Do long-term conservation pasture management practices influence microbial diversity and antimicrobial resistant genes in runoff

Authors: YANG, YICHAO - University Of Arkansas; Ashworth, Amanda; Durso, Lisa; SAVIN, MARY - University Of Arkansas; DEBRUYAN, JENNIFER - University Of Tennessee; Cook, Kimberly - Kim; Moore, Philip; Owens, Phillip

Submitted to: Frontiers in Microbiology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/15/2021
Publication Date: 4/8/2021
Citation: Yang, Y., Ashworth, A.J., Durso, L.M., Savin, M., Debruyan, J., Cook, K.L., Moore Jr., P.A., Owens, P.R. 2021. Do long-term conservation pasture management practices influence microbial diversity and antimicrobial resistant genes in runoff. Frontiers in Microbiology. 12. Article 617066. https://doi.org/10.3389/fmicb.2021.617066.
DOI: https://doi.org/10.3389/fmicb.2021.617066

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 manure. Following land application, AMR bacteria 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 pasture best management strategies (e.g., rotational grazing, filter strips at the edge of fields) can minimize AMR gene movement and affect the microbial communities in surface water runoff. All fields received the same rate of poultry litter, with business as usual practices (continuous grazing and haying) being evaluated against best management strategies. The greatest number of different microbial species was found under hay field management (no cattle grazing). This could be due to more poultry litter remaining on the soil surface from less incorporation in the absence of cattle, as cattle hooves act as tillage in these systems. In addition, pasture best management strategies did not reduce AMR gene abundance in runoff. These results illustrate that conservation pasture management practices may influence the microbial communities in water runoff, but AMR gene presence is affected to a lesser extent in the U.S’ largest land-use category.

Technical Abstract: There is a global concern that antimicrobial resistant (AMR) genes may be transmitted through the food chain from animal manures to soil to surface water. However, details are lacking on the ecology of AMR genes in water runoff, as well as how conservation management practices may minimize the movement of AMR genes and affect the runoff microbiome. The aim of this study was to enumerate AMR genes and identify microbial community structure and diversity in water runoff following 14-years of poultry litter and cattle manure deposition and evaluate if pasture management [hayed (H), continuously grazed (CG), rotationally grazed (R), rotationally grazed with a buffer strip (RB), rotationally grazed with a fenced riparian buffer (RBR), and a control represented by nearby non-agricultural water samples from a wild and scenic river)] minimized the presence and amount of AMR genes. Since 2004, all pastures received annual poultry litter at a rate of 5.6 Mg ha-1. Surface runoff samples were collected from each watershed from 2018-2019 and quantitative PCR was performed to enumerate four AMR-associated genes (ermB, sulI, intlI, and blactx-m-32). Runoff bacterial communities were additionally characterized using Illumina 16S rRNA gene amplicon sequencing. Overall, long-term pasture management influenced water microbial community structure, with effects differing by year (P<0.05). Bacterial richness (Chao index) was influenced by pasture management, with lowest richness occurring in the control and greatest under H. Bacterial community structure differed between pasture management and the control. Bacterial richness increased in runoff following poultry litter application. However, there was no impact (P >0.05) from pasture management on the abundance of these four AMR associated genes, therefore, conservation pasture management did not reduce AMR gene abundance in runoff for these targets. These results illustrate that conservation pasture management practices may influence the bacterial richness in water runoff, but AMR gene dissemination to a lesser extent, in the U.S’ largest land-use category.