Soil microbial function in a time of global change: effect of dairy antibiotics on soil microbial communities and ecosystem function

Abstract

Antibiotic resistance is ubiquitous due to high usage of antibiotics and the capability of bacteria to transfer genes both horizontally and vertically. While this has dire implications for human health, the potential to disturb microbial communities and ecosystem functions they regulate is under appreciated. Antibiotics are commonly used in the livestock sector, accounting for 80% of antibiotic use domestically. This dissertation addresses three facets of this problem. Chapter 2 is a nation-wide survey of antibiotic resistance at dairy operations, aimed at understanding how ecosystem function is affected in situ. Chapter 3 describes a field-experiment, seeking to determine whether antibiotics have effects beyond soil through impacts on plant-microbe-soil feedbacks, thus potentially altering terrestrial ecosystem function. Chapter 4 investigates how rising global temperature interacts with antibiotic exposure through a microcosm-incubation experiment. These multiple stressors (i.e. temperature and antibiotics) could alter microbial community composition or physiology with repercussions on function. Additionally, chapter 4 seeks to determine whether microbes acclimate to continued antibiotic exposure. In chapter 2 I present evidence that increased antibiotic resistant gene (ARG) abundance with exposure to antibiotics and manure, and a correlation between ARGs and microbial stress. This increase in microbial stress results in elevated soil carbon loss. Chapter 3 shows that antibiotic exposure can change plant function – presumably through impacts on rhizospheric microbial community composition. Plants assimilate more nitrogen, but more carbon is lost from the system overall seemingly due to plant-soil-microbe tradeoffs. Chapter 4 shows a temporally dependent temperature–antibiotic interactive effect. Initially, pirlimycin increased microbial respiration at high temperatures, however this diminishes with time. Additional studies of microbial respiration at a range of temperatures show that microbial acclimation to antibiotic exposure may be taking place. However, interactive effects of high temperature and antibiotics appear to inhibit active microbial biomass production. Possible explanations to both of these patterns are the underlying differences in microbial community composition, specifically the fungal:bacterial. My results show that antibiotics not only lead to increased ARG abundance, but also have wide ranging effects on communities and ecosystem processes that are likely to be compounded in the face of global change.