Soil microbial and plant responses to increasing antibiotic concentration: a case study of five antibiotics

Abstract

ABSTRACT Antibiotic contamination from biogenic waste in agricultural soils poses a significant threat to soil health and crop productivity. We investigated the effect of antibiotics on the soil microbial community, antibiotic resistance genes, and mobile genetic elements (MGEs) and plant productivity in a 6-week greenhouse trial. Here, Spinacia oleracea (spinach) and Raphanus sativus (radish) were grown from seeds, and a mix of five antibiotics, namely sulfamethoxazole, trimethoprim, enrofloxacin, clarithromycin, and chlortetracycline, was added to the soil at concentrations of 0, 0.1, 1, and 10 mg kg −1 soil dry weight (c0, c0.1, c1, and c10, respectively). Overall, we found that the antibiotic treatments significantly impacted prokaryotic α-diversity and prokaryotic and fungal β-diversity. The relative abundance of human and plant pathogens did not increase under antibiotic exposure, but there was a significant reduction in plant growth-promoting bacteria. Moreover, the c10 treatment significantly increased the abundance of MGE intI1, indicative of horizontal gene transfer and sulfonamide resistance gene sul1, and significantly lowered radish biomass and nitrogen uptake, while spinach biomass and nitrogen uptake were unaffected. In summary, our study showed that antibiotic exposure significantly changed prokaryotic community diversity, while fungi remained largely unaffected. The reduction of plant growth-promoting bacteria may have a significant impact on soil nutrient cycling and crop productivity, but more research is needed to understand the long-term impact of these co-applied antibiotics on food production. Additionally, more studies are needed to understand the effect of antibiotics on realistic, field-scale conditions to fully understand the impact on environmental and human health. IMPORTANCE Agricultural soils are frequently contaminated with complex mixtures of antibiotics from various biogenic sources, yet we lack a clear understanding of their specific ecological impact. While many studies investigate antibiotics, they are often studied in pollution sources like manure, which contain confounding factors like heavy metals. To provide a mechanistic understanding of antibiotic-specific responses, we investigated the effects of a complex, five-antibiotic mixture on the soil-plant system, independent of other contaminants. As expected, antibiotics reduced prokaryotic diversity and increased the abundance of some genes related to antibiotic resistance. Additionally, antibiotic exposure reduced plant growth-promoting bacteria, which may have subsequent detrimental effects on plant and soil health. Moreover, we found that antibiotic exposure can reduce plant biomass and nitrogen uptake, but this is highly plant dependent. This research highlights the critical need to monitor antibiotic pollution due to its potential detrimental effect on plant health and alterations to the soil microbiome.

Key findings

• ▸Antibiotic treatments significantly impacted prokaryotic alpha-diversity and both prokaryotic and fungal beta-diversity.
• ▸There was a significant reduction in plant growth-promoting bacteria under antibiotic exposure.
• ▸The relative abundance of human and plant pathogens did not increase despite antibiotic treatment.

Keywords

Identifiers

DOI

10.1128/aem.01581-25

Journal

Applied and Environmental Microbiology

Year

2026