Preferential flow reduces water residence times and allows rapid transport of pollutants such as organic contaminants. Thus, preferential flow is considered to reduce the influence of soil matrix-solute interactions during solute transport. While this claim may be true when rainfall directly follows solute application, forcing rapid chemical and physical disequilibrium, it has been perpetuated as a general feature of solute transport—regardless of the magnitude preferential flow. A small number of studies have alternatively shown that preferential transport of strongly sorbing solutes is reduced when solutes have time to diffuse and equilibrate within the soil matrix. Here we expand this inference by allowing solute sorption equilibrium to occur and exploring how physiochemical properties affect solute transport across a vast range of preferential flow. We applied deuterium-labeled rainfall to field plots containing manure spiked with eight common antibiotics with a range of affinity for the soil after 7 days of equilibration with the soil matrix and quantified preferential flow and solute transport using 48 soil pore water samplers spread along a hillslope. Based on > 700 measurements, our data showed that solute transport to lysimeters was similar—regardless of antibiotic affinity for soil—when preferential flow represented less than 15% of the total water flow. When preferential flow exceeded 15%, however, concentrations were higher for compounds with relatively low affinity for soil. We provide evidence that (1) bypassing water flow can select for compounds that are more easily released from the soil matrix, and (2) this phenomenon becomes more evident as the magnitude of preferential flow increases. We argue that considering the natural spectrum preferential flow as an explanatory variable to gauge the influence of soil matrix-solute interactions may improve parsimonious transport models.

Compared to surface application, manure subsurface injection reduces surface runoff of nutrients, antibiotic resistant microorganisms, and emerging contaminants. Less is known regarding the impact of both manure application methods on surface transport of antibiotic resistance genes (ARGs) in manure-amended fields. We applied liquid dairy manure to field plots by surface application and subsurface injection and simulated rainfall on the first or seventh day following application. The ARG richness, relative abundance (normalized to 16s rRNA), and ARG profiles in soil and surface runoff were monitored using shotgun metagenomic sequencing. Within 1 day of manure application, compared to unamended soils, soils treated with manure had 32.5–70.5% greater ARG richness and higher relative abundances of sulfonamide (6.5–129%) and tetracycline (752–3766%) resistance genes (p ≤ 0.05). On day 7, soil ARG profiles in the surface-applied plots were similar to, whereas subsurface injection profiles were different from, that of the unamended soils. Forty-six days after manure application, the soil ARG profiles in manure injection slits were 37% more diverse than that of the unamended plots. The abundance of manure-associated ARGs were lower in surface runoff from manure subsurface injected plots and carried a lower resistome risk score in comparison to surface-applied plots. This study demonstrated, for the first time, that although manure subsurface injection reduces ARGs in the runoff, it can create potential long-term hotspots for elevated ARGs within injection slits.

Land application of manure, while beneficial to soil health and plant growth, can lead to an overabundance of nutrients and introduction of emerging contaminants into agricultural fields. Compared with surface application of manure, subsurface injection has been shown to reduce nutrients and antibiotics in surface runoff. However, less is known about the influence of subsurface injection on the transport and persistence of antibiotic‐resistant microorganisms. We simulated rainfall to field plots at two sites (one in Virginia and one in Pennsylvania) 1 or 7 d after liquid dairy manure surface and subsurface application (56 Mg ha–1) and monitored the abundance of culturable antibiotic‐resistant fecal coliform bacteria (ARFCB) in surface runoff and soils for 45 d. We performed these tests at both sites in spring 2018 and repeated the test at the Virginia site in fall 2019. Manure subsurface injection, compared with surface application, resulted in less ARFCB in surface runoff, and this reduction was greater at Day 1 after application compared with Day 7. The reductions of ARFCB in surface runoff because of manure subsurface injection were 2.5–593 times at the Virginia site in spring 2018 and fall 2019 and 4–5 times at the Pennsylvania site in spring 2018. The ARFCB were only detectable in the 0‐to‐5‐cm soil depth within 14 d of manure surface application but remained detectable in the injection slits of manure subsurface‐injected plots even at Day 45. This study demonstrated that subsurface injection can significantly reduce surface runoff of ARFCB from manure‐applied fields.

To address concerns regarding the potential impact of antibiotic use in animal husbandry on antibiotic resistance in humans, we conducted a greenhouse-based study examining uptake of the veterinary antibiotics oxytetracycline (OTC) and monensin (MON) by Tifton 85 Bermudagrass (T85), the most commonly grown forage grass in the southeastern U.S.A. Since oxytetracycline is used in both veterinary and human medicine, its accumulation in animal products could impact human resistance to this antibiotic. Monensin is not used in human medicine but has a high potential for accumulating in the environment. Our research examined antibiotic uptake by forage grass T85, the effect of dairy manure application on its uptake, and antibiotic retention in soil. We compared unspiked, wet dairy manure to wet dairy manure spiked with MON or OTC that was soil surface applied to pots or incorporated into soil. After 6 wk, plant stem/leaf and root tissue, as well as soil samples, were assessed for antibiotic residues using enzyme-linked immunosorbent assay (ELISA). Results confirmed Tifton 85 MON and OTC uptake. Six weeks after adding the antibiotics, the greatest plant matter OTC and MON contents were 157.9 ± 70.6 and 234.4 ± 19.6 µg kg−1, respectively, and 17.6 and 369.5 µg kg−1, respectively, for soil. When spiked with OTC, manure incorporation led to decreased OTC uptake by T85 tissue. Bioaccumulation of these antimicrobials in livestock and in the environment is a potential concern for animal, environmental, and human health.

The overuse of antibiotics has led to considerable increases of antibiotic resistance genes (ARGs) that have spread throughout the entire food supply chain. ARGs often transfer from processing facilities to food, causing major public health concerns. The current standard for detecting ARGs typically depends on quantitative polymerase chain reaction (qPCR) and gene sequencing. However, the reliance on experienced personnel and complicated readout equipment substantially inhibits the expansion of ARGs testing in nonlaboratory settings. Improved on-site testing will help monitor the spread of ARGs contamination to ensure food safety and address public health concerns. Herein, we developed a CRISPR-Cas12a-based assay for the colorimetric detection of ARGs in washing water collected from a food processing plant. In our assay, DNA-functionalized gold nanoparticles (AuNPs) were cross-linked with a ssDNA cross-linker. Target-induced Cas12a trans-cleavage was utilized for degradation of the cross-linkers, shifting the optical properties of the AuNPs to produce a facile visual readout. Without DNA amplification, we were able to detect three representative ARGs with a detection limit of 5 nM or lower. In addition, our assay was extended to a more complex medium, where as few as 10 3 gene copies in washing water from a fruit washing facility were visually detected. Based on our results, our method is both highly specific and sensitive. Due to the affordability and simplicity of our assay, this method can improve ARGs detection to monitor and prevent the immense spread of antimicrobial resistance among the food supply chain.