Biogeochemistry Commons^™

Gone With The Wind: Soil Moisture Effects On Gaseous Nitrogen Removal From Wastewater, Faith L. Anderson

Senior Honors Projects

Onsite wastewater treatment systems (OWTS), or septic systems, release nitrogen (N), which can be detrimental to aquatic ecosystems. The final step in the treatment of wastewater is dispersal onto a drainfield, where it percolates through the soil. Part of the N is removed from wastewater and released into the atmosphere as N₂ and N₂O by denitrification, which requires anoxic conditions. Previous studies looking at the effect of soil water-filled pore space (WFPS) on denitrification using clean water with a high level of dissolved O₂ (DO) have identified a minimum of 60% WFPS for denitrification to take …

Photocatalytic Reduction Of Fumarate To Succinate On Zns Mineral Surfaces, Ruixin Zhou, Marcelo I. Guzman

Chemistry Faculty Publications

The reductive tricarboxylic acid (rTCA) cycle is an important central biosynthetic pathway that fixes CO₂ into carboxylic acids. Among the five reductive steps in the rTCA cycle, the two-electron reduction of fumarate to succinate proceeds nonenzymatically on the surface of photoexcited sphalerite (ZnS) colloids suspended in water. This model reaction is chosen to systematically study the surface photoprocess occurring on ZnS in the presence of [Na₂S] (1–10 mM) hole scavenger at 15 °C. Experiments at variable pH (5–10) indicate that monodissociated fumaric acid is the primary electron acceptor forming the monoprotic form of succinic acid. The following …

The Ecologist's Field Guide To Sequence-Based Identification Of Biodiversity, Simon Creer, Kristy Deiner, Serita D. Frey, Dorota Porazinska, Pierre Taberlet, W. Kelley Thomas, Caitlin Potter, Holly M. Bik

Faculty Publications

The past 100 years of ecological research has seen substantial progress in understanding the natural world and likely effects of change, whether natural or anthropogenic. Traditional ecological approaches underpin such advances, but would additionally benefit from recent developments in the sequence-based quantification of biodiversity from the fields of molecular ecology and genomics. By building on a long and rich history of molecular taxonomy and taking advantage of the new generation of DNA sequencing technologies, we are gaining previously impossible insights into alpha and beta diversity from all domains of life, irrespective of body size. While a number of complementary reviews …

Quantifying The Global N2o Emissions From Natural Ecosystems Using A Mechanistically-Based Biogeochemistry Model, Tong Yu

Open Access Theses

Nitrous oxide (N2O) has a great influence on atmospheric chemistry and climate. It is not only a major greenhouse gas, but also one of the largest ozone-depleting substances emitted from the biosphere. Process-based biogeochemistry modeling constrained by site-level observations is a feasible approach to quantifying its emissions at large temporal and spatial scales. This study developed a process-based biogeochemistry model of N2O emissions based on an extant biogeochemistry model, the Terrestrial Ecosystem Model (TEM). The model development includes: 1) incorporating the effects of physical conditions on both nitrification and denitrification and 2) implementing principles of the stoichiometry of carbon and …

Iron Concretions In The Cretaceous Dakota Formation, Anthony Kohtz, Richard Kettler, David Loope

UCARE: Research Products

The Cretaceous Dakota Formation contains abundant iron oxide concretions. The precursors to the iron concretions are siderite (FeCO3) nodules that formed in a reducing floodplain environment. A variety of concretion morphologies formed when the precursor siderite nodules were dissolved by oxidizing groundwater in a paleoaquifer. Iron-oxidizing bacteria are able to oxidize aqueous Fe(II) to Fe(III) oxy-hydroxide at microaerophilic and neutrophilic conditions. This study investigated these concretions to determine if there was a microbial element in their formation and to characterize the concretion morphologies present in the Dakota. This is important for complete paleoenvironment interpretations and astrobiology pursuits.

The Marine Cyanate Cycle, Brittany Widner

OES Theses and Dissertations

Cyanate (OCN-) is a reduced nitrogen compound with the potential to serve as a nitrogen and carbon source for marine microbes. Evidence from genomes and culture studies indicated that several marine cyanobacterial groups, including representatives of the globally important genera Synechococcus and Prochlorococcus, might be capable of cyanate assimilation. However, prior to this study, the distribution, bioavailability, and production pathways of cyanate were unknown in natural systems due to the absence of a sensitive cyanate assay; and the ability of organisms to assimilate cyanate on relevant timescales was unknown because we lacked a suitable tracer for measuring uptake. I developed …

A Comparison Of Soil Hydrothermal Properties In Zonal And Uniform Tillage Systems Across The Us Corn Belt, Alwyn Williams, Adam S. Davis, Patrick M. Ewing, A. Stuart Grandy, Daniel A. Kane, Roger T. A. Koide, David A. Mortensen, Richard G. Smith, Sieglinde S. Snapp, Kurt A. Spokas, Anthony C. Yannarell, Nicholas R. Jordan

Faculty Publications

Zonal tillage (e.g. ridge tillage, RT) separates management of row and inter-row positions, while non-zonal tillage (e.g. chisel plough, CP) applies management uniformly across a field. This may have large effects on soil hydrothermal properties, affecting soil processes and crop development. We examined the effects of RT versus CP on soil hydrothermal conditions under maize (Zea mays L.) at four sites spanning the US Corn Belt over two growing seasons (2012–2013). We also investigated whether RT, as a result of changes in hydrothermal conditions, could stimulate greater soil nitrogen (N) availability during peak maize N demand. We captured wide variation …

Patterns And Sources Of Anthropogenic Contaminants In The Otter Creek Watershed, Madison County, Kentucky, Elijah D. Wolfe, Walter S. Borowski, Jacob L. Robin

EKU Faculty and Staff Scholarship

Stream systems are often affected by anthropogenic contaminants that affect water quality and stream ecosystems. Land use determines the type and quantity of contaminants present in natural waters. The Otter Creek watershed (170 km²; Madison County, Kentucky) consists predominantly of pasture and rural housing, with some cropland. The basin also receives runoff from the town of Richmond and a sewage treatment plant operates within the watershed. We measured concentrations of nutrients (phosphate, ammonium, nitrate) and fecal microbes to discover levels of anthropogenic contaminants affecting water quality and to identify contaminant sources.

We sampled 4 times in the summer …

Soil Functional Zone Management: A Vehicle For Enhancing Production And Soil Ecosystem Services In Row-Crop Agroecosystems, Alwyn Williams, Daniel A. Kane, Patrick M. Ewing, Lesley W. Atwood, Andrea Jilling, Meng Li, Yi Lou, Adam S. Davis, A. Stuart Grandy, Sheri C. Huerd, Mitchell C. Hunter, Roger T. Koide, David A. Mortensen, Richard G. Smith, Sieglinde S. Snapp, Kurt A. Spokas, Anthony C. Yannarell, Nicholas R. Jordan

Faculty Publications

There is increasing global demand for food, bioenergy feedstocks and a wide variety of bio-based products. In response, agriculture has advanced production, but is increasingly depleting soil regulating and supporting ecosystem services. New production systems have emerged, such as no-tillage, that can enhance soil services but may limit yields. Moving forward, agricultural systems must reduce trade-offs between production and soil services. Soil functional zone management (SFZM) is a novel strategy for developing sustainable production systems that attempts to integrate the benefits of conventional, intensive agriculture, and no-tillage. SFZM creates distinct functional zones within crop row and inter-row spaces. By incorporating …

Marine Ecoregion And Deepwater Horizon Oil Spill Affect Recruitment And Population Structure Of A Salt Marsh Snail, Steven C. Pennings, Scott Zengel, Jacob Oehrig, Merryl Alber, T. Dale Bishop, Donald R. Deis, Donna Devlin, A. Randall Hughes, John J. Hutchens, Jr., Whitney M. Kiehn, Caroline R. Mcfarlin, Clay L. Montague, Sean P. Powers, C. Edward Proffitt, Nicholle Rutherford, Camille L. Stagg, Keith Walters

University Faculty and Staff Publications

Marine species with planktonic larvae often have high spatial and temporal variation in recruitment that leads to subsequent variation in the ecology of benthic adults. Using a combination of published and unpublished data, we compared the population structure of the salt marsh snail, Littoraria irrorata, between the South Atlantic Bight and the Gulf Coast of the United States to infer geographic differences in recruitment and to test the hypothesis that the Deepwater Horizon oil spill led to widespread recruitment failure of L. irrorata in Louisiana in 2010. Size-frequency distributions in both ecoregions were bimodal, with troughs in the distributions consistent …

Juvenile Survival And Adult Return As A Function Of Freshwater Rearing Life History For Coho Salmon In The Klamath River Basin, Molly Gorman

Cal Poly Humboldt theses and projects

The Scott and Shasta rivers, Klamath River tributaries, experience spatial disparity in habitat quality in spring and summer as a result of historical and current land-use. Juvenile Coho Salmon (Oncorhynchus kisutch) born in the upper tributary reaches often rear in natal streams before migrating to sea. However, those born in the lower reaches often encounter unsuitable habitat and emigrate during their first spring to seek non-natal rearing habitats. It is assumed that these early outmigrants are population losses. This study evaluated first-summer survival, and contribution to the adult population, of non-natal rearing juveniles in the Klamath River Basin. …

An Alignment-Free "Metapeptide" Strategy For Metaproteomic Characterization Of Microbiome Samples Using Shotgun Metagenomic Sequencing, Damon H. May, Emma Timmins-Schiffman, Molly P. Mikan, H. Rodger Harvey, Elhanan Borenstein, Brook L. Nunn, William S. Noble

OES Faculty Publications

In principle, tandem mass spectrometry can be used to detect and quantify the peptides present in a microbiome sample, enabling functional and taxonomic insight into microbiome metabolic activity. However, the phylogenetic diversity constituting a particular microbiome is often unknown, and many of the organisms present may not have assembled genomes. In ocean microbiome samples, with particularly diverse and uncultured bacterial communities, it is difficult to construct protein databases that contain the bulk of the peptides in the sample without losing detection sensitivity due to the overwhelming number of candidate peptides for each tandem mass spectrum. We describe a method for …

Perchlorate Variations Over 300 Years: Influence Of Human Activities, Volcanic Eruptions And Bolide Events, Kari Peterson

Electronic Theses and Dissertations

Perchlorate, which derives from both anthropogenic and natural sources in the current environment, constitutes a significant health risk to humans because it competitively inhibits iodine uptake by the thyroid gland. Thus, there has been considerable interest in reducing the human exposure to environmental perchlorate by limiting the release of perchlorate from anthropogenic sources. However, a lack of understanding of the relative contributions from anthropogenic and natural sources has prevented widespread regulation. A 300-year ice core perchlorate record from Summit Station, Greenland (1700-2007 C.E.) that extends beyond the onset of the Industrial Revolution (1850 C.E.) is used to assess the anthropogenic …

Mobility Of Escherichia Coli Within Karst Terrains, Kentucky, Usa, Ashley M. Bandy

Theses and Dissertations--Earth and Environmental Sciences

Bacterial contamination of karst aquifers is a concern as water quality across the globe deteriorates in the face of decreasing water security. This study examined the transport and attenuation of two non-virulent isolates of Escherichia coli in relation to traditional groundwater tracers such as rhodamine WT dye and latex microspheres in two karst regions in Kentucky. Differential movement between the four tracers was observed in both epikarst and karst aquifer traces, with differences in behavior dependent on flow conditions. Attenuation was greater for the bacterial isolate containing the iha gene, compared to the isolate containing the kps gene. Microspheres of …

Effects Of Epichloë Coenophiala−Tall Fescue Symbiosis On Plant-Microbe-Soil Interactions In A Temperate Pasture, Lindsey C. Slaughter

Theses and Dissertations--Plant and Soil Sciences

Plants interact in myriad ways with microorganisms to influence ecosystem processes such as nutrient cycling, which can regulate ecosystem response to global change. One important plant-microbe symbiosis occurs between cool-season grasses and asexual fungal Epichloë endophytes, such as tall fescue (Schedonorus arundinaceus) and Epichloë coenophiala. Because the common toxic strain of the endophyte (CTE) harms grazing livestock, non-livestock toxic endophyte (NTE) strains have been developed and are increasingly deployed in pastures. Little is known about how these symbioses impact other plant-microbe interactions and microbe-mediated soil processes in grassland ecosystems. I conducted three studies to determine how E. …

Synthesis Of Satellite Microwave Observations For Monitoring Global Land-Atmosphere Co2 Exchange, Lucas Alan Jones

Graduate Student Theses, Dissertations, & Professional Papers

This dissertation describes the estimation, error quantification, and incorporation of land surface information from microwave satellite remote sensing for modeling global ecosystem land-atmosphere net CO₂ exchange. Retrieval algorithms were developed for estimating soil moisture, surface water, surface temperature, and vegetation phenology from microwave imagery timeseries. Soil moisture retrievals were merged with model-based soil moisture estimates and incorporated into a light-use efficiency model for vegetation productivity coupled to a soil decomposition model. Results, including state and uncertainty estimates, were evaluated with a global eddy covariance flux tower network and other independent global model- and remote-sensing based products.

Evaluating The Biogeochemical Functioning Of A Constructed Fen On The Post-Mining Landscape Of Athabasca Oil Sands Region, Fort Mcmurray, Alberta, Canada, Felix C. Nwaishi

Theses and Dissertations (Comprehensive)

Peatlands have a unique biogeochemical function, characterized by an imbalance between the rates of biomass accumulation and decomposition. These characteristics facilitate the ability of peatlands to support the sequestration of nutrients and carbon. In disturbed peatlands, these functions are compromised. Thus, reclamation targets amongst other key functions, the recovery of biogeochemical functioning. These functions could serve as a measure of recovery to conditions that are present in natural analogues. This thesis examines the recovery of microbially-mediated nutrient transformation processes in a fen peatland that was constructed on a post-mining landscape in the Athabasca oil sands region, Fort McMurray, Alberta. The …

The Role Of Amino Acids In The Nitrogen Cycle Of Peatlands, Tia Scarpelli

Dissertations, Master's Theses and Master's Reports

Future release of carbon from peatlands in response to climate change may be impacted by nitrogen limitation. The current study considers the role of amino acids as a nitrogen source in peatlands. The total free amino acid (TFAA) concentration for peats ranged from 0-2.3 µM, and leucine was the primary contributor. The dominance of sedge or ericaceous shrub plant types did not significantly impact the TFAA pool. Ammonium concentrations were much greater than TFAA and nitrate concentrations. TFAA concentrations were greatest in spring and least in fall. The springtime maxima and summer decrease in concentrations were simulated in a modeling …

Mycorrhizal Roots In A Temperate Forest Take Up Organic Nitrogen From 13c- And 15n-Labeled Organic Matter, Matthew A. Vadeboncoeur, Andrew P. Ouimette, Erik A. Hobbie

All Materials

Background and Aims

The importance of the uptake of nitrogen in organic form by plants and mycorrhizal fungi has been demonstrated in various ecosystems including temperate forests. However, in previous experiments, isotopically labeled amino acids were often added to soils in concentrations that may be higher than those normally available to roots and mycorrhizal hyphae in situ, and these high concentrations could contribute to exaggerated uptake.

Methods

We used an experimental approach in which we added ¹³C-labeled and ¹⁵N-labeled whole cells to root-ingrowth cores, allowing proteolytic enzymes to release labeled organic nitrogen at a natural rate, as …

Thermodynamic Modeling Of Aqueous Geochemistry Of Chlorine Salts: Application To Stability And Habitability Of Liquid Brines On Mars, Amira Elsenousy

Graduate Theses and Dissertations

The WCL (Wet Chemistry Lab) instrument on board the Mars’s Phoenix Lander has identified the soluble ionic composition of the soil at the landing site. Two important ions were detected at the landing site; perchlorates (ClO4-) with a concentration of ~ 2.4 wt% and chlorides (Cl-) with a concentration of 0.54 wt%. Between chloride and perchlorate ions three other oxidized ions exist and called chlorine ions: hypochlorite ClO - (ox. state +1), chlorite ClO2- (ox. state +3) and chlorate ClO3- (ox. state +5). These oxidized ions might be existed as intermediate species on the surface of Mars but remained undetected. …

Convergence Of Microbial Assimilations Of Soil Carbon, Nitrogen, Phosphorus And Sulfur In Terrestrial Ecosystems, Xiaofeng Xu, Dafeng Hui, Anthony W. King, Xia Song, Peter E. Thornton, Lihua Zhang

Biology Faculty Research

How soil microbes assimilate carbon-C, nitrogen-N, phosphorus-P and sulfur-S is fundamental for understanding nutrient cycling in terrestrial ecosystems. We compiled a global database of C, N, P and S concentrations in soils and microbes and developed relationships between them by using a power function model. The C:N:P:S was estimated to be 287:17:1:0.8 for soils and 42:6:1:0.4 for microbes. We found a convergence of the relationships between elements in soils and in soil microbial biomass across C, N, P and S. The element concentrations in soil microbial biomass follow a homeostatic regulation curve with soil element concentrations across C, N, P …

Mercury In Coniferous And Deciduous Upland Forests In Northern New England, Usa: Implications Of Climate Change, J. B. Richardson, A. J. Friedland

Dartmouth Scholarship

Climatic changes in the northeastern US are expected to cause coniferous stands to transition to deciduous stands over the next hundred years. Mercury (Hg) sequestration in forest soils may change as a result. In order to understand potential effects of such a transition, we studied aboveground vegetation and soils at paired coniferous and deciduous stands on eight mountains in Vermont and New Hampshire, USA.

A Comparative Analysis Of Portable X-Ray Fluorescence Spectrometry And Stable Isotopes In Assessing Ancient Coastal Peruvian Diets, Theresa Jane Gilbertson

USF Tampa Graduate Theses and Dissertations

This dissertation explores a cross-cultural analysis of the dietary signatures of four coastal cultures of prehistoric Peru. A combination of elemental analysis based on portable x-ray fluorescence spectrometry (pXRF), testing trace elements presented in 209 individuals’ skulls representing the Nazca (38), Cañete (33), Lima (40), and Moche (98) valleys and/or cultures of the first millennium AD, is weighed in conjunction with isotope ratio mass spectrometry (IRMS) to analyze human bone collagen and bone apatite derived from a portion of the individuals represented in the Nazca, Cañete, and Lima cranial samples.

Evidence from the results of both tests are weighed using …

In Situ Studies Of Limestone Dissolution In A Coastal Submarine Spring, Rachel Marie Schweers

USF Tampa Graduate Theses and Dissertations

Limestone dissolution in karst environments is likely due to geochemistry of the water, the actions of microbial communities, and the effect of water flow. We explored the rate of limestone dissolution and will examine here the microbial communities associated with the limestone. A conduit within the brackish cave, Double Keyhole Spring, on the coast of central west Florida was the site of the experiment. PVC pipes (5cm x 16cm) were filled with crushed limestone that was screened to a 1.9cm – 2.54cm size range. There were three treatments (5 replicates each): Control - sealed autoclaved controls with limestone and conduit …

Patterns Of Anthropogenic Nutrient Contaminants In The Otter Creek Watershed, Madison County, Kentucky, Elijah D. Wolfe, Walter S. Borowski, Jacob L. Robin

EKU Faculty and Staff Scholarship

We measured nutrient concentrations within the Otter Creek watershed (Madison County, Kentucky) to: (1) discover levels of anthropogenic contaminants affecting the water quality; (2) compare these measurements to a national data set; and (3) identify nutrient sources. The watershed mainly drains rural land characterized by cattle grazing, but also drains the town of Richmond. We sampled throughout the watershed to gain a representative perspective of nutrient levels and specifically targeted localities of suspected anthropogenic nutrient sources. Water samples were passed through a 0.45 mm filter, placed in pre-acidified vials, and measured one to two days after collection. Nutrients – ammonium, …

Changes In Litter Quality Caused By Simulated Nitrogen Deposition Reinforce The N-Induced Suppression Of Litter Decay, Linda T. A. Van Diepen, Serita D. Frey, Christopher M. Sthultz, Eric W. Morrison, Rakesh Minocha, Anne Pringle

Faculty Publications

Rates of nitrogen (N) deposition are increasing in industrialized and rapidly developing nations. Simulated N deposition suppresses plant litter decay rates, in particular for low quality (high lignin) litter. Litter quality is a primary driver of litter decomposition; however, it is not clear how changes in litter quality caused by long-term ecosystem exposure to chronic N additions interact with altered soil N-availability to influence litter decay dynamics. To document the effects of simulated N deposition on litter quality, we conducted a meta-analysis of available litter nutrient data from simulated N deposition experiments in temperate forests. To directly test whether changes …

Source-Specific Molecular Signatures For Light-Absorbing Organic Aerosols, Amanda Susan Willoughby

Chemistry & Biochemistry Theses & Dissertations

Organic aerosols (OA) are universally regarded as an important component of the atmosphere based on quantitative significance as well as the far-reaching impact they have on global climate forcing and human health. Despite the acknowledged importance, OA amounts and impacts remain the largest uncertainties regarding radiative forcing estimates. Incomplete chemical characterization of aerosol organic matter (OM) and a lack of concrete source apportionment is a major source of this uncertainty. The primary focus of this study is to provide much needed molecular details regarding ambient OA from key emission sources, and establish links between molecular and optical properties.

Complete chemical …

Development Of Enzymatic Biofuel Cell For Glucose Sensor Application, Ashar Turky Abd

Theses and Dissertations

For several decades, biological fuel cells have drawn significant attention as alternative power sources since they are environmentally friendly and less expensive, compared to the conventional noble metal-based fuel cells. Some enzymatic biocatalysts such as glucose dehydrogenase and glucose oxidase consume glucose as fuel, generating electric currents if paired with an oxygen reduction electrode. While microbial biofuel cells inevitably require a physical barrier or proton exchange membrane between anode and cathode, enzyme-based biofuel cells allow a membraneless or single compartment design, since enzymes are very selective on redox species. For example, glucose dehydrogenase oxidizes the glucose fuel only, while it …

Is Atmospheric Phosphorus Pollution Altering Global Alpine Lake Stoichiometry?, Janice Brahney, Natalie Mahowald, Daniel S. Ward, Ashley P. Ballantyne, Jason C. Neff

Ecosystem and Conservation Sciences Faculty Publications

Anthropogenic activities have significantly altered atmospheric chemistry and changed the global mobility of key macro-nutrients. Here we show that contemporary global patterns in nitrogen (N) and phosphorus (P) emissions drive large hemispheric variation in precipitation chemistry. These global patterns of nutrient emission and deposition (N:P) are in turn closely reflected in the water chemistry of naturally oligotrophic lake (r² = 0.81, p < 0.0001). Observed increases in anthropogenic N deposition play a role in nutrient concentrations (r² = 0.02, p < 0.05); however, atmospheric deposition of P appears to be major contributor to this pattern (r² = 0.65, p < 0.0001). Atmospheric simulations indicate a global increase in P deposition by 1.4 times the pre-industrial rate largely due to increased dust and biomass burning emissions. Although changes in the mass flux of global P deposition are smaller than for N, the impacts on primary productivity may be greater because, on average, one unit of increased P deposition has 16 times the influence of one unit of N deposition. These stoichiometric considerations, combined with the evidence presented here, suggest that increases in P deposition may be a major driver of alpine Lake trophic status, particularly in the Southern Hemisphere. These results underscore the need for the broader scientific community to consider the impact of atmospheric phosphorus deposition on the water quality of naturally oligotrophic lakes.

Predicting Landscape-Scale Co 2 Flux At A Pasture And Rice Paddy With Long-Term Hyperspectral Canopy Reflectance Measurements, J. H. Matthes, S. H. Knox, C. Sturtevant, O. Sonnentag

Dartmouth Scholarship

Measurements of hyperspectral canopy reflectance provide a detailed snapshot of information regarding canopy biochemistry, structure and physiology. In this study, we collected 5 years of repeated canopy hyperspectral reflectance measurements for a total of over 100 site visits within the flux footprints of two eddy covariance towers at a pasture and rice paddy in northern California. The vegetation at both sites exhibited dynamic phenology, with significant interannual variability in the timing of seasonal patterns that propagated into interannual variability in measured hyperspectral reflectance. We used partial least-squares regression (PLSR) modeling to leverage the information contained within the entire canopy reflectance …