Posts Tagged ‘ribosomal DNA’

Unexpected high fungal diversity in forest soils

August 28th, 2009

hetraieSoil fungi play a major role in ecological and biogeochemical processes in forest ecosystems. Little is known, however, about the structure and richness of different fungal communities and the distribution of functional ecological groups (pathogens, saprobes and symbionts). Within the framework of our metagenomics project aimed to assess the microbial diversity in temperate forests, we surveyed the fungal diversity in six different forest soils at the Breuil-Chenue long-term observatory using tag-encoded 454 pyrosequencing of the nuclear ribosomal internal transcribed spacer-1 (ITS-1). The paper reporting this study is now online on the New Phytologist Early View pages.

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 (MOTU). Most MOTUs (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 MOTUs showed the highest sequence similarity to Ceratobasidium sp., Cryptococcus podzolicus, Lactarius sp. and Scleroderma sp.

This study, together with two other surveys exploring the diversity of fungal communities in  Quercus macrocarpa phyllosphere (Jumpponen & Jones, 2009) and the diversity of arbuscular mycorrhiza fungi in a boreonemoral forest (Öpik et al., 2009), 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 likely accelerate the study of the spatiotemporal dynamics of fungal communities in forest ecosystems.

Buée et al. (2009) 454 Pyrosequencing analyses of forest soils reveal an unexpectedly high fungal diversity. New Phytologist, doi: 10.1111/j.1469-8137.2009.03003.x

Jumpponen & Jones (2009) Massively parallel 454 sequencing indicates hyperdiverse fungal communities in temperate Quercus macrocarpa phyllosphere. New Phytologist, doi: 10.1111/j.1469-8137.2009.02990.x

Öpik et al. (2009) Large-scale parallel 454 sequencing reveals host ecological group specificity of arbuscular mycorrhizal fungi in a boreonemoral forest. New Phytologist, doi: 10.1111/j.1469-8137.2009.02920.x