Soil Fungal Community Metagenomics In Large-Scale Ecological Studies.

The soil fungal community plays critical roles in plant health and carbon cycling. Recent developments in fungal genome and community DNA sequencing now allow characterization of the fungal community in terrestrial ecosystems. Using a combination of targeted metagenomics (rRNA gene fragments, functional genes), shotgun and metatranscriptome approaches, coupled with other molecular measures, we are exploring the responses of the soil fungal community to a decade of elevated CO2 in six different ecosystems, through the US Department of Energy Free Air CO2 Enrichment (FACE) and Open Top Chamber (OTC) manipulation experiments. By sequencing fragments of the rRNA large subunit gene (LSU) and cellobiohydrolase 1 gene (cbh1) from replicated field samples, we explored heterogeneity in fungal community composition between the sites, within each site, and across soil depth. Despite local heterogeneity, there appears to be a fungal meta-community specific for each ecosystem. Changes in fungal biomass or community composition in response to elevated CO2 were detected in some, but not all, of the ecosystems. Where multiple factors were included in the field site experiments (plant species, soil depth, N fertilization, ozone treatment), the observed community responses associated with those factors were often larger than the response to elevated CO2. To facilitate identification of target fungal gene sequences, we are developing a naïve Bayesian classifier and curated training sets for fungal LSU, ITS, and cbh1 genes. Use of shotgun and metatranscriptome approaches are being developed for comparative analysis of soil fungal communities in these field experiments. They can be useful for detecting changes in community composition. However, our ability to identify gene functions in these datasets requires a deeper knowledge of genomes from dominant soil fungi. Genomes of several fungi are currently being sequenced, which should greatly facilitate the use of ‘omics techniques for fungal communities in soils.