Effects of plant-derived and manure-derived fertilizers on soil antibiotic resistome: in-situ investigation under growth stages

Antibiotic resistance problem prompted by manure land application is urgent. Due to free of antibiotics, plant-derived fertilizer may be a safer alternative for manure. However, little is known about the effects of plant-derived fertilizer on soil antibiotic resistome. Here, yeast fertilizer, an organic fertilizer derived from sugarcane and beet fermented by yeast, was investigated to confirm its effects on antibiotic resistance genes (ARGs) in a soybean field by comparing with chicken manure. Yeast fertilizer and chicken manure were applied at two dose levels. ARG variations were investigated at seedling and harvest stages of soybean. For total ARGs, significant increments (P < 0.05) of ARG abundance and diversity were observed in both the two high-dose amended soils at seedling stage, while increments disappeared at harvest stage. For individual ARGs, 31 and 32 ARGs were significantly enriched (P < 0.05) at seedling stage, 9 and 5 ARGs remained enriched by harvest stage in high-dose yeast fertilizer and chicken manure amended soils, respectively, with discriminative distributions in ARG types. Genes conferring resistance to critically important antibiotics like aminoglycoside, beta-lactam, macrolide-lincosamide-streptogramin, sulfonamide and tetracycline gained larger proportions among enriched ARGs in manured soils, indicating chicken manure posed higher antibiotic resistance risk than yeast fertilizer. Variation of enriched ARGs in yeast fertilizer amended soils were largely dependent on the change of soil properties, while in manured soils were largely constrained to direct introduction of manure-borne antibiotic resistome. Our study provided useful information on evaluating environmental safety of plant-derived fertilizer in terms of soil antibiotic resistance.