Antibiotics Used in Farm Animals Alter the Soil Microbiome

May 1, 2018

The common practice of treating livestock animals with antibiotics has led to the selection and spread of antibiotic-resistant bacteria and increased resistance in human clinical infections. But what about the antibiotics not absorbed by either the treated animal or its microbes? Livestock antibiotics may have an even greater effect on agriculture than previously appreciated, by affecting the soil microbes of crops treated with animal manure containing residual antibiotics. A new Applied and Environmental Microbiology report demonstrates that antibiotic exposure specifically alters the population of Bradyrhyzobium bacteria that are part of the nitrogen-fixing nodules of crops like soybeans.

AppEnvMicro: Long-term exposure of agricultural soil to veterinary antibiotics changes the population structure of symbiotic nitrogen-fixing rhizobacteria occupying nodules of soybeans (Glycine max)

Soybeans are legumes that are a globally important food source for both people and animals. Here, first author Cécile Revellin and senior scientist Edward Topp looked at the Bradyrhizobium populations in soil plots treated annually since 1999 with a mixture of antibiotics similar to those found in swine manure. The scientific team were investigating whether the nearly 20-year treatment changed the different Bradyrhizobium species present.

To do this, they amplified and read the population RSα sequences, present in most Bradyrhizobium species that nodulate soybeans, from four different soils: an untreated soil and three plots that had been treated with low, intermediate, or high concentrations of antibiotics (see figure, right). The antibiotic-treated soils all showed higher proportions of B. liaoningense than untreated soil, but the antibiotic-exposed bacteria showed no difference in drug resistance. The authors hypothesize that in addition to potential antibacterial effects, the antibiotics may act on the plants to change the plant-microbe interactions in the rhizosphere. 

Distributions of RSα fingerprints of isolates obtained from plants
grown in plots receiving the indicated antibiotic treatments. 
Distributions of RSα fingerprints of isolates obtained from plants grown in plots receiving the indicated antibiotic treatments. 

Bradyrhizobium species fix atmospheric nitrogen and provide it to their host plant, but different species of Bradyrhizobium have specialized metabolic functions conferred by unique genomic and plasmid sequences. The research team plans to study the functional effects of these antibiotics to see whether different species compositions lead to differences in nitrogen fixation and subsequent plant growth. Understanding the role played by antibiotics in the complex soil microbial composition may help protect plant health and improve crop yields.  

Treating soil directly with antibiotics may not mimic the way that antibiotics in manure influence the rhizosphere composition, and the authors hope to pursue this in future studies. 

Author: Julie Wolf

Julie Wolf
Dr. Julie Wolf is in science communications at Indie Bio, and was a former ASM employee. Follow Julie on Twitter for more ASM and microbiology highlights at @JulieMarieWolf.