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Listeria monocytogenes is a serious foodborne pathogen that can harbor the pathogenicity islands Listeria pathogenicity island 3 (LIPI-3) and LIPI-4. Intriguingly, these have also been reported in nonpathogenic L. innocua from food and farm environments, though limited information is available for strains from the natural environment.

Soil organic carbon (SOC) is traditionally measured through dry combustion of soil but is inaccurate in soils recently limed or containing carbonates. Soils of south central Idaho contain carbonates therefore 3 alternative methods are typically used. Walkley-Black titration (WBTIT) has an extensive history but generates a large volume of hazardous waste for each sample analyzed. Low temperature loss on ignition (LOI360°C) may be utilized but requires frequent sample manipulation and is therefore prone to human error. A pressure calcimeter (Pcal) may be used, however the sample container may leak leading to inaccurate results. Therefore, a new method of SOC determination (WBSPEC) utilizing a microplate spectrophotometer was compared to LOI360°C, Pcal, and WBTIT in 75 south central Idaho soils and 10 standard soils. First, it was confirmed that soils of south central Idaho contain carbonates leading to inaccurate SOC determination by dry combustion. During the alternative method comparison, the WBSPEC method reduced waste production over the traditional WBTIT method by 89% while reducing sample handling over LOI360°C. The LOI360°C and WBTIT methods were most similar, however, the WBSPEC method performed adequately; the Pcal method often overestimated SOC compared to each other method. As the low SOC soils of south central Idaho were of particular interest, the methods were compared a second time on low SOC (

Greenhouse gas (GHG) emissions data from irrigated cropping systems utilizing dairy manure are needed in semiarid western regions. The objectives of this field study were to (i) determine the effect of synthetic N fertilizer (urea), enhanced-efficiency synthetic fertilizer (SuperU), composted dairy manure, dairy manure applications (fall and spring applied), and a control (no fertilizer or manure) on GHG losses over the growing season and overall global warming potential (GWP) and (ii) evaluate the influence of irrigation and field/crop management practices on GHG fluxes. The treatments were not applied to alfalfa (2017) but were applied to corn (2018; except SuperU) and barley (2019). Cumulative N2O-N losses over the 3-year rotation ranged from 2.8 to 5.2 kg/ha, with the fall and spring manure losing the greatest amounts of N2O-N. Emission factors indicated that -1.5 to 0.79% of the total N applied was lost as N2O-N during the growing seasons. Cumulative losses of CO2-C and CH4-C over the rotation were on average 12,170 and -0.77 kg/ha, respectively, with no significant differences among the treatments. Major N2O-N pulses were associated with early-season irrigation events and incorporation of fertilizer and manure, but overall fluxes tended to increase during the summer months when soil temperatures were highest. When accounting for increases in soil organic carbon (SOC) over the three growing seasons, the net GWPs were determined to be negative for the compost (-35.4), fall manure (-130.4), and spring manure (-48.9) treatments. As a result, these manure treatments should be considered as an alternative to synthetic N fertilizer use in southern Idaho due to their ability to increase SOC and help reduce agricultural climate impacts, while maintaining high crop yields.

Extracellular and intracellular antibiotic resistance genes (eARGs and iARGs) possess significant differences with respect to their mobility and availability to bacteria, thus it is important to understand their partitioning, persistence, and fate in the environment. The objectives of this study were to: (i) modify the protocol of a commercial DNA extraction kit to sequentially extract extracellular and intracellular DNA (eDNA and iDNA) from the same soil sample; and (ii) determine the effect of temperature (5, 20, and 35C), water holding capacity (25, 50, and 75% of WHCmax), and freeze-thaw (-20/20C) on the abundance of two ARGs [sul1 and tet(M)], class 1 integron-integrase gene (intI1), and 16S rRNA gene in soils treated with dairy manure. To assess the efficiency of the eDNA/iDNA method, we performed spiking and recovery experiments with a gene that codes for a green fluorescent protein (gfp). When soils were spiked with a whole-cell preparation of gfp-containing E. coli, the recovery of the gfp gene was on average 0.2% and 1.2% for eDNA and iDNA, respectively. Soils were also spiked with the gfp gene itself, which showed that nearly 80% of the DNA could not be recovered. Results from the microcosm experiments indicate that extracellular and intracellular sul1, tet(X), intI1, and 16S rRNA genes are resilient and not readily affected by temperature, WHC, or freeze-thaw cycles. The intracellular gene levels decreased only slightly during the 56-day incubation period. The extracellular gene levels (when detectable) decreased dramatically by day 7, then leveled off thereafter, which may have been caused by adsorption to soil particles and/or degradation. Absolute gene abundances (per g of dry soil) were one to two orders of magnitude higher in iDNA than in eDNA fractions, but were similar when normalized to the 16S rRNA gene throughout the incubation period, indicating that enrichment of eARGs and iARGs did not occur. It is important for the scientific community to standardize total, as well as, extracellular/intracellular DNA extractions in order to readily compare results between laboratories.

Antimicrobial resistance associated with the spread of plasmid-encoded extended-spectrum β-lactamase (ESBL) genes conferring resistance to third generation cephalosporins is increasing worldwide. However, data on the population of ESBL producing E. coli in different animal sources and their antimicrobial characteristics are limited. The purpose of this study was to investigate potential reservoirs of ESBL-encoded genes in E. coli isolated from swine, beef, dairy, and poultry collected from different regions of the United States using whole-genome sequencing (WGS). Three hundred isolates were typed into different phylogroups, characterized by BOX AIR-1 PCR and tested for resistance to antimicrobials. Of the 300 isolates, 59.7% were resistant to sulfisoxazole, 49.3% to tetracycline, 32.3% to cephalothin, 22.3% to ampicillin, 20% to streptomycin, 16% to ticarcillin, resistance to the remaining 12 antimicrobials was less than 10%. Phylogroups A and B1 were most prevalent with A (n = 92, 30%) and B1 (87 = 29%). A total of nine E. coli isolates were confirmed as ESBL producers by double-disk synergy testing and multidrug resistant (MDR) to at least three antimicrobial drug classes. Using WGS, significantly higher numbers of ESBL-E. coli were detected in swine and dairy manure than from any other animal sources, suggesting that these may be the primary animal sources for ESBL producing E. coli. These isolates carry plasmids, such as IncFIA(B), IncFII, IncX1, IncX4, IncQ1, CollRNAI, Col440I, and acquired ARGs aph(6)-Id, aph(3″)-Ib, aadA5, aph(3′)-Ia, blaCTX-M-15, blaTEM-1B, mphA, ermB, catA1, sul1, sul2, tetB, dfrA17. One of the E. coli isolates from swine with ST 410 was resistant to nine antibiotics and carried more than 28 virulence factors, and this ST has been shown to belong to an international high-risk clone. Our data suggests that ESBL producing E. coli are widely distributed in different animal sources, but swine and dairy cattle may be their main reservoir.

Irrigation return flows (IRFs) collect surface runoff and subsurface drainage, causing them to have elevated contaminant and bacterial levels, and making them a potential source of pollutants. The purpose of this study was to determine antimicrobial susceptibility among Escherichia coli and enterococcal isolates that were collected from IRFs in a south-central Idaho watershed. Environmental isolates can be a potentially important source of antimicrobial resistance (AMR) and IRFs may be one way resistance genes are transported out of agroecosystems. Water samples were collected from nine IRFs and one background site (canal water from Snake River) on a biweekly basis during 2018. Escherichia coli and enterococci were enumerated via a most probable number (MPN) technique, then subsamples were plated on selective media to obtain isolates. Isolates of E. coli (187) or enterococci (185) were tested for antimicrobial susceptibility using Sensititre broth microdilution plates. For E. coli, 13% (25/187) of isolates were resistant to tetracycline, with fewer numbers being resistant to 13 other antimicrobials, with none resistant to gentamicin. While 75% (141/187) of the E. coli isolates were pan-susceptible, 12 multidrug resistance (MDR) patterns with 17 isolates exhibiting resistance to up to seven drug classes (10 antimicrobials). For the enterococcal species, only 9% (16/185) of isolates were pan-susceptible and the single highest resistance was to lincomycin (138/185; 75%) followed by nitrofurantoin (56/185; 30%) and quinupristin/dalfopristin (34/185; 18%). In addition, 13 enterococcal isolates belonging to Enterococcus faecalis, Enterococcus faecium, Enterococcus casseliflavus, and Enterococcus thailandicus, were determined to be MDR to up to six different antimicrobial drug classes. None of the enterococcal isolates were resistant to gentamycin, linezolid, tigecycline, and vancomycin.

Dairy concentrated animal feeding operations (CAFO) are required to implement nutrient management plans enforced by environmental protection agencies to minimizing the risk of water resource degradation and to report gaseous emissions when they exceed certain threshold values. Although tools exist to aid in completing such tasks, few of the tools integrate the impact of on-farm manure treatment unit operations such as anaerobic digestion, solids separation, and nutrient recovery. Furthermore, existing tools do not estimate the nutrient value of recovered products and effluent leaving the dairy system or the nutrient fate after effluent is applied to crop fields. Dairy-CropSyst is a decision support tool for researchers and CAFO managers aimed at evaluating the effects of different manure treatment unit operations on gaseous emission and nutrient fate in dairy systems. The model tracks nutrients through the dairy system, including inorganic and organic forms of carbon, nitrogen, and phosphorus. This is accomplished by integrating established transformation and emission equations, performance parameters of manure treatments from industrial data and literature, and using a cropping system model for the land application evaluation. Comparison of simulated values with observed emissions indicated that model performance was reasonable. The overall correlation coefficient of observed and predicted ammonia and methane emission from dairy manure management was 0.72 and 0.58 respectively. Simulated and observed N2O emission were found in close agreement before and after the irrigation event, however, the model over estimated N2O emission after irrigation events (Coefficient of Residual Mass = −0.87). The use of Dairy-CropSyst has the potential to assist the dairy industry in decision making on manure management treatment strategies and as a tool for reporting GHG and ammonia emissions.

Information on greenhouse gas (GHG) emissions from manure application in cropping systems of the irrigated mountain west region is needed. The effects of manure application rate and timing on GHG emissions from a four-year commercial rotation under sprinkler irrigation was investigated. Treatments included dry manure rates of 52 or 18 Mg/ha applied annually or 36 Mg/ha applied biennially as well as fertilizer and control treatments. Cumulative losses of N2O-N over the rotation ranged from 1.4 to 8.4 kg/ha with the 52 Mg/ha manure application losing the greatest amount of N2O-N. Calculated emission factors indicated that 0.13 to 0.24% of total N applied was lost as N2O-N, much less than the emission factor of 1% used by the IPCC. Cumulative CO2-C losses were greater in the manure treatments compared to the fertilizer and controls, with approximately 7% of carbon added lost as CO2-C. These soils acted as a sink for CH4-C with average fluxes ranging from -0.1 to -0.3 kg/ha. Maximum N2O-N flux levels occurred at soil moisture contents ranging from 0.3 to 0.4 m3/m3 and temperature near 25 °C, while CO2-C emissions occurred over broader soil moisture and temperature conditions. The overall global warming potential (GWP) associated with manure application indicated that the manure treatments had a net negative GWP while fertilizer treatment was near neutral. A better understanding of regional soil and climatic conditions that affect GHG emissions will enable the development of emission factors more appropriate for use in GHG inventory efforts.

Insufficient characterization of soil organic carbon (SOC) dynamics in semi-arid climates contributes uncertainty to SOC sequestration estimates. This study estimated changes in SOC (0–30 cm depth) due to variations in manure management, tillage regime, winter cover crop, and crop rotation in southern Idaho (USA). Empirical data were used to drive the Denitrification Decomposition (DNDC) model in a “default” and calibrated capacity and forecast SOC levels until 2050. Empirical data indicates: (i) no effect (p = 0.51) of winter triticale on SOC after 3 years, (ii) SOC accumulation (0.6 ± 0.5 Mg ha–1 year–1) under a rotation of corn-barley-alfalfax3 and no change (p = 0.905) in a rotation of wheat-potato-barley-sugarbeet, (iii) manure applied annually at rate 1X is not significantly different (p = 0.75) from biennial application at rate 2X, and (iv) no significant effect of manure application timing (p = 0.41, fall vs. spring). The DNDC model simulated empirical SOC and biomass C measurements adequately in a default capacity, yet specific issues were encountered. By 2050, model forecasting suggested: (i) triticale cover resulted in SOC accrual (0.05–0.27 Mg ha–1 year–1), (ii) when manure is applied, conventional tillage regimes are favored, and (iii) manure applied treatments accrue SOC suggesting a quadratic relationship (all R2 &gt, 0.85 and all p &lt, 0.0001), yet saturation behavior was not realized when extending the simulation to 2100. It is possible that under very large C inputs that C sequestration is favored by DNDC which may influence “NetZero” C initiatives.

Advanced soil tests are being developed to help improve the estimation of plant available nutrients in order to better match fertilizer additions with plant needs as well as provide a measure of soil health, in some instances. The Soil Health Tool (SHT) has been developed with both goals in mind, yet it has not been tested for use in semi-arid regions such as southern Idaho. In the present study, we compared the use of the SHT for making fertilizer recommendations vs. using the standard regional method as well as evaluated the SHT soil health score (SHS) relative to crop yields and quality. The SHT was designed to analyze samples for 0-15 cm depth and regional guidelines call for deeper soil sampling (0-30 cm or 0-60 cm). In order to determine N fertilizer applications, use of the tool without accounting for depth, would recommend greater N application (~138 kg/ha) than the current regional methodology. However, it does appear that by accounting for depth in the SHT can provide similar available N estimates for the top 30 cm of soil. While N mineralization was not well predicted utilizing the method included in the SHT or from the regional methodology, the average estimated available N for these soils (47 kg/ha) was similar to the N mineralization value used in the current regional methodology (50 kg/ha). The P fertilizer recommendations were more similar between the two methodologies with the SHT recommending, on average 4.7 kg/ha less P than the regional method. The lower P recommendation are likely due to a lack of accounting for the effects of high calcium carbonate levels on the P availability from fertilizers in this region. The SHS was highly correlated with measures of soil C but was not positively correlated to crop yield. In some instances, increasing SHS resulted in decreases in crop quality as the addition of manure increased soil C but also created other potential problems such as high salt contents and release of late season N. With modification to more accurately represent irrigation conditions and including sampling to greater soil depths, this test may be tailored to better estimate soil nutrient status and provide better fertilizer recommendations for the region.

Dairy manure is regularly applied to crop fields as a solid or liquid to improve the soil nutrient status. However, pathogens may survive during manure storage and enter the environment during application. In this study, three storage practices were evaluated to understand the survival patterns of O157:H7 and spp. in dairy manure using a culture-based approach. To replicate common farm manure storage techniques, solid manure was stacked as piles with periodic turning or as static piles without turning, whereas liquid manure (feces, urine, and water) was stored as a slurry in small tanks to simulate lagoon conditions. The and levels in the manure samples were determined for 29 wk. Results showed that there was an initial reduction in bacteria levels in the first month; however, both and managed to survive in the solid manure piles for the full study period. In slurry samples, was not detected after 14 wk, but survived until the end of the experiment at relatively lower levels than in the solid manure piles. Ambient weather and pile size were identified as the main reasons for bacteria survival during the course of the experiment. The outcome of this study is important in terms of understanding pathogen survival in manure piles and slurries prior to their application to crop fields.

Ammonia (NH3) emissions from dairy liquid storage systems can be a source of reactive nitrogen (N) released to the environment, with a potential to adversely affect sensitive ecosystems and human health. However, little on-farm research has been conducted to estimate these emissions and determine the factors that may affect these emissions. Six lagoons in south-central Idaho were monitored for one year using open-path Fourier transform spectrometry, with NH3 emissions estimated using inverse dispersion modeling (WindTrax software). Lagoon physicochemical characteristics thought to contribute to NH3 emissions were also monitored over this period. Average total emissions from the lagoons ranged from 12 to 43 kg NH3 ha-1 d-1, or 5.4 to 85 kg NH3 d-1. Emissions from the settling basin on one dairy were 30% of the total emissions from the liquid storage system, indicating that basins are important sources of on-farm NH3 emissions. Emissions generally trended greater during the summer, when temperatures were greater. High wind events and agitation of the lagoons created temporary increases in NH3 emissions irrespective of temperature. Lagoon physicochemical characteristics, such as total Kjeldahl nitrogen (TKN) and total ammoniacal nitrogen (TAN), were highly correlated with emissions (r = 0.52 and 0.55, respectively). Regression models were developed to predict on-farm NH3 emissions and indicated that TKN, TAN, wind speed, air temperature, and pH were the main drivers of these emissions. An on-farm N balance suggested that lagoon NH3-N losses represented 9% of total N lost from the facility, 65% of total lagoon N, and 5% of dairy herd N intake. A process-based model (Integrated Farm System Model) estimated values for N excretion and NH3-N loss from the lagoon within 5% of that measured on-farm. More on-farm research is needed to better refine both process-based models and emission factor estimates to more accurately predict NH3 emissions from lagoons on dairies in the western U.S. Keywords: Ammonia, Emission, Inverse dispersion, Manure.

Altering dairy cattle diets to reduce both enteric methane (CH4) production and nitrogen (N) excretion are valuable tools for mitigating the environmental impact of dairy production. We examined the impact of altering diets on changes in physicochemical properties of manure during storage, short term plant N availability, and overall system N use efficiency. Manure collected from cattle fed diets with differing forage and crude protein (CP) content were stored via three methods (slurry, static pile, turned pile) for 29 weeks and sampled at week 0, 1, 2, 3, 4, 9, 14, 19, 24, and 29. Mass losses of total carbon (C) ranged from 28 to 50% and followed the trend static pile > slurry > turned pile (P < 0.01). Total N losses ranged from 20 to 47% with the slurry and static pile treatments having larger (but similar) losses than the turned pile treatment (P < 0.01). The soil 2-week plant available N was similar in the static pile and turned pile treatments and were 67% less than the slurry treatment. The short-term plant N use efficiency was similar for both the static pile and slurry treatments (22-24%), which were greater than that of the turned pile treatment (16%). Overall estimated system N use efficiencies were 5% greater for lower CP diets compared to high CP diets. While rapidly drying manure may conserve C and N, there may be a tradeoff with plant N utilization which could affect overall system efficiencies.

The polar organic compound integrative sampler (POCIS) is a tool that has been effectively used to passively sample organic pollutants over long periods in aquatic environments. In this study, POCIS were used to investigate the spatial and temporal occurrence of 21 antibiotics in irrigation return flows and upstream sites of an intensively managed agricultural watershed in south-central Idaho. The antibiotic metabolite, erythromycin-HO, and the antibiotics monensin, oxytetracycline, sulfadimethoxine, sulfamethazine, sulfamethoxazole, trimethoprim, and tylosin were detected at frequencies ranging from 3.1 to 62.5%, with monensin having the highest rate of detection. The fact that monensin was the most frequently detected compound indicates that it is entering return flows in runoff from fields that had received livestock manure or wastewater. Antibiotics (except oxytetracycline, sulfamethazine, and tylosin) were also detected at an upstream site that consisted of diverted Snake River water and is the source of irrigation water for the watershed. Therefore, even cropped soils that are not treated with manure are still receiving low-level antibiotics during irrigation events. This study provides the first set of evidence that surface waters within this agricultural watershed contain antibiotic residues associated with veterinary and human uses.

Methane generation from dairy liquid storage systems is a major source of agricultural greenhouse gas emissions. However, little on-farm research has been conducted to estimate and determine the factors that may affect these emissions. Six lagoons in south-central Idaho were monitored for 1 yr, with CH4 emissions estimated by inverse dispersion modeling. Lagoon characteristics thought to contribute to CH4 emissions were also monitored over this time period. Average emissions from the lagoons ranged from 30 to 126 kg/ha per day or 22 to 517 kg/d. Whereas we found a general trend for greater emissions during the summer, when temperatures were greater, events such as pumping, rainfall, freeze or thaw of lagoon surfaces, and wind significantly increased CH4 emissions irrespective of temperature. Lagoon physicochemical characteristics, such as total solids, chemical oxygen demand, and volatile solids, were highly correlated with emission. Methane prediction models were developed using volatile solids, wind speed, air temperature, and pH as independent variables. The US Environmental Protection Agency methodology for estimating CH4 emissions from manure storage was used for comparison of on-farm CH4 emissions from 1 of the lagoon systems. The US Environmental Protection Agency method underestimated CH4 emissions by 48%. An alternative methodology, using volatile solids degradation factor, provided a more accurate estimate of annual emissions from the lagoon system and may hold promise for applicability across a range of dairy lagoon systems in the United States.

Information is needed regarding the effect of nitrogen source on greenhouse gas (GHG) emissions from irrigated semiarid agricultural soils. We report nitrous oxide, carbon dioxide, and methane emissions from a silage corn (Zea mays L.) (2013)–barley (Hordeum vulgare L.) (2014)–alfalfa (Medicago sativa L.) (2015) rotation under conventional tillage and sprinkler irrigation. We evaluated the effectiveness of an enhanced-efficiency fertilizer (SuperU, a stabilized granular urea with urease and nitrification inhibitors) to reduce nitrous oxide emissions compared with granular urea and to determine GHG emissions from fall-applied dairy manure or composted dairy manure and spring-applied dairy manure. Nitrogen was applied during the first 2 yr of the study. SuperU plots emitted 53% less nitrous oxide than urea with corn, whereas no emission reductions occurred in 2014 with barley. The nitrous oxide -N emission losses as a percentage of total nitrogen applied were 0.21 and 0.04% for urea and SuperU in 2013, respectively, with losses of 0.05% from both urea fertilizers in 2014. On average, nitrous oxide fluxes from fall and spring manure were statistically similar and greater than the other nitrogen treatments in 2014 and a lasting manure treatment effect on emissions occurred under alfalfa. Carbon dioxide fluxes were greatest from fall- and spring-applied manure during the first 2 yr. Methane fluxes were negative, indicating microbial oxidation, and no differences occurred among the treatments. Corn, barley, and alfalfa yields were similar among all nitrogen treatments. This work demonstrates that SuperU can reduce nitrous oxide emissions from irrigated cropping systems in the semiarid western United States without affecting yields.

The shedding of Escherichia coli O157:H7 and Listeria monocytogenes in the feces of ruminants and the consequential risk to the public and environmental health is well reported. However, the influence of dietary manipulation on the shedding of fecal bacteria is not well understood. This study was conducted to improve understanding of the relationship between dietary feed composition and shedding of E. coli O157:H7 and Listeria spp. in dairy feces. Twelve cows were randomly assigned to four treatment diets of two dietary forage levels: low forage (37.4% dry matter, DM) vs. high forage (53.3% of DM) and two dietary crude protein (CP) levels: low protein (15.2% of DM) vs. high protein (18.5% of DM) in a 4×4 replicated Latin square design with four periods each including a 14 d adaptation and 3 d sample collection periods. Generic E. coli was detected in some of the feed ingredients, such as cotton seed, alfalfa hay, almond, and CaCO 3 , while Listeria was detected in the alfalfa hay and mineral mix. A significant interaction effect was observed between dietary forage and CP on the presence of fecal E. coli O157:H7 ( P =0.01) but not with Listeria . On average, the greatest E. coli O157:H7 level (6.6 log 10 CFU/g of feces) was observed from the high forage and high protein diet and the lowest level was 6.1 log 10 CFU/g from the low forage and high protein diet. The average Listeria shedding rate was within the range of 1.7–2.3 log 10 CFU/g among the dietary forage and CP treatments. For the CP treatments, significantly low levels of Listeria were observed from cows fed the high protein (0.9−1.6 log 10 CFU/g) compared to the low protein (1.3–2.1 log 10 CFU/g) diet. Considering temporal fluctuations, no significant diurnal pattern was observed for either E.coli O157:H7 or Listeria . In addition, no time of sampling over day by dietary forage or CP content interaction on fecal E.coli O157:H7 or Listeria level was observed. This study showed that diets can influence the shedding of potentially pathogenic bacteria in dairy cow excreta.

Although historically, antibiotic resistance has occurred naturally in environmental bacteria, many questions remain regarding the specifics of how humans and animals contribute to the development and spread of antibiotic resistance in agroecosystems. Additional research is necessary to completely understand the potential risks to human, animal, and ecological health in systems altered by antibiotic-resistance-related contamination. At present, analyzing and interpreting the effects of human and animal inputs on antibiotic resistance in agroecosystems is difficult, since standard research terminology and protocols do not exist for studying background and baseline levels of resistance in the environment. To improve the state of science in antibiotic-resistance-related research in agroecosystems, researchers are encouraged to incorporate baseline data within the study system and background data from outside the study system to normalize the study data and determine the potential impact of antibiotic-resistance-related determinants on a specific agroecosystem. Therefore, the aims of this review were to (i) present standard definitions for commonly used terms in environmental antibiotic resistance research and (ii) illustrate the need for research standards (normalization) within and between studies of antibiotic resistance in agroecosystems. To foster synergy among antibiotic resistance researchers, a new surveillance and decision-making tool is proposed to assist researchers in determining the most relevant and important antibiotic-resistance-related targets to focus on in their given agroecosystems. Incorporation of these components within antibiotic-resistance-related studies should allow for a more comprehensive and accurate picture of the current and future states of antibiotic resistance in the environment.

Collection fluids used in liquid-based bioaerosol samplers can influence the viability of microorganisms. In this study we determined the recovery efficiency of vegetative E. coli O157:H7 cells that were spiked into low viscosity evaporating collection fluids during operation of a BioSampler® for up to 90 min at room temperature. The collection fluids tested were deionized (DI) water, DI water with 0.1% (w/w) antifoam B (AFB), phosphate-buffered saline (PBS), and osmoprotectants consisting of peptone (with and without AFB) or betaine at .1% (w/w) in DI water. Using DI water, there was a rapid decline in the recovery of culturable E. coli, with only 11, 3, and 0% being recovered after 30, 60, and 90 min, respectively. Recoveries were substantially greater with use of PBS (53, 25, and 16%, respectively) but not as high as with use of the osmoprotectants or AFB. Peptone and AFB alone or together allowed for the greatest recovery of E. coli, with average values ranging from 87 to 98% at 90 min. Betain...

Surface waters could be a dominant route by which antibiotic resistance genes (ARGs) are disseminated. In the present study we explored the prevalence and abundance of ARGs [blaCTX-M-1, erm(B), sul1, tet(B), tet(M), and tet(X)], class 1 integron-integrase gene (intI1), and IncP-1 and IncQ-1 plasmids in eight irrigation return flows (IRFs) and a background site (Main Line Canal, MLC) in the Upper Snake Rock watershed in southern Idaho. Grab samples were collected on a monthly basis for a calendar year, which were processed to extract microbial DNA, followed by droplet digital PCR to quantify the gene copies on an absolute (per 100 mL) and relative (per 16S rRNA gene copies) basis. The antibiotic resistance and intI1 genes and IncP-1/IncQ-1 plasmids were recovered at all IRF sampling sites with detections ranging from 55 to 81 out of 81 water sampling events. The blaCTX-M-1 gene was detected the least frequently (68%), while the other genes were detected more frequently (88–100%). All of the genes were also detected at MLC from April to Oct when water was present in the canal. The genes from lowest to greatest relative abundance in the IRFs were: blaCTX-M-1

There are limited numbers of Escherichia coli isolate panels that represent United States food animal production. The majority of existing Escherichia coli isolate panels are typically designed: (i) to optimize genetic and/or phenotypic diversity; or (ii) focus on human isolates. To address this shortfall in agriculturally-related resources, we have assembled a publicly-available isolate panel (AgEc) from the four major animal production commodities in the United States, including beef, dairy, poultry, and swine, as well as isolates from agriculturally-impacted environments, and other commodity groups. Diversity analyses by phylotyping and Pulsed-field Gel Electrophoresis revealed a highly diverse composition, with the 300 isolates clustered into 71 PFGE sub-types based upon an 80% similarity cutoff. To demonstrate the panel's utility, tetracycline and sulfonamide resistance genes were assayed, which identified 131 isolates harboring genes involved in tetracycline resistance, and 41 isolates containing sulfonamide resistance genes. There was strong overlap in the two pools of isolates, 38 of the 41 isolates harboring sulfonamide resistance genes also contained tetracycline resistance genes. Analysis of antimicrobial resistance gene patterns revealed significant differences along commodity and geographical lines. This panel therefore provides the research community an E. coli isolate panel for study of issues pertinent to U.S. food animal production.

Improving our understanding of antibiotic resistance in soils is important for the protection of human, animal and ecological health. In south-central Idaho, antibiotic resistance genes (ARGs) [blaCTX-M-1, erm(B), sul1, tet(B), tet(M) and tet(X)] and a class 1 integron-integrase gene (intI1) were quantified in agricultural and non-agricultural soils (96 total sites) under various land use practices (cropland, forestland, inactive cropland, pastureland, rangeland, recreational, residential). We hypothesized that gene occurrence and abundance would be greater in intensively managed agricultural soils. The ARGs (except blaCTX-M-1) and intI1 gene were detected in many of the soils (15 to 58 out of 96 samples), with sul1 and intI1 being detected the most frequently (60% of samples). All of the genes were detected more frequently in the cropland soils (46 sites) and at statistically greater relative abundances (per 16S rRNA gene) than in soils from the other land use categories. When the cropland gene data was separated by sites that had received dairy manure, dairy wastewater, and/or biosolids (27 sites), it was revealed that the genes [except tet(B)] were found at statistically greater abundances (7- to 22-fold higher on average) than in soils that were not treated. The results from this study provide convincing evidence that manure/biosolids use in Idaho cropland soils increases the expansion of antibiotic resistance-related determinants.

The application of dairy wastewater to agricultural soils is a widely used practice to irrigate crops and recycle nutrients. In this study, small-scale field plots were irrigated monthly (6 times) with dairy wastewater (100%), wastewater diluted to 50% with irrigation (canal) water, and diluted wastewater spiked with copper sulfate (50 mg Cu L−1), while control plots were irrigated with canal water. In addition, half of all plots were either planted with wheat or were left as bare soil. Biweekly soil samples were collected during this period and processed to determine the occurrence and abundance of antibiotic resistance genes [blaCTX-M-1, erm(B), sul1, tet(B), tet(M), and tet(X)] and a class 1 integron-integrase gene (intI1) via quantitative real-time PCR (qPCR). Only sul1 and tet(X) were detected in soil (3 out of 32 samples) before the wastewater treatments were applied. However, the occurrence and relative abundance (normalized to 16S rRNA gene copies) of most genes [erm(B), intI1, sul1, and tet(M)] increased dramatically after wastewater irrigation and levels were maintained during the entire study period. blaCTX-M-1 was the only gene not detected in wastewater-treated soils, which is likely related to its absence in the dairy wastewater. Relative gene levels in soil were found to be statistically similar among the treatments in most cases, regardless of the wastewater percentage applied and presence or absence of plants. The key result from this study is that dairy wastewater irrigation significantly enlarges the reservoir of ARGs and intI1 in soils, while detection of these genes rarely occurred in soil irrigated only with canal water. In addition, elevated levels of Cu in the wastewater and treated soil did not produce a concomitant increase of the ARG levels.

Animal manures are commonly used to enhance soil fertility, but there are growing concerns over the impact of this practice on the development and dissemination of antibiotic resistance. The aim of this study was to determine the effect of annual dairy manure applications on the occurrence and abundance of antibiotic resistance genes (ARGs) in an agricultural soil under crop production. The experimental design was a randomized complete block with four replications, which included the following treatments: i) control (no fertilizer); ii) inorganic fertilizer; and iii) stockpiled dairy manure. Inorganic fertilizer was applied in the spring, while dairy manure was applied in the fall of 2012–2015 at 17.2, 34.5, and 52.0 Mg (dry wt.)/ha. Soil samples were collected in the spring (pre-plant) and fall (post-harvest) to a depth of 120 cm. DNA extracted from the soils was used in a quantitative real-time PCR reaction to determine absolute abundances (per g dry soil) and relative abundances (per 16S rRNA gene copies) of ARGs. The ARGs targeted were blaCTX-M-1, erm(B), sul1, tet(A), tet(W), and tet(X) and a class 1 integron-integrase gene (intI1), but only sul1, tet(W), tet(X), and intI1 were detected in enough samples to run statistics and draw conclusions. This study found that: i) manure application increases ARG abundances above background soil levels; ii) the higher the manure application rate, the higher the ARG abundance in soil; iii) the amount of manure applied is more important than reoccurring annual applications of the same amount of manure; iv) absolute abundance and occurrence of ARGs decreases with increasing soil depth, but relative abundances remained constant; and v) ARGs correlated with each other and a number of soil chemical parameters, but not with soil moisture or 16S rRNA gene. Overall, this study demonstrated that dairy manure applications significantly increase the abundance of clinically relevant ARGs when compared to soil that received inorganic fertilizer or no fertilizer/manure.

With increased concern over the effects of livestock production on the environment, a number of new technologies have evolved to help scientists evaluate the environmental footprint of beef cattle. The objective of this review was to provide an overview of some of those techniques. These techniques include methods to measure individual feed intake, enteric methane emissions, ground-level greenhouse gas and ammonia emissions, feedlot and pasture emissions, and identify potential pathogens. The appropriate method to use for measuring emissions will vary depending upon the type of emission, the emission source, and the goals of the research. These methods should also be validated to assure they produce accurate results and achieve the goals of the research project. In addition, we must not forget to properly use existing technologies and methods such as proper feed mixing, feeding management, feed/ingredient sampling, and nutrient analysis.

Foundries around the world discard millions of tons of sand each year even though they can be beneficially used in manufactured soils and geotechnical applications. Despite their usefulness as an aggregate replacement, some environmental authorities are concerned over potential negative impacts associated with residual organic binders in waste foundry sands (WFSs). In this study, chemically bound molding and core sands were obtained from aluminum, bronze and iron foundries that used alkyd urethane, phenolic urethane, Novolac, and natural organic binders. The aim was to use mid-infrared (MIR) spectrometry to assess binder changes within the sands during the casting process. Bands associated with C H stretching were detected in most WFSs. Mid-infrared spectra and total carbon data demonstrated that organic binders closest to the molten metal interface and subjected to the highest casting temperatures exhibited the most thermal degradation. Our results also provided preliminary evidence that MIR spectroscopy could potentially be used as a method to quantify residual binder in WFSs.

In the western United States where dairy wastewaters are commonly land applied, there are concerns over individuals being exposed to airborne pathogens. In response, a quantitative microbial risk assessment (QMRA) was performed to estimate infectious risks after inhalation exposure of pathogens aerosolized during center pivot irrigation of diluted dairy wastewaters. The dispersion of pathogens (Campylobacter jejuni, Escherichia coli O157:H7, non-O157 E. coli, Listeria monocytogenes, and Salmonella spp.) was modeled using the atmospheric dispersion model, AERMOD. Pathogen concentrations at downwind receptors were used to calculate infectious risks during one-time (1, 8, and 24 h) and multiday (7 d at 1 h d(-1)) exposure events using a β-Poisson dose-response model. This assessment considered risk of infection in residential populations that were 1 to 10 km from a center pivot operation. In the simulations, infectious risks were estimated to be the greatest in individuals closest to the center pivot, as a result of a higher pathogen dose. On the basis of the results from this QMRA, it is recommended that wastewaters only be applied during daylight hours when inactivation and dilution of airborne pathogens is highest. Further refinement of the dispersion and dose-response models should be considered to increase the utility of this QMRA.

Shedding of Escherichia coli O157:H7 and Listeria monocytogenes in ruminant manure is well reported. However, the influence of dietary manipulation on the shedding of the pathogens is not well understood. This study was conducted to improve the understanding of the relationship between dietary feed composition and pathogen shedding in dairy feces, particularly E. coli O157:H7 and L. monocytogenes. Twelve cows were randomly assigned to a 2 Ã 2 factorial arrangement of 2 dietary forage levels: low forage (37.4% of dry matter [DM]) vs. high forage (HF, 53.3% of DM) and two dietary crude protein (CP) levels: low protein (LP, 15.2% of DM) vs. high protein (HP, 18.5% of DM) in a 4 Ã 4 replicated Latin square design with four periods each including 15 d adaptation and 3 d sample collection. In CP treatments, significantly low concentrations of L. monocytogenes were observed from cows fed the HP (0.9-1.6 log10 cfu/g) compared to the LP diet (1.3â2.1 log10 cfu/g). Significant interaction effect was observed between dietary forage and crude protein on the presence of E. coli O157:H7 (P < 0.05) but not on L. monocytogenes. On average, the highest E. coli O157:H7 concentration (6.5 log10 cfu/g of feces) was observed from the HF and HP diet and the lowest concentration was 6.2 log10cfu/g from the HF and LP diet. The average L. monocytogenes shedding was within the range of 1.8 to 2.4 log 10cfu/g among the treatments. The study showed that diet has an influence on the shedding of pathogenic bacteria in dairy excreta.

Zoonotic pathogens in land-applied dairy wastewaters are a potential health risk. The occurrence and abundance of 10 pathogens and 3 fecal indicators were determined by quantitative real-time PCR (qPCR) in samples from 30 dairy wastewaters from southern Idaho. Samples tested positive for Campylobacter jejuni , stx 1 - and eaeA -positive Escherichia coli , Listeria monocytogenes , Mycobacterium avium subsp. paratuberculosis , and Salmonella enterica , with mean recoveries of genomic DNA corresponding to 10 2 to 10 4 cells ml −1 wastewater. The most predominant organisms were C. jejuni and M. avium , being detected in samples from up to 21 and 29 of 30 wastewater ponds, respectively. The qPCR detection limits for the putative pathogens in the wastewaters ranged from 16 cells ml −1 for M. avium to 1,689 oocysts ml −1 for Cryptosporidium. Cryptosporidium and Giardia spp., Yersinia pseudotuberculosis , and pathogenic Leptospira spp. were not detected by qPCR.

The presence of antibiotic drug residues, antibiotic resistant bacteria, and antibiotic resistance genes in agroecosystems has become a significant area of research in recent years and is a growing public health concern. While antibiotics are used in both human medicine and agricultural practices, the majority of their use occurs in animal production where historically they have been used for growth promotion, in addition to the prevention and treatment of disease. The widespread use of antibiotics and the application of animal wastes to agricultural lands play major roles in the introduction of antibiotic-related contamination into the environment. Overt toxicity in organisms directly exposed to antibiotics in agroecosystems is typically not a major concern because environmental concentrations are generally lower than therapeutic doses. However, the impacts of introducing antibiotic contaminants into the environment are unknown, and concerns have been raised about the health of humans, animals, and ecosystems. Despite increased research focused on the occurrence and fate of antibiotics and antibiotic resistance over the past decade, standard methods and practices for analyzing environmental samples are limited and future research needs are becoming evident. To highlight and address these issues in detail, this special collection of papers was developed with a framework of five core review papers that address the (i) overall state of science of antibiotics and antibiotic resistance in agroecosystems using a causal model, (ii) chemical analysis of antibiotics found in the environment, (iii) need for background and baseline data for studies of antibiotic resistance in agroecosystems with a decision-making tool to assist in designing research studies, as well as (iv) culture- and (v) molecular-based methods for analyzing antibiotic resistance in the environment. With a focus on the core review papers, this introduction summarizes the current state of science for analyzing antibiotics and antibiotic resistance in agroecosystems, discusses current knowledge gaps, and develops future research priorities. This introduction also contains a glossary of terms used in the core reivew papers of this special section. The purpose of the glossary is to provide a common terminology that clearly characterizes the concepts shared throughout the narratives of each review paper. Agriculture and Food Research Initiative Competitive from USDA National Institute of Food and Agriculture [2013-68003-21256] We thank all of the authors who contributed papers to this special section, which would not have been possible without their efforts. This project was supported by the Agriculture and Food Research Initiative Competitive Grant no. 2013-68003-21256 from the USDA National Institute of Food and Agriculture. Public domain – authored by a U.S. government employee

© American Society of Agronomy, Crop Science Society of America, and Soil Science Society of America. 5585 Guilford Rd., Madison, WI 53711 USA. All rights reserved. Nitrogen excreted in dairy manure can be potentially transformed and emitted as NH3, which can create livestock and human respiratory problems and be an indirect source of N2O. The objectives of this study were to: (i) investigate environmental factors influencing NH3emissions from dairy housing; and (ii) identify key explanatory variables in the NH3emissions prediction from dairy housing using a meta-analytical approach. Data from 25 studies were used for the preliminary analysis, and data from 10 studies reporting 87 treatment means were used for the meta-analysis. Season and flooring type significantly affected NH3emissions. For nutritional effect analysis, the between-study variability (heterogeneity) of mean NH3emission was estimated using random-effect models and had a significant effect (P < 0.01). Therefore, random-effect models were extended to mixedeffect models to explain heterogeneity regarding the available dietary and animal variables. The final mixed-effect model included milk yield, dietary crude protein, and dry matter intake separately, explaining 45.5% of NH3emissions heterogeneity. A unit increase in milk yield (kg d-1) resulted in a 4.9 g cow-1d-1reduction in NH3emissions, and a unit increase in dietary crude protein content (%) and dry matter intake (kg d-1) resulted in 10.2 and 16.3 g cow-1d-1increases in NH3emissions, respectively, in the scope of this study. These results can be further used to help identify mitigation strategies to reduce NH3emissions from dairy housing by developing predictive models that could determine variables with strong association with NH3emissions.

A fresh green sand, spent green sand, and a weathered spent green sand (wSGS) from a foundry landfill were analyzed using diffractometry, electron microscopy, fluorometry, granulometry, spectrometry, and thermogravimetry (TG). Our objective was to understand how the physicochemical properties of the foundry green sands change from their original form after being subjected to the casting process, then after weathering at the landfill. A quantitative phase composition model was also postulated for each material based on the TG results and it was found to be the most reliable and informative quantitative data for this type of residue. The weathered sample, that remained in a landfill for two years, was found to be composed of almost pure sand. Because of the weathering process, it may be possible to use the wSGS as a virgin sand replacement in the regeneration system or in geotechnical applications where bentonite would affect the properties of the final product.

Animal manures are known to harbor a variety of zoonotic pathogens, which are suspected of being transported off-site as aerosols from confined feeding operations. In this study, aerosols were collected using a high-volume sampler downwind from a 10,000 cow open-freestall dairy and nearby fields being sprinkler irrigated with wastewater. DNA extracts were prepared from the aerosol samples, then a region of the16S ribosomal RNA gene was sequenced for bacterial identification and phylogenetic classification. At the dairy and irrigation sites, Proteobacteria (α-, β-, and γ-subdivisions) was the most abundant phylum, representing 78% and 69% of all sequences, respectively, while Actinobacteria, Bacteroidetes and Firmicutes represented only 10% or less of the sequences. Of the 191 clones sequenced from the dairy aerosol samples, 6 sequences were found to be homologous with uncultured bacteria from cow milk, rumen, and fecal samples. However, none of the sequence matches was affiliated with bacteria known to be pathogenic to otherwise healthy humans. Although our results do suggest a high diversity among the aerosolized bacteria, the sampling strategy employed in this study may not account for the variable nature of bioaerosol emissions. Keywords: Aerosol, Dairy, Manure, PCR, Spray irrigation, Wastewater

Our objective was to establish doses of orally administered NaClO(3) that reduced the presence of generic Escherichia coli in intestines of ewes and neonatal lambs managed in a shed-lambing system. Neonatal lambs (n = 32; age = 7.1 ± 1.2 d; BW = 6.8 ± 1.0 kg) and yearling ewes (n = 44; BW = 74.8 ± 5.6 kg) were used in 2 experiments. In both experiments, lambs and ewes were randomly assigned to 1 of 4 groups, and groups were randomly assigned to 1 of 4 treatments. In Exp. 1, neonatal lambs were given single, aqueous, oral doses of saline (control; NaCl, 30 mg·kg of BW(-1)) or 30, 60, or 90 mg of NaClO(3)·kg(-1) of BW. At 25.9 ± 1.3 h after treatment, lambs were euthanized, and intestinal contents were collected aseptically. In Exp. 2, ewes were given single, aqueous, oral doses of saline (NaCl, 150 mg·kg of BW(-1)) or 150, 300, or 450 mg of NaClO(3)·kg(-1) of BW. At 24.0 ± 0.8 h after treatment, fecal samples were collected aseptically from the rectum of each ewe. For both experiments, generic E. coli were enumerated from intestinal contents and feces within 4 to 12 h after collection. In Exp. 1, the effect (P = 0.08) of NaClO(3) on the presence of generic E. coli in colon contents was dose-dependent. This effect was linear (P < 0.01) and negative, which indicated that as NaClO(3) dose increased, generic E. coli that could be isolated from colon contents decreased. Specifically, lambs dosed with 60 and 90 mg of NaClO(3)·kg(-1) of BW had fewer E. coli cfu·g(-1) of content than control lambs (P < 0.06). Lambs dosed with 90 mg of NaClO(3)·kg(-1) of BW had fewer E. coli cfu·g(-1) of content than lambs dosed with 30 mg of NaClO(3)·kg(-1) of BW (P = 0.09). Sodium chlorate dose did not influence (P = 0.58) the presence of generic E. coli in contents collected from the cecum. In Exp. 2, the effect (P < 0.0001) of NaClO(3) on the presence of E. coli in fecal contents from ewes was dose-dependent. This effect was quadratic (P < 0.0001) and negative; ewes dosed with 150, 300, and 450 mg of NaClO(3)·kg(-1) of BW had fewer E. coli cfu·g(-1) of feces than control ewes. No differences in E. coli cfu·g(-1) of feces were detected between NaClO(3) treatments (P = 0.88 to 0.97). Based on these results, a single oral dose of at least 60 and 150 mg of NaClO(3)·kg(-1) of BW in neonatal lambs and yearling ewes, respectively, significantly decreased the presence of generic E. coli in contents from the lower intestine.

The objective of this study was to phylogenetically analyze microorganisms from the domains Bacteria and Archaea in hypersaline sediment from Death Valley National Park. Using domain-specific primers, a region of the 16S rRNA gene was amplified using polymerase chain reaction (PCR), and the product was subsequently used to create a clone library. A total of 243 bacterial clones, 99 archaeal clones, and 209 bacterial isolates were examined. The 243 clones from Bacteria were affiliated with the following groups: the Bacilli (59 clones) and Clostridia (1) of the Firmicutes, Bacteroidetes (90), Proteobacteria (27), Cyanobacteria (18), Gemmatimonadetes (41), candidate division OP1 (5), Actinobacteria (1), and the Deinococcus-Thermus division (1). Within the class Bacilli, 46 of 59 clones were tentatively identified as 10 unclassified species. The majority of bacterial isolates (130 of 209) were more closely related to the Bacillus subtilis–B. licheniformis clade than to any other recognized taxon, and an Ecotype Simulation analysis of B. subtilis relatives identified four previously unknown ecotypes. Several new genera were discovered within the Bacteroidetes (4) and the Gemmatimonadetes (2). Of the 99 archaeal clones, 94 were tentatively identified as belonging to 3 new genera within the Halobacteriaceae; other clones represented novel species within each of 4 established genera.

Confined animal production systems produce increased bioaerosol concentrations, which are a potential respiratory health risk to individuals on site and downwind. In this longitudinal study, airborne endotoxin and microorganisms were collected during the spring, summer, and fall at a large, open-freestall dairy in southern Idaho. Compared with the background ambient atmosphere, both endotoxin and culturable heterotrophic bacteria concentrations were up to several-hundred-fold greater 50 m downwind from the facility, then decreased to near background concentrations at 200 m. However, downwind fungi concentrations were not increased above background concentrations. At 50 m downwind, the average inhalable endotoxin concentration ranged from 5 to 4,243 endotoxin units per m⁻³, whereas bacteria concentrations ranged from 10² to 10⁴ cfu per m⁻³ of air. Although the bioaerosol concentrations did not follow a seasonal trend, they did significantly correlate with meteorological factors. Increasing temperature was found to be positively correlated with increasing bacteria (r = 0.15, P < 0.05), fungi (r = 0.14, P < 0.05), and inhalable endotoxin (r = 0.32, P < 0.001) concentrations, whereas an inverse relationship occurred between the concentration and solar radiation. The airborne concentrations at 50 m were also found to be greatest at night, which can likely be attributed to changes in animal activity and wind speed and reduced exposure of the airborne microorganisms to UV radiation.

The expansion of the dairy industry in southern Idaho has lead to increased application of manures to meet crop nutrient demands which can alter the uptake pattern of both macro- and micro-nutrients. A greenhouse study was conducted to determine the effects of dairy manure, composted dairy manure, and fertilizer (mono-ammonium phosphate, MAP) application on soil test phosphorus (P), microbial activity, and nutrient uptake by silage corn. Two Portneuf soils, having either a low or high soil test P concentration, were amended with the three treatments at four application rates (25, 50, 100, and 200 mg P kg-1) with four replications of each treatment in a randomized complete design. Treatments were incubated for two weeks, then planted with corn grown for approximately three weeks. Soil samples were analyzed prior to planting, whereas plant samples were analyzed at the end of the growing period. Increases in Olsen P from P additions were greatest in the MAP and least in the manure treated soils. Plant dry matter production and tissue P concentration did not differ with treatment. Tissue K increased with manure and compost addition while tissue Ca decreased; there was also a decrease in tissue Mg with compost application. Tissue Zn increased with manure applications, while tissue Mn decreased with manure and compost application on the Low-P soil. It is important to consider plant nutrient interactions when applying manure and compost to feed-crops as imbalances in K, Ca, and Mg can have a negative impact on animal health.

Airborne endotoxins in occupational environments are a potential respiratory hazard to individuals. In this study, airborne endotoxins were collected using open-face and button aerosol samplers from inside animal housing units and downwind from agricultural production sites and a wastewater treatment plant. Filter extracts were then diluted to examine the effect of interfering substances on the kinetic Limulus amebocyte lysate (LAL) assay. In most cases, the overall endotoxin concentration was shown to decrease with increasing dilution up to 1000-fold, suggesting the presence of enhancing substances in the filter extracts. This dilution-dependent effect was most prominent in the open-face endotoxin samples, while button samples displayed little effect. Using a joinpoint regression model, it was determined that a dilution factor of 50 to 100 was generally sufficient to eliminate the presence of enhancing substances. After screening the data for dilution dependent effects, the airborne endotoxin concentrations were determined. The highest endotoxin concentrations, ranging from 2841 to 49,066 endotoxin units m(-3) of air, were found inside swine farrowing and finishing barns. Airborne endotoxin concentrations were 10- to 100-fold lower inside a dairy barn and downwind of other agricultural production sites and the wastewater treatment plant. Examination of dilution-dependent effects should be considered essential when utilizing the LAL assay, especially if values are to be used for regulatory purposes.

In this study, we conducted simulated spray irrigation events of dairy wastewater to assess the impact of pressure and sprinkler type on post-sprinkler culturable microorganism concentrations. Dairy wastewater was sampled before and after it was pumped through sprinklers typically used on center-pivot irrigation systems. Three different sprinklers types were used at three different operating pressures to give a range of water drop sizes. The microorganisms quantified in this study were total coliforms, Escherichia coli, Clostridium perfringens, heterotrophic bacteria, and coliphages. In most cases, the pre- and post-sprinkler concentrations were determined to be statistically similar, suggesting that culturable viability was not affected when wastewater flowed through these sprinklers. When an impact was found to occur, there was usually an increase in the post-sprinkler microorganism concentration. While this increase can be attributed to the disruption of microbial aggregates during the spraying process, there was no apparent relationship with pressure setting or spray plate. Understanding impacts at the sprinkler level should be considered an integral part of the dispersion modeling process, as it may influence the number of viable microorganisms that become aerosolized during pressurized irrigation events.