For intensive production systems like the Blue Ridge Aquaculture (BRA), based in Martinsville, VA, there are significant economic incentives to reuse the waste by diverting it into a cropping system that would increase the total productivity and total resource-reuse efficiency, and decrease the environmental, ecological, and financial costs of aquacultural waste disposal. In order to facilitate the reuse of effluent from the tilapia production at the BRA, a green house was developed. On this site, sludge waste from recirculating aquaculture was separated and composted using a vermicomposting technique and the resulting compost was utilized as an amendment to conventional greenhouse potting mixes. These aquacultural waste products were compared to conventional greenhouse culture of a common ornamental annual plant. It was hypothesized that (1) vermicomposted aquaculture sludge would increase the growth of plants over conventional greenhouse potting mixes, and (2) recycled aquacultural wastewater can serve as a quality source of irrigation water, and plant response would differ with irrigation method. Plant growth and 11 out of 12 plant tissue nutrients were greater when compost was increased in the substrate. Plant root growth and 3 out of 12 tissue nutrients were increased when irrigated with wastewater. Plant shoot mass and total mass was greater when irrigated by ebb and flow irrigation compared to overhead mist irrigation, and 4 out of 12 tissue nutrients were greater when irrigated with mist irrigation. Overall plant performance was greatest with 15% vermicomposted sludge in the substrate and watered with wastewater by ebb and flow irrigation. / Master of Science

Considerable concern has developed over the possible pollution from poultry litter storage methods. This study was conducted to evaluate three different storage scenarios; covered stockpiles, uncovered stockpiles, and litter sheds. The stockpiles were monitored over two rainfall simulation events, in both the Ridge and Valley and the Piedmont physiographic provinces, with both surface and subsurface flows analyzed. An observational study, where subsurface water was sampled for a nine-month period was conducted using six litter sheds, three in each of the above provinces. Samples were analyzed for nutrients, fecal coliforms, and solids. Concentrations of NHx, TKN, OP, TP, VSS, and FC in surface runoff from uncovered litter piles were all statistically higher than that from covered piles, with NO3 being the exception. However, increased runoff volumes originating from the covered litter piles caused mass loadings from both covered and uncovered piles to be similar enough that statistical significance was not obtained, except in the case of FC. Soil water samples from litter stockpiles did not show a statistically significant treatment effect for concentration data, but uncovered piles did exhibit higher nitrogen concentration estimates than the covered piles. Sample collection frequency showed a statistically significant increase in the number of samples that could be obtained from the edge lysimeter under uncovered litter piles from the Piedmont experimental site. This result indicates uncovered piles are releasing the precipitation absorbed during the rainfall simulation into the sub-surface environment. In the storage shed study, a greater number of samples were collected per attempt at the Piedmont sheds compared to those at the Ridge and Valley site. While both areas were undergoing a significant drought, Piedmont porous-cup lysimeters yielded samples 63% of the time, compared to 10% for Ridge and Valley lysimeters. Lysimeters located near the edge of the shed were also more likely to yield a sample than those in the center or a background location. Unknown interferences within the litter shed samples prevented three laboratories from obtaining valid nutrient concentrations. / Master of Science

Carried out in collaboration with the Occoquan Water Monitoring Lab, this thesis presents the results of research that sought to ascertain the spatial distribution of chlorophyll-a concentrations in the Lake Manassas Reservoir using a combination of Landsat TM satellite imagery and ground based field measurements. Images acquired on May 14, 1998 and March 8, 2000 were analyzed with chlorophyll-a measurements taken on 13, 1998 and March 7, 2000. A ratio of Landsat TM band 3: Landsat Band 4 was used in a regression with data collected at eight water quality monitoring stations run by the Occoquan Watershed Monitoring Lab. Correlation coefficients of 0.76 for the 1998 data and 0.73 for the 2000 data were achieved. Cross validation statistical analysis was used to check the accuracy of the two models. The standard error and error of the estimate were reasonable for the models from both years. In each instance, the ground data was retrieved approximately 24 hours before the Landsat Image acquisition and was a potential source of error. Other sources of error were the small sample size of chlorophyll-a concentration measurements, and the uncertainty involved in the location of the water quality sampling stations. / Master of Science

<p dir="ltr">Interactions between drinking water quality and delivery systems, pipe materials, and attitudes</p>

Antimicrobial resistance (AMR) is a One-Health (human, animal, environment) challenge that requires collaborative, interdisciplinary action. Comparable surveillance data are needed to effectively inform policy interventions aimed at preventing the spread of AMR. Environmental monitoring lags behind that of other One Health sectors and is in need of agreed upon targets and standardized methods. A challenge is that there are numerous microorganisms, antibiotic resistance genes (ARGs), and mobile genetic elements and corresponding methods that have been proposed. In this dissertation, a framework for AMR monitoring of aquatic environments was developed through a combination of literature review and stakeholder input, via surveys and a workshop. Through this process, three targets were selected for standardization: the sulfonamide resistance gene (sul1), the class 1 integron integrase gene (intI1), and cefotaxime-resistant Escherichia coli. Quantitative polymerase chain reaction (qPCR)- and culture-based protocols were developed and pilot tested in two independent laboratories on a set of six water matrices: wastewater, recycled water, and surface water from six different wastewater utilities engaging in water reuse located in five states across the USA. The impact of wastewater treatment and advanced water treatment processes was examined in terms of removal of these targets. Finally, qPCR and culture methods were used to examine the relationship between sul1, intI1, E. coli, and fecal indicators in private household wells across four states in the Southern USA that were identified as susceptible to storm events. The overall findings provide a useful baseline occurrence of the proposed AMR monitoring indicators across a range of water types and protocols that are accessible to water utilities. / Doctor of Philosophy / Life-saving drugs and treatments are failing at an increasing rate because of antimicrobial resistance (AMR). Antimicrobials, such as antibiotics, are a double-edged sword, because they are an effective weapon for killing disease-causing pathogens, but the more they are used the greater the likelihood that microbes that are resistant to them will survive, reproduce, and spread. National action plans for AMR have been created by a majority of countries, emphasizing the importance of antibiotic stewardship and other mitigation strategies. However, numerous data gaps need to be addressed in order to identify strategies that are most likely to be effective and to implement them. Environmental surveillance, including wastewater influent, wastewater effluent, and surface water, could prove an informative means to track AMR trends with time and relate them to human activities and corresponding mitigation efforts. The purpose of this dissertation was to develop a framework for AMR surveillance of aquatic environments and to test it across an array of sample types. We considered an array of possible culture- and DNA-based targets from available scientific literature and engaged experts and stakeholders in narrowing down the list to options that were both informative and feasible. We developed protocols for quantifying an antibiotic resistance gene (sul1), a mobile genetic element that has been implicated in the spread of multi-antibiotic resistance (intI1), and an extended spectrum beta-lactamase (ESBL) producing form of Escherichia coli. We compared the methods between two independent laboratories on untreated wastewater, treated wastewater, recycled water, and surface water collected from six locations across five states. We additionally did a survey of private household well water that was hypothesized to be vulnerable to contamination due to storms and lack of resources for maintenance. The results of this research can help to support environmental monitoring of AMR across the US and globally.

Coastal environments are among the most threatened ecosystems globally, with water quality degradation constituting a major scientific and management issue that requires addressing. Burrowing sandprawns (Kraussillichirus kraussi) have been shown in past research to improve water quality by removing microalgae from the water column. Their burrows are thought to act as biofiltration systems, with water-borne phytoplankton particles being adsorbed onto burrow walls during bi-directional water pumping. However, not much is known about ecological repercussions of this hypothesised mechanism and whether it indiscriminately impacts all microorganisms in the water column. This issue forms the foundation of my research, which aimed to experimentally determine whether potential filtration effects of sandprawns are consistent across pelagic bacterial and phytoplankton assemblages or whether there are any discriminatory responses. Findings demonstrated that increasing sandprawn density did not significantly reduce the abundance of bacterial water quality indicators (Escherichia coli and total heterotrophic bacteria). However, sandprawns were found to reduce the abundance of phytoplankton cells. At the end of the experiment, the relative abundance of phytoplankton in the controls were 1.9 times higher relative to the 100% treatment. Similarly, the concentrations of nitrite were 17.7 times higher in controls relative to 100% treatment at the end of the experiment. Furthermore, increasing sandprawn abundance induced a phytoplankton sizebased shift from pico- to nano dominance, with nanophytoplankton contributing 17.76% at the beginning of the experiment, but shifting to 58.07% at the end of the experiment in the maximum sandprawn density treatment. Additionally, sandprawn presence had no significant impact on cryptophytes or Prochlorococcus-like algal abundance. These results demonstrate that sandprawns disproportionately impact certain groups and influence phytoplankton assemblages beyond biomass decline. These findings are novel as such discriminatory effects on pelagic assemblages have previously not been attributed to endobenthic deposit-feeding ecosystem engineers. This study therefore provides novel insights into mechanisms by which these organisms may alter coastal ecosystems and influence bentho-pelagic coupling processes. This is especially significant when viewed in the context of global change, where understanding the factors that influence phytoplankton dynamics are important for predicting ecosystem functioning under projected climatic conditions. Given the overall top-down impact of sandprawns on phytoplankton, this study supports the idea of sandprawns being effective nature-based tools that can mitigate the global challenge of eutrophication in coastal ecosystems. The results of this study ultimately emphasises the need for protection and conservation of sandprawns (and functionally similar endobenthic engineers) and their habitats from threats such as habitat loss.

Improved agricultural productivity due to use of fertilizers over the last century has resulted in yield of cash crops, such as corn (Zea mayes L), to be increased on a per hectare basis. Consequently, inadequate fertilizer management such as improper timing or over application has led to infiltration into aquatic environments which can be detrimental to the ecology of such systems. Agricultural systems within the Mississippi River Basin have contributed to large-scale eutrophication in the Gulf of Mexico through surface and dissolved fertilizer loading in upstream tributaries. In response to these concerns, nutrient loss reduction strategies (NLRS), have developed in order to minimize these contributions of eutrophication to aquatic environments. Among adjustments in agricultural practices, one solution is the implementation of cover crops at the end of the cash crop growing season. The primary purpose of cover crops is to increase retention of nutrients during the fall and spring through soil stabilization and nutrient uptake which can prevent erosion and dissolved pathways to fertilizer loading in aquatic environments. Common types of cover crops able to achieve these goals are categorized as winter cereal cover crops (WCCC) and namely, winter cereal rye (Secale cereale) (WCR) is preferred in the state of Illinois. Using WCR has provides addition potential benefits such as cold hardiness establishment, carbon sequestration, weed suppression, and altering hydrological conditions before or during the cash crop. Although there are a variety of benefits from WCR, there are documented tradeoffs due to the presence of WCR, namely, reduced corn yields due to diminished stand population and decreased nitrogen availability through the process of immobilization which results from a carbon to nitrogen ration (C:N) which is greater than 25:1. Our research centered around solutions to maximize benefits of WCR while minimizing negative tradeoffs to the subsequent corn. We hypothesized that reduced seeding rate and higher quality cultivars of WCR would lead to quicker decomposition of biomass (Chapter 1) and would result in corn yields (Chapter 2) that were higher than the alternative treatments of high seeding rates and typical cultivars of WCR. Additionally, we hypothesized that selecting alternative cover crop species such as crimson clover (Trifolium incarnatum), integrating crimson clover with WCR, and reducing seeding rate through precision planting of cover crops off of the corn row would lead to quicker decomposition and result in higher corn yields than the WCR treatment planted normally (Chapter 3). All research was conducted with two site-years for each study. Chapter 1 consisted of two studies (Study A and Study B) where WCR seeding rate was modified and consisted of five treatments of 0, 34, 56, 84, and 112 kg ha-1 of WCR (Study A), and where WCR seeding rate as well as cultivar was modified and consisted of five treatments (Study B). Treatments consisted of an initial no cover crop control and two cultivars, one typical rye considered as “normal” and a hybrid variety (KWS) considered as “hybrid” that were planted at rates of 67 kg ha-1, considered as “low”, and 100 kg ha-1, considered as “high”. The objective of both studies in Chapter 1 was to evaluate the influence of seeding rate (Study A) as well as seeding rate × cultivar had on (i) WCR biomass and nutrient composition, (ii) decomposition and C:N dynamics, and (iii) soil nitrogen dynamics during the growing season in 2021 (Year 1) and 2022 (Year 2). In Study A, it was found that overall biomass was higher as seeding rate increased linearly (R2 = .94) over the two years from 34, 56, 84, to 112 kg ha-1 (2810.43, 3022.14, 3179.89, 3416.52 kg ha-1, respectively). The seeding rate did not influence the rate at which WCR biomass decomposed due to similarities in carbon and nitrogen concentrations within WCR. Fluctuations in C:N ranged from a high of 37:1 at the beginning of the decomposition phase to a minimum of 21:1 by the end of the decomposition phase. Soil NO3-N and NH4-N measured lowest in the 112 kg ha-1 treatment at 15-30 cm in Year 1. Treatments with no cover crop had the highest soil NO3-N from 0-30 cm in Year 2. Overall biomass of WCR was consistently higher during both years in the hybrid WCR treatments at both seeding rates compared to the normal rye of the respective seeding rate. The ratio of carbon to nitrogen was higher in hybrid varieties (42:1) in Year 1 but not in Year 2. The decomposition rate of all WCR in Study B were similar and not influenced by the various treatments. Fluctuations of C:N ranged from a high of 42:1 in the beginning of decomposition to a minimum of 17:1 by the end of the decomposition phase. Estimated N release of all treatments were similar. Both NO3-N and NH4-N were higher in the no cover crop treatment at the end of the season from 0-30 cm during Year 1, while there was no end of year difference in Year 2. In conjunction with the results of Chapter 1, our objectives in Chapter 2 were to see how treatments from Study A and B influenced (i) corn grain yield, (ii) corn stand count, near difference vegetation index (NDVI), leaf area index (LAI), corn N uptake, corn ear composition, as well as end of year N balance, and (iii) to analyze how those components related to overall corn yield. We additionally included how the treatments’ influence on corn could impact soil N dynamics. In Study A, overall corn yield was influenced by WCR seeding rate (p < .05) as the no cover crop and 34 kg ha-1 treatment (11.57, 11.61 Mg ha-1, respectively) were significantly different from the 112 kg ha-1 treatment (10.73 Mg ha-1). Stand count for corn was also influenced by WCR seeding rate (p < .05) as it linearly decreased with increasing seeding rate (R2 = .90) from 70,0009 to 62,552 plants ha-1. The seeding rate influenced the NDVI reading as it was lower in the 84 and 112 kg ha-1 treatments, indicating greater potential soil N immobilization. It was found that yield was most strongly correlated with corn stand count and 1000 kernel weight. In Study B, corn stand count was the only variable influenced by treatment, which was highest in the no cover crop treatment and was lower in the hybrid WCR when compared to the normal WCR at their respective seeding rates. Yield, kernel weight, number, N uptake were all higher in Year 1 and N balance was lower in Year 1. Chapter 3 investigated how cover crop selection, integration, and planting method influenced all of the aforementioned objectives from Chapter 1 and 2. One study made up Chapter 3 (Study C) and consisted of six treatments which were a no cover crop control, WCR monoculture planted at a rate of 67 kg ha-1, crimson clover monoculture planted normally (CNP) at a rate of 28 kg ha-1, crimson clover monoculture precision planted off of the subsequent corn row (CPP) at a rate of 20 kg ha-1, a mixture of the WCR and crimson clover planted normally (RCNP) at a rate of 33 and 22 kg ha-1, respectively, and a mixture of WCR and crimson clover precision planted with crimson clover on the subsequent corn row (RCPP) at a rate of 50 and 7 kg ha-1, respectively. It was observed that overall biomass was driven by presence of WCR but was not significantly different from the mixture treatments in either year. The biomass of crimson clover was not impacted by precision planting, indicating the ability to lower seeding rate. Presence of crimson clover was responsible for the C:N ratio of the treatment as all crimson clover monoculture treatments, aside from Year 1 CNP due to presence of weeds biomass, were lower in C:N (17:1) than all other treatments. Decomposition rate was influenced by cover crop selection as CPP had the highest decay rate of all treatments in both years (-0.00111, -0.00118 in Year 1 and 2, respectively) and RCPP treatment decomposed quicker than WCR in Year 2. The ratio of carbon to nitrogen was lowest for crimson clover monoculture treatments, followed by mixture treatments. By the end of the decomposition phase in Year 1, all treatments had similar C:N ratios indicating biomass decomposition and higher N content in WCR. Year 2 had a lower amount of N concentration in all treatments which influenced C:N ratio of WCR associated treatments. Estimated N release was higher in the mixture treatments as their N content was higher than the WCR monoculture with more biomass than the crimson clover monocultures. Over the two years of the study, crimson clover monoculture treatments resulted in the highest yields (10.16 and 10.11 Mg ha-1 for CNP and CPP, respectively) which were significantly different than the RCPP and WCR treatments, resulting in higher N balances in the RCPP and WCR treatments. Year 2 had lower corn stand count, yield, kernel weight, kernel number, NDVI. Yield was strongly correlated with CSD (.81), diameter (.91) and length (-.91). During both years, soil NO3-N and NH4-N were similar in all treatments by the end of the season indicating uptake by corn. We conclude that in Southern Illinois it may not be fiscally responsible for a grower to use seeding rates over 34 kg ha-1 or hybrid cultivars if their intention is to use WCR as a cover crop before corn in their cropping system. Although the biomass was higher, decomposition was not quicker than lower seeding rate of WCR or typical varieties of WCR. Integrating WCR with crimson clover did not result in lower biomass which may be a practical solution to lowering C:N in the cover crop system, aiding in decomposition so the biomass associated N is able to accessed by corn without being loss to early in the growing season through leaching. Precision planting of cover crops did not impede biomass accumulation which indicates seeding rates and planting design possibilities for WCR, and crimson clover cover cropping systems. Corn stand density was highly impacted by the presence of WCR which indicates the need for adjusting rate and cover crop selection in order to minimize yield reduction in corn.

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Globally, water bodies are increasingly affected by undesirable harmful algal blooms. This dissertation contributes to research methodology pertaining to quantification of the algal blooms in multiple water bodies of Mississippi using in situ, analytical, and remote sensing techniques. The main objectives of this study were to evaluate the potential of several techniques for phytoplankton enumeration and to develop remote sensing algorithms for several sensors and evaluate the performance of the sensors for quantifying phytoplankton in several water bodies. Analytical techniques such as “FlowCam”, an imaging flow cytometer; “HPLC”, high performance liquid chromatography with the chemical taxonomy program “ChemTax”; spectrofluorometric analyses; and “ELISA” assay were used to quantify a suite of parameters on algal blooms. Additionally, in-situ algal pigment biomass was measured using fluorescence probes. It was found that that each technique has unique potential. While some of the rapid and simpler techniques can be used instead of more involved techniques, sometimes use of several techniques together is beneficial for managing aquatic ecosystems and protecting human health. Algorithms were developed to quantify chlorophyll a using five remote sensing sensors including three currently operational satellite sensors and two popular sensors onboard the Unmanned Aerial Systems (UASs). Empirical band ratio algorithms were developed for each sensor and the best algorithms were chosen. Cluster analysis helped in differentiating the water types and linear regression was used to develop algorithms for each of the water types. The UAS sensor- Micasense was found to be most useful among the UAS sensors and the best overall with highest R2 value 0.75 with p<0.05 and minimum %RMSE of 28.22% and satellite sensor OLCI was found to be most efficient among the three satellite sensors used in the study for chlorophyll a estimation with R2 of 0.75 with p<0.05 and %RMSE 13.19%. The algorithms developed for these sensors in this study represent the best algorithms for chlorophyll a estimation in these water bodies based on R2 and %RMSE. The applicability of the algorithms can be extended to other water bodies directly or the approach developed in this study can be adopted for estimating Chl a in other water bodies.

Classification of remotely sensed imagery for reliable land use and land cover (LULC) change information remains a challenge in areas where spectrally similar LULC features occur. Dissolved organic matter (DOM) influences the biogeochemistry of aquatic environments and its quantity and quality are due, in large part, to the surrounding LULC. Thus, objectives were to improve the accuracy of LULC classification and quantify seasonal variations of water quality in a watershed dominated by agriculture and determine the controls for the variations in water quality. Support vector machine classification scheme with post classification correction yielded highest accuracy for LULC classifications and four distinct DOM components were found that changed seasonally and were controlled by hydrology and LULC. The microbial component was the main fraction of the DOM pool due in large part to agricultural practices. This DOM can influence the water quality significantly as it moves downstream and causes increased biological activity.