonia angusta, and Frontonia anatolica species isolated from aquatic environments of Van in Turkey were investigated in detail using morphological, morphometrical, and molecular methods. Although there were minor differences, the Frontonia populations were morphologically similar to the other previously reported populations of the 4 species. Frontonia leucas differed from the other populations by the following combination of characters: about 200 somatic and only 3 vestibular kineties, and a single micronucleus. The Turkish population of Frontonia acuminata had just 4 vestibular kineties and the large micronucleus was always located to the anterior of the carrot-shaped macronucleus. The ratio of the oral apparey size to the cell size of Frontonia angusta in this study was about 18%, with 3 vestibular kineties, and 1 excretory pore. Phylogenetic trees based on small-subunit rRNA gene sequences were constructed using Bayesian inference and maximum-likelihood. Frontonia anatolica was more closely related to Apofrontonia dohrni and Paramecium spp. than to its congeners, while F. acuminata, like F. terricola, was also more closely related to the family Stokesiidae. The results indicated that Frontonia is a non-monophyletic genus consisting of 3 groups. We presented the systematic relationships of the genera and families of Peniculida with new data of genus Frontonia herein. 

scholarly journals New insights into the phylogeny of Entamoeba species provided by analysis of four new small-subunit rRNA genes

2006 ◽  
Vol 56 (9) ◽  
pp. 2235-2239 ◽  
Author(s):  
C. Graham Clark ◽  
Farrokh Kaffashian ◽  
Blessing Tawari ◽  
Jeffrey J. Windsor ◽  
Anke Twigg-Flesner ◽  
...  
Keyword(s):  
Phylogenetic Analyses ◽  
Small Subunit ◽  
Rrna Genes ◽  
Recent Common Ancestor ◽  
Small Subunit Rrna ◽  
Entamoeba Dispar ◽  
Single Nucleus ◽  
Entamoeba Moshkovskii ◽  
Entamoeba Suis ◽  
Entamoeba Polecki

Sequences of small-subunit rRNA genes have been obtained for four new isolates of Entamoeba. Phylogenetic analyses give new insights into the evolution of these organisms. A novel Entamoeba from pigs in Vietnam that produces uninucleate cysts proved to be unrelated to other uninucleated cyst-producing species. Revival of the name Entamoeba suis for this organism is proposed. Instead of being related to Entamoeba polecki, it shares a recent common ancestor with the non-encysting Entamoeba gingivalis in a lineage that is basal to the tetranucleate cyst-producing clade. This suggests that species producing cysts with four nuclei are descended from an ancestor that produced cysts with a single nucleus. An Entamoeba from a horse was isolated in culture. No cysts were observed in the original stool sample but the sequence is placed unequivocally within the clade of tetranucleate cyst-producing species with no other sequences being specifically related. Revival of the name Entamoeba equi for this organism is proposed. The Entamoeba ecuadoriensis sequence was found to be the most closely related to Entamoeba histolytica and Entamoeba dispar, as predicted, despite the organism having been an environmental isolate originally assigned to Entamoeba moshkovskii. Finally, a partial E. polecki gene sequence from a pig proved to be virtually identical to that of Entamoeba struthionis from an ostrich, suggesting that the latter name is a synonym.

scholarly journals The phylogenetic position of enteromonads: a challenge for the present models of diplomonad evolution

2005 ◽  
Vol 55 (4) ◽  
pp. 1729-1733 ◽  
Author(s):  
Martin Kolisko ◽  
Ivan Cepicka ◽  
Vladimír Hampl ◽  
Jaroslav Kulda ◽  
Jaroslav Flegr
Keyword(s):  
Molecular Phylogenetics ◽  
Small Subunit ◽  
The Other ◽  
Rrna Genes ◽  
Phylogenetic Position ◽  
Single Event ◽  
Small Subunit Rrna

Unikaryotic enteromonads and diplokaryotic diplomonads have been regarded as closely related protozoan groups. It has been proposed that diplomonads originated within enteromonads in a single event of karyomastigont duplication. This paper presents the first study to address these questions using molecular phylogenetics. The sequences of the small-subunit rRNA genes for three isolates of enteromonads were determined and a tree constructed with available diplomonad, retortamonad and Carpediemonas sequences. The diplomonad sequences formed two main groups, with the genus Giardia on one side and the genera Spironucleus, Hexamita and Trepomonas on the other. The three enteromonad sequences formed a clade robustly situated within the diplomonads, a position inconsistent with the original evolutionary proposal. The topology of the tree indicates either that the diplokaryotic cell of diplomonads arose several times independently, or that the monokaryotic cell of enteromonads originated by secondary reduction from the diplokaryotic state.

scholarly journals Endophytic microbial diversity in coffee cherries ofCoffea arabicafrom southeastern Brazil

2013 ◽  
Vol 59 (4) ◽  
pp. 221-230 ◽  
Author(s):  
Marcelo N.V. Oliveira ◽  
Thiago M.A. Santos ◽  
Helson M.M. Vale ◽  
Júlio C. Delvaux ◽  
Alexander P. Cordero ◽  
...  
Keyword(s):  
Microbial Diversity ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Phylogenetic Analyses ◽  
Critical Role ◽  
Geographic Location ◽  
Small Subunit ◽  
Rrna Genes ◽  
Southeastern Brazil ◽  
Small Subunit Rrna ◽  
Microbial Composition

The microbiota associated with coffee plants may play a critical role in the final expression of coffee quality. However, the microbial diversity in coffee cherries is still poorly characterized. Here, we investigated the endophytic diversity in cherries of Coffea arabica by using culture-independent approaches to identify the associated microbes, ultimately to better understand their ecology and potential role in determining coffee quality. Group-specific 16S rRNA and 26S rRNA genes polymerase chain reaction – denaturing gradient gel electrophoresis and clone library sequencing showed that the endophytic community is composed of members of the 3 domains of life. Bacterial sequences showing high similarity with cultured and uncultured bacteria belonged to the Betaproteobacteria, Gammaproteobacteria, and Firmicutes phyla. Phylogenetic analyses of cloned sequences from Firmicutes revealed that most sequences fell into 3 major genera: Bacillus, Staphylococcus, and Paenibacillus. Archaeal sequences revealed the presence of operational taxonomic units belonging to Euryarchaeota and Crenarchaeota phyla. Sequences from endophytic yeast were not recovered, but various distinct sequences showing high identity with filamentous fungi were found. There was no obvious correlation between the microbial composition and cultivar or geographic location of the coffee plant. To the best of our knowledge, this is the first report demonstrating internal tissue colonization of plant fruits by members of the Archaea domain. The finding of archaeal small-subunit rRNA in coffee cherries, although not sufficient to indicate their role as active endophytes, certainly expands our perspectives toward considering members of this domain as potential endophytic microbes.

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