Cross-comparison of methods for quantifying antibiotic resistance in agricultural soils amended with dairy manure and compost

Agricultural soils are often amended with livestock manure, making them a key reservoir of antibiotic resistance genes (ARGs). Given that among the most microbially-diverse environments on planet; effective characterization and quantification effects manure-derived amendments soil resistomes is major challenge. This study examined dairy agricultural via two strategies: anthropogenic ARG markers qPCR shotgun metagenomic resistome profiling; these strategies were compared to previously published resistant fecal coliform dataset. Soil samples collected throughout 120 day complete block field experiment compare amendment type resistance. Results all three measurements consistent hypothesis application composted manure reduced in relative raw although some differences noted comparing patterns time. Raw manure-amended yielded high sul1 tet(W) abundances Day 0 (following application), but significantly decreased background levels by 67 (harvest) (study completion). Shotgun metagenomics similarly detected decrease sulfonamide tetracycline-associated ARGs over time manure- compost-amended soils; however, lower than those estimated qPCR. Interestingly, tetracycline culturable coliforms echoed observed metagenomics; erythromycin directly recovered culture soils, corresponding not or metagenomics. supports both composting restrictions as means reducing potential for spread application. suggest finer conclusions drawn depending which monitoring target selected.