Shifts of Antibiotic Resistomes in Soil Following Amendments of Antibiotics-Contained Dairy Manure

Int J Environ Res Public Health. 2022 Aug 30;19(17):10804. doi: 10.3390/ijerph191710804.


Dairy manure is a nutrition source for cropland soils and also simultaneously serves as a contamination source of antibiotic resistance genes (ARGs). In this study, five classes of antibiotics including aminoglycosides, beta-lactams, macrolides, sulfonamides, and tetracyclines, were spiked in dairy manure and incubated with soil for 60 days. The high throughput qPCR and 16S rRNA amplicon sequencing were used to detect temporal shifts of the soil antibiotic resistomes and bacterial community. Results indicated dairy manure application increased the ARG abundance by 0.5-3.7 times and subtype numbers by 2.7-3.7 times and changed the microbial community structure in soils. These effects were limited to the early incubation stage. Selection pressure was observed after the addition of sulfonamides. Bacterial communities played an important role in the shifts of ARG profiles and accounted for 44.9% of the resistome variation. The incubation period, but not the different antibiotic treatments, has a strong impact on the bacteria community. Firmicutes and Bacteroidetes were the dominant bacterial hosts for individual ARGs. This study advanced our understanding of the effect of dairy manure and antibiotics on the antibiotic resistome in soils and provided a reference for controlling ARG dissemination from dairy farms to the environment.

Keywords: antibiotic resistance genes; antibiotics; dairy manure; microbial communities; soil.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Anti-Bacterial Agents / analysis
  • Anti-Bacterial Agents / pharmacology
  • Bacteria / genetics
  • Genes, Bacterial
  • Manure* / analysis
  • RNA, Ribosomal, 16S / genetics
  • Soil Microbiology
  • Soil* / chemistry
  • Sulfonamides


  • Anti-Bacterial Agents
  • Manure
  • RNA, Ribosomal, 16S
  • Soil
  • Sulfonamides

Grants and funding

This research was funded by National Key Research and Development Program (2021YFD1800700) and Innovation Project of Chinese Academy of Agricultural Sciences (CAAS-FRI-06).