Antibiotic-contaminated wastewater in agroecosystems: Soil microbiome resistome interactions and CRISPR phage engineering for microbiome restoration

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Abstract

Antibiotic-contaminated wastewater has become a significant environmental challenge driving the dissemination of antibiotic resistance genes (ARGs) and disrupting soil microbial ecology in agroecosystems. Wastewater from hospitals, livestock production systems, slaughterhouses, and wastewater irrigation introduces antibiotic residues, antibiotic-resistant bacteria (ARB), and mobile genetic elements (MGEs) into agricultural soils, accelerating selective pressure and horizontal gene transfer (HGT) within microbial communities. This review examines the major sources and environmental fate of antibiotics in soil systems and discusses their impacts on microbiome-resistome interactions, nutrient cycling, soil fertility, agroecosystem resilience, and food safety. We also explore how antibiotic exposure alters microbial community structure and promotes the persistence of resistant pathogens in agricultural environments. Advanced mitigation strategies, including membrane technologies, membrane bioreactors, advanced oxidation processes, constructed wetlands, and biochar-based remediation, are evaluated for reducing antibiotic and ARG dissemination. In addition, emerging CRISPR-based engineering and bacteriophage-mediated approaches are discussed as precision tools for targeted resistome suppression and soil microbiome restoration. Finally, an integrated One Health framework linking wastewater regulation, antimicrobial stewardship at farm level, sustainable manure management, and soil microbiome surveillance is proposed to support sustainable agriculture and mitigate environmental antimicrobial resistance.

Graphical abstract

Keywords

antibiotic-contaminated wastewater / antibiotic resistance genes / soil microbiome / agroecosystems / CRISPR based engineering / bacteriophage therapy

Highlight

	● Wastewater antibiotics disrupt soil microbiome resistome balance.
	● ARGs spread through wastewater, manure, and irrigation pathways.
	● Antibiotic pollution reduces soil fertility and agroecosystem resilience.
	● CRISPR phage systems enable targeted suppression of resistant bacteria.
	● One Health strategies support sustainable AMR mitigation in agriculture.

CHANGE HISTORY

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