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Naturally occurring bacterial populations are capable of detoxifying chlorinated compounds and immobilizing the radionuclide uranium via reductive processes. This study addressed the following three knowledge gaps in the fields of chlorinated solvent and uranium bioremediation, 1) the risks and benefits of coupling bioremediation with thermal treatment for clean-up of chlorinated ethene-contaminated sites, 2) the accuracy of available techniques for the monitoring of chlorinated solvent bioremediation, and 3) the role of gram positive Desulfitobacterium spp. in uranium immobilization. Experiments demonstrated that thermal treatment increases electron donor availability, but the increased electron donor was not used to fuel reductive dechlorination and was actually consumed for methanogenesis. Two approaches for monitoring chlorinated solvent bioremediation were investigated, molecular techniques and compound-specific isotope analysis (CSIA). Results demonstrated that while Dehalococcoides (Dhc) gene expression was up-regulated under conditions inhibitory to dechlorination, the isotope effects associated with dechlorination reactions catalayzed by Dhc populations in consortia and in pure cultures were similar. U(VI) reduction by multiple Desulfitobacterium isolates was demonstrated. Interestingly, while almost all U(VI)-reducing populations have been reported to produce uraninite (UO2), the product of U(VI) reduction by Desulfitobacterium isolates was a unique form of insoluble mononuclear U(IV).

Contaminated aquatic sediments pose health risks to fish, wildlife, and humans and can limit recreational and economic uses of surface waters. Technical and cost effective in situ approaches for sediment management and remediation have been identified as a research need. Subaqueous in situ capping is a promising remedial approach; however, little is known regarding its impact on underlying sedimentary processes and the feasibility of bioaugmented caps at sites subject to contaminated groundwater seepage. This work specifically addresses (1) the impact of capping on biogeochemical processes at the sediment-water interface, (2) the ability and degree to which indigenous sediment microorganisms colonize an overlying cap, (3) the effect of advective flow direction on redox conditions within a cap, (4) natural contaminant bioattenuation processes within capped sediment, and (5) limitations toward a functional bioreactive in situ cap. Laboratory-scale experiments with capped sediment columns demonstrated that emplacement of a sand-based in situ cap induced an upward, vertical shift of terminal electron accepting processes into the overlying cap while simultaneously conserving redox stratification. Upflow conditions simulating a groundwater seep compressed anaerobic processes towards the cap-water interface. Microorganisms indigenous to the underlying sediment colonized cap material and spatial population differences generally reflected redox stratification. Downflow of oxic surface water through the cap, simulating tidally-induced recharge, created fully oxic conditions within the cap, demonstrating that flow direction strongly contributes to redox conditions. Experiments simulating capped sediment subject to contaminated groundwater seepage revealed a reduction of natural bioattenuation processes with time, stemming from the elimination of labile organic matter deposition to the sediment and a subsequent lack of electron donor. Thus, parent contaminants within groundwater seeps will be subject to minimal biotransformations within the sediment before entering a reducing cap. A bioreactive cap, inoculated with microorganisms capable of reductive dehalogenation, was established to reductively dechlorinate tetrachloroethene present in the groundwater; however electron donor amendments to sediment effluent were required to achieve complete dechlorination of tetrachloroethene to non-toxic ethene. Results from this work improve understanding of biogeochemical and bioattenuation processes within capped aquatic sediments and should aid in the development of active capping technologies.

abstract: DehaloR^2 is a previously characterized, trichloroethene (TCE)-dechlorinating culture and contains bacteria from the known dechlorinating genus, Dehalococcoides. DehaloR^2 was exposed to three anthropogenic contaminants, Triclocarban (TCC), tris(2-chloroethyl) phosphate (TCEP), and 1,1,1-trichloroethane (TCA) and two biogenic-like halogenated compounds, 2,6-dibromophenol (2,6-DBP) and 2,6-dichlorophenol (2,6-DCP). The effects on TCE dechlorination ability due to 2,6-DBP and 2,6-DCP exposures were also investigated. DehaloR^2 did not dechlorinate TCC or TCEP. After initial exposure to TCA, half of the initial TCA was dechlorinated to 1,1-dichloroethane (DCA), however half of the TCA remained by day 100. Subsequent TCA and TCE re-exposure showed no reductive dechlorination activity for both TCA and TCE by 120 days after the re-exposure. It has been hypothesized that the microbial TCE-dechlorinating ability was developed before TCE became abundant in groundwater. This dechlorinating ability would have existed in the microbial metabolism due to previous exposure to biogenic halogenated compounds. After observing the inability of DehaloR^2 to dechlorinate other anthropogenic compounds, DehaloR^2 was then exposed to two naturally occurring halogenated phenols, 2,6-DBP and 2,6-DCP, in the presence and absence of TCE. DehaloR^2 debrominated 2,6-DBP through the intermediate 2-bromophenol (2-BP) to the end product phenol faster in the presence of TCE. DehaloR^2 dechlorinated 2,6-DCP to 2-CP in the absence of TCE; however, 2,6-DCP dechlorination was incomplete in the presence of TCE. Additionally, when 2,6-DBP was present, complete TCE dechlorination to ethene occurred more quickly than when TCE was present without 2,6-DBP. However, when 2,6-DCP was present, TCE dechlorination to ethene had not completed by day 55. The increased dehalogenation rate of 2,6-DBP and TCE when present together compared to conditions containing only 2,6-DBP or only TCE suggests a possible synergistic relationship between 2,6-DBP and TCE, while the decreased dechlorination rate of 2,6-DCP and TCE when present together compared to conditions containing only 2,6-DCP or only TCE suggests an inhibitory effect. / Dissertation/Thesis / M.S. Civil and Environmental Engineering 2012

Tetrachloroethylene and its daughter-products represent a group of contaminations which are frequently found at sites with industrial activities, such as metal processing, electrotechnical and pharmaceutical industries as well as dry cleaning of clothing and the production of colours, paints and laquers. Due to their toxicity and persistence under natural conditions "denser-than-water" non aqueous phase liquids are substantial threats to the subsurface environment as well as the surface ecosystems including human beings. During the last two decades a number of technical solutions has been presented to enhance the situation of contaminated areas. One of the more recently established concepts are permeable reactive barriers. Permeable reactive barriers are passive in situ treatment zones containing a reactive material suitable to remove the contamination from the groundwater. They are installed downgradient from the pollution source perpendicular to the groundwater flow direction to immobilise or degrade the dissolved pollutants in the groundwater as it flows through. This project was organised in two main parts. The first part assessed seven different iron powders in batch experiments to determine the most efficient powder in terms of degradation velocity. The second part of the study employed this powder in a column experiment using different mixing ratios with sand to evaluate its performance under simulated subsurface conditions in a permeable reactive barrier. The aim of this experiment was to obtain a more detailed description of the behaviour and performance of the selected material. In the batch experiment the most promissing iron powder produced a half-life of tetrachloroethylene of 2.36 h. The column study demonstrated that cis-dichloroethylene has the longest half-life compared to tetrachlorethylene and trichloroethylene with 1.65 h. Having the longest half-life of all chloroethylenes included in this investigation the cis-dichloroethylene concentration will determine the dimensioning of a permeable barrier for remediation purposes.

Reductive dechlorination is a significant natural attenuation process in chloroethene-contaminated aquifers where organic carbon combined with reducing redox conditions support active dechlorinating microorganisms. At sites where natural organic carbon (NOC) associated with the aquifer matrix provides fermentable organics, the ability to measure the NOC is needed to assess the potential for the long-term sustainability of reductive dechlorination. This study focused on developing a method to measure the potentially bioavailable organic carbon (PBOC) associated with aquifer sediment. To measure NOC and evaluate its biodegradability, liquid extraction techniques on aquifer sediment were investigated. Single extractions with different extracting solutions showed that extractable organic carbon associated with the sediment ranged from 1-38% of the total organic carbon content (TOCs). Bioassay experiments demonstrated that 30-60% of the extractable organic carbon can be utilized by a microbial consortium. Alternating between 0.1% pyrophosphate and base solutions over multiple extractions increased the rate of removal efficiency and targeted two organic carbon pools. The result of the investigation was a laboratory method to quantify organic carbon from the aquifer matrix in terms of the PBOC. In the second part, the extractable PBOC was shown to biodegrade under anaerobic conditions, to produce H2 at levels necessary to maintain reductive dechlorination, and to support reductive dechlorination in enrichment cultures. For the third part of the research, the difference in extractable organic carbon inside and outside of a chloroethene-contaminated plume was examined through the combination of PBOC laboratory data and field parameters. Supported by ground-water constituent data, the PBOC extraction and bioassay studies showed that less extractable organic carbon was present inside than outside of the chloroethene plume. The final part of the research investigated the distribution of PBOC extractions across six contaminated sites. PBOC extractions were directly correlated to the TOCs, soft carbon content, and level of reductive dechlorination activity at the sites. Based on these correlations, a range for organic carbon potentially available to subsurface microorganisms was proposed where the upper bound consisted of the soft carbon and the lower bound consisted of the PBOC. / Ph. D.

Groundwater remediation strategies have advanced toward more effective and economical remedial technologies. Monitored natural attenuation (MNA) has become accepted by federal regulatory agencies as a viable remediation strategy for contaminants under site-specific conditions. At chloroethene contaminated sites where MNA is used as a remediation strategy, microbially-mediated reductive dechlorination is typically the dominant pathway for natural attenuation. The efficacy of reductive dechlorination at sites with no anthropogenic carbon sources is often influenced by the availability of readily-biodegradable natural organic carbon along with favorable geochemical conditions for supporting microbial dehalogenation. Recent research studies have suggested that the pool of labile natural organic carbon, operationally defined as potentially bioavailable organic carbon (PBOC), may be a critical component related to sustaining reductive dechlorination at MNA sites. The objective of this study was to evaluate PBOC as a quantitative measure of the labile organic carbon fraction of aquifer sediments in relation to microbial reductive dechlorination of chlorinated solvents. In the first phase of this study, the variability of PBOC in aquifer sediments was examined among 15 chloroethene contaminated sites. Results showed that PBOC displayed considerable variability among the study sites, ranging over four orders of magnitude. Regression results demonstrated that a positive correlation existed between PBOC, solid phase total organic carbon (TOCs), and reductive dechlorination activity at the sites. Results supported that greater levels of PBOC and TOCs corresponded to higher reductive dechlorination activity at the sites. Composition results showed that 6-86% of PBOC consisted of proteins and amino acids. Results also suggested a positive relationship existed between PBOC, concentrations of potentially bioavailable organic compounds present in the aquifer system, expressed as hydrolyzable amino acids (HAA), and the natural attenuation capacity (NAC) at the sites. Higher PBOC levels were consistently observed at sites with greater NAC and levels of HAA. The results of this study suggested that the variability of PBOC in the aquifer sediments exhibited a reasonable correlation with TOCs, hydrolyzable amino acids, and chloroethene transformation among the selected sites. In the second phase of this study, the relationship between PBOC in aquifer sediments and site specific performance data was evaluated among 12 chloroethene contaminated sites. Results demonstrated that PBOC in aquifer sediments was directly correlated to independent field metrics associated with reductive dechlorination. Levels of PBOC demonstrated direct relationships with hydrogen (H2) and dissolved oxygen (DO) concentrations within the groundwater system at the selected study sites. Results also indicated that PBOC demonstrated positive relationships with reductive dechlorination activity and the natural attenuation capacity of the sites. The findings of this study suggested that the level of PBOC in aquifer sediments may be a key factor in sustaining conditions favorable for microbial reductive dechlorination. In the third phase of this study, the distribution of PBOC was investigated at a chloroethene contaminated site. PBOC was measured in surficial aquifer sediment samples collected at varying depths in the vicinity of a chloroethene plume. Results demonstrated that levels of PBOC were consistently higher in aquifer sediments with minimal chloroethene exposure relative to samples collected in the PCE-contaminated source zone. Regression results demonstrated that a statistically significant inverse correlation existed between PBOC levels and chloroethene concentrations for selected temporary wells in the contaminated source zone at the study site. Consistent with these findings, results also indicated a similar trend of increased PBOC in aquifer sediments outside the chloroethene plume relative to aquifer sediments inside the plume. Results from this study further suggested that differences in extracted carbon levels at the site for surficial aquifer sediment samples in the PCE-contaminated source zone could impact the extent of reductive dechlorination within the hydrographic unit. / Ph. D.

abstract: This dissertation explores the use of bench-scale batch microcosms in remedial design of contaminated aquifers, presents an alternative methodology for conducting such treatability studies, and - from technical, economical, and social perspectives - examines real-world application of this new technology. In situ bioremediation (ISB) is an effective remedial approach for many contaminated groundwater sites. However, site-specific variability necessitates the performance of small-scale treatability studies prior to full-scale implementation. The most common methodology is the batch microcosm, whose potential limitations and suitable technical alternatives are explored in this thesis. In a critical literature review, I discuss how continuous-flow conditions stimulate microbial attachment and biofilm formation, and identify unique microbiological phenomena largely absent in batch bottles, yet potentially relevant to contaminant fate. Following up on this theoretical evaluation, I experimentally produce pyrosequencing data and perform beta diversity analysis to demonstrate that batch and continuous-flow (column) microcosms foster distinctly different microbial communities. Next, I introduce the In Situ Microcosm Array (ISMA), which took approximately two years to design, develop, build and iteratively improve. The ISMA can be deployed down-hole in groundwater monitoring wells of contaminated aquifers for the purpose of autonomously conducting multiple parallel continuous-flow treatability experiments. The ISMA stores all sample generated in the course of each experiment, thereby preventing the release of chemicals into the environment. Detailed results are presented from an ISMA demonstration evaluating ISB for the treatment of hexavalent chromium and trichloroethene. In a technical and economical comparison to batch microcosms, I demonstrate the ISMA is both effective in informing remedial design decisions and cost-competitive. Finally, I report on a participatory technology assessment (pTA) workshop attended by diverse stakeholders of the Phoenix 52nd Street Superfund Site evaluating the ISMA's ability for addressing a real-world problem. In addition to receiving valuable feedback on perceived ISMA limitations, I conclude from the workshop that pTA can facilitate mutual learning even among entrenched stakeholders. In summary, my doctoral research (i) pinpointed limitations of current remedial design approaches, (ii) produced a novel alternative approach, and (iii) demonstrated the technical, economical and social value of this novel remedial design tool, i.e., the In Situ Microcosm Array technology. / Dissertation/Thesis / Ph.D. Biological Design 2013

Die toxische sowie kanzerogene Verbindung 1,2-Dichlorpropan (DCP) ist weit verbreitet in Industrie und Landwirtschaft. Die Verbindung zeigt eine geringe chemische Reaktivität, ist nur mäßig wasserlöslich und unter aeroben Bedingungen weitestgehend beständig gegenüber mikrobiellen Abbauprozessen in der Umwelt. Als Folge reichert sich DCP in Grundwässern, Sedimenten und Böden an und gefährdet über die Nahrungskette die Gesundheit von Mensch und Tier. Um DCP effizient und ökonomisch zu unbedenklichen Verbindungen abzubauen, wurden mikrobielle Mischkulturen aus belasteten Sedimenten angereichert und in einen Wirbelschichtreaktor überführt. Dieses Verfahren ermöglichte eine kontinuierliche anaerobe Dechlorierung von DCP zu Propen. Grundsätzlich stellen biologische Abbauverfahren, bei denen komplexe mikrobielle Mischpopulationen eingesetzt werden, einen vielversprechenden Weg zur Transformation chlororganischer Verbindungen dar. Jedoch liegen üblicherweise nur wenige Informationen über die Zusammensetzung der betreffenden Populationen vor, so daß eine Optimierung bzw. effiziente Steuerung des Prozesses erheblich erschwert wird. Gegenstand der vorliegenden Arbeit war die Bestimmung der mikrobiellen Zusammensetzung der DCP-dechlorierenden Bioreaktorpopulation. Aufgrund der bekannten Limitierungen klassisch-mikrobiologischer Nachweisverfahren wurde eine Kombination mehrerer molekulargenetischer Methoden eingesetzt, die auf der vergleichenden Sequenzanalyse ribosomaler RNA beruhten. Die Untersuchungen zeigten, daß die Bakterienpopulation des Reaktors außerordentlich divers zusammengesetzt war und im wesentlichen aus bislang nicht-kultivierten Arten bestand. Es dominierten "Grüne nicht-schwefelhaltige Bakterien" (green nonsulfur bacteria) sowie Grampositive Bakterien mit niedrigem GC-Gehalt. Die Archaea hingegen waren fast ausschließlich durch zwei bekannte methanogene Spezies vertreten, Methanosaeta concilii sowie Methanomethylovorans hollandica. Der Vergleich der gewonnenen rDNA-Daten mit denen anderer Lebensräume ergab, daß Süßwasserhabitate, in denen chlororganische Verbindungen reduktiv umgesetzt werden, offenbar eine spezifische Populationsstruktur aufweisen. Es konnten spezifische 16S rDNA-Gruppen definiert werden (SHA-Cluster), die auch nach längerem Reaktorbetrieb noch nachgewiesen werden konnten. Darüber hinaus wurden Dehalobacter restrictus- sowie Dehalococcoides ethenogenes-ähnliche Bakterien in der DCP-dechlorierenden Bioreaktorpopulation gefunden. Beide Spezies sind in der Lage, chlororganische Verbindungen unter Verwendung von Wasserstoff als alleinigem Elektronendonor reduktiv zu dechlorieren. Es ist davon auszugehen, daß Dehalobacter und Dehalococcoides spp. aufgrund ihrer Physiologie an der reduktiven Umsetzung des DCPs beteiligt sind. Die Untersuchung der Population über einen längeren Zeitraum zeigte überdies, daß Bakterien der Gattung Dehalobacter überproportional angereichert und daraufhin zur dominierenden Spezies im Reaktor wurden. Dieser Befund läßt auf eine zentrale Rolle von Dehalobacter spp. bei der Transformation von DCP zu Propen schließen. Konsequenterweise führte die Zugabe von Wasserstoff zum Reaktor zur einer deutlichen Steigerung des DCP-Umsatzes. Dehalobacter und Dehalococcoides spp. sowie die anderen durch SHA-Cluster repräsentierten Bakterien stellen potentielle Indikatororganismen für die DCP-Transformation im Reaktor dar. Ein kontinuierliches Monitoring dieser Bakterien würde zu einer effizienteren Steuerung des Dechlorierungsprozesses und damit zu einer Optimierung des Verfahrens führen. / The toxic and carcinogenic compound 1,2-dichloropropane (DCP) is widely used in industry and agriculture. DCP shows a low chemical reactivity. It is only moderately soluble in aqueous systems and almost recalcitrant to microbial degradation under aerobic conditions. As a consequence DCP accumulates in groundwater, sediments and soil, thus endangering humans and animals via the food chain. To efficiently transform DCP to harmless organic compounds microbial mixed cultures have been enriched from sediments and were subsequently transferred into a fluidized bed bioreactor. This process allowed a continuous anaerobic dechlorination of DCP to propene. Bioreactor processes using complex microbiota represent a promising technology for transformation of chlorinated compounds. However, the composition of the used population is usually unknown, hence hindering both optimization and control of the degradation process. Subject of this work was the analysis of the microbial diversity of the DCP-dechlorinating bioreactor population. Conventional culture-dependent microbiological methods are often limited if used for the analysis of complex communities. Therefore, a combination of different molecular methods based on comparative 16S rRNA analysis was applied. It was found that the bioreactor population was highly diverse and consisted mainly of as yet-uncultured bacteria. Members of the green nonsulfur bacteria and the gram-positive bacteria with low G+C content dominated the consortium. In contrast the archaea were represented by only two species, Methanosaeta concilii and Methanomethylovorans hollandica. The comparison of the rDNA data with those of other biotopes revealed that reductively dechlorinating freshwater habitats show a specific community structure. 16S rDNA-clusters were defined, which could still be detected after a longer operation time of the bioreactor. Furthermore, Dehalobacter restrictus- and Dehalococcoides ethenogenes-like bacteria were found in the DCP-dechlorinating bioreactor population. Both species are capable of reductive dechlorination using hydrogen as the sole electron source. Therefore, it could be assumed that these bacteria were also involved in the dechlorination of DCP. The investigation of the bioreactor population for a longer period of time revealed that Dehalobacter-like bacteria were significantly enriched and subsequently became the most frequently found bacterium within the bioreactor. This indicates a major role of Dehalobacter spp. within the transformation process of DCP to propene. Consequently, the addition of hydrogen to the bioreactor led to an increase of the DCP transformation rate. Dehalobacter und Dehalococcoides spp. as well as the bacteria represented by the specific SHA-clusters are possibly suitable as indicator organisms for the transformation of DCP within the bioreactor. A continuous monitoring of these bacteria would lead to a more efficient control and hence, to an optimization of the transformation process.

The method of using stimulated reductive dechlorination when remediating sites contaminated with chlorinated solvents is not unusual, but not many studies have been done on the overall process outside of a controlled environment. In order to investigate the process, principal component analysis (PCA) and partial least square (PLS) regression was used to identify the most important parameters for the degradation of the chlorinated solvents. The most important parameter for all chlorinated compounds turned out to be oxygen, with levels of degradation products increasing with decreasing levels of dissolved oxygen. Dissolved oxygen was deemed the most important variable to measure during a control program on the site. The degradation dynamics of the process were investigated to examine the behaviour of the chlorinated solvents and their degradation products. The degradation products of the main contaminant TCE were found in all observation points, which indicates an ongoing reductive dechlorination all over the site. A large amount of the mother product, TCE, was found in two observation points, which were believed to be situated close to the sources of the TCE contamination. Over the observation period of 2,5 years the levels of TCE in the source areas decreased significantly to below the remediation goal. However, the levels of TCE increased in another observation point further downstream, with concentrations still increasing at the end of this study. The levels in this point were lower than those measured initially in the source area, but still much higher than the accepted values. Possible reasons for this appearance of TCE could be an isolated sheet of contaminants being pushed into the observation point from a nearby location or transport of the contaminants from the source area in units of higher conductivity such as sand lenses or fractures in the clayey soil. / Att använda stimulerad reduktiv deklorering som metod för att sanera fastigheter förorenade med klorerade lösningsmedel är inte ovanligt, men få studier har undersökt det övergripande saneringsförloppet utanför de kontrollerade förhållanden i en labbmiljö. För att undersöka nedbrytningsprocessen användes principalkomponentsanalys (PCA) och partial least square (PLS) regression i syfte att identifiera de parametrar som hade störst påverkan på nedbrytningen av de klorerade föroreningarna. Den enskilt viktigaste parametern visade sig vara halten löst syre i grundvattnet, då halterna av nedbrytningsprodukter ökade med minskande syrehalt. Därför ses syre som den viktigaste parametern för att följa förloppet och är den parameter som bör mätas i kontrollprogram över nedbrytningsprocessen.   Nedbrytningsdynamiken analyserades under en observationsperiod på 2,5 år för att studera hur de klorerade föroreningarna betedde sig under nedbrytningsförloppet. Nedbrytningsprodukter hittades i provtagningspunkter över hela fastigheten vilket visar på en pågående reduktiv deklorering. En stor mängd av moderprodukten TCE hittades i två punkter som bedömdes vara källor till TCE-spridningen. Under observationsperioden sjönk halterna av TCE i dessa två punkter till under gränsen för åtgärdsmålet, dock ökade koncentrationen av TCE i en annan provpunkt längre nedströms källområdet. Halterna i provpunkten var inte lika höga som de initiala halterna i källområdet, men de var långt högre än det fastställda åtgärdsmålen och ökade fortfarande när undersökningen avslutades. Möjliga förklaringar till varför halterna ökade i denna provpunkt är att ett sjok av TCE från omkringliggande sediment har transporterats till provpunkten, eller att en föroreningstransport har skett från källområdet via områden med högre konduktivitet i till exempel sandlinser eller sprickor.