Contamination of long-term manure-fertilized Indian paddy soils with veterinary antibiotics: Impact on bacterial communities and antibiotics resistance genes

In the present study, we investigated the implication of long-term fertilization of Indian rice paddies with animal manures on the prevalence of veterinary antibiotics (VAs) residues, enrichment of soil microorganisms, and abundance of antibiotic resistance genes (ARGs). The most frequently detected antibiotics in Indian paddy soils were tetracyclines followed by sulfonamides. The soils long-term fertilized with poultry manure (PM) and cow manure (CM) contained significant amounts of VAs (137.20 & mu;g kg-1) in soil. Members of Actinobacteria, Streptomyces, Rubrobacter, Pseudonocardia, Pseudomonas and Rhizobium were predominant in soils that received PM or CM. ARGs such as mtrA, arlR, bcrA, novA, oleC, sul4 and kdpE that confer resistance mostly to macrolides, aminocoumarins, multi-drugs, and sulfonamides were predominant, and the main phyla that contributed ARGs included Actinobacteria (55 %) and Proteobacteria (22 %). Antibiotic modification/degradation was the major (58.30 %) antibiotic resistance mechanism in bacteria enriched in long-term fertilized soils. Residues of tetracyclines, quinolones, sulfonamides, Cu and Cd in soils positively correlated with ARGs. Notably, this study is the first evidence on the prevalence of VAs, antibiotic-resistant microbes, and ARGs in paddy soils of India long-term fertilized with PM or CM and shed light on the interactions between antibiotics, heavy metals and ARGs.

Automated summary

In this study, we investigated the presence of veterinary antibiotic residues, soil microorganisms, and antibiotic resistance genes (ARGs) in Indian rice paddies fertilized with animal manures. The most frequently detected antibiotics were tetracyclines and sulfonamides. Soils fertilized with poultry manure and cow manure contained significant amounts of veterinary antibiotics. Actinobacteria, Streptomyces, Rubrobacter, Pseudonocardia, Pseudomonas, and Rhizobium were the dominant soil microorganisms in these fertilized soils. ARGs conferring resistance to macrolides, aminocoumarins, multi-drugs, and sulfonamides were found in abundance, with Actinobacteria and Proteobacteria being the main phyla contributing to ARGs. Antibiotic modification/degradation was the major antibiotic resistance mechanism in bacteria enriched in long-term fertilized soils. Residues of tetracyclines, quinolones, sulfonamides, copper, and cadmium in soils were positively correlated with ARGs. This study provides the first evidence of the prevalence of veterinary antibiotics, antibiotic-resistant microbes, and ARGs in Indian rice paddies fertilized with animal manures and sheds light on the interactions between antibiotics, heavy metals, and ARGs.