Implications of the use of organic fertilizers for antibiotic resistance gene distribution in agricultural soils and fresh food products. A plot-scale study

• Published in: The Science of the total environment Vol. 815; p. 151973
• Main Authors: Sanz, Claudia, Casado, Marta, Navarro-Martin, Laia, Cañameras, Núria, Carazo, Núria, Matamoros, Victor, Bayona, Josep Maria, Piña, Benjamin
• Format: Journal Article
• Language: English
• Published: Netherlands Elsevier B.V 01.04.2022
• Subjects: 16S sequencing; Agriculture; Animals; Anti-Bacterial Agents - pharmacology; Circular economy; Drug Resistance, Microbial - genetics; Fertilizers - analysis; Fluoroquinolone; Manure; Microbiomes; qPCR; Soil; Soil Microbiology; Sulfonamide; Swine; Tetracycline; Sulfonamide; Circular economy; Microbiomes; 16S sequencing; Fluoroquinolone; qPCR; Tetracycline
• ISSN: 0048-9697; 1879-1026
• DOI: 10.1016/j.scitotenv.2021.151973

The spread of antibiotic resistance genes (ARG) into agricultural soils, products, and foods severely limits the use of organic fertilizers in agriculture. In order to help designing agricultural practices that minimize the spread of ARG, we fertilized, sown, and harvested lettuces and radish plants in experimental land plots for two consecutive agricultural cycles using four types of fertilizers: mineral fertilization, sewage sludge, pig slurry, or composted organic fraction of municipal solid waste. The analysis of the relative abundances of more than 200,000 ASV (Amplicon Sequence Variants) identified a small, but significant overlap (<10%) between soil's and fertilizer microbiomes. Clinically relevant ARG were found in higher loads (up to 100 fold) in fertilized soils than in the initial soil, particularly in those treated with organic fertilizers, and their loads grossly correlated to the amount of antibiotic residues found in the corresponding fertilizer. Similarly, low, but measurable ARG loads were found in lettuce (tetM, sul1) and radish (sul1), corresponding the lowest values to samples collected from minerally fertilized fields. Comparison of soil samples collected along the total period of the experiment indicated a relatively year-round stability of soil microbiomes in amended soils, whereas ARG loads appeared as unstable and transient. The results indicate that ARG loads in soils and foodstuffs were likely linked to the contribution of bacteria from organic fertilizer to the soil microbiomes, suggesting that an adequate waste management and good pharmacological and veterinarian practices may significantly reduce the presence of these ARGs in agricultural soils and plant products. [Display omitted] •Fertilization increased loads of clinically relevant ARGs.•Measurable ARG loads in lettuce (tetM, sul1) and radish (sul1)•Soil and food ARG loads strongly depended on the type of fertilizer.•Lowest ARG loads found in minerally-fertilized soils and crops.•Bacteria from organic fertilizers may increase ARG loads in soils and crops.