Inorganic and organic fertilizers impact the abundance and proportion of antibiotic resistance and integron-integrase genes in agricultural grassland soil

Hiie Nõlvak*, Marika Truu, Kärt Kanger, Mailiis Tampere, Mikk Espenberg, Evelin Loit, Henn Raave, Jaak Truu

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

88 Citations (Scopus)


Soil fertilization with animal manure or its digestate may facilitate an important antibiotic resistance dissemination route from anthropogenic sources to the environment. This study examines the effect of mineral fertilizer (NH4NO3), cattle slurry and cattle slurry digestate amendment on the abundance and proportion dynamics of five antibiotic resistance genes (ARGs) and two classes of integron-integrase genes (intI1 and intI2) in agricultural grassland soil. Fertilization was performed thrice throughout one vegetation period. The targeted ARGs (sul1, tetA, blaCTX-M, blaOXA2 and qnrS) encode resistance to several major antibiotic classes used in veterinary medicine such as sulfonamides, tetracycline, cephalosporins, penicillin and fluoroquinolones, respectively. The non-fertilized grassland soil contained a stable background of tetA, blaCTX-M and sul1 genes. The type of applied fertilizer significantly affected ARGs and integron-integrase genes abundances and proportions in the bacterial community (p < 0.001 in both cases), explaining 67.04% of the abundance and 42.95% of the proportion variations in the grassland soil. Both cattle slurry and cattle slurry digestate proved to be considerable sources of ARGs, especially sul1, as well as integron-integrases. Sul1, intI1 and intI2 levels in grassland soil were elevated in response to each organic fertilizer's application event, but this increase was followed by a stage of decrease, suggesting that microbes possessing these genes were predominantly entrained into soil via cattle slurry or its digestate application and had somewhat limited survival potential in a soil environment. However, the abundance of these three target genes did not decrease to a background level by the end of the study period. TetA was most abundant in mineral fertilizer treated soil and blaCTX-M in cattle slurry digestate amended soil. Despite significantly different abundances, the abundance dynamics of bacteria possessing these genes were similar (p < 0.05 in all cases) in different treatments and resembled the dynamics of the whole bacterial community abundance in each soil treatment.

Original languageEnglish
Pages (from-to)678-689
Number of pages12
JournalScience of the Total Environment
Publication statusPublished - 15 Aug 2016

Bibliographical note

Funding Information:
This research was supported by Estonian Ministry of Agriculture , project number 372 ; Estonian Ministry of Education and Research (grants IUT2-16 and 3.2.0801.11-0026 ); and by Estonian Doctoral School of Earth Science and Ecology project. “The effect of cattle slurry and cattle slurry digestate on the grassland microbial community”. Authors are grateful to Dr. Matthew Copley for his suggested manuscript revisions.

Publisher Copyright:
© 2016 .


  • Antibiotic resistance
  • Digestate fertilization
  • Grassland soil
  • Integron-integrases
  • Manure slurry fertilization


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