Alterations in soil microbial communities caused by treatments with penicillin or neomycin

Environ Sci Pollut Res Int. 2017 Aug;24(22):18651-18662. doi: 10.1007/s11356-017-9530-3. Epub 2017 Jun 25.


Antibiotic residues in soils can lead to serious health risk and ecological hazards. In this study, the effects of penicillin and neomycin, two antibiotics widely used in animal production, were investigated on soil bacterial communities. Changes in the community structure were monitored using three 16S ribosomal DNA (rDNA) polymerase chain reaction-based approaches, including denaturing gradient gel electrophoresis (DGGE), amplified rDNA restriction analysis (ARDRA), and terminal-restriction fragment length polymorphism (T-RFLP) analysis. The prominent DGGE bands were excised from gels and sequenced, and the data indicated the prevalence of Gammaproteobacteria in the soils. The total soil bacterial community, including uncultured bacteria, exhibited a higher diversity than that of cultured bacteria. Some microbial strains were capable of surviving and even subsisting on penicillin or neomycin. We also observed toxic effects of the antibiotics on the indigenous soil bacterial communities since some genotypes disappeared after the treatments (e.g., Pseudomonas sp., Stenotrophomonas sp., Salinimonas, and uncultured Acinetobacter sp.). The implications of these findings are that the functions of soil bacterial communities may be negatively affected if key microbial community members are lost.

Keywords: ARDRA; DGGE; Neomycin; Penicillin; Soil microbial community; T-RFLP.

MeSH terms

  • Bacteria / classification
  • Bacteria / drug effects*
  • Bacteria / genetics
  • Biodiversity*
  • DNA, Bacterial / genetics
  • Microbial Consortia / drug effects*
  • Neomycin / toxicity*
  • Penicillins / toxicity*
  • RNA, Ribosomal, 16S / genetics
  • Sequence Analysis, DNA
  • Soil Microbiology*
  • Soil Pollutants / toxicity


  • DNA, Bacterial
  • Penicillins
  • RNA, Ribosomal, 16S
  • Soil Pollutants
  • Neomycin