Effects of prescription antibiotics on soil- and root-associated microbiomes and resistomes in an agricultural context

• Published in: Journal of hazardous materials 2020-12, Vol.400, p.123208-123208, Article 123208
• Main Authors: Cerqueira, Francisco, Christou, Anastasis, Fatta-Kassinos, Despo, Vila-Costa, Maria, Bayona, Josep Maria, Piña, Benjamin
• Format: Article
• Language: English
• Subjects: Angiotensin Receptor Antagonists; Angiotensin-Converting Enzyme Inhibitors; Anti-Bacterial Agents - pharmacology; Antibiotic resistance; Drug Resistance, Microbial - genetics; Genes, Bacterial; Humans; Lactuca sativa L; Metagenomics; Microbiome; Microbiota; Prescriptions; Resistome; Root endosphere; Soil; Soil Microbiology
• ISSN: 0304-3894; 1873-3336
• DOI: 10.1016/j.jhazmat.2020.123208

[Display omitted] •Soil microbiome composition changed due to antibiotics in irrigation water.•Antibiotics (AB) affected abundance of specific bacterial Orders in the roots.•Rhizobiales abundance reduced in roots exposed to anbitiotics.•AB increased intrinsic (mex), acquired (phoP, parC,E) resistance in root endophytes.•Confirmed the impact of AB in soil and plants' microbiomes and resistomes. The use of treated wastewater for crop irrigation is rapidly increasing to respond to the ever-growing demands for water and food resources. However, this practice may contribute to the spread of antibiotic resistant bacteria (ARB) and antibiotic resistant genes (ARGs) in agricultural settings. To evaluate this potential risk, we analyzed microbiomes and resistomes of soil and Lactuca sativa L. (lettuce) root samples from pots irrigated with tap water spiked with 0, 20, or 100 μg L−1 of a mixture of three antibiotics (Trimethoprim, Ofloxacin, Sulfamethoxazole). The presence of antibiotics induced changes in bacterial populations, particularly in soil, as revealed by 16S rDNA sequence analysis. Parallel shotgun sequencing identified a total of 56 different ARGs conferring resistance against 14 antibiotic families. Antibiotic -treated samples showed increased loads of ARGs implicated in mutidrug resistance or in both direct and indirect acquired resistance. These changes correlated with the prevalence of Xantomonadales species in the root microbiomes. We interpret these data as indicating different strategies of soil and root microbiomes to cope with the presence of antibiotics, and as a warning that their presence may increase the loads of ARBs and ARGs in edible plant parts, therefore constituting a potential risk for human consumers.