L'extraction de la tourbe pour en produire des substrats horticoles entraine la perte de leur capacité à séquestrer le carbone (C) dans les sols. Cependant, depuis plus d’une trentaine d’années, de nombreuses tourbières se sont vues restaurées et dans certains cas des mares sont intégrées. Les mares de tourbières sont présentes surtout dans les régions côtières et maritimes et sont généralement émettrices de C, à l’inverse des tourbières. Or, les mares sont des micro-habitats ayant un grand potentiel lié à la biodiversité et jouent ainsi un rôle très important pour de nombreuses espèces. De manière générale, la mesure du succès de la restauration des mares se concentre surtout sur le retour des espèces végétales typiques des mares naturelles et la présence d’un niveau d’eau constant à l’année. Très peu d’études se concentrent sur la biogéochimie des mares pour évaluer le succès de la restauration. Mon projet de recherche vise à évaluer le succès de la création des mares dans les projets de restauration de tourbière en utilisant des variables biogéochimiques. La recherche vise donc à identifier les différences biogéochimiques entre les mares créées et naturelles en plus de déterminer la trajectoire biogéochimique des mares créées dans le temps. Pour ce faire, nous avons mesuré différentes variables biogéochimiques telles le pH, les concentrations d’azote (N), de phosphore (P), de carbone organique dissout (DOC), de cations basiques – calcium (Ca), sodium (Na), magnésium (Mg) et potassium (K) et des gaz dissouts - méthane (CH4), dioxyde de carbone (CO2) et protoxyde d’azote (N2O) -. L’échantillonnage s’est fait dans 62 mares réparties au sein de 7 tourbières situé au Québec et au Nouveau-Brunswick : des mares naturelles et des mares créées il y a entre 3 et 22 ans. Les mares naturelles et créées ont des caractéristiques biogéochimiques différentes, et ce sans prendre en compte l’année de création. De ce fait, l’eau des mares créées est moins acide (pH >5) et plus concentrée en nutriments - N et P - que les mares naturelles. Cependant, les mares créées les plus anciennes ont tendance à se rapprocher des caractéristiques biogéochimiques des mares naturelles où la variation de la nappe phréatique et par le fait même la profondeur des mares viendraient jouer un rôle important sur les variables biogéochimiques. Des mares créées plus profondes et plus grandes pourraient ainsi permettre une présence d’eau permanente sans qu’elles s’assèchent durant l’été et ainsi favoriser le retour des conditions biogéochimiques similaires aux mares naturelles. / The extraction of peat to produce horticultural substrates leads to the loss of their ability to sequester carbon (C) in soils. However, over the past 30 years, many peatlands have been restored and open-water pools have been incorporated in some cases. Pools are naturally present in some bogs, especially in coastal and maritime regions, and are generally net C emitters, unlike peatlands. Pools are known to be micro-habitats with great potential for biodiversity and play a very important role for many species. In general, the measurement of the success of pool creation focuses on the return of bog plant species and a constant presence of water throughout the year. Currently, very few studies focus on the biogeochemistry of created pools to assess success. My research project uses biogeochemical variables to evaluate the success of created pools in peatland restoration projects. The research aims to identify biogeochemical differences between created and natural pools and to determine the biogeochemical trajectory of created pools over time. We measured different biogeochemical variables such as pH, nitrogen (N), phosphorus (P), dissolved organic carbon (DOC), base cations - calcium (Ca), sodium (Na), magnesium (Mg) and potassium (K) and dissolved gases - methane (CH4), carbon dioxide (CO2) and nitrous oxide (N2O) -. Sampling was done in 62 pools located in 7 peatlands in Quebec and New Brunswick. We sampled both natural pools and pools created between 3 and 22 years ago. Natural and created pools have different biogeochemical characteristics, without considering the year of creation. Water in created pools is less acidic (pH >5) and more concentrated in nutrients - N and P - than in natural pools. However, the oldest created pools tend to be closer to the biogeochemical characteristics of natural pools. The variation of the water table and the depth of the pools play an important role for the return towards natural biogeochemical characteristics. Deeper and larger created pools could allow a permanent water presence during dry periods in summer and thus promote the return of biogeochemical conditions similar to natural pools.

Master of Science / Department of Biology / John M. Blair / Anthropogenic activities impact ecosystems in numerous direct and indirect ways, affecting the cycling of carbon (C) and nitrogen (N) on local, regional and global scales. North America tallgrass prairie is an ecosystem profoundly altered by anthropogenic activities, with most native prairie converted to alternate land uses or heavily impacted by other environmental changes. While aboveground responses to anthropogenic drivers have received much attention, the responses of belowground biota, ecological processes, and nutrient allocation to land management and environmental change are poorly documented, especially over long timeframes. This research builds upon a long-term experiment (the Belowground Plot Experiment) initiated in 1986 at Konza Prairie Biological Station (Manhattan, KS). I utilized a subset of treatments to address the effects of annual burning vs. fire suppression and/or chronic N additions on soil C and N dynamics and microbial communities in tallgrass prairie. I measured a suite of soil variables related to C and N cycling during the 2012 growing season, including total soil C and N, microbial biomass C and N, in situ net N mineralization, potential N mineralization, in situ CO2 efflux, and potentially mineralizable soil C. I also assessed changes in microbial community composition using microbial phospholipid fatty acids (PLFA) profiles. Annual burning significantly (p≤0.05) increased the soil C:N ratio and in situ CO2 efflux, while decreasing potential ammonification and nitrification rates. Annual burning also increased total PLFA mass and relative abundance of fungi. Chronic N addition (100 kg N ha-1 year-1) significantly reduced the soil C:N ratio, while increasing total soil N and potential nitrification and ammonification rates. Chronic N addition reduced potential C mineralization, microbial biomass C and N, and altered microbial community composition by increasing abundance of bacterial PLFAs and reducing fungal PLFAs. Sampling date also significantly affected many variables. These results indicate that different fire regimes and chronic N enrichment over decades affects soil C and N pools and transformations, as well as microbial biomass and composition. In total, this study highlights the importance of long-term ecological research and identifies likely changes in tallgrass prairie nutrient dynamics and soil microbial communities under increased N and frequent burning.

Doctor of Philosophy / Department of Agronomy / Gary M. Pierzynski / The bioavailability of Pb and Zn is linked to the solubility of solid phases and other soil chemical characteristics, which is associated with their environmental risk, suggesting that in situ stabilization of these elements can be accomplished by influencing their chemistry. However, more research is needed to investigate the effectiveness of different soil amendments on reducing Pb and Zn bioavailability. A lab study was conducted to evaluate the effects of five different P amendments and time on Pb/Zn speciation in a contaminated soil using synchrotron-based techniques, while a field investigation studied the effects of composted beef manure on plant biomass production and the influence on microbial function, size, and community shifts. In the lab study, the Pb-phosphate mineral plumbogummite was found as an intermediate phase of pyromorphite formation, which has not been documented until now. Additionally, all fluid and granular P sources were able to induce Pb-phosphate formation, but fluid phosphoric acid (PA) was the most effective with time and distance from the treatment. However, acidity from PA increased the prescence of soluble Zn species, which can have negative environmental consequences. Granular phosphate rock (PR) and triple super phosphate (TSP) reacted to generate both Pb- and Zn-phosphates, with TSP being more effective at greater distances than PR. In the field study, compost additions of 269 Mg ha[superscript]1 significantly decreased bioavailable Zn, while increasing estimated available water, plant nutrients, and plant biomass as compared to a contaminated control and low addition of compost (45 Mg ha[superscript]1) over three years. Additionally, compost additions of 269 Mg ha[superscript]1 significantly increased microbial enzyme activities, nitrification, and microbial biomass over the contaminated control through the duration of the study. Increases in microbial activity and biomass are related to increases in total C, available water, and extractable P, while negative relationships were found with electrical conductivity and with bioavailable Zn. The addition of lime or lime plus bentonite with compost did not further reduce metal availability, increase plant biomass, or improve the size or function of microbial communities. High compost additions caused a slight shift in microbial community structure according to phospholipids fatty acid analysis. Increases in the mole percents of both Gram-positive (Gm[superscript]+) and Gram negative (Gm[superscript]-) bacteria were found depending on site. Microbial biomass of Gm[superscript]+, Gm[superscript]-, and fungi were also increased by high compost additions. Results indicate that large additions of compost are needed to increase microbial biomass, improve microbial activity, and re-establish a healthy vegetative community. This study proposes that organic matter and P amendments can be used to stabilize and reduce the bioavailability of heavy metals in soils and mine waste materials, but must be managed carefully and intelligently.

Doctor of Philosophy / Department of Chemical Engineering / Larry E. Erickson / Chlorinated solvents are the second most ubiquitous contaminants, next to petroleum hydrocarbons, and many are carcinogens. Tetrachloroethylene or perchloroethene (PCE) has been employed extensively in the dry cleaning industry and carbon tetrachloride (CT) has been used as a fumigant in grain storage facilities. In this work, remediation feasibility studies were conducted by mesocosm experiments; a chamber was divided into six channels and filled with soil, and plants were grown on top. Each channel was fed with contaminated water near the bottom and collected at the outlet, simulating groundwater flow conditions. The contaminants were introduced starting from March 12, 2004. PCE was introduced at a concentration of about 2 mg/L ([similar to]12 [Mu]moles/L) in three channels, two of them with alfalfa plants and the other with grass. CT was introduced at a concentration of about 2 mg/L ([similar to]13 [Mu]moles/L) in the other three channels, two of them with alfalfa plants and the other with grass. After the system had attained steady state, the concentrations of PCE and CT at inlet and outlet were monitored and the amount of PCE and CT disappearing in the saturated zone was studied. Since no degradation products were found at the outlet after about 100 days, one channel-each for PCE and CT (with alfalfa) was made anaerobic by adding one liter of 0.2 % glucose solution. The glucose solution was fed once every month starting from July 1, 2004 and continued until February 2005. From October 1, 2004, one liter of 0.1 % emulsified soy oil methyl esters (SOME) was fed to two other channels (with alfalfa), one exposed to PCE and another exposed to CT. The SOME addition dates were the same as that for glucose. The outlet liquid of the channel fed with PCE and SOME started to contain some of the degradation compounds of PCE; however, the extent of degradation was not as great as that of the glucose fed channel. No degradation compounds were observed in the outlet solution of the channel (grass grown on top) in which no carbon and energy supplements were added. Similar trend was observed in the CT fed channels also. KB-1, a commercially available microbial culture (a consortium of dehalococcoides) that degrades dichloroethene (DCE), was added through the inlet of the PCE fed channels, but this did not lead to sufficient conversion of DCE. Addition of KB-1 at well 3, located approximately in the middle of the channel, had a greater impact in the degradation of DCE, in both glucose and SOME amended channels, compared to addition at the inlet. KB-1 culture added to the channel was active even 155 days later, suggesting that there is sustainable growth of KB-1 when provided with suitable conditions and substrates. A pilot field study was conducted for remediation of a tetrachloroethylene (PCE) contaminated site at Manhattan, KS. The aquifer in the pilot study area has two distinct zones, termed shallow zone and deep zone, with groundwater velocities of about 0.3 m/day and 0.1 m/day. Prior to the pilot study, PCE concentration in groundwater at the pilot study area was about 15 mg/L (ppm) in the deep zone and 1 mg/L in the shallow zone. Nutrient solution comprising soy oil methyl esters (SOME), lactate, yeast extract and glucose was added in the pilot study area for biostimulation, on August 18, 2005. Potassium bromide (KBr) was added to the nutrient solution as a tracer. PCE was converted to DCE under these conditions. To carry out complete degradation of PCE, KB-1, a consortium of Dehalococcoides, and a second dose of nutrient solution were added on October 13, 2005. After addition of KB-1, both PCE and DCE concentrations decreased. Nutrients were again injected on March 3, 2006 (with KBr) and on August 1, 2006. The total chlorinated ethenes (CEs) have decreased by about 80 % in the pilot study area due to bioremediation. Biodegradation of CEs continued for a long time (several months) after the addition of nutrients. The insoluble SOME may be retained at the feeding area and provide a long time source of electron donors. Biostimulation and bioaugmentation of PCE contaminated soil and groundwater was evaluated in the laboratory and this technique was implemented successfully in the pilot field study. Modeling of the tracer study was performed using an advection-dispersion equation (ADE) and traditional residence time distribution (RTD) methods. The dispersion coefficient, groundwater velocity and hydraulic conductivity were estimated from the experimental data. The groundwater velocities vary from 1.5 cm/d to 10 cm/d in the deep zone and 15 cm/d to 40 cm/d in the shallow zone. The velocities estimated from the 2004 tracer study and 2005 tracer study were higher compared to the velocity estimated from the 2006 tracer study, most likely because of microbial growth and product formation that reduced the hydraulic conductivity. Based on data collected from several wells the hydrologic parameter values obtained from tracer studies appear to vary spatially.

Master of Science / Department of Biology / Walter K. Dodds / Human-induced stressors such as increased nitrogen (N) loadings, altered watershed land-use, and biodiversity losses are a few of the numerous threats to aquatic systems. Prairie streams experience natural disturbances, such as flooding and desiccation, which may alter responses to anthropogenic stressors. Denitrification, the dissimilatory reduction of NO3- to N gas (N2O or N2), is the only permanent form of N removal from terrestrial or aquatic ecosystems, and is important in mitigating N pollution to streams and downstream waters. Little is known about the relationships between denitrification and riparian prairie vegetation or large consumers. In the first chapter, I used outdoor mesocosms to determine the impact of a grazing minnow, Campostoma anomalum, on structural and functional responses of prairie streams to a simulated flood, focusing on denitrification. In terrestrial ecosystems, grazing can stimulate denitrification, but this has not been studied in streams. Ammonium (NH4+) enrichments, used to simulate fish excretion, alleviated N limitations on denitrification. Both fish and NH4+ affected algal biomass accrual, but only fish affected algal filament lengths and particulate organic matter. In a second experiment, I examined the impact of woody vegetation expansion, a primary threat to tallgrass prairie, on riparian and benthic denitrification. Expansion of woody vegetation in these grasslands is due primarily to altered fire regimes, which historically inhibited woody vegetation growth. To determine the effect of woody vegetation expansion on benthic and riparian denitrification, woody vegetation was removed from the riparian zone of a grazed and an ungrazed watershed. Both soil and benthic denitrification rates from this removal buffer were compared to rates in grassy or woody riparian zones. Riparian soil denitrification was highly seasonal, with greatest rates occurring during early spring, and rates being low throughout the remainder of the year. Benthic denitrification was also temporally variable but did not exhibit seasonal trends, suggesting benthic denitrification is driven by factors other than water temperature. Removal of woody vegetation stimulated soil and benthic denitrification rates over rates found in naturally vegetated riparian zones. Elevated N loadings will continue to affect aquatic ecosystems, and these effects may be exacerbated by biodiversity losses or changing riparian vegetation.

Climate change is predicted to be the most pronounced in high latitude ecosystems, however very little is known about their vulnerability to the projected warmer temperatures. In particular, natural organic matter (NOM) in the high latitude cryosphere which includes dissolved organic matter (DOM) and cryoconite organic matter (COM) from glaciers and soil organic matter (SOM) in permafrost, is highly susceptible to climate change which may lead to severe consequences on both local and global carbon biogeochemical cycles. Examination of DOM in glacier ice by a novel 1H nuclear magnetic resonance (NMR) water suppression pulse sequence at its natural abundance revealed and quantified the composition and the organic constituents in ice samples from Antarctica. 1H NMR spectra of samples from several glaciers were acquired and compared to the dominant fluorescent DOM fraction. This comprehensive approach showed that glacier ice DOM was mainly composed of small, labile biomolecules associated with microbes. Examination of the organic debris found on glacier surfaces (COM) from both Arctic and Antarctic glaciers were determined to be derived from microbes. Samples from Arctic glaciers were more chemically heterogeneous with small inputs of plant-derived material detected after targeted extractions. Therefore the COM carbon composition was determined to be dependent on the local glacier environment, suggesting a site specific contribution to the carbon cycle. Finally, the distribution of extracted branched glycerol dialkyl glycerol tetraether (GDGT)microbial membrane lipids and the deuterium incorporation of plant-wax n-alkane biomarkers extracted from dated permafrost SOM (paleosols) were independently applied for Canadian Arctic climate reconstruction during the last glacial maximum. Overall, the branched GDGT based temperature reconstructions from the Arctic paleosols reconstruct higher temperatures, likely when bacterial activity was optimal. The deuterium composition of the C29 n-alkane plant lipids appears to integrate an average annual signal. Further analysis by both non-selective NMR spectroscopic and targeted biomarker techniques on these paleosol samples revealed that the major vegetative sources from this paleoecosystem originated from woody and non-woody angiosperms. This thesis demonstrates several novel analytical characterization techniques, along with the major sources and composition of NOM in the cryosphere while demonstrating its use in paleoclimate applications.

Climate change is predicted to be the most pronounced in high latitude ecosystems, however very little is known about their vulnerability to the projected warmer temperatures. In particular, natural organic matter (NOM) in the high latitude cryosphere which includes dissolved organic matter (DOM) and cryoconite organic matter (COM) from glaciers and soil organic matter (SOM) in permafrost, is highly susceptible to climate change which may lead to severe consequences on both local and global carbon biogeochemical cycles. Examination of DOM in glacier ice by a novel 1H nuclear magnetic resonance (NMR) water suppression pulse sequence at its natural abundance revealed and quantified the composition and the organic constituents in ice samples from Antarctica. 1H NMR spectra of samples from several glaciers were acquired and compared to the dominant fluorescent DOM fraction. This comprehensive approach showed that glacier ice DOM was mainly composed of small, labile biomolecules associated with microbes. Examination of the organic debris found on glacier surfaces (COM) from both Arctic and Antarctic glaciers were determined to be derived from microbes. Samples from Arctic glaciers were more chemically heterogeneous with small inputs of plant-derived material detected after targeted extractions. Therefore the COM carbon composition was determined to be dependent on the local glacier environment, suggesting a site specific contribution to the carbon cycle. Finally, the distribution of extracted branched glycerol dialkyl glycerol tetraether (GDGT)microbial membrane lipids and the deuterium incorporation of plant-wax n-alkane biomarkers extracted from dated permafrost SOM (paleosols) were independently applied for Canadian Arctic climate reconstruction during the last glacial maximum. Overall, the branched GDGT based temperature reconstructions from the Arctic paleosols reconstruct higher temperatures, likely when bacterial activity was optimal. The deuterium composition of the C29 n-alkane plant lipids appears to integrate an average annual signal. Further analysis by both non-selective NMR spectroscopic and targeted biomarker techniques on these paleosol samples revealed that the major vegetative sources from this paleoecosystem originated from woody and non-woody angiosperms. This thesis demonstrates several novel analytical characterization techniques, along with the major sources and composition of NOM in the cryosphere while demonstrating its use in paleoclimate applications.

Doctor of Philosophy / Department of Agronomy / Ganga M. Hettiarachchi / The milling and mining operations of metal ores are one of the major sources of heavy metal contamination at earth’s surface. Due to historic mining activities conducted in the Tri-State mining district, large area of land covered with mine waste, and soils enriched with lead (Pb), zinc (Zn) and cadmium (Cd) remain void of vegetation influencing ecosystem and human health. It has been hypothesized that if these minewaste materials are disposed of in the flooded subsidence pits; metals can be transformed into their sulfide forms under reduced conditions limiting their mobility, and toxicity. These mine waste materials are high in pH, low in organic carbon (OC) and sulfur (S). The objective of this study was to examine the effect of OC and S addition on the biogeochemical transformations of Pb, Zn and Cd in submerged mine waste containing microcosms. Advanced molecular spectroscopic and microbiological techniques were used to obtain a detail, mechanistic, and molecular scale understanding of the effect of natural and stimulated redox conditions on biogeochemical transformation and dynamics of Pb, Zn and Cd essential for designing effective remediation and mitigation strategies. The results obtained from these column studies indicated that Pb, Zn and Cd were effectively immobilized upon medium (119-day) and long-term (252-day) submergence regardless of treatment. The OC plus S treatment enhanced sulfide formation as supported by scanning electron microscopy- energy dispersive X-ray technique, and synchrotron based bulk-, and micro-X-ray fluorescence and absorption spectroscopy analyses. Microbial community structure changed with OC and S addition with the enhancement sulfur reducing bacteria genes (dsrA/B), and decreased metal resistance genes over time. The long-term submergence of existing mine tailings with OC plus S addition reduced trace metals mobility most likely through dissimilatory sulfate reduction under stimulated reduced conditions. Colloidal assisted metal transportation (<1% of both Pb and Cd) occurred during initial submergence. Retention filters are suggested to avoid colloidal metal transport in order to meet the maximum concentration limit for Pb and Cd in surface and groundwater. This research enhances our understanding of the redox processes associated with the sequestration of non-redox sensitive metals through dissimilatory reduction of sulfates in mine waste materials and/or waste water and provides regulators with useful scientific evidence for optimizing remediation goals.