<p> Smallholder farms in central Uganda do not reach their agronomic potential in large part due to declining soil fertility. Continuous cultivation and soils that are susceptible to degradation lead to yield declines that threaten household food security. Improvements in soil management are needed to produce both the quantity and quality of food required to reduce food insecurity. However, this requires active farmer participation in the identification and evaluation of different soil management strategies. On-farm and participatory approaches to research were used to evaluate the potential benefits of using Integrated Soil Fertility Management (ISFM) to improve the quantity and nutritional quality of an indigenous vegetable crop, <i>Solanum aethiopicum</i> or nakati, in Uganda's Lake Victoria Crescent. There is increasing recognition of the complementary roles organic and mineral fertilizers play in both short- and long-term soil management. ISFM emphasizes strategically targeted mineral fertilizer use combined with organic inputs to ensure fertilizer use efficiency and crop productivity given the limited availability of all nutrient resources in smallholder systems. Greater yield benefits can be achieved with the combined application of organic and mineral fertilizers compared to either resource applied alone. The ISFM framework also recognizes the influence of social factors on organic and mineral input management. A greater understanding of farmers' soil management decision-making process can guide the development of robust solutions to declining soil fertility.</p><p> Yield responses of nakati to organic (composted cow manure) and mineral fertilizers (urea), applied separately and in combination, were measured on farmer-managed plots to evaluate the efficacy of using IFSM on indigenous vegetables. Yield benefits from combined fertility sources were only observed under high fertility application rates with little difference between single or combined sources observed at low fertility rates. Low soil pH led to a significant decline in yields. Yields significantly increased when farmers actively participated in the trials, demonstrating the importance of overall good agronomic practices in achieving yield responses to fertilizer applications. </p><p> Measuring the effect of edaphic factors and fertility management strategies on the nutritional value of nakati indicated that uptake of nitrogen and micronutrients were affected primarily by soil pH and fertilizer nitrogen source. Foliar iron and zinc concentrations decreased significantly as soil pH increased, but other soil properties did not affect foliar nutrient concentrations. Foliar nitrogen increased significantly with the use of mineral fertilizer. The practical implications of this are most likely overshadowed when mineral fertilizer applications lead to increasing biomass and foliar nitrogen concentrations are diluted. Smallholder farmers can best attain nutritional benefits from nakati by increasing yields rather than modifying soil environments or fertilizer practices.</p><p> A participatory approach was used to document the knowledge and perceptions of farmers regarding their soils and soil management practices. Farmers participated in an ISFM demonstration program where they were exposed to Western scientific soil concepts. Pre-program focus group discussions were used to analyze farmers' existing soil knowledge and perceptions followed by participant observation, post-program interviews and focus group discussions to evaluate if and how scientific soil concepts were assimilated into farmers' soil knowledge. Farmers shared many 'structural similarities' with scientists in how they perceive soil, yet these similarities were often not recognized and utilized when scientists talked to farmers about soil. Thus potentially beneficial technologies, such as the use of mineral fertilizer as part of an ISFM framework, could be at odds with farmers' existing perceptions of fertilizer and remain an underutilized tool in soil fertility management.</p>

<p> Knowledge of colloid mobility is important for understanding nutrient cycling, the transport of some contaminants, and for developing environmental remediation systems such as geologic filters. The interaction forces between colloids and soil materials are central to colloid transport and immobilization. These forces act at the microscale (nanometers to microns) and include: fluid drag (friction), Brownian motion, gravity and buoyancy, and fluid chemical forces (including DLVO and van der Waals mechanisms). Most vadose zone studies, however, consider colloids at the continuum scale in terms of solute transport mechanisms using parametrized forms of the advection-dispersion equation and absorption isotherms. A comprehensive, generally applicable, well-documented and publicly available framework for simulating colloids at the microscale is still lacking. </p><p> Colloid transport and mobility are mechanisms that fundamentally occur at the microscale. As such, representation of the pore-structure needs to be obtained that is meaningful for the pore-scale fluid flow field and colloid mobility (pore-scale colloidal force balances cause the colloidal transport field to be different from the fluid flow field). At the same time, the pore-structure needs to be relevant for continuum-scale experiments or simulations. There are two ways by which a pore-structure can be obtained: by direct three-dimensional imaging (typically with x-ray tomographic techniques) or by reconstruction techniques that yield a synthetic, but presumably representative, pore-structure. Both techniques are examined in this dissertation, but the synthetic route must be used if little micro-scale information is available. </p><p> This dissertation addresses three main objectives. In chapter 2 it addresses the relation between image quality obtained with two different x-ray tomography techniques (a synchrotron and an industrial scanner) and the obtained flow field. Chapter 3 discusses the development of the LB-Colloids software package, while chapter 4 applies the code to data obtained from a breakthrough experiment of nanoparticulate TiO₂. </p><p> In chapter 2, pore-scale flow fields for Berea sand stone and a macropore soil sample were obtained with lattice Boltzmann simulations which were volume-averaged to a sample-scale permeability and verified with an observed sample-scale permeability. In addition, the lattice Boltzmann simulations were verified with a Kozeny-Carman equation. Results indicate that the simulated flow field strongly depends on the quality of the x-ray tomographic imagery and the segmentation algorithm used to convert gray-scale tomography data into binary pore-structures. More complex or advanced segmentation algorithms do not necessarily produce better segmentations when dealing with ambiguous imagery. It was found that the KC equation provided a reliable initial assessment of error when predicting permeability and can be used as a quick evaluation of whether simulations of the micro-scale flow field should be pursued. In the context of this study, this chapter indicated that LB is able to generate relevant pore-scale flow fields that represent sample-scale permeabilities. However, because the remainder of the study was focused on the development of a pore-scale colloid mobility framework we decided to focus primarily on synthetically-generated pore-structures. This also allowed us to focus on actual mechanisms that were free of imaging and segmentation artifacts. </p><p> Chapter 3 discusses the development of the LB-Colloids package. This simulation framework is able to simulate large collections of individual colloids through pore representations and porous media. The general workflow for users is as follows: 1) Obtain a pore structure by tomographic imaging or by synthetic means. The latter can be accomplished though the included PSPHERE module which is able to generate a random porous medium using user-supplied porosity and particle size. 2) The pore-scale fluid flow field in the porous medium is generated with a lattice Boltzmann method and a user-specified body force that controls the volume averaged Darcy velocity. 3) Mobility and attachment/detachment of colloids is simulated by accounting of the force balance (fluid drag, Brownian motion, gravity and buoyancy forces, and fluid-chemical forces including DLVO and van der Waals mechanisms). Colloid mobility is carried out at a submicron to nanometer scale and requires grid refinement of the LB flow field. To speed up computations the fluid-chemical forces are precomputed for every grid cell. </p><p> Because of computational considerations, the LB-Colloids package is presently only able to deal with 2D representations of the porous medium. Code-development and testing (chapter 4) would have taken too long for a full 3D approach. The main draw-back of the 2D approach is that these cannot accurately represent 3D pore-structures. However, no fundamental &ldquo;new&rdquo; mechanisms are needed for a 3D approach and we expect that this can be easily built into the clean and well-documented LB-colloids code. The LB-Colloids framework is applied on data obtained from a break-through experiment of TiO₂ nanoparticles. (Abstract shortened by ProQuest.) </p><p>

<p> If given the correct remotely sensed information, machine learning can accurately describe soil moisture conditions in a heterogeneous region at the large scale based on soil moisture readings at the small scale through rule transference across scale. This paper reviews an approach to increase soil moisture resolution over a sample region over Australia using the Soil Moisture Active Passive (SMAP) sensor and Landsat 8 only and a validation experiment using Sentinal-2 and the Advanced Microwave Scanning Radiometer (AMSR-E) over Nevada. This approach uses an inductive localized approach, replacing the need to obtain a deterministic model in favor of a learning model. This model is adaptable to heterogeneous conditions within a single scene unlike traditional polynomial fitting models and has fixed variables unlike most leaning models. For the purposes of this analysis, the SMAP 36 km soil moisture product is considered fully valid and accurate. Landsat bands coinciding in collection date with a SMAP capture are down sampled to match the resolution of the SMAP product. A series of indices describing the Soil-Vegetation-Atmosphere Triangle (SVAT) relationship are then produced, including two novel variables, using the down sampled Landsat bands. These indices are then related to the local coincident SMAP values to identify a series of rules or trees to identify the local rules defining the relationship between soil moisture and the indices. The defined rules are then applied to the Landsat image in the native Landsat resolution to determine local soil moisture. Ground truth comparison is done via a series of grids using point soil moisture samples and air-borne L-band Multibeam Radiometer (PLMR) observations done under the SMAPEx-5 campaign (Panciera 2013). This paper uses a random forest due to its highly accurate learning against local ground truth data yet easily understandable rules. The predictive power of the inferred learning soil moisture algorithm did well with a mean absolute error of 0.054 over an airborne L-band retrieved surface over the same region. The validation experiment also demonstrated a strong linkage to the soil moisture, but the algorithm suffered from a lack of training data over such a small site. However, soil moisture estimation still exhibited a mean average error (MAE) of 0.028, compared to a 0.129 MAE of a deterministic model built upon the Air Force Weather Model.</p><p>

<p> Land-use change has significantly contributed to rising global atmospheric carbon dioxide (CO₂) concentrations by reducing carbon (C) storage and increasing C emissions from soils. Soils represent the second largest C pool on Earth, with drylands comprising approximately 21% of the globe&rsquo;s soil organic carbon (SOC). While research regarding the effects of land-use change on SOC in more mesic regions has typically shown an overall reduction in SOC, it is relatively unclear how the land use change from native vegetation to irrigated cropland will affect SOC dynamics in semi-arid regions. Surface soils (0-10 cm) and subsoils (90-100 cm) of an alfalfa field that has been under irrigation for more than five decades, and of an adjacent unmanaged shrubland were collected at the University of Nevada, Reno Main Station Field Laboratory on the eastern boundary of Reno, Nevada. Soils were fractionated using particle size and density fractionation methods and each fraction was analyzed for C, nitrogen (N) content and C and N isotopic composition. Soil CO₂ concentrations and effluxes were measured monthly in the same sites for the 12-month duration of the study.</p><p> Carbon and N analysis of particle size and density fractions revealed that irrigation and management significantly reduced the amount of C and N in the soil. The amount of C in the labile fractions from both the particle size fractionation and density fractionation was significantly smaller and the relative amount of C in recalcitrant fractions was larger in the alfalfa field compared to the native vegetation. The differences in &delta;¹³C values of both stable and labile soil organic matter reflected differences between dominant vegetation types, but these differences were only significant for density fractions. Both fractionation methods revealed differences in &delta;¹⁵N values between soil types, again reflecting differences in vegetation. An eight-week laboratory incubation at constant temperature and water content revealed that the shrubland soil had a higher potential rate of decomposition than the alfalfa field soil, even though alfalfa SOM had a lower C/N ratio, likely as a result of water limitations at the field site allowing for greater accumulation of labile C in the shrubland soil. Additionally, decomposition of organic matter in the buried A horizon from each site was limited by substrate quality rather than environmental conditions. Land conversion to irrigated agriculture resulted in larger soil CO₂ concentrations and effluxes, especially during the growing season. This was true despite shrubland soils having larger amounts of labile C available for decomposition. The source of respired CO₂ for each soil type remains unclear, though CO₂ &delta;¹³C values reflected differences in &delta;¹³C isotopic values for the SOM and vegetation between the two sites. The results from this study suggest that converting a semi-arid shrubland into irrigated cropland may cause an overall loss of SOC that can contribute to rising atmospheric CO₂ levels, though the relative amounts of recalcitrant C may increase in semi-arid soils following management.</p><p>

<p> Nutrient cycling plays a critical role in maintaining biodiversity and ecosystem services in agricultural, urban, and natural lands. However, across landscapes there is substantial unexplained heterogeneity in nutrient cycling. Classic thinking holds that abiotic factors are the source of this spatial heterogeneity with a secondary role of plant biomass. However, recent work suggests that higher trophic levels or variation in traits at the level of plant genotype may also play an important role in structuring nutrient environments. For instance, herbivores may indirectly create heterogeneity in cycling through the induction of chemical and structural changes in plants traits. Phenotypic plasticity due to anti-herbivore defense may then alter nutrient cycling rates by changing the microbial breakdown of plant litter inputs. Alternatively, variation among plant genotypes in the expression of these same traits may overwhelm the influence of phenotypic plasticity on soil processes. Both genetic and environmentally based changes in plant traits have separately been demonstrated to alter soil processes, but their interaction and the relative importance of these sources of variation across local landscapes is unknown.</p><p> I address this question by developing a plant trait-mediated, conceptual framework of nutrient cycling. I then evaluate this framework within an old-field ecosystem by focusing on the dominant plant species, <i>Solidago altissima </i>, and its dominant grasshopper herbivore, <i>Melanoplus femurrubrum </i>, using a combination of lab assays, a greenhouse pot experiment, a field mesocosm experiment, and field surveys. First, I demonstrate that goldenrod individuals exhibit both genotypic variation and phenotypic plasticity in plant defensive trait responses across a nutrient and herbivory gradient in the greenhouse. At low nutrient supply, genotypes tolerate herbivory (inducing plant physiological changes that decrease the negative impact on fitness) while at high nutrient supply, the same genotypes induce a resistance response detectable through lower herbivore growth rates. These environmentally mediated changes in plant trait expression then altered the ability of a common microbial community to decompose senesced litter harvested from the same plants. Induced resistance in the population of genotypes grown at high nutrient levels led to decreased litter decomposition of herbivore legacy litter. In contrast, at low nutrient supply, herbivore legacy litter decomposed more efficiently compared to control litter. This suggests that the interaction between herbivory and nutrient supply could cause context-dependent acceleration or deceleration of nutrient cycling. As a result, trait plasticity may mediate effects of multiple environmental conditions on ecosystem processes in this system.</p><p> I tested this hypothesis using a three-year, raised bed, field experiment examining the effect of plasticity and locally relevant genetic variation on ecosystem processes in a naturalistic setting. Genotype clone clusters were planted in homogenized soil in enclosed cages with varying nutrient supply and grasshopper herbivory. Again, I documented strong genetically and environmentally-based trait variation in plant allocation, growth, and leaf traits. I next explicitly linked these genetic and plastic functional trait changes to concurrent changes in a variety of soil processes (microbially available carbon, plant available nitrogen, nitrogen mineralization potential, and microbial biomass) and litter decomposition rates. Importantly, partitioning functional trait variation into genetic and environmental components improved explanatory power. I also documented potential differences in herbivore effects on "slow" vs. "fast" cycling in soil microbially available C pools. Within both experiments the magnitude of trait variation measured was similar to the variation expressed by individuals across a focal field.</p><p> Taken together, this dissertation demonstrates that plant genotype, herbivores, and nutrients can all modify litter decomposition and other soil processes within ecosystems through differential expression of plant functional traits. Due to the spatially clumped, clonal, and dominant nature of goldenrod, the genetic and herbivory-driven changes documented here could lead to a predictable mosaic of soil process rates across a single old field landscape. This work also highlights the complex interplay between genetically and environmentally-based trait variation in determining population and ecosystem processes within landscapes and improves our understanding of the often-overlooked indirect effects of plant/herbivore interactions on nutrient cycling It suggests that herbivores may shape not only the evolution of plant populations, but also the soil nutrient environment and microbial community in which plants live. This sets up the potential for eco-evolutionary feedbacks between plant defense expression and soil nutrient availability. More broadly, it suggests that biotic factors, in addition to abiotic ones, play a key role in determining local-scale soil nutrient availability patterns and should potentially be accounted for within ecosystem models. These results are particularly salient in a world where anthropogenic nitrogen inputs continue to rise and climate change is predicted to increase herbivory and thus plant defensive trait induction on landscapes. </p>

Phytoremediation is a tool that uses plants that can absorb and accumulate metals in harvestable portions of the plant to cleanse contaminated soils. Most metals are more soluble in soils with an acidic pH. Nitrogen fertilizers acidify pH by different reactions in the soil. Goals of this research were: (1) develop a zinc-contaminated soil; (2) determine effects of nitrogen fertilizers on soil-zinc availability; (3) determine Zn-phytoextraction potential of Brassica juncea Czern. and Festuca arundinacea Schreb.; and (4) determine concentrations of nitrogen fertilizers needed to maximize Zn solubility in soils. After a 14-day incubation period, very little Zn in the soil was water-extractable, which suggested that Zn was reacting with the soil; therefore, an incubation time of 14 days was utilized. Morgan's solution, extracted higher concentrations of Zn than water. If soils were sequentially extracted with water, Morgan's solution, and Mechlich-3 solution, water extracted the least amount of Zn, Morgan's solution extracted higher concentrations than water or Mehlich 3, but Mehlich 3 extracted higher concentrations than water. Lowest pH values occurred with additions of urea (pH 5.18), sludge (pH 4.89), or calcium nitrate (5.26) than with compost (pH 5.33), manure (pH 5.50), or no fertilizer (pH 5.40) or if N was supplied at 400 mg/kg (pH 4.91). Brassica did not germinate well or survive in soil-Zn concentrations greater than 125 mg/kg. Soil-Zn concentrations utilized with brassica were 0 to 100 mg/kg. Highest accumulation of Zn was 0.29% of the dry mass, which occurred at 100 mg Zn/kg or in soils with urea added. Water-extractable Zn at this level averaged 1.1 mg/kg and Morgan's extractable Zn averaged 18 mg/kg. Fescue germinated well in soil-Zn concentrations ranging from 0 to 2000 mg/kg. The soil-Zn concentrations utilized with fescue were 0 to 1000 mg/kg. Highest accumulation of Zn by fescue was 0.33%, which occurred at 1000 mg Zn/kg or in soils with urea or sludge added. Water-extractable concentrations of Zn at this level averaged 11 mg/kg and Morgan's extractable Zn concentrations averaged 290 mg/kg. This research showed that fescue has phytoremediation potential that is as good or better than that of brassica.

Incorporation of organic fertilizers/amendments on turfgrass management has been, and continues to be, a popular strategy of integrated pest management (IPM) program to reduce environmental impacts by pesticide and nitrate leaching. Most of the research on organic fertilizers for the turfgrass industry has focused upon disease suppression, improving soil physical, chemical and biological properties, and the fertility effect on high-cut turfgrass. However, little information has been reported on the response of highly maintained golf turfgrass, such as common on golf courses. The current research studied the effects of organic fertilizer as a sole source on turfgrass performance on highly maintained golf turf and its short-term effects on total soil microbial dynamics on different soil profiles. In addition, environmental impact by organic fertilizer derived dissolved organic matter (DOM) on pesticide sorption and transport in soil was also investigated. Four natural organic fertilizers were evaluated in this study which includes Milorganite (6-2-0), NatureSafe (8-3-5) and SoylMicrobial (F as flowable and G as granular, 14-1-1) and one synthetic organic fertilizer Scotts (29-3-4). In soil microbial dynamics study, application of all natural organic fertilizers increased soil bacterial populations within 4 days after fertilizer treatment (DAT) while little or no effect with the synthetic organic fertilizer was observed on all three soil profiles for the growth chamber experiment. Similar results were observed for the 2 year field trials, however, only the SoylMicrobial (F) fertilizer treatment increased total bacterial populations at 2nd and 4th DAT. In turfgrass response under organic fertilizer application experiment, weekly applications increased clipping an average of 43% compared with bi-weekly applications. Overall, native soils provided higher clipping yields than USGA sand and mixed soil profiles. SoylMicrobial provided sufficient N for acceptable turfgrass growth and Milorganite was ineffective as a sole turfgrass fertilizer. These results suggested that selected natural organic fertilizers can be used as a sole source for turfgrass fertility and the application rates and frequencies need to be adjusted for the different soil profiles. Batch equilibrium techniques were used to evaluate relative effects of organic fertilizer-derived DOM on sorption transport of three organic chemicals (2,4-D, naphthalene and chlorpyrifos) in soils. Sorption capacity was significantly reduced with additional DOM in solution for all three chemicals. The higher the concentration of DOC in solution, the more sorption was reduced. Column experiment results were consistent with batch equilibrium results suggesting that organic fertilizer-derived DOM might lead to enhanced transport of applied chemicals in soil. Results also suggested that organic fertilizers should not be applied on turf directly after pesticide application, which would reduce the impact of organic fertilizer-DOM facilitated transport of applied pesticides.

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