Aquaculture has great potential to help supply the nutritional needs of a growing population. To date, however, the benefits that aquaculture can have, have largely been overshadowed by the environmental degradation some segments of the industry have caused. The following body of work describes my efforts to help reduce the environmental impacts of aquaculture. By integrating aquaculture production into traditional agriculture, the impact of farming on already limited water resources and the reliance on chemical fertilizers can be reduced. Recent expansion of the aquaculture industry in Arizona has made it possible to study the integration of olive groves with marine shrimp culture. In chapter 3, I describe the characterization and evaluation of the effluent from an inland, low-salinity shrimp farm as a potential source of irrigation water. I found that 0.41 kg of ammonia-nitrogen, 0.698 kg of nitrite-nitrogen, 8.7 kg of nitrate-nitrogen and 0.93 kg of total phosphorus (TP) were made available as fertilizer each day in the effluent water. Based on the results of this first study, I decided to conduct a farm trial to quantify the effects of these shrimp farm effluents on olive trees. This work is described in chapter 4. Trees in all treatment groups grew an average of 40.1 cm over the four month study period. While growth of trees irrigated with shrimp farm effluent did not improve in respect to the other treatments, our results do indicate that irrigating with low-salinity water had no noticeable negative effects. Chapter 5 describes work conducted in Idaho, as part of a larger study aimed at reducing the effluent loads of phosphorus (P) from high density, flow-through aquaculture facilities. Research steps were taken to establish a relationship between TP and the carbon 12/13 isotope ratio (δ¹³C) and/or the nitrogen 14/15 isotope ratio (δ¹⁵N). Our findings suggest that both δ¹⁵N and δ¹³C are good better proxies for P, after correcting for P retention. A linear regression of %P (corrected) on δ¹³C and δ¹⁵N resulted in R2 values of 0.843 and 0.8622, respectively. This suggests that by tracking δ¹⁵N and/or δ¹³C through a high-density, flow-through aquaculture facility over time I will be able to determine the residence time of P with a high degree of accuracy.

Three soils were tested as possible substrates for an evapotranspiration cover for a Uranium mill tailings disposal site in Moab, Utah. Small weighing field lysimeters were used to determine the field capacity of soils with the effect of a coarse-grained capillary barrier placed beneath the soil to increase water retention. Water was ponded on each lysimeter and then covered with plastic to prevent evaporation. Lysimeters were drained and weighed periodically throughout the experiment. Field capacity was determined by the weight of the lysimeter when drainage stopped. Results were compared to a mathematical model for estimating water storage of capillary barriers. Results from particle size analyses were also compared to water storage results and we found that both sand and clay were significant factors (p <0.05) in explaining water storage. After determining the water-holding capacity of the soils, recommendations on the most suitable soil for the Moab evapotranspiration cap will be made.

Aquatic nuisance species (ANS) represent a growing problem in Arizona that is receiving little funding attention. With the objective of addressing this problem in a coordinated manner between state and federal agencies, the task of writing the Arizona State Aquatic Nuisance Species Management Plan was undertaken, this process and its results will be discussed. Section 1204 of the Nonindigenous Aquatic Nuisance Prevention and Control Act of 1990 (P.L. 101-646), provides opportunity for federal cost-share upon adoption of a state management plan. Methodology included gathering input towards reworking an early draft of the plan at a number of meetings, including the Lower Colorado Giant Salvinia Task Force, the Salvinia molesta National Convention, and Southwest Vegetation Management Association, and researching the format and process used in writing plans recently adopted in other states. Developments in management needs were incorporated, several of the plan's tasks were initiated and the plan was presented to agency members for comments and review. The resulting management plan is now ready to be signed into action, requiring approval by the state governor as a final step towards providing additional funds to fight ANS.

The primary objective of this study was to evaluate the applicability of polymerase chain reaction (PCR) for the detection of enteroviruses in groundwater impacted by reclaimed wastewater. Samples were analyzed by conventional cell culture assay and the reverse transcriptase polymerase chain reaction (RT-PCR), semi-nested PCR, sequencing and dot blot probe hybridization. Viruses were detected in 4/20 samples by cell culture compared to 9/20 by RT-PCR. Semi-nested PCR and probe hybridization increased detection sensitivity to 11/20 and 12/20, respectively. Sequencing of seminested PCR products confirmed enteroviral origin of the amplified sequences, suggesting no cross-reactivity of the primers. Chlorine inactivated viruses were not concentrated as efficiently as cell culture detectable virus (90 percent less efficient). Their ability to be detected by PCR decreased by 90% after five days in secondary effluent and nine days in tap water. These results suggest that PCR is a more sensitive approach for the detection of enteroviruses in the environment. Also, chlorine inactivated viruses are less likely to be detected by PCR than cell culture infectious viruses.

A study was conducted in Maricopa, AZ over three field cropping seasons from December 2001 through April 2003 in order to determine the effects of fish effluent irrigations on field crops and to determine the sustainability of nutrient recycling through an integrative aquaculture-agriculture system. Treatments were designed to compare current fertilization and irrigation methods to possible integrative strategies in order to conserve natural resources. The discharged outflow from two sources of irrigation water, (well water and effluent from a fish pond/reservoir), were tested throughout the duration of the study. Maricopa's NO3-rich well water, was consistently found to contain slightly higher total N concentrations than the fish effluent, which contained higher NH4, organic N, and PO4 concentrations. Unfavorable spatial distribution of pond sludges (containing significantly higher amounts of N and P than well water) resulted in the remainder of large stores of nutrients along the pond bottom. Because a nutrient sink was created within these pond reservoirs, fish effluent irrigations were found to have no significant effect on cotton or barley yields. Vegetative plant growth, however, was significantly affected in several instances, probably by the slow, yet advantageous process of organic matter degradation near soil surfaces. Any significant increases in vegetative growth were found only in effluent-irrigated plots and occurred later in crop seasons. Analysis of the pond sludge confirmed that if pond sediments could be more efficiently removed and applied to land, the benefits from such an integrative system could have great ecological and financial benefits (i.e. decreasing chemical fertilizer use, using water to a greater potential, producing an extra crop of fish, and having lower fertilization costs).

Land surface albedo is the ratio of reflected to incident solar radiation. It is a function of several surface parameters including soil color, moisture, roughness and vegetation cover. A better understanding of albedo and how it changes in relation to variations in these parameters is important in order to help improve our ability to model the effects of land surface modifications on climate. The objectives of this study were 1) To determine empirical relationships between smooth bare soil albedo and soil color, 2) To develop statistical relationships between albedo and ground-based thematic mapper (TM) measurements of spectral reflectances, 3) To determine how increased surface roughness caused by tillage reduces bare soil albedo and 4) To empirically relate albedo with TM data and other physical characteristics of mixed grass/shrubland sites at Walnut Gulch Watershed. Albedos, colors and spectral reflectances were measured by Eppley pyranometer, Chroma Meter CR-200 and a Spectron SE-590, respectively. Measurements were made on two field soils (Gila and Pima) at the Campus Agricultural Center (CAC), Tucson, AZ. Soil surface roughness was measured by a profile meter developed by the USDA/ARS. Additional measurements were made at the Maricopa Agricultural Center (MAC) for statistical model testing. Albedos of the 15 smooth, bare soils (plus silica sand) were determined by linear regression to be highly correlated (r²=0.93, p>0.01) with color values for both wet and dry soil conditions. Albedos of the same smooth bare soils were also highly correlated (r²≥0.86, p>0.01) with spectral reflectances. Testing of the linear regression equations relating albedo to soil color and spectral reflectances using the data from MAC showed a high correlation. A general nonlinear relationship given by y=8.3661n(x)+37.802 r²=0.71 was determined between percent reduction in albedo (y) and surface roughness index (x) for wet and dry Pima and Gila field soils. Measurements of albedo, color and spectral reflectance at the Walnut Gulch Watershed indicated that albedo values were highly correlated with percent rock & gravel, color value and reflectance data (TM bands 1-4).

Recent studies have proposed that images from Synthetic Aperture Radar (SAR) sensors can be used to map spatially distributed soil moisture patterns within 5 cm of the surface. Unfortunately, many hydrologic applications require vadose zone soil moisture measurements rather than surface soil moisture measured by the SAR sensor. By combining SAR-derived surface soil moisture maps with a Soil-Vegetation-Atmosphere- Transfer (SVAT) model, it may be possible to obtain spatially distributed, temporally continuous information on vadose zone soil moisture. The first step in developing such a combined approach is to investigate the accuracy and precision of a SVAT model to estimate surface and vadose zone soil moisture over time. In this experiment, we evaluated the Simultaneous Heat and Water (SHAW) model by comparing its soil moisture estimates to a calibrated, one year, hourly soil moisture data set at three different depths under bare soil and shrub cover surfaces. Analysis indicated that the SHAW model overestimated soil moisture at each depth by an average of 0.02 M^3M&-3 under bare soil and underestimated soil moisture at each depth under shrub cover by an average of 0.02 m^3m^-3 . Based on this research, future studies should focus on calibration of the SHAW model and the assimilation of remotely sensed data as a primary model input.

Understanding the extent of microbial transport, distribution and activity in the subsurface is paramount for effective in-situ bioremediation. In one study, we investigated the impact a substrate pulse has on the movement of inoculated or indigenous bacteria through saturated porous media. In another study, we developed a method to visualize the distribution of bacteria on soil surfaces. The elution of either inoculated or indigenous bacteria was monitored from model (homogenous) sand or natural (heterogenous) soil column systems. Sand columns receiving salicylate resulted in enhanced elution of inoculated P. putida. However, the salicylate pulse did not result in enhanced elution of P. putida from a natural system. For natural heterogenous systems, the salicylate pulse significantly affected the elution of certain indigenous bacteria. Specifically, more heterotrophs were eluted from soil columns receiving salicylate than from those that did not for both loamy sand soils tested. On the other hand, there were consistently fewer salicylate-degrading cells eluted in the presence of salicylate from one of the two soils tested. These data suggest that bacterial transport is a function of both the porous medium and the microbial population(s) under investigation. In the second study, an agar lift-DNA/DNA hybridization technique was developed to visualize the distribution of eubacteria on soil surfaces. Briefly, a single layer of soil was lifted from the surface of soil microcosms onto agar slabs and allowed to incubate. Bacterial colonies were lifted from the agar slabs onto membranes. The location of individual colonies was detected on the membranes by hybridization with a probe complementary to a conserved region of the eubacterial genome. This method was able to detect active microorganisms on different soil surfaces. The probe signal correlated well with the number of metabolically active microorganisms found in soils amended with a carbon source. This technique also allowed for visualization of localized microbial activity. A combined approach utilizing both soil column studies and the agar-lift technique should allow researchers to better elucidate microbial transport, distribution and activity in subsurface environments.

The spatial and temporal responses of natural landscape ecosystems in the Northeast region of Brazil (NEB) to changes in rainfall conditions over the last two decades of the 20th century have not been fully examined. The NEB ecosystems are highly dynamic landscape responding to weather conditions, of which rainfall is the most important variable. The research described in this dissertation was conducted to test whether or not the impact of rainfall fluctuations on the vegetation dynamics can be spatially and temporally differentiated within the NEB ecosystems. This was achieved in two phases: In phase one, the spatial and temporal consistency of the response of monthly normalized difference vegetation index (NDVI) derived from Advanced Very High Resolution Radiometer (AVHRR) data records to monthly rain gauge data records for the period 1982-1993 was assessed. This assessment of the spatial and temporal responses of the NDVI time series data to rainfall time series data tested the hypotheses that responses of NEB ecosystems to rainfall conditions can occur with different time lags and can be spatially heterogeneous. This was achieved by using correlation coefficients with different time lags and by applying factor analysis through the use of Varimax rotation. In phase two, the spatial and temporal variability of the NDVI responses to NEB land surface conditions for the period 1982-2001 was quantified. This quantification of temporal and spatial variability in NDVI across the NEB ecosystems tested the hypothesis that responses of NDVI variability to land surface conditions of the NEB can be temporally and spatially heterogeneous by combining statistical parameters of monthly series of NDVI (minimum, mean, maximum, anomalies and coefficient of variation) and by using annual NDVI images. The results of phase one of this research showed that the direct response (i.e., no lagged response) of the NEB ecosystems to rainfall was associated with different land cover types. A strong positive relation was found in rainfall-limited NEB ecosystems that are associated with Caatinga biome. Particularly, the disturbance of the landscape reduced the significance of the relationship. Over the Cerrado biome and Atlantic rain forest (evergreen tropical forest), significant negative relations between NDVI and rainfall were found where there are no moisture availability constraints. However, the NDVI responses of the NEB ecosystems to changing rainfall conditions were found to be strongly positive for the correlation of NDVI with rainfall in the concurrent plus one previous month. This was demonstrated for most of the NEB ecosystems, except for the southeastern NEB that is formed by the Atlantic rain forest that, in certain areas, has been converted to cropland. In general, there is a good spatial agreement between the NEB ecosystems and the patterns of NDVI variability on both the annual basis and the interannual basis as the temporal responses of the NEB ecosystems are affected by both positive and negative correlations with rainfall. In phase two, the results show clear indications that, for the inter-annual NDVI variability in the interval between 20% and 45% variability a positive response of ND VI to changes in rainfall exist for most of NEB ecosystems where main annual rainfall amounts vary from 300 to 750 mm. A strong decrease of response was found in the monthly NDVI anomalies trend over the period of September 1988 to August 1997. The decrease might be interpreted as a response of NEB ecosystems caused by the impact of enhanced aridity over the 1990s. Overall, in the first phase, it was observed that responses of different land cover types of the NEB to rainfall conditions appeared to occur with different time lags and appeared to be spatially heterogeneous. In the second phase, the inter-annual NDVI variability in the NEB ecosystems to land surface variations appeared to be temporally and spatially heterogeneous. These results suggest that vegetation responses over the NEB ecosystems to changing rainfall conditions, as measured by changes in NDVI to rainfall fluctuations, may have a potential for predicting the impact of rainfall conditions on the NEB landscape dynamics.

Sixty-three of 435 (14.5%) samples collected from broiler chickens were positive for C. jejuni. Twenty-two of 55 samples were from organic chickens (40%) and 41 of 380 samples were from conventional chickens (10.8%). Isolates were subjected to macrorestriction profiling using SmaI and analyzed for their ability to survive in macrophage cells and invade in epithelial cells. Antibiotic testing to cefaclor, ciprofloxacin, tetracycline, erythromycin, gentamicin, trimethroprim/sulfamethoxazole, and ampicillin were performed. Finally, 5 isolates of varying putative in vitro virulence traits were chosen for experimental inoculation of newborn piglets. Five piglets per isolate were tested and examined macroscopically and microscopically upon necropsy. Genotyping of isolates indicated 1 to 3 profiles per flock. Of the 22 organic isolates from chickens, only 3 (13.6%) were able to survive within macrophages. For the conventional isolates, 21 out of 41 (51.2%) were able to survive. However, the majority of isolates (90.5%) from both organic and conventional isolates were not capable of invading epithelial cells. No isolates exhibited resistance to ciprofloxacin or gentamicin. One isolate out of 63 (1.6%) was resistant to erythromycin, 52 (82.5%) to tetracycline, 28 (44.4%) to trimethroprim/sulfamethoxazole, and 6 (9.5%) to cefaclor. In terms of the piglet studies, regardless of the combination of in vitro invasion or survival results or type of flock, most piglets (16/25) in all groups exhibited hyperemia, edema, and hemorrhage in the small intestine or colon upon gross examination. Microscopic examination revealed congested mucosa and erosion of the epithelium in 10 of the 25 piglets from 4 of the 5 groups. In conclusion, this study suggests that C. jejuni isolated from broiler chickens are virulent in piglets and are probably capable of causing disease in humans. Furthermore, the results of the survival and invasion assays did not correlate with the results of the piglet studies and cannot be relied upon to predict degree of virulence. Therefore, another virulence factor is responsible for the pathogenesis, such as a toxin(s). As this is the first study to confirm putative in vitro virulence traits with an animal model, further research is recommended with the piglet model to assess pathogenicity.