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UBC Theses and Dissertations

Unearthing the influence of soil organic matter removal on population structure and metabolism of soil microbial communities Hahn, Aria Stefanee


Microorganisms are the stewards and creators of Earth's ecosystems, driving planetary nutrient and energy cycles. As such, the interactions and metabolic processes of microbial communities have emerged as a fundamental area of scientific research. Through the use of multi-omic (e.g.; metagenomics, metatranscriptomics, proteomics) sequence information, it is possible to reconstruct the compositional, regulatory, and distributed metabolic processes connecting microbial community members. This dissertation develops an interpretative framework for the joint analysis of compositional network patterns and metabolic pathway reconstruction using metagenomic and metatranscriptomic data from soils collected from lodgepole pine forests 13 years post-harvesting and soil organic matter removal and adjacent undisturbed lodgepole pine forests and Interior Douglas-fir forests at two Long Term Soil Productivity (LTSP) sites located near Kamloops, and Williams Lake B.C., Canada. Further, this dissertation serves to improve the accuracy with which environmental sequence data are analyzed by leveraging the work of statisticians to overcome known biases in canonical approaches to data normalization. Finally, this work provides a systematic approach to the functional annotation of unassembled data, and extends an existing diversity index to accept data types common in studies involving uncultivated microbial annotation. Together the data indicated spatiotemporal variation in, and forest harvesting impact on, metabolic interactions and genomic potential for plant biomass degradation and carbon cycling. However, redundant metabolic capacity combined with genetic variation within the microbial community ensures natural and anthropogenically-induced environmental change had disparate effects across community members thereby moderating the consequences of localized extinctions or niche space reduction, and guarding against the loss of metabolic functions within the soil ecosystem. Indeed, environmental change can result in the reshuffling of trophic relationships and information exchange (e.g.; H+, metabolites, and horizontal gene transfer) allowing new and novel interactions between organisms to form and increase the community's ability to tolerate disturbance. This work represents an important step in understanding how environmental changes impact microbial communities and ecosystem function within the soil milieu. Ultimately, data and findings from this dissertation can be integrated with future analyses of biogeochemical parameter information and thermodynamic principles to enable time variable forecasts of microbial adaptive response to environmental change.

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