Stockpiling versus Composting: Effectiveness in Reducing Antibiotic-Resistant Bacteria and Resistance Genes in Beef Cattle Manure.

Manure storage methods can affect the concentration and prevalence of antibiotic-resistant bacteria (ARB) and antibiotic resistance genes (ARGs) in cattle manure prior to land application. The objective of this study was to compare stockpiling and composting with respect to their effectiveness in reducing ARB and ARGs in beef cattle manure in a field-scale study. Field experiments were conducted in different seasons with different bulking agents for composting. For both the winter-spring cycle and the summer-fall cycle, ARB concentrations declined below the limit of quantification rapidly in both composting piles and stockpiles; however, ARB prevalence was significantly greater in the composting piles than in the stockpiles. This was likely due to the introduction of ARB from bulking agents. There was no significant change in ARG concentrations between initial and final concentrations for either manure storage treatment during the winter-spring cycle, but a significant reduction of the ARGs erm(B), tet(O), and tet(Q) over time was observed for both the composting pile and stockpile during the summer-fall cycle. Results from this study suggest that (i) bulking agent may be an important source of ARB and ARGs for composting; (ii) during cold months, the heterogeneity of the temperature profile in composting piles could result in poor ARG reduction; and (iii) during warm months, both stockpiling and composting can be effective in reducing ARG abundance. IMPORTANCE Proper treatment of manure is essential to reduce the spread of antibiotic resistance and protect human health. Stockpiling and composting are two manure storage methods which can reduce antibiotic-resistant bacteria and resistance genes, although few field-scale studies have examined the relative efficiency of each method. This study examined the ability of both methods in both winter-spring and summer-fall cycles, while also accounting for heterogeneity within field-scale manure piles. This study determined that bulking agents used in composting could contribute antibiotic-resistant bacteria and resistance genes. Additionally, seasonal variation could hinder the efficacy of composting in colder months due to heterogeneity in temperature within the pile; however, in warmer months, either method of manure storage could be effective in reducing the spread of antibiotic resistance.

Influence of Setback Distance on Antibiotics and Antibiotic Resistance Genes in Runoff and Soil Following the Land Application of Swine Manure Slurry.

The environmental spread of antibiotics and antibiotic resistance genes (ARGs) from the land application of livestock wastes can be a potential public health threat. The objective of this study was to assess the effects of setback distance, which determines how close manure may be applied in relation to surface water, on the transport of antibiotics and ARGs in runoff and soil following land application of swine manure slurry. Rainfall simulation tests were conducted on field plots covered with wheat residues, each of which contained an upslope manure region where slurry was applied and an adjacent downslope setback region that did not receive slurry. Results show that all three antibiotics (chlortetracycline, lincomycin, and tiamulin) and seven out of the ten genes tested (erm(B), erm(C), intI1, tet(O), tet(Q), tet(X), and the 16S rRNA gene) decreased significantly in runoff with increased setback distance. Only blaTEM, chlortetracycline, and tiamulin decreased significantly in surface soil with increased setback distance, while the other analytes did not exhibit statistically significant trends. By using linear regression models with field data, we estimate that a setback distance between 34-67 m may allow manure-borne antibiotics and ARGs in runoff to reach background levels under the experimental conditions tested.

Resistome and mobilome in surface runoff from manured soil as affected by setback distance.

Land application of livestock manure introduces antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs) into the soil environment. The objectives of this study were to examine the changes of resistome and mobilome in runoff and soil as a function of setback distance, i.e., the distance between manured soil and surface water, and to quantify the contributions of manure and background soil to the ARGs and MGEs in surface runoff. The resistome and mobilome in runoff and soil from a field-scale plot study were characterized using a high throughput quantitative polymerase chain reaction (HT-qPCR) array. It was estimated that a setback distance of ~40 m is required to reduce the total abundance of ARGs and MGEs in runoff from amended plots to that in control runoff. The resistome and mobilome of the soil in the setback region was not affected by manure-borne ARGs and MGEs. SourceTracker analyses revealed that background soil gradually became the predominant source of the ARGs and MGEs in runoff as setback distance increased. The results demonstrate how manure-borne ARGs and MGEs dissipated in agricultural runoff with increasing setback distance and had limited impacts on the resistome and mobilome of soil within the setback region.

Antibiotic resistance genes in swine manure slurry as affected by pit additives and facility disinfectants.

Manure storage facilities are critical control points to reduce antibiotic resistance genes (ARGs) in swine manure slurry before the slurry is land applied. However, little is known about how exogenous chemicals entering the manure storage facilities may affect the fate of ARGs. The objective of this study was to analyze the impact of six commonly used pit additives and four facility disinfectants on the concentration of ARGs in swine manure slurry. Bench scale reactors, each containing approximately 50 L of liquid swine manure, were dosed with additives or disinfectants and were sampled for 40 days. Seven antibiotic resistance genes along with the intI1 gene and the 16S rRNA gene were monitored. Out of the six additives tested, Sludge Away significantly reduced the time-averaged absolute abundance of erm(C), erm(F), tet(Q), and the 16S rRNA gene as compared to the no additive control. Out of the four disinfectants tested, Tek-Trol significantly reduced the time-averaged absolute abundance of erm(B), erm(C), erm(F), intI1, tet(Q), and tet(X) than did the no-disinfectant control. According to Spearman's rank correlation, three genes erm(F), tet(Q), and tet(X) showed a strong to perfectly positive correlation and the two genes erm(B) and tet(O) showed a moderate to strong correlation in both the additive and disinfectant tests. Overall, the disinfectants were more effective in controlling the absolute abundance of ARGs than were the pit additives.

Simulated Winter Incubation of Soil With Swine Manure Differentially Affects Multiple Antimicrobial Resistance Elements.

Gastrointestinal bacteria that harbor antibiotic resistance genes (ARG) become enriched with antibiotic use. Livestock manure application to cropland for soil fertility presents a concern that ARG and bacteria may proliferate and be transported in the environment. In the United States, manure applications typically occur during autumn with slow mineralization until spring planting season. A laboratory soil incubation study was conducted mimicking autumn swine manure application to soils with concentrations of selected ARG monitored during simulated 120-day winter incubation with multiple freeze-thaw events. Additionally, the effects of two soil moistures [10 and 30% water holding capacity (WHC)] and two manure treatments [raw versus hydrated lime alkaline stabilization (HLAS)] were assessed. Fourteen tetracycline resistance genes were evaluated; tet(D), tet(G), and tet(L) were detected in background soil while swine manure contained tet(A), tet(B), tet(C), tet(G), tet(M), tet(O), tet(Q), and tet(X). By day 120, the manure-borne tet(M) and tet(O) were still detected while tet(C), tet(D), tet(L), and tet(X) genes were detected less frequently. Other tet resistance genes were detected rarely, if at all. The sum of unique tet resistance genes among all treatments decreased during the incubation from an average of 8.9 to 3.8 unique tet resistance genes. Four resistance elements, intI1, bla ctx-m-32, sul(I), erm(B), and 16s rRNA genes were measured using quantitative PCR. ARG abundances relative to 16S abundance were initially greater in the raw manure compared to background soil (-1.53 to -3.92 log abundance in manure; -4.02 to <-6.7 log abundance in soil). In the mixed manure/soil, relative abundance of the four resistance elements decreased (0.87 to 1.94 log abundance) during the incubation largely because 16S rRNA genes increased by 1.21 log abundance. Throughout the incubation, the abundance of intI1, bla ctx-m-32, sul(I), and erm(B) per gram in soil amended with HLAS-treated manure was lower than in soil amended with raw manure. Under low initial soil moisture conditions, HLAS treatment reduced the abundance of intI1 and resulted in loss of bla ctx-m-32, sul(I), and erm(B)] compared to other treatment-moisture combinations. Although one might expect antibiotic resistance to be relatively unchanged after simulated winter manure application to soil, a variety of changes in diversity and relative abundance can be expected.

Swine slurry characteristics as affected by selected additives and disinfectants.

Current swine industry practice is to house animals in confinement facilities which capture and store feces and urine as slurry in pits below the production area. Additives and disinfectants may be introduced into the manure pits. This study was conducted to measure the effects of additives and disinfectants on temporal changes in swine slurry characteristics. Slurry from a commercial swine production facility in southeast Nebraska, USA was collected and transferred to 57 L reactors located within a greenhouse. Selected additives and disinfectants were added to the reactors and physical properties, chemical characteristics, and antibiotic concentrations were monitored for 40 days. Concentrations of dry matter (DM), total nitrogen (TN), phosphorus pentoxide (P2O5), calcium (Ca), magnesium (Mg), zinc (Zn), iron (Fe), manganese (Mn), and copper (Cu) were significantly greater than the Control in each of the reactors containing additives. The reactors in which the additives MOC-7, More Than Manure®, Sludge Away, and Sulfi-Doxx were introduced had significantly greater values of chemical oxygen demand (COD), total volatile solids (TVS), total suspended solids (TSS), total solids (TS), dry matter (DM), TN, P2O5, Ca, Mg, Zn, Fe, Mn, Cu and chlortetracycline than the other additive treatments. Concentrations of TVS and TSS were significantly lower in the reactors containing Clorox® and Virkon™ than the other disinfectant treatments. The total dissolved solids (TDS) concentration of 26,500 mg L-1 and pH value of 7.27 obtained for the reactors containing Tek-Trol were significantly greater than measurements obtained for the other treatments. Concentrations of chlortetracycline and tiamulin of 8840 and 28.8 ng g-1, respectively, were significantly lower for the treatments containing Tek-Trol. The sodium (Na) concentration of 1070 mg L-1 measured in the reactors containing Clorox® was significantly greater than values for the other disinfectant treatments. The introduction of selected additives and disinfectants may influence certain physical properties, chemical characteristics, and antibiotic concentrations of swine slurry.

Fate and transport of antibiotics and antibiotic resistance genes in runoff and soil as affected by the timing of swine manure slurry application.

Land application of swine manure slurry is a common practice to supplement nutrients to soil for crop production. This practice can introduce antibiotic residues and antibiotic resistance genes (ARGs) into the environment. Field testing is critical in identifying manure management practices effective in minimizing the environmental impacts of manure-borne antibiotic and ARGs. The objective of this study was to determine how the timing of swine manure application relative to rainfall events impacts the fate and transport of antibiotics and ARGs in surface runoff and manure-amended soil. Swine manure slurry was either broadcast or injected on test plots in the field. A set of three 30-min simulated rainfall events, 24 h apart, were initiated on manured plots 1 day, 1 week, 2 weeks, or 3 weeks after the manure application. Results showed that an interval longer than 2 weeks between application and rainfall often significantly reduced the levels of antibiotics and ARGs tested in runoff with the exception of tet(X). For soil samples from broadcast plots, concentrations of two of the three antibiotics tested (lincomycin and tiamulin) decreased substantially in the first two weeks after manure application. In contrast, concentrations of most of the ARGs tested (tet(Q), tet(X), and erm(A)) in soil did not change significantly during the test period. Information obtained from the study can be beneficial in designing manure management practices and estimating the environmental loading of antibiotics and ARGs resulting from manure application.

Methane and carbon dioxide emission from two pig finishing barns.

Agricultural activities are an important source of greenhouse gases. However, comprehensive, long-term, and high-quality measurement data of these gases are lacking. This article presents a field study of CH(4) and CO(2) emission from two 1100-head mechanically ventilated pig (Sus scrofa) finishing barns (B1 and B2) with shallow manure flushing systems and propane space heaters from August 2002 to July 2003 in northern Missouri. Barn 2 was treated with soybean oil sprinkling, misting essential oils, and misting essential oils with water to reduce air pollutant emissions. Only days with CDFB (complete-data-full-barn), defined as >80% of valid data during a day with >80% pigs in the barns, were used. The CH(4) average daily mean (ADM) emission rates were 36.2 +/- 2.0 g/d AU (ADM +/- 95% confidence interval; animal unit = 500 kg live mass) from B1 (CDFB days = 134) and 28.8 +/- 1.8 g/d AU from B2 (CDFB days = 131). The CO(2) ADM emission rates were 17.5 +/- 0.8 kg/d AU from B1 (CDFB days = 146) and 14.2 +/- 0.6 kg/d AU from B2 (CDFB days = 137). The treated barn reduced CH(4) emission by 20% (P < 0.01) and CO(2) emission by 19% (P < 0.01). The CH(4) and CO(2) released from the flushing lagoon effluent were equivalent to 9.8 and 4.1% of the CDFB CH(4) and CO(2) emissions, respectively. The emission data were compared with the literature, and the characteristics of CH(4) and CO(2) concentrations and emissions were discussed.

Quality assured measurements of animal building emissions: gas concentrations.

Comprehensive field studies were initiated in 2002 to measure emissions of ammonia (NH3), hydrogen sulfide (H2S), carbon dioxide (CO2), methane (CH4), nonmethane hydrocarbons (NMHC), particulate matter <10 microm in diameter, and total suspended particulate from swine and poultry production buildings in the United States. This paper focuses on the quasicontinuous gas concentration measurement at multiple locations among paired barns in seven states. Documented principles, used in air pollution monitoring at industrial sources, were applied in developing quality assurance (QA) project plans for these studies. Air was sampled from multiple locations with each gas analyzed with one high quality commercial gas analyzer that was located in an environmentally controlled on-farm instrument shelter. A nominal 4 L/min gas sampling system was designed and constructed with Teflon wetted surfaces, bypass pumping, and sample line flow and pressure sensors. Three-way solenoids were used to automatically switch between multiple gas sampling lines with > or =10 min sampling intervals. Inside and outside gas sampling probes were between 10 and 115 m away from the analyzers. Analyzers used chemiluminescence, fluorescence, photoacoustic infrared, and photoionization detectors for NH3, H2S, CO2, CH4, and NMHC, respectively. Data were collected using personal computer-based data acquisition hardware and software. This paper discusses the methodology of gas concentration measurements and the unique challenges that livestock barns pose for achieving desired accuracy and precision, data representativeness, comparability and completeness, and instrument calibration and maintenance.

Quality-assured measurements of animal building emissions: particulate matter concentrations.

Federally funded, multistate field studies were initiated in 2002 to measure emissions of particulate matter (PM) < 10 microm (PM10) and total suspended particulate (TSP), ammonia, hydrogen sulfide, carbon dioxide, methane, nonmethane hydrocarbons, and odor from swine and poultry production buildings in the United States. This paper describes the use of a continuous PM analyzer based on the tapered element oscillating microbalance (TEOM). In these studies, the TEOM was used to measure PM emissions at identical locations in paired barns. Measuring PM concentrations in swine and poultry barns, compared with measuring PM in ambient air, required more frequent maintenance of the TEOM. External screens were used to prevent rapid plugging of the insect screen in the PM10 preseparator inlet. Minute means of mass concentrations exhibited a sinusoidal pattern that followed the variation of relative humidity, indicating that mass concentration measurements were affected by water vapor condensation onto and evaporation of moisture from the TEOM filter. Filter loading increased the humidity effect, most likely because of increased water vapor adsorption capacity of added PM. In a single layer barn study, collocated TEOMs, equipped with TSP and PM10 inlets, corresponded well when placed near the inlets of exhaust fans in a layer barn. Initial data showed that average daily mean concentrations of TSP, PM10, and PM2.5 concentrations at a layer barn were 1440 +/- 182 microg/m3 (n = 2), 553 +/- 79 microg/m3 (n = 4), and 33 +/- 75 microg/m3 (n = 1), respectively. The daily mean TSP concentration (n = 1) of a swine barn sprinkled with soybean oil was 67% lower than an untreated swine barn, which had a daily mean TSP concentration of 1143 +/- 619 microg/m3. The daily mean ambient TSP concentration (n = 1) near the swine barns was 25 +/- 8 microg/m3. Concentrations of PM inside the swine barns were correlated to pig activity.

Feasibility and costs of phosphorus application limits on 39 U.S. swine operations.

Concerns about manure P and water quality have prompted new regulations imposing P limits on land application of manure. Previous research established that P limits increase land needs for animal feeding operations. We evaluated the effect of N, annual P, and rotation P limits on the feasibility of manure management. A mechanistic model characterized manure management practices on 39 swine operations (20 unagitated lagoon and 19 slurry operations) in five states (Iowa, Missouri, North Carolina, Oklahoma, and Pennsylvania). Extensive information collected from each operation was used to determine effects of manure storage type, ownership structure, and application limits on attributes of manure management. Phosphorus limits had substantially greater effect on slurry operations, increasing land needs 250% (0.3 hectares per animal unit [AU]) and time for manure application 24% (2.5 min AU(-1)) for rotation P limits and 41% (4.4 min AU(-1)) for annual P limits. Annual P limits were infeasible for current land application equipment on two operations and had the greatest effect on time and costs because they required all but three slurry operations to reduce discharge rate. We recommend implementing rotation P limits (not to exceed crop N need) to minimize time effects, allow most farmers to use their current manure application methods, and allow manure to fulfill crop N and P needs in the year of application. Phosphorus limits increased potential manure value but would require slurry operations to recover at least 61% of manure value through manure sales. Phosphorus limits are likely to shape the U.S. swine industry through differential effects on the various sectors of the swine industry.

An assessment of nitrogen-based manure application rates on 39 U.S. swine operations.

Water quality concerns and revised regulations are changing how confined animal feeding operations manage manure. Devising acceptable and feasible changes in manure practices requires a full understanding of the forces shaping current manure management decisions. Previous theoretical models have shown that a wide range of factors influence the lowest cost solution for manure management. We used a mechanistic model to characterize the manure management practices on 39 swine operations (20 unagitated lagoon and 19 slurry operations) in five states (Iowa, Missouri, North Carolina, Oklahoma, and Pennsylvania). Information was collected from each operation about animal numbers, feed and water use, manure handling and storage characteristics, field locations, crop rotation, fertilizer need, and equipment inventory and usage. Collected data were used as input and to validate results from a mechanistic model that determined acres required for manure application, manure application rate, time required for manure application, value of manure, and costs of manure management. The 39 farms had a mean of 984 animal units (AU) per operation, 18.2 AU ha(-1) (7.4 AU acre(-1)), and manure application costs of dollar 10.49 AU(-1) yr(-1). Significant factors affecting manure management included operation size, manure handling system, state, and ownership structure. Larger operations had lower manure management costs (r2 = 0.32). Manure value potentially exceeded manure application costs on 58% of slurry and 15% of lagoon operations. But 38% of slurry operations needed to apply manure off the farm whereas all lagoon operations had sufficient land for N-based manure management. Manure management was a higher percentage of gross income on contract operations compared with independents (P < 0.01). This research emphasized the importance of site-specific factors affecting manure management decisions and the economics of U.S. swine operations.