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Taxonomic Analysis (taxonomic + analysis)
Selected Abstracts454 Pyrosequencing analyses of forest soils reveal an unexpectedly high fungal diversityNEW PHYTOLOGIST, Issue 2 2009M. Buée Summary ,,Soil fungi play a major role in ecological and biogeochemical processes in forests. Little is known, however, about the structure and richness of different fungal communities and the distribution of functional ecological groups (pathogens, saprobes and symbionts). ,,Here, we assessed the fungal diversity in six different forest soils using tag-encoded 454 pyrosequencing of the nuclear ribosomal internal transcribed spacer-1 (ITS-1). No less than 166 350 ITS reads were obtained from all samples. In each forest soil sample (4 g), approximately 30 000 reads were recovered, corresponding to around 1000 molecular operational taxonomic units. ,,Most operational taxonomic units (81%) belonged to the Dikarya subkingdom (Ascomycota and Basidiomycota). Richness, abundance and taxonomic analyses identified the Agaricomycetes as the dominant fungal class. The ITS-1 sequences (73%) analysed corresponded to only 26 taxa. The most abundant operational taxonomic units showed the highest sequence similarity to Ceratobasidium sp., Cryptococcus podzolicus, Lactarius sp. and Scleroderma sp. ,,This study validates the effectiveness of high-throughput 454 sequencing technology for the survey of soil fungal diversity. The large proportion of unidentified sequences, however, calls for curated sequence databases. The use of pyrosequencing on soil samples will accelerate the study of the spatiotemporal dynamics of fungal communities in forest ecosystems. [source] Pseudozyma jejuensis sp. nov., a novel cutinolytic ustilaginomycetous yeast species that is able to degrade plastic wasteFEMS YEAST RESEARCH, Issue 6 2007Hyuk-Seong Seo Abstract An ustilaginomycetous anamorphic yeast, isolated from orange leaves on Jeju island in South Korea, represents a novel Pseudozyma species according to morphologic and physiologic findings and molecular taxonomic analysis using the D1/D2 domains of the large subunit (26S) rRNA gene and the internally transcribed spacer (ITS) 1+2 regions. The name Pseudozyma jejuensis sp. nov. is proposed for this novel species, with OL71T (=KCTC 17482T=CBS 10454T) as type strain. In the present study, we have also demonstrated that Pseudozyma jejuensis OL71 is capable of producing cutinase and degrading polycaprolactone. These results suggest that Pseudozyma jejuensis or its cutinase may be useful for the biological degradation of plastic waste. [source] DNA barcodes to identify species and explore diversity in the Adelgidae (Insecta: Hemiptera: Aphidoidea)MOLECULAR ECOLOGY RESOURCES, Issue 2009R. G. FOOTTIT Abstract The Adelgidae are relatively small, cryptic insects, exhibiting complex life cycles with parthenogenetic reproduction. Due to these characteristics, the taxonomy of the group is problematic. Here, we test the effectiveness of the standard 658-bp barcode fragment from the 5,-end of the mitochondrial cytochrome c oxidase 1 gene (COI) in differentiating among 17 species of Adelgidae, in associating life-cycle stages, and in assessing patterns of geographical variation in selected species. Species of Adelgidae are well-differentiated by DNA barcodes, enabling the identification of different morphological forms, immature stages and individuals on different hosts and at different periods of the life cycle. DNA barcodes have uncovered cryptic diversity within taxa and, in other cases, a lack of sequence divergence in species pairs previously separated by life-cycle characteristics, indicating a need for further taxonomic analysis. [source] The North American cranberry fruit rot fungal community: a systematic overview using morphological and phylogenetic affinitiesPLANT PATHOLOGY, Issue 6 2009J. J. Polashock Cranberry fruit rot (CFR) is caused by many species of fungi, with the contribution of any given species to the disease complex varying among plantings of Vaccinium macrocarpon within a site, sites within regions, and among regions and years. This study assessed the morphological and molecular variability of five widespread CFR-causing fungi: Phyllosticta vaccinii, Coleophoma empetri, Colletotrichum acutatum, Colletotrichum gloeosporioides and Physalospora vaccinii. Although the majority of isolates had morphological characteristics consistent with published descriptions, some were atypical. For example, non-chromogenic isolates of C. acutatum were recovered from British Columbia and white isolates of Physalospora vaccinii were recovered in addition to the more common dark isolates. On the basis of sequence analysis of the ITS and large subunit rDNA (LSU), it appears that Phyllosticta vaccinii, C. empetri, C. gloeosporioides and C. acutatum are genetically uniform on cranberry in North America. This suggests the possibility that these fungal species were introduced to cultivated cranberries and concomitantly moved with planting material to new locations. In contrast, white isolates of Physalospora had ITS and LSU sequences distinct from those of their dark counterparts, with phylogenetic analyses suggesting that these isolates represent either different species or distinct members of highly divergent populations. Taxonomic placement of all species based on phylogenetic relationships was consistent with morphological placement, with the exception of Physalospora vaccinii. Unlike other Physalospora species, CFR isolates of Physalospora vaccinii were not allied with the Xylariomycetidae; instead, these fungi were members of the Sordariomycetidae. A deeper taxonomic analysis is needed to resolve this inconsistency in familial affiliation. [source] | ||||||||||