Biogeochemistry Commons^™

The Microbiome Stress Project: Toward A Global Meta-Analysis Of Environmental Stressors And Their Effects On Microbial Communities, Jennifer D. Rocca, Marie Simonin, Joanna R. Blaszczak, Jessica G. Ernakovich, Sean M. Gibbons, Firas S. Midani, Alex D. Washburne

Faculty Publications

Microbial community structure is highly sensitive to natural (e.g., drought, temperature, fire) and anthropogenic (e.g., heavy metal exposure, land-use change) stressors. However, despite an immense amount of data generated, systematic, cross-environment analyses of microbiome responses to multiple disturbances are lacking. Here, we present the Microbiome Stress Project, an open-access database of environmental and host-associated 16S rRNA amplicon sequencing studies collected to facilitate cross-study analyses of microbiome responses to stressors. This database will comprise published and unpublished datasets re-processed from the raw sequences into exact sequence variants using our standardized computational pipeline. Our database will provide insight into general response patterns …

Characterizing Freshwater Phytoplankton Dynamics With Electro-Optical Remote Sensing, Michael Sayers

Dissertations, Master's Theses and Master's Reports

Freshwater lakes are an important component contributing to ecosystem health and biodiversity on local, regional, and global scales. And while lakes only represent <5% of the global surface area, they are often very productive systems which contribute significantly to carbon cycling dynamics and freshwater fish production on a number of spatial scales. Due to the remote location and sheer size of some of these lakes it has proven difficult to adequately document changes in water quality. Significant challenges exist to adequately monitor water quality, and in particular phytoplankton dynamics, over large spatial and temporal scales using traditional in situ methods. Satellite electro-optical remote sensing offers a potential tool to provide better characterization of phytoplankton dynamics for a variety of freshwater systems. This work resulted in an approach to quantify global summer phytoplankton abundance using a newly developed remote sensing derived chlorophyll-a product. This product was also used in conjunction with a newly created carbon fixation model to assess global freshwater phytoplankton production which provided new insights into the role freshwater systems play in the …

Spatiotemporal Dynamics Of Nitrogen And Carbon Biogeochemistry In A Wetland-Stream Sequence, Patrick E. Hurley

Graduate Student Theses, Dissertations, & Professional Papers

Studies of aquatic ecosystems often segregate streams from the influential ponds, lakes, and wetland zones that act as important transitions between terrestrial and fluvial systems. Across the aquatic landscape, these zones interact to form linked ecosystems that function as discrete nutrient processing domains, shifting biogeochemical signals due to spatial and temporal variability in hydrologic and biologic controls. Using a mass-balance approach, we profiled nutrient dynamics along a 23-km wetland-stream sequence over three seasons. Hydrologic, morphologic, and biologic conditions, as well as landscape attributes, were quantified to determine potential controls on biogeochemical cycling in a tributary of the Upper Clark Fork …

Carbon In The Deep Biosphere: Forms, Fates, And Biogeochemical Cycling, Susan Q. Lang, Magdalena R. Osburn, Andrew D. Steen

Faculty Publications

Building on the synthesis of carbon reservoirs in Earth's subsurface, this chapter focuses on the forms, cycling, and fate of the carbon supporting microbial life in the terrestrial and marine subsurface. As the subsurface is estimated to host a vast reservoir of life on Earth, identifying the carbon compounds that life uses for energy and growth is key to understanding ecosystem functioning in the past and at present, and also for extrapolating these findings to the search for life in the universe. This chapter highlights advances in quantifying small carbon compounds, measuring rates of carbon turnover, and the fate of …

The Role Of Small Reservoirs In Reducing Reactive N Export Via Denitrification, Margaret Phillips, Wil Wollheim

Honors Theses and Capstones

Reactive nitrogen (N), which harms ecosystem health, has been increasing in the biosphere, leading to higher N export to coastal ecosystems. Although man-made reservoirs can be significant sources of greenhouse gases, they can also retain N, thus reducing N export. Because many dams are relics from industrial hydropower, their removal is becoming increasingly common. It is therefore crucial to understand the ecological tradeoffs of man-made reservoirs. While previous studies have examined nutrient budgets and denitrification at inputs and outputs of large reservoirs, small reservoir dynamics remain understudied. In this study, we measured inputs and outputs of NO₃ and N …

Fishers' Ecological Knowledge And Stable Isotope Analysis: A Social-Ecological Systems Approach To Endangered Species Conservation, Kathryn Rose Wedemeyer-Strombel

Open Access Theses & Dissertations

Identifying developmental habitat is essential for understanding population structure and species resiliency, especially for critically endangered species. In long-lived, oceanic, migratory animals such as sea turtles, elucidating developmental grounds is particularly difficult. When data are deficient or challenging to acquire, scientists often lean towards traditional quantitative methods when a social-ecological systems approach could better provide crucial baseline data and guiding information. Fishers’ ecological knowledge (FEK), the combination of experiential and culturally transmitted knowledge, is expert knowledge and should be treated as such. In 2008, FEK led to the “rediscovery” of the critically endangered eastern Pacific (EP) population of hawksbill sea …

Biogeochemical Response To Vegetation And Hydrologic Change In An Alaskan Boreal Fen Ecosystem, Danielle L. Rupp

Dissertations, Master's Theses and Master's Reports

Boreal peatlands store approximately one third of the earth’s terrestrial carbon, locked away in currently waterlogged and frozen conditions. Peatlands of boreal and arctic ecosystems are affected increasingly by shifting hydrology caused by climate change. The consequences of these relatively rapid ecosystem changes on carbon cycling between the landscape and the atmosphere could provide an amplifying feedback to climate warming. Alternatively, the advancement of terrestrial vegetation into once waterlogged soils could uptake carbon as a sink. Previous work suggests that fens will become an increasingly dominant landscape feature in the boreal. However, studies investigating fens, their response to hydrologic and …

Resuscitation Of Microalgae From Mississippi River Plume Sediments, Chase C. Chaplin, Marnie Tabor, Israel A. Marquez, Kanchan Maiti, Jeffrey W. Krause

Gulf and Caribbean Research

No abstract provided.

Compositions And Structures Of Particulate And Colloidal Organic Matter In Aquatic Environment By Advanced Analytical Techniques, Yong Ran, Dainan Zhang, Shujie Hu, Yu Yang, Jingdong Mao

Chemistry & Biochemistry Faculty Publications

Dissolved, colloidal and particulate organic matter (DOM, COM and POM) is important in the global carbon cycle and knowledge of their sources and structures can be critical to understanding their roles in biogeochemical cycles. This study explored the sources and chemical structures of COM and POM samples from the Pearl River Basin, China by elemental, chlorophyll a (Chl a), radiocarbon and stable carbon isotopic analyses, NMR techniques, and Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) analysis. The chemical and nano-sclae structures of two ultrafiltered dissolved organic matter (UDOM) samples from surface seawater of the Pacific and Atlantic Ocean …

Utilizing Lipid Biomarkers To Understand The Microbial Community Structure Of Deep Subsurface Black Shale Formations, Rawlings Akondi

Graduate Theses, Dissertations, and Problem Reports (ETD)

The deep subsurface environment has been known to host microbes as early as 1926 and has also been suggested to potentially account for as much as 50% of the Earth`s biomass. Researchers have shown that microbes alter their membrane lipid components in response to physiological stress, producing stress indicative lipid biomarkers. However, little effort has been made to understand the subsurface microbial community of the shale ecosystem which is increasingly being exploited and altered by addition of drilling and hydraulic fluids to meet our growing energy needs. Phospholipid fatty acids (PLFAs) are microbial lipid biomarkers and are found in all …

Compound-Specific Isotope Analysis Of Amino Acids In Biological Tissues: Applications In Forensic Entomology, Food Authentication And Soft-Biometrics In Humans, Mayara Patricia Viana De Matos

Graduate Theses, Dissertations, and Problem Reports (ETD)

In this work we demonstrate the power of compound-specific isotope analysis (CSIA) to analyze proteinaceous biological materials in three distinct forensic applications, including: 1) linking necrophagous blow flies in different life stages to their primary carrion diet; 2) identifying the harvesting area of oysters for food authentication purposes; and 3) the ability to predict biometric traits about humans from their hair.

In the first application, we measured the amino-acid-level fractionation that occurs at each major life stage of Calliphora vicina (Robineau-Desvoidy) (Diptera: Calliphoridae) blow flies. Adult blow flies oviposited on raw pork muscle, beef muscle, or chicken liver. Larvae, pupae …

Clarifying The Interpretation Of Carbon Use Efficiency In Soil Through Methods Comparison, Kevin M. Geyer, Paul Dijkstra, Robert Sinsabaugh, Serita D. Frey

Faculty Publications

Accurate estimates of microbial carbon use efficiency (CUE) are required to predict how global change will impact microbially-mediated ecosystem functions such as organic matter decomposition. Multiple approaches are currently used to quantify CUE but the extent to which estimates reflect methodological variability is unknown. This limits our ability to apply or cross-compare published CUE values. Here we evaluated the performance of five methods in a single soil under standard conditions. The microbial response to three substrate amendment rates (0.0, 0.05, and 2.0 mg glucose-C g−1 soil) was examined using: 13C and 18O isotope tracing approaches which estimate CUE based on …

Seasonal Soil Carbon Fluxes In Transitioning Agricultural Soils In Central Washington State: Relations To Land-Use, Environmental Factors And Soil Carbon-Nitrogen Characteristics, Brandon Kautzman

All Master's Theses

Changing agricultural land-use practices to increase soil carbon sequestration contributes to climate change mitigation and improved food security by moving CO₂ from the atmosphere into soil as soil organic carbon (SOC). In 2016, a farm in Thorp, Washington, Spoon Full Farm, began converting land historically farmed using conventional methods of tillage and synthetic fertilizers to conservation farming methods with direct seeding and organic soil amendments with a goal of sequestering carbon in the soil. This project evaluates relationships of soil CO₂ respiration and net ecological exchange (NEE) with land-use types, seasonal environmental factors (air temperature, relative humidity, soil …

Colloidal And Truly Dissolved Metal(Loid)S In Wastewater Lagoons And Their Removal With Floating Treatment Wetlands, Lauren Sullivan

Graduate Student Theses, Dissertations, & Professional Papers

Climate change is predicted to cause continuing declines in late-season streamflow, thus increasing the relative contribution of wastewater effluent to surface water flows. Wastewater effluent represents a critical point source of metal and metalloid contamination to aquatic ecosystems and wastewater lagoons are the most common wastewater treatment system in the rural United States. Although the fraction of total wastewater metals and metalloids in "dissolved" forms (defined here asnm) likely drives the potential for negative effects on receiving waters, this broad operational definition lumps truly dissolved solutes (nm) with small colloids and nanomaterials (1-450 nm; hereafter colloids). This size distinction may …

Influence Of Ligand Complexation On Nickel Toxicity, Speciation And Bioavailability In Marine Waters, Samantha Sherman

Theses and Dissertations (Comprehensive)

Currently there are no site-specific bioavailability-based prediction models for assessing the impacts of nickel (Ni) in marine environments although there are indications that these may be warranted. The aim of this research was to characterize the complexation of Ni in relation to toxicity and speciation. Various complexing ligands were used, and it was predicted that the binding affinity (logKf) of ligands would be inversely correlated to toxicity based on dissolved Ni concentrations ([NiD]) but that on a free ion concentration ([Ni2+]) basis, toxicity would not vary. A two-phased approach was used; the first was a proof of principle where synthetic …

Using Paleolimnology To Establish Baseline Conditions For Metal Contaminants In Advance Of Proposed Mining To Inform A Northern Community-Led Aquatic Monitoring Program, Tłı̨Chǫ Lands, Northwest Territories, Canada., James Telford

Theses and Dissertations (Comprehensive)

The Marian Watershed Stewardship Program (MWSP), a community-driven aquatic ecosystem monitoring program, was developed by the Tłı̨chǫ Government to address concerns regarding the cumulative impacts of multiple potential stressors. In particular, the MWSP aims to develop methods that will be effective for detecting potential pollution from the proposed cobalt-gold-copper-bismuth NICO mine within Tłı̨chǫ Lands. In collaboration with the MWSP, paleolimnological methods and geochemical normalization are used to establish pre-mine baselines of lake sediment metals concentrations in the Marian River watershed prior to mine development. This baseline framework can be used to assess for pollution from surficial sediment once the mine …

Evaluating Stable Isotope And Geochronologic Techniques For Paleoclimate Reconstruction: Case Study Of The Santa Cruz Formation, Argentina, Robin B. Trayler

Boise State University Theses and Dissertations

Stable isotope analysis has become the method of choice for many studies investigating the paleoecology and paleoclimate of fossil mammal faunas. While organic tissues (collagen, keratins, proteins) persist for < 10⁵ years highly mineralized tooth enamel is resistant to alteration and degradation and faithfully preserves its isotopic composition for millions (> 10⁶) years. Reconstructing past climates from these records relies on both understanding both micro-scale mechanisms of isotope incorporation into individual teeth, and macro-scale changes in isotope compositions over hundreds of thousands or millions of years. In this dissertation I address three questions.

First, how does the geometry and …

Investigating Smoke Aerosol Emission Coefficients Using Modis Active Fire And Aerosol Products – A Case Study In The Conus And Indonesia, Xiaoman Lu, Xiaoyang Zhang, Fangjun Li, Mark Cochrane

Global Land Surface Season Data Sets

This data set is in relation to the paper of the same title, which has been submitted to the Journal of Geophysical Research: Biogeosciences.

Instructions for viewing the data in “Readme.txt”

Relating Cyanobacteria And Physicochemical Water-Quality Properties In Willow Creek Lake, Nebraska, 2012–14, David L. Rus, Brent M. Hall, Steven A. Thomas

United States Geological Survey: Water Reports and Publications

Document abstract

Cyanobacteria (also referred to as blue-green algae) are naturally present members of phytoplankton assemblages that may detract from beneficial uses of water because some strains produce cyanotoxins that pose health hazards to people and animals. Cyanobacteria populations observed in Willow Creek Lake during 2012 through 2014 were compared to external nutrient loading from the Willow Creek drainage basin and several other physicochemical properties within the lake, including internal nutrient loading. This report is part of a cooperative study between the United States Geological Survey, the Lower Elkhorn Natural Resources District, the Nebraska Department of Environmental Quality, the Nebraska …

Reduced Carbon Use Efficiency And Increased Microbial Turnover With Soil Warming, Jianwei Li, Gangsheng Wang, Melanie A. Mayes, Steven D. Allison, Serita D. Frey, Zheng Shi, Xiao-Ming Hu, Yiqi Luo, Jerry M. Melillo

Faculty Publications

Global soil carbon (C) stocks are expected to decline with warming, and changes in microbial processes are key to this projection. However, warming responses of critical microbial parameters such as carbon use efficiency (CUE) and biomass turnover (rB) are not well understood. Here, we determine these parameters using a probabilistic inversion approach that integrates a microbial-enzyme model with 22 years of carbon cycling measurements at Harvard Forest. We find that increasing temperature reduces CUE but increases rB, and that two decades of soil warming increases the temperature sensitivities of CUE and rB. These temperature sensitivities, which are derived from decades-long …

Are The Oxygen Isotope Values Of The Late Cretaceous Western Interior Seaway Different From The Open Ocean?, Camille H. Dwyer, Corinne Myers, Viorel Atudorei

Shared Knowledge Conference

The Western Interior Seaway (WIS) was a North American epicontinental sea that was connected to the open ocean through the passage of the northern Boreal Sea and the southern Tethys Sea from the early Albian (~113 million years ago) to the early Paleogene (~65 million years ago). The WIS began to recced and lost its connection to the southern Tethys Sea in the late Campanian (~72 million years ago). In the early Paleogene, the WIS dried up completely. The oxygen isotopic composition (δ18O) of benthic bivalves was measured from the upper Campanian and lower Maastrichtian (75 million years ago to …

Groundwater Contamination At Coal Ash Deposit Sites In Kentucky, Brandon Rose

Scholars Week

No abstract provided.

Clio: An Autonomous Vertical Sampling Vehicle For Global Ocean Biogeochemical Mapping, Michael V. Jakuba, John A. Breier, Daniel Gomez-Ibanez, Kaitlyn Tradd, Mak A. Saito

School of Earth, Environmental, & Marine Sciences Faculty Publications

We report the design, sea trials, and scientific operation of a fast vertical profiling autonomous underwater vehicle, called Clio, designed to cost-effectively improve the understanding of marine microorganism ecosystem dynamics on a global scale by collecting high-volume filter samples autonomously, in contrast to conventional techniques that require a ship’s wire.

Characterizing Diatom Biofilms And Their Influence On The Sand Biogeochemistry Of High Energy Beaches, Logan C. Jarrell

Honors Theses

High energy beaches are among the most dynamic ecological settings on Earth. Compared to mudflats, diatoms of high energy beaches have been more neglected in the literature, particularly true of the intertidal biofilms that form and dissipate with nutrient cycling and light intensity over the tidal cycle. Although short lived, the productivity of these biofilms may be critical to the organic-poor sand. Through sediment coring and subsequent analyses of the uppermost sand of three suspected biofilm stations—non-runnel, runnel crest, and runnel trough—along with seemingly bare sand as a control, this study sought to verify the presence of diatom biofilms and …

Guidelines And Considerations For Designing Field Experiments Simulating Precipitation Extremes In Forest Ecosystems, Heidi Asbjornsen, John L. Campbell, Katie A. Jennings, Matthew A. Vadeboncoeur, Cameron Mcintire, Pamela H. Templer, Richard P. Phillips, Taryn L. Bauerle, Michael C. Dietze, Serita D. Frey, Peter M. Groffman, Rosella Guerrieri, Paul J. Hanson, Eric P. Kelsey, Alan K. Knapp, Nathan G. Mcdowell, Patrick Meir, Kimberly A. Novick, Scott V. Ollinger, Will T. Pockman, Paul G. Schaberg, Stan D. Wullschleger, Melinda D. Smith, Lindsey E. Rustad

Faculty Publications

Precipitation regimes are changing in response to climate change, yet understanding of how forest ecosystems respond to extreme droughts and pluvials remains incomplete. As future precipitation extremes will likely fall outside the range of historical variability, precipitation manipulation experiments (PMEs) are critical to advancing knowledge about potential ecosystem responses. However, few PMEs have been conducted in forests compared to short-statured ecosystems, and forest PMEs have unique design requirements and constraints. Moreover, past forest PMEs have lacked coordination, limiting cross-site comparisons. Here, we review and synthesize approaches, challenges, and opportunities for conducting PMEs in forests, with the goal of guiding design …

Cover Crops May Cause Winter Warming In Snow-Covered Regions, Danica L. Lombardozzi, Gordon B. Bonan

Faculty Publications

Cover crops, grown between cash crops when soil is fallow, are a management strategy that may help mitigate climate change. The biogeochemical effects of cover crops are well documented, as they provide numerous localized benefits to farmers. We test potential biogeophysical climate impacts of idealized cover crop scenarios by assuming that cover crops are planted offseason in all crop regions throughout North America. Our results suggest that planting cover crops increases wintertime temperature up to 3 °C in central North America by decreasing albedo in regions with variable snowpack. Cover crops with higher leaf area indices increase temperature more by …

Sulfur (34S/32S) Isotope Composition Of Gypsum And Implications For Deep Cave Formation On The Nullarbor Plain, Australia, Matej Lipar, Mateja Ferk, Sonja Lojen, Milo Barham

International Journal of Speleology

Large deep caves with little relation to surface topography are distinctive karst features on the Nullarbor Plain of Australia. The presence of gypsum deposits and chemoautotrophic bacteria within the caves have been suggested as evidence for cave formation and (or) enlargement via sulfuric acid speleogenesis. To test this hypothesis, the stable sulfur isotope compositions (δ³⁴S) of both cave gypsum and surface gypsum were measured. Analyses yielded relatively high, positive δ³⁴S values from both cave gypsum and surface gypsum, arguing against gypsum genesis via microbial chemoautotrophy, and more broadly, sulfuric acid speleogenesis. Instead, the gypsum is interpreted …

Investigation Of Biogeochemical Mechanisms Of Greenhouse Gas Production In The Urban Hudson River Estuary, Brian Alan Brigham

Dissertations, Theses, and Capstone Projects

Coastal megacities deposit significant amounts of carbon (C), nitrogen (N) and other pollutants into surrounding waters. These inputs, including wastewater and surface water runoff, may affect estuarine and adjacent wetland biogeochemical cycles, microbial production and ultimately greenhouse gas (GHG) efflux. In many megacities pollutant loading is typically greatest after periods of precipitation when the volume of wastewater and storm water runoff exceeds local sanitation capacity, resulting in the discharge of raw sewage into adjacent waters. These combined sewage overflow (CSO) events have received considerable attention primarily due to their potential impact on human health and eutrophication. However, whether these events …

High-Dimensional Isotope Relationships, Yuyang He

LSU Doctoral Dissertations

High-dimensional isotope relationships describes the relationships of two or more element or position-specific (PS) elements in the same molecule or ion. It provides us more powerful tools to study reaction mechanisms and dynamics. Chapter 1 is about dual or multiple stable isotope relationship on δ-δ (or δ'-δ') space. While temporal data sampled from a closed-system can be treated by a Rayleigh Distillation Model (RDM), spatial data should be treated by a Reaction-Transport Model (RTM). Here we compare the results of a closed-system RDM to a RTM for systems with diffusional mass transfer by simulating the trajectories on nitrate's δ'^{18 …}

Geotraces And Beyond: Studies Of Trace Elements In Coastal And Open Ocean Waters With An Emphasis On The Effects Of Oxygen Depletion And Hydrothermal Plumes, Peng Ho

Dissertations

We investigated various dissolved trace element (dTE) distributions in two distinct areas: the coastal northern Gulf of Mexico and the eastern tropical Pacific Ocean.

A multi-year (2007‒2011) chemical time series of eight stations in the western Mississippi Sound (MS) and northwestern Mississippi Bight (MB) was undertaken to examine the factors affecting chemical distributions in this dynamic region. Key findings include the frequent development of bottom water hypoxia in MB during late spring-summer, the likely contribution of submarine groundwater discharge (SGD) to the material flows, and observation of effects of episodic events including tropical storms and the opening of the Bonnet …