Browsing by Author "Xia, Kang"

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    AgroSeek: a system for computational analysis of environmental metagenomic data and associated metadata
    Liang, Xiao; Akers, Kyle; Keenum, Ishi M.; Wind, Lauren L.; Gupta, Suraj; Chen, Chaoqi; Aldaihani, Reem; Pruden, Amy; Zhang, Liqing; Knowlton, Katharine F.; Xia, Kang; Heath, Lenwood S. (2021-03-10)
    Background Metagenomics is gaining attention as a powerful tool for identifying how agricultural management practices influence human and animal health, especially in terms of potential to contribute to the spread of antibiotic resistance. However, the ability to compare the distribution and prevalence of antibiotic resistance genes (ARGs) across multiple studies and environments is currently impossible without a complete re-analysis of published datasets. This challenge must be addressed for metagenomics to realize its potential for helping guide effective policy and practice measures relevant to agricultural ecosystems, for example, identifying critical control points for mitigating the spread of antibiotic resistance. Results Here we introduce AgroSeek, a centralized web-based system that provides computational tools for analysis and comparison of metagenomic data sets tailored specifically to researchers and other users in the agricultural sector interested in tracking and mitigating the spread of ARGs. AgroSeek draws from rich, user-provided metagenomic data and metadata to facilitate analysis, comparison, and prediction in a user-friendly fashion. Further, AgroSeek draws from publicly-contributed data sets to provide a point of comparison and context for data analysis. To incorporate metadata into our analysis and comparison procedures, we provide flexible metadata templates, including user-customized metadata attributes to facilitate data sharing, while maintaining the metadata in a comparable fashion for the broader user community and to support large-scale comparative and predictive analysis. Conclusion AgroSeek provides an easy-to-use tool for environmental metagenomic analysis and comparison, based on both gene annotations and associated metadata, with this initial demonstration focusing on control of antibiotic resistance in agricultural ecosystems. Agroseek creates a space for metagenomic data sharing and collaboration to assist policy makers, stakeholders, and the public in decision-making. AgroSeek is publicly-available at https://agroseek.cs.vt.edu/ .
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    Alternative and Improved Cropping Systems for Virginia
    Chim, Bee Khim (Virginia Tech, 2016-04-27)
    Feed grain consumption in Virginia and the mid-Atlantic region is more than double the total production. Producing more feed grains in this region could generate more profit for grain growers and lower costs for end-users. Increased feed grain production in this region will necessitate improved corn (Zea mays L.) management techniques and adoption of alternative feed grains such as grain sorghum (Sorghum bicolor L.). In order to achieve our overall objective of increased corn and grain sorghum production in the region, experiments were conducted to assess tools with the ability to increase the efficiency of sidedress nitrogen (N) application for corn and to test the performance of grain sorghum in both full season and double-crop rotations in this region. For the corn studies, seven field experiments were established in 2012-2014 with four replications in a randomized complete block design. Treatments included a complete factorial of four different preplant N rate (0, 45, 90, 134 kg ha-1) with three different approach simulation model-prescribed rates (Virginia Corn Algorithm, Maize-N, Nutrient Expert-Maize) and the standard Virginia yield-goal based approach. No differences in corn yield were found between the different simulation model and preplant N rate, however the prescribed sidedress N rate varied significantly due to the simulation model, preplant N rate and the interaction between them. The nitrogen use efficiency (NUE) was estimated based on partial factor productivity (PFP) of nitrogen. The greatest PFP resulted from use of the Virginia Corn Algorithm (VCA), which produced 68 kg grain kg N-1 compared with 49 kg grain kg N-1 for the yield-goal based approach. While the VCA shows promise as a tool for improving NUE of sidedress applications in corn, more research is needed to validate performance. Soybean (Glycine max L.) is often double-cropped after small grain in the mid-Atlantic region. Growing grain sorghum in this niche in the cropping system instead could result in greater overall feed grain production. In order to assess the performance of grain sorghum as an alternative in common cropping systems, four field experiments were established at the Southern Piedmont Agriculture Research and Extension Center (SPAREC) and Tidewater Agriculture Research and Extension Center (TAREC), near Blackstone and Holland, Virginia, respectively. The experiments were conducted using a split plot design with four replications and fourteen treatments. Main plot was winter small grain crop; either barley (Hordeum vulgare L.), triticale (x Triticosecale.), wheat (Triticum aetivum L.) or winter-fallow and the subplot either soybean or sorghum. In three of four instances, full season sorghum yields were greater than double-cropped sorghum after small grain. At two locations, sorghum yields following triticale were lower than when following barley, possibly indicating an antagonistic or allelopathic effect of triticale. The most profitable cropping system was wheat-soybean based on the price assumptions and measure yields in this experiment. Among the sorghum cropping system, the most profitable system was also wheat-sorghum. Sorghum can be successfully grown in both full-season and double-crop systems and offers good potential to increase feed grain production in this region.
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    Antimicrobial resistance in soil: long-term effects on microbial communities, interactions with soil properties, and transport of antimicrobial elements
    Shawver, Sarah Elizabeth (Virginia Tech, 2022-06-08)
    Since penicillin was discovered in 1928, antibiotic usage in human and veterinary medicine and prevalence of antibiotic resistant bacteria (ARB), has been increasing. While antibiotics and antibiotic resistance genes (ARGs) naturally occur in soils, increasing abundances of ARGs correlate with increased antibiotic usage in agricultural settings. When livestock are treated with antibiotics, the antibiotic compounds, ARB, and ARGs can enter soil via manure excreted onto pastures or applied to other fields as fertilizer, thereby spreading antimicrobial resistance (AMR) in the environment. In addition to human health implications, increased AMR has negative impacts on ecosystem services such as carbon and nitrogen cycling. While many studies have researched antibiotic persistence in agricultural systems and their impacts on soil microbial communities, there are still significant knowledge gaps around the long-term effects of antibiotic exposure in soils, how those impacts differ among soils, and how elements of AMR may differentially transport through soil. To address these knowledge gaps, our objectives were to 1) examine the impact of multi-year repeated additions of manure from cattle administered antibiotics on soil microbial communities, 2) determine the interactive effects of soil moisture and type on soil microbial communities exposed to antibiotics and manure, and 3) differentiate between vertical transport of AMR in the form of viable ARB or ARGs in extracellular plasmids. Our results demonstrate that soil bacterial community structures were consistently altered by 3-year additions of manure from cattle administered antibiotics compared to soil amended with antibiotic-free manure. Furthermore, ARG abundances were higher in soils with manure additions compared to soil without manure, although this was true regardless of whether the cattle were administered antibiotics, suggesting that manure and antibiotic impacts on soil microbial communities can persist over multi-year of repeated manure applications. Additionally, in microcosms, effects of manure from cattle administered antibiotics on ARG abundances, microbial community structures, respiration, and nitrogen pools in soil were seen across multiple soil types and moisture contents, suggesting environmental conditions can alter how manure and antibiotics impact microbial community structure and nutrient cycling. Finally, ARB flowed readily through saturated soil, but were also detectable in the top 5 cm of soil columns. However, ARGs on extracellular plasmids did not flow through soil columns and were not detected in soil, indicating that extracellular DNA does not persist or transport through the soil to any meaningful degree. Overall, these results indicate a nuanced approach is required to mitigate the environmental spread of AMR. Soil management strategies for addressing the AMR crisis should consider the broader context of manure management, as high ARG abundances can come from application of manure from antibiotic-free cattle, and soil microbial communities in individual environments may have varied responses to manure antibiotic exposure. Furthermore, the transport of AMR through soil is complex and dynamic, as elements of AMR may transport differently through soil and require separate consideration in modeling and management. Future AMR management practices that consider diverse factors that affect persistence and spread of AMR in the environment can help protect livestock productivity and maintain the efficacy of antibiotics to protect human and animal health.
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    Antimicrobial Resistance Mitigation [ARM] Concept Paper
    Vikesland, Peter J.; Alexander, Kathleen A.; Badgley, Brian D.; Krometis, Leigh-Anne H.; Knowlton, Katharine F.; Gohlke, Julia M.; Hall, Ralph P.; Hawley, Dana M.; Heath, Lenwood S.; Hession, W. Cully; Hull, Robert Bruce IV; Moeltner, Klaus; Ponder, Monica A.; Pruden, Amy; Schoenholtz, Stephen H.; Wu, Xiaowei; Xia, Kang; Zhang, Liqing (Virginia Tech, 2017-05-15)
    The development of viable solutions to the global threat of antimicrobial resistance requires a transdisciplinary approach that simultaneously considers the clinical, biological, social, economic, and environmental drivers responsible for this emerging threat. The vision of the Antimicrobial Resistance Mitigation (ARM) group is to build upon and leverage the present strengths of Virginia Tech in ARM research and education using a multifaceted systems approach. Such a framework will empower our group to recognize the interconnectedness and interdependent nature of this threat and enable the delineation, development, and testing of resilient approaches for its mitigation. We seek to develop innovative and sustainable approaches that radically advance detection, characterization, and prevention of antimicrobial resistance emergence and dissemination in human-dominated and natural settings...
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    Application of biochar to soils may result in plant contamination and human cancer risk due to exposure of polycyclic aromatic hydrocarbons
    Wang, Jian; Xia, Kang; Waigi, Michael Gatheru; Gao, Yanzheng; Odinga, Emmanuel Stephen; Ling, Wanting; Liu, Juan (2018-12)
    Biochars are added to soil to improve agronomic yield. This greenhouse- and field-scale study evaluated poly cyclic aromatic hydrocarbon (PAH) contamination in 35 commercial and laboratory-produced biochars, and assessed the effects of biochar amendment of soils on PAH accumulation in vegetables and the risk for cancer. The total and bioavailable PAH concentrations in biochars varied from 638 to 12,347 mu g/kg and from below the detection limit (BDL) to 2792 mu g/kg, respectively. PAH formation in biochars decreased with increasing production temperature (350-650 degrees C). Root exudates enhanced PAH release from biochars. The total PAH concentrations in eight edible vegetables growing in biochar-amended soil varied according to biochar and vegetables type from BDL to 565 mu g/kg. A health risk assessment framework was integrated with the benzo [a] pyrene toxic equivalency quotient and the incremental lifetime cancer risk (ILCR) to estimate the exposure risk for human beings via ingestion of PAH-contaminated vegetables. The total ILCR for adults was above 10(-6), which suggests a risk to human health from direct exposure to PAHs in vegetables grown in biochar-amended soil. These results demonstrate that biochar application may lead to contamination of plants with PAHs, which represents a risk to human health. The PAH levels in biochars produced using different conditions and/or feed-stocks need to be evaluated and biochars should be pretreated to remove PAHs before their large-scale agronomic application.
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    ARGem: a new metagenomics pipeline for antibiotic resistance genes: metadata, analysis, and visualization
    Liang, Xiao; Zhang, Jingyi; Kim, Yoonjin; Ho, Josh; Liu, Kevin; Keenum, Ishi M.; Gupta, Suraj; Davis, Benjamin; Hepp, Shannon L.; Zhang, Liqing; Xia, Kang; Knowlton, Katharine F.; Liao, Jingqiu; Vikesland, Peter J.; Pruden, Amy; Heath, Lenwood S. (Frontiers, 2023-09-15)
    Antibiotic resistance is of crucial interest to both human and animal medicine. It has been recognized that increased environmental monitoring of antibiotic resistance is needed. Metagenomic DNA sequencing is becoming an attractive method to profile antibiotic resistance genes (ARGs), including a special focus on pathogens. A number of computational pipelines are available and under development to support environmental ARG monitoring; the pipeline we present here is promising for general adoption for the purpose of harmonized global monitoring. Specifically, ARGem is a user-friendly pipeline that provides full-service analysis, from the initial DNA short reads to the final visualization of results. The capture of extensive metadata is also facilitated to support comparability across projects and broader monitoring goals. The ARGem pipeline offers efficient analysis of a modest number of samples along with affordable computational components, though the throughput could be increased through cloud resources, based on the user’s configuration. The pipeline components were carefully assessed and selected to satisfy tradeoffs, balancing efficiency and flexibility. It was essential to provide a step to perform short read assembly in a reasonable time frame to ensure accurate annotation of identified ARGs. Comprehensive ARG and mobile genetic element databases are included in ARGem for annotation support. ARGem further includes an expandable set of analysis tools that include statistical and network analysis and supports various useful visualization techniques, including Cytoscape visualization of co-occurrence and correlation networks. The performance and flexibility of the ARGem pipeline is demonstrated with analysis of aquatic metagenomes. The pipeline is freely available at https://github.com/xlxlxlx/ARGem.
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    Artificial topography changes the growth strategy of Spartina alterniflora, case study with wave exposure as a comparison
    Hong, Hualong; Dai, Minyue; Lu, Haoliang; Liu, Jingchun; Zhang, Jie; Chen, Chaoqi; Xia, Kang; Yan, Chongling (Springer Nature, 2017-11-17)
    This paper reports findings about the growth of Spartina alterniflora (Loisel.) near an engineered coastal protection defences to discover the potential influences on vegetation growth from the artificial topography. Impacts of the artificial topography on the sediment element composition were detected by comparing the fixed effects caused by artificial topography and wave exposure using linear mixed models. Surficial sediments under the impacts of artificial topography contain elevated levels of biogenic elements and heavy metals, including C (and organic carbon), N, S, Al, Fe, Mn, Cu, Zn, As, Cd, Cr, Ni, and Pb. The results showed that element enrichment caused by artificial topography reduced the vegetation sexual reproduction. Contrary to the potential inhibition caused by direct wave exposure, which was due to the biomass accumulation limit, the inhibition caused by artificial topography was related to the transition of growth strategy. The contents of Cu, Mn, N, Ni, S and As in the sediments were critical in considering the relationship between the change in the sediment element composition and the alteration in the plant growth. Our study emphasizes the importance of rethinking the impacts of coastal development projects, especially regarding the heterogeneity of sediment element composition and its ecological consequences.
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    Assessing Per- and Polyfluoroalkyl Substances (PFAS) Presence and Distribution in the Stormwater Systems of Socioeconomically Disadvantaged Coastal Communities
    Blackburn, Savanna; Harrison, Michael (Virginia Tech, 2024-05-01)
    This interdisciplinary study investigates the presence of Per- and Polyfluoroalkyl Substances (PFAS) in socioeconomically disadvantaged communities within two coastal municipalities in the Virginia Coastal Plain. Utilizing a field and laboratory approach, the research aims to assess the distribution and concentration of 30 PFAS compounds across multiple environmental receptors. Initial grab-sampling conducted across four distinct sites provided preliminary data on a wide range of PFAS, employing targeted analytical techniques to evaluate their presence. The significance of the study is underscored by the ecological and public health risks associated with PFAS contamination. Results from the analysis revealed variable concentrations of PFAS compounds across the sampled locations, suggesting a relationship between urban infrastructure, environmental justice areas, and PFAS distribution. These findings contribute to the existing body of knowledge on PFAS environmental behavior, risks, and management, highlighting the need for continued monitoring and research. Additionally, the study demonstrates the critical role of interdisciplinary collaboration in addressing complex environmental health issues, providing a foundation for future research and targeted sampling strategies to mitigate PFAS risks in urban coastal settings.
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    Assessing Potential Solutions to Mitigate Pollution from Neonicotinoid Seed Coatings
    Morrison, Benjamin Anthony (Virginia Tech, 2020-12-08)
    Thiamethoxam and clothianidin are two neonicotinoids used in seed coatings for crops such as corn and soybeans. Both neonicotinoids have high solubility in water, so they are prone to transport via leaching and runoff. This thesis is comprised of two studies that evaluated potential solutions to mitigate neonicotinoid transport from fields. The first study examined the relationship between soil organic carbon content and neonicotinoid transport in a field planted in soybeans. Soils with increased organic carbon leached less thiamethoxam and clothianidin during early growing season leaching peaks; however, at the end of the season, higher organic carbon content only decreased leached mass of clothianidin. The second study was to determine neonicotinoid uptake of different ground covers used as cover crops or edge-of-field buffer strips, as well as the partitioning of thiamethoxam and clothianidin throughout the plants. Ground covers, such as crimson clover, had the highest recovery of applied thiamethoxam, meaning that it may be a good candidate to retain this pesticide in fields. Thiamethoxam and clothianidin concentrations were higher in leaf tissues than in stems or roots, indicating that above-ground biomass removal may be an effective way to reduce neonicotinoid loading in the environment. From these studies, I concluded 1) practices that raise the amount of organic carbon in the soil may help decrease early-season neonicotinoid transport, resulting in lower concentrations in surrounding waterways, and 2) careful selection of plant species, such as crimson clover, may help reduce neonicotinoid transport in the environment, while potentially reducing exposure to beneficial insects.
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    Biosolids as a source of soil conditioning and fertility for turfgrass
    Badzmierowski, Mike J. (Virginia Tech, 2019-11-04)
    Wastewater treatment plants are shifting towards producing exceptional quality (EQ) biosolids to increase recycling rates to land, especially urban areas. Other methods of improving the environmental impact of wastewater treatment includes additions of iron (Fe) to reduce phosphorus (P) concentrations in outgoing treated water and precipitate the P into the biosolids. Proper management of biosolids to rehabilitate anthropogenically disturbed urban soils for improved plant growth and effects on the cycling of nutrients requires further study. Our objectives were: 1) to determine whether various EQ biosolids could be managed to improve degraded soil properties and turfgrass quality while minimizing risk of P loss in a field study; and 2) to use spectral reflectance data to compare relationships of vegetation indices to soil and turfgrass parameters. We found that after an initial lag-time of one year, biosolids amendments increased turfgrass clipping biomass and aesthetic quality greater than did synthetic fertilizer. Repeated topdressing applications of biosolids reduced soil bulk density and increased soil organic carbon (OC) and nitrogen (N) stocks. Biosolids applied at the agronomic N rate did not increase water-soluble P (15 and 18 mg P kg-1 of soil) compared to biosolids applied at the agronomic P rate (9.6 mg P kg-1 of soil) and synthetic fertilizer (13 mg P kg-1 of soil) after five years. We further demonstrated at this field site that collecting continuous data improves spectral reflectance vegetation indices relationships to turfgrass quality, clipping biomass, and tissue N accumulation. Soil volumetric water content was best correlated to the water band index (r = 0.60) and the green-to-red ratio index (r = 0.54) vegetation indices. Differences in soil and turfgrass measured parameters were best detected when there was drought-stressed versus irrigated turfgrass.
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    BOHEMIA: Broad One Health Endectocide-based Malaria Intervention in Africa—a phase III cluster-randomized, open-label, clinical trial to study the safety and efficacy of ivermectin mass drug administration to reduce malaria transmission in two African settings
    Chaccour, Carlos; Casellas, Aina; Hammann, Felix; Ruiz-Castillo, Paula; Nicolas, Patricia; Montaña, Julia; Mael, Mary; Selvaraj, Prashant; Duthaler, Urs; Mrema, Sigilbert; Kakolwa, Mwaka; Lyimo, Issa; Okumu, Fredros; Marathe, Achla; Schürch, Roger; Elobolobo, Eldo; Sacoor, Charfudin; Saute, Francisco; Xia, Kang; Jones, Caroline; Rist, Cassidy; Maia, Marta; Rabinovich, N. R. (2023-02-21)
    Background Residual malaria transmission is the result of adaptive mosquito behavior that allows malaria vectors to thrive and sustain transmission in the presence of good access to bed nets or insecticide residual spraying. These behaviors include crepuscular and outdoor feeding as well as intermittent feeding upon livestock. Ivermectin is a broadly used antiparasitic drug that kills mosquitoes feeding on a treated subject for a dose-dependent period. Mass drug administration with ivermectin has been proposed as a complementary strategy to reduce malaria transmission. Methods A cluster randomized, parallel arm, superiority trial conducted in two settings with distinct eco-epidemiological conditions in East and Southern Africa. There will be three groups: human intervention, consisting of a dose of ivermectin (400 mcg/kg) administered monthly for 3 months to all the eligible population in the cluster (>15 kg, non-pregnant and no medical contraindication); human and livestock intervention, consisting human treatment as above plus treatment of livestock in the area with a single dose of injectable ivermectin (200 mcg/kg) monthly for 3 months; and controls, consisting of a dose of albendazole (400 mg) monthly for 3 months. The main outcome measure will be malaria incidence in a cohort of children under five living in the core of each cluster followed prospectively with monthly RDTs Discussion The second site for the implementation of this protocol has changed from Tanzania to Kenya. This summary presents the Mozambique-specific protocol while the updated master protocol and the adapted Kenya-specific protocol undergo national approval in Kenya. BOHEMIA will be the first large-scale trial evaluating the impact of ivermectin-only mass drug administration to humans or humans and cattle on local malaria transmission.
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    Chip-Scale Gas Chromatography
    Akbar, Muhammad (Virginia Tech, 2015-09-04)
    Instrument miniaturization is led by the desire to perform rapid diagnosis in remote areas with high throughput and low cost. In addition, miniaturized instruments hold the promise of consuming small sample volumes and are thus less prone to cross-contamination. Gas chromatography (GC) is the leading analytical instrument for the analysis of volatile organic compounds (VOCs). Due to its wide-ranging applications, it has received great attention both from industrial sectors and scientific communities. Recently, numerous research efforts have benefited from the advancements in micro-electromechanical system (MEMS) and nanotechnology based solutions to miniaturize the key components of GC instrument (pre-concentrator/injector, separation column, valves, pumps, and the detector). The purpose of this dissertation is to address the critical need of developing a micro GC system for various field- applications. The uniqueness of this work is to emphasize on the importance of integrating the basic components of μGC (including sampling/injection, separation and detection) on a single platform. This integration leads to overall improved performance as well as reducing the manufacturing cost of this technology. In this regard, the implementation of micro helium discharge photoionization detector (μDPID) in silicon-glass architecture served as a major accomplishment enabling its monolithic integration with the micro separation column (μSC). For the first time, the operation of a monolithic integrated module under temperature and flow programming conditions has been demonstrated to achieve rapid chromatographic analysis of a complex sample. Furthermore, an innovative sample injection mechanism has been incorporated in the integrated module to present the idea of a chip-scale μGC system. The possibility of using μGC technology in practical applications such as breath analysis and water monitoring is also demonstrated. Moreover, a nanotechnology based scheme for enhancing the adsorption capacity of the microfabricated pre-concentrator is also described.
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    Culturable antibiotic-resistant fecal coliform bacteria in soil and surface runoff after liquid dairy manure surface application and subsurface injection
    Hilaire, Sheldon Shervon; Chen, Chaoqi; Radolinski, Jesse; Leventhal, Talia; Preisendanz, Heather; Kleinman, Peter J. A.; Maguire, Rory O.; Stewart, Ryan D.; Saporito, Lou S.; Xia, Kang (Wiley, 2022-02-05)
    Land application of manure, while beneficial to soil health and plant growth, can lead to an overabundance of nutrients and introduction of emerging contaminants into agricultural fields. Compared with surface application of manure, subsurface injection has been shown to reduce nutrients and antibiotics in surface runoff. However, less is known about the influence of subsurface injection on the transport and persistence of antibiotic-resistant microorganisms. We simulated rainfall to field plots at two sites (one in Virginia and one in Pennsylvania) 1 or 7 d after liquid dairy manure surface and subsurface application (56 Mg ha–1) and monitored the abundance of culturable antibiotic-resistant fecal coliform bacteria (ARFCB) in surface runoff and soils for 45 d. We performed these tests at both sites in spring 2018 and repeated the test at the Virginia site in fall 2019. Manure subsurface injection, compared with surface application, resulted in less ARFCB in surface runoff, and this reduction was greater at Day 1 after application compared with Day 7. The reductions of ARFCB in surface runoff because of manure subsurface injection were 2.5–593 times at the Virginia site in spring 2018 and fall 2019 and 4–5 times at the Pennsylvania site in spring 2018. The ARFCB were only detectable in the 0-to-5-cm soil depth within 14 d of manure surface application but remained detectable in the injection slits of manure subsurface-injected plots even at Day 45. This study demonstrated that subsurface injection can significantly reduce surface runoff of ARFCB from manure-applied fields.
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    CyberBioSecurity through Leadership-as-Practice Development
    Kaufman, Eric K.; Adeoye, Samson; Batarseh, Feras; Brown, Anne M.; Drape, Tiffany A.; Duncan, Susan; Rutherford, Tracy; Strawn, Laura K.; Xia, Kang (2022-03-28)
    CyberBioSecurity is an emerging field at the interface of life sciences and digital worlds (Murch, 2018). The solution to the global cyberbiosecurity challenge is not merely technical; society needs cyberbiosecurity professionals who engage in leadership with a boundary-crossing approach that involves collective effort. Such an approach emerges from leadership-as-practice development (LaPD), characterized by its efforts to “change patterns and thinking that could transform a culture of mediocrity to one of excellence and resilience'' (Raelin, 2020, p. 2). While LaPD has been used in some professional learning contexts and it aligns with some signature pedagogies of the professions, the opportunity remains for embedding LaPD in graduate education to meet the needs of emerging fields. The objective of this proposed project is to catalyze transformative cyberbiosecurity graduate education in a way that increases cognitive integrative capability among cyberbiosecurity scientists and professionals. As noted by Pratch (2014), “leaders who possess integrative capacity are better able to assess problems and find workable solutions than those who do not” (p. 1). In this project, we intend to embedding LaPD in online graduate and train-the-trainer modules, testing various pedagogies associated with boundary-crossing graduate education. The approach will include use of collaborative leadership learning groups (CLLGs), which are “anchored in practice, bringing together learners who can identify and work together on the challenges they face collectively” (Denyer & Turnbull James, 2016, p. 269). Our specific research questions include: What signature pedagogies best support the emerging discipline of CyberBioSecurity education? To what extent do collaborative leadership learning groups (CLLGs) increase students’ cognitive integrative capability?
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    Development and Validation of a UPLC-MS/MS Method to Monitor Cephapirin Excretion in Dairy Cows following Intramammary Infusion
    Ray, Partha; Knowlton, Katharine F.; Shang, Chao; Xia, Kang (PLOS, 2014-11-06)
    Cephapirin, a cephalosporin antibiotic, is used by the majority of dairy farms in the US. Fecal and urinary excretion of cephapirin could introduce this compound into the environment when manure is land applied as fertilizer, and may cause development of bacterial resistance to antibiotics critical for human health. The environmental loading of cephapirin by the livestock industry remains un-assessed, largely due to a lack of appropriate analytical methods. Therefore, this study aimed to develop and validate a cephapirin quantification method to capture the temporal pattern of cephapirin excretion in dairy cows following intramammary infusion. The method includes an extraction with phosphate buffer and methanol, solid-phase extraction (SPE) clean-up, and quantification using ultra performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS). The LOQ values of the developed method were 4.02 µg kg−1 and 0.96 µg L−1 for feces and urine, respectively. This robust method recovered >60% and >80% cephapirin from spiked blank fecal and urine samples, respectively, with acceptable intra- and inter-day variation (<10%). Using this method, we detected trace amounts (µg kg−1) of cephapirin in dairy cow feces, and cephapirin in urine was detected at very high concentrations (133 to 480 µg L−1). Cephapirin was primarily excreted via urine and its urinary excretion was influenced by day (P = 0.03). Peak excretion (2.69 mg) was on day 1 following intramammary infusion and decreased sharply thereafter (0.19, 0.19, 0.08, and 0.17 mg on day 2, 3, 4, and 5, respectively) reflecting a quadratic pattern of excretion (Quadratic: P = 0.03). The described method for quantification of cephapirin in bovine feces and urine is sensitive, accurate, and robust and allowed to monitor the pattern of cephapirin excretion in dairy cows. This data will help develop manure segregation and treatment methods to minimize the risk of antibiotic loading to the environment from dairy farms.
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    Effect of antibiotic use and composting on antibiotic resistance gene abundance and resistome risks of soils receiving manure-derived amendments
    Chen, Chaoqi; Pankow, Christine A.; Oh, Min; Heath, Lenwood S.; Zhang, Liqing; Du, Pang; Xia, Kang; Pruden, Amy (Elsevier, 2019-05-03)
    Manure-derived amendments are commonly applied to soil, raising questions about whether antibiotic use in livestock could influence the soil resistome (collective antibiotic resistance genes (ARGs)) and ultimately contribute to the spread of antibiotic resistance to humans during food production. Here, we examined the metagenomes of soils amended with raw or composted manure generated from dairy cows administered pirlimycin and cephapirin (antibiotic) or no antibiotics (control) relative to unamended soils. Initial amendment (Day 1) with manure or compost significantly increased the diversity (richness) of ARGs in soils (p < 0.01) and resulted in distinct abundances of individual ARG types. Notably, initial amendment with antibiotic-manure significantly increased the total ARG relative abundances (per 16S rRNA gene) in the soils (2.21×unamended soils, p < 0.001). After incubating 120 days, to simulate a wait period before crop harvest, 282 ARGs reduced 4.33- fold (median) up to 307-fold while 210 ARGs increased 2.89-fold (median) up to 76-fold in the antibioticmanure- amended soils, resulting in reduced total ARG relative abundances equivalent to those of the unamended soils. We further assembled the metagenomic data and calculated resistome risk scores, which was recently defined as a relative index comparing co-occurrence of sequences corresponding to ARGs, mobile genetic elements, and putative pathogens on the same scaffold. Initial amendment of manure significantly increased the soil resistome risk scores, especially when generated by cows administered antibiotics, while composting reduced the effects and resulted in soil resistomes more similar to the background. The risk scores of manure-amended soils reduced to levels comparable to the unamended soils after 120 days. Overall, this study provides an integrated, high-resolution examination of the effects of prior antibiotic use, composting, and a 120-day wait period on soil resistomes following manure-derived amendment, demonstrating that all three management practices have measurable effects and should be taken into consideration in the development of policy and practice for mitigating the spread of antibiotic resistance.
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    Effect of composting and soil type on dissipation of veterinary antibiotics in land-applied manures
    Chen, Chaoqi; Ray, Partha P.; Knowlton, Katharine F.; Pruden, Amy; Xia, Kang (2018)
    The objective of this study was to determine the fate of commonly used veterinary antibiotics in their naturally excreted form when manure-based amendments are applied to soil. Beef cattle were administered sulfamethazine, tylosin, and chlortetracycline and dairy cows were treated with pirlimycin. The resulting manure was composted for 42 d under static or turned conditions and applied at agronomic N rates to sandy, silt, and silty clay loam soils and compared with amendment with corresponding raw manures in sacrificial microcosms over a 120-day period. Antibiotic dissipation in the raw manure-amended soils followed bi-phasic first order kinetics. The first phase half-lives for sulfamethazine, tylosin, chlortetracycline, and pirlimycin ranged from 6.0 to 18, 2.7 to 3.7, 23 to 25, and 5.5–8.2 d, respectively. During the second phase, dissipation of sulfamethazine was negligible, while the half-lives for tylosin, chlortetracycline, and pirlimycin ranged from 41 to 44, 75 to 144, and 87–142 d, respectively. By contrast, antibiotic dissipation in the compost-amended soils followed single-phase first order kinetics with negligible dissipation of sulfamethazine and half-lives of tylosin and chlortetracycline ranging from 15 to 16 and 49–104 d, respectively. Pirlimycin was below the detection limit in the compost-amended soils. After incubating 120 d, antibiotics in compost-amended soils (up to 3.1 μg kg−1) were significantly lower than in manure-amended soils (up to 19 μg kg−1, p < .0001), with no major effect of soil type on the dissipation. Risk assessment suggested that composting can reduce antibiotic resistance selection potential in manure-amended soils.
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    Effect of Golf Course Turfgrass Management on Water Quality of Non-tidal Streams in the Chesapeake Bay Watershed
    Wilson, Chantel (Virginia Tech, 2015-04-09)
    Turfgrass management activities on golf courses have been identified as a possible source of Chesapeake Bay nutrient pollution. Total Maximum Daily Load goals are in place to reduce nutrient amounts entering the Bay. Dissertation investigations include (1) the role of golf course turfgrass management in nutrient deposition or attenuation in local streams, (2) estimations of total nitrogen (N) discharging to the watershed from stream outlet points as a function of land use and watershed area, and (3) other factors potentially affecting water quality on golf courses, including soil characteristics and use of best management practices (BMPs). Total N, nitrate-N, ammonium-N, phosphate-phosphorus (P), streamwater temperature, specific conductance (SpC), pH and dissolved oxygen (DO) were sampled at 12-14 golf course stream sites in the James River and Roanoke River watersheds during baseflow conditions. Discharge was determined at outflow locations. Unit-area loads (UALs) were calculated from monitoring data. These UALs were then compared to UALs from Chesapeake Bay Watershed Model land use acreages and simulated loads for corresponding watershed segments. Virginia golf course superintendents were also surveyed to determine BMP use. No consistent impairment trends were detected for streamwater temperature, SpC, pH, or DO at any of the sites. Outflow NO3-N was below the 10 mg L-1 EPA drinking water standard. However, some sites may be at increased risk for benthic impairment with total N concentrations >2 mg L-1, as suggested by VADEQ. Significant increases in nitrate-N at OUT locations were measured at four sites, whereas decreases were measured at two sites. Ammonium-N significantly decreased at two sites. Golf course N UALs calculated from baseflow monitoring were lower than or similar to UALs estimated for forested areas in the associated watershed segment at seven out of the 12 sites. Golf course UALs ranged from 1.3-87 kg N ha-1 yr-1. Twenty-one of 32 surveyed BMPs had an adoption rate ≥50% among survey respondents. In most cases, presence of golf courses generally does not appear to significantly degrade baseflow water quality of streams in this study. Management level appears to be an influencing factor on water quality and concerns may be heightened in urban areas.
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    Effect of Soil Type, Composting, and Antibiotic Use on Fate of Antibiotic Resistance Genes and Microbial Community Composition in Dairy and Beef Manure Applied Soils
    Pankow, Christine Ann (Virginia Tech, 2017-07-20)
    Manure is a commonly used soil fertilizer, but there are concerns that this practice could affect the spread of antibiotic resistance genes (ARGs) from farm to fork. A microcosm-scale study evaluated the effect of prior antibiotic use (manure-based soil amendments generated from dairy and beef cattle with or without antibiotic administration), composting, and soil type on the quantity of ARGs and the microbial community composition of dairy and beef manure applied soil. ARGs were analyzed through novel metagenomic techniques and quantitative polymerase chain reaction of sul1, tet(W), and 16S rRNA gene, while the microbial community composition was determined via 16S rRNA amplicon sequencing. The results indicated that while prior antibiotic administration elevated the relative abundance of ARGs and changed the microbial community of raw manure applied soils, composting reduced this effect. However, compost applied soils still had a higher relative abundance of ARGs than the unamended soils and occasionally soil applied with raw manure of untreated cattle. Soil type may be a mediating factor as there were differences observed between the three soil types (sandy loam, silty clay loam, and silty loam) with sandy loam amended soils often having the least attenuation of ARGs. As the relative abundance of ARGs was still elevated and the microbial community composition still significantly different from the unamended soils after 120 days, these results suggest that 120 days is not a long enough waiting period between biological soil amendments and crop harvest for ARG dissipation.
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    Effects of Manure Injection on Transport and Transformation of Nutrient and Antibiotics
    Kulesza, Stephanie Brooke (Virginia Tech, 2015-10-13)
    Overapplication of manure in sensitive watersheds is an issue of increasing environmental concern due to increased nutrient loading and antibiotic release into aquatic environments. Manure is typically surface applied, leaving nutrients and antibiotics vulnerable to loss at the soil surface. Elevated nutrient and antibiotic loading into water bodies can increase the rate of eutrophication and occurrence of antibiotic resistance genes in areas of high animal agriculture production, such as the Chesapeake Bay watershed. Manure injection is a new technology that incorporates manure into the soil with minimal disturbance, and management strategies that reduce manure loss from agricultural fields could prevent the transport of nutrients and antibiotics to sensitive waterways. However, little is known about the efficacy of dry litter injection to decrease nitrogen (N) loss when compared to surface application. Also, there are no studies that determine the effects of injection on antibiotic transport and transformation after manure application. Therefore, this project focused on changes in N cycling, orchardgrass hay yield and quality, and transport and transformation of pirlimycin and cephapirin, two common antibiotics in dairy production, when manure is injected. Subsurface injection eliminated ammonia volatilization and N loss in runoff and increased soil inorganic N when compared to surface application after volatilization, incubation, and rainfall simulation studies. Although these benefits did not translate to higher yields in orchardgrass hay, protein increased when poultry litter was injected, indicating greater N uptake. Injection of dairy manure decreased losses of pirlimycin to levels of the control when compared to surface application. Although, pirlimycin had a slower degradation rate within the injection slit compared to surface application, potentially increasing the amount of time soil microbes are exposed to antibiotics. In an incubation study, pirlimycin concentrations decreased after 7 days, but concentrations increased sharply after 14 days. This indicates that conjugates formed in the liver or digestive tract of dairy cows may revert back to the parent compound after manure application. With increased retention of nutrients and antibiotics, injection could be a best management practice used to reduce the loss of these compounds to the environment while increasing the quality of crops produced.