Mineral-associated organic carbon (MAOC) is a vital component of soil health and ecosystem productivity, playing a key role in carbon (C) sequestration and nutrient cycling. This dissertation investigates how plant root traits, nitrogen (N) fertilization, and cover cropping influence soil organic carbon (SOC) and MAOC. In the first chapter, a greenhouse experiment with 30 herbaceous plant species found that non-N-fixing plants exhibited stronger positive correlations with MAOC compared to N-fixing species, which were more closely linked to SOC. Root biomass contributed to decreases in MAOC, while specific root length (SRL), and coarse root traits were found to significantly contribute to increases in MAOC, highlighting the importance of plant root architecture in stabilizing C. In the second chapter which focused on relationships among N-fertilization, root traits, and MAOC, moderate N fertilization (56 and 112 kg N/ha) was found to enhance total SOC (∆SOC) and MAOC (∆MAOC) accumulation in the system, while higher N inputs (168 kg/ha) reduced C gains. Notably, the use of stable isotopes allowed for the quantification of fresh C additions, with results that indicate plant-added MAOC (PA-MAOC) was influenced more by plant species and root traits, such as coarse root length and aboveground biomass, rather than N fertilization. In the third chapter, a long-term field study demonstrated the effectiveness of cover cropping in increasing both SOC and MAOC by 43–59% and 27–36%, respectively, compared to conventional and no-till systems without cover crops. Despite triennial additions of N fertilizer over nine years, no significant increases in SOC or MAOC was observed. Additionally, root biomass exhibited positive trends with MAOC. These findings suggest that cover cropping, combined with no till practices, plays a pivotal role in enhancing MAOC by minimizing soil disturbance and promoting root-driven C inputs. This research highlights the importance of integrating plant species selection, root morphological traits, N management, and conservation practices to optimize long-term C storage (i.e., MAOC) and support sustainable soil management. Future studies should continue to include MAOC and particulate organic carbon fractions as these functional C sub pools may respond differently than bulk SOC pool. Including further studies on the interactions between root morphology, environmental factors, and C/N dynamics is necessary to develop more resilient agroecosystems capable of mitigating C losses and improving long-term soil health. / Doctor of Philosophy / This dissertation explores soil organic carbon, an important component of soil organic matter, which is vital for soil health and fertility. Soil organic matter promotes plant growth and agricultural productivity, and is critical for mitigating climate change by acting as a carbon sink, absorbing carbon dioxide from the atmosphere, which is why maintaining and building soil carbon is important. Soil carbon that is bound to minerals such as clays, is referred to as mineral-associated carbon (MAOC), which holds the largest pool of carbon on land and is often believed to persist over longer time-scales. Cover crops, their plant roots, and nitrogen fertilizer may have different relationships with MAOC when compared to total soil carbon, and these responses are not well understood. To address some of these knowledge gaps, this dissertation measured MAOC, plant root traits such as root size and structure, among different types of plants commonly used in agriculture and land reclamation practices. Results from this work show that root traits play an important role in increasing MAOC during short-term plant growth, with different effects depending on whether the plants can fix nitrogen from the air. Nitrogen fertilization was found to strongly impact MAOC, with moderate levels increasing amounts of MAOC, but low or too much nitrogen caused losses. Additionally, plant traits like root and stem biomass had a stronger influence on fresh carbon inputs from plants to the soil versus nitrogen alone. Cover crops proved to be a highly effective strategy for improving MAOC storage over 9 years, while additional nitrogen fertilizer had little long-term effect. These findings highlight the importance of balancing plant selection, fertilization, and sustainable practices to maintain healthy, carbon-rich soils.

Mangrove stands and oyster reefs are two common coastal habitats in the Indian River Lagoon. Each habitat provides diverse ecosystem services, including carbon sequestration and carbon storage. A decrease in freeze events and an increase in sea levels are leading to mangrove habitat expansion, including encroachment onto live oyster reefs in the IRL’s northernmost portion, Mosquito Lagoon. This study investigates how the encroachment of black mangroves (Avicennia germinans) and red mangroves (Rhizophora mangle) on eastern oyster reefs (Crassostrea virginica) impacts the abundance and stability of soil carbon relative to each habitat alone. Soil and sediment samples (0-10cm) were collected from three locations in Mosquito Lagoon, each containing a mangrove-only, oyster-only, and mangrove-encroached oyster reef habitat. Total and active carbon were quantified, and stable carbon was determined through physical and density fractionation that isolates persistent mineral-associated organic matter (MAOM). Results showed total, active, and MAOM-carbon averaged 2-3 times greater in mangroves than oyster reefs, while mangrove-encroached oyster reefs were intermediate in concentration. However, mangrove-oyster soils have the highest proportion of the total carbon pool protected as MAOM (54.9%), compared to each habitat alone (mangrove-only, 35.3%, oyster-only, 30.3%). This research is the first to provide data on blue carbon storage in areas where mangroves encroach on oyster reefs, including differentiating total carbon based on its stability in the soil.