The Effect of Manure Application Rates on the Vertical Distribution of Antibiotic Resistance Genes in Farmland Soil

Abstract

Manure application is the primary input route for antibiotic resistance genes (ARGs) in farmland soil. This study investigated the effects of varying the rates of five chicken manure applications on the accumulation and distribution of ARGs across different soil depths (0–20, 20–40, and 40–60 cm) using metagenomic sequencing. The results revealed that the distribution of ARGs in farmland soil was closely linked to soil depth and influenced to some extent by the fertilizer quantity after 30 days of fertilization. ARGs were predominantly concentrated in the surface soil and exhibited a significant decrease in type and abundance with an increased soil depth. Compared with soil treated with chemical fertilizers alone, chicken manure-treated surface soil presented a higher diversity and abundance of ARGs. However, the diversity and abundance of ARGs did not increase proportionally with the increasing ratios of chicken manure application (0, 25, 50, 75, and 100%). ARGs in soil primarily conferred resistance to host bacteria through antibiotic efflux pumps (~33%), antibiotic target alteration (~31%), antibiotic inactivation (~20%), and antibiotic target protection (~8%). Correlation analysis involving ARGs and soil microorganisms revealed widespread multidrug resistance among soil microorganisms. Furthermore, two genera of human pathogenic bacteria (Pseudomonas sp. and Listeria sp.) were identified as potential microbial hosts of ARGs in all treatments. Correlation analysis involving ARGs and environmental factors indicated that soil ARGs are predominantly influenced by heavy metals and microorganisms. This paper offers valuable insights for environmental risk assessments regarding the utilization of livestock manure resources. Additionally, it furnishes a scientific foundation for farmland application strategies pertaining to livestock manure.