Microbiome mediating methane dynamics in coastal ecosystems

Sebastian Euler

doi:10.25918/thesis.348

In coastal ecosystems, prokaryotic communities play an important role in regulating the cycling of methane (CH₄) and related compounds. These areas are comprised of complex and delicately balanced ecosystem zones containing a multitude of specific ecological niches for resident microorganisms. Our understanding of the archaeal and bacterial players governing CH₄ cycling processes in coastal environments continues to evolve, however significant knowledge gaps remain. This thesis used 16S metagenomics sequencing and bioinformatics pipelines paired with cavity ring-down spectrometry and other high-resolution temporal and spatial evaluations of greenhouse gases (GHGs) and nutrients in a set of interconnected coastal ecosystems. Hypotheses around anthropogenic impact, vegetation and sediment characteristics as well as subterranean estuary nutrient transformations are explored in the microbiome context using this approach. This thesis highlights that methanogenic archaea were most abundant in the highly urbanized sites of the studied river estuary, and had a positive correlation with elevated CH₄ concentrations. Dissolved organic carbon (DOC) and carbon dioxide (CO₂) abundances, coupled with a scarcity of other electron acceptors like dissolved oxygen (DO) and nitrate (NO₃-) likely facilitated methanogen niches in these sites. Along a pristine mangrove continuum, methanogens primarily occurred in vegetated ecosystem zones and were confined to low/below rhizosphere depths, as well as in an atypical salt marsh niche in the upper tidal zone. Correspondingly, the dense mangrove forest exhibited the highest CH₄ emissions as well as forest floor methanotroph abundances. Pneumatophores and crab burrows were proposed as conduits, facilitating CH₄ transport from deeper sediments. The studied subterranean estuary (STE) revealed complex zonation, ecological niches, and microbiome distributions. Methanogens were most prevalent at the terrestrial end of the transect along with the highest concentrations of CH₄, CO₂ and DOC. Rapidly decreasing CH₄ and ammonium (NH4+) concentrations corresponded with higher abundances of methanotrophs as well as ammonia oxidizing and nitrifying prokaryotes in the mixing zone, likely representing a sink for CH₄ and bioavailable nitrogen. The results suggest that previous studies which deduced coastal CH₄ and nutrient fluxes using only terrestrial endmembers may have overestimated these fluxes by neglecting microbially mediated transformations throughout the STE. Overall, this thesis highlights the most important microbiological niches and environmental conditions mediating coastal CH₄ cycling in the face of a changing climate and provides a platform for future research.

Microbiome mediating methane dynamics in coastal ecosystems

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Microbiome mediating methane dynamics in coastal ecosystems

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