Publication Date


Document Type


Committee Members

Abinash Agrawal (Advisor), Donald Cipollini (Committee Member), Hailiang Dong (Committee Member), Mark Goltz (Committee Member), Michael Shelley (Committee Member)

Degree Name

Doctor of Philosophy (PhD)


Bench-scale microcosms with wetland plant roots were investigated to characterize the microbial contributions to contaminant degradation of halogenated aliphatic hydrocarbons (HAHs) with ammonium. The batch system microcosms consisted of a known mass of wetland plant roots in aerobic growth media where the roots provided both an inoculum of root-associated ammonium-oxidizing microorganisms and a microbial habitat. Aqueous growth media, ammonium, and HAHs including trichloroethene (TCE), cis-1,2-dichloroethene (cis-DCE), chloroform (CF), 1,1,2-trichloroethane (1,1,2-TCA), ethylene dibromide (EDB, or 1,2-dibromoethane, 1,2-DBA) and 1,2-dichloroethane (1,2-DCA) were replaced weekly in batch microcosms while retaining roots and root-associated biomass.

Molecular biology results indicated that ammonium-oxidizing bacteria (AOB) were enriched from wetland plant roots while analysis of contaminant and oxygen concentrations showed that those microorganisms can degrade HAHs by aerobic cometabolism.

Cometabolism of TCE, at 29 and 46 µg/L, was sustainable over the course of 9 weeks, with 20-30 mg/L ammonium-N. However, at 69 µg/L of TCE, ammonium oxidation and TCE cometabolism were completely deactivated in two weeks. This indicated that between 46 and 69 µg/L TCE with 30 mg/L ammonium-N there is a threshold [TCE] below which sustainable cometabolism can be maintained with ammonium as the primary substrate. However, cometabolism-induced microbial deactivation of ammonium oxidation and TCE degradation at 69 µg/L TCE did not result in a lower abundance of the amoA gene in the microcosms.

In the following experiments with TCE and elevated concentration of 75 mg/L ammonium-N, the deactivation of cometabolism with TCE was observed again when TCE reached from ~50 to ~70 µg/L. The cometabolic system was activated again one week after the system was replaced by a TCE-free medium culture. Rate constants did not change significantly during the inactivation cycle if normalized by X. It can be inferred that the drop in ammonium and TCE degradation at certain [TCE] are due to the activity shut down by ammonia oxidizers. Similar deactivation trends were observed in microcosm amended with cis-DCE, 1,1,2-TCA and EDB when HAHs concentration increased above ~150 µg/L. No deactivation was observed in the reactors with CF and 1,2-DCA.

A shift of ammonium oxidation production from nitrite of nitrate after HAHs were added was observed in all the HAHs batch systems and those shifts all coincided with a moderate decrease in ammonium and HAHs degradation kinetics. Following sequencing analysis on a cometabolic system with TCE showed that the relative abundance of nitrite oxidizers (especially Nitrospira) changed significantly after 14 weeks, which suggest that the microbial community changed with the addition of elevated concentration of TCE. The relative abundance of previous dominance genera Nitrosomonas decreased at higher TCE concentrations while the abundance of nitrite oxidizers Nitrospira increased significantly due to the weakened competence for oxygen from Nitrosomonas.

This research indicates that microorganisms associated with wetland plant roots can assist in the natural attenuation of HAHs in contaminated aquatic environments, such as urban or treatment wetlands, and wetlands impacted by industrial solvents.

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Department or Program

Department of Earth and Environmental Sciences

Year Degree Awarded


Creative Commons License

Creative Commons Attribution-Noncommercial-Share Alike 3.0 License
This work is licensed under a Creative Commons Attribution-Noncommercial-Share Alike 3.0 License.