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

Abstract

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 Bacillus anthracis, Bordetella pertussis, and B. anthracis (sulfonamide resistance gene, sul1), respectively. The corresponding findings in greenhouse soils were Mycobacterium tuberculosis and M. ulcerans, M. tuberculosis (macrolide-lincosamide-streptogramin resistance protein, MLSRP), and B. anthracis (sul1), 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.

Long-term field application of sewage sludge increases the abundance of antibiotic resistance genes in soil

“…Previous studies have suggested that dominant human pathogens in manure were Bacillus anthracis and Bordetella pertussis (Fang et al, 2015), and those in sewage sludge were Escherichia coli and Klebsiella pneumoniae (Ye and Zhang, 2011), however, we did not detect these in our samples. One reasonable explanation is that these pathogens detected in sewage sludge or manures could not successfully establish in the present soil.…”

“…One reasonable explanation is that these pathogens detected in sewage sludge or manures could not successfully establish in the present soil. This hypothesis is supported by a recent study, in which, it was reported that although Bacillus anthracis and Bordetella pertussis were detected in manure, they were not detected in manure-amended soil (Fang et al, 2015). In this study, the identification of bacterial pathogens was based on the use of the 16S rRNA gene sequence from each sample blast against the bacterial pathogen 16S rRNA database.…”

“…Based on the taxonomic list derived from the virulence factors database (http://www.mgc.ac.cn/VFs/) and some references (Fang et al, 2015;Li et al, 2015a;Ye and Zhang, 2011), the bacterial pathogens database including 557 pathogenic species (Table S2) was constructed. All the 16S rRNA gene sequences of the selected bacterial pathogens are publicly available from the NCBI GenBank (http:// www.ncbi.nlm.nih.gov/).…”

Impact of bioaccessible pyrene on the abundance of antibiotic resistance genes during Sphingobium sp.- and sophorolipid-enhanced bioremediation in soil

“…The four resistance genes investigated in this study have been reported among the most frequently detected resistance genes in soil [20,34]. Although we did not detect the existence of antibiotics in the soil, we identified ARGs conferring resistance to tetracycline and sulfonamide (tetW and tetM, and sulI and sulII, respectively).…”

Iron-incorporated mesoporous silica for enhanced adsorption of tetracycline in aqueous solution

“…[2][3][4] Recently, the detection of TC in aquatic environments has raised concern about its potential to promote the development of antibiotic resistance genes and pose a risk to humans. [5][6][7][8] As shown in Fig. S1, † TC possesses tricarbonylamide, phenolic diketone, and dimethylamine groups, which cause complexity in its behavior in aquatic media.…”