Understanding and controlling microbial community assembly is critical to developing novel bioprocesses for nutrient and energy recovery from wastewater and preparing for global climate change. As molecular biology tools and DNA sequencing improve, microbial ecologists can progress from answering qualitative questions about “who is there, and what are they doing?” to rationally designing microbial communities for specific functions. Despite our increasing ability to monitor microbial community phylogenetic and functional composition, parsing the impact of community interactions, abiotic factors, dispersal limitations, and stochastic factors in complex microbial consortia remains a major challenge. This thesis first lays out important fundamental concepts and contemporary ‘omics and computational tools in microbial ecology. Next it investigates community assembly mechanisms at regional and watershed scales and then applies these concepts to designing a microbial electrochemical cell (MEC) based bioprocess and investigating MEC community structure. Chapters 1 and 2 introduce the background and methods for molecular microbial ecology, respectively. In chapter 3, a longitudinal field study was used to test for regional synchrony in population dynamics in activated sludge bioreactors. Using a nested experimental approach, longitudinal sampling of multiple reactors per site across several regional plants was performed. Community beta diversity over time and between sites was compared and temperature driven seasonal variation was the dominant process observed. This trend was consistent across multiple community scales in activated sludge systems and visible in nitrifier populations. In chapter 4, the amplicon sequencing, multivariate ordination and variance partitioning approaches developed previously were applied to study soil hydrology driven community assembly in an intensively managed landscape. In the final chapter, ongoing work integrating native prairie microbial ecology with a novel longitudinal and spatially resolved groundwater monitoring system is discussed. The focus of these sections is demonstrating the impact of hydrology & soil moisture on community structure. The next two chapters are devoted to lab-scale bioreactor studies of microbial electrochemical cells for H2O2 production. Exoelectrogenic biofilms were enriched in 3D-printed bioreactors and biological acetate oxidation was coupled to H2O2 electrosynthesis via oxygen reduction. Buffer composition, electrode composition and hydraulic residence time were optimized for H2O2 titer and pH. The produced H2O2 was utilized for tandem catalytic sulfoxidation of a model aromatic thioether compound with a heterogeneous niobium(V)-catalyst, and demonstrated similar activity to commercially produced H2O2. While this last finding is expected, the process demonstrates a novel approach for wastewater valorization through continuous production of H2O2 and its immeditate use as a selective oxidant in aqueous conditions for green chemistry applications. Finally, a genome-centric metagenomic approach is used to investigate the relationship between electron donor availability and MEC community structure, an open community assembly question of relevance for MEC scale-up. The methodologies applied in this thesis have applications for rationally designing other bioprocesses based on underlying microbial community assembly rules as well as investigating physiological niches of keystone microbes for existing processes.

Creator

• Grifin, James

DOI

• https://doi.org/10.21985/n2-6pgs-2a16

Subject

• Environmental engineering
• Bioinformatics

Language

• en

Alternate Identifier

• http://dissertations.umi.com/northwestern:14462
• etdadmin_upload_626962

Keyword

• metagenomics
• microbial electrochemical cells
• microbial ecology
• activated sludge
• amplicon sequencing

Date created

• 2018-01-01

Resource type

• Dissertation

Rights statement

• In Copyright