UBC Theses and Dissertations
Illuminating phylogeny and function of microbial dark matter in Sakinaw Lake Gies, Esther Anna
Microorganisms are the most abundant and diverse forms of life on Earth. Interconnected microbial communities drive matter and energy transformations integral to ecosystem functions and services through distributed metabolic networks innovated over 3.5 billion years of evolution. To effectively harness this metabolic potential it is necessary to chart uncultivated microbial community structure and function. Cultivation-independent studies indicate that over half of the microbial diversity on Earth belongs to uncultivated candidate divisions, also known as microbial dark matter (MDM). Here, I illuminate MDM structure and function in meromictic Sakinaw Lake on the Sunshine Coast of British Columbia Canada. Sakinaw Lake water column conditions quantified over 8 field campaigns were intimately associated with unprecedented abundance and diversity of MDM. Using network analysis and single cell genomics, co-occurrence patterns between MDM including OP9/JS-1, OP8 and methanogenic Archaea were linked with potential to perform syntrophic acetate oxidation, an important process in anaerobic digestion of organic matter in natural and engineered ecosystems. Single-cell and metagenome analysis revealed previously unrecognized nitrate reduction potential in candidate division OP3 and uncovered a novel archaeal lineage. In addition, numerous Fe-S oxidoreductases associated with MDM in Sakinaw Lake indicate the potential to couple sulfur oxidation to iron reduction. Taken together, my work establishes Sakinaw Lake as a natural laboratory in which to explore MDM structure and function, shines a spotlight on known and novel interactions and metabolic capabilities among these most enigmatic microorganisms, and points to potential biotechnological innovations based on cooperative interactions between MDM populations.
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Attribution-NonCommercial-NoDerivs 2.5 Canada