First Advisor

William Fish

Date of Publication


Document Type


Degree Name

Doctor of Philosophy (Ph.D.) in Environmental Sciences and Resources


Environmental Sciences and Resources




Anaerobic bacteria, Creosote -- Environmental aspects, Methane -- Environmental aspects, Polycyclic aromatic hydrocarbons -- Biodegradation



Physical Description

1 online resource (ix, 83 p.) : ill. (some col.)


The overall goal of this work was to investigate microbial activity leading to the anaerobic degradation of polycyclic aromatic hydrocarbons and an organophilic clay sediment cap used at a creosote-contaminated Superfund site. To determine whether or not PAHs were being degraded under anaerobic conditions in situ, groundwater and sediment porewater samples were analyzed for metabolic biomarkers, or metabolites, formed in the anaerobic degradation of naphthalene (a low-molecular weight PAH). In addition, a groundwater push-pull method was developed to evaluate whether the transformation of deuterated naphthalene to a deuterated metabolite could be monitored in situ and if conservative rates of transformation can be defined using this method. Metabolites of anaerobic naphthalene degradation were detected in all samples that also contained significant levels of naphthalene. Anaerobic degradation of naphthalene appears to be widespread in the upland contaminated aquifer, as well as within the adjacent river sediments. A zero-order rate of transformation of naphthalene-D₈ to naphthoic acid-D₇was calculated as 31 nM·d-¹. This study is the first reported use of deuterated naphthalene to provide both conclusive evidence of the in situ production of breakdown metabolites and an in situ rate of transformation. Methane ebullition was observed in areas of the sediment cap footprint associated with organophilic clay that was used a reactive capping material to sequester mobile non-aqueous phase liquid (NAPL) at the site. Anaerobic slurry incubations were constructed using sediment core samples to quantify the contribution of the native sediment and the different layers of capping material (sand and organophilic clay) to the overall methane production. Substrate addition experiments using fresh, unused organophilic clay, as well as measured changes in total carbon in organophilic clay over time supported the hypothesis that microbes can use organophilic clay as a carbon source. Quantitative PCR (qPCR) directed at the mcrA gene enumerated methanogens in field samples and incubations of native sediment and capping materials. Denaturing gradient gel electrophoresis (DGGE) was also performed on DNA extracted from these samples to identify some of the predominant microorganisms within the sediment cap footprint. The organophilic clay incubations produced up to 1500 times more methane than the native sediment and sand cap incubations. The organophilic clay field sample contained the greatest number of methanogens and the native sediment contained the least. However, the native sediment incubations had greater numbers of methanogens compared to their respective field sample and comparable numbers to the organophilic clay incubation. An increase in methane production was observed with the addition of fresh, unused organophilic clay to the already active organophilic clay incubations indicating that organophilic clay stimulates methanogenesis. In addition, organophilic clay retrieved from the field lost about 10% of its total carbon over a 300-day incubation period suggesting that some component of organophilic clay may be converted to methane. DGGE results revealed that some of the predominant groups within the native sediment and sediment cap were Bacteriodetes, Firmicutes, Chloroflexi, and Deltaproteobacteria. An organism 98% similar to Syntrophus sp. was identified in the organophilic clay suggesting this organism may be working in concert with methanogens to convert the organic component of organophilic clay ultimately to methane. The capacity of organophilic clay to sequester organic contaminants will likely change over time as the organic component is removed from the clay. This, in turn, affects the use of this material as a long-term remedial strategy in reduced, contaminated environments.


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Portland State University. Environmental Sciences and Resources Ph. D. Program

Persistent Identifier