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. …

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 …

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 …

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. …