Implications of the use of organic fertilizers for Antibiotic Resistant Gene dissemination in agricultural soils and fresh food products. A plot-scale study

The spread of antibiotic resistance genes (ARG) into agricultural soils, products, and foods severely limits the use of organic fertilizers in agriculture. In this study, experimental land plots were fertilized, sown, and harvested for two consecutive agricultural cycles using either mineral or three types of organic fertilizers: 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) allowed the identification of a small, but significant (<10%) overlap between soil and fertilizer microbiomes, particularly in soils sampled the same day of the harvest (post-harvest soils). Loads of clinically relevant ARG were significantly higher (up to 100 fold) in fertilized soils relative to the initial soil. The highest increases corresponded to post-harvest soils treated with organic fertilizers, and they correlated with the extend of the contribution of fertilizers to the soil microbiome. Edible products (lettuce and radish) showed low, but measurable loads of ARG (sul1 for lettuces and radish, tetM for lettuces). These loads were minimal in mineral fertilized soils, and strongly dependent on the type of fertilizer. We concluded that at least part of the observed increase on ARG loads in soils and foodstuffs were actual contributions from the fertilizer microbiomes. Thus, we propose that adequate waste management and good pharmacological and veterinarian practices may significantly reduce the potential health risk posed by the presence of ARG in agricultural soils and plant products. The nature of the study was to analyse the incorporation rate of Antibiotic Resistance Genes from organic fertilisers (sludge, slurry, USW) to the soil by means of 16s rDNA amplicon sequencing approaches. We used soil fertilised with a chemical fertiliser as our control. We sequenced the organic fertilizers and the soils ammended with these, plus chemically fertilised soils and a couple of "initial soil" with any kind of fertilisation, to have a initial idea fo the ARGs presence in the soil prior to the experiments. Definitions: SLUDGE: Soil amended (fertilized) with water treatment plant sludge SLURRY: Soil amended (fertilized) with pig slurry USW: Soil amended (fertilized) with Urban Solid Waste MINERAL: Soil amended (fertilized) with the commonly used chemical fertilizer