Antimicrobial resistance in escherichia coli and enterococcal isolates from irrigation return flows in a high-desert watershed

Irrigation return flows (IRFs) are of interest because they collect surface runoff and subsurface drainage, causing them to have elevated contaminant and bacterial levels, and making them a potential point source of pollutants. The purpose of this study was to determine antibiotic susceptibility profiles of E. coli and Enterococcus spp. that were collected from IRFs in south-central Idaho. Environmental isolates can be a potentially important source of antibiotic resistance (AR) 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 Enterococcus were enumerated via a Most Probable Number technique, then subsamples were plated on selective media to obtain isolates. About 185 of 800 unique isolates for E. coli and Enterococcus were tested for antimicrobial susceptibility using the Sensititre broth microdilution plates. For E. coli, 11% of the isolates were resistant to tetracycline, with fewer numbers being resistant to the 13 other antibiotics, with none resistant to gentamicin. While 77% of the E. coli isolates were pan-susceptible, 9 MDR patterns with resistance up to 7 drug classes (10 antibiotics) occurred in 11 isolates. For the enterococcal species, only 9% of isolates were pan-susceptible and the single highest resistance was to lincomycin (75%) followed by nitrofurantoin (31%) and tetracycline (11%). In addition, 13 enterococcal isolates were determined to be MDR to up to 5 different drug classes and it was only prevalent among E. faecalis, E. faecium, E. casseliflavus, and E. thailandicus. Due to the potential for human contact, routine monitoring of E. coli and Enterococcus in the IRFs could be a useful tool to understand the long-term trends of AR in this mixed-use watershed

Antibiotic resistance genes, class 1 integrons, and IncP-1/IncQ-1 plasmids in irrigation return flows

Antibiotic resistance is encoded by antibiotic resistance genes (ARGs) and surface waters could be a dominant route by which they are disseminated. In the present study we aimed to explore 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 south-central 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 to 100%). All of the genes were also detected at MLC from April to October when water was present in the canal. The genes from lowest to greatest relative abundance in the IRFs were: blaCTX-M-1 < erm(B) < tet(B) < IncQ-1 < tet(M) < sul1 < intI1 = IncP-1 < tet(X). When compared to the average annual relative gene abundances in MLC water samples, they were found to be at statistically greater levels (P = 0.008) except that of the IncP-1 and IncQ-1 plasmids (P = 0.8 and 0.08, respectively). The fact that most IRFs contained higher levels than found in the canal water, indicates that IRFs can be a point source of ARGs that ultimately discharge into surface waters. It was also found that ARG levels were not strongly correlated with the intI1 gene, nor IncP-1 and IncQ-1 plasmids, suggesting that the ARGs were not enriched as a result of horizontal gene transfer among or replication within environmental bacteria

Year-Long Assessment of Airborne Endotoxin at a Concentrated Dairy Operation

In this study, we monitored total airborne endotoxins at upwind and downwind sites at a large open-lot dairy each month for a year. At the upwind site, the average airborne concentration was 28.5 endotoxin units (EU) m-3, while at the downwind edge of the lot and 200 m from the lot edge, the average concentrations were 169 and 72 EU m-3, respectively. At the downwind edge of the lot, there was a significant correlation between the airborne endotoxin concentration and wind speed or air temperature. A comparison between total and inhalable airborne endotoxin concentrations, near the end of the study, revealed no significant differences between the two endotoxin collection methods. Our data suggest that endotoxin exposure can be reduced as one increases their distance from the open-lot dairy

Concentrations of Airborne Endotoxin and Microorganisms at a 10,000 Cow Open-Freestall Dairy

Confined animal production systems produce elevated bioaerosol concentrations, which are a potential respiratory health risk to individuals on site and downwind. In this study, airborne endotoxin and microorganisms were collected during the spring, summer, and fall at a large open-freestall dairy in southern Idaho. Compared to 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 elevated above background concentrations. At 50 m downwind, the average inhalable endotoxin concentration ranged from 4.6 to 4243 endotoxin units/cubic meter of air, while bacteria concentrations ranged from 102 to 104 colony forming units (CFU)/cubic meter. 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 endotoxin, bacteria, and fungi concentrations, while 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 ultraviolet radiation

Effect of Sprinkler Pressure and Spray Plate on Culturable Microorganism Concentrations During Simulated Irrigation of Dairy Wastewater

In this study we conducted simulated spray irrigation events of dairy wastewater to assess the impact of pressure and sprinkler type upon 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 coliphage. 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

Spatial and temporal variation in physicochemical properties of dairy lagoons in south-central Idaho

There are large quantities of wastewater generated on dairies in south-central Idaho, which can be a source of valuable nutrients as well contribute to air quality and climate change issues via ammonia (NH3) and greenhouse gas (GHG) emissions. The objective of this study was to examine the range of lagoon water properties among dairies in the region and to determine how they varied spatially and temporally. Twenty-seven lagoons were sampled twice in a blind trial to determine physicochemical characteristics, while 6 lagoons were sampled (3 to 27 times) over a longer period of time to determine how these characteristics changed with time and space. Lagoon properties measured consisted of total solids (TS), volatile solids (VS), chemical oxygen demand (COD), total Kjeldahl nitrogen (TKN), total ammoniacal nitrogen (TAN), total phosphorus (P), total potassium (K), temperature, pH, dissolved oxygen (DO), and specific conductivity. Results indicate that all lagoon characteristics varied greatly between dairies and with sampling date. Seasonal trends indicated that N decreased from spring to fall, while specific conductivity, total P, total K, and in some instances TS and VS increased over the same time period. There was an effect of housing on these properties with freestall dairies having higher concentrations of TS, VS, COD, TKN, TAN, and specific conductivity than dry-lot dairies. There was little effect of dairy size on physicochemical characteristics measured. These results suggest that it is important to account for nutrients applied with lagoon waters in nutrient budgets in order to prevent over-application of N and K which could lead to N leaching and forage quality issues. In addition, capturing the temporal variation in lagoon properties is important to accurately model seasonal variations in NH3 and GHG emissions

Growing and non-growing season nitrous oxide emissions from manured soil under irrigation

Dairy manure is used in semiarid southern Idaho to improve soil fertility, but campaigns to measure resulting nitrous oxide (N2O) emissions over the complete year have not been conducted to date. The objective of this study was to measure N2O fluxes throughout the growing and non-growing seasons in 2020 (sugar beet) and 2021 (corn silage) in a field that received inorganic N fertilizer or was previously treated with dairy manure solids on an annual and biennial basis for 8 years. Gas fluxes were measured daily using automated chambers that were connected to a gas chromatograph for in situ analysis of N2O. The N2O emissions were found to be highly episodic and major pulses were associated with freeze-thaw events in the winter, irrigation events during the growing season, and soil disturbance at harvest. Emissions were greatest from soil that had received manure at the highest annual application rate of 52 Mg/ha (dry wt.), with cumulative totals of 3.6 and 3.0 kg N2O-N/ha in 2020 and 2021, respectively. These cumulative totals were about 3-fold greater than emissions from plots treated with inorganic fertilizer or manure at 17 Mg/ha annually or 35 Mg/ha biennially. This outcome can be attributed to high concentrations of nitrate produced through mineralization of organic N in manure. Emission factors indicated that 0.6 to 0.9% of the total N applied was lost as N2O-N over the two years. When breaking down the emissions by season, anywhere from 49 to 63% (2020) and 37 to 58% (2021) of the N2O-N emissions occurred during the non-growing season. Cumulative growing and non-growing season N2O emissions were found to be statistically equivalent in the inorganic fertilizer and manure treatments. This finding stresses the need to also measure N2O emissions during the non-growing season as a way to improve the accuracy of annual emission estimates

Evaluation of center pivot sprinkler wind drift and evaporation measurement technique

Wind drift and evaporation losses (WDELs) are an often discussed topic in regards to center pivot sprinkler irrigation efficiency. Opinions on the magnitude of WDELs vary widely, in part due to the wide variation in WDEL values published in the literature. The magnitude of WDELs reported in the literature range from 2 to 45%. The common technique employed to measure WDEL is to use catch cans and compare the measured volume of catch with the volume of water applied based on sprinkler nozzle size, operating pressure and spacing with the difference being WDEL. The inaccuracies of catch cans resulting from wind effects on catch efficiency and evaporation of water from the catch can prior to measurement have led to the wide range in WDEL reported in the literature. The objective of this project was to develop and evaluate a methodology for measurement of WDEL from center pivot sprinklers using a combination of applied water collectors, bromide tracer and air samplers. The evaluation criteria were the magnitude of water volume balance error. A methodology for measuring wind drift and evaporation loss from center pivot sprinklers was developed and field tested under limited wind speed conditions. Volume balance errors ranged from 0.1 to 7.1%. The cause for the large errors on two occasions has not yet been determined. The percent of applied water aerosolized and measured as drift was found to be linearly correlated with wind speed. Overall, the limited tests show the methodology to be feasible for measuring WDEL from center pivot sprinklers. Tests in higher wind speeds are needed to validate the methodology as is determination and elimination of the cause for the high volume balance errors

Case Study: Seasonal and Spatial Distribution of Ambient Ammonia Concentrations Measured at a Large Open-Lot Dairy

The volatilization of NH3 from dairy production facilities is not only a loss of valuable N, but also an air quality concern because NH3 plays a role in the formation of airborne particulate matter, which can be a health hazard. The ambient NH3 concentrations over several seasons at 3 locations (open lots, compost yard, lagoon) throughout a large openlot dairy were determined, as well as the spatial distribution of NH3 over the open-lot area. There was a significant main effect of location (P lagoon = compost > background, with averages of 0.58, 0.33, 0.30, and 0.04 mg NH3/m3, respectively. The effect of weather and lot conditions on the spatial distribution of NH3 across the lots was evident, with lower concentrations and less spatial variability in winter months when the lots were frozen compared with wetter warmer months. Lower NH3 concentrations and less spatial variability were also measured when manure stockpiles were removed from the open lots and the lots were dry. Significantly greater NH3 concentrations were generated in the lot area versus the compost and lagoon areas, which were not significantly different. Because the lots are greater in size by a factor of approximately 6, it is evident that NH3 emissions from this sector of the dairy contribute the greatest amount of NH3 to the atmosphere

Potential of winter cover crops and tillage for managing manure-based nutrient loading

Increased utilization of manure resulting from the expansion of the dairy industry has culminated in a soil nutrient surplus in southern Idaho. The objective of this study was to investigate the combined effect of winter cover crops and tillage practice on nutrient cycling, yield, and overall forage quality under annual manure applications. The 2 x 4 split plot study (2015 -2021) consisted of main treatments of conventional (ConTill) vs minimal (MinTill) tillage, and secondary treatment combinations of (1) manure (M) vs no manure (NM) and (2) winter triticale ( X Triticosecale) (CC) vs fallow (NCC) for each tillage type. Corn (Zea mays) and triticale whole plant tissue were collected for annual yield, tissue concentrations, nutrient removal rates, and forge quality. CC reduced corn yields (-1.65 M/ha) while M increased triticale yield (+13.6 Mg/ha). For both forages, M had greater tissue P (+0.483 and +2.21 g/kg) and K (+4.18 and +19.91 g/kg) and reduced Ca (-0.60 and -0.54 g/kg). Corn with M had smaller Mg (-0.43 g/kg) and triticale had greater Mg (+0.22 g/kg). Forages with M removed greater N (+39.93 and +109.84 kg/ha), P (+12.98 and +21.18 kg/ha), and K (+99.81 and +187.48 kg/ha). Corn with M removed less Mg (-7.85 kg/ha) and Ca (-11.24 kg/ha) and triticale removed greater Mg (+6.06 kg/ha) and Ca (+10.00 kg/ha). For both forages, M removed greater Zn and Na. M had greater corn CP (+0.89%), EE (+0.16%), and ash (+0.41%), and less ADF (-0.84%) and starch (-0.74%). CC had greater corn ADF (+0.50%) and less starch (-0.76%). M had greater triticale DM (+0.23%), CP (+4.21%), ADF (+4.27%), aNDFom (+6.46%), and lignin (+0.68), but smaller starch (-0.13%) and WSC (-9.46%). Use of triticale as a winter cover crop has strong potential for adding significantly to annual nutrient removal rates but may require nutrient additions for adequate plant growth. Producers should carefully consider the trade-offs in soils with high nutrient status. Triticale may exhibit increased risk of excess tissue concentrations that can be detrimental to animal health when grown on manured soils, but can be mitigated through well-balance feed rationing