Biogeochemistry Commons^™

Overview And Methods Of Molecular Paleontology: A Review, Shelby Touchstone

Williams Honors College, Honors Research Projects

Molecular paleontology—the study of ancient biomolecules preserved in fossils and sediments, including ancient DNA, lipids, and proteins—has motivated researchers since the 1950s, inspiring both scientific inquiry and broader cultural imagination. Think Jurassic Park. This honors thesis presents a comprehensive review of the history, current state, and methods of the field of molecular paleontology. Drawing on peer-reviewed literature and scholarly resources accessed through databases such as EBSCO and Bierce library, this review examines key techniques such as Next Generation Sequencing and amino acid racemization and will go over limitations and controversies in the field. It will also explore potential new …

High Algal Biomass Is Decoupled From Metabolism In The Gallatin River, Cora Mae Steinbach

Graduate Student Theses, Dissertations, & Professional Papers

Assessing eutrophication in rivers is difficult compared to lakes and coastal waters, because most algal biomass occurs on the riverbed and flows interact and co-vary with production (Biggs and Close, 1989; Bernhardt et al., 2018). Riverine eutrophication is typically assessed using algal biomass and water column nutrients (U.S. Environmental Protection Agency, 2000), but biomass is highly variable and labor-intensive to measure, while nutrient concentrations often underestimate enrichment due to rapid biological uptake (Dodds and Smith, 2016). Reach-scale river metabolism can help evaluate long-term functional change in rivers recovering from nutrient enrichment (Arroita et al., 2019; Jankowski et al., 2021; Diamond …

Flood-Season Surface Water-Groundwater Interactions Across Distinct Geomorphic Units In A Yellow River Great Bend Tributary Basin, Yinlong Wang, Ruizhong Gao, Debin Jia, Xixi Wang, Tingxi Liu, Xiaomin Liu, Shiming Bai

Civil & Environmental Engineering Faculty Publications

Surface water-groundwater interactions are complex in the Great Bend region of the Yellow River. Clarifying water exchange and source differences among geomorphic units is important for understanding regional hydrological processes and improving water resources management. In this study, the Wulanmulun River Basin, a typical tributary of the Yellow River, was selected as the study area. A total of 90 water samples were collected, including 25 river water samples, 43 groundwater samples, and 22 precipitation samples. Gibbs diagrams, multivariate statistical analysis, PMF, and MixSIAR models were used to investigate the hydrochemical and isotopic characteristics, source contributions, and transformation relationships of surface …

Seasonal And Geologic Controls On Submarine Groundwater Discharge-Derived Nutrient Fluxes To Two Coastal Embayments, Moira Taylor, Joseph J. Tamborski, Aaron Alorda-Kleinglass, Nathaniel Maynard

OES Faculty Publications

Submarine groundwater discharge and porewater exchange are critical but often overlooked sources of nutrients to coastal systems. This study investigates how sediment permeability and summer-winter seasonal dynamics influence the magnitude and biogeochemistry of nutrient fluxes from submarine groundwater discharge and porewater exchange. Reaction rates in the subterranean estuary were used to identify the transformations and drivers of nutrient loading in two geologically distinct embayments in the U.S. East Coast: the highly permeable Peconic Bay estuary (NY), and the surficially fine-grained coastal embayments of the southern Delmarva Peninsula (VA). We applied radium isotope mass balances to distinguish total submarine groundwater discharge …

Diatom Community Response To High And Low Iron Upwelling Plumes In The California Current System, Sveinn V. Einarsson, Kimberly Powell, Claire Till, Tyler Coale, P. Dreux Chappell

OES Faculty Publications

Diatoms are important primary producers, accounting for most of the oceanic production and carbon export relative to other photosynthetic eukaryotes. There are important differences among diatom species that enable them to proliferate in different environments. Some have nutrient storage capabilities or lower nutrient quotas suited for oligotrophic oceans. Bloom-forming diatoms are typically found in nutrient-rich coastal waters where they respond quickly to nutrient pulses and can influence biogeochemical cycling in the ocean after blooms. As many physiological differences affect biomass and export, it is important to better understand how physical and chemical parameters influence diatom community composition, especially in dynamic …

Characterizing The Unique Chemical Imprint Of On-Axis, Lower-Temperature Hydrothermal Flow To The Deep Ocean (Southern East Pacific Rise, 16.5°-18.0°S), Laura E. Moore, Randelle M. Bundy, Joseph A. Resing, Scott White, Tamara Baumberger, Peter N. Sedwick, Nathaniel J. Buck, Anson M. Antriasian, Isaac Keohane, Bettina M. Sohst, Sharon L. Walker, Christopher R. German

OES Faculty Publications

In addition to high-temperature vents, lower-temperature flow (LTF) (< 300°C) is abundant along mid-ocean ridges and contributes globally-important fluxes of heat and water along with largely-unconstrained geochemical influences on the ocean. We examined the impact of on-axis LTF on the chemical composition of the overlying water column (< 40 m above seafloor) along the 16.5°-18.0°S sector of the ultrafast-spreading southern East Pacific Rise using autonomous underwater vehicle Sentry surveys and conductivity-temperature-depth rosette casts. LTF sites were typically spatially isolated from high-temperature systems and imparted unique chemical signatures to the overlying ocean. Water column samples impacted by LTF exhibited low particulate iron:sulfur ratios and high methane: total-dissolvable manganese ratios, whereas samples influenced by high-temperature venting exhibited opposite trends. We confirmed that LTF imparts a distinct and measurable chemical signature to the water column, independent from high-temperature vents. Isolated, on-axis LTF will be important to consider when assessing hydrothermal circulation impacts upon ocean biogeochemistry.

Autonomous Float Data Reveal Decoupled Trends In Chlorophyll And Stratification In The Indian Ocean, Marufa Ishaque, Sophie Clayton, John Klinck

OES Faculty Publications

Recent studies have shown that the Indian Ocean is warming significantly, but how this warming impacts primary production is largely unresolved due to a relative lack of depth-resolved biological observations. In this study, we have used Biogeochemical-Argo data from 2013 to 2022, comprising over 9,000 individual profiles, to examine regional patterns and trends in depth-integrated chlorophyll, depth-integrated net primary production and stratification in the northern and Equatorial Indian Ocean. Our analysis shows that water column stratification is increasing in the majority of the study area, with the highest rate of increase observed in the western Bay of Bengal. At the …

Recirculated Submarine Groundwater Discharge Dominates Nutrient Inputs And Enhances Eutrophication Risk In A Coastal Lagoon, Júlia Rodriguez-Puig, Clara Ruiz-González, Marc Diego-Feliu, Irene Alorda-Montiel, Aaron Alorda-Kleinglass, Daniel Romano-Gude, Andrea G. Bravo, Júlia Dordal-Soriano, Javier Gilabert, Sophia Bergeler, Celine Lavergne, Gemma Casas, Marisol Manzano, Jordi Garcia-Orellana, Valentí Rodellas

OES Faculty Publications

Submarine groundwater discharge (SGD) is a widely recognized pathway for nutrient transport to coastal systems. Prior studies overlook the unique biogeochemical signatures of different SGD pathways, neglecting their differences in biogeochemical transformations and spatiotemporal factors. Here, we present an integrated assessment of nutrient delivery through three SGD pathways (fresh SGD, long‐scale recirculated SGD, and short‐scale porewater exchange), alongside surface water inputs, to evaluate their seasonality and impact on nutrient dynamics in a coastal lagoon. We conducted five field surveys in March, July, and November 2021, July 2024, and March 2025 in the Mar Menor lagoon, an ecosystem facing severe ecological …

Visualizing The Barely Detectable: Particle Characteristics Of The Elusive Aquatic Gel Phase In The Northeastern Subtropical Atlantic, Huanqing Huang, María Couret, Santiago Hernández-León, Alexander B. Bochdansky

OES Faculty Publications

Marine gels constitute a large yet poorly explored ocean carbon pool. Shadow imaging was tuned to detect particles at two sensitivity levels: high–optical density particles (HODP), resembling the particles captured by most imaging systems, and low–optical density particles (LODP), representing a vastly more abundant and gel-dominated pool. This method enabled us to map and characterize a portion of oceanic gels without filtration and staining. In the subtropical northeast Atlantic, LODP outnumbered HODP of the same size by one or two orders of magnitude. Morphology and particle number spectra differed greatly between the two pools, with LODP showing greater morphological homogeneity …

Assessing Dissolved Organic Matter Sources And Dynamics In Urban Stormwater: Implications For Greenhouse Gases, Harper W. Schmalz

Theses and Dissertations (Comprehensive)

Stormwater management ponds (SWMPs) are important aspects of land-use planning and increasingly recognized as active sites of biogeochemical processing that influence carbon cycling; however, little research has investigated the controls on dissolved organic and dissolved inorganic carbon (DOC and DIC) within these systems. This thesis examined the processing and transformations of dissolved carbon between three compartments to support the development of a greenhouse gas (GHG) box-model for urban stormwater ponds, including SWMP sediment, surface water, and vegetation. The objective of this thesis was to assess the biogeochemical processes that govern the rate and transformation of DOC and DIC between these …

Impacts Of Burn Severity On The Hydro-Physical, Chemical And Thermal Properties Of Sub-Arctic Peat, Joshua B. Meyer Mr

Theses and Dissertations (Comprehensive)

Under current climate change, summer season in the boreal regions of Canada is becoming increasingly warmer and drier. This shift is driving increases in the frequency and intensity of naturally occurring wildfires and allowing access to areas not normally susceptible to fire such as wetlands. In peatland areas, these increasingly large fires can create complex burn scars, which contain a wide variety of different burn severities across different landcover types. This variety calls for a greater understanding of how varying fire intensity affects the hydro physical, chemical, and thermal characteristics of boreal peat. This study aims to deepen that understanding …

Direct And Satellite-Based Quantification Of Greenhouse Gas Fluxes In Small Ponds., Mark Christopher Tierney

Electronic Theses and Dissertations

As evidenced by their historic losses due to anthropogenic activities, wetlands are undervalued ecosystems that provide numerous ecosystem services, from recreational opportunities to carbon (C) storage. However, these wetlands are also the largest natural source of atmospheric methane (CH₄). Additionally, small water bodies (< 10,000 m²) are disproportionately large emitters relative to larger lakes and reservoirs. As construction and restoration efforts proceed, it is crucial to identify wetlands that need restoration and to understand the factors driving both greenhouse gas (GHG) fluxes and the C balance of these systems. This dissertation investigates the drivers of greenhouse gas fluxes …

Modeling Aerosol Transport During High Particulate Matter Episodes In El Paso-Juarez Region And Mitigating Mining-Related Emissions Of Rare Earth Elements (Rees) To The Air, Suzan Aranda Luna

Open Access Theses & Dissertations

This dissertation examines the use of the HYSPLIT model to develop a methodology for the transport and dispersion of air masses affecting particulate matter (PM) concentrations in the El Paso Region, and bioleaching experiments as an alternative to mitigating rare-earth concentrations in the air. Chapter 2 describes the study methodology, 3 and 4 cover the modeling methodology using two-representative high PM2.5 episodes, occurring on February 28, 2024, and June 19, 2024, respectively. These sections encompass the analysis of backward trajectories using four different meteorological datasets to build trajectory frequency maps, the exploratory model analysis of modeled outputs from lower to …

What Limits Dryland Ecosystems? Patterns Of Soil Fertility And Resource Limitation In The Chihuahuan Desert, Dylan Stover

Open Access Theses & Dissertations

Human activities are substantially altering global resource cycles with widespread implications for biogeochemistry and ecosystem functioning globally. Drylands, regions where precipitation is outweighed by water losses, are especially sensitive to these large shifts in resource cycles due to their inherently low and variable resource availability. In these regions, resource availability and biological activity are often concentrated around plants – or fertile islands – and predominantly driven by pulses of water. However, our knowledge of the processes influencing biological productivity in drylands – patterns of soil fertility and resource limitation – remains lacking, and their unique biogeochemical and biological processes create …

Tracing The Journey Of Dissolved Organic Matter: From Leaf Litter Photodegradation To Microbial Processing In Tropical Streams, Samantha Nicole Sullivan

Chemistry & Biochemistry Theses & Dissertations

Dissolved organic matter (DOM) is a major reservoir of organic carbon in aquatic ecosystems and plays a central role in global carbon cycling through its transformation and remineralization to carbon dioxide (CO₂). As DOM moves from terrestrial environments into streams and rivers, its chemical composition is altered by a combination of microbial and photochemical oxidation processes that regulate both its reactivity and its persistence during transport. However, the molecular mechanisms governing these oxidative transitions, particularly in tropical ecosystems characterized by strong hydrologic seasonality and substantial inputs of plant-derived material, remain insufficiently resolved. This dissertation integrates ultrahigh-resolution mass spectrometry, optical characterization, …

Aluminum As A Tracer Of Dust Deposition To The Ocean: A Case Study From The Bermuda Region, Tara Elizabeth Williams

OES Theses and Dissertations

Aluminum (Al), a major component of mineral aerosol (dust), partially dissolves in seawater and is widely used as a tracer for estimating time‐averaged dust fluxes to the ocean. Such estimates rely on dissolved Al (DAl) inventories in the surface mixed layer (SML), an assumed SML residence time of DAl (_TDAl), the fractional solubility of Al in dust (Al_S), and the mass fraction of Al in dust. In this study, dust flux estimated from seasonal, water-column DAl data from the Bermuda Atlantic Time-series Study (BATS) region are compared with direct dust flux estimated from contemporaneous measurements of …

A Bioarchaeological Study Of The Individuals From The Városfalva Burial Mound In Transylvania, Romania (15th-19th Century), Vanessa C. Reeves

USF Tampa Graduate Theses and Dissertations

This study explores the lives and deaths of the Szekler people recovered from a burial mound in the Transylvanian village of Városfalva. The Transylvanian plateau is located in present day Romania, and is protected on the east and the south by the Carpathian Mountains. The Szekler people arrived in this area around 1000 CE, and were a nomadic group originating in the Asian Steppes region who later intermarried with various migratory groups as they moved across the Eurasian plains. The Szeklers eventually banded together with the proto-Hungarian Magyar peoples and settled in the Carpathian Basin, the easternmost frontier of the …

Spatio-Temporal Characterization Of Trace Metals Across The West Florida Shelf And During The Decline Of The North Atlantic Spring Bloom, Delfina Paola Navarro-Estrada

USF Tampa Graduate Theses and Dissertations

Phytoplankton in the marine environment require the trace metals manganese (Mn), iron (Fe), cobalt (Co), nickel (Ni), copper (Cu), zinc (Zn), and cadmium (Cd) to catalyze cellular processes driving photosynthesis, including macronutrient (nitrogen, phosphorus, and carbon) acquisition, light harvesting, and protection from oxidative stress. The high biological demand for these elements, coupled with their low concentrations in the ocean, can limit primary production and shape community composition in marine ecosystems, highlighting the need to understand the drivers behind trace metal distributions and their interplay with phytoplankton growth across biogeochemical regimes. This dissertation characterizes the spatial and temporal distributions of dissolved …

Mcl1 And Hexokinase 2 Form A Glucose Metabolic Regulatory Axis, Robert Lee

All ETDs from UAB

Hexokinase 2 (HK2) initiates glucose metabolism by catalyzing the conversion of glucose to glucose-6-phosphate providing the starting substrate for a vast array of metabolic pathways such as glycolysis, pentose phosphate pathway (PPP), amino acid biosynthesis and others. While HK2’s metabolic role in normal physiologic function (such as in cardiomyocytes) and cancers (through driving the Warburg Effect) are well established, there is emerging evidence that supports HK2 is also a critical mediator of protein-protein interactions that regulate cell survival. Through comprehensive review, we explore how HK2 contributes to cell survival through metabolic and protein scaffolding roles. We also investigate a novel …

Effect Of Seasonal Variability In Methane Emissions And Iron Redox Chemistry At Terrestrial-Aquatic Interfaces, Hermes C. Ruiz

Master's Theses

Methane (CH₄) emissions at terrestrial–aquatic interfaces (TAIs) are significant contributors to the global carbon budget, yet the mechanisms driving methanogenesis remain poorly understood. Limited data exist on how seasonal variations and redox processes influence CH₄ fluxes in these dynamic ecosystems. This study addressed two questions: (1) How are CH₄ fluxes in riverine floodplains and adjacent hillslopes impacted by seasonal variations? (2) What roles do metal redox processes (e.g., iron (Fe)) play in regulating methanogenesis?

In-situ CH₄ flux and solid-phase Fe speciation were quantified in East River, CO, under flooded and drained conditions. Groundwater chemistry, gas flux, and soil physical properties …