Molecular analysis of basidiomycete diversity in agricultural soils

Bahnmann, B. and R.G. Thorn

Presented at the ASM at Estes Park (2006-09-01 to 2012-09-23 )

Improving our understanding of the taxonomic composition of soil microbial communities is essential to understanding microbial contributions to ecosystem functioning. Of particular interest is the soil basidiomycete community as they play an important role in nutrient cycling. This role is especially significant in the agriculture and forestry sectors where nutrient supply and turnover is a limiting factor to long term primary productivity. The filamentous growth form of basidiomycetes and their copious production of extracellular mucopolysaccharides might also have related benefits to soil stabilization and carbon storage. Advancements in molecular techniques and DNA extraction methods from soils are allowing researchers to explore soil microbial communities at much greater taxonomic resolution than direct microscopy methods and without the biases associated with traditional culture-based sampling approaches. We used molecular techniques to study the basidiomycete community within four agriculturally-related treatments at KBS-LTER. Soil extracted DNA was amplified with basidiomycete-specific primers and the resulting mixed template was cloned. Plasmids were extracted from selected clones and digested using restriction enzymes. Plasmids yielding unique digest patterns were sequenced and placed within a phylogenetic tree for nearest-neighbour identification. Ninety-eight unique sequences were obtained from 320 clones, with representatives from five of the eight clades of homobasidiomycetes described by Hibbett and Thorn (2001). The majority of the sequences (69% of all clones) belong to the euagarics clade. Preliminary analyses indicate that the overall diversity of homobasidiomycetes followed similar patterns to earlier studies by Lynch & Thorn (in press) on the same treatments, suggesting a possible levelling off of the species accumulation curves in some treatments sampled.

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