Beef cattle feedlot runoff impacts on soil antimicrobial resistance

Authors: SPEICHER, SCOTT - University Of Nebraska; Miller, Daniel; Durso, Lisa; LI, XU - University Of Nebraska; Woodbury, Bryan; ESKRIDGE, KENT - University Of Nebraska; MILLMIER SCHMIDT, AMY - University Of Nebraska

Submitted to: Agrosystems, Geosciences & Environment
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/4/2024
Publication Date: 4/14/2024
Citation: Speicher, S., Miller, D.N., Durso, L.M., Li, X., Woodbury, B.L., Eskridge, K., Millmier Schmidt, A. 2024. Beef cattle feedlot runoff impacts on soil antimicrobial resistance. Agrosystems, Geosciences & Environment. 7. Article e20498. https://doi.org/10.1002/agg2.20498.
DOI: https://doi.org/10.1002/agg2.20498

Interpretive Summary: Antibiotic resistance threatens the treatment of everything from minor scrapes to major illnesses. In a practical sense, the term “antibiotic resistance” refers to the decreasing ability of antibiotic drugs to fight bacterial infections. Efforts are required across human, animal, and environmental health sectors to control antibiotic resistance. There are two different ways to study antibiotic resistance in the environment, either by culturing the bacteria themselves, or by targeting the DNA instructions that code for antibiotic resistance, the antibiotic resistance genes. In this instance, we used both methods to address questions related to how bacteria in general, fecal indicators, and antibiotic resistant bacteria specifically, move through the soil following the application of beef cattle feedlot runoff, down to 1.8 m depth. This is because when applied to soil, one concern is the potential for vertical transport through soil to groundwater. In this study, the number of bacteria in soil decreased with depth, both for the runoff-amended field and the control field. Long-term runoff application did not impact the recovery of cefotaxime resistant or tetracycline resistant bacteria compared to a control field, but erythromycin resistant bacteria and erm(C) and tet(Q) genes were significantly higher in treated compared to control fields. Two other genes, erm(A) and tet(X) were not detected in any soil samples. Based upon these results we conclude that long-term applications of stored beef cattle feedlot runoff impact the surface and shallow soil microbial community, but the degree of impact was dependent upon the type of resistance evaluated, and more specifically, the genes targeted for analysis.

Technical Abstract: Field application of beef cattle feedlot runoff may transport manure-borne microbes and antibiotic resistant (AR) bacteria to agricultural soils eventually impacting deeper soils and groundwater. To evaluate this potential, total soil, AR, and fecal indicator bacteria (Escherichia coli and Enterococcus) and the presence/abundance of AR genes were examined to a depth of 1.8 m in an agricultural field receiving long-term application of feedlot runoff and compared to a nearby pasture receiving no runoff. While plate counts of total soil bacteria and cefotaxime-resistant, erythromycin-resistant, and tetracycline-resistant bacteria decreased with depth on both fields (P < 0.001) by an average 2-log10 CFU g-1 to 1.8 m depth, field differences were only observed with greater abundances of total soil and erythromycin-resistant bacteria (P = 0.026) in the runoff-amended versus control field soils. Soil bacterial and fecal indicator bacterial isolates evaluated phenotypically for resistance to 12 antibiotics varied in range and sensitivity. Using a culture-independent approach, erm(C) and tet(Q) were detected using PCR in 31% and 58% of runoff-field samples throughout the soil profile. Detection of erm(C) and tet(Q) in the control field soil profile was less frequent (0% and 11%, respectively). Two other genes, erm(A) and tet(X) were not detected in any soil samples. Based upon these results, long-term applications of beef cattle feedlot runoff may increase the total abundance of microorganisms in the surface and shallow soil, but the relative enrichment of antibiotic resistance was dependent upon the type of resistance evaluated, and more specifically, the genes targeted for analysis.