The application of nitrogen (N) fertilizers and manure to agricultural soil is essential for crop production, but has in turn introduced environmental impacts including: eutrophication, contamination of groundwater, freshwater acidification, and an increase in greenhouse gas emissions. The movement of nitrogen was observed following liquid swine manure applications at six fields in Winchester, ON employing controlled tile drainage and denitrifying bioreactors. The manure was mainly in the form of ammonium during application where it was transformed to other N species including nitrate and nitrous oxide (N2O) by microbial activity in soil. Large soil N2O fluxes occurred in fields throughout 2012 and 2013, and total N of soil in the fields was enriched in 15N, indicating denitrification. Soil nitrate was also leached and collected by drainage tiles, and a portion of the tile water was treated by denitrifying bioreactors. Previous studies have demonstrated that denitrification of nitrate in bioreactors elicits the production of N2O, which is emitted from the overlying soil surface and/or is released as dissolved N2O in tile effluent. In this study, it is found that a decrease in nitrate was associated with decreasing levels of nitrous oxide during a rain event, and no significant N2O flux was recorded above bioreactors throughout either year. The δ15N and δ18O signatures of nitrate did not change significantly following bioreactor treatment and did not exhibit the 15N and 18O enrichment that is characteristic of denitrification. The data demonstrates that the decrease in nitrate through the bioreactors was due to dilution, likely from the accumulation of rainfall in reactor beds employing controlled tile drainage. Further work is needed to examine the conditions under which dilution may occur in place of denitrification.

A wastewater treatment and reuse system consisting of a tile drainage system, a constructed treatment wetland (CTW), a reservoir, and an irrigation system was established. The system supplied 780 mm of irrigation water for the 1.8 ha of drained land for the 2008 growing season. A hydraulic tracer study conducted in the CTW supported the use of a length to width ratio of 10:1. During 2008, annual nitrate-nitrogen (NO3--N) and Escherichia coli (E. coli) mass reductions were 67.6 and 63.3%, respectively. Elevated E. coli levels were observed in the reservoir during the warm season. Therefore, water may not be safe for irrigating crops consumed raw. The mean first-order areal uptake rate constants generated for NO3--N and E. coli were 8.0 and 6.4 m y-1, respectively, and are recommended for similar CTWs. A wetland area to drainage area ratio of 4.5% is recommended to achieve ? 70 % mass reduction of NO3--N and E. coli

<p><a>Subsurface tile drainage is a commonly used practice to lower the water table in poorly drained soils, and is often done to improve soil conditions for agricultural operations. Tile drainage has been shown to increase cash crop yield, allow for more timely field operations, and reduce erosion.</a> However, few studies have evaluated the potential long-term changes in soil physical and chemical properties as a result of subsurface tile drainage. This study was conducted on a naturally poorly drained Clermont silt loam soil located at the Southeast Purdue Ag Center near Butlerville Indiana. The intent of this study was to characterize possible evolution of soil physical and chemical properties after 35 years of subsurface drainage. <a>The field site was established in the spring of 1983 with tile drains installed in 2 blocks with tile spacings of 5, 10, 20, and 40m, with the 40-m spacing used as the undrained control</a>. Soil samples were collected in May of 2018 to a depth of 1 meter and were analyzed for carbon and nitrogen content, aggregate stability, and fertility at depth increments of 0-5, 5-15, 15-30, 30-50, 50-75 and 75-100cm. In-field measurements were also taken in May of 2018 for vane shear resistance and in May of 2019 for cone penetration resistance. Total carbon content was found to be significantly higher in the 5-m tile spacing than the 40-m tile spacing in the 0-5cm and 5-15cm depths, with the 10-m and 20-m tile spacings being intermediate. Conversely, in the 75-100cm depth the inverse trend was observed, where the 40-m tile spacing was found to have significantly greater carbon content than narrower tile spacings. Trends observed with carbon stocks per depth increment closely followed trends observed with carbon content at the same depth. However, no significant differences were observed among treatments with the summation of carbon stocks to the 1-m depth. Tile spacing did not have a significant effect on aggregate stability at any depth. The soil fertility data showed some indication of the potential translocation of soil calcium from the soil surface to lower depths in the soil profile resulting in significantly higher soil pH in the 5-m tile spacing than the 40-m tile spacing in all depths below 30cm. No consistent differences related to treatment were found with the cone penetrometer or vane shear penetrometer measurements. After 35 years of drainage history, tile drain spacing did not have a significant effect on total carbon stocks to the 1-m depth, but rather seems to have had a significant effect on the vertical distribution of soil carbon content throughout the soil profile.</p>

In agriculture-dominated areas, water pollution resulting from nutrients migrating from farms to water bodies is a major concern. The migration is further exacerbated by traditional tile drain known as Uncontrolled Tile Drainage (UCTD), which removes excess water from areas to keep the water table low enough for crops to grow. UCTD, commonly used in Ontario, Canada, is believed to contribute to water quality issues, whereas Controlled Tile Drainage (CTD) is an alternative technique in which a structure controls the outlets of the drains so that water only leaves a field when the water table level exceeds a desired threshold. Considered as a Best Management Practice (BMP), CTD has been documented as an efficient practice preventing nutrients from migrating out of agricultural fields. This thesis aims to improve our understanding of the environmental benefits of replacing UCTD with CTD. Three significant contributions were achieved. The first contribution of the thesis is the improvements of the algorithm for calculating nitrates in tile flows in the Soil and Water Assessment Tool (SWAT) model. Researchers have simulated CTD by dynamically changing tile depth to mimic the operation of outlet structure gates, but it has been demonstrated that doing so results in inaccuracies, and so the algorithm in the model has been improved subsequently. The current author proposed and tested a new algorithm for calculating nitrates in tile flows that better represents the dynamics of water and nutrients in soil layers for the SWAT model. A model for the South Nation watershed, located in Ontario, Canada, was then developed and successfully calibrated using the improved SWAT model. The second contribution was the extension of the SWAT model to simulate riverine hydraulic and water quality processes by coupling it with the QUAL2Kw model. In this thesis, a procedure is developed to couple the SWAT model and the QUAL2Kw model to enable continuous simulations of 13 water quality parameters in the South Nation River system. The coupled model was calibrated and verified at various observed locations along the river during the five seasons of growth from 2006 to 2010. The simulation results suggested that CTD also improved the water quality of the river by lowering biologically available N levels of NO2--N, and NO3--N, thereby impeding phytoplankton growth in the river. The third contribution is the verification of the benefits of replacing UCTD with CTD in the future climates. The confirmation was done using the SWAT model alone, and then the coupled SWAT/QUAL2K models, using a matrix of climate change experiments performed with several Global Climate Models and Regional Climate Models. The results suggest that nutrient loading from the watershed will increase in the 2021–2050 period compared to the 1985–2006 period. Thus, pollution from agricultural fields will worsen with the current UCTD approach, while the results also show that CTD would perform effectively and stably in future climate scenarios and could counterbalance the effects of climate change on water quality. To the author’s knowledge, this study is the first attempt to date to assess the environmental effects of CTD on a watershed and river by coupling the SWAT and QUAL2Kw models. The findings expand the current scope of knowledge on the environmental effects of CTD on watersheds and rivers under current and future climate change regimes. Long periods of continuous simulation and a matrix of climate change scenarios also make this study stand out from other studies. It laid a foundation for future investigations.

Quantifying effectiveness of soil management practices on surface and subsurface water quality at the field scale is becoming increasingly important in the Lake Champlain Basin and other agricultural watersheds. During 2012 and 2013, field plots (22.9 x 45.7 m) were established at the Lake Alice Wildlife Area in Chazy, NY to begin a long-term water quality monitoring study. Plots were established in a cool season grass field (1 ha) leased and managed by the William H. Miner Agricultural Research Institute in Chazy, NY. The soil type transitions from an excessively drained outwash soil on the upslope to a very poorly drained silty clay series at the toeslope. Tile drainage lines were installed in each plot and drained to concrete manholes at the corner of each plot where water was sampled and measured. Plots were randomly assigned to a tile-drained (TD) or naturally-drained treatment (UD). Tile outlets were plugged in the UD treatment to enable natural drainage conditions. Surface runoff water was collected at the lower boundary of each plot by shallow PVC-lined trenches that outlet to the manholes. Continuous water flow from each hydrologic pathway was measured in 5-gallon buckets with v-notch weirs and pressure transducers. Total phosphorus (TP), soluble reactive phosphorus SRP), unreactive phosphorus (UP) and sediment (TSS) loads were estimated by multiplying the mean hourly runoff volume by the respective sample concentration for each hydrologic pathway. Data were collected April 21, 2014 through June 30, 2015. Loading rates were unable to be calculated from February 22, 2015 through April 9, 2015 due to freeze/thaw cycles preventing accurate water flow data collection. Event-based loading for TP, SRP, UP, TSS, and water yield were calculated in addition to cumulative losses over the study duration. No significant differences in cumulative TP exports were found between treatments (UD = 230.9 g ha-1; TD = 233.9 g ha-1). Approximately 55% more SRP and 158% more TSS was exported by UD (130.8 g ha-1; 168.8 kg ha-1) than TD (84.2 g ha-1; 65.5 kg ha-1). Unreactive P exports from TD (149.7 g ha-1) were 50% greater than UD (100.1 g ha-1). Two runoff events dominated the treatment response. An intense rain storm on May 16, 2014 generated the greatest sediment losses in both treatments during an individual event, contributing 65 and 67% of the cumulative losses from TD and UD, respectively. This event was also responsible for 40% of UP losses from TD. A 3 d rain/snowmelt event beginning on December 24, 2014 resulted in 61 and 84% of all SRP losses for TD and UD, respectively. The results of this study indicate that tile drainage may not have a negative impact on water quality relative to a naturally drained field. However, additional years of data are needed to develop more robust conclusions as different management strategies and weather conditions could result in different outcomes.

Over the past century of settlement, the landscapes of the Midwestern United States have experienced extensive anthropogenic modifications in order to convert prior wetlands-lowlands to subsequent fruitful croplands. The hydrologic responses of these landscapes have been significantly altered by the installation of artificial drainage (surface ditches and subsurface tile drains) and the change in natural preferential flow paths (increased cracks or root holes due to land use practices). Changes to peak stream flow behaviors is a result of many different inter-related variables; however, intensified agricultural drainage remains one of the largest suspects. Though the effects of subsurface drainage (primarily in the form of tile drains) on landscape, hydrology, ecology, and economy have been questioned, theories of hydrologic controls continue to be vague at best. Soil-Water-Atmosphere-Plant, known as SWAP, was developed to simulate the interaction of vegetation development with the transport of water, solutes, and heat in the unsaturated zone. It is a one-dimensional, vertically directed model with a domain reaching from a plane just above the canopy to a plane in the shallow saturated zone. In the horizontal direction, the model's main focus is the field scale since most transport processes can be described in a deterministic way. The SWAP model was calibrated and validated for simulating flow regimes of drained and undrained landscapes in Iowa. A new term `flashiness' is used to characterize flow data. The Richards-Baker Flashiness Index quantifies the frequency and intensity of short term changes in streamflow. From the simulated results, the effect of anthropomorphic modifications to a landscape is determined to be strongly influenced by soil structural properties and hydraulic properties, along with rainfall regimes. Adding subsurface drains to soils with lower hydraulic conductivities, such as clay, tends to reduce peak flows during precipitation events. Conversely, adding drainage to soils with higher hydraulic conductivities, such as sand, increases peak flows. During years with heavy precipitation, soils with lower permeability show a `saddle shape' relationship between the flashiness index and the distance between tile drains produces. The lowest point of the `saddle' determines the ideal drain spacing for mitigating flashiness. When the shrinking and cracking of clay soils is considered, macropores dominate water flow pathways into the soil matrix and tile drains have a minimal effect on the flow regime. The volume of macropores at the surface of the soil profile is indirectly proportional to flashiness index. Independent of rainfall regimes, cropping season, and soil type, subsurface flows of drained landscapes always exceed that of undrained landscapes. Continuance of comprehensive studies of artificial subsurface drainage can produce positive impacts on engineering, economic, and ecological environments.

The influence of precipitation on runoff characteristics of tile drainage systems and nitrate concentrations in drainage water were evaluated in this thesis. The Jeninsky stream catchment is located at the foothill of Sumava Mountains near the border checkpoint Dolni Dvoriste. Extensive agriculture (pasture) is practised in the catchment as well as surrounding areas. Above mentioned evaluated characteristics were measured on two closure profiles of tile drained subcatchments. Discharges were measured continously, water quality was sampled forthnigtly. Evaluated hydrologic year 2007 was rich in rainfall {--} the precipitation amounted to 892 mm, which is classified as a wet year, despite of 41 days long dry period. Runoff characteristics don{\crq}t vary much in both subcatchments, due to similar area and land use on researched catchments. Long dry period did not cause zero discharges. The progress of nitrate concentrations in subcatchments is characterized by low variations in values. Relatively low values (90-percentil of nitrate concentrations in individual catchments belong to II. and III. class of water quality limits set by Czech legislative) occured in the catchment. These values correspond or slightly exceed values monitored on surrounding simirarly used areas, but are significantly lower than values monitored in areas, where intensive agriculture is practised. This confirms positive influence of grassing on nitrate pollution of drainage and surface water.

Controlled tile drainage (CTD) is an agricultural management practice with well-documented water quality and agronomic benefits, however, by virtue of its effect upon soil hydrology, CTD could potentially impact soil greenhouse gas (GHG: CO2, CH4, N2O) emissions. This study aimed to determine whether: (1) CTD affects soil GHG emissions throughout a dry (2012) and a wet (2013) growing season for corn, soybean, and forage fields in eastern Ontario, and (2) the location in a field with respect to a tile drain (over tile (OT) versus between tile (BT)) is important in GHG emissions. Non-steady state chambers were used for sampling soil GHG emissions in order to analyze GHG fluxes, the δ13C of soil-respired CO2 (RT), and for separating total soil respiration into its rhizosphere and soil components. There was no significant difference in average GHG emissions from CTD and UTD fields (except for 1/5 field pairs studied for N2O) and from OT and BT locations. The means of δ13C of RT were not statistically different (p>0.05) between 4/5 CTD and UTD field pairs, and between OT and BT locations in 4/5 CTD fields. The mean contributions from rhizosphere respiration and soil respiration did not differ (p>0.05) in 3/4 CTD and UTD field pairs. This lack of difference in GHG emissions is believed to have resulted from their being no difference in surface soil water contents among CTD and UTD fields and among OT and BT locations. It is believed that surface soil moisture did not vary because: (1) the water table was too low in 2012 for effective water table control, and (2) significant precipitation created equally wet surface soil in 2013. In 2013, the surface soil moisture was approximately 10% greater and this may be why there was an approximate 5 kg C/ha/day greater CO2 flux from soybean fields in 2013 than in 2012. δ13C was useful for distinguishing the source of CO2 emissions (rhizosphere versus soil respiration) in CTD fields when the crop and plant δ13C signatures varied. The results are useful for helping to capture the carbon footprint of tile drainage management practices imposed at field-scale.

Subsurface tile drainage is a common management practice implemented by farmers throughout the Midwest in fields that have poorly drained soils. Tile drainage has several benefits including increased productivity, reduced erosion, and increased trafficability. However, relatively little is known about the long-term change of soil properties that may occur as a result of subsurface drainage. Careful monitoring of tile drains at the long-term experimental site at the Southeast Purdue Agricultural Center led to the observation of faster drain flow than in the past, with hydrographs of the flow showing flashier peaks, suggesting that more preferential flow paths have developed over time. The overall goal of this study was to characterize possible evolution of physical and hydraulic properties of this silt loam soil after 35 years of subsurface drainage. Bulk density and water retention were measured in May of 2018 at 0-5 cm, 5-15 cm, and 15-30 cm in all plots and again in July of 2019 in the 5 m and 40 m spacings at four different horizons down to depths of approximately 100 cm, rather than set depth increments. Bulk density results from both sets of sampling show the 5 m spacing to have a significantly lower bulk density than the 40 m spacing in the top 30 cm of soil, although the difference was small. Differences in water retention among treatments were too small to be physically meaningful. Saturated hydraulic conductivity results measured by three different methods were highly variable and no differences were detected. In soils with naturally weak structure, low organic matter, and low clay content, like the soil in this study, the processes responsible for soil aggregation, structure stabilization, and lowering bulk density are inherently slow and may require longer than 35 years of subsurface drainage to produce significant changes in the physical properties measured.

Agricultural management is essential for achieving optimum crop production and maintaining soil quality. Soil microorganisms are responsible for nutrient cycling and are an important consideration for effective soil management. The overall goal of the present research was to better understand microbial communities in agricultural soils as they relate to soil management practices. For this, we evaluated the differential impact of two contrasting drainage practices on microbial community composition and characterized active denitrifiers from selected agricultural sites. Field drainage is important for crop growth in arable soils. Controlled and uncontrolled tile drainage practices maintain water in the field or fully drain it, respectively. Because soil water content influences nutrient concentration, moisture, and oxygen availability, the effects of these two disparate practices on microbial community composition was compared in paired fields that had diverse land management histories. Libraries of the 16S rRNA gene were generated from DNA from 168 soil samples collected from eight fields during the 2012 growing season. Paired-end sequencing using next-generation sequencing was followed by read assembly and multivariate statistical analyses. Results showed that drainage practice exerted no measureable effect on the bacterial communities. However, bacterial communities were impacted by plant cultivar and applied fertilizer, in addition to sampled soil depth. Indicator species were only recovered for depth; plant cultivar or applied fertilizer type had no strong and specific indicator species. Among indicator species for soil depth (30-90 cm) were Chloroflexi (Anaerolineae), Betaproteobacteria (Janthinobacterium, Herminiimonas, Rhodoferax, Polaromonas), Deltaproteobacteria (Anaeromyxobacter, Geobacter), Alphaproteobacteria (Novosphingobium, Rhodobacter), and Actinobacteria (Promicromonospora). Denitrification in agricultural fields transforms nitrogen applied as fertilizer, reduces crop production, and emits N2O, which is a potent greenhouse gas. Agriculture is the highest anthropogenic source of N2O, which underlines the importance of understanding the microbiology of denitrification for reducing greenhouse gas emissions by altered management practices. Existing denitrifier probes and primers are biased due to their development based mostly on sequence information from cultured denitrifiers. To circumvent this limitation, this study investigated active and uncultivated denitrifiers from two agricultural sites in Ottawa, Ontario. Using DNA stable-isotope probing, we enriched nucleic acids from active soil denitrifiers by exposing intact replicate soil cores to NO3- and 13C6-glucose under anoxic conditions using flow-through reactors, with parallel native substrate controls. Spectrophotometric chemistry assays and gas chromatography confirmed active NO3- depletion and N2O production, respectively. Duplicate flow-through reactors were sacrificed after one and four week incubation periods to assess temporal changes due to food web dynamics. Soil DNA was extracted and processed by density gradient ultracentrifugation, followed by fractionation to separate DNA contributed by active denitrifiers (i.e., “heavy” DNA) from that of the background community (i.e., “light” DNA). Light and heavy DNA samples were analyzed by paired-end sequencing of 16S rRNA genes using next-generation sequencing. Multivariate statistics of assembled 16S rRNA genes confirmed unique taxonomic representation in heavy fractions from flow-through reactors fed 13C6-glucose, which exceeded any site-specific or temporal shifts in putative denitrifiers. Based on high relative abundance in heavy DNA, labelled taxa affiliated with the Betaproteobacteria (71%; Janthinobacterium, Acidovorax, Azoarcus, Dechloromonas), Alphaproteobacteria (8%; Rhizobium), Gammaproteobacteria (4%; Pseudomonas), and Actinobacteria (4%; Streptomycetaceae). Metagenomic DNA from the original soil and recovered heavy fractions were subjected to next-generation sequencing and the results demonstrated enrichment of denitrification genes with taxonomic affiliations to Brucella, Ralstonia, and Chromobacterium in heavy fractions of flow-through reactors fed 13C6-glucose. The vast majority of heavy-DNA-associated nitrite-reductase reads annotated to the copper-containing form (nirK), rather than the heme-containing enzyme (nirS). Analysis of recovered nirK genes demonstrated low sequence identity across common primer-binding sites used for the detection and quantification of soil denitrifiers, indicating that these active denitrifiers would not have been detected in molecular surveys of these same soils.