Long-term manure inputs induce a deep selection on agroecosystem soil antibiotic resistome

Area of Science:

• Environmental microbiology
• Soil science
• Agricultural science

Background:

• Antibiotic resistance genes (ARGs) enrichment in soils is known, but ecological processes in long-term organically fertilized soils are understudied.
• Understanding ARG composition in typical agricultural regions requires further investigation.

Purpose of the Study:

• To investigate the distribution and assembly of ARG profiles in three agricultural soils under contrasting long-term fertilization regimes.
• To compare the effects of chemical-only versus organic-only fertilization on ARGs and mobile genetic elements (MGEs).

Main Methods:

• High-throughput quantitative PCR (HT-qPCR) was employed.
• Analysis was conducted on black soil, fluvo-aquic soil, and red soil.
• Contrasting fertilization regimes (chemical-only vs. organic-only) were applied long-term.

Main Results:

• Organic manure significantly increased ARG abundance and number compared to chemical fertilizer.
• Organic manure application enriched mobile genetic elements (MGEs), positively associated with ARGs.
• Long-term organic fertilizer enriched opportunist and specialist ARGs in fluvo-aquic and red soils, but not black soils. Generalist ARGs remained largely unchanged.
• ARG profiles showed more deterministic assembly in organically fertilized soils.

Conclusions:

• Long-term organic fertilization enriches ARGs and MGEs in agricultural soils.
• Organic fertilization influences the assembly processes of soil antibiotic resistomes.
• Long-term organic fertilizer application may increase the persistence and health risks associated with soil antibiotic resistance, particularly for specialist ARGs.