The effect of long-term application of nitrogen-rich fertilizers on soil resistome: A study of conventional and organic cropping systems

Soil resistomes of conventional and organic systems were similar in terms of ARG biodiversity. Soil resistomes of conventional and organic systems were different regarding individual ARGs. Uncultivated bacteria and archaea can contribute significantly to soil resistome. Metagenomic studies of various soil environments have previously revealed the widespread distribution of antibiotic resistance genes (ARGs) around the globe. In this study, we applied shotgun metagenomics to investigate differences in microbial communities and resistomes in Chernozem soils that have been under long-term organic and conventional cropping practices. The organic cropping system was seeded with Triticum spelta without any fertilizer. The conventional cropping system was seeded with Triticum durum Desf and used mineral fertilizer (NPK), that resulted in an increased amount of total and available carbon and nitrogen in soils. Across all samples, we identified a total of 21 ARG classes, among which the dominant were vancomycin, tetracycline and multidrug. Profiling of soil microbial communities revealed differences between the studied fields in the relative abundances of 14 and 53 genera in topsoil and subsoil, respectively. Correlation analysis showed significant correlations (positive and negative) among 18 genera and 6 ARGs, as well as between these ARGs and some chemical properties of soils. The analysis of metagenome-assembled genomes revealed that Nitrospirota, Thermoproteota, Actinobacteriota and Binatota phyla of archaea and bacteria serve as hosts for glycopeptide and fluoroquinolone/tetracycline ARGs. Collectively, the data obtained enrich knowledge about the consequences of human agricultural activities in terms of soil microbiome modification and highlight the role of nitrogen cycling taxa, including uncultivated genera, in the formation of soil resistome.