Impact of organic soil amendments in antibiotic levels, antibiotic resistance gene loads, and microbiome composition in corn fields and crops

The potential spreading of antibiotic resistance genes (ARG) into agricultural fields and crops represent a fundamental limitation on the use of organic fertilization in food production systems. We present here a study of the effect of spreading four types of organic soil amendments (raw pig slurry, liquid and solid fractions, and a digested derivative) on demonstrative plots in two consecutive productive cycles of corn harvest (Zea mays), using a mineral fertilizer as a control, following the application of organic amendments at 32-62 T per ha (150 kg total N/ha) and allowing 5-8 months between fertilization and harvest. A combination of qPCR and high-throughput 16S rDNA sequencing methods showed a small, but significant impact of the fertilizers in both ARG loads and microbiomes in soil samples, particularly after the second harvesting cycle. The slurry solid fraction showed the largest impact on both ARG loads and microbiome variation, whereas its digestion derivatives showed a much smaller impact. Soil samples with the highest ARG loads also presented increased levels of tetracyclines, indicating a potential dual hazard by ARG and antibiotic residues linked to some organic amendments. Unlike soils, no accumulation of ARG or antibiotics was observed in corn leaves (used as fodder) or grains, and no grain sample reached detection limits for neither parameter. These results support the use of organic soil amendments in corn crops, while proposing the reduction of the loads of ARGs and antibiotics from the fertilizers to greatly reduce their potential risk.

This work was supported by grants from the LIFE Program of the European Union (LIFE17 ENV/ES/000439), the Spanish Ministry of Science, Innovation and University (MCIN/AEI/10.13039/501100011033, grant RTI2018-096175-B-I00), and the Generalitat de Catalunya (2017SGR902). CSL was supported by a FI predoctoral fellowship from the Generalitat de Catalunya and the European Social Fund (2018 FI B 00368, ESF Investing in your future). IDAEA-CSIC is a Center of Excellence Severo Ochoa (Spanish Ministry of Science and Innovation, Project CEX2018-000794-S, ERDF A way of making Europe).

Peer reviewed