Systems analysis of engineered and natural microbial consortia

Abstract

Microorganisms are ubiquitous and typically exist within complex interacting communities or consortia. Microbial consortia are capable of cooperating in a coordinated fashion to extract mass and free energy from their environment. Chemical and biological engineers have long been keen to harness microbial processes for the development of technologies with applications ranging from energy capture to environmental remediation to human health. The pursuit of novel microbial biotechnologies has given rise to the relatively new discipline of microbial consortia engineering, which differs from and expands upon more traditional monoculture based practices. Many successful examples of applied and/or engineered microbial consortia mimic fundamental ecological strategies observed from nature, highlighting the importance for engineers to study natural biological phenomena. The overarching goal for this dissertation was to observe and quantitatively characterize interactions and physical phenomena occurring within select microbial consortial systems. The technical research presented here explores microbial consortia on three main fronts: (i) metabolically engineered heterotrophic systems, (ii) photoautotrophic-heterotrophic biofilm systems and (iii) naturally occurring thermo-acidophilic microbial mat systems. The metabolically engineered systems were designed to mimic a common ecological strategy involving syntrophic metabolite exchange via primary-productivity coupled with secondary consumption of potentially inhibitory byproducts (i.e., acetic acid). This system exhibited enhanced biomass productivity as compared to monoculture controls. The primary-productivity concept was also explored, in a more traditional sense, by characterizing production, consumption and exchanges of oxygen within photoautotrophic-heterotrophic biofilm systems. Tight spatial coupling of oxygenic-photosynthesis and aerobic-respiration was observed in both biofuel producing and waste-water remediating biofilm communities. The role of oxygen as an important terminal electron acceptor was also investigated in pristine Fe(III)-oxide microbial mats from geothermal springs located in Yellowstone National Park (USA). For these systems, oxygen availability defines ecological niche environments that spatially govern specific community member abundances and activities. Classical chemical engineering reaction and diffusion analysis was used to model concentration dependent oxygen consumption kinetics and establish that these mats are likely mass transfer limited. Both primary-productivity and microbially mediated oxygen reactions are interrelated, cross-cutting themes throughout this dissertation. The research described here is interdisciplinary chemical engineering that utilizes fundamental microbial ecology as a foundational platform.