Understanding the biogeographic and environmental controls of antibiotic resistance in soils

Background/Question/Methods

Soils contain immense diversity and support terrestrial ecosystem functions, but soil health and function is being threatened by both anthropogenic and environmental stressors. One prevalent stressor that has the potential to dramatically change the community composition and function of soils is the introduction of antibiotics through human use and livestock management. Though antibiotic production and resistance is a natural process, humans are changing the distribution and prevalence of these compounds and the associated resistance. While many studies have demonstrated how human management can increase antibiotic inputs and resistance, we surprisingly still lack a fundamental understand of the ecology and biogeography of antibiotics. Here, we performed a nation-wide assessment of environmental antibiotic resistance to shed light on when and where there compounds and their associated resistance are most prevalent. We collected soil from 220 locations across the US and analyzed their community composition and the diversity and abundance of antibiotic production and resistance genes using a novel molecular technique called targeted gene capture. We also collected metadata about the land use history and vegetation, and analyzed the chemical composition of the soils to link how abiotic factors and management shapes soil antibiotic resistance.

Results/Conclusions

We found that the abiotic template, soil edaphic characteristics and land use history all shape the diversity and prevalence of antibiotic production and resistance. We also demonstrate a distinct biogeography to antibiotic resistance abundance and biodiversity. This is strongly related to both soil community composition and the soil type found across our sampling locations. Interestingly, the prevalence of soil C was positively correlated with the abundance of antibiotic resistance, which may be due to higher microbial competition in high C environments. We also find that history of livestock management can cause large increases in the abundance and diversity of antibiotic resistance, regardless of geographic location. These results emphasize that antibiotic production and resistance is a natural component of our ecosystems, but human interference is changing the diversity and distribution of these genetic elements. This study also provides important insight into which soil environments are most likely to harbor high rates of antibiotic resistance and should therefore be of high priority in terms of bioremediation management.