Phenotypic traits that enhance microbial habitability of antibiotic gradients in a porous network under nitrate reducing conditions




Alcalde, Reinaldo Enrique

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Antibiotic contamination of terrestrial and aquatic environments can promote the selection of antibiotic-resistant bacteria that threaten the efficacy of antibiotic treatment and can impact the function of nontarget native bacteria that modulate biogeochemical processes, such as nitrogen turnover. The latter is an important ecological function for the maintenance of soil and water quality. Antibiotics that enter the environment occur in spatial concentration gradients due to solute transport phenomena. However, the environmental side effects of antibiotic compounds have mostly been interpreted through laboratory models where this spatial dimension is not considered. These observations motivated us to develop a microfluidic reactor that mimics this diffusive aspect of nature to probe the microbial response to antibiotic concentration gradients under nitrate-reducing conditions. In Chapter 2, we present the microfluidic gradient chamber (MGC), a reactor that generates diffusive gradients of solutes across an interconnected porous network. We find that swimming motility and migration of Shewanella oneidensis MR-1 cells allow for habitability and metabolic activity in highly toxic regions of a ciprofloxacin gradient. Moreover, our results show that S. oneidensis MR-1 remains metabolically active for five days without observed inheritable antibiotic resistance. Chapter 3 begins to explore the underlying mechanisms that allow for such adaptive survival. We find that S. oneidensis MR-1 requires a chemotactic gene (cheA) for this habitability to occur. We then explore the role of transient adaptive resistance via resistance-nodulation-division (RND) efflux pumps; ancient elements of bacterial physiology and virulence. Contrary to expectations, we show that S. oneidensis MR-1 does not require RND efflux pumps for habitability. Lastly, in Chapter 4, we explore the role of antibiotic biodegradation on habitability in the MGC. We find that the extracellular electron transfer pathway, Mtr, enhances the degradation rate of the antibiotic sulfamethoxazole. We then provide evidence that suggests that antibiotic biodegradation is not a determinant factor for habitability in the MGC. Our work contributes to an emerging body of knowledge deciphering the effects of antibiotic spatial heterogeneity on microorganisms and highlights differences of microbial response in these systems versus well-mixed batch conditions.


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