Application of organic fertilizers increases antibiotics in soil

A brief summary of the manuscript, Use of commercial organic fertilizer increases the abundance of antibiotic resistance genes and antibiotics in soil by Zhou et al. (2016)

Key Points:

  • Residual antibiotics can persist in soil for months following the application of manure-based, commercial organic fertilizers.
  • Antimicrobial resistance and antibiotic residues decreased significantly over the first 60 days following fertilizer application but did not return to background levels until four months after application.


Pelletized and composted manures are the primary sources of nutrients for fertilizers used in organic crop and vegetable production. Image by Ernesto Rodriquez, from Pixabay

Demand for organic crops and products has become a global phenomenon. A study conducted in China investigated the presence of antibiotic residues and AMR genes in soil on organic farms fertilized by manure-based, commercial organic fertilizers (COF). Bacterial genes that are resistant to antibiotics (AMR genes) are pieces of DNA that give the carrying bacteria the ability to survive the effects of antibiotics designed to kill them. Many COFs are produced by composting raw manure with sawdust, straw, or hay. After the composting process has ceased, the compost may be further dried and pelletized for packaging and sale (Fig 1). While the composting process decreases or eliminates live pathogens present in manure, it may not produce enough heat to destroy DNA, and therefore, AMR genes may survive. Although the threats of AMR are a current global concern, there are differences in the regulatory framework for managing antibiotics in agriculture or lack of any regulations in some instances. As the concentration of antibiotics and the AMR genes will vary widely between manure sources, it can be difficult to predict their presence in COF.

This study found that in fields where COFs had been applied, antibiotics were present in relatively low concentrations, and persisted for up to 4 months following fertilizer application. Antibiotics were not found in control plots (those receiving no fertilizer), however, the control plots contained some AMR genes. The application of COFs significantly increased the AMR gene concentrations in soil, but like the antibiotics, AMR gene concentrations returned to background levels within four months of application.

These results indicate that while manure-based COFs are an improvement over raw manure from an AMR perspective, COFs still carry some risk of transferring antibiotics and AMR genes to soil and soil-dwelling microbes. As antibiotics undergo degradation within the soil environment, the selective pressure and competitive advantage for resistant soil microbial populations will be removed, which may decrease the survival of resistant bacteria in an antibiotic-free environment. Based on the study results presented, organic farmers should leave a window between final fertilizer application and harvest to limit the risk of AMR genes or antibiotics transferred to crops.

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Written by Eric Henning while an Undergraduate Researcher in the Dept. of Biological Systems Engineering, University of Nebraska. Reviewed by: Stephanie Lansing, University of Maryland and Emmanuel Okelo, University of California-Davis.

The scientific research summarized in this article was published as:

Zhou, Xue, Min Qiao, Feng-Hua Wang, and Youn-Guan Zhu. 2016. Use of commercial organic fertilizer increases the abundance of antibiotic resistance genes and antibiotics in soil. Environ Sci Pollut Res 24, 701–710 (2017).

This article presents the author’s interpretation of the published research for a general audience and should not be considered a reflection of the position or opinion of the researchers.