The overuse of antibiotics in agriculture is an emerging concern, due to their potential detrimental impact to the environment. This study focuses on exploring antimicrobial properties of lignin derived compounds. Lignin is of interest as a feedstock to replacing some petroleum-based chemicals and products because it is the most abundant source of renewable aromatic compounds on the planet. Two lignin rich streams, residues from the enzymatic hydrolysis of dilute acid and alkaline pretreated corn stover, were decomposed via pyrolysis and hydrogenolysis, respectively. The resulting liquid oils were subjected to sequential extractions using a series of solvents with different polarities. Chemical compositions of the extracted fractions were characterized through HPLC and GC/MS. These extracted compounds were screened against Saccharomyces cerevisiae (S. cerevisiae), Escherichia coli, and Lactobacillus amylovorus for antimicrobial properties. Six lignin model monomers: guaiacol, vanillin, vanillic acid, syringaldehyde, 2,6-dimethoxyphenol, and syringic acid were compared to the oils and extracted fractions for antimicrobial properties. Development of lignin-derived chemicals with antimicrobial properties could provide a novel use for this underutilized natural resource.

Hydrothermal liquefaction is a thermochemical technique for obtaining crude bio-oil from lignocellulosic biomass with moderate temperature and pressure. The crude bio-oil can then be upgraded to various biofuels and bioproducts. Hydrothermal liquefaction is amenable to use of biomass feedstocks that have high-moisture. The overall goal of this research is to demonstrate the effectiveness of white rot fungus (WRF) as a pretreatment option in the production of bio-oil from switchgrass through hydrothermal liquefaction. If WRF is an effective pretreatment, it could be a cost-effective option for commercialization, allowing hydrothermal liquefaction to be used on an industrial scale to produce high quality bio-oil capable of replacing some of the fossil fuel liquids used today. This thesis specifically focuses on the investigation of the effects of particle size and culture time on lignin degradation using Phanerochaete chrysosporium as a pretreatment method on switchgrass. In addition, the conversion efficiency of WRF treated switchgrass was compared to that of torrefied switchgrass and untreated switchgrass after the pyrolysis conversion process. The results indicate that WRF outperforms torrefaction as a pretreatment method for the conversion of sugar-based components, thus may be an attractive alternative for fermentation conversion processes, but probably not for thermochemical processes.

Due to their small size and ectothermic biology, the heat production of insects and insect larvae is hard to quantify. However, knowing the amount of heat production, as well as ammonia production of insects may be beneficial for commercial production of valuable insect species. Black soldier fly larvae (BSFL) are of interest in the agricultural industry because they quickly consume organic waste and have high amounts of protein and fat in their bodies. It has been proposed that BSFL be used to manage livestock waste, while serving as a high-protein feed source for livestock animals. To efficiently rear BSFL, it is necessary to design rearing facilities, which maintain optimal conditions for the larvae. To design such a facility, it is necessary to know the amount of heat and ammonia that BSFL produce. A gradient calorimeter was used to measure the heat and ammonia production rates of black soldier fly larvae. The study determined that BSFL heat production changes significantly with the age and weight of the larvae. Aggregations produce the most total heat when larvae are older and larger. The study also found that larvae produce less heat per individual and per gram of body weight as they grow. Larvae also produce significantly different amounts of heat depending on the size of the groups they are in, and do not produce consistent amounts of heat per individual or per gram of body weight, even if maintained at a consistent population density. Larvae in group sizes of 100, 300, and 500 produced an average and standard deviation of 0.00107±0.000295, 0.00067±0.00014, and 0.00049±0.00020 W/larva, respectively. Likewise, larvae in groups of 100, 300 and 500 produced an average of 0.01826±0.00010, 0.01023±0.00565, and 0.00575±0.00371 W/g, respectively. The differences in heat produced per individual and per gram is troublesome when trying to estimate a total heat production for large populations. The largest heat production rate observed in this study was 0.407 W, and was produced by a group of 500 BSFL. Frass analysis indicated that between 4.80 and 7.79 lbs of ammoniacal-nitrogen is emitted for every ton of frass produced. These data could be used to estimate the total heat and ammonia produced from a larger population of BSFL being reared inside a closed facility, allowing engineers to design HVAC systems to keep the larvae at their optimal growing condition year-round. Placing BSFL rearing accommodations at livestock facilities could be beneficial to livestock, poultry, and fishery producers, because BSFL can be used to dispose of animal wastes and are also a good source of protein-rich animal feed.

A general systematic framework with several sub-frameworks was developed to help managers make informed decisions related to the reuse of treated wastewater in agricultural irrigation. The framework involves the identification and evaluation of the short- and long-term effects of using treated wastewater with some common constituents of concern ( e.g. salts and some specific ions, nutrients, heavy metals, organic compounds, and microorganisms) on the environmental elements ( crop , soils, surface water, and groundwater), and on the public health. Local and/ or international standards, criteria, and guidelines related to agricultural reuse are applied to the evaluation of the effects. Based on the evaluation results, decisions are made and management alternatives are proposed. The management alternatives include improving the wastewater treatment level , blending treated wastewater with good-quality water, using an appropriate irrigation method, using different reuse schemes, and zero discharging from specific industries. The framework demonstration includes the data input, information processing, output, evaluation, and decision-making phases. Data related to the plant-soil system (crop, soil, and any other assimilation pathway), and the behavior and fate of treated wastewater constituents are necessary for the identification of the effect on the environmental elements. Jordan was selected as a case study for the demonstration of the general systematic framework. Due to the lack of data related to the different constituents, some of the hazardous heavy metals were considered in the demonstration with the worst condition of accumulating the whole quantity of metals in the soil. The demonstration results showed that, at least for the coming 40 years Jordan can practice the reuse of the treated wastewater for agricultural irrigation without exceeding the maximum allowable limits in the agricultural soils based on the USEPA for biosolid application. With regard to blending and system efficiency, the demo result s also showed that they do not have an effect on the long-term accumulation of the hazardous metals in the soil. The general systematic framework is a decision tool, which is able to answer questions related to water treatment level and type , when to blend with freshwater, the recommended blending ratio, the recommended irrigation method, selection of the optimum reuse scheme, as well as providing answers to questions related to industrial wastewater constituents.

The production of alternative transportation fuels is imperative to meet future energy demands without contributing to global climate change. Advances in alternative processing techniques that have emerged due to interest in microalgae as a feedstock have led to a variety of potential processing pathways for the production of bio-based fuels. A major hurdle in the algal production process is maintaining a fast and stable algae culture. Monocultures, developed for their high lipid content, suffer from low productivity, are susceptible to crashes and require a constant supply of carbon dioxide to maintain productivity. In an effort to circumvent these obstacles, algal turf scrubber systems (ATS) are now being targeted not only for water purification, but as a means of producing algae feedstocks for fuel conversion. The resulting algae are capable of being harvested at a much higher density, requiring less energy for dewatering purposes. ATS systems do present other drawbacks that downstream technologies need to account for to make this system a viable means for fuel conversion. While polyculture algae species display great growth characteristics, they contain high percentages of nitrogen containing proteins and low lipid content. If not removed this nitrogen pollutes any resulting biocrude making it unacceptable for diesel fuel blends. This study investigates a processing method which reduces the nitrogen content of the resulting fuel by fermenting both carbohydrates and proteins into intermediate compounds. By tuning the E. coli fermentation stain it is hoped that the process will yield higher value co-products than those investigated in this study. The research contained herein incorporates laboratory experimentation with engineering systems modeling to assess the economic feasibility and environmental impacts of generating biofuels from ATS cultivated algae. Results show a minimum fuel selling price of $5.93 per gasoline gallon equivalent and greenhouse gas emissions of -0.0185 kg CO2eq per MJ fuel. Discussion points include process optimization in terms of minimum fuel selling price and global warming potential.

Algae can be used to treat wastewater and manure while producing a feedstock for renewable energy. Algae require nutrients to achieve their maximum growth and manure could provide those nutrients, thereby reducing the cost of algae production and the impact of manure treatment. Algae concentration during cultivation is a critical variable that is difficult to measure due to the high concentration of suspended solids present in manure. This dissertation addresses methods to measure algae concentration in the presence of manure solids. Quantifying the algae concentration gravimetrically or by optical density was unreliable due to manure solids interfering with the measurement. Cell counting to determine algae concentration was accurate but time consuming, subjective, required dilution of concentrated samples and only small sample volumes could be measured. Chlorophyll extraction was a consistent method to determine algae concentration in manure based media, but the model had to be adjusted to account for solids interference. The proposed equation predicted chlorophyll concentration from Chlorella vulgaris in dairy manure better than the reference equation. Different algae strains (Chlorella vulgaris, Cylindrocystis sp, and Scenedesmus sp.) and manure sources (dairy, beef, swine, and sheep) were used to validate the proposed equation and all combinations had a linear relationship between actual and predicted chlorophyll concentration, but not all comparisons followed a 1:1 reference line. Even with chlorophyll extraction the manure solids interfered with the chlorophyll measurement and calibrations had to be developed based on manure type. A method based on spectral deconvolution was used to quantify algae concentration in the presence of manure without chlorophyll extraction. Various manure-algae mixtures were scanned with a spectrophotometer. Algae concentration was accurately determined with the four manure sources. Measuring algae concentration required absorbance spectra from 600 to 700 nm and manure solids concentration between 280 and 350 nm. Spectral deconvolution was able to differentiate algae concentration and manure solids concentration with a Pearson coefficient of 95.3% and 99.8% respectively. This method proved to be an accurate and efficient method for estimating algae and manure solids content in unprocessed samples. A critical factor was utilizing appropriate reference spectra.

Two contour weep berms systems were designed and implemented to evaluate their performance at mitigating water quantity problems from a horse muck composting operation. The field-scale study focused on the hydrologic response of a standard contour weep berm and a modified contour weep berm. The modified contour weep berm incorporated a woodchip trench upgradient of a typical standard contour weep design. Monitoring occurred from July 2011 through spring 2012. Eight storm events produced measureable runoff for the standard contour weep berm; however, only five storm events produced measurable runoff for the modified contour weep berm. The largest storm event occurred on November 27, 2012 with rainfall depth of 49.0 mm. This storm event generated a total runoff volume of 183.1 m3 and 188.5 m3 for the standard and modified contour weep berms, respectively. All runoff produced from the storm events during the monitoring period was completely detained and infiltrated. No runoff was released from the horse muck composting facility through the passive dewatering system to down-gradient vegetative filter strips during the monitoring period.

In recent years, there has been a concern for the amount of carbon dioxide released into the atmosphere and how it will be captured. One way to capture carbon dioxide is with algae. In this study, algae's growth was measured at different temperatures. The first part of the study was to grow Scenedesmus and Chlorella with M8 or urea growth media at a temperature of 25, 30 or 35ºC. It was found that 30ºC had the best growth rates for both algae. The second part studied Scenedesmus growth with urea, more in-depth, and found the optimum growth temperature to be 27.5ºC with a growth rate of 0.29 1/hr. The last part of the study was a heat transfer model which predicted the temperature of a greenhouse and an outdoor unit. The model could also predict the growth rate of the algae and the temperature if flue gas is mixed in with the algae.

Cheese products are manufactured more consistently and with better quality if the curd cutting time can be consistently selected. An optical sensor that accurately predicts cutting time has been developed for large cheese vats, but the initial cost of these sensors makes them uneconomical for small artisan cheese manufacturers. The small artisan cheese vats require an inexpensive sensor technology that can be implemented simply. The initial cost of purchasing a sensor and installing these sensors plus the need for a computational program for implementing the algorithm make this technology excessively expensive for these smaller cheese manufacturers. The objective of this research was to develop a simpler sensor technology that can be implemented inexpensively by artisan cheese makers. A prototype sensor has been developed and shown to measure the coagulation of milk in initial experiments. This sensor uses the same concepts for estimating cutting time and much of the same technology as the light backscatter technology; however, it is considerably more cost effective than a light backscatter sensor welded permanently into a vat. The results will show the unique and novel design and characterize its performance on unhomogenized milk.

Antibiotics are commonly used in animal agriculture to treat and prevent diseases and promote growth. Unfortunately, large amounts of antibiotics are not metabolized, but instead are excreted in urine and feces. Rainfall simulation studies were used to investigate the transport of the antibiotic oxytetracycline and various constituents in runoff and the ability of alum to reduce pollutant transport. Runoff samples were collected at several points during the simulated storm event from each of four treatments: control (C), manure only (M), manure and antibiotics (MA), and manure, antibiotics and alum (MAA). Flow-weighted composite samples were created and compared to the flow weighted mean concentration (FWMC). Constituents with concentrations well-above the detection limits (E. coli, NH4-N, turbidity, TSS, TOC, and EC) showed a strong correlation between flow-weighted composite samples and FWMC. When constituent concentrations were at or near the detection limits, errors associated with the composite samples were magnified. Oxytetracycline concentrations had the strong correlation to E. coli, Cl, TOC, TSS, and turbidity suggesting that a BMP effective at trapping sediment or particulates may work best for reducing oxytetracycline concentrations in runoff. Alum (1%) did not reduce levels of oxytetracycline in runoff. It is recommended that higher doses of alum be tested.