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Loyola University Chicago

Department of Biology

Samantha Lindemann Thesis Defense: Project Description

Title: Denitrification in Urban Coastal Environments: A Functional Gene Study



Eutrophication is a major anthropogenic stressor on aquatic ecosystems worldwide. Jamaica Bay is located in the southeastern portion of New York City, NY (NYC). Like many other estuaries, Jamaica Bay is impacted by anthropogenic N inputs from various sources. Despite eutrophic conditions, improvements in water quality over the last few decades have prompted government agencies to promote oyster restoration to help reduce anthropogenic N in NYC waters. The effect of eastern oysters on sediment bacterial communities responsible for denitrification in Jamaica Bay was previously unknown. Those samples exposed to oysters were predicted to have high denitrification gene abundances, and thus a high potential for denitrification; however no significant relationship was found.  Abundance of key denitrification genes were quantified using qPCR. Our results showed oysters’ effect on abundance of denitrifiers was variable by site and season with no significant overall impact. A significant factor for denitrifier abundance in Jamaica Bay was availability of organic matter. 

This project also explored post-hurricane Sandy denitrification dynamics in a nearby estuary, the Western Long Island South Shore estuary (WLISS). Following the damage caused by this superstorm, 68 million gallons of raw sewage were released into WLISS. This massive release of sewage was the result of damage caused to the Bay Park Sewage Treatment Plant which is responsible for wastewater treatment serving 5 million people. The release of this sewage greatly increased the nutrient load in the WLISS estuary and the environmental impacts are of interest. Our analyses showed a mixed effect of site and season on the bacterial denitrifying community. Unlike Jamaica Bay, there is a significant correlation between denitrifier abundance and denitrification rate. This study employed methods that more directly assayed the samples in conditions similar to those found in the environment and therefore may be more indicative of natural denitrification rates.



I owe many thanks to my thesis advisors Dr. Domenic Castignetti and Dr. Timothy Hoellein. They have put in a great deal of time guiding me in the lab, answering questions, and providing me with invaluable advice. I would not have been able to complete my graduate education without their continual support.  I'd also like to thank the Castignetti and Hoellein lab members; in particular Elizabeth Humphrey and Mike Hassett for their help throughout my thesis project. Another thank you is owed to Dr. Stefan Kanzok. The use of his laboratory as well as his advisement on my research methods were extremely important to my project.  Finally, I'd like to thank my third committee member, Dr. John Kelly, for all the time he spent advising me throughout my thesis research.



Samantha Lindemann of Montevideo, Minnesota, graduated from the University of Minnesota Duluth in 2011 with a Bachelor of Science degree in Cell and Molecular Biology.  After working at Era Laboratories as an aquatic toxicology technician for one year, she began the Master of Science program at Loyola University Chicago in 2012 where she joined the labs of Dr. Domenic Castignetti and Dr. Timothy Hoellein


Committee Members 

Dr. Domenic Castignetti

Dr. Timothy Hoellein

Dr. John Kelly





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