Silent heroes of the sediment: unearthing the bioremediation potential of microbes from contaminated sites

This dissertation work aimed to assess the bioremediation potential for two contaminated sites in New Jersey, USA. The first site is the Passaic River, which is historically contaminated with the toxic chlorinated compound, 2,3,7,8-tetrachlorodibenzo-p-dioxin (2,3,7,8-TeCDD), among other contaminants, and the second site is a large industrial site contaminated with many toxic, recalcitrant compounds including benzene. We created anaerobic microcosms using sediments from the Passaic River and observed dechlorination, and hence detoxification, of 2,3,7,8-TeCDD to the di-chlorinated product 2,7-dichlorodibenzo-p-dioxin. In separate microcosms, we observed dechlorination of 2,7-dichlorodibenzo-p-dioxin to the non-chlorinated dibenzo-p-dioxin, which indicates that bacteria native to these sediments are capable of completely dechlorinating the toxic parent compound 2,3,7,8-TeCDD. 16S rRNA gene sequencing and qPCR revealed an increase in a phylotype, named PR_dA.O., in 2,3,7,8-TeCDD dechlorinating cultures, hinting at an active role in dechlorination. PR_dA.O. likely represents a new genus within the Dehalococcoidia class separate from Dehalogenimonas and Dehalococcoides, well-established dechlorinators. DNA from the most active 2,3,7,8-TeCDD dechlorinating bottle was shotgun sequenced to obtain reads for a metagenome. Many partial reductive dehalogenase homologous (rdh) genes were identified; however, few full length rdh could be identified. Of interest, seventeen high-coverage rdhA encoding the catalytically active portion of reductive dehalogenases were identified, most with accompanying rdhB predicted membrane anchor protein genes. These rdh genes can be candidates for heterologous expression in a more quickly growing host organism. We analyzed multidisciplinary datasets focused on a contaminated section of a large industrial site in Southern New Jersey. The data included groundwater geochemical species data, X-ray fluorescence (XRF), and 16S rRNA gene sequencing data obtained through interrogation of thin slices of an anaerobic sediment core. We hypothesized zones of biodegradation activity based on aligning data trends and potential microbial metabolisms. This study was unique in its fine-scale resolution of the data due to the separate analyses of over 300 slices of the core by collaborators. Our results suggest that an iron-reducing bacterium from a 4-inch region of the core was capable of benzene oxidation and produced the observed geochemical and contaminant profiles seen within the corresponding depth at the site.Ph.D.Includes bibliographical reference