Does a lower dosage of sewage sludge affect the microbiome and resistome of agricultural soils?

Abstract

Amendment of soils with sewage sludge are a common practice in agriculture to improve crop yields. Sewage sludge could carry hazardous elements, including prokaryotes that are resistant to antibiotics and heavy metals. The amendment dosage is an important element impacting on the soil microbiome and its resistome, although, rarely discussed. This study aimed to investigate changes in the composition of prokaryotes, antibiotic resistance genes (ARGs), mobile elements (integrons), and heavy metal resistance genes (HMRGs) using a metagenomic approach. Agricultural soils were fertilized with sewage sludge (3 tons.ha) from small, medium, large and very large wastewater treatment plants (WWTPs). Results indicated that the dosage inflicted no significant changes in the microbiome and resistome between the fertilized soils and the control soil. Significant differences were registered for the sewage sludges samples. Proteobacteria ( ~ 54%) followed by Actinobacteria ( ~ 23%) were more abundant in sewage sludges, while Actinobacteria ( ~ 40%) was more abundant than Proteobacteria ( ~ 37%) in fertilized soils. Sewage sludges showed significantly higher abundances of ARGs and integrons when compared to fertilized soils. Most populated ARGs were tetracyclines, macrolides, fluoroquinolones and aminoglycosides. The smallest sized WWTPs contained the most populated resistome. Interestingly, only ARGs conferring resistance to vancomycines (vanAEHX) presented higher abundances in fertilized soils. Furthermore, the concentration of Zn and Cu in sludge samples had a significant positive correlation with the abundances of HMRGs (merA, TcrB, PcoB and zntA) and several ARGs conferring resistance to tetracyclines, fluoroquinolones and macrolides. These results suggest that Zn and Cu play a crucial role in shaping the microbiome and resistome in WWTPs. This study is an example that a lower dosage of sewage sludge could be an important factor in reducing the risk of transporting hazardous elements during agricultural soil amendment.