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UBC Theses and Dissertations

A multi-omic perspective on microbial mediated methane oxidation in the Saanich Inlet water column Mónica, Torres Beltrán


Microbial communities play an integral role in the biogeochemical cycling of carbon, nitrogen and sulfur throughout the biosphere. These communities interact, forming metabolic networks that change and adapt in response to availability of electron donors and acceptors. Oxygen minimum zones (OMZs) are regions of the ocean where oxygen (O₂) is naturally depleted. In OMZs microbial communities use alternative terminal electron acceptors such as nitrate, sulfate and carbon dioxide, resulting in fixed nitrogen loss and production of greenhouse gases including methane (CH₄). In this thesis, I explored microbial community structure, dynamics and metabolic interactions as they relate to CH₄ cycling in Saanich Inlet, a seasonally anoxic fjord on the coast of British Columbia Canada that serves as a model ecosystem for studying microbial processes in OMZs. Leveraging decadal time series observations in Saanich Inlet, I developed a geochemical dataset consisting of nutrient and gas measurements, coupled with multiomic (DNA, RNA and protein) sequence information to chart microbial community structure and dynamics along defined redox gradients. I conducted methods optimization comparing in situ and on-ship sampling paradigms and used correlation analysis to infer putative microbial interaction networks in relation to water column CH4 oxidation. Methanotrophic bacteria in Saanich Inlet were identified associated with three uncultivated Gammaproteobacteria clades termed OPU1, OPU3 and symbiont-related that partitioned in the water column during periods of prolonged stratification. Water column distribution of the OPU3 clade was found to correlate with nitrite (NO₂-). Based on these results, I conducted incubations with labelled CH₄ and NO₂- to test this correlation and constrain potential metabolic interactions between methanotrophs and other one-carbon utilizing microorganisms under low O₂ conditions. Using multi-omic information derived from these incubations I confirmed the role of OPU3 in coupling CH₄ oxidation to NO₂- reduction and uncovered potential metabolic interactions between OPU3 and other co-occurring microorganisms including Methylophilales, Planctomycetes and Bacteroidetes. Evidence for a communal function in CH₄ oxidation expands the role of OPU3 in the global carbon budget and provides a conceptual foundation for the development of numerical models to predict CH₄ flux from OMZs as they expand throughout the global ocean.

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