Logan, Merritt N., authorBorch, Thomas, advisorRappé, Anthony, committee memberNeilson, James, committee memberConant, Richard, committee member2025-09-012025-09-012025https://hdl.handle.net/10217/241886https://doi.org/10.25675/3.02206Permafrost—perennially frozen ground covering approximately one-fifth of the Northern Hemisphere's land—plays a crucial role in global biogeochemical cycles. These frozen soils are vast reservoirs, holding roughly twice the organic carbon found in the atmosphere and about half of the global subterranean organic nitrogen. However, rising temperatures, particularly in the Arctic where warming is two to four times faster than the global average, threaten permafrost stability. This thawing exposes previously sequestered organic matter to decomposition, potentially releasing billions of tons of carbon and nitrogen-containing greenhouse gases (GHGs). The unpredictable, long-term behavior of permafrost during and after thaw makes it extremely challenging to forecast its impact on global climate, leading to significant uncertainties and frequent omissions from Earth system models. While historical permafrost thaw occurred gradually, rising temperatures are now driving rapid thaw events, accelerating permafrost loss within just a few years. These rapidly thawing areas are identified as highly active GHG emitters, expected to contribute nearly half of permafrost-derived GHGs by 2300, despite impacting only about 1% of the permafrost area. Though carbonaceous GHGs often dominate research, emerging studies highlight that released nitrous oxide—formed through the mineralization of nitrogen reserves from deep, previously frozen soils—may also have a significant impact. The biogeochemical cycling of nitrogen in thawing permafrost is complex, influenced by organic matter composition, thaw rate, soil saturation, and microbial activity. Chapter 2 addresses these complexities by characterizing organic nitrogen across a permafrost thaw gradient at Stordalen Mire, Sweden. Employing Fourier Transform Ion Cyclotron Resonance Mass Spectrometry (FT-ICR MS) alongside Nuclear Magnetic Resonance (1H NMR) spectroscopy and metatranscriptomic analyses, we found elevated ammonium and dissolved organic nitrogen concentrations in the thaw front, with a reduced proportion of peptide-like or carbohydrate molecules. These findings are critical for understanding how the molecular composition of nitrogen changes during thaw, directly impacting its bioavailability and subsequent GHG emissions. The analytical techniques utilized for characterizing organic matter in environmental systems are further described in Chapter 3, which provides a critical review of FT-ICR MS applications. This methodological framework addresses analytical challenges and offers recommendations for sample collection, preparation, analysis, and data interpretation, serving as a vital resource for the field. This provides valuable guidelines for the continued and broader application of FT-ICR MS in a variety of environmental systems. Returning to permafrost, Chapter 4 investigates the interactions between iron minerals and organic carbon across the thaw transition. Reactive iron minerals in permafrost soils sequester organic carbon but can release it upon thaw through reductive dissolution. Using FT-ICR MS, we identified a significant pulse of dissolved organic carbon and Fe2+(aq) at the thaw front, with a higher proportion of aliphatic molecules observed in both dissolved and mineral–adsorbed fractions before thawing. These results suggest that reactive iron minerals at the thaw front play a crucial role as electron acceptors for anaerobic respiration, directly influencing the fate and mobility of released organic carbon and its potential for GHG production. Finally, Chapter 5 extends the application of FT−ICR MS to assess the environmental impact of agricultural sulfur use. In an independent study, we examined dissolved organic sulfur (DOS) in California vineyards and their downstream watersheds. Combining FT−ICR MS with sulfur isotope (δ34S) analysis, we detected vineyard-derived DOS in non-agricultural water systems. Our findings highlight that the mobilization of agriculturally derived organic sulfur can influence critical downstream biogeochemical processes, such as mercury methylation, underscoring the broader environmental consequences of land management practices. In summary, this dissertation demonstrates the power of FT-ICR MS, combined with a comprehensive suite of complementary analytical methodologies, to elucidate the complex molecular transformations of organic carbon, nitrogen, and sulfur in dynamic environmental systems. This molecular-level understanding is crucial for improving predictions of future climate impacts and informing environmental management strategies in a warming world.born digitaldoctoral dissertationsengCopyright and other restrictions may apply. User is responsible for compliance with all applicable laws. For information about copyright law, please see https://libguides.colostate.edu/copyright.organic carbonorganic nitrogenFT-ICR MSpermafrostorganic matterText