Long-term impacts of conservation pasture management in manuresheds on system-level microbiome and antibiotic resistance genes

Authors: SEYOUM, MITIKU - University Of Arkansas; Ashworth, Amanda; Feye, Kristina; Owens, Phillip; Moore, Philip; RICKIE, STEVEN - University Of Arkansas; SAVIN, MARY - University Of Arkansas

Submitted to: Frontiers in Microbiology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 9/13/2023
Publication Date: 9/29/2023
Citation: Seyoum, M., Ashworth, A.J., Feye, K.M., Owens, P.R., Moore Jr, P.A., Rickie, S., Savin, M. 2023. Long-term impacts of conservation pasture management in manuresheds on system-level microbiome and antibiotic resistance genes. Frontiers in Microbiology. 14. Article 1227006. https://doi.org/10.3389/fmicb.2023.1227006.
DOI: https://doi.org/10.3389/fmicb.2023.1227006

Interpretive Summary: Livestock manures from cattle and poultry are valuable fertilizer sources but may also contain antimicrobial resistant (AMR) bacteria. As depending on antibiotic properties, up to 90% of antibiotics pass un-degraded through animals to feces following land application, AMR bacteria from manure may move from soil through water runoff, however, the extent of this is unknown, particularly in pastures (animal grazing systems). Therefore, researchers conducted a study to evaluate if long-term pasture best management strategies (e.g., rotational grazing, filter strips at the edge of fields) can minimize AMR gene movement relative to common practices (e.g., contentiously grazed and hay systems), as well as identify how microbial diversity changed based on conservation practices. All fields received the same rate of poultry litter and all runoff from fields was collected over a 15-year period, as were soil and manure (cattle and poultry) in efforts to quantify AMR gene movement from animals-soil-water. Results demonstrated that business as usual practice (overgrazing) increased AMR presence compared to conservation practices in the soil. Similarly, soil microbial communities increased following long-term overgrazing compared to conservation systems, which was attributed to continuous manure additions from animal excreta. Taken together, conservation practices (unfertilized grass buffer strips and riparian filter strips) could reduce risks of AMR dissemination in the soil and downstream environment, thus improving water quality and human health.

Technical Abstract: Animal manure improves soil fertility and organic carbon, but, long-term deposition may contribute to antibiotic resistance genes (ARGs) entering the soil-water environment. Further, little is known about the long-term impacts of animal manure inputs on the soil-water microbiome, which is an important aspect of soil health and fertility. The aim of this study is to assess: 1) impacts of long-term conservation practices on the distribution of ARGs and microbial community dynamics in soil, manure, and runoff; and 2) associations between bacterial taxa, soil health indicators, ARGs, and heavy metals in manure (cattle and poultry), soils, and surface runoff in a longitudinal study following 15 years of continuous management (two conventional and three conservation pasture management strategies, all receiving annual poultry litter). Cattle manure, poultry litter, soil, and runoff samples were collected from each watershed 2018 to 2019 and characterized using 16S rRNA gene sequencing. In addition, four representative ARGs (ermB, sul1, intl1, and blactx-m-32) were quantified from cattle and poultry manure, soil, and runoff using quantitative PCR. Results revealed that ARGs were strongly correlated with each other in cattle manure and soil, but not in runoff. Similarly, after 15-years of conservation practices, relationships existed between heavy metals and ARGs. For example, Cu, Fe and Mn were positively linked to intl1, sul1, and ermB in the soil, but trends varied in runoff. These findings were further supported by network analyses that indicated complex co-occurrence patterns between bacteria taxa, ARGs, heavy metals, and physicochemical parameters in cattle manure, soil, and surface runoff. Overall, this study provides system-level linkages of microbial communities, the resistome, and physicochemical conditions based on long term conservation practices at the soil-water-animal nexus.