Charles E. Via Jr. Department of Civil and Environmental Engineering
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The Charles E. Via, Jr. Department of Civil and Environmental Engineering, which is ranked in the top 10 accredited civil and environmental engineering departments by the US News and World Report survey, is one of the largest programs in the United States. The Department has 46 full-time faculty, 657 undergraduate, and 400 graduate students. Civil engineers are the principal designers, constructors, operators, and caretakers of many of the constructed facilities and systems that contribute to the high quality of life enjoyed in the United States. The Charles E. Via, Jr. Department of Civil and Environmental Engineering offers educational programs in all areas of civil engineering practice.
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Browsing Charles E. Via Jr. Department of Civil and Environmental Engineering by Department "Biological Systems Engineering"
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- AgroSeek: a system for computational analysis of environmental metagenomic data and associated metadataLiang, 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/ .
- Comparison of Two Alternative Methods for Developing TMDLs to Address Sediment ImpairmentsWallace, Carlington W.; Benham, Brian L.; Yagow, Eugene R.; Gallagher, Daniel L. (2018-12)While excessive sediment is a leading cause of aquatic life use impairments in free-flowing rivers in Virginia, there is no numeric sediment-water quality criterion. As a result, total maximum daily load (TMDL) sediment loads are often established using a comparable, nonimpaired reference watershed. Selecting a suitable reference watershed can be problematic. This case study compared the reference watershed approach (RWA) which uses the Generalized Watershed Loading Function and the disaggregate method (DM) which uses output from Phase 5.3 of the Chesapeake Bay Watershed Model. In this case study, the two methods were used to develop sediment TMDLs for three impaired watersheds in Virginia (Taylor Creek, Turley Creek, and Long Meadow Run). In this case study comparison, the RWA required between 12.8 and 14.7 times greater sediment load reductions (t/year) to reach the TMDL load (Taylor Creek > Long Meadow Run > Turley Creek) when compared to the reductions called for using the DM. While each TMDL development method has inherent limitations, the DM uses output from the Chesapeake Bay Watershed Model to establish TMDL target loads. This means that the application of the DM is restricted to the Chesapeake Bay Watershed.
- The effects of dietary protein content and manure handling technique on ammonia emissions during short-term storage of dairy cow manureSparks, 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.
- Effects of Large Wood on Floodplain Connectivity in a Headwater Mid-Atlantic StreamKeys, Tyler A.; Governer, Heather; Jones, C. Nathan; Hession, W. Cully; Hester, Erich T.; Scott, Durelle T. (2018-05-08)Large wood (LW) plays an essential role in aquatic ecosystem health and function. Traditionally, LW has been removed from streams to minimize localized flooding and increase conveyance efficiency. More recently, LW is often added to streams as a component of stream and river restoration activities. While much research has focused on the role of LW in habitat provisioning, geomorphic stability, and hydraulics at low to medium flows, we know little about the role of LW during storm events. To address this question, we investigated the role of LW on floodplain connectivity along a headwater stream in the Mid-Atlantic region of the United States. Specifically, we conducted two artificial floods, one with and one without LW, and then utilized field measurements in conjunction with hydrodynamic modeling to quantify floodplain connectivity during the experimental floods and to characterize potential management variables for optimized restoration activities. Experimental observations show that the addition of LW increased maximum floodplain inundation extent by 34%, increased floodplain inundation depth by 33%, and decreased maximum thalweg velocity by 10%. Model results demonstrated that different placement of LW along the reach has the potential to increase floodplain flow by up to 40%, with highest flooding potential at cross sections with high longitudinal velocity and shallow depth. Additionally, model simulations show that the effects of LW on floodplain discharge decrease as storm recurrence interval increases, with no measurable impact at a recurrence interval of more than 25 years.
- Environmental health disparities in the Central Appalachian region of the United StatesKrometis, Leigh-Anne H.; Gohlke, Julia M.; Kolivras, Korine N.; Satterwhite, Emily M.; Marmagas, Susan West; Marr, Linsey C. (De Gruyter, 2017-09-26)Health disparities that cannot be fully explained by socio-behavioral factors persist in the Central Appalachian region of the United States. A review of available studies of environmental impacts on Appalachian health and analysis of recent public data indicates that while disparities exist, most studies of local environmental quality focus on the preservation of nonhuman biodiversity rather than on effects on human health. The limited public health studies available focus primarily on the impacts of coal mining and do not measure personal exposure, constraining the ability to identify causal relationships between environmental conditions and public health. Future efforts must engage community members in examining all potential sources of environmental health disparities to identify effective potential interventions.
- Fecal Indicator Bacteria and Antibiotic Resistance Genes in Storm Runoff from Dairy Manure and Compost-Amended Vegetable PlotsJacobs, Kyle; Wind, Lauren L.; Krometis, Leigh-Anne H.; Hession, W. Cully; Pruden, Amy (American Society for Agronomy, 2019-07-01)Given the presence of antibiotics and resistant bacteria in livestock manures, it is important to identify the key pathways by which land-applied manure-derived soil amendments potentially spread resistance. The goal of this field-scale study was to identify the effects of different types of soil amendments (raw manure from cows treated with cephapirin and pirlimycin, compost from antibiotic-treated or antibiotic-free cows, or chemical fertilizer only) and crop type (lettuce [Lactuca sativa L.] or radish [Raphanus sativus L.]) on the transport of two antibiotic resistance genes (ARGs; sul1 and ermB) via storm runoff from six naturally occurring storms. Concurrent quantification of sediment and fecal indicator bacteria (FIB; Escherichia coli and enterococci) in runoff permitted comparison to traditional agricultural water quality targets that may be driving factors of ARG presence. Storm characteristics (total rainfall volume, storm duration, etc.) significantly influenced FIB concentration (two-way ANOVA, p < 0.05), although both effects from individual storm events (Kruskal-Wallis, p < 0.05) and vegetative cover influenced sediment levels. Composted and raw manure-amended plots both yielded significantly higher sul1 and ermB levels in runoff for early storms, at least 8 wk following initial planting, relative to fertilizer-only or unamended barren plots. There was no significant difference between sul1 or ermB levels in runoff from plots treated with compost derived from antibiotic-treated versus antibiotic-free dairy cattle. Our findings indicate that agricultural fields receiving manure-derived amendments release higher quantities of these two “indicator” ARGs in runoff, particularly during the early stages of the growing season, and that composting did not reduce effects of ARG loading in runoff.
- Generalized Likelihood Uncertainty Estimation and Markov Chain Monte Carlo Simulation to Prioritize TMDL Pollutant AllocationsMishra, Anurag; Ahmadisharaf, Ebrahim; Benham, Brian L.; Wolfe, Mary Leigh; Leman, Scotland C.; Gallagher, Daniel L.; Reckhow, Kenneth H.; Smith, Eric P. (2018-12)This study presents a probabilistic framework that considers both the water quality improvement capability and reliability of alternative total maximum daily load (TMDL) pollutant allocations. Generalized likelihood uncertainty estimation and Markov chain Monte Carlo techniques were used to assess the relative uncertainty and reliability of two alternative TMDL pollutant allocations that were developed to address a fecal coliform (FC) bacteria impairment in a rural watershed in western Virginia. The allocation alternatives, developed using the Hydrological Simulation Program-FORTRAN, specified differing levels of FC bacteria reduction from different sources. While both allocations met the applicable water-quality criteria, the approved TMDL allocation called for less reduction in the FC source that produced the greatest uncertainty (cattle directly depositing feces in the stream), suggesting that it would be less reliable than the alternative, which called for a greater reduction from that same source. The approach presented in this paper illustrates a method to incorporate uncertainty assessment into TMDL development, thereby enabling stakeholders to engage in more informed decision making.
- Microbiota and Antibiotic Resistome of Lettuce Leaves and Radishes Grown in Soils Receiving Manure-Based Amendments Derived From Antibiotic-Treated CowsFogler, Kendall; Guron, Giselle K.P.; Wind, Lauren L.; Keenum, Ishi M.; Hession, W. Cully; Krometis, Leigh-Anne H.; Strawn, Laura K.; Pruden, Amy; Ponder, Monica A. (Frontiers, 2019-04-10)Cattle are commonly administered antibiotics, resulting in excretion of antibiotics, antibiotic-resistant bacteria (ARB), and antibiotic resistance genes (ARGs). The aim of this study was to determine if the use of dairy manure collected during antibiotic administration influences the bacterial microbiota of lettuce and radishes, including carriage of ARB and ARGs, when applied as a soil amendment and if composting mitigates the effects. Lettuce and radishes were grown in field-plots amended with raw manure from antibiotic-treated (cephapirin, pirlimycin) cows, composted manure from antibiotic-treated cows, composted manure from antibiotic-free cows, or an inorganic chemical fertilizer (control; 12 plots, n = 3). Surficial vegetable bacteria and antibiotic resistomes (i.e., total ARGs) were characterized using heterotrophic plate counts (HPCs) on antibiotic-containing media, 16S rRNA gene amplicon sequencing, quantitative polymerase chain reaction (qPCR), and shot-gun metagenomics. The different manure and compost amendments did not result in significant changes to the surficial vegetable bacteria at the phylum level; however, some minor changes at the class and family level were observed. Beta-diversities of the ARGs detected by shotgun metagenomic sequencing were distinctly different between vegetable type (R = 0.30, p = 0.04), with small separations between the resistomes associated with amendment type in unrarefied analysis (R = 0.27, p = 0.02), but not rarefied analysis, of the data. Network analysis highlighted that multi-drug ARG classes commonly co-occurred with plasmid-associated genes and could be a driver of co-and cross-selection of ARGs in the different conditions. Carriage of sul1 and tet(W) ARGs on vegetables quantified by qPCR were strong indicators of manure-based amendment relative to chemical fertilizer, with some reduction incurred via composting (p < 0.05). Also, increased HPCs resistant/tolerant to clindamycin, a class of antibiotics administered to cattle, were on lettuce grown in biological soil amendments relative to chemical fertilizer (p < 0.05). This study demonstrates that amending soil with rawmanure collected fromdairy cows during antibiotic administration may affect the composition of microbiota and resistomes associated with vegetable surfaces. Composting may be an important strategy to reduce some ARGs on fresh produce, but differences in the resistomes of lettuce and radishes suggest the extent of soil contact should be considered.
- Two-phase Monte Carlo simulation for partitioning the effects of epistemic and aleatory uncertainty in TMDL modelingMishra, Anurag; Ahmadisharaf, Ebrahim; Benham, Brian L.; Gallagher, Daniel L.; Reckhow, Kenneth H.; Smith, Eric P. (ASCE, 2018-10-29)A two-phase Monte Carlo simulation (TPMCS) uncertainty analysis framework is used to analyze epistemic and aleatory uncertainty associated with simulated exceedances of an in-stream fecal coliform (FC) water quality criterion when using the Hydrological Simulation Program-FORTRAN (HSPF). The TPMCS framework is compared with a single-phase or standard Monte Carlo simulation (SPMCS) analysis. Both techniques are used to assess two total maximum daily load (TMDL) pollutant allocation scenarios. The application of TPMCS illustrates that cattle directly depositing FC in the stream is a greater source of epistemic uncertainty than FC loading from cropland overland runoff, the two sources specifically targeted for reduction in the allocation scenario. This distinction is not possible using SPMCS. Although applying the TPMCS framework involves subjective decisions about how selected model parameters are considered within the framework, this uncertainty analysis approach is transparent and the results provide information that can be used by decision makers when considering pollution control measure implementation alternatives, including quantifying the level of confidence in achieving applicable water quality standards. © American Society of Civil Engineers (ASCE).