Prevalence of Antibiotic Resistance Genes and Bacterial Pathogens in Long-Term Manured Greenhouse Soils As Revealed by Metagenomic Survey

Antibiotic resistance genes (ARGs), human pathogenic bacteria (HPB), and HPB carrying ARGs pose a high risk to soil ecology and public health. Here, we used a metagenomic approach to investigate their diversity and abundance in chicken manures and greenhouse soils collected from Guli, Pulangke, and Hushu vegetable bases with different greenhouse planting years in Nanjing, Eastern China. There was a positive correlation between the levels of antibiotics, ARGs, HPB, and HPB carrying ARGs in manures and greenhouse soils. In total, 156.2–5001.4 μg/kg of antibiotic residues, 22 classes of ARGs, 32 HPB species, and 46 species of HPB carrying ARGs were found. The highest relative abundance was tetracycline resistance genes (manures) and multidrug resistance genes (greenhouse soils). The dominant HPB and HPB carrying ARGs in the manures were <i>Bacillus anthracis</i>, <i>Bordetella pertussis</i>, and <i>B. anthracis</i> (sulfonamide resistance gene, <i>sul1</i>), respectively. The corresponding findings in greenhouse soils were <i>Mycobacterium tuberculosis</i> and <i>M. ulcerans</i>, <i>M. tuberculosis</i> (macrolide-lincosamide-streptogramin resistance protein, MLSRP), and <i>B. anthracis</i> (<i>sul1</i>), respectively. Our findings confirmed high levels of antibiotics, ARGs, HPB, and HPB carrying ARGs in the manured greenhouse soils compared with those in the field soils, and their relative abundance increased with the extension of greenhouse planting years