Biogeochemistry Commons^™

Unraveling Sources Of Cyanate In The Marine Environment: Insights From Cyanate Distributions And Production During The Photochemical Degradation Of Dissolved Organic Matter, Rui Wang, Jihua Liu, Yongle Xu, Li Liu, Kenneth Mopper

Chemistry & Biochemistry Faculty Publications

Cyanate is a nitrogen and energy source for diverse marine microorganisms, playing important roles in the nitrogen cycle. Despite the extensive research on cyanate utilization, the sources of this nitrogen compound remain largely enigmatic. To unravel the sources of cyanate, distributions and production of cyanate during photochemical degradation of natural dissolved organic matter (DOM) were investigated across various environments, including freshwater, estuarine, coastal areas in Florida, and the continental and slope regions of the North American mid-Atlantic Ocean (NATL). Cyanate production was also examined during the photochemical degradation of exudates from a typical strain of Synechococcus, an important phytoplankton …

Soil Biogeochemistry In Riparian And Restored Tidal Wetlands: Monitoring And Method Evaluation, Joseph Anthony Loffredo

Open Access Master's Theses

Although soils are essential for sustaining ecosystems, they are often overlooked in routine monitoring efforts during restoration projects. This thesis tries to address the interest in and challenges of measuring and monitoring soil biogeochemical properties and processes to evaluate restoration trajectories. In the first part of this thesis (Chapter 1), I monitored tidal marsh vegetation and soil biogeochemical responses to restoration by thin-layer placement (TLP) of dredged sediments in a greenhouse mesocosm study and a parallel field study at an active restoration site in southern RI. In the greenhouse, aboveground plant biomass in mesocosms treated with +5 cm and +10 …

Examining The Role Of Microbial Communities In Soil Carbon Cycling Across Levels Of Complexity, Chansotheary Dang

Graduate Theses, Dissertations, and Problem Reports (ETD)

Microorganisms provide the foundation for many ecosystem processes and are important drivers of carbon and nutrient cycling. The advancement of next generation sequencing has allowed researchers to lift open the lid on the ‘black box’ in microbial ecology. While previously unculturable microbes can now be characterized with the 16S rRNA gene, answering ‘who’s there?’ is only part of the challenge. Hidden inside the ‘black box’ remains the question, ‘who’s doing what?’. Recent development in trait-based methods like quantitative stable isotope probing (qSIP) equipped microbial ecologists with the tool to connect taxon-specific traits to ecosystem processes. Despite the growing body of …

Tracing Past Climate Signals Through Multi-Proxy Analysis: Insights From Sedimentary Plant Wax Hydrogen Isotope Data And Long-Term Hydroclimate Records In Estonia, Mariliis Eensalu

Graduate Research Theses & Dissertations

In light of the rising global temperatures, there is an increasing need to understand the potential shifts in hydroclimate. Past climate reconstructions offer a glimpse into the possible temperature-moisture dynamics by providing quantitative constraints for hydroclimate variability under different temperature conditions, which can ultimately aid in decreasing the uncertainty in future climate projections. The research presented in this dissertation focuses on utilizing various proxies to reconstruct past hydroclimate conditions, particularly in the Baltic region, with a specific emphasis on Estonia. The second and third chapter aim to improve the understanding of sedimentary plant wax hydrogen isotope (δ2H) data by first …

Dust-Driven Mechanism For Marine Particle Aggregation: Interactions Between Clay Minerals, Heterotrophic Bacteria And Organic Matter Influences Aggregation In Marine Systems, Vignesh Gokuladas Menon

Dartmouth College Master’s Theses

Atmospheric dust deposition plays a crucial role in marine biogeochemical cycles, yet mechanisms underlying its impact on particle dynamics remain unclear. This study investigates the synergistic interactions between marine heterotrophic bacteria and clay minerals in seawater, focusing on their effect on Transparent Exopolymer Particles (TEP) production and organoclay aggregation. Field experiments in the Gulf of Maine and laboratory roller tank studies were conducted using natural microbial communities and model heterotrophic bacterial strains (Alteromonas sp. EZ55, Marinobacter adhaerens HP15, and Sulfitobacter sp. NAS-14.1). Results demonstrate that clay exposure significantly enhances TEP production by bloom-associated heterotrophic bacteria, with increases up to …

Supply And Consumption Of Dissolved Organic Phosphorus Across The Subtropical Indian Ocean, Corinne Richard

Honors Theses and Capstones

The Indian Ocean is an understudied region for marine phosphorus (P) biogeochemistry. Emerging evidence indicates marine phytoplankton can adapt to decreasing supplies of inorganic P, a required nutrient for growth, by alternatively utilizing organic forms of P. Here we investigate the dissolved organic phosphorus concentration ([DOP]) distribution across the southern Indian Ocean using observations collected on the I05 US GO-SHIP Cruise (2023) across ~33ºS latitude. We quantify the longitudinal variability of [DOP] in the upper 350 m of the Indian Ocean and infer its rate of biological consumption from surface waters, contributing as an organic nutrient to sustain marine autotrophs …

Novel Analytical Approaches For The Study Of Energy And Nutrient Flow In Streams, Michelle Catherine Kelly

Dissertations, Master's Theses and Master's Reports

This dissertation applied novel modeling, experimental and statistical approaches to overcome the challenges of measuring and analyzing energy and nutrient cycling in streams through 3 studies: (1) determining the predictors of respiration and denitrification in streams across the United States, (2) simultaneous estimation of denitrification and nitrogen (N) fixation rates, and (3) the impact of C lability metrics on the interpretation of C degradation in DOM incubation experiments. In the first study, I used predictive modeling approaches to show that respiration and denitrification were positively correlated across the landscape but were predicted by factors at different spatial scales. Denitrification rates …

Evaluating The Risk Posed By Gadolinium In The Grand River Watershed, Johann Memmel

Theses and Dissertations (Comprehensive)

Gadolinium (Gd) is a rare earth element (REE), primarily used in contrast agents for magnetic resonance imaging (MRI), with additional applications in metallurgy, phosphors, neutron shielding, and other niche applications. Both Gd and Gd-based contrast agents (GBCAs, the form used for MRIs) have been detected downstream of wastewater effluent discharges and there is currently little research into the risk this poses to aquatic ecosystems. This study investigated the potential environmental risks of Gd and GBCAs using the Grand River watershed (GRW) in southwestern Ontario as a model ecosystem due to it containing a variety of land uses (urban, industrial, agricultural) …

Permafrost Carbon: Progress On Understanding Stocks And Fluxes Across Northern Terrestrial Ecosystems, Claire C. Treat, Anna-Maria Virkkala, Eleanor Burke, Lori Bruhwiler, Abhishek Chatterjee, Joshua B. Fisher, Josh Hashemi, Frans-Jan W. Parmentier, Brendan M. Rogers, Sebastian Westermann, Jennifer D. Watts, Elena Blanc-Betes, Matthias Fuchs, Stefan Kruse, Avni Malhotra, Kimberley Miner, Jens Strauss, Amanda Armstrong, Howard E. Epstein, Bradley Gay, Mathias Goeckede, Aram Kalhori, Dan Kou, Charles E. Miller, Susan M. Natali, Youmi Oh, Sarah Shakil, Oliver Sonnentag, Ruth K. Varner, Scott Zolkos, Edward A.G. Schuur, Gustaf Hugelius

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Significant progress in permafrost carbon science made over the past decades include the identification of vast permafrost carbon stocks, the development of new pan-Arctic permafrost maps, an increase in terrestrial measurement sites for CO₂ and methane fluxes, and important factors affecting carbon cycling, including vegetation changes, periods of soil freezing and thawing, wildfire, and other disturbance events. Process-based modeling studies now include key elements of permafrost carbon cycling and advances in statistical modeling and inverse modeling enhance understanding of permafrost region C budgets. By combining existing data syntheses and model outputs, the permafrost region is likely a wetland methane …

Reducing Food Scarcity: The Benefits Of Urban Farming, S.A. Claudell, Emilio Mejia

Journal of Nonprofit Innovation

Urban farming can enhance the lives of communities and help reduce food scarcity. This paper presents a conceptual prototype of an efficient urban farming community that can be scaled for a single apartment building or an entire community across all global geoeconomics regions, including densely populated cities and rural, developing towns and communities. When deployed in coordination with smart crop choices, local farm support, and efficient transportation then the result isn’t just sustainability, but also increasing fresh produce accessibility, optimizing nutritional value, eliminating the use of ‘forever chemicals’, reducing transportation costs, and fostering global environmental benefits.

Imagine Doris, who is …

Wonderstone And Its Connection To Liesegang, Microbes, And Beyond, Haden S. Mandery

Department of Earth and Atmospheric Sciences: Dissertations, Theses, and Student Research

In the western and southwestern United States, the term wonderstone is used to describe volcanic, volcaniclastic, and sedimentary rocks with variegated banding produced by iron oxide mineralization or staining. This iron oxide mineralization is typically described as Liesegang banding. In this paper I will (1) test if the banding in wonderstone follows the spacing and width laws characteristic of Liesegang, (2) identify the source of iron that ultimately precipitated in the bands, and (3) examine the role that microbes played in the formation of the mineralization in these rocks. I conclude that the iron oxide mineralization is not Liesegang banding. …

The Discovery Of Diverse Picophytoplankton Populations In The Columbia And Willamette Rivers Using Flow Cytometry, Kylee M. Lamberson

Chemistry Undergraduate Departmental Honors Theses

As important primary producers, picophytoplankton determine the flow of carbon and energy in aquatic ecosystems. Picocyanobacteria are one picophytoplankton group known to be dominant in oceans and lakes, but they are still poorly understood in river systems. This project examined picophytoplankton communities in two distinct river systems: the Columbia and Willamette Rivers in Portland, Oregon. I aimed to characterize and quantify the picophytoplankton populations in the context of the environmental conditions of the two rivers. I used flow cytometry to detect cells based on their relative size and pigment fluorescence. I sampled nearly weekly for ten months to capture population …

Enhancing Our Understanding Of Ancient Oceans Through The Investigation Of Molybdenum Behavior Under Sulfidic Conditions, Rachel Faye Phillips

Open Access Theses & Dissertations

The most abundant trace metal in the ocean today, molybdenum (Mo), exhibits distinct behavior in oxygenated water, where it remains predominantly dissolved, compared to euxinic (i.e., oxygen-free and sulfidic) water, in which it is sequestered into the sediment. This dissimilar behavior allows us to use Mo concentrations and isotopic compositions in sediment to reconstruct marine oxygenation conditions throughout geologic history. However, Mo sequestration mechanisms under euxinic conditions remain unresolved, which limits the accuracy and precision of reconstructions made using Mo signatures in the rock record. For my doctoral research, I experimentally investigated abiotic and biotic Mo sequestration mechanisms under various …

Quantifying The Role Of Water Quality On Nitrogen Cycling In A Trophic Estuary, Kayla Gonzalez-Boy

Symposium of Student Scholars

Jobos Bay Estuary is an intertidal, tropical estuary located in southern Puerto Rico. The estuary covers about 12 km² and has a variety of habitats, such as seagrass beds, mangroves, mud flats, and coral reefs, which play important roles in sediment trapping and water quality maintenance. Seagrasses also serve as nursery and feeding grounds and provide shelter for macrofauna. Currently, the role of seagrasses and water quality on nitrogen (N) cycling in trophic estuaries is not well constrained. Understanding variations in sediment-based effects on N cycling rates and transformations, and how they are associated with water quality, is an …

Volcanic Diffuse Volatile Emissions Tracked By Plant Responses Detectable From Space, Robert R. Bogue, Peter M. J. Douglas, Joshua B. Fisher, John Stix

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Volcanic volatile emissions provide information about volcanic unrest but are difficult to detect with satellites. Volcanic degassing affects plants by elevating local CO2 and H2O concentrations, which may increase photosynthesis. Satellites can detect plant health, or a reaction to photosynthesis, through a Normalized Difference Vegetation Index (NDVI). This can act as a potential proxy for detecting changes in volcanic volatile emissions from space. We tested this method by analyzing 185 Landsat 5 and 8 images of the Tern Lake thermal area (TLTA) in northeast Yellowstone caldera from 1984 to 2022. We compared the NDVI values of the thermal area with …

Reply To: Beyond Microbial Carbon Use Efficiency, Feng Tao, Johannes Lehmann, Ying-Ping Wang, Lifen Jiang, Bernhard Ahrens, Kostiantyn Viatkin, Stefano Manzoni, Benjamin Z. Houlton, Yuanyuan Huang, Bruce A. Hungate, Serita D. Frey, Michael W. I. Schmidt, Markus Reichstein, Nuno Carvalhais, Philippe Ciais, Umakant Mishra, Gustaf Hugelius, Toby D. Hocking, Xingjie Lu, Zheng Shi, Ronald Vargas, Yusuf Yigini, Christian Omuto, Ashish A. Malik, Guillermo Peralta, Rosa Cuevas-Corona, Luciano E. Di Paolo, Isabel Luotto, Cuijuan Liao, Yi-Shuang Liang, Vinisa S. Saynes, Xiaomeng Huang

Faculty Publications

In their commentary, Xiao et al. cautioned that the conclusions on the critical role of microbial carbon use efficiency (CUE) in global soil organic carbon (SOC) storage in a paper by Tao et al. (2023) might be too simplistic. They claimed that Tao et al.’s study lacked mechanistic consideration of SOC formation and excluded important datasets. Xiao et al. brought up important points, which can be largely reconciled with our findings by understanding the differences in expressing processes in empirical studies and in models.

A New View Of Chlorophyll Dynamics In The Southern Mid-Atlantic Bight From A Two-Year High-Resolution Spray Glider Survey, Francesco Lane

OES Theses and Dissertations

The southern Mid-Atlantic Bight (MAB) near Cape Hatteras, NC, USA, is likely a hotspot for the episodic export of carbon-rich shelf waters to the open ocean. Over a 2 year period, from March 2017 to May 2019, Spray gliders repeatedly occupied transects, along the slope and across the shelf, generating high-resolution chlorophyll fluorescence (fChl) data in the southern MAB. This study implements an fChl calibration method utilizing remotely sensing ocean color as a standard. We validate the method’s utility by demonstrating a reduction in post-calibration cross-mission fChl variability and demonstrating close correspondence between the calibrated fChl data and an in …

Approaches To Assessing Nutrient Coupling In Open Ocean Datasets, James M. Moore, Claire P. Till

IdeaFest: Interdisciplinary Journal of Creative Works and Research from Cal Poly Humboldt

Nutrient coupling describes a process where the biogeochemical cycles of two elements are linked by being incorporated similarly into biomass. This paper uses data from the GEOTRACES GP16 cruise (Eastern Pacific Zonal Transect) to investigate the relationship between certain macronutrients generally coupled to trace elements in terms of their oceanic distributions with the notable exception of in an oxygen minimum zone: cadmium-phosphate and zinc-silicate. There are many methods applied to oceanographic data to correlate analyte concentrations; while they are often presented independently in literature, here we attempt to use them in conjunction for a more thorough interpretation. By compiling 1) …

What Is Microbial Dormancy, Mark D. Mcdonald, Carlos Owusu-Ansah, Jared B. Ellenbogen, Zachary D. Malone, Michael P. Ricketts, Steve E. Frolking, Jessica G. Ernakovich, Michael Ibba, Sarah C. Bagby, J. L. Weissman

Faculty Publications

Life can be stressful. One way to deal with stress is to simply wait it out. Microbes do this by entering a state of reduced activity and increased resistance commonly called ‘dormancy’. But what is dormancy? Different scientific disciplines emphasize distinct traits and phenotypic ranges in defining dormancy for their microbial species and system-specific questions of interest. Here, we propose a unified definition of microbial dormancy, using a broad framework to place earlier discipline-specific definitions in a new context. We then discuss how this new definition and framework may improve our ability to investigate dormancy using multi-omics tools. Finally, we …

Reply To: Contribution Of Carbon Inputs To Soil Carbon Accumulation Cannot Be Neglected, Feng Tao, Benjamin Z. Houlton, Serita D. Frey, Johannes Lehmann, Stefano Manzoni, Yuanyuan Huang, Lifen Jiang, Umakant Mishra, Bruce A. Hungate, Michael W. I. Schmidt, Markus Reichstein, Nuno Carvalhais, Philippe Ciais, Ying-Ping Wang, Bernhard Ahrens, Gustaf Hugelius, Toby D. Hocking, Xingjie Lu, Zheng Shi, Kostiantyn Viatkin, Ronald Vargas, Yusuf Yigini, Christian Omuto, Ashish A. Malik, Guillermo Peralta, Rosa Cuevas-Corona, Luciano E. Di Paolo, Isabel Luotto, Cuijuan Liao, Yi-Shuang Liang, Vinisa S. Saynes, Xiaomeng Huang, Yiqi Luo

Faculty Publications

In the accompanying Comment1, He et al. argue that the determinant role of microbial carbon use efficiency in global soil organic carbon (SOC) storage shown in Tao et al. (2023)2 was overestimated because carbon inputs were neglected in our data analysis while they suggest that our model-based analysis could be biased and model-dependent. Their argument is based on a different choice of independent variables in the data analysis and a sensitivity analysis of two process-based models other than that used in our study. We agree that both carbon inputs and outputs (as mediated by microbial processes) matter when predicting SOC …