Browsing by Author "Wilkins, Mike, committee member"
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Item Open Access Acid mine drainage impacts in the Upper Arkansas River Basin: a study of water quality, treatment efficiency, and predicted longevity(Colorado State University. Libraries, 2019) Moore, Megan, author; Covino, Tim, advisor; Ross, Matthew, committee member; Wilkins, Mike, committee member; Rhoades, Charles, committee memberMining activity in the Sugarloaf and Leadville mining districts of Leadville, Colorado has impaired water quality in the Upper Arkansas River Basin. Tributary and main channel waters are often out of compliance with state water quality standards, and stream flora and fauna as well as human use of these waterways is threatened by acid mine drainage. This study aims to describe the impact historical mining activity has had on the waters of the Upper Arkansas River Basin by characterizing water quality, analyzing metal removal efficiency from both active and passive treatment sites in the area, and estimating the time it will take for drainage from mining tunnels to naturally comply with state water quality standards. A comparison of instream dissolved concentrations of cadmium, copper, iron, lead, manganese, and zinc to state water quality standards shows waters of the Upper Arkansas River Basin are often out of compliance with chronic and/or acute standards. This is seen more frequently upstream from treatment sites and higher up in the tributary system than at tributary mouths or in the main channel of the Arkansas River. An examination of metal removal from the Leadville Mine Drainage Tunnel and Yak Tunnel water treatment plants along East Fork and California Gulch shows dissolved metal reduction between 33 and 100 percent compared with 0 to 84 percent at the passive Dinero Wetland Complex along Lake Fork. Finally, an analysis of projected longevity highlights the importance of clean-up plans for future mining projects with estimated impaired water quality continuing upwards of 2000 years at Yak Tunnel.Item Open Access Evaluating post-fire woody mulch effects on soil and stream nitrogen(Colorado State University. Libraries, 2024) Richardson, Mikaela, author; Kampf, Stephanie, advisor; Rhoades, Chuck, advisor; Ross, Matt, committee member; Wilkins, Mike, committee memberSevere wildfires often increase nitrogen (N) loss from burned watersheds, impacting downstream water quality, water treatability, and aquatic habitat. Woody mulch is commonly applied to mitigate soil erosion and enhance revegetation post-fire, but it also provides a source of labile carbon (C) that may stimulate microbial immobilization and limit N release from soils. The objective of our study was to evaluate whether mulch application influenced turnover and loss of soil C and N in laboratory leaching trials and hillslope field settings, and then compared post-fire C and N in streams draining mulched and unmulched catchments. In the laboratory, we quantified C and N inputs and leaching outputs from mulched and unmulched soil columns. Within the Cameron Peak fire burn scar in northern Colorado, we compared soil N availability and potential leaching losses between mulched and unmulched hillslope plots. We also measured C, N, and other chemical constituents in streams draining three mulched and three unmulched catchments. In the laboratory leaching studies, mulch added high concentrations of dissolved organic carbon (> 500 mg L-1) and decreased nitrate leaching from soil columns by 27% during repeated simulated rainfall events. In hillslope plots, mulching also reduced soil nitrate, with greater impacts following spring snowmelt when N losses from soils to streams was highest. However, the effect of mulching was not measurable at the catchment scale due to low application rates and mulch extent, paired with high topographic and geomorphic variability amongst the catchments. Our findings show that C inputs from woody mulch can influence soil N retention in burned watersheds when applied at a minimum rate of 5 Mg ha-1; however practical constraints on aerial application may make it challenging to apply enough mulch for any downstream response to be detectable. Coupled with physical erosion protection, the biogeochemical impacts of mulching may facilitate soil and vegetation recovery following severe wildfire and reduce post-fire N losses to streams if sufficiently applied. Therefore, further post-fire rehabilitation efforts should optimize mulch operations by prioritizing sensitive watersheds and treating them with adequate mulch.Item Open Access Evaluating the effects of fire on carbon and nitrogen biogeochemistry in forested ecosystems(Colorado State University. Libraries, 2023) Roth, Holly, author; Borch, Thomas, advisor; Henry, Chuck, committee member; Reynolds, Melissa, committee member; Prenni, Jessica, committee member; Wilkins, Mike, committee memberForests provide ecosystem services (e.g., carbon storage, nutrient processing, and water filtration) valued at ~$5 trillion per year which are vulnerable to disturbances such as wildfire. Although fires are a natural component of healthy forests, climate change has begun to increase the size, frequency, and severity of wildfires outside of their historic range. Expected increases in burn severity have implications for carbon (C) and nitrogen (N) cycling, with the potential to shift forests from C sinks to C sources due to long delays in tree re-establishment. There is great interest in resolving changes to soil organic matter (SOM) composition, especially organic nitrogen, to predict how forests respond to wildfires. Therefore, the purpose of the work included in this dissertation was to improve nitrogen analysis in fire-impacted forest systems and apply these methods to soil and water samples. In the following work, a suite of advanced analytical approaches were used to determine the molecular composition of SOM, which was evaluated for the impacts of severe wildfires on microbially-mediated SOM processing and water quality in fire-impacted watersheds. Field-based soil and water samples were collected from subalpine forests in the Colorado Rocky Mountains and investigated for shifts in the water-soluble and solid fractions of SOM in lodgepole pine-dominated forests and their influence on microbial processing and water quality was determined. The objectives of this study were to leverage ultrahigh mass spectrometry to improve N analysis in fire-impacted systems (Objective 1), determine the post-fire changes to surface water C and N chemistry in reducing conditions (Objective 2) and to characterize how fire severity influences SOM composition along soil burn severity gradients (Objective 3). Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) currently achieves the highest mass resolving power in the world, which allows for the study of complex mixtures with tens of thousands of compounds that are separated by the mass of an electron across a wide molecular weight range. The most widely used FT-ICR MS analytical approach uses negative-ion mode electrospray ionization (-ESI) to selectively ionize highly abundant carboxylic acids in SOM. The application of this approach has allowed for rigorous analysis of C composition; however, -ESI FT-ICR MS vastly underestimates N-dense species which are formed during combustion. The biases associated with ionization are propagated in chemical property calculations that are determined by elemental compositions and which must be fully understood for proper use in C and N cycling models. We compared traditional -ESI with positive-ion mode electrospray ionization (+ESI) of burned soil extracts and found that +ESI increased compositional coverage by 87%, including nearly 10,000 additional N species (Objective 1). We applied our +ESI FT-ICR MS findings on a burn severity gradient (low, moderate, and high severity) to evaluate the compositional changes to SOM with increasing severity, with a specific focus on organic nitrogen. We collected soils from burned lodgepole pine forests along the Colorado-Wyoming border from two depths to characterize changes to organic N chemistry. Since organic N is the most abundant form of soil N in conifer forests, a better understanding of post-fire organic N will help address a critical gap in our understanding of fire severity-induced changes in the molecular composition of soil organic nitrogen. Nuclear magnetic resonance spectroscopy and FT-ICR MS analysis showed that N content and aromaticity of water-extractable SOM (0-5 cm depth) increased with burn severity, while minimal changes to the 5-10 cm depth were observed. Heterocyclic N species are generally higher in toxicity compared to their non-nitrogenated counterparts, which prompted soil toxicity measurements. We used Microtox ® to determine that soil toxicity increased with increasing burn severity, which may be partly attributed to newly formed N-species (Objective 2). In conjunction with increased fire activity, North American beaver (C. canadensis) populations have steadily increased since the early 1900s. The ponds that beavers create slow or impound hydrologic and elemental fluxes, increase soil saturation, and have a high potential to transform redox active elements (e.g., oxygen, nitrogen, sulfur, and metals). While surface water runoff composition has been studied in many environments, the effects of reducing conditions (i.e., beaver ponds) on these products are not well known. We collected surface water and sediment samples to investigate the impact of beaver ponds on the chemical properties and molecular composition of dissolved forms of C and N, and the microbial functional potential encoded within these environments from a combination of FT-ICR MS and metagenomics. We found that N-containing compounds and aromaticity increased in the surface water of burned beaver ponds, and that C/N and O/C ratios decreased. Microbial communities within the ponds did not have the capacity to process aromatic species, but they did have the potential for anaerobic metabolism and the potential to respire on microbial necromass (Objective 3). Fires burn heterogeneously across the landscape, and overstory vegetation likely plays a large role both in the way fires burn and how soils recover post-fire. Site factors such as soil type affect the interactions of SOM with abiotic soil components and can have cascading effects on soil C storage, including SOM partitioning between particulate organic matter (POM) and mineral associated organic matter (MAOM). POM is generally considered to have a faster turnover time than MAOM, which is physically protected from microbial degradation. Soil under two common trees in Colorado (lodgepole pine and aspen) are known to differ in SOM quantity and composition, including their relative proportions of POM and MAOM but post-fire products in these soils are relatively uncharacterized. To determine the differences in post-fire SOM between aspen and pine soils, we collected soils from under aspen and pine stands and burned them in open-air pyrocosms to minimize environmental variables which confound field-based studies. We concluded that fire influenced the dissolved fraction of the soils, with higher concentrations of dissolved organic carbon, dissolved total nitrogen, ammonium-N, and nitrate-N in burned aspen soil extracts. To determine the implications for less bioavailable carbon fractions, we will determine %C and %N in soils that have only been dried and sieved, as well as separated into POM and MAOM. We will also characterize the dissolved fractions using FT-ICR MS and NMR to evaluate differences in soil functional groups. Complementary microbiome analyses will be performed to determine the implications of shifts in soil functionality for microbial processing and C and N sequestration. The novel application of +ESI in this dissertation allowed for the identification of increasingly N-dense species at high burn severities which were not previously observed in field samples. N-dense species are enriched under reducing conditions as they are unable to be processed by local microbial communities. In total, these findings contribute to our understanding of newly formed organic C and N species in soils, with implications for microbial activity in fire-affected watersheds.Item Embargo The adventures of Lactobacillus acidophilus: evaluating a recombinant probiotic rotavirus vaccine from host and microbial perspectives(Colorado State University. Libraries, 2024) Gilfillan, Darby L., author; Vilander, Allison, advisor; Dean, Gregg, advisor; Abdo, Zaid, committee member; Wilkins, Mike, committee memberRotavirus is an enteric infection of global importance causing diarrheal-associated illness that can be fatal in young children and the elderly. There is a gap in vaccine efficacy between high- and lower-middle-income countries (LMIC) with LMIC often experiencing diminished vaccine-conferred protection. Rotaviruses, whether attenuated vaccine strains or primary pathogens, do not exist in isolation within the host's gastrointestinal tract. Other actors present within the microbiome can inhibit or augment vaccine efficacy by influencing the vaccine itself or the mucosal immune response. Understanding and exploiting interactions between host and microbe is a promising frontier for mucosal vaccinology. This dissertation will explore the probiotic Lactobacillus acidophilus (LA) as a vaccine platform for a microbiome-minded, next-generation approach to rotavirus immunization. We developed and confirmed a novel recombinant LA (rLA) vaccine expressing rotavirus antigens of the VP8* domain from the rotavirus EDIM VP4 capsid protein along with the adjuvants FimH and FliC. Rotavirus naïve adult BALB/cJ mice were orally immunized followed by murine rotavirus strain ECWT viral challenge. Antirotavirus serum IgG and antigen-specific antibody-secreting cell responses were detected in rLA-vaccinated mice. A day after the oral rotavirus challenge, fecal antigen shedding was significantly decreased in the rLA group. These results demonstrate the potential of rLA platforms to generate protective mucosal immunity. Additionally, metagenomic and metatranscriptomic analyses of exogenous probiotic administration within the murine small intestine revealed differences between LA genome expression and the whole metatranscriptome in recombinant- versus wild-type LA-vaccinated mice. LA genome expression in rLA-vaccinated mice had decreased carbohydrate metabolism and increased stress responses. We also detected antigen and adjuvant transcript expression only in mice exposed to the rLA platform. There was relative enrichment of probiotic species in the wild-type group with overall increased α- and β-diversity in the buffer compared to probiotic groups. These results highlight the interactions between an exogenous probiotic and the host microbiome at an immune inductive site. Finally, we used an in vitro model to evaluate modulation of polyunsaturated fatty acid (PUFA) metabolism on host cell and (r)LA interactions. Both (r)LA and PUFA treatments significantly changed pathogen recognition receptor expression. (r)LA treatment mainly altered inflammatory cytokine expression while PUFA supplementation primarily influenced mucin expression. rLA strains adhered more to host cells than wild-type LA while the rLA strain expressing both antigens and adjuvants may better prevent E. coli adhesion. These results and methodologies provide a starting point for further investigation into PUFA metabolism as a mechanism for improving rLA immunogenicity and competition against other enteric pathogens.