Deciphering decomposition and the effects of disturbance in forest soil microbial communities with metagenomics and stable isotope probing

Forest industries are expected to bolster the renewable resource economy, but must contend with ecological challenges in maintaining the long-term fertility of forest plantation soils, and technological challenges in converting forest biomass into industrially relevant sources of carbon and energy. This thesis advances research related to both, first by describing the broad changes in soil microbial communities in the decades following timber harvesting, their implications for soil processes and the influence of biomass retention for mitigation (Chapter 3) and, second, by conducting the first comprehensive culture-independent survey of lignocellulolytic organisms in forest soils to expand knowledge of their diversity and catabolic capabilities (Chapter 4). Analysis of over 1,300 bacterial (16S rRNA gene) and fungal (ITS region) pyrotag libraries demonstrated consistent changes in microbial communities at harvested sites across North America, such as i) the increase of desiccation- and heat-tolerant organisms, ii) the general decline of ectomycorrhizal (EM) fungi with a rise of select EM genera (Suillus and Thelephora), iii) the moderation of population shifts by organic matter retention and iv) changes in the functional character of harvested soils, including reduced methanotrophic populations and cellulolytic activity. Biogeographical differences in community structure revealed the potential for variation in the impacts of harvesting. Overall, a number of taxonomic groups were identified that may be important indicators for assessing the long-term impact of timber harvesting. Stable isotope probing revealed the degradation of model hemicellulose, cellulose and lignin substrates by specialized taxa, active on a sole substrate, and groups capable of degrading all three plant polymers, such as members of Burkholderiales and Caulobacteraceae. Bacterial lignin-degraders were more active than fungi in soil microcosms, represented by taxa with characterized lignolytic capability (Sphingobacteriaceae and Sphingomonadaceae) and novel taxa, such as members of Elusimicrobia and Acidobacteria. Differences in lignocellulolytic populations were observed among ecozones and soil layers. Mineral soils harboured a greater proportion of poorly characterized functional taxa and represent reservoirs of unexplored catabolic diversity. Metagenome assembly was ~3 to 20-fold higher as a result of SIP, providing a trove of sequence data containing carbohydrate- and lignin-active enzymes from lignolytic and cellulolytic taxa for future characterization.Science, Faculty ofMicrobiology and Immunology, Department ofGraduat