Hidden versatility, competition, and cooperation: Methanogenesis and nitrification drive unexpected carbon and nitrogen cycle linkages

Abstract

Wetlands serve as crucial nodes in the carbon (C) and nitrogen (N) cycles by sequestering ~30% of global soil organic matter (SOM) and contributing to ~20% of annual global methane emissions despite accounting for only ~6% of global land area. The degradation, release, and retention of organic carbon and nitrogen in wetlands is facilitated by the activity of microorganisms that assemble into microbial communities within the pore network of wetland sediment aggregates. However, biogeochemical nutrient gradients will impose selective pressures that control the structure and function of the microbial community responsible for greenhouse gas emissions and SOM storage. The complex feedback between microbial activity and biogeochemistry makes it difficult to predict how increasing anthropogenic activity will influence nutrient cycling in wetland ecosystems. This dissertation aims to address this critical gap by linking single-cell microbial ecophysiology and community structure to ecosystem-scale biogeochemistry while developing predictive understanding of how microbial communities respond to environmental change. This work aims to investigate both the microbial interactions governing the degradation of organic carbon to methane by methanogenic communities in wetland sediments and the ecophysiology of ammonia-oxidizing microorganisms (AOM)—major contributors to terrestrial nitrous oxide (N2O) emissions and the global nitrogen cycle. Methane (CH4) and N2O are potent greenhouse gases (GHG) with global warming potentials 27 and 273 times greater than carbon dioxide (CO2) over a 100-year timescale, respectively. These important environmental processes were studied in laboratory enrichments and isolates with a combination of culture-based, isotopic, multi-omic, and mathematical modeling approaches. Wetland sediment chemostat enrichments were used in the first two sections to investigate spatial community structure, carbon degradation, and links between the carbon and nitrogen cycle. This thesis begins with a comprehensive overview of methanogenesis and nitrification and their connections to global carbon and nitrogen cycles within wetland ecosystems (Chapter 1). Synthetic wetland sediment aggregate chemostat enrichments and mathematical models of lactate degrading methanogenic communities demonstrated spatial community structuring and highlighted the importance of spatial proximity for methanogenesis (Chapter 2). Aerobic and anaerobic necromass degrading wetland communities reverted to their prior states after oxygen perturbations demonstrating the resiliency of these functionally redundant communities, while emphasizing necromass recycling as an underappreciated link between the carbon and nitrogen cycle (Chapter 3). Next, the physiological mechanisms underlying nitrogen removal in a novel partial nitritation-anammox reactor using high affinity AOM were evaluated (Chapter 4). This physiological investigation led to the discovery of hydroxylamine-dependent nitrate reduction and the biotic mechanism of N2O production by the complete ammonia-oxidizing (comammox) bacteria Nitrospira inopinata (Chapter 5). These results highlight the spatial dimension of metabolic niche partitioning, link the carbon and nitrogen cycles through necromass degradation, and uncover previously unknown nitrogen cycling metabolic versatility.