BioFun: Biodiversity in the dark: High-throughput sequence analyses of arctic fungal communities
Research methods and ethics
During the summer 2013 a field cruise will be conducted at Svalbard, where a research ship will be hired and used during a two-week field campaign (it lies outside the applied project and is covered by other funds, but it forms a basis for the subsequent analyses and is hence reported here). During this field trip, fungal fruit bodies will be sampled for establishing arctic reference sequence data (WP1). Sanger sequencing will be used to obtain ITS and LSU sequences from the collected material, which will be accessioned in UNITE. Moreover, environmental samples will be collected for the high throughput sequence analyses in WP2 and WP5, with a main focus on ectomycorrhizal plants like Dryas octopetala, Salix polaris and Bistorta vivipara. In WP5, minibus trips will be performed to sample soils in Scandinavia, especially at high latitudes of Norway and boreal and mixed forests of Sweden, Finland and Baltic states. From ca. 50 2500 m2-plots, 40 soil cores (diam=5 cm; 5 cm depth) will be pooled and used for 454 (tentatively) and soil nutrient analyses (as established for ca. 400 samples collected from all over the world). Most of the soil samples are prepared for sequencing in Estonia. In WP2, various high throughput sequence analyses will be conducted, including Illumina MiSeq, GS FLX (454), Ion Torrent PGM and PacBio. The Norwegian Sequencing Centre at the University of Oslo will perform these analyses in collaboration with the project participants.
Various bioinformatics approaches will be used to analyze the sequence data including QIIME, MEGA, and the elaborated tools. The bioinformatics analyses will be conducted in collaboration with staff at the Norwegian Sequencing Centre as established in previous studies of the Norwegian partner. Phylogenetic analyses and comparative analyses will be run using RAxML and picante package of R, respectively. Univariate and multivariate analyses will be performed using nlme, and vegan packages of R that are routinely used in the Estonian group’s publications in addressing similar hypotheses at the global scale. The Estonian group led the build-up of UNITE database, PlutoF workbench and it has a good programming capability. Certain members of both Estonian (UK) and Norwegian (KHL) groups are among the top taxonomic experts in specific groups of ectomycorrhizal and saprotrophic fungi relevant to this project. The complementary skills and previous collaborative experience (13 co-authored papers) render integration of this knowledge highly fruitful.
This project has no adverse effects on the environment and it does not involve animal or human testing. Sampling of soils, plants and fungi will follow the regulations of governments involved and international standards. This project will increase our knowledge about arctic terrestrial ecosystems and, hence, provide a better basis for a sustainable management of these ecosystems in the changing climate.