Scholarly Works, Biological Systems Engineering

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Research articles, presentations, and other scholarship

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Browsing Scholarly Works, Biological Systems Engineering by Department "Dairy Science"

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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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    The effects of dietary protein content and manure handling technique on ammonia emissions during short-term storage of dairy cow manure
    Sparks, J. A.; Ogejo, Jactone Arogo; Cyriac, J.; Hanigan, Mark D.; Knowlton, Katharine F.; Gay, S. W.; Marr, Linsey C. (American Society of Agricultural and Biological Engineers, 2011)
    An improved understanding of the potential for dietary protein manipulation to reduce ammonia emissions from dairy farms during various stages of manure handling is needed for both modeling and policy-making efforts. The objective of this study was to assess the effects of dietary protein manipulation on ammonia emissions from relatively freshly voided dairy cow manure in three types of removal systems: scraped manure removal systems, flushed manure removal systems, and flushed manure removal systems with a solids separator. Emissions were measured using a dynamic flux chamber for 12 h or more. Ammonia fluxes and emission factors per mass of manure were not affected by dietary protein content because fluxes depended mainly on total ammoniacal nitrogen (TAN) concentration, which did not vary with diet. However, emissions on a per-cow basis were 12% lower with the diet containing 15.0% crude protein as compared to the one with 17.8% (a change in crude protein of 16%) due to reduced urine output. The largest absolute impact of dietary protein manipulation would be with separated liquids because their emission factor was approximately four times higher than for the other types of manure. While dietary protein manipulation can reduce ammonia emissions from manure during long-term storage, its effectiveness in the hours immediately after manure is excreted is limited because emissions are more sensitive to other factors, including temperature and extent of mixing of the manure, that vary widely under real operating conditions on a farm.
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    Sorption of estrogen to three agricultural soils from Virginia, USA
    Kozarek, Jessica Lindberg; Wolfe, Mary Leigh; Love, Nancy G.; Knowlton, Katharine F. (American Society of Agricultural and Biological Engineers, 2008)
    Land-applied manures and grazing livestock are sources of estrogens to the environment. Natural steroid estrogens such as 17 beta-estradiol (E2) in low concentrations (ng L(-1)) can adversely affect the reproductive health of aquatic organisms. The goal of this research was to quantify the sorption of E2 to three agricultural soils form different physiographic regions in Virginia, a critical step in predicting transport of estrogens in runoff from agricultural fields. Batch equilibrium experiments were conducted with a range of E2 concentrations (50 to 2000 mu g L(-1)) in a background solution of 5 mM calcium chloride and 100 mg L(-1) sodium azide added to samples of Groseclose loam, Myatt sandy loam, and Cecil loam soils collected from the plow layer (0 to 15 cm) in addition to samples of Groseclose loam, Myatt sandy loam, and Cecil loam soils collected from the plow layer (0 to 15 cm) in addition to a Cecil soil sample from the Bt horizon. The concentration of E2 in the liquid phase was measured by gas chromatography/mass spectrometry (GC-MS) and was used to develop sorption isotherms for each soil. The time required to reach apparent equilibrium for all soils was less than 24 h. In general, the linear isotherm provided a good fit to model the sorption of E2 to agricultural soils from the plow layer (R(2) > 0.9). The sorption of E2 to agricultural soil was correlated to the organic carbon content of each soil (Pearson coefficient, 0.79) with log K(oc) values ranging from 2.90 to 3.99.
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    The Waste Solutions Forum: An Innovative and Cooperative Approach to Support the Agricultural Community and Protect Water Quality
    Bendfeldt, Eric S.; Knowlton, Katharine F.; Denckla Cobb, Tanya; Dukes, Franklin; Holm, Kathy; Ogejo, Jactone Arogo (2007-12)
    Nitrogen (N) and phosphorus (P) contamination of water resources is a significant concern for the Chesapeake Bay and threatens the economic viability of farming communities within the Shenandoah Valley. Nutrient reduction challenges in the Shenandoah Valley are greater because the excess nutrients in the region are largely in the form of manure and poultry litter, which have traditionally been applied to cropland and are difficult and expensive to transport long distances. Poultry is Virginia's top revenue earner for receipts in the agricultural sector and employs 12,000 people statewide. Dairy farming generates about $300 million in farm receipts in Virginia and 40 percent of the state's 795 dairy farms are located in the Shenandoah Valley. The Waste Solutions Forum was convened in April 2005 by Virginia Tech faculty and a planning committee comprised of individuals representing the agricultural and environment conservation communities and other interest groups to explore innovative, economically viable, and long-term solutions to these nutrient challenges and issues. Nearly 80 invitees from the agricultural, business, regulatory, environmental, and academic communities participated in a facilitated "outcome-based" discussion that resultedin a detailed strategy for addressing excess manure and litter, including specific priority actions for research, pilot projects, policy, and education. The Forum and its steering committee continue to focus on these strategies and long-term solutions to the nutrient challenge facing animal agriculture in an effort to support the agricultural community and protect water quality. This collaborative approach of traditional and non-traditional partnerships has allowed the Forum to make significant progress toward long-term solutions and achieving the defined priority actions, including receipt of over $2 million in grant funds, implementation of multiple on-the-ground pilot projects, numerous educational events, and coordinated policy to support agriculture and improve water quality.