Nozomi Ytow

The Species API of the Global Biodiversity Information Facility (GBIF) provides public access to taxonomic data aggregated from multiple data sources. Each data source follows its own classification which can be inconsistent with classifications from other sources. Even with a reference classification e.g. the GBIF Backbone taxonomy, a comprehensive method to compare classifications in the data aggregation is essential, especially for non-expert users. A Java application was developed to compare multiple taxonomies graphically using classification data acquired from GBIF’s ChecklistBank via the GBIF Species API. It uses a table to display taxonomies where each column represents a taxonomy under comparison, with an aligner column to organise taxa by name. Each cell contains the name of a taxon if the classification in that column contains the name. Each column also has a cell showing the hierarchy of the taxonomy by a folder metaphor where taxa are aligned and synchronised in the aligner column. A set of those comparative tables shows taxa categorised by relationship between taxonomies. The result set is also available as tables in an Excel format file.

Japan's largest platform for academic e-journals: J-STAGE is a full text database for reviewed academic papers published by Japanese societies

Japan's largest platform for academic e-journals: J-STAGE is a full text database for reviewed academic papers published by Japanese societies

Japan's largest platform for academic e-journals: J-STAGE is a full text database for reviewed academic papers published by Japanese societies

Microbial diversity in forage crop seeds was examined using culture-independent methods. Environmental DNA samples were extracted from the surface of the seeds, and the intergenic spacer region between small subunit and large subunit RNA genes was then amplified by ribosomal intergenic spacer analysis (RISA) for the profiling of microbial community structures. The results suggested the presence of stable microbial communities in seeds and sequencing of the RISA amplicons identified a total of 33 unique microbial sequences in 1.6 g of seed material from Italian ryegrass (Lolium multiflorum) and timothy (Phleum pretense). These included several sequences showing high similarity to known plant-associated microbes, such as Pseudomonas fluorescens and Clavibacter michiganensis, the Cladosporium and Dioszegia group of fungi, and also several uncultured bacteria.

Japan's largest platform for academic e-journals: J-STAGE is a full text database for reviewed academic papers published by Japanese societies

Japan's largest platform for academic e-journals: J-STAGE is a full text database for reviewed academic papers published by Japanese societies

Ribosomal intergenic spacer analysis (RISA) has been applied to the microbial community analysis of agronomic products in combination with a simple and rapid DNA extraction method, consisting of a one-step extraction and two-step purification, for a variety of agronomic products. RISA appears to be a useful tool for the study of the community structures of food-associated microbes and their use as a unique fingerprinting signature for each agronomic product. Sequencing analyses of amplicons generated from RISA suggest that this method can detect conventional microbes. In the case of RISA of wasabi paste DNA, the sequences of the amplicons showed high similarity to the plant pathogen Xanthomonas campestris and the soil bacterium Bacillus subtilis, whereas several food-associated bacteria (Lactococcus lactis, Lactococcus raffinolactis, and Lactococcus sakei) were detected using this technique in sausage DNA. Unexpectedly, the sequencing analyses also revealed the presence of several microbes that possessed high similarity to human bacterial pathogens such as Weissella confusa and Yersinia pestis. The results suggest that RISA will be a useful method for routine microbial community analysis in agronomic products. Keywords: Microbial community analysis; ribosomal intergenic spacer analysis

In the present study, we examined the feasibility of using a simplified ribosomal intergenic spacer analysis (RISA) technique to investigate the impact of chrysanthemum genotypes, including Bt transgenic lines, the control parental line and a wild species, on microbial communities in their rhizospheric soils. Differential bands among the plant genotypes were identified from RISA profiles. Sequence data revealed that some bands showed high levels of similarity to known species, such as a fungal group of Exidiopsis and Exidia and a protozoan, Tetrahymena tropicalis. None, however, shared homology to either pathogenic or beneficial microbes that have previously been identified in association with both animals and plants.