Eighty-two percent of the United States population reside in urban areas. The centralized treatment of the municipal wastewater produced by this population is a huge energy expenditure, up to three percent of the entire energy budget of the country. A portion of this energy is able to be recovered through the process of anaerobic sludge digestion. Typically, this technology converts the solids separated and generated during the wastewater treatment process into methane, a combustible gas that may be burned to generate electricity. Designing and optimizing anaerobic digestion systems requires the measurement of degradation rates for waste-specific kinetic parameters. In this work, I discuss the ways these kinetic parameters are typically measured. I recommend and demonstrate improvements to these commonly used measuring techniques. I provide experimental results of batch kinetic experiments exploring the effect of sludge pretreatment, a process designed to facilitate rapid breakdown of recalcitrant solids, on energy recovery rates. I explore the use of microbial electrochemical cells, an alternative energy recovery technology able to produce electricity directly from sludge digestion, as precise reporters of degradation kinetics. Finally, I examine a fundamental kinetic limitation of microbial electrochemical cells, acidification of the anode respiring biofilm, to improve their performance as kinetic sensors or energy recovery technologies.

Engineered nanomaterials (ENMs) are added to numerous consumer products to enhance their effectiveness, whether it be for environmental remediation, mechanical properties, or as dietary supplements. Uses of ENMs include adding to enhance products, carbon for strength or dielectric properties, silver for antimicrobial properties, zinc oxide for UV sun-blocking properties, titanium dioxide for photocatalysis, or silica for desiccant properties. However, concerns arise from ENM functional properties that can impact the environment and a lack of regulation regarding ENMs leads to potential public exposure to ENMs and results in ill-informed public or manufacturer perceptions of ENMs. My dissertation evaluates the environmental, human health, and societal impacts of using ENMs, with a focus on ionic silver and nanosilver, in consumer and industrial products. Reproducible experiments served as functional assays to assess ENM distributions among various environmental matrices. Functional assay results were visualized using radar plots and aid in a framework to estimate likely ENM disposition in the environment. To assess beneficial uses of ENMs, bromide ion removal from drinking waters to limit disinfection by-product formation was studied. Silver-enabled graphene oxide materials were capable of removing bromide from water, and exhibited less competition from background solutes (e.g. natural organic matter) when compared against solely ionic silver addition to water for bromide removal. To assess complex interactions of ENMs with the microbiome, batch experiments were performed using fecal samples spiked with ionic silver or commercial dietary silver nanoparticles. Dietary nanosilver and ionic silver exposures to the fecal microbiome for 24 hours reduce short chain fatty acid (SCFA) production and changes the relative abundance of the microbiota. To understand the social perceptions of ENMS, statistically rigorous surveys were conducted to assess related perceptions related to the use of ENMs in drinking water treatment devices the general public and, separately, industrial manufacturers. These stakeholders are influenced by costs and efficiency of the technologies, consumer concerns of the safety of technologies, and environmental health and safety of the technologies. This dissertation represents novel research that took an interdisciplinary approach, spanning from wet-lab engineering bench scale testing to social science survey assessments to better understand the environmental, human health, and societal impacts of using ENMs such as nanosilver and ionic silver in industrial processes and consumer products.

Electro-Selective Fermentation (ESF) combines Selective Fermentation (SF) and a Microbial Electrolysis Cell (MEC) to selectively degrade carbohydrate and protein in lipid-rich microalgae biomass, enhancing lipid wet-extraction. In addition, saturated long-chain fatty acids (LCFAs) are produced via β-oxidation. This dissertation builds understanding of the biochemical phenomena and microbial interactions occurring among fermenters, lipid biohydrogenaters, and anode respiring bacteria (ARB) in ESF. The work begins by proving that ESF is effective in enhancing lipid wet-extraction from Scenedesmus acutus biomass, while also achieving “biohydrogenation” to produce saturated LCFAs. Increasing anode respiration effectively scavenges short chain fatty acids (SCFAs) generated by fermentation, reducing electron loss. However, the effectiveness of ESF depends on biochemical characteristics of the feeding biomass (FB). Four different FB batches yield different lipid-extraction performances, based on the composition of FB’s cellular structure. Finally, starting an ESF reactor with a long solid retention time (SRT), but then switching it to a short SRT provides high lipid extractability and volumetric production with low lipid los. Lipid fermenters can be flushed out with short a SRT, but starting with a short SRT fails achieve good results because fermenters needed to degrading algal protective layers also are flushed out and fail to recover when a long SRT is imposed. These results point to a potentially useful technology to harvest lipid from microalgae, as well as insight about how this technology can be best managed.

The objective of this study was to evaluate possible bioremediation strategy for aerobic aquifers by combining ZVI chemical reduction and microbial reductive dechlorination for TCE and ClO4-. To achieve this objective, continuous flow-through soil columns were used to test the hypothesis that bioaugmentation with dechlorinating enrichment cultures downstream of the ZVI injection can lead to complete reduction of TCE and ClO4- in aerobic aquifers. We obtained soil and groundwater from a Superfund site in Arizona. The experiments consisted of 205 cm3 columns packed with soil and ZVI, which fed 1025 cm3 columns packed with soil, biostimulated with fermentable substrates and bioaugmented. Aerobic groundwater was pumped through the ZVI columns. The ZVI reduced the oxidation-reduction potential (ORP) of groundwater from +150 mV to -190 mV. The reduced groundwater and biostimulation with fermentable substrates created anaerobic conditions in the bioaugmentation columns favorable for anaerobic microbial activity. Perchlorate (ClO4-) reduction to non-detectable levels occurred after biostimulation. Reduction of TCE to cis-dichloroethene, vinyl chloride and ethene was observed only after bioaugmentation. Within ~120 days of continuous columns operation, ethene was produced in the bioaugmentation columns this dechlorination activity was sustained until the end of experiments. The groundwater from the Superfund site had high concentration of sulfate (~1000 mg/L). Substantial sulfate reduction occurred in the bioaugmentation columns. Complete microbial reduction of TCE and perchlorate is usually challenging in the presence of high sulfate concentration; however, the strategy tested in this study suggests that a bioremediation scheme for simultaneous reduction of TCE and perchlorate in aerobic aquifers containing high sulfate concentration is feasible.

Widespread use of chlorinated solvents for commercial and industrial purposes makes co-occurring contamination by 1,1,1-trichloroethane (TCA), trichloroethene (TCE), and 1,4-dioxane (1,4-D) a serious problem for groundwater. TCE and TCA often are treated by reductive dechlorination, while 1,4-D resists reductive treatment. Aerobic bacteria are able to oxidize 1,4-D, but the biological oxidation of 1,4-D could be inhibited TCA, TCE, and their reductive transformation products. To overcome the challenges from co-occurring contamination, I propose a two-stage synergistic system. First, anaerobic reduction of the chlorinated hydrocarbons takes place in a H2-based hollow-fiber “X-film” (biofilm or catalyst-coated film) reactor (MXfR), where “X-film” can be a “bio-film” (MBfR) or an abiotic “palladium-film” (MPfR). Then, aerobic removal of 1,4-D and other organic compounds takes place in an O2-based MBfR. For the reductive part, I tested reductive bio-dechlorination of TCA and TCE simultaneously in an MBfR. I found that the community of anaerobic bacteria can rapidly reduce TCE to cis-dichloroethene (cis-DCE), but further reductions of cis-DCE to vinyl chloride (VC) and VC to ethene were inhibited by TCA. Also, it took months to grow a strong biofilm that could reduce TCA and TCE. Another problem with reductive dechlorination in the MBfR is that mono-chloroethane (MCA) was not reduced to ethane. In contrast, a film of palladium nano-particles (PdNPs), i.e., an MPfR, could the simultaneous reductions of TCA and TCE to mainly ethane, with only small amounts of intermediates: 1,1-dichloroethane (DCA) (~3% of total influent TCA and TCE) and MCA (~1%) in continuous operation. For aerobic oxidation, I enriched an ethanotrophic culture that could oxidize 1,4-D with ethane as the primary electron donor. An O2-based MBfR, inoculated with the enriched ethanotrophic culture, achieved over 99% 1,4-D removal with ethane as the primary electron donor in continuous operation. Finally, I evaluated two-stage treatment with a H2-based MPfR followed by an O2-MBfR. The two-stage system gave complete removal of TCA, TCE, and 1,4-D in continuous operation.

This dissertation critically evaluated methodologies and devices for assessing and protecting the health of human populations, with particular emphasis on groundwater remediation and the use of wastewater-based epidemiology (WBE) to inform population health. A meta-analysis and assessment of laboratory-scale treatability studies for removing chlorinated solvents from groundwater found that sediment microcosms operated as continuous-flow columns are preferable to batch bottles when seeking to emulate with high fidelity the complex conditions prevailing in the subsurface in contaminated aquifers (Chapter 2). Compared to monitoring at the field-scale, use of column microcosms also showed (i) improved chemical speciation, and (ii) qualitative predictability of field parameters (Chapter 3). Monitoring of glucocorticoid hormones in wastewater of a university campus showed (i) elevated stress levels particularly at the start of the semester, (ii) on weekdays relative to weekend days (p = 0.05) (161 ± 42 μg d-1 per person, 122 ± 54 μg d-1 per person; p ≤ 0.05), and (iii) a positive association between levels of stress hormones and nicotine (rs: 0.49) and caffeine (0.63) consumption in this student population (Chapter 4). Also, (i) alcohol consumption determined by WBE was in line with literature estimates for this young sub-population (11.3 ± 7.5 g d-1 per person vs. 10.1 ± 0.8 g d-1 per person), whereas caffeine and nicotine uses were below (114 ± 49 g d-1 per person, 178 ± 19 g d-1 per person; 627 ± 219 g d-1 per person, 927 ± 243 g d-1 per person). The introduction of a novel continuous in situ sampler to WBE brought noted benefits relative to traditional time-integrated sampling, including (i) a higher sample coverage (93% vs. 3%), (ii) an ability to captured short-term analyte pulses (e.g., heroin, fentanyl, norbuprenorphine, and methadone), and (iii) an overall higher mass capture for drugs of abuse like morphine, fentanyl, methamphetamine, amphetamine, and the opioid antagonist metabolite norbuprenorphine (p ≤ 0.01). Methods and devices developed in this work are poised to find applications in the remediation sector and in human health assessments.

Petroleum contamination is ubiquitous during extraction, transportation, refining, and storage. Contamination damages the soil’s ecosystem function, reduces its aesthetics, and poses a potential threat to human beings. The overall goals of this dissertation are to advance understanding of the mechanisms behind ozonation of petroleum-contaminated soil and to configure an effective integrated bioremediation + ozonation remedial strategy to remove the overall organic carbon. Using a soil column, I conducted batch ozonation experiments for different soils and at different moisture levels. I measured multiple parameters: e.g., total petroleum hydrocarbons (TPH) and dissolved organic carbon (DOC), to build a full understanding of the data that led to the solid conclusions. I first demonstrated the feasibility of using ozone to attack heavy petroleum hydrocarbons in soil settings. I identified the physical and chemical hurdles (e.g., moisture, mass transfer, pH) needed to be overcome to make the integration of chemical oxidation and biodegradation more efficient and defines the mechanisms behind the experimental observations. Next, I completed a total carbon balance, which revealed that multiple components, including soil organic matter (SOM) and non-TPH petroleum, competed for ozone, although TPH was relatively more reactive. Further experiments showed that poor soil mixing and high soil-moisture content hindered mass transfer of ozone to react with the TPH. Finally, I pursued the theme of optimizing the integration of ozonation and biodegradation through a multi-stage strategy. I conducted multi-stages of ozonation and bioremediation for two benchmark soils with distinctly different oils to test if and how much ozonation enhanced biodegradation and vice versa. With pH and moisture optimized for each step, pre-ozonation versus post-ozonation was assessed for TPH removal and mineralization. Multi-cycle treatment was able to achieve the TPH regulatory standard when biodegradation alone could not. Ozonation did not directly enhance the biodegradation rate of TPH; instead, ozone converted TPH into DOC that was biodegraded and mineralized. The major take-home lesson from my studies is that multi-stage ozonation + biodegradation is a useful remediation tool for petroleum contamination in soil.

The gastrointestinal (GI) tract is home to a complex and diverse microbial ecosystem that contributes to health or disease in many aspects. While bacterial species are the majority in the GI tract, their cohabitants, fungal species, should not be forgotten. Children with autism spectrum disorder (ASD) often suffer from GI disorders and associated symptoms, implying a role the bacterial and fungal gut microbiota play in maintaining human health. The irregularities in GI symptoms can negatively affect the overall quality of life or even worsen behavioral symptoms the children present. Even with the increase in the availability of next-generation sequencing technologies, the composition and diversities of fungal microbiotas are understudied, especially in the context of ASD. We therefore aimed to investigate the gut mycobiota of 36 neurotypical children and 38 children with ASD. We obtained stool samples from all participants, as well as autism severity and GI symptom scores to help us understand the effect the mycobiome has on these symptoms. By targeting the fungal internal transcribed spacer (ITS) and bacterial 16S rRNA V4 regions, we obtained fungal and bacterial amplicon sequences, from which we investigated the diversities, composition, and potential link between two different ecological clades. From fungal amplicon sequencing results, we observed a significant decrease in the observed fungal OTUs in children with ASD, implying a lack of potentially beneficial fungi in ASD subjects. We performed Bray-Curtis principal coordinates analysis and observed significant differences in fungal microbiota composition between the two groups. Taxonomic analysis showed higher relative abundances of Candida , Pichia, Penicillium , and Exophiala in ASD subjects, yet due to a large dispersion of data, the differences were not statistically significant. Interestingly, we observed a bimodal distribution of Candida abundances within children with ASD. Candida's relative abundance was not significantly correlated with GI scores, but children with high Candida relative abundances presented significantly higher Autism Treatment Evaluation Checklist (ATEC) scores, suggesting a role of Candida on ASD behavioral symptoms. Regarding the bacterial gut microbiota, we found marginally lower observed OTUs and significantly lower relative abundance of Prevotella in the ASD group, which was consistent with previous studies. Taken together, we demonstrated that autism is closely linked with a distinct gut mycobiota, characterized by a loss of fungal and bacterial diversity and an altered fungal and bacterial composition.

Background
Syngas fermentation, the bioconversion of CO, CO[subscript 2], and H[subscript 2] to biofuels and chemicals, has undergone considerable optimization for industrial applications. Even more, full-scale plants for ethanol production from syngas fermentation by pure cultures are being built worldwide. The composition of syngas depends on the feedstock gasified and the gasification conditions. However, it remains unclear how different syngas mixtures affect the metabolism of carboxidotrophs, including the ethanol/acetate ratios. In addition, the potential application of mixed cultures in syngas fermentation and their advantages over pure cultures have not been deeply explored. In this work, the effects of CO[subscript 2] and H[subscript 2] on the CO metabolism by pure and mixed cultures were studied and compared. For this, a CO-enriched mixed culture and two isolated carboxidotrophs were grown with different combinations of syngas components (CO, CO:H[subscript 2], CO:CO[subscript 2], or CO:CO[subscript 2]:H[subscript 2]).
Results
The CO metabolism of the mixed culture was somehow affected by the addition of CO[subscript 2] and/or H[subscript 2], but the pure cultures were more sensitive to changes in gas composition than the mixed culture. CO[subscript 2] inhibited CO oxidation by the Pleomorphomonas-like isolate and decreased the ethanol/acetate ratio by the Acetobacterium-like isolate. H[subscript 2] did not inhibit ethanol or H[subscript 2] production by the Acetobacterium and Pleomorphomonas isolates, respectively, but decreased their CO consumption rates. As part of the mixed culture, these isolates, together with other microorganisms, consumed H[subscript 2] and CO[subscript 2] (along with CO) for all conditions tested and at similar CO consumption rates (2.6 ± 0.6 mmol CO L[superscript −1] day[superscript −1]), while maintaining overall function (acetate production). Providing a continuous supply of CO by membrane diffusion caused the mixed culture to switch from acetate to ethanol production, presumably due to the increased supply of electron donor. In parallel with this change in metabolic function, the structure of the microbial community became dominated by Geosporobacter phylotypes, instead of Acetobacterium and Pleomorphomonas phylotypes.
Conclusions
These results provide evidence for the potential of mixed-culture syngas fermentation, since the CO-enriched mixed culture showed high functional redundancy, was resilient to changes in syngas composition, and was capable of producing acetate or ethanol as main products of CO metabolism.

On average, our society generates ~0.5 ton of municipal solid waste per person annually. Biomass waste can be gasified to generate synthesis gas (syngas), a gas mixture consisting predominantly of CO, CO2, and H2. Syngas, rich in carbon and electrons, can fuel the metabolism of carboxidotrophs, anaerobic microorganisms that metabolize CO (a toxic pollutant) and produce biofuels (H2, ethanol) and commodity chemicals (acetate and other fatty acids). Despite the attempts for commercialization of syngas fermentation by several companies, the metabolic processes involved in CO and syngas metabolism are not well understood. This dissertation aims to contribute to the understanding of CO and syngas fermentation by uncovering key microorganisms and understanding their metabolism. For this, microbiology and molecular biology techniques were combined with analytical chemistry analyses and deep sequencing techniques. First, environments where CO is commonly detected, including the seafloor, volcanic sand, and sewage sludge, were explored to identify potential carboxidotrophs. Since carboxidotrophs from sludge consumed CO 1000 faster than those in nature, mesophilic sludge was used as inoculum to enrich for CO- and syngas- metabolizing microbes. Two carboxidotrophs were isolated from this culture: an acetate/ethanol-producer 99% phylogenetically similar to Acetobacterium wieringae and a novel H2-producer, Pleomorphomonas carboxidotrophicus sp. nov. Comparison of CO and syngas fermentation by the CO-enriched culture and the isolates suggested mixed-culture syngas fermentation as a better alternative to ferment CO-rich gases. Advantages of mixed cultures included complete consumption of H2 and CO2 (along with CO), flexibility under different syngas compositions, functional redundancy (for acetate production) and high ethanol production after providing a continuous supply of electrons. Lastly, dilute ethanol solutions, typical of syngas fermentation processes, were upgraded to medium-chain fatty acids (MCFA), biofuel precursors, through the continuous addition of CO. In these bioreactors, methanogens were inhibited and Peptostreptococcaceae and Lachnospiraceae spp. most likely partnered with carboxidotrophs for MCFA production. These results reveal novel microorganisms capable of effectively consuming an atmospheric pollutant, shed light on the interplay between syngas components, microbial communities, and metabolites produced, and support mixed-culture syngas fermentation for the production of a wide variety of biofuels and commodity chemicals.