Do Long-Term Conservation Pasture Management Practices Influence Microbial Diversity and Antimicrobial Resistant Genes in Runoff?

Abstract

Runoff from land-applied manure and poultry litter is one mechanism by which manure-borne bacteria are transported over large distances in the environment. 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 affect the runoff microbiome or minimize the movement of AMR genes. The aim of this study was to identify microbial community structure and diversity in water runoff following 14-years of poultry litter and cattle manure deposition and to evaluate the amount of AMR genes under five conventional and conservation pasture management strategies. Since 2004, all watersheds received annual poultry litter at a rate of 5.6 Mg ha−1 and were consistently managed. Surface runoff samples were collected from each watershed from 2018 to 2019, characterized using Illumina 16S rRNA gene amplicon sequencing and enumerated for four AMR-associated genes (ermB, sulI, intlI, and blactx-m-32) using quantitative PCR. Overall, long-term pasture management influenced water microbial community structure, with effects differing by year (p < 0.05). Bacterial richness (Chao1 index) was influenced by pasture management, with the lowest richness occurring in the control (nearby non-agricultural water source) and the greatest under fields that were hayed (no cattle presence). Runoff bacterial richness in watersheds increased following poultry litter applications, indicating poultry litter is a possible source of bacteria and altered runoff community structure. The blactx-m-32 gene was not detected in any surface water sample. The remaining three AMR genes were absent in the non-agricultural control, but present in agricultural samples. However, there was no impact (p > 0.05) from pasture management on the abundance of these genes, indicating both conventional and conservation practices have similar ecologies for these targets; however, there was a greater detection of sulI genes from runoff in continuously grazed systems in 2019, with hay being lowest in 2019. Results illustrate that the edge of field buffer strips may increase bacterial richness in water runoff, but these changes in richness do not greatly impact target AMR genes in the United States largest land-use category.

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

“…The field setup utilized 15 sloped and individually isolated manuresheds at the USDA-ARS Research Center in Booneville, Arkansas that have been previously described ( Pilon et al, 2017a , b , 2019 ; Anderson et al, 2020 ; Yang et al, 2021 ) ( Supplementary Figure S2 ). Three different agricultural conservation management practices were evaluated, including rotationally grazed (R), rotationally grazed with a buffer strip (RB), and rotationally grazed with a fenced riparian buffer (RBR).…”

“…Sampling, filtration, and processing of 100 mL samples from every 95 litter of surface runoff water ( n = 60) were conducted in 2018 and 2019 as previously described ( Yang et al, 2021 ). To prepare for DNA extraction and subsequent analyses, each runoff sample from the manuresheds was passed through a filtration system.…”

“…These ARGs were targeted because they encodes for antibiotics categorized as “Critically Important” for human health according to world health organization reports ( WHO, 2014 ). The standards, primers, amplifications and thermocycling conditions were performed as previously described ( Yang et al, 2020 , 2021 ; Gurmessa et al, 2021 ).…”

“…This can occur within both the animal gastrointestinal tract (GIT) and in crop production environment, like soil, and can be further facilitated by transferable genetic elements and selective chemical agents (pharmaceuticals, heavy metals and disinfectants) ( Frost et al, 2005 ; Gillings, 2014 ; Zhao et al, 2019 ; Wang et al, 2020 ). Further, in soil fertilized with manure, the longevity of antibiotic-resistant bacteria and their corresponding resistance genes may be extended ( Li et al, 2017 ; Chen et al, 2018 ; Rahman et al, 2018 ; Cheng et al, 2019 ; Yang et al, 2020 , 2021 ). This prolonged survival can be attributed to selective agents that favor their growth, coupled with the extra nutrients the manure provides ( Guber et al, 2005 ; Tien et al, 2017 ; He et al, 2020 ; Mware et al, 2022 ).…”

“…In addition, the effects of cattle manure and poultry litter on the transfer of ARGs through surface transport, and the potential impact of agricultural conservation management practices on the soil and surface runoff microbiome, and the reduction of the spread of ARGs is not well understood. Previous analyses evaluated ARGs and/or microbial communities within specific production environments [i.e., manure ( Gurmessa et al, 2021 ), soil ( Yang et al, 2019a , b , 2020 ), or water ( Yang et al, 2021 ) only]; however, no study has thoroughly evaluated system-level impacts from conservation and conventional practices on ARG dissemination and the manure-soil-water microbiome in long-term.…”