20,775 research outputs found
Congruence of chloroplast- and nuclear-encoded DNA sequence variations used to assess species boundaries in the soil microalga Heterococcus (Stramenopiles, Xanthophyceae).
BackgroundHeterococcus is a microalgal genus of Xanthophyceae (Stramenopiles) that is common and widespread in soils, especially from cold regions. Species are characterized by extensively branched filaments produced when grown on agarized culture medium. Despite the large number of species described exclusively using light microscopic morphology, the assessment of species diversity is hampered by extensive morphological plasticity.ResultsTwo independent types of molecular data, the chloroplast-encoded psbA/rbcL spacer complemented by rbcL gene and the internal transcribed spacer 2 of the nuclear rDNA cistron (ITS2), congruently recovered a robust phylogenetic structure. With ITS2 considerable sequence and secondary structure divergence existed among the eight species, but a combined sequence and secondary structure phylogenetic analysis confined to helix II of ITS2 corroborated relationships as inferred from the rbcL gene phylogeny. Intra-genomic divergence of ITS2 sequences was revealed in many strains. The 'monophyletic species concept', appropriate for microalgae without known sexual reproduction, revealed eight different species. Species boundaries established using the molecular-based monophyletic species concept were more conservative than the traditional morphological species concept. Within a species, almost identical chloroplast marker sequences (genotypes) were repeatedly recovered from strains of different origins. At least two species had widespread geographical distributions; however, within a given species, genotypes recovered from Antarctic strains were distinct from those in temperate habitats. Furthermore, the sequence diversity may correspond to adaptation to different types of habitats or climates.ConclusionsWe established a method and a reference data base for the unambiguous identification of species of the common soil microalgal genus Heterococcus which uses DNA sequence variation in markers from plastid and nuclear genomes. The molecular data were more reliable and more conservative than morphological data
Pyrosequencing analysis of fungal assemblages from geographically distant, disparate soils reveals spatial patterning and a core mycobiome
Identifying a soil core microbiome is crucial to appreciate the established microbial consortium, which is not usually subjected to change and, hence, possibly resistant/resilient to disturbances and a varying soil context. Fungi are a major part of soil biodiversity, yet the mechanisms driving their large-scale ecological ranges and distribution are poorly understood. The degree of fungal community overlap among 16 soil samples from distinct ecosystems and distant geographic localities (truffle grounds, a Mediterranean agro-silvo-pastoral system, serpentine substrates and a contaminated industrial area) was assessed by examining the distribution of fungal ITS1 and ITS2 sequences in a dataset of 454 libraries. ITS1 and ITS2 sequences were assigned to 1,660 and 1,393 Operational Taxonomic Units (OTUs; as defined by 97% sequence similarity), respectively. Fungal beta-diversity was found to be spatially autocorrelated. At the level of individual OTUs, eight ITS1 and seven ITS2 OTUs were found in all soil sample groups. These ubiquitous taxa comprised generalist fungi with oligotrophic and chitinolytic abilities, suggesting that a stable core of fungi across the complex soil fungal assemblages is either endowed with the capacity of sustained development in the nutrient-poor soil conditions or with the ability to exploit organic resources (such as chitin) universally distributed in soils
Sequence analysis of the second internal Transcribed spacer (ITS2) region of rDNA for species identification of trichostrongylus nematodes isolated from domestic livestock in Iran
Background: Infectivity of herbivores with Trichostrongylus nematodes is widespread in many countries, having a major economic impact on breeding, survivability, and productivity of domestic livestock. This study was carried out on Trichostrongylus species isolated from domestic livestock in order to develop an easy-to-perform method for species identification. Methods: Trichostrongylus isolates were collected from sheep, goat, cattle, and buffaloes in Khuzestan Province, southwest Iran. Primary species identification was carried out based on morphological characterization of male worms. PCR amplification of ITS2-rDNA region was performed on genomic DNA and the products were sequenced. Phylogenetic analysis of the nucleotide sequence data was conducted employing Bayesian Inference approach. Consequently, a restriction fragment length polymorphism (RFLP) profile was designed to differentiate Trichostrongylus species. Results: A consensus sequence of 238 nucleotides was deposited in the GenBank for Iranian isolates of Trichostrongylus species including T. colubriformis, T. capricola, T. probolurus and T. vitrinus. The designated RFLP using restriction enzyme TasI could readily differentiate among species having different ITS2 sequence. The molecular analysis was in concordance with morphological findings. Conclusion: Phylogenetic analysis indicated a close relationship among the sequences obtained in this study and reference sequence of relevant species. ITS2-RFLP with TasI is recommended for molecular differentiation of common Trichostrongylus species
Molecular detection of parasites (Trematoda, Digenea: Bucephalidae and Monorchiidae) in the European flat oyster Ostrea edulis (Mollusca: Bivalvia)
Members of the globally distributed bivalve family Ostreidae (oysters) have a significant role in marine ecosystems and include species of high economic importance. In this work, we report the occurrence of digenean parasites of the families Bucephalidae (Prosorhynchoides sp.) and Monorchiidae (Postmonorchis sp.) in Mediterranean native populations of Ostrea edulis (but not in the introduced Magallana gigas). Molecular detection was based on DNA sequencing of the ribosomal intergenic spacer 2 (ITS2) marker. The importance of detecting the presence of overlooked digenean parasites in Mediterranean oysters is discussed. © 2018 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group
Molecular key to seven Brazilian species of Trichogramma (Hymenoptera: Trichogrammatidae) using sequences of the ITS2 region and restriction analysis
Is there any genetic variation among native mexican and argentinian populations of Dalbulus maidis (Hemiptera: Cicadellidae)?.
The corn leafhopper Dalbulus maidis (Delong & Wolcott) (Hemiptera: Cicadellidae) originated in Mexico, but is found from southeastern and southwestern USA to Argentina. Differences in reproductive and phenotypic traits between Mexican (native) and Argentinian (adventive) populations have been previously reported, but information on their genetic variation is currently unavailable. The objective was to investigate possible genetic variability among D. maidis populations collected in Mexico on maize and maize relatives (annual and perennial teosintes) and on maize in Argentina. A region of the mitochondrial gene coding for the cytochrome oxidase subunit I (mtCOI) and the ribosomal internal transcribed spacer (ITS2) were sequenced and analyzed. We developed the forward and reverse primers for the DNA amplification of COI in D. maidis (dalCOI). Twenty two and 17 sequences for dalCOI and ITS2, respectively, were generated and analyzed. No genetic variation among Mexican and Argentinian populations was found in the ribosomal region and low genetic variation was found in the mitochondrial region. These results could be explained by the short evolutionary time scale, since both maize and the corn leafhopper moved throughout the Americas only in the most recent millenia, or in part to the limited host range, and thus a limited change in the corn leafhopper associated bacteria.Fil: Palomera, Veronica. Universidad de Guadalajara; MéxicoFil: Bertin, Sabrina. Universidad de Torino ; ItaliaFil: Rodriguez, Aaron. Universidad de Guadalajara; MéxicoFil: Bosco, Domenico. Universidad de Torino; ItaliaFil: Virla, Eduardo Gabriel. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Tucumán. Planta Piloto de Procesos Industriales Microbiológicos; ArgentinaFil: Moya-Raygoza, Gustavo. Universidad de Guadalajara; Méxic
Diagnosis of centrocestus formosanus infection in zebrafish (Danio rerio) in Italy: A window to a new globalization-derived invasive microorganism
Centrocestus formosanus is a digenetic trematode with a complex life cycle, involving invertebrate and vertebrate hosts, humans included. In particular, it causes gill lesions and mortality in freshwater fish species, and gastrointestinal symptoms in infected humans. Here, we describe the occurrence of C. formosanus infection in zebrafish imported in Italy and propose a newly designed species-specific primer pair to ameliorate the diagnostic investigations for C. formosanus. Gill arches of 30 zebrafish were examined for the presence of encysted metacercariae under a stereomicroscope and processed through molecular analyses targeting the ribosomal internal transcribed sequence 2 (ITS2). Although C. formosanus distribution was originally restricted to Asia, it has been subsequently reported in new countries, revealing itself as an invasive species and raising important concerns for biodiversity, economy, scientific research, as well as animal and public health. Given the crucial role played by the ornamental fish industry in spreading this parasite, there is an urgent need for control measures to prevent the introduction and establishment of C. formosanus in non-endemic areas, including Europe. We also suggest developing new strategies in microbiology and epidemiology to better explore this new globalization-derived invasive species
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Native and invasive inoculation sources modify fungal community assembly and biomass production of a chaparral shrub
Feedbacks between plants and surrounding soil microbes can contribute to the establishment and persistence of invasive annual grasses as well as limit the success of restoration efforts. In this study, we aim to understand how three sources of soil inocula – native, invasive (from under Bromus diandrus) and sterile – affect the growth response and fungal community composition in the roots of a chaparral shrub, Adenostoma fasciculatum. We grew A. fasciculatum from seed in a greenhouse with each inoculum source and harvested at six months. We measured above- and below-ground biomass, arbuscular mycorrhizal fungal (AMF) colonization and conducted targeted-amplicon sequencing of the 18S and ITS2 loci to characterize AMF and general fungal community composition, respectively. Native inoculum resulted in roots with richer communities of some groups of AMF and non-AMF symbionts, when compared to roots grown with invasive or sterile inoculum. Seedlings grown with invasive and native inoculum did not have different growth responses, but both produced more biomass than a sterile control. These findings suggest that inoculation with soil from native species can increase the diversity of multiple groups of fungal symbionts and inoculation with live soil (invasive or native) can increase seedling biomass. Moreover, future work would benefit from assessing if a more diverse community of fungal symbionts increases seedling survival when planted in field restoration sites
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Comparisons of host mitochondrial, nuclear and endosymbiont bacterial genes reveal cryptic fig wasp species and the effects of Wolbachia on host mtDNA evolution and diversity
Background
Figs and fig-pollinating wasp species usually display a highly specific one-to-one association. However, more and more studies have revealed that the "one-to-one" rule has been broken. Co-pollinators have been reported, but we do not yet know how they evolve. They may evolve from insect speciation induced or facilitated by Wolbachia which can manipulate host reproduction and induce reproductive isolation. In addition, Wolbachia can affect host mitochondrial DNA evolution, because of the linkage between Wolbachia and associated mitochondrial haplotypes, and thus confound host phylogeny based on mtDNA. Previous research has shown that fig wasps have the highest incidence of Wolbachia infection in all insect taxa, and Wolbachia may have great influence on fig wasp biology. Therefore, we look forward to understanding the influence of Wolbachia on mitochondrial DNA evolution and speciation in fig wasps.
Results
We surveyed 76 pollinator wasp specimens from nine Ficus microcarpa trees each growing at a different location in Hainan and Fujian Provinces, China. We found that all wasps were morphologically identified as Eupristina verticillata, but diverged into three clades with 4.22-5.28% mtDNA divergence and 2.29-20.72% nuclear gene divergence. We also found very strong concordance between E. verticillata clades and Wolbachia infection status, and the predicted effects of Wolbachia on both mtDNA diversity and evolution by decreasing mitochondrial haplotypes.
Conclusions
Our study reveals that the pollinating wasp E. verticillata on F. microcarpa has diverged into three cryptic species, and Wolbachia may have a role in this divergence. The results also indicate that Wolbachia strains infecting E. verticillata have likely resulted in selective sweeps on host mitochondrial DNA
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