Project description:Three new species of Phyllosticta, P. hostae on Hosta plantaginea (China), P. schimae on Schima superba (China), and P. ilicis-aquifolii on Ilex aquifolium (UK), are described and illustrated in this study. They are compared with morphologically similar and phylogenetically closely related species. A polyphasic approach using phylogeny, host association, disease symptoms, colony and morphological characteristics, is employed to justify the introduction of the new taxa. Phylogenetic relationships of the new species with other Phyllosticta species are revealed by DNA sequence analyses based on the nrDNA-internal transcribed spacer (ITS) regions and a combined multilocus alignment of the ITS, partial translation elongation factor 1-alpha (TEF1), actin (ACT), and glyceraldehyde 3-phosphate dehydrogenase (GPDH) gene regions.
Project description:Two new species, Penicillium krskae (isolated from the air as a lab contaminant in Tulln (Austria, EU)) and Penicillium silybi (isolated as an endophyte from asymptomatic milk thistle (Silybum marianum) stems from Josephine County (Oregon, USA)) are described. The new taxa are well supported by phenotypic (especially conidial ornamentation under SEM, production of red exudate and red pigments), physiological (growth at 37 °C, response to cycloheximide and CREA), chemotaxonomic (production of specific extrolites), and multilocus phylogenetic analysis using RNA-polymerase II second largest subunit (RPB2), partial tubulin (benA), and calmodulin (CaM). Both new taxa are resolved within the section Exilicaulis in series Restricta and show phylogenetic affiliation to P. restrictum sensu stricto. They produce a large spectrum of toxic anthraquinoid pigments, namely, monomeric anthraquinones related to emodic and chloremodic acids and other interesting bioactive extrolites (i.e., endocrocin, paxilline, pestalotin, and 7-hydroxypestalotin). Of note, two bianthraquinones (i.e., skyrin and oxyskyrin) were detected in a culture extract of P. silybi. Two new chloroemodic acid derivatives (2-chloro-isorhodoptilometrin and 2-chloro-desmethyldermoquinone) isolated from the exudate of P. krskae ex-type culture were analyzed by nuclear magnetic resonance (NMR) and liquid chromatography-mass spectrometry (LC-MS).
Project description:Soybean bradyrhizobia (Bradyrhizobium spp.) are bacteria that fix atmospheric nitrogen within the root nodules of soybean, a crop critical for meeting global nutritional protein demand. Members of this group differ in symbiotic effectiveness, and historically both phenotypic and genotypic approaches have been used to assess bradyrhizobial diversity. However, agreement between various approaches of assessment is poorly known. A collection (n=382) of soybean bradyrhizobia (Bradyrhizobium japonicum, B. diazoefficiens, and B. elkanii) were characterized by Internal Transcribed Spacer - Restriction Fragment Length Polymorphism (ITS-RFLP), cellular fatty acid composition (fatty acid methyl esters, FAME), and serological reactions to assess agreement between phenotypic and genotypic methods. Overall, 76% of the accessions demonstrated identical clustering with each of these techniques. FAME was able to identify all 382 accessions, whereas 14% were non-reactive serologically. One ITS-RFLP group, containing 36 Delaware isolates, produced multiple ITS amplicons indicating they possess multiple ribosomal RNA (rrn) operons. Cloning and sequencing revealed that these strains contained as many as three heterogenous rrn operons, a trait previously unknown in bradyrhizobia. A representative subset of 96 isolates was further characterized using 16S rRNA and Internal Transcribed Spacer (ITS) amplicon sequencing. ITS sequences showed better inter- and intra-species discrimination (65-99% identity) than 16S sequences (96-99% identity). This study shows that phenotypic and genotypic approaches are strongly correlated at the species level but should be approached with caution. We also suggest using combined 16S and ITS genotyping data to obtain better inter- and intra-species resolution in bradyrhizobia classification.
Project description:Key chili and maize growing areas of Pakistan were selected for a focused baseline study of the levels of Aspergillus spp. Investigations were undertaken using a combination of molecular and culture-based techniques. Samples investigated included soil samples, one-year-old corn cobs, and fresh chili from selected locations. Aspergillus strains obtained from corn cobs were screened using coconut milk agar, resulting in one strain that was positive for aflatoxin production. Whole genome sequencing (WGS) with low coverage techniques were employed to screen the isolates for differences in the ribosomal RNA gene cluster and mitochondrial genome, with the aflatoxigenic strain proving to have a distinctive profile. Finally, strains were subjected to matrix-assisted laser-desorption and ionization time-of-flight mass spectrometry (MALDI-ToF-MS) in order to obtain a proteomic 'fingerprint' which was used to distinguish the aflatoxigenic strain from the other isolates. The next generation sequencing (NGS) study was broadened to incorporate metabarcoding with ITS rRNA for determining the microbial biodiversity of the soil samples and presumptive screening for the presence of aflatoxigenic strains. Using information gleaned from the WGS results, a putative aflatoxigenic operational taxonomic unit (OTU) was observed in four of the 15 soil samples screened by metabarcoding. This method may have beneficial applications in early detection and surveillance programs in agricultural soils and commodities.
Project description:Paramecium (Ciliophora) systematics is well studied, and about twenty morphological species have been described. The morphological species may include several genetic species. However, molecular phylogenetic analyses revealed that the species diversity within Paramecium could be even higher and has raised a problem of cryptic species whose statuses remain uncertain. In the present study, we provide the morphological and molecular characterization of two novel Paramecium species. While Paramecium lynni n. sp., although morphologically similar to P. multimicronucleatum, is phylogenetically well separated from all other Paramecium species, Paramecium fokini n. sp. appears to be a cryptic sister species to P. multimicronucleatum. The latter two species can be distinguished only by molecular methods. The number and structure of micronuclei, traditionally utilized to discriminate species in Paramecium, vary not only between but also within each of the three studied species and, thus, cannot be considered a reliable feature for species identification. The geographic distribution of the P. multimicronucleatum and P. fokini n. sp. strains do not show defined patterns, still leaving space for a role of the geographic factor in initial speciation in Paramecium. Future findings of new Paramecium species can be predicted from the molecular data, while morphological characteristics appear to be unstable and overlapping at least in some species.