Mining-influenced water (MIW) is an acidic stream containing a typically acidic pH (e.g., 2.5), sulfate, and dissolved metal(loid)s. MIW has the potential to affect freshwater ecosystems and thus MIW requires strategies put in place for containment and treatment. Lignocellulosic sulfate-reducing biochemical reactors (SRBRs) are considered a cost-effective passive treatment for MIW and have been documented to continuously treat MIW at the field-scale. However, long-term operation (> 1 year) and reliable MIW treatment by SRBRs at mining sites is challenged by the decline in sulfate-reduction, the key treatment mechanism for metal(loid) immobilization. This dissertation addresses operational designs and materials suited to promote sulfate reduction in lignocellulosic SRBRs treating MIW. In this dissertation I demonstrated that lignocellulosic SRBRs containing spent brewing grains and/or sugarcane bagasse can be acclimated in continuous mode at hydraulic retention times (HRTs) of 7-12 d while simultaneously removing 80 ± 20% – 91 ± 3% sulfate and > 98% metal(loid)s. Additionally, I showed that decreasing the HRT to 3 d further yields high metal(loid) removal (97.5 ± 1.3% – 98.8 ± 0.9%). Next, I verified the utility of basic oxygen furnace slag to increase MIW pH in a two-stage treatment involving a slag stage and an SRBR stage containing spent brewing grains or sugarcane bagasse. The slag reactor from the two-stage treatment increased MIW pH from 2.6 ± 0.2 to 12 ± 0.3 requiring its re-combination with fresh MIW to reduce pH to 5.0 ± 1.0 prior to entering the lignocellulosic SRBRs. The lignocellulosic SRBRs from the two-stage treatment successfully continued to remove metal(loid)s, most notably cadmium, copper, and zinc at ≥ 96%. In additions to these outcomes, I performed a metadata analysis of 27 SRBRs employing brewers spent grains, sugarcane bagasse, rice husks and rice bran, or a mixture of walnut shells, woodchips, and alfalfa. I found that sugarcane bagasse SRBRs can remove between 94 and 168 mg metal(loid) kg–1 lignocellulose d–1. In addition, Bacteroidia relative abundances showed a positive correlation with increasing sulfate removal across all 27 SRBRs and are likely essential for the degradation of lignocellulose providing electron donors for sulfate reduction. Clostridia and Gammaproteobacteria were negatively correlated with sulfate reduction in the 27 SRBRs, however SRBRs that received alkalinized MIW had lower relative abundances of Clostridia, Gammaproteobacteria, and methanogenic archaea (known competitors for sulfate-reducing bacteria). Overall, my dissertation provides insight into lignocellulosic materials and operational designs to promote long-term sulfate-reduction in lignocellulosic SRBRs treating MIW.

The world currently faces hundreds of millions of cubic meters of soil contaminated with petroleum crude oil residuals. The application of ozone gas (O3) to contaminated soil is an effective means to oxidize petrogenic compounds and, when used with bioremediation, remove the oxidized byproducts. The overarching goal of this dissertation was to evaluate two areas of potential concern to large-scale O3 deployment: the capacity of O3-treated petroleum contaminated soils to support seed germination before bioremediation and the transport characteristics of O3 in soil columns. A matched study comparing the germination outcomes of radish (Raphanus sativus L.), grass (Lagurus ovatus), and lettuce (Lactuca sativa) in soils contaminated with three crude oils at various O3 total-dose levels showed that radish germination was sensitive to the soluble byproducts of oxidized petroleum (assayed as dissolved organic carbon [DOC]), but not sensitive to the unreacted petroleum (total petroleum hydrocarbon [TPH]). A multivariable logistic regression model based on the radish results showed that adverse germination outcomes varied with the DOC concentration and that DOC ecotoxicity decreased with increasing O3 dose-level and background organic material. The model was used to create a risk management map of conditions that created 10%, 25%, and 50% extra risks of adverse radish germination. Thus, while O3 effectively lowered TPH in soils, the byproducts exhibited ecotoxicity that inhibited radish germination. On the other hand, the sensitivity of radish germination to oxidized petroleum byproducts could be utilized to assess ecological risk. The feasibility of gas transport in the soil matrix is also of paramount concern to field-scale utilization of O3. A matched study comparing TPH removal at three field-relevant loading rates (4, 12, or 36 mgozone/ gsoil/ hr) and various total dose-levels showed an anisotropic pattern along the axial distance favoring the column inlet end. The asymmetry decreased as loading rate decreased and with concurrent improvements in O3-transport distance, O3 utilization, and heat balance. Overall, a low O3 loading rate significantly improved O3 transport and utilization efficiency, while also better distributing reaction-generated heat along the gas flow path for a depth typically utilized in bioremediation field settings.

Trichloroethene (TCE) and hexavalent chromium (Cr (VI)) are ubiquitous subsurface contaminants affecting the water quality and threatening human health. Microorganisms capable of TCE and Cr (VI) reductions can be explored for bioremediation at contaminated sites. The goal of my dissertation research was to address challenges that decrease the efficiency of bioremediation in the subsurface. Specifically, I investigated strategies to (i) promote improve microbial reductive dechlorination extent through the addition of Fe0 and (ii) Cr (VI) bio-reduction through enrichment of specialized microbial consortia. Fe0 can enhance microbial TCE reduction by inducing anoxic conditions and generating H2 (electron donor). I first evaluated the effect of Fe0 on microbial reduction of TCE (with ClO4– as co-contaminant) using semi-batch soil microcosms. Results showed that high concentration of Fe0 expected during in situ remediation inhibited microbial TCE and ClO4– reduction when added together with Dehalococcoides mccartyi-containing cultures. A low concentration of aged Fe0 enhanced microbial TCE dechlorination to ethene and supported complete microbial ClO4– reduction. I then evaluated a decoupled Fe0 and biostimulation/bioaugmentation treatment approach using soil packed columns with continuous flow of groundwater. I demonstrated that microbial TCE reductive dechlorination to ethene can be benefitted by Fe0 abiotic reactions, when biostimulation and bioaugmentation are performed downstream of Fe0 addition. Furthermore, I showed that ethene production can be sustained in the presence of aerobic groundwater (after Fe0 exhaustion) by the addition of organic substrates. I hypothesized that some lessons learned from TCE Bioremediation can be applied also for other pollutants that can benefit from anaerobic reductions, like Cr (VI). Bioremediation of Cr (VI) has historically relied on biostimulation of native microbial communities, partially due to the lack of knowledge of the benefits of adding enriched consortia of specialized microorganisms (bioaugmentation). To determine the merits of a specialized consortium on bio-reduction of Cr (VI), I first enriched a culture on lactate and Cr (VI). The culture had high abundance of putative Morganella species and showed rapid and sustained Cr (VI) bio-reduction compared to a subculture grown with lactate only (without Morganella). Overall, this dissertation work documents possible strategies for synergistic abiotic and biotic chlorinated ethenes reduction, and highlights that specialized consortia may benefit Cr (VI) bio-reduction.

Water is a vital resource, and its protection is a priority world-wide. One widespread threat to water quality is contamination by chlorinated solvents. These dry-cleaning and degreasing agents entered the watershed through spills and improper disposal and now are detected in 4% of U.S. aquifers and 4.5-18% of U.S. drinking water sources. The health effects of these contaminants can be severe, as they are associated with damage to the nervous, liver, kidney, and reproductive systems, developmental issues, and possibly cancer. Chlorinated solvents must be removed or transformed to improve water quality and protect human and environmental health. One remedy, bioaugmentation, the subsurface addition of microbial cultures able to transform contaminants, has been implemented successfully at hundreds of sites since the 1990s. Bioaugmentation uses the bacteria Dehalococcoides to transform chlorinated solvents with hydrogen, H2, as the electron donor. At advection limited sites, bioaugmentation can be combined with electrokinetics (EK-Bio) to enhance transport. However, challenges for successful bioremediation remain. In this work I addressed several knowledge gaps surrounding bioaugmentation and EK-Bio. I measured the H2 consuming capacity of soils, detailed the microbial metabolisms driving this demand, and evaluated how these finding relate to reductive dechlorination. I determined which reactions dominated at a contaminated site with mixed geochemistry treated with EK-Bio and compared it to traditional bioaugmentation. Lastly, I assessed the effect of EK-Bio on the microbial community at a field-scale site. Results showed the H2 consuming capacity of soils was greater than that predicted by initial measurements of inorganic electron acceptors and primarily driven by carbon-based microbial metabolisms. Other work demonstrated that, given the benefits of some carbon-based metabolisms to microbial reductive dechlorination, high levels of H2 consumption in soils are not necessarily indicative of hostile conditions for Dehalococcoides. Bench-scale experiments of EK-Bio under mixed geochemical conditions showed EK-Bio out-performed traditional bioaugmentation by facilitating biotic and abiotic transformations. Finally, results of microbial community analysis at a field-scale implementation of EK-Bio showed that while there were significant changes in alpha and beta diversity, the impact of EK-Bio on native microbial communities was minimal.

Soil impacts from crude oil spills in the United States are regulated at the state level using the analytical group total petroleum hydrocarbons (TPH) as the primary regulatory metric. TPH concentration in soil is used to enforce and verify compliance with cleanup levels (CULs). While there are significant differences between states concerning TPH CULs based on land use, most states enforce an action level of 100 mg TPH kg⁻1. The most common standard method for quantification of TPH in soils is EPA Method 8015, which entails extraction of petroleum hydrocarbons by dichloromethane and analysis by gas chromatography with flame ionization detection (GC-FID). Using Method 8015 or similar methods, TPH is defined as the cumulative area of all peaks within a defined analytical range (typically C6-C36). A limitation of TPH standard methods is their lack of specificity for petroleum hydrocarbons (i.e., these methods can also detect and quantify compounds that are an inherent part of natural soil organic matter (SOM)). While the interference of SOM compounds with TPH quantification is known, documentation regarding the extent of this interference is almost absent in the peer-reviewed literature. In this thesis, 15 biogeochemically-diverse soils, uncontaminated by crude oil hydrocarbons, were sampled from geographically diverse locations and investigated in an effort to determine the concentration of SOM that registers as TPH. Solvent extractions using dichloromethane or n-pentane in conjunction with GC-FID analysis showed that all soils had detectable concentrations of TPH ranging from 160 to 2700 mg TPH kg–1. Based on the results from this study, it can be concluded that many soils have a higher apparent TPH concentration than most US state-level CULs. In addition, the data from this study show that soils with a lower pH and/or a higher organic carbon content also have higher concentrations of apparent TPH. Findings from this thesis show that uncontaminated soils have a significant apparent TPH concentration that would be considered part of the TPH originating from contamination and should be accounted for in the regulatory landscape.

The goal of this research was to study the effect of dilution on ammonium and potassium removal from real hydrolyzed urine. The performance of two natural zeolites, clinoptilolite and chabazite, was studied and compared with the help of batch equilibrium experiments at four dilution levels: 100%, 10%, 1% and 0.1% (urine volume/total solution volume). Further, the sorption behavior of other exchangeable ions (sodium, calcium and magnesium) in clinoptilolite and chabazite was studied to improve the understanding of ion exchange stoichiometry. Ammonium and potassium removal were highest at undiluted level in samples treated with clinoptilolite. This is a key finding as it illustrates the benefit of urine source separation. Chabazite treated samples showed highest ammonium and potassium removal at undiluted level at lower doses. At higher doses, potassium removal was similar in undiluted and 10% urine solutions whereas ammonium removal was the highest in 10% urine solutions. In general, chabazite showed higher ammonium and potassium removal than clinoptilolite. The result showed that ion exchange was stoichiometric in solutions with higher urine volumes.

Mineral weathering and industrial activities cause elevated concentration of hexavalent chromium (Cr(VI)) in groundwater, and this poses potential health concern (>10 ppb) to southwestern USA. The conversion of Cr(VI) to Cr(III) – a fairly soluble and non-toxic form at typical pH of groundwater is an effective method to control the mobility and carcinogenic effects of Cr(VI). In-situ chemical reduction using SnCl2 was investigated to initiate this redox process using jar testing with buffered ultrapure water and native Arizona groundwater spiked with varying Cr(VI) concentrations. Cr(VI) transformation by SnCl2 is super rapid (<60 seconds) and depends upon the molar dosage of Sn(II) to Cr(VI). Cr(VI) removal improved significantly at higher pH while was independent on Cr(VI) initial concentration and dissolved oxygen (DO) level. Co-existing oxyanions (As and W) competed with Cr(VI) for SnCl2 oxidation and adsorption sites of formed precipitates, thus resulted in lower Cr(VI) removal in the challenge water. SnCl2 reagent grade and commercial grade behaved similarly when freshly prepared, but the reducing strength of the commercial product decreased by 50% over a week after exposing to atmosphere. Equilibrium modeling with Visual MINTEQ suggested redox potential < 400 mV to reach Cr(VI) treatment goal of 10 ppb. Kinetics of Cr(VI) reduction was simulated via the rate expression: r=-k[H+]-0.25[Sn2+]0.5[Cr2O72-]3 with k = 0.146 uM-2.25s-1, which correlated consistently with experimental data under different pH and SnCl2 doses. These results proved SnCl2 reductive treatment is a simple and highly effective method to treat Cr(VI) in groundwater.

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.

This research explores microbial chain elongation as a pathway for production of complex organic compounds in soils with implication for the carbon cycle. In chain elongation, simple substrates such as ethanol and short chain carboxylates such as acetate can be converted to longer carbon chain carboxylates under anaerobic conditions through cyclic, reverse β oxidation. This pathway elongates the carboxylate by two carbons. The chain elongation process is overall thermodynamically feasible, and microorganisms gain energy through this process. There have been limited insights into the versatility of chain elongating substrates, understanding the chain elongating microbial community, and its importance in sequestering carbon in the soils.

We used ethanol, methanol, butanol, and hydrogen as electron donors and acetate and propionate as electron acceptors to test the occurrence of microbial chain elongation in four soils with different physicochemical properties and microbial communities. Common chain elongation products were the even numbered chains butyrate, caproate, and butanol, the odd numbered carboxylates valerate and heptanoate, along with molecular hydrogen. At a near neutral pH and mesophilic temperature, we observed a stable and sustained production of longer fatty acids along with hydrogen. Microbial community analysis show phylotypes from families such as Clostridiaceae, Bacillaceae, and Ruminococcaceae in all tested conditions. Through chain elongation, the products formed are less biodegradable. They may undergo transformations and end up as organic carbon, decreasing the greenhouse gas emissions, thus, making this process important to study.

The advantages and challenges of combining zero-valent iron (ZVI) and microbial reduction of trichloroethene (TCE) and perchlorate (ClO4-) in contaminated soil and groundwater are not well understood. The objective of this work was to identify the benefits and limitations of simultaneous application of ZVI and bioaugmentation for detoxification of TCE and ClO4- using conditions relevant to a specific contaminated site. We studied conditions representing a ZVI-injection zone and a downstream zone influenced Fe (II) produced, for simultaneous ZVI and microbial reductive dechlorination applications using bench scale semi-batch microcosm experiments. 16.5 g L-1 ZVI effectively reduced TCE to ethene and ethane but ClO4- was barely reduced. Microbial reductive dechlorination was limited by both ZVI as well as Fe (II) derived from oxidation of ZVI. In the case of TCE, rapid abiotic TCE reduction made the TCE unavailable for the dechlorinating bacteria. In the case of perchlorate, ZVI inhibited the indigenous perchlorate-reducing bacteria present in the soil and groundwater. Further, H2 generated by ZVI reactions stimulated competing microbial processes like sulfate reduction and methanogenesis. In the microcosms representing the ZVI downstream zone (Fe (II) only), we detected accumulation of cis-dichloroethene (cis-DCE) and vinyl chloride (VC) after 56 days. Some ethene also formed under these conditions. In the absence of ZVI or Fe (II), we detected complete TCE dechlorination to ethene and faster rates of ClO4- reduction. The results illustrate potential limitations of combining ZVI with microbial reduction of chlorinated compounds and show the potential that each technology has when applied separately.