Date of Graduation


Document Type


Degree Name

Doctor of Philosophy in Biology (PhD)

Degree Level



Biological Sciences


Steven Stephenson

Committee Member

Frederick Spiegel

Second Committee Member

Burt Bluhm

Third Committee Member

Ravi Barabote


Biodiversity, Bioinformatics, Community Ecology, Ion Torrent, Mycology


Global importance of forests is difficult to overestimate, given their role in oxygen production, ecological roles in nutrient cycling and supporting numerous living species, and economic value for industry and as recreational zones. Fitness of the forest-forming trees strongly depends on microbial communities associated with tree roots. In particular, fungi impact tree fitness: mycorrhizal species provide water and nutrients for the trees in exchange for C, endophytic fungi play key roles in host defense against pathogenic organisms, and saprotrophic fungi decompose dead organic matter and facilitate nutrient cycling. In addition, pathogenic fungal species strongly affect forest fitness. Despite their importance, fungal communities associated with forest trees are largely unknown because the typical morphological assay takes into consideration a scarce portion of fungal diversity: species that produce visible fruiting bodies at relatively frequent intervals. A more accurate assessment of fungal diversity in forests has become possible with the development of next-generation sequencing, where fungal species are being identified based on the presence of their DNA in the sample. In this work, DNA-metabarcoding was utilized to assess the diversity of fungi associated with roots of forest-forming trees within the families Fagaceae and Betulaceae (Europe), and Fagaceae, and Juglandaceae (North America). The data obtained provided unprecedented insight into hidden richness of root-associated fungi, which approached 1756 OTUs (a proxy for species) in the European dataset, and 2769 – in the North American dataset. Variation in fungal community composition was largely explained by geographical location (ca. 30%). However, the effect of host specificity (ca. 9-15% of variation) was significant as well. DNA-based data revealed strong positive and negative patters in fungal co-occurrence (e.g., a positive relationship was observed between Cenococcum geophilum and species of Russulaceae), which could indicate interactions between fungal species. In addition to diversity assays, fungal responses to acid precipitation were quantified, and revealed strong declines in fungal richness and abundance, including ectomycorrhizal species. I conclude that compositional shifts in root-associated fungal communities could be particularly suitable for monitoring of forest ecosystems, given an optimal response time in fungi (not too slow as in wooded plants and not as high as in bacteria).