Assemblage of Bacteria Communities and Resistome Enrichment by Dairy Flurries Along the Rhizosphere–Bulk Soil Continuum on Dairy Farms

The use of dairy slurries as organic fertilizer amendments is a common practice in agriculture as a cost-saving measure, as well as a residue management strategy. However, concerns related to the increase in antibiotic resistance in the environment under the scope of the One Health strategy are increasing. In this study, we aimed to assess resistome enrichment driven by dairy slurry application in four southern Chile dairy farms. Slurry pits, rhizospheres of Lolium perenne amended with those slurries, and bulk soils were sampled. Thirteen antibiotic-resistance genes (ARGs, tetA, tetG, tetM, tetQ, tetW, tetX, sul1, sul2, blaCTXM, blaOXA-1, blaTEM, ermB, and dfrA1) for five antibiotic classes (tetracyclines, sulfonamides, beta-lactams, macrolides, and trimethoprim–sulfamethoxazole), two related integrases (intl1 and intl2), and total bacteria (16S rRNA) abundance was measured by quantitative PCR (qPCR). Then, the abundance profiles of two enzyme-inactivated ARGs (tetX and blaTEM) were determined. The differences between the bacterial communities inhabiting the different sample types were explored with 16S rRNA metabarcoding. In general, all measured ARGs were detected in slurries. A decreasing trend in ARG copy numbers was observed with increasing soil depth, with the exception of tetX, whose abundance increased in the bulk soil at specific farms. The tetX and blaTEM communities revealed no differences in the relative abundance of variants in any of the samples. Finally, taxonomic and structural differences were found among all sample types. Thus, the enrichment of the sampled farm soil resistomes was driven by the application of the raw slurries as fertilizer.