Tidying Up International Nucleotide Sequence Databases: Ecological, Geographical and Sequence Quality Annotation of ITS Sequences of Mycorrhizal Fungi

Sequence analysis of the ribosomal RNA operon, particularly the internal transcribed spacer (ITS) region, provides a powerful tool for identification of mycorrhizal fungi. The sequence data deposited in the International Nucleotide Sequence Databases (INSD) are, however, unfiltered for quality and are often poorly annotated with metadata. To detect chimeric and low-quality sequences and assign the ectomycorrhizal fungi to phylogenetic lineages, fungal ITS sequences were downloaded from INSD, aligned within family-level groups, and examined through phylogenetic analyses and BLAST searches. By combining the fungal sequence database UNITE and the annotation and search tool PlutoF, we also added metadata from the literature to these accessions. Altogether 35,632 sequences belonged to mycorrhizal fungi or originated from ericoid and orchid mycorrhizal roots. Of these sequences, 677 were considered chimeric and 2,174 of low read quality. Information detailing country of collection, geographical coordinates, interacting taxon and isolation source were supplemented to cover 78.0%, 33.0%, 41.7% and 96.4% of the sequences, respectively. These annotated sequences are publicly available via UNITE (http://unite.ut.ee/) for downstream biogeographic, ecological and taxonomic analyses. In European Nucleotide Archive (ENA; http://www.ebi.ac.uk/ena/), the annotated sequences have a special link-out to UNITE. We intend to expand the data annotation to additional genes and all taxonomic groups and functional guilds of fungi

Socio-Economic factors influencing deforestation on the Uluguru mountains, Morogoro, Tanzania

No Abstract.Discovery and Innovation Vol. 19 (1&2) 2007: pp. 139-14

Forest Gardens as an 'intermediate' land-use system in the nature-culture continuum: Characteristics and future potential

Forest gardens are reconstructed natural forests, in which wild and cultivated plants coexist, such that the structural characteristics and ecological processes of natural forests are preserved, although the species composition has been adapted to suit human needs. These agroforests include a range of modified and transformed forests, and form an integral part of local land-use systems. They lie between natural forests and tree-crop plantations in terms of their structure and composition, and low intensity of forest extraction systems and the high intensity plantation systems in terms of their management intensity. Their management is characterized by combined use of silvicultural and horticultural operations, and spatial and temporal variations. These ecologically sustainable systems are often dynamic in species composition in response to changing socioeconomic conditions. Evolved over a long period of time as a result of local community's creativity, forest gardens have still received little attention in agroforestry research, just as in the case of the more intensively domesticated homegardens. The study of forest gardens offers good opportunities for obtaining a better understanding of the 'nature-analogous' agroforestry systems and for developing multifunctional agroforestry systems combining production and biodiversity values