Independent terrestrial origins of the Halosphaeriales (marine Ascomycota)

A phylogenetic study of marine ascomycetes was initiated to test and refine evolutionary hypotheses of marine-terrestrial transitions among ascomycetes. Taxon sampling focused on the Halosphaeriales, the largest order of marine ascomycetes. Approximately 1050 base pairs (bp) of the gene that codes for the nuclear small subunit (SSU) and 600 bp of the gene that codes for the nuclear large subunit (LSU) ribosomal RNAs (rDNA) were sequenced for 15 halosphaerialean taxa and integrated into a data set of homologous sequences from terrestrial ascomycetes. An initial set of phylogenetic analyses of the SSU rDNA from 38 taxa representing 15 major orders of the phylum Ascomycota confirmed a close phylogenetic relationship of the halosphaerialean species with several other orders of perithecial ascomycetes. A second set of analyses, which involved more intensive taxon sampling of perithecial ascomycetes, was performed using the SSU and LSU rDNA data in combined analyses. These second analyses included 15 halosphaerialean taxa, 26 terrestrial perithecial fungi from eight orders, and five outgroup taxa from the Pezizales. In these analyses the Halosphaeriales were polyphyletic and comprised two distinct lineages. One clade of Halosphaeriales comprised 12 taxa from 11 genera and was most closely related to terrestrial fungi of the Microascales. The second clade of halosphaerialean fungi comprised taxa from the genera Lulworthia and Lindra and was an isolated lineage among the perithecial fungi. Both the main clade of Halosphaeriales and the Lulworthia/Lindra clade are supported by the data as being independently derived from terrestrial ancestors.     

新科Rhizoplacopsidaceae中的新属及新种Rhizoplacopsis weichingii

本文描述了位于新科盾叶科 Rhizoplacopsidaceae(Umbilicariales,Lecanoromycetes,Ascomycota)中的新属盾叶属 Rhizoplacopsis 和新种蔚青盾叶 Rhizoplacopsis weichingii。蔚青盾叶取名于著名中国真菌学家王云章教授之字“蔚青”,作为庆祝教授百岁生日之纪念。该新种在外形上与 Rhizoplaca 属地衣极为相似,但位于地衣体上的子囊盘却为网衣型。此外,它的子囊顶器结构非常接近于 Umbilicaria-type。基于分子数据,对 Rhizoplacopsis weichingii 及其它相关地衣进行的系统发育分析支持成立新属盾叶属 Rhizoplacopsis 和新科盾叶科 Rhizoplacopsidaceae。     

Phylogenetic relationships within the superfamily Desmodoroidea (Nematoda: Desmodorida), with descriptions of two new and one known species

Three nematode species of the superfamily Desmodoroidea Filipjev, 1922, were isolated from beach sediments in Wellington, New Zealand, for morphological and molecular analyses. Two of these species, D esmodorella verscheldei sp. nov. and D racograllus ngakei sp. nov. , were new to science and are described herein. Epsilonema rugatum Lorenzen, 1973, comb. nov. , which was originally described from New Zealand material as a subspecies of Epsilonema dentatum from Chile, is redescribed and elevated to the rank of species based on cuticular ornamentation. The phylogenetic relationships amongst the three Desmodoroidea families are investigated based on new and existing sequences of the D2 and D3 expansions segments of large subunit (LSU) 28S rRNA gene and small subunit (SSU) of 18S rDNA gene. Our analyses suggest that the Draconematidae is a sister taxon to the Desmodorinae and Spiriniinae, with the Draconematidae forming a monophyletic crown group and the Desmodorinae and Spiriniinae forming a paraphyletic stem group. Phylogenetic relationships between the Epsilonematidae and Stilbonematinae, however, could not be determined with certainty. The SSU and D2‐D3 of LSU consensus trees indicate that the morphological resemblance between the Draconematidae and Epsilonematidae, which are both characterized by swollen pharyngeal body regions and mid‐posterior body regions with specialized setae, reflects distinct and independently evolved adaptations to their unusual mode of locomotion, with differences in the structure and distribution of specialized setae between the two families also consistent with convergent evolution. We show that the family Desmodoridae and superfamily Desmodoroidea as currently defined are not monophyletic. It was not possible to determine whether the Prodesmodorinae are more closely related to the Desmodoroidea or Microlaimoidea, although it is clear that they do not belong to the Desmodoridae. The single Molgolaiminae sequence available formed a distinct clade together with the superfamily Microlaimoidea, and should therefore be placed with the latter. Clarifying the phylogenetic relationships within the Desmodoroidea will require greater focus on the Pseudonchinae, Molgolaiminae, and Epsilonematidae, for which no or very few sequences are available at present. © 2016 The Linnean Society of London     

Culture and Phylogenetic Characterization of Trichomitus trypanoides Duboscq & Grassè 1924, n. comb.: a Trichomonad Flagellate Isolated from the Hindgut of the Termite Reticulitermes santonensis Feytaud

ABSTRACT. A trichomonad flagellate strain R1 was isolated from the hindgut contents of the termite Reticulitermes santonensis Feytaud. The flagellate was cultivated at 28° C in anaerobic medium containing yeast extract, minerals and vitamins. The isolate fed on living bacteria. It showed the typical morphological and ultrastructural features of the trichomonads. closely resembling Trichomitus trypanoides. In order to determine its phylogenetic position the small subunit ribosomal DNA (SSU rDNA) of the flagellate was amplified in vitro using the polymerase chain reaction (PCR), cloned in a plasmid vector and sequenced. Comparison of the obtained sequence with so far available SSU rRNA/rDNA sequences showed strongest similarity (89%) to the sequence of Tritrichomonas foetus. The phylogenetic analysis with parsimony and distance matrix methods placed Trichomitus trypanoides strain R1 near by the root of the phylogenetically so far analyzed eukaryotic organisms. This confirms that termites harbour hindgut symbionts, which originate from very early evolved eukaryotes.     

Complete rRNA gene sequences reveal that the microsporidium Nosema bombi infects diverse bumblebee (Bombus spp.) hosts and contains multiple polymorphic sites

Characterisation of microsporidian species and differentiation among genetic variants of the same species has typically relied on ribosomal RNA (rRNA) gene sequences. We characterised the entire rRNA gene of a microsporidium from 11 isolates representing eight different European bumblebee (Bombus) species. We demonstrate that the microsporidium Nosema bombi infected all hosts that originated from a wide geographic area. A total of 16 variable sites (all single nucleotid polymorphisms (SNPs)) was detected in the small subunit (SSU) rRNA gene and 42 (39 SNPs and 3 indels) in the large subunit (LSU) rRNA sequence. Direct sequencing of PCR-amplified DNA products of the internal transcribed spacer (ITS) region revealed identical sequences in all isolates. In contrast, ITS fragment length determined by PAGE and sequencing of cloned amplicons gave better resolution of sequences and revealed multiple SNPs across isolates and two fragment sizes in each isolate (six short and seven long amplicon variants). Genetic variants were not unique to individual host species. Moreover, two or more sequence variants were obtained from individual bumblebee hosts, suggesting the existence of multiple, variable copies of rRNA in the same microsporidium, and contrary to that expected for a class of multi-gene family under concerted evolution theory. Our data on within-genome rRNA variability call into question the usefulness of rRNA sequences to characterise intraspecific genetic variants in the Microsporidia and other groups of unicellular organisms.     

A Molecular Perspective on Ecological Differentiation and Biogeography of Cyclotrichiid Ciliates

ABSTRACT. Cyclotrichiids are of ecological and evolutionary interest by virtue of their importance in red tide formation, their highly divergent small subunit (SSU) ribosomal RNA (rRNA) genes, kleptoplastidy, and utility as indicators of eutrophication. However, only seven strains have had their SSU rRNA genes sequenced and their environmental diversity and distribution are largely unknown. We probed 67 globally dispersed freshwater column/sediment and soil DNA samples (eDNAs) and constructed 24 environmental gene libraries using polymerase chain reaction primers specific to an uncharacterised cyclotrichiid subgroup. We reveal a novel, globally ubiquitous freshwater clade comprising 25 genetically distinct SSU ribosomal DNA (rDNA) sequences (SSU-types). Some identical SSU-types were detected at globally widely distributed sites. The SSU-types form four distinct phylogenetic clusters according to marine or non-marine provenance, suggesting at least one major marine–freshwater evolutionary transition within the cyclotrichiids. We used the same primers to sample intensively 18 sampling points in 13 closely situated lakes, each characterised by 14 environmental variables, and showed that molecular detection or non-detection of cyclotrichiids was most significantly influenced by levels of total phosphorus, dissolved organic carbon, and chlorophyll a . Within the subset of lakes in which cyclotrichiids were detected, closely related SSU-types differed in their ecological preferences to pH, total phosphorus, and sample depth.     

Evolutionary relationships among heterokont algae (the autotrophic stramenopiles) based on combined analyses of small and large subunit ribosomal RNA

In order to study the phylogenetic relationships within the stramenopiles, and particularly among the heterokont algae, we have determined complete or nearly complete large-subunit ribosomal RNA sequences for different species of raphidophytes, phaeophytes, xanthophytes, chrysophytes, synurophytes and pinguiophytes. With the small- and large-subunit ribosomal RNA sequences of representatives for nearly all known groups of heterokont algae, phylogenetic trees were constructed from a concatenated alignment of both ribosomal RNAs, including more than 5,000 positions. By using different tree construction methods, inferred phylogenies showed phaeophytes and xanthophytes as sister taxa, as well as the pelagophytes and dictyochophytes, and the chrysophytes/synurophytes and eustigmatophytes. All these relationships are highly supported by bootstrap analysis. However, apart from these sister group relationships, very few other internodes are well resolved and most groups of heterokont algae seem to have diverged within a relatively short time frame.     

Phylogeny of the Poorly Known Ciliates,Microthoracida, a Systematically Confused Taxon (Ciliophora), with Morphological Reports of Three Species

Three species of Microthoracids, Lopezoterenia paratorpens n. sp., Trochiliopsis australis Foissner et al., 1988 and Discotricha papillifera Tuffrau, 1954, collected from Chinese coastal waters, were investigated using live observation and protargol staining methods. Lopezoterenia paratorpens n. sp. was characterized by its squarely shaped cortical papillae and by dorsal kineties which contained loosely distributed basal bodies. Trochiliopsis australis was revealed to have two oral membranelles, which was not recorded in the original report. Phylogenetic analyses were carried out based on SSU rRNA gene sequence data from each of the three species, and on other available data for microthoracids. The results showed that the order Microthoracida is not monophyletic because the family Discotrichidae, which contains L. paratorpens and D. papillifera, forms a clade separated from the “core” Microthoracids clade. The topologies of the maximum likelihood and Bayesian inference trees, along with the distinct morphological characteristics found previously, suggest that the family Discotrichidae should not be assigned to the order Microthoracida. We propose to designate a new order, Discotrichida n. ord. which diagnosed as: flattened ciliates with conspicuous cortical papillae on both dorsal and ventral faces, rod‐shaped mucocysts, and an asymmetric cytopharyngeal basket. Also, the fact that Leptopharynx clusters with the assemblage including T. australis, and Pseudomicrothorax is located distantly from Leptopharynx indicates that the classification of Pseudomicrothoracidae and Microthoracidae by Foissner (1985) is justified.     

Medicago species affect the community composition of arbuscular mycorrhizal fungi associated with roots

Sequencing of the 5' end of the large ribosomal subunit (LSU rDNA) and quantitative polymerase chain reaction (qPCR) were combined to assess the impact of four annual Medicago species (Medicago laciniata, Medicago murex, Medicago polymorpha and Medicago truncatula) on the genetic diversity of arbuscular mycorrhizal (AM) fungi, and on the relative abundance of representative AM fungal genotypes, in a silty-thin clay soil (Mas d'Imbert, France). Two hundred and forty-six Glomeromycete LSU rDNA sequences from the four plant species and the bulk soil were analysed. The high bootstrap values of the phylogenetic tree obtained allowed the delineation of 12 operational taxonomic units (OTUs), all belonging to Glomus. Specific primers targeting Glomeromycetes and major OTUs were applied to quantify their abundance by qPCR. Glomeromycetes and targeted OTUs were significantly more abundant in the root tissues than in the bulk soil, and the frequencies of three of them differed significantly in the root tissues of the different plant species. These differences indicate that, despite the absence of strict host specificity in mycorrhizal symbiosis, there was a preferential association between some AM fungal and plant genotypes.     

Length and Sequence Heterogeneity in the Mitochondrial Internal Transcribed Spacer of Acanthamoeba spp.

ABSTRACT. The internal transcribed spacer (ITS) between the mitochondrial large (23S rRNA; rnl ) and small (16S rRNA; rns ) subunit ribosomal RNA genes of Acanthamoeba castellanii strain Neff was sequenced previously and was uniquely interesting because it contained tRNA genes with acceptor stem mismatches that underwent RNA editing repair. Our interest in this ITS region was to determine its phylogenetic potential in differentiating between closely related isolates. We analyzed the mitochondrial ITS region for 17 Acanthamoeba isolates and observed extensive sequence and length variability, making this region difficult to align. Acanthamoeba griffini strain S-7 had the shortest ITS (i.e. 559 base pairs [bp]) compared with Acanthamoeba palestinensis strain Reich, which had the longest (i.e. 1,360 bp). The length disparity occurred predominantly between the spacer region of the aspartic acid ( trnD ) and methionine ( trnM ) tRNA genes. Unexpectedly, this region in A. palestinensis Reich was found to contain a duplication of the trnM gene. Additionally, like A. castellanii strain Neff, all isolates examined had tRNAs with mismatches in their acceptor stem. Also, the potential for an additional type of editing not described previously for Acanthamoeba , involving purine to pyrimidine transversions was observed.     

Structural Insights into the Role of Diphthamide on Elongation Factor 2 in mRNA Reading-Frame Maintenance

One of the most critical steps of protein biosynthesis is the coupled movement of mRNA, which encodes genetic information, with tRNAs on the ribosome. In eukaryotes, this process is catalyzed by a conserved G-protein, the elongation factor 2 (eEF2), which carries a unique post-translational modification, called diphthamide, found in all eukaryotic species. Here we present near-atomic resolution cryo-electron microscopy structures of yeast 80S ribosome complexes containing mRNA, tRNA and eEF2 trapped in different GTP-hydrolysis states which provide further structural insights into the role of diphthamide in the mechanism of translation fidelity in eukaryotes.     

Description of Hemicaloosia graminis n. sp. (Nematoda: Caloosiidae) Associated with Turfgrasses in North and South Carolina,USA

A new nematode species was discovered during a diversity survey of plant-parasitic nematodes on turfgrass conducted in North and South Carolina in 2010 and 2011. It is described herein as Hemicaloosia graminis n. sp. and is characterized by two annuli in the lip region, one lateral line, body 610.0–805.0 μm long, stylet 65.0–74.6 μm long, vulva at 84.1% –85.8% of the body , 254–283 annuli, vulva at the 38–53^rd annulus from tail terminus, 12–14 annuli between vulva and anus, tail elongate-pointed, 67.5–84.8 μm long in females and spicule straight, 31.0 μm long, caudal alae well developed, two lateral lines in males. The newly described species is morphologically closest to H. paradoxa, but has a longer stylet (65.0–74.6 vs 61.0–65.0 μm) and a higher V-value (84.1–85.8 vs 78.1–84.0%), less RV (38–53 vs 50–56), higher RVan (12–14 vs 10) in females, and a shorter tail (30.1 vs 36.7 μm) and more anteriorly located excretory pore (105.9 vs 140.0 μm) in the male. It was easily differentiated from other species based on near-full-length small subunit rRNA gene (SSU) and ITS1 sequences. Phylogenetic analysis from SSU supports placement in a monophyletic clade with the genus Caloosia. An identification key and a table of distinguishing characteristics are presented for all seven species of Hemicaloosia.     

The presence and synthesis of the NADPH-protochlorophyllide oxidoreductase in barley leaves with a high temperature-induced deficiency of plastid ribosomes

High-temperature-induced deficiency of plastid ribosomes in barley plants (Hordeum vulgare L.) was used as a system for studying the role of the cytoplasm in the synthesis of the NADPH-protochlorophyllide oxidoreductase. The enzyme is present in 33° C-grown plants. The failure of high-temperature-grown plants to accumulate chlorophyll during illumination is not caused by the absence of the protochlorophyllide-reducing enzyme. The synthesis of the NADPH-protochlorophyllide oxidoreductase was studied by feeding [³⁵S]methionine to the seedling and by following the incorporation of the radioactively labeled amino acid into plastid proteins. The NADPH-protochlorophyllide oxidoreductase was labeled in high-temperature-grown barley plants to the same extent as in control plants grown at 25° C. It is concluded that the 36,000-M_r polypeptide of the NADPH-protochlorophyllide oxidoreductase is synthesized outside the plastid on cytoplasmic 80S ribosomes.     

Morphology and molecular phylogeny of Thalassiosira sinica sp. nov. (Bacillariophyta) with delicate areolae and fultoportulae pattern

Thalassiosira Cleve is one of the most species-rich marine diatom genera. Previous studies have mainly focused on polar and temperate areas, but recent studies on material from Asian waters suggested that a high and undescribed species diversity of Thalassiosira occurs in Asia. On the basis of plankton samples collected from the South China Sea, a new species, T. sinica sp. nov. Y. Li & Y. Q. Guo is described. The morphology of the cells was examined by light and scanning electron microscopy. The hypervariable region of the nuclear large-subunit ribosomal DNA and the relatively conserved region of the nuclear small-subunit ribosomal DNA were sequenced for information on phylogenetic relationships. The living cells are usually solitary and drum-shaped. The areolae on the valve are delicate, small and arranged in fascicles. In addition to a regular ring of marginal fultoportulae on the valve edge, T. sinica possesses one central fultoportula and a number of fultoportulae arranged into 2–3 irregular rings on the valve face. A rimoportula located inside the ring of marginal fultoportulae possesses a long and strong external tube. The valvocopula and the copulae have rows of pores, but the pores on the valvocopula are larger than those on the copulae. Thalassiosira sinica appears to be included in subgroup C sensu Gedde because of a rimoportula with a distinct external tube located on the valve face. The molecular phylogeny, inferred from both SSU and LSU sequences, does, however, not support the validity of subgroup C, as the closest allies of T. sinica here turned out to be T. diporocyclus and T. lundiana, species in which the rimoportulae are located on the valve margin.