SSU rRNA
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The small subunit ribosomal RNA (SSU rRNA) gene is a widely used molecular marker to study the diversity of life. Sequencing of SSU rRNA gene amplicons has become a standard approach for the investigation of the ecology and diversity of microbes. However, a well-curated database is necessary for correct classification of these data. While available for many groups of Bacteria and Archaea, such reference databases are absent for most eukaryotes. The primary goal of the EukRef project (eukref.org) is to close this gap and generate well-curated reference databases for major groups of eukaryotes, especially protists. Here we present a set of EukRef-curated databases for the excavate protists-a large assemblage that includes numerous taxa with divergent SSU rRNA gene sequences, which are prone to misclassification. We identified 6121 sequences, 625 of which were obtained from cultures, 3053 from cell isolations or enrichments and 2419 from environmental samples. We have corrected the classification for the majority of these curated sequences. The resulting publicly available databases will provide phylogenetically based standards for the improved identification of excavates in ecological and microbiome studies, as well as resources to classify new discoveries in excavate diversity.
- MeSH
- Archaea * MeSH
- Bacteria genetika MeSH
- Eukaryota * genetika MeSH
- fylogeneze MeSH
- geny rRNA MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
Small subunit rRNA sequences were obtained from 38 representatives mainly of the nematode orders Spirurida (Camallanidae, Cystidicolidae, Daniconematidae, Philometridae, Physalopteridae, Rhabdochonidae, Skrjabillanidae) and, in part, Ascaridida (Anisakidae, Cucullanidae, Quimperiidae). The examined nematodes are predominantly parasites of fishes. Their analyses provided well-supported trees allowing the study of phylogenetic relationships among some spirurine nematodes. The present results support the placement of Cucullanidae at the base of the suborder Spirurina and, based on the position of the genus Philonema (subfamily Philoneminae) forming a sister group to Skrjabillanidae (thus Philoneminae should be elevated to Philonemidae), the paraphyly of the Philometridae. Comparison of a large number of sequences of representatives of the latter family supports the paraphyly of the genera Philometra, Philometroides and Dentiphilometra. The validity of the newly included genera Afrophilometra and Caranginema is not supported. These results indicate geographical isolation has not been the cause of speciation in this parasite group and no coevolution with fish hosts is apparent. On the contrary, the group of South-American species of Alinema, Nilonema and Rumai is placed in an independent branch, thus markedly separated from other family members. Molecular data indicate that the skrjabillanid subfamily Esocineminae (represented by Esocinema bohemicum) should be either elevated to the rank of an independent family or Daniconematidae (Mexiconema africanum) should be decreased to Daniconematinae and transferred to the family Skrjabillanidae. Camallanid genera Camallanus and Procamallanus, as well as the subgenera Procamallanus and Spirocamallanus are confirmed to be paraphyletic. Paraphyly has also been found within Filarioidea, Habronematoidea and Thelazioidea and in Cystidicolidae, Physalopteridae and Thelaziidae. The results of the analyses also show that Neoascarophis, Spinitectus and Rhabdochona are monophyletic, in contrast to the paraphyletic genus Ascarophis. They further confirm the independence of two subgenera, Rhabdochona and Globochona, in the genus Rhabdochona. The necessity of further studies of fish-parasitizing representatives of additional nematode families not yet studied by molecular methods, such as Guyanemidae, Lucionematidae or Tetanonematidae, is underscored.
- MeSH
- DNA helmintů genetika chemie MeSH
- financování organizované MeSH
- fylogeneze MeSH
- hlístice genetika klasifikace patogenita MeSH
- molekulární sekvence - údaje MeSH
- nematodózy parazitologie veterinární MeSH
- nemoci ryb parazitologie MeSH
- ribozomální DNA genetika chemie MeSH
- ryby MeSH
- sekvence nukleotidů MeSH
- sekvenční analýza DNA veterinární MeSH
- zvířata MeSH
- Check Tag
- zvířata MeSH
Marine alveolates (MALVs) are diverse and widespread early-branching dinoflagellates, but most knowledge of the group comes from a few cultured species that are generally not abundant in natural samples, or from diversity analyses of PCR-based environmental SSU rRNA gene sequences. To more broadly examine MALV genomes, we generated single cell genome sequences from seven individually isolated cells. Genes expected of heterotrophic eukaryotes were found, with interesting exceptions like presence of proteorhodopsin and vacuolar H+-pyrophosphatase. Phylogenetic analysis of concatenated SSU and LSU rRNA gene sequences provided strong support for the paraphyly of MALV lineages. Dinoflagellate viral nucleoproteins were found only in MALV groups that branched as sister to dinokaryotes. Our findings indicate that multiple independent origins of several characteristics early in dinoflagellate evolution, such as a parasitic life style, underlie the environmental diversity of MALVs, and suggest they have more varied trophic modes than previously thought.
Apicomplexan parasites represent one of the most important groups of parasitic unicellular eukaryotes comprising such important human parasites such as Plasmodium spp. and Toxoplasma gondii. Apicomplexan radiation as well as their adaptation to the parasitic style of life took place before the era of vertebrates. Thus, invertebrates were the first hosts of apicomplexan parasites that switched to vertebrates later in evolution. Despite this fact, apicomplexan parasites of invertebrates, with the exception of gregarines, have so far been ignored in phylogenetic studies. To address this issue, we sequenced the nuclear SSU rRNA genes from the homoxenous apicomplexan parasites of insects Adelina grylli and Adelina dimidiata, and the heteroxenous Aggregata octopiana and Aggregata eberthii that are transmitted between cephalopods and crustaceans, and used them for phylogenetic reconstructions. The position of the adelinids as a sister group to Hepatozoon spp. within the suborder Adeleorina was stable regardless of the phylogenetic method used. In contrast, both members of the genus Aggregata possess highly divergent SSU rRNA genes with an unusual nucleotide composition. Because of this, they form the longest branches in the tree and their position is variable. However, the genus Aggregata branches together with adelinids and hepatozoons in most of the analyses, although their position within the scope of this cluster is unstable.
The archamoebae form a small clade of anaerobic/microaerophilic flagellates or amoebae, comprising the pelobionts (mastigamoebids and pelomyxids) and the entamoebae. It is a member of the eukaryotic supergroup Amoebozoa. We examined 22 strains of 13 species of Mastigamoeba, Pelomyxa and Rhizomastix by light-microscopy and determined their SSU rRNA gene sequences. The SSU rRNA gene sequences of Pelomyxa palustris and Mastigella commutans in GenBank are shown to belong to P. stagnalis and Mastigamoeba punctachora, respectively. Five new species of free-living archamoebae are described: Mastigamoeba abducta, M. errans, M. guttula, M. lenta, and Rhizomastix libera spp. nov. A species of Mastigamoeba possibly living endosymbiotically in Pelomyxa was identified. Rhizomastix libera, the first known free-living member of that genus, is shown to be an archamoeba. R. libera possesses an ultrastructure unique within archamoebae: a rhizostyle formed from a modified microtubular cone and a flagellum with vanes. While many nominal species of pelobionts are extremely hard to distinguish by light microscopy, transient pseudopodial characters are worthy of further investigation as taxonomic markers.
- MeSH
- Archamoebae klasifikace genetika ultrastruktura MeSH
- druhová specificita MeSH
- Endolimax klasifikace genetika ultrastruktura MeSH
- Entamoeba klasifikace genetika ultrastruktura MeSH
- fylogeneze MeSH
- geny rRNA MeSH
- mikroskopie MeSH
- molekulární evoluce * MeSH
- protozoální DNA analýza MeSH
- sekvenční analýza DNA MeSH
- zvířata MeSH
- Check Tag
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
This study describes cryptosporidiosis in an overwintering group of 15 European hedgehogs (Erinaceus europaeus), comprising 3 adults and 12 juveniles. Four juvenile hedgehogs were hospitalised with anorexia, malodorous diarrhoea and dehydration. Immediate parasitological examinations revealed the presence of Cryptosporidium sp. in these animals and also in 5 other juveniles. All hedgehogs were coproscopically monitored for 4 months over the winter season. Shedding of Cryptosporidium oocysts persisted from 6 to 70 days. Repeated shedding of Cryptosporidium oocysts occurred in 3 animals after 4 months subsequent to the first outbreak. Clinical signs were observed only at the beginning of the outbreak (apathy, anorexia, general weakness, mild dehydration, and malodorous faeces with changed consistence - soft/diarrhoea) in the 4 hospitalised juveniles. Overall 11 hedgehogs were Cryptosporidium-positive, both microscopically and by PCR methods. Sequence analyses of SSU rRNA and gp60 genes revealed the presence of C. parvum IIdA18G1 subtype in all positive hedgehogs. Moreover, 3 hedgehogs had a mixed infection of the zoonotic C. parvum and C. erinacei XIIIaA19R13 subtype. Cryptosporidium infections can be rapidly spread among debilitated animals and the positive hedgehogs released back into the wild can be a source of the infection for individuals weakened after hibernation.
- MeSH
- Cryptosporidium parvum klasifikace genetika fyziologie MeSH
- Cryptosporidium klasifikace genetika fyziologie MeSH
- feces parazitologie MeSH
- fylogeneze MeSH
- geny rRNA genetika MeSH
- ježkovití parazitologie MeSH
- kryptosporidióza parazitologie patologie MeSH
- nemocnice veterinární MeSH
- zvířata MeSH
- Check Tag
- mužské pohlaví MeSH
- ženské pohlaví MeSH
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- kazuistiky MeSH
A strain of naked amoeba isolated from pikeperch (Sander lucioperca (L.)) kidney tissue has been characterized using light- and transmission electron microscopy. Sequencing of SSU rDNA and phylogenetic analysis based on a broad dataset of sequences completed our study. All data obtained suggest that this strain belongs to a species that has not been described before. As none of the existing genera of amoebae is applicable to this organism, the new genus Grellamoeba is established and the type species Grellamoeba robusta is described. Although the phylogenetic position of the SSU rDNA sequence of the type strain of G. robusta is sensitive to the method of analysis applied, a tendency to group with Acramoeba dendroida Smirnov, Nassonova et Cavalier-Smith, 2008 is evident.
- MeSH
- Amoebozoa klasifikace genetika izolace a purifikace ultrastruktura MeSH
- fylogeneze MeSH
- geny rRNA MeSH
- ledviny parazitologie MeSH
- mikroskopie MeSH
- molekulární sekvence - údaje MeSH
- okounovití parazitologie MeSH
- protozoální DNA chemie genetika MeSH
- ribozomální DNA chemie genetika MeSH
- RNA protozoální genetika MeSH
- RNA ribozomální 18S genetika MeSH
- sekvenční analýza DNA MeSH
- shluková analýza MeSH
- transmisní elektronová mikroskopie MeSH
- zvířata MeSH
- Check Tag
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
We isolated and cultivated 31 strains of free-living heterolobosean flagellates and amoebae from freshwater, brackish, and marine sediments with low concentrations of oxygen. Phylogenetic analysis of small subunit (SSU) rDNA showed that the strains constitute a single clade, the Psalteriomonadidae. According to combined light-microscopic morphology plus molecular phylogeny, our isolates belong to seven species and five genera, from which three species and two genera are new. In addition, previously described anaerobic species Percolomonas descissus and Vahlkampfia anaerobica are transferred to the Psalteriomonadidae. We identified a flagellate stage of Monopylocystis visvesvarai which was reported to produce only amoebae. Two environmental sequences previously obtained from acidic environments belong to the Psalteriomonadidae as well, suggesting a broad ecological importance of the Psalteriomonadidae. The ultrastructure of two psalteriomonadid species was also studied. Unifying features of the Psalteriomonadidae are acristate mitochondrial derivates, flagellates with a ventral groove and four flagella, and a harp-like structure in the mastigont. A new overall classification of the Psalteriomonadidae is proposed. Our data show that the Psalteriomonadidae are much more diverse than previously thought and constitute the main anaerobic lineage within the Heterolobosea.
- MeSH
- Eukaryota klasifikace cytologie genetika MeSH
- fylogeneze MeSH
- geny rRNA MeSH
- mikrobiologie vody * MeSH
- mikroskopie MeSH
- molekulární sekvence - údaje MeSH
- protozoální DNA chemie genetika MeSH
- ribozomální DNA chemie genetika MeSH
- RNA protozoální genetika MeSH
- RNA ribozomální 18S genetika MeSH
- sekvenční analýza DNA MeSH
- shluková analýza MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
Although experiments show a positive association between vascular plant and arbuscular mycorrhizal fungal (AMF) species richness, evidence from natural ecosystems is scarce. Furthermore, there is little knowledge about how AMF richness varies with belowground plant richness and biomass. We examined relationships among AMF richness, above- and belowground plant richness, and plant root and shoot biomass in a native North American grassland. Root-colonizing AMF richness and belowground plant richness were detected from the same bulk root samples by 454-sequencing of the AMF SSU rRNA and plant trnL genes. In total we detected 63 AMF taxa. Plant richness was 1.5 times greater belowground than aboveground. AMF richness was significantly positively correlated with plant species richness, and more strongly with below- than aboveground plant richness. Belowground plant richness was positively correlated with belowground plant biomass and total plant biomass, whereas aboveground plant richness was positively correlated only with belowground plant biomass. By contrast, AMF richness was negatively correlated with belowground and total plant biomass. Our results indicate that AMF richness and plant belowground richness are more strongly related with each other and with plant community biomass than with the plant aboveground richness measures that have been almost exclusively considered to date.
- MeSH
- biodiverzita * MeSH
- biomasa * MeSH
- DNA fungální genetika MeSH
- geny hub MeSH
- geny rRNA MeSH
- kořeny rostlin mikrobiologie MeSH
- mykorhiza klasifikace genetika MeSH
- pastviny * MeSH
- rostliny klasifikace MeSH
- sekvenční analýza DNA MeSH
- výpočetní biologie MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Geografické názvy
- Saskatchewan MeSH
