Control of PDD in dairy herds in the United States is essential for maximizing animal health, production, and profitability. A survey was conducted to determine use of footbaths on dairy farms in Northeastern NY and VT. The survey found, significantly more farms were using footbaths than were not (71 versus 27 farms, respectively). Copper sulfate (n = 59) was most frequently reported product used and footbath waste was disposed of to manure storage by 83.8% of farms. Research was conducted to examine these animal management and waste disposal practices on crop growth, soil, and manure storage. Greenhouse studies were conducted with objectives of determining effects of application of high Cu dairy manure on growth and quality of forage grasses and effect of excess of Cu applied from dairy manure on soil Cu concentrations. In 3 experiments, orchardgrass (Dactylis glomerata L.) and timothy (Phleum pretense L.), were tested. Treatments were 0, 5.6, and 11.2 kg Cu/ha from CuSO4 in dairy manure that was incorporated into a sandy loam (Study 1 and 2) or a silt loam (Study 2) soil. Study 3 evaluated 0, 27.1, 54.3, and 81.4 kg/ha of Cu incorporated in a silt loam soil. Two years of research were conducted with the objectives of evaluating effects of the application of dairy manure with high Cu concentrations on growth and yield of corn (Zea mays L.) for silage and soil Cu concentrations. Treatments were 0, 9.12, and 18.23 kg Cu/ha and were applied to the same plots in 2006 and 2007. The 3 treatment were tested on early and late maturity corn hybrids. Two studies were conducted to examine the effects of excess Cu on manure in storage. Study 1 was conducted in the summer of 2006 to examine the effects over time of excess Cu on stored manure. Study 2 was conducted in the summer of 2007 to examine the effects of excess Cu on manure after 2 weeks of storage and subsequent effects of application to orchardgrass, timothy, reed canarygrass (Phalaris arundinacea L.), and alfalfa (Medicago sativa L.). Finally, soils collected from all research projects were used to evaluate the relationship of the extraction of Cu by CaCl2, Modified Morgan’s, and Mehlich-3 to total Cu measured by nitric acid digestion, soil CEC (meq/100g), SOM (%), and Cu applications. From the greenhouse studies it was found that orchardgrass appeared to be more tolerant to high Cu application from dairy manure than timothy and root Cu concentration was consistently higher than shoot Cu concentration. Two annual applications of high-Cu dairy manure had no effects on growth, yield, or composition of corn. There was no evidence of vertical movement of Cu in the soil after 2 annual applications to corn. Copper treatments did not change manure composition and did not change manure differently over time. Total bacterial counts were not affected by increasing the Cu concentration in the manure. The concentration of available Cu in the manure increased as the Cu treatment and total Cu in the manure increased. A single application of high Cu manure did not affect the yield or quality of orchardgrass, timothy, reed canarygrass, or alfalfa that it was applied to. As reported in other research the Cu concentration of alfalfa was higher than that of the grasses. Overall, Cu application rate has a large affect on the measure of Cu concentration in the soil and the strongest relationship to Cu extracted by Mehlich-3. The Mehlich-3 and Modified Morgan’s extractions are both good predictors of Cu extracted by CaCl2. Mehlich-3 is a very good predictor of Cu extracted by Modified Morgan’s.

Research was conducted to compare the effects of composted dairy manure and raw dairy manure alone, or in combination with supplemental inorganic fertilizer, on soil chemical properties and Coastal bermudagrass [Cynodon dactylon (L.) Pers.] yield and nutritive value. Composted dairy manure was surface applied at rates of 14 (125 kg N ha-1), 29 (250 kg N ha-1) and 57 (500 kg N ha-1) Mg dry matter (DM) ha-1, and raw dairy manure was surface applied at a rate of 54 (420 kg N ha-1) Mg DM ha-1 to established bermudagrass. Selected compost and manure plots received supplemental inorganic N at rates of 56, 84 and 112 kg ha-1 cutting-1 or 112 kg ha-1 cutting-1 of supplemental N with supplemental inorganic phosphorus or potassium at rates of 112 kg P2O5 ha-1 yr-1 and 112 kg K2O ha-1 cutting-1, respectively. Composted dairy manure (29 and 57 Mg DM ha-1) or raw manure alone increased cumulative forage yields compared to the untreated check in both years of the study, but were less than those obtained using only inorganic fertilizer. Application of 56 kg N ha-1 cutting-1 or more of supplemental N to compost (29 and 57 Mg DM ha-1) or iv manure produced forage yields that were equal to or greater than those obtained using inorganic fertilizer alone. However, increasing compost rate did not increase tissue N concentrations regardless of supplemental inorganic N rate. Yield and tissue K concentrations were increased in the second growing season when supplemental inorganic K was applied to 29 Mg ha-1 of compost or 54 Mg ha-1 of raw dairy manure. No yield response was observed when supplemental inorganic P was applied to compost or manure. Soil pH and concentrations of NH4, NO3, K, Ca, Mg and Mn were increased by application of compost or manure. Soil P concentrations in the 0 to 5-cm zone exceeded 200 mg kg-1 when compost was applied at the high rate. Dairy manure compost was an effective nutrient source for bermudagrass hay production, but will require the use of supplemental N and, in some cases, K to achieve yields comparable to inorganic fertilizer.

A pilot scale nitrogen (N) removal system was constructed and operated for approximately 365 days and was designed to remove inorganic total ammonia nitrogen (TAN) from solids-separated dairy manure. An anaerobic fermenter, upstream of the N removal reactor, produced volatile fatty acids (VFAs), to be used as an electron donor to fuel denitrification, and TAN at a COD:N ratio of 18:1. However, sufficient amounts of non-VFA COD was produced by the fermenter to fuel the denitrification reaction at an average NO3- removal rate of 5.3 ± 2 mg/L NO₃--N. Total ammonia N was removed from the fermenter effluent in an N removal reactor where a series of aerobic and anoxic zones facilitated aerobic TAN oxidation and anoxic NO₃- and NO₂- reduction. The minimum dissolved oxygen (DO) concentration allowing for complete TAN removal was found to be 0.8 mg/L. However, TAN removal rates were less than predicted using default nitrifying kinetic parameters in BioWin®, a biological modeling simulator, which indicated the presence of a nitrification inhibitor in fermented dairy manure. Furthermore, an N balance during the aerobic zone indicated that simultaneous nitrification-denitrification (SND) was occurring in the aerobic zone of the N removal reactor and was most apparent at DO concentrations below 1.3 mg/L. A series of nitrite generation rate (NGR) experiments confirmed the presence of an inhibitor in fermented dairy manure. A model sensitivity analysis determined that the most sensitive ammonia oxidizing bacteria (AOB) kinetic parameters were the maximum specific growth rate, , and the substrate half saturation coefficient, . Nitrifying inhibition terms of competitive, non-competitive, mixed competitive, and un-competitive were applied to the growth rate equation in BioWin® but an accurate representation of the observed TAN removal rates in the pilot scale system could not be found by adjusting the kinetic parameters alone. Reducing the default BioWin® hydrolysis rate by approximately 50% produced a more accurate calibration for all inhibition terms tested indicating that the hydrolyization of organic N in dairy manure is less than typical municipal waste water. / Master of Science

Regulations for total maximum daily loads require management of phosphorus loading from farms and municipalities. This study evaluated environmental impacts of a system for using and exporting the phosphorus in composted dairy manure (CDM) and composted municipal biosolids (CMB) through turfgrass sod. Responses of soil physical, chemical, and biological properties within and below the sod layer were monitored during turfgrass establishment in two experiments under greenhouse conditions. During turf establishment in column lysimeters, phosphorus and nitrogen leaching from an amended surface layer through soil were evaluated. In addition, growth of turf was related to the observed changes in soil nutrients and properties. In the first experiment, four replications of a factorial design comprised three soil types (USGA greens sand, Windthorst fine sandy loam [fine, mixed, thermic Udic Paleustalf], Houston black clay [fine, smectitic, thermic, Udic Hapustert]), two dairy manure rates ( 200 kg P ha-1, 400kg P ha-1), and two turf species (St. Augustinegrass (Stenotaphrum secundatum [Walt.] Kuntze var. Raleigh) and Tifway 419 Bermudagrass (Cynodon dactylon [L.] Pers. x C. transvaaleensis Burtt-Davy). Columns received three separate leaching events in which a 9-cm depth of distilled water was applied. A similar experimental design was implemented for Experiment 2 in January 2004. Treatments consisted of the same three soils and three volume-based rates of CDM and CMB (0, 150, 250 cm3 L-1) during establishment of St. Augustinegrass turf. Columns received one pore volume of distilled water on three separate occasions. In both experiments, soil physical properties (bulk density, water infiltration rate, and water content) and microbial populations were unaffected by CDM or CMB. Applications of CDM at P-based rates utilized in the first experiment yielded no variation of leaching loss among rates of P or N. Most of the P applied was retained in the top 10 cm of soil. When large volume-based rates were used, leaching losses of P and N varied among CDM or CMB application rates. Leaching losses were only observed in the USGA sand and were highest for the 250 cm3 L-1 rate of CDM or CMB. Regardless of compost source, applications of organic amendments at volume-based rates can increase leaching loss of P and N on sandy soils. However, if P-based rates are used there is little risk for leaching loss of N and P during sod establishment.

Regulations for total maximum daily loads require management of phosphorus loading from farms and municipalities. This study evaluated environmental impacts of a system for using and exporting the phosphorus in composted dairy manure (CDM) and composted municipal biosolids (CMB) through turfgrass sod. Responses of soil physical, chemical, and biological properties within and below the sod layer were monitored during turfgrass establishment in two experiments under greenhouse conditions. During turf establishment in column lysimeters, phosphorus and nitrogen leaching from an amended surface layer through soil were evaluated. In addition, growth of turf was related to the observed changes in soil nutrients and properties. In the first experiment, four replications of a factorial design comprised three soil types (USGA greens sand, Windthorst fine sandy loam [fine, mixed, thermic Udic Paleustalf], Houston black clay [fine, smectitic, thermic, Udic Hapustert]), two dairy manure rates ( 200 kg P ha-1, 400kg P ha-1), and two turf species (St. Augustinegrass (Stenotaphrum secundatum [Walt.] Kuntze var. Raleigh) and Tifway 419 Bermudagrass (Cynodon dactylon [L.] Pers. x C. transvaaleensis Burtt-Davy). Columns received three separate leaching events in which a 9-cm depth of distilled water was applied. A similar experimental design was implemented for Experiment 2 in January 2004. Treatments consisted of the same three soils and three volume-based rates of CDM and CMB (0, 150, 250 cm3 L-1) during establishment of St. Augustinegrass turf. Columns received one pore volume of distilled water on three separate occasions. In both experiments, soil physical properties (bulk density, water infiltration rate, and water content) and microbial populations were unaffected by CDM or CMB. Applications of CDM at P-based rates utilized in the first experiment yielded no variation of leaching loss among rates of P or N. Most of the P applied was retained in the top 10 cm of soil. When large volume-based rates were used, leaching losses of P and N varied among CDM or CMB application rates. Leaching losses were only observed in the USGA sand and were highest for the 250 cm3 L-1 rate of CDM or CMB. Regardless of compost source, applications of organic amendments at volume-based rates can increase leaching loss of P and N on sandy soils. However, if P-based rates are used there is little risk for leaching loss of N and P during sod establishment.

The purpose of this research was to characterize a flushed dairy manure wastewater and to develop the kinetic and stoichiometric parameters associated with nitrogen removal from the wastewater, as well as to demonstrate experimental and simulated nitrogen removal from the wastewater. The characterization showed that all the wastewaters had carbon to nitrogen ratios large enough for biological nitrogen removal. Analysis of carbon to phosphorus ratios showed that enough carbon is available for phosphorus removal but enough may not be available for both nitrogen and phosphorous removal in anaerobically pretreated wastewater. In addition, kinetic and stoichiometric parameters were determined for the biological nitrogen removal in sequencing batch reactors for the dairy manure wastewater. Results showed that many parameters are similar to those of municipal wastewater treatment systems. This characterization and the derived kinetic and stoichiometric parameters provided some of the information necessary for development of a nitrogen removal process in a sequencing batch reactor. Lab scale treatment of a 1:2 dilution of the anaerobically pretreated wastewater was demonstrated. Treatment was able to achieve between 89 and 93% removal of soluble inorganic nitrogen as well as up to 98% removal of biodegradable soluble and colloidal COD. In addition, a solids removal efficiency of between 79 and 94% was achieved. The lab scale treatment study demonstrated that sequencing batch reactors are capable of achieving high nitrogen removal on wastewaters with the carbon to nitrogen ratios of the dairy manure wastewater. Model simulations of the treatment process were used to develop a sensitivity analysis of the reactor feed configuration as well as the kinetic and stoichiometric parameters. The analysis of the feed configuration demonstrated the advantage of decreasing the amount of feed that is fed in the last feed period so that the effluent nitrate will be minimized. The analysis indicated that the autotrophic growth rate is one of the most important parameters to measure while error in the heterotrophic decay or yield values can lead to miscalculations of oxygen required for treatment. / Master of Science

Phosphorus (P) recovery and re-use is very important today for sustainable nutrient cycling and water quality protection due to the declining global P reserves and increasingly stringent wastewater treatment regulations. P recovery as struvite (MgNH4PO4·6H2O) is a promising technology because it can be used as a slow-release fertilizer. The objective of this study was to investigate different pretreatment methods to enhance struvite precipitation in dairy manure. Generally there are two challenges that need to be overcome to precipitate struvite in liquid dairy manure. The first is the relatively high calcium (Ca) concentration. The present study investigated the effectiveness of two calcium binding reagents to reduce the calcium inhibitory effects to enhance the struvite precipitation. A chemical equilibrium model (Visual MINTEQ 2.60) was used to determine the pH to acidify manure and to precipitate struvite. Then, bench-scale experiments were conducted to validate the model results using synthetic and untreated manure. First, the manure was acidified (pH 4.5) to liberate the particulate-bounded Mg2+, Ca2+ and inorganic P. Second, EDTA and/or oxalate compounds were added to the manure. Third, pH was increased to 7.5 for struvite precipitation from the liquid filtrate. Results showed that struvite-containing crystals were obtained from the samples treated with calcium removal compounds, with a total suspended solids (TSS) concentration less than 4,000 mg/L. The second challenge is the low dissolved reactive P (DRP, i.e. PO4-P) to total P (TP) ratio. This study investigated different pretreatment methods for P release to enhance struvite precipitation in liquid dairy manure: enhanced biological phosphorus removal (EBPR), microwave heating (MW) and anaerobic digestion (AD). All of the pretreatment methods resulted in P release but struvite crystals were observed only in precipitates obtained in manure pretreated with MW+H2SO4 acidification. Without oxalic acid to reduce the Ca2+ effects, all the other pretreatment methods were not effective in enhancing struvite precipitation in liquid dairy manure. Hardly any struvite or crystalline-like solids were found in the non-centrifuged samples, regardless of any pretreatment, indicating the effects of suspended solids and organic matter on struvite precipitation. A partial economic analysis was conducted to assess the chemical costs of P recovery from liquid dairy manure with different pretreatment methods; P recovery amounts as struvite were modeled by Visual Minteq 2.61.Three pretreatment conditions (untreated manure + oxalic acid, MW + H2SO4 acidification, and AD) were selected based on the precipitation results. MW + H2SO4 acidification produced the highest struvite quantities among the pretreatment methods to enhance struvite recovery, also with the lowest chemical addition costs. / Master of Science

Animal manures are land applied in agronomic systems to supply essential crop nutrients and decrease dependency on chemical fertilizers. Liquid manures are traditionally surface broadcast to fields and sometimes incorporated to reduce odor and nutrient losses; however, incorporation is incompatible with no-till agriculture. Subsurface manure injection is a no-till compatible alternative application method which addresses these concerns, but likely changes the dynamics of nutrient cycling. Comparison of the two application methods has yielded mixed results and warrants further research. Therefore, the objectives of this research were to contrast the surface broadcast and subsurface injection of dairy slurry on nitrogen and carbon cycling, crop yield, and biologic responses to proxy soil health. In a forced air-flow laboratory incubation, manure injection reduced ammonia volatilization by 87% and 98% in a sandy loam and clay loam soil, respectively. The increased ammoniacal nitrogen recovery resulted in increases of soil nitrate of 13% for the sandy loam and 26% for the clay loam after 40 days of incubation. Microbial measurements were inconclusive in the laboratory. In 7 site-years of field study, soil nitrate was greater in 7 of 25 measurements under manure injection and 30% higher under injection on average during the corn pre side-dress nitrate test (PSNT) time. Soil nitrate sampling methods were assessed for fields injected with manure; a standard random sampling method had a coefficient of variation (C.V.) of 28% and was as equally repeatable as utilizing an equi-spaced distribution of cores taken across an injection band, C.V. of 30%. Both biological responses, carbon mineralization (C-min) and substrate induced respiration (SIR), were not different between application methods; both were highly variable and C-min was especially intensive logistically. Corn yield showed no consistent response to application method, but probably was not nitrogen limited. In 2 years of field study conducted on a university research farm injection resulted in greater 0-15cm soil nitrate levels than surface broadcast 1 week after application and persisted for 9 additional weeks. In injected plots, nitrate was concentrated in the injection band; nitrate movement was significant only 10cm lateral to the injection band but overall distribution fit well to a second degree polynomial, especially 2 and 4 weeks after application, R2>0.80. Evidence of leaching was observed in one year after receiving considerable rainfall in weeks 1 and 2 after application. When corn grain yield was averaged year over year, injection was 26% greater than the no- manure control, and 15% greater than surface application. Both biological metrics, C-min and microbial biomass, were stratified by depth; C-min was concentrated within the manure band leading to greater mineralization under injected applications. Microbial biomass was significantly higher under injection at the 15-30cm depth. Overall biological response to manure application method was inconclusive, however manure injection is superior to surface application in terms of nitrogen recovery. / Doctor of Philosophy / Animal manures supply nutrients essential to crop growth (notably nitrogen and phosphorous); liquid manures (pigs and dairy cattle) are commonly applied by spraying them on soils before tillage. Where no-tillage is used as a conservation measure subsurface injection can be used as an alternative to leaving manure on the soil surface. The purpose of this research was to assess nutrient cycling, crop yield, and soil health impacts of surface applied and injected dairy manure applications. Manure injection greatly reduces a nitrogen loss pathway, and as a result supplies more plant available nitrogen to the crop. Methods of soil sampling fields using injection were compared and a recommended sampling method was defined. Transport of a form of nitrogen vulnerable to movement in the ground was found to only travel 10cm away from where manure was injected. Transport of this form of nitrogen below the injection area was observed after abundant rainfall. Crop yields were sometimes higher under injection however, yields are also determined by factors other than nitrogen. Soil health was not repeatably improved under one application method, but microbial activity was greater at shallower soil depths.

Anaerobic digestion and struvite precipitation are two effective ways of treating dairy manure for recovering biogas and phosphorus. Anaerobic digestion of dairy manure is commonly limited by slow fiber degradation, while one of the limitations to struvite precipitation is the availability of orthophosphate. The aim of this work was to study the use of microwave-based thermochemical pretreatment to simultaneously enhance manure anaerobic digestibility (through fiber degradation) and struvite precipitation (through phosphorus solubilization). Microwave heating combined with different chemicals (NaOH, CaO, H₂SO₄, or HCl) enhanced solubilization of manure and degradation of glucan/xylan in dairy manure. However, sulfuric acid-based pretreatment resulted in a low anaerobic digestibility, probably due to the sulfur inhibition and side reactions. The pretreatments released 20-40% soluble phosphorus and 9-14% ammonium. However, CaO-based pretreatment resulted in lower orthophosphate releases and struvite precipitation efficiency as calcium reacts with phosphate to form calcium phosphate. Collectively, microwave heating combined with NaOH or HCl led to a high anaerobic digestibility and phosphorus recovery. Using these two chemicals, the performance of microwave- and conventional-heating in thermochemical pretreatment was further compared. The microwave heating resulted in a better performance in terms of COD solubilization, glucan/xylan reduction, phosphorus solubilization and anaerobic digestibility. Lastly, temperature and heating time used in microwave treatment were optimized. The optimal values of temperature and heating time were 147°C and 25.3 min for methane production, and 135°C and 26 min for orthophosphate release, respectively. Applying manure or slurry directly to the land can contribute to pathogen contamination of land, freshwater and groundwater. Thus it is important to study the fate of pathogens in diary manure anaerobic digestion systems. The goal of the project was to establish a molecular based quantitative method for pathogen identification and quantification, compare the molecular based method with culture based method and study pathogen fate in dairy manure and different anaerobic digesters. Result showed that molecular based method detected more E.coli than the culture based method with less variability. Thermophilic anaerobic digestion can achieve more than 95% pathogen removal rate while mesophilic anaerobic digester had increased E.coli number than fresh manure, indicating temperature is a key factor for pathogen removal. In general, the overall goal of the study is to develop an integrated dairy manure treatment system. The microwave based pretreatment enhanced the subsequent biogas production and struvite precipitation, and the molecular tool based method provided a more precise and faster way to study the pathogen fate in various anaerobic digestions. / Ph. D.

Loss of nitrogen (N) from dairy manure during storage is an issue of economic, environmental, and social concern for farming communities. The lost N 1) decreases the value of manure as a fertilizer and is an economic loss because supplemental inorganic N fertilizer is purchased to meet N needs on farms; 2) produces the potential pollution for water and air systems, thereby damaging the associated ecosystems; 3) causes challenges to human health. Thus, it is vital to manage and use N in an efficient and eco-friendly manner. N mineralization is a pathway in the N cycle, which converts organic N to inorganic N that is more susceptible to loss. The objective of this study was to conduct lab-scale experiments to assess the effects of temperature, manure solids content, using manure seed and autoclave sterilization operation at the start of storage, and storage time on the N mineralization and the associated microbial community during the storage of liquid dairy manure. Manure scrapped from the barn floor of a commercial dairy farm and diluted to make experimental stocks with high (46 to 78 g/L) and low (19 to 36 g/L) total solids (TS), to simulate what is typically transported to the manure storage pit was used. The manure was incubated in the laboratory at three temperatures (10, 20, and 30°C) for two storage periods (60 and 180 days). Manure samples were taken at different storage time for analyses. The results showed that temperature and using sterilization operation at the start of storage had significant effects on N mineralization for both storage periods (p < 0.05). The highest N mineralization rate occurred at 30℃, which rate constant (k) was 0.096 week-1. While, the lowest N mineralization occurred at 10℃, and its corresponding k was 0.013 week-1. The concentrations of mineralized N (Nm) with non-sterilized (R) manure were significantly higher than that with sterilized (R0) manure (p < 0.05). Compared to that with high TS (H) manure, the concentrations of Nm were significantly higher with low TS (L) manure after 180-d storage (p < 0.05). Raw manure augmented with manure seed (MS) had significantly higher Nm than the manure seed only (SO) (p < 0.05). In order to investigate the changes of microbial community in manure, samples were collected on days 0, 30, 90, and 180 for the 180-d storage experiment, and days 0, 30, and 60 for the 60-d storage experiment, and then manure DNA under different condition was successfully extracted from collected samples and used for 16S rRNA sequencing. This study provided a more comprehensive understanding of the impact factors for manure storage, and was expected to clarify the relationship between N mineralization and the associated microbial community. / Master of Science / Loss of nitrogen (N) from dairy manure during storage is rooted in the process of degradation via microbial activities. During storage of dairy manure, up to 60% of N can be lost to the environment (the air, rivers, groundwater, etc.), causing damages such as global warming and water pollution. However, it is challenging to manage and reduce the N lost during manure storage because of lack of comprehensive knowledge of the complex microbial activities in manure storage structures. Thus, the long-term goal of this study is to discern the interactions of the physical, chemical, and microbial processes that affect the N transformation. The generated information will help to mitigate/minimize the loss of nitrogenous gases during storage of dairy manure. The specific objectives included: 1) to evaluate the effects of selected factors (including storage time, temperature, manure solids content, using manure seed and sterilization operation at the beginning of storage) on N mineralization during storage of liquid dairy manure and determine the associated N mineralization rate; 2) to reveal the microbial communities in stored liquid dairy manure under different conditions (listed above). The outcome of this study could be used to refine N mineralization input parameter of manure storage submodules of the process-based models such as Manure DeNitrification-DeComposition model (Manure-DNDC) and Integrated Farm System Model (IFSM) with the goal to improve their accuracy of estimating or accounting for the fate or cycling of N in dairy manure during storage.