Surrogate organisms have been used to study highly pathogenic organisms, or organisms that cannot be cultured in the laboratory. Surrogates are selected based on multiple similarities to the pathogen, such as morphology, genome size and structure, and environmental characteristics. This dissertation utilized MS2 coliphage as a surrogate for norovirus and Ebola virus in three environments. MS2 is an icosahedral, single-stranded RNA bacteriophage. It is a male-specific coliphage that infects the bacteria Escherichia coli. Its properties, such as morphology and survival in the environment, have been likened to those of many enteric viruses. Because of this, it has been used as a surrogate for pathogenic enteric viruses for disinfection testing on surfaces, in water and in food; modeling the movement and survival of pathogens in different environments; and transfer properties from surfaces. This dissertation utilized MS2 as a surrogate in three different studies. In the first, MS2 is used as a surrogate for human enteric viruses in irrigation canals to predict the re-suspension of pathogenic viruses from bed sediment into overlying irrigation water using a flume to re-create field conditions in the laboratory. MS2 re-suspension into the overlying water was characterized at varying flow rates and velocities using two sediment types. Its overall re-suspension was not statistically significantly different (p > 0.05) between flow rates. The additional studies in this dissertation used MS2 as a surrogate for Ebola virus in human waste. Ebola virus is a BSL-4 organism that is spread through direct contact with bodily fluids. It is found in bodily fluids in concentrations between 10^5.5 and 10⁸ genome copies per milliliter. In the first study using MS2 as a surrogate for Ebola virus, efficacies of four disinfectants were tested using 10¹² PFU of MS2 in one liter containing 2.25% (w/v) organic matter at three contact times (1, 15 and 30 minutes). The purpose of this study was to assess the disinfectants on reducing virus in waste before toilet flushing. Peracetic acid and quaternary ammonium formulation were found to reduce the concentration of MS2 in the toilet bowl the fastest (within one minute) with the greatest reduction (2.26 and 1.99 log₁₀), when compared with the other disinfectants. Reductions observed from hydrogen peroxide were significantly less than those from peracetic acid and quaternary ammonium (p < 0.05). The contamination of restroom surfaces by MS2 was also evaluated after toilet flushing with and without disinfectant treatment. All four disinfectants were found to significantly reduce the viral concentrations on fomites after 15 minutes of contact (p < 0.05). Despite disinfectant use, three sites were contaminated in 100% of trials (N = 18). These were the toilet bowl rim, the toilet seat top and underside. The final study evaluated the inactivation of MS2 and several other viruses by thermophilic and mesophilic anaerobic digestion. Little information is available on the influence of the wastewater treatment process, specifically anaerobic digestion, on emerging viruses, such as Ebola virus. It is important to evaluate this process due to the environmental disposal and discharge of wastewater and solids into the environment. All viruses were recoverable after mesophilic digestion (reductions from 1.8-6.6 log₁₀ per mL), except the lipid-containing bacteriophage Φ6. Thermophilic digestion inactivated all viruses significantly (p = 0.0011) more than mesophilic digestion. The reductions by thermophilic digestion ranged from 2.8-7.1 log₁₀ per mL. The inactivation between the initial concentration and both digestion types was statistically significant (p = 0.007).

Soil water content (SWC) measurements are crucial worldwide for hydrological predictions, agricultural activities, and monitoring the progress of reclamation on disturbed land from industrial activities. In colder climates, snow water equivalent (SWE) measurements are equally important, and directly contribute to improved spring water supply forecasting. Both these variables, SWC and SWE, are commonly measured with either point-scale (e.g. soil cores for SWC and snow tubes for SWE) or large-scale (remote sensing) methods. The cosmic-ray soil moisture probe (CRP) was recently developed to fill this gap between small- and large-scale measurements. The CRP provides an average SWC reading in a landscape-scale measurement footprint (300 m radius) by taking advantage of the relationship between aboveground neutrons and soil water. Although the CRP has proved accurate in relatively homogenous sites, it has not been validated at highly heterogeneous sites. Since snow is simply frozen water, the CRP also has the potential for monitoring SWE at the landscape-scale. However, no calibration has been developed for measuring SWE with the CRP. This thesis aimed to further validate the use of a CRP for measuring SWC at a highly heterogeneous site, and calibrate a CRP for monitoring landscape-scale SWE at an agriculture field. The heterogeneous site used to validate the CRP for SWC measurement was an oil sand reclamation site made up of multiple test plots of varying soil layer treatments. Despite the clear differences in soil texture at the site, the CRP-monitored SWC compared accurately to sampled soil water content and a network of soil moisture probes. With the use of modeling, it was also possible to downscale the CRP measurement to the plot scale. For calibrating the CRP for monitoring SWE, an empirical calibration function was developed based on the relationship between the CRP-measured neutrons and SWE from snow surveys with snow tubes. Using the calibration equation, CRP-estimated SWE closely matched SWE measured from snow surveys. Differences were attributed to mid winter and spring melting of the snowpack along with varying soil water content in the top of the soil profile. This research demonstrates the usefulness of the CRP for monitoring SWC at unique sites and its ability to monitor SWE at the landscape-scale.

Thesis (MScAgric)--Stellenbosch University, 2013. / ENGLISH ABSTRACT: Soil amelioration and conditioning is desirable and in many cases essential, due to increasing food demand and the deterioration and exhaustion of soils. A new soil ameliorant, consisting of orange oil as a base and a mixture of surfactants, is on the global agricultural market. Use of this soil ameliorant by farmers has made an impact on crop production and plant growth on many farms. The effects of this soil ameliorant on selected soil properties as well as plant traits were evaluated by a field trial, a pot trial and a Water Characteristic Curve experiment. A field trial was performed in the Firgrove area near Somerset West, Western Cape (South Africa). It entailed the evaluation of the water content and lateral movement of water in a sandy soil after the application of the soil ameliorant. The field was already planted with Capsicum annuum crop at the initiation of the trial. The trial was performed in a drip irrigated field by taking soil water measurements using a Diviner 2000 probe over a nine week period. The trial showed significant increases in water content on the plots treated with the soil ameliorant. These increases are indicative of an increase in the lateral movement of the soil water, as the measurements were taken between two drippers. On average, the ameliorant treated soil had 17% higher water content than that of the control. A Water Characteristic Curve (WCC) experiment was conducted, which entailed establishing the WCC for a sandy soil treated with the soil ameliorant. The Sandbox apparatus, from Eijkelkamp Agrisearch Equipment, was used to perform the experiment and provides suction values of 0.1 to 10.1 KPa. The WCC showed that the ameliorant application increased water retention over all suctions, especially for the 10 l/ha ameliorant application. This substantiated the Field trial where water retention was increase in a sandy soil. A pot trial was performed in a greenhouse to evaluate the effect of the soil ameliorant on selected soil properties and certain plant traits. This experiment consisted of an ameliorant treatment and a control with a combination of four different Plant Available Water Depletion (PAWD) regimes namely, 10% depletion, 50% depletion, 80% depletion and 50%C depletion, where “C” refers to covered. The trial layout, with five single pot replicates per treatment combination, was according to a randomized block design. The surface covering of one of the 50% PAWDs was a plastic sheet which to prevent evaporation from the soil surface. The ameliorant treatment resulted in significant improvements in overall plant growth, total biomass production, especially dry root biomass. Leaf Area Index and plant height were also improved. The Biomass Water Use Efficiency was improved with the ameliorant application, especially for the 50%C PAWD illustrating the beneficial use of a mulch. Bulk density was decreased with application of the ameliorant but this difference was not statistically significant. Aggregate stability for the moist soils (10% and 50%C PAWD) was significantly improved with the ameliorant application. The application of this soil ameliorant made significant improvements in various facets of plant growth and certain soil physical properties. Especially water holding capacity in sandy soils and the overall improvement in plant growth. There is still much opportunity for research in this field and many questions remain, especially those pertaining to the mechanisms involved in the workings of a soil ameliorant containing a mixture of ingredients. / AFRIKAANSE OPSOMMING: Die bestuur van besproeingswater en die optimisasie van gewasproduksie is `n studieveld wat baie aandag verg, aangesien varswater bronne bedreig word. As gevolg van die stygende vraag na voedsel en die agteruitgang en uitputting van die grond, is grondverbetering en-kondisionering aanbeveelbaar en in sommige gevalle noodsaaklik. `n Nuwe grond verbeteraar, bestaande uit lemoen olie as `n basis en ‘n mengsel van benattingsmiddels, is beskikbaar op die wêreld landbou mark. Die gebruik van die grondverbeteraar deur boere het ‘n impak gemaak op gewasproduksie en plantegroei op baie plase. Die effek van die grondverbeteraar op geselekteerde grond-eienskappe sowel as plantkenmerke is geevalueer deur ‘n veld proef, ‘n pot proef en ‘n Water Karakeristieke Kurwe eksperiment. `n Veldproef is uitgevoer in die Firgrove omgewing naby Somerset Wes in die Wes-Kaap Provinsie, Suid Afrika. Die veldproef het die evaluasie van die grondwater inhoud en die laterale beweging van water in `n sanderige grond behels. Die gewas Capsicum annuum was alreeds in die veld aangeplant voor die begin van die proef. Die proef was uitgevoer in `n drup besproeide veld deur grondwater metings wat geneem is met `n Diviner 2000 peilstif oor `n periode van nege weke. Die proewe het `n beduidende verhoging in die groundwater-inhoud getoon waar die grond met die grondverbeteraar behandel is. Die verhogings was `n aanduiding van `n toename in die laterale vloei van grond water, aangesien die lesings tussen twee druppers geneem is. Die grond, wat met die grondverbeteraar behandel is, het gemiddeld 17% hoёr groundwater-inhoud gehad as die kontrole. `n Water Karakteristieke Kurwe (WKK) eksperiment is uitgevoer, wat bestaan het uit die opstel van die WKK vir `n sanderige grond behandel met die grondverbeteraar. Die “Sandbox” apparaat van Eijkelkamp, Agrisearch Equipment is gebruik wat negatiewe druk waardes van 0.1 tot 10.1 KPa toon. Die WKK het getoon dat die toediening van die grondverbeteraar die water retensie verhoog het oor al die drukke, veral in die 10 l/ha toediening. Dit staaf die resultate van die Veld eksperiment waar water retensie verhoog is in die sanderige grond. Die pot-eksperiment is uitgevoer in `n tonnel om die effek van die grondverbeteraar op geselekteerde grond eienskappe en verskeie plant eienskappe te evalueer. Die eksperiment het bestaan uit ‘n grondverbeteraar behandeling en ‘n kontrole met ‘n kombinasie van vier verskillende plantbeskikbare wateronttrekkings naamlik, 10%, 50%, 80% onttrekking, en ‘n 50%C onttrekking, waar “C” verwys na “covered”. Die proef uiteensetting, met vyf enkel pot herhalings per behandeling kombinasie was volgens ‘n ewekansig blok uitleg. Die oppervlakte dekking van 50%C plantbeskikbare waterottrekking was `n 60 μm plastiek-vel wat verdamping vanaf die grondoppervlak verhoed het. Die grondverbeteraar behandeling het `n beduidende verbetering in algehele plantgroei, totale biomassa produksie en spesifiek droё wortel biomassa getoon. Die blaararea indeks en planthoogte het ook `n verbetering getoon. Die biomassa-watergebruiksdoeltreffendheid het verbeter met die toediening van die grondverbeteraar, spesifiek vir die 50%C plantbeskikbarewaterottrekking wat die voordele van die gebruik van oppervlakdekking illustreer. Die brutodigtheid is verminder deur die toediening van die grondverbeteraar, maar die verskil was statisties nie wesenlik nie. Agregaat-stabiliteit vir die grond met `n hoёr vogregime (10% en 50%C plantbeskikbare waterottrekking) is wesenlik verbeter met die toediening van die grondverbeteraar. Die toediening van die grondverbeteraar het wesenlike verbeteringe in verskeie plantegroei- en grondfisiese-eienskappe getoon. Spesifiek laterale beweging in sanderige grond en die verbettering van algehele plantegroei. Daar is nog baie geleenthede vir navorsing in die veld en baie vrae bly onbeantwoord, veral in verband met die meganismes met bretrekking tot die werking van die grondverbeteraar wat uit `n mengsel van bestandele bestaan.

The study was aimed to provide information on local biomass development during crop growth using ground based optical sensors and to incorporate the local crop status to a crop growth simulation model to improve understanding on inherent variability of crop field. The experiment was conducted in a farmer’s field located near Princeton in Caldwell County, Western Kentucky. Data collection on soil, crop and weather variables was carried out in the farm from 2006 December to 2008 October. During this period corn (Zea mays L.) and winter wheat (Triticum sp) were grown in the field. A 450 m long representative transect across the field consisting of 45 locations each separated by 10 m was selected for the study. Soil water content was measured in a biweekly interval during crop growth from these locations. Measurements on crop growth parameters such as plant height, tiller count, biomass and grain yield were able to show spatial variability in crop biomass and grain yield production. Crop reflectance measured at important crop growth stages. Soil water sensing capacitance probe was site specifically calibrated for each soil depth in each location. Various vegetation indices were calculated as proxy variables of crop growth. Inherent soil properties such as soil texture and elevation were found playing a major role in influencing spatial variability in crop yield mainly by affecting soil water storage. Temporal persistence of spatial patterns in soil water storage was not observed. Optimum spatial correlation structure was observed between crop growth parameters and optical sensor measurements collected early in the season and aggregated at 2*2 m2 sampling area. NDVI, soil texture, soil water storage and different crop growth parameters were helpful in explaining the spatial processes that influence grain yield and biomass using state space analysis. DSSAT was fairly sensitive to reflect site specific inputs on soil variability in crop production.

Water quality, and therefore human health, may be significantly affected by the presence of pathogenic enteric microorganisms derived for improper disposal of wastewater to aquatic environments. Detection of waterborne viruses is complex due to the difficulties in concentrating the sample and then in detecting the virus by cell culture or molecular techniques. Methods used to concentrate enteric viruses from water have remained largely unchanged for nearly 30 years. The U.S. Environmental Protection Agency requires the use of 1MDS electropositive filters for concentrating enteric viruses from water; however, these filters are expensive for routine viral monitoring. The NanoCeram® filter, an electropositive cartridge filter, has been proposed as a new alternative for large volumes of water. The objective of the study was: to evaluate the effectiveness of NanoCeram® filters for the concentration of poliovirus-1 from wastewater samples and compare to 1MDS cartridge filters. This study suggested that NanoCeram® filters are a viable alternative to the use of 1MDS filters for viral monitoring in surface waters and wastewaters. L. monocytogenes outbreaks with Latin-style soft cheese have been well-documented; however, more information to characterize the human health risk associated with the consumption of queso fresco (QF) using unpasteurized milk is needed. The objectives of the study were: i) to evaluate the prevalence of Listeria, Escherichia coli, Salmonella and fecal coliforms in QF obtained from markets in the northwestern state of Sinaloa, Mexico, and ii) to address the human health impact associated with the consumption of QF contaminated with L. monocytogenes using quantitative microbial risk assessment (QMRA). The study suggested that QF produced in Culiacan, Sinaloa, Mexico have microbial loads above the maximum values recommended by the Official Mexican Regulations; and QMRA can be used to interpret microbial contamination data for impacts on public health.

Copper cast alloys de-activate antibiotic-resistant bacteria on contact and could be very effective in decreasing potentially harmful microorganisms in the environment. In this study copper alloys with varying copper contents were utilized to evaluate their antimicrobial effects on Pseudomonas aeruginosa, Escherichia coli, and Enterococcus faecium in changing environmental conditions. The survival rates of P. aeruginosa wild type and its derivative transposon mutants of the cin operon on copper cast alloys were investigated in order to demonstrate the influence of genes involved in copper resistance. The gene disruption of the response regulator of the cin operon resulted in shorter survival rates on copper alloys, which was also influenced by temperature and method of exposure. Bacteria often have acquired copper resistance mechanisms in order to withstand higher copper concentrations in their surroundings, which may be a factor in their survival rates on copper surfaces. Copper- and antibiotic-resistant E. coli and E. faecium strains were obtained from pigs raised on feeds containing copper sulfate and antibiotics. Survival rates of these bacteria were influenced by the percentage of copper in the alloys, varying moisture conditions on copper surfaces, suspension media used, and differences between strains. Survival was also dependent on copper corrosion rates since corrosion inhibition with benzotriazole or a thick surface layer of thermal oxide resulted in prolonged survival on copper surfaces. Corrosion of copper surfaces releases copper ions which directly affect bacterial survival on copper alloys. The results obtained in this study emphasize that copper alloys are effective as antimicrobial materials but changing environmental conditions can significantly influence bacterial survival on copper surfaces. These findings can be applied to a better utilization of copper alloys in water, food, and healthcare environments. Antibiotic- and copper ion-resistant bacteria can be killed on contact with copper alloys which makes the proliferation of these microorganisms less likely and reduces the risk to human health. However, in a very different environment copper ion-resistant microbes can be useful for plant-microbe associations in bioremediation of copper mining wastelands.

In the current study, the antibacterial efficacy of zeolites containing silver or copper ions or a combination of these metals was assessed against several diverse copper resistant (CuR) and copper sensitive (CuS) strains of clinically relevant bacterial species. CuR Pseudomonas putida was significantly reduced in comparison to the unamended zeolite control. Unexpectedly, a CuS P. putida strain with no reported metal resistance appeared to be more resistant to the zeolite containing either Ag or Ag/Cu than the CuR strain. Contrary to expectations, after three and six hours of exposure, the CuS Escherichia coli displayed significantly more resistance to the Ag/Cu and Cu treatments than the reportedly CuR E. coli. All three reportedly CuR strains of Salmonella enterica exhibited resistance to Cu and Ag, as well as to the combination of the two metals after three and six hours of exposure. The reductions observed after 24 hours for all three CuR strains with Cu alone were still statistically significant compared to that of the CuS S. enterica strain. In addition, two of the CuR strains were more resistant to silver after 24 hours of exposure, suggesting a shared resistance mechanism such a copper efflux pump that also removes silver ions from the cell. Both the CuR and CuS strains of E. faecium were highly resistant to all of the treatments. In general, after comparison of all the resistances with all the treatments, E. faecium was the most resistant species, P. putida was the least resistant species, and the Salmonella strains were more resistant than E. coli in most cases.

In this study, the relationship of above-ground net primary productivity (ANPP) with precipitation using the enhanced vegetation index (EVI) from satellite data as surrogate for ANPP was assessed. To use EVI as a proxy for ANPP we extracted the satellite data from areas with uniform vegetation in a 2x2 km area for the multi-site approach.In the multi-site analysis in the United States our results showed a strong exponential relationship between iEVI and annual precipitation across the sites and climate regimes studied. We found convergence of all sites toward common and maximum rain use efficiency under the water-limited conditions represented by the driest year at each site. Measures of inter-annual variability in iEVI with rainfall variation across biomes were similar to that reported by Knapp and Smith (2001) in which the more herbaceous dominant sites were found to be most sensitive to interannual variations in precipitation with no relationships found in woodland sites.The relationship was also evaluated in the southern hemisphere using a multi-site analysis with information from satellite TRMM for precipitation and MOD13Q1 from MODIS for EVI values at calendar and hydrologic year periods. The tested sites were located across the 6 major land cover types inAustralia, obtained from MODIS MCD12Q1 product and used to compare the relationship across different biomes. The results showed significant agreement between the annual iEVI and annual precipitation across the biomes involved in this study showing non-significant differences between the calendar and hydrologic years for the 24 sites across different climatic conditions.At the regional scale we also assessed the ANPP-precipitation relationship across all of Australia. Precipitation data from TRMM was obtained at 0.25x0.25 degrees spatial resolution and monthly temporal resolution and EVI values were obtained from the CGM (Climate Grid Modeling) MOD13C1-16-days and 5.6km temporal and spatial resolutions, respectively. Our results were in fair agreement with those from our first two studies and previous research and provided specific insights regarding the use iEVI as a proxy for productivity over extended regions as well as its combination with data sets from TRMM sensor for precipitation data.

Throughout the arid and semi-arid regions, researchers have been looking at different ways to deal with the salinity problem of the soil and water as well as feed for the livestock. Study 1 focused on a pilot project conducted in an irrigation district in Marana, AZ, USA, looking at using Reverse Osmosis (RO) concentrate on Atriplex lentiformis (quailbush) and then harvesting the plant to be tested for its possible use as a supplement in feed for livestock. Three irrigation treatments were tested based on the potential evapotranspiration rate (ET(o)): (1) plots irrigated at ET(o) adjusted daily via an on-site micrometeorology station; (2) plots irrigated at 1.5 ET(o) adjusted daily; (3) plots irrigated at a constant rate throughout the year based on the mean of annual ET(o). The plants produced 15-24 tons ha⁻¹ year⁻¹ of biomass and could be irrigated at the rate of ET(o), ca. 2 m yr⁻¹ at this location. It was concluded that irrigation of halophyte forage crops provide a viable strategy for extending water supplies and disposing of saline water in arid-zone irrigation districts. Study 2 focused on a field data from Study 1 and two greenhouse experiments. The greenhouse experiments were conducted in 2007 and 2010. The 2010 greenhouse trials, under well-watered conditions, showed that the apparent zero-point-salinity for yield was 47.3 g L⁻¹ TDS. An additional greenhouse experiment was conducted in which plants in sealed pots were grown to the wilting point on a single application of water. The experiment was conducted at different salinities to see if salinity and water stress were additive factors in reducing yield and Water Use Efficiency (WUE). To the contrary, yield and WUE actually increased as a function of salinity, perhaps due to conversion from C3 to C4 photosynthesis over the salinity range (noted in other studies with A. lentiformis). We conclude that xerohalophytes such as A. lentiformis could greatly extend the useful range of salinities under which forage crops can be grown in arid-zone irrigation districts.

Rhamnolipids are surface-active molecules produced by Pseudomonas aeruginosa as congener mixtures. They are considered “green” alternatives to synthetic surfactants used in many applications. Optimizing yield and controlling congener distribution are necessary steps for successful commercialization. Studies have noted that vegetable oils, composed of a mixture of fatty acids, increase rhamnolipid yield. The physiological explanation for this is not yet understood. Furthermore the exact effects of various fatty acid components in the oils on rhamnolipid production have not been reported. The first part of the dissertation was to investigate rhamnolipid biosynthesis when fatty acid substrates are present. A combination of stable isotope tracing and gene expression assays were used to identify rhamnolipid lipid precursors and potential lipid metabolic pathways used in rhamnolipid synthesis. Result suggests that an octanoyl-CoA intermediate of β-oxidation is diverted from β-oxidation to de novo fatty acid synthesis via a “bypass route”, and is incorporated into either a 2-carbon or a 4 carbon β-ketoacyl- ACP, which can then be recognized by the RhlA enzyme for the biosynthesis of rhamnolipid lipid moiety. The second part of the dissertation focuses on studying how fatty acid substrates of different chain length (C₁₂ to C₂₂) and saturation (C(18:1) and C(18:2)) affect rhamnolipid yield, carbon conversion rate, and congener distribution. Results showed that stearic acid significantly increased rhamnolipid yield. A positive linear correlation between the mass percent of stearic acid used and the carbon conversion rate was observed. For all treatments, the RhaC₁₀C₁₀ was the most abundant and RhaC₁₀C(12:1) was the least abundant of the major congeners produced. However, the relative amounts of RhaC₁₀C₈ and RhaC₁₀C₁₂ congeners were dependent on several factors. In general, fatty acid substrates with relatively short chain length (C₁₂ and C₁₄), the unsaturated fatty acid C(18:2), and longer cultivation times resulted in a higher RhaC₁₀C₈/ RhaC₁₀C₁₂ ratio. The studies presented here demonstrate that the medium composition, in particular the organic substrate component, can affect rhamnolipid biosynthesis, yield, and congener distribution. Furthermore, this work presents evidence that C₁₈ fatty acids as co-substrates increase rhamnolipid yield by draining rhamnolipid intermediates directly from the β-oxidation pathway.