Angie David UNIV 391 Reflection A January 19, 2012 My research projects are interested in the idea of oyster

restoration as a method to clean up polluted waters. In urban and agricultural rivers and estuaries, nitrogen accumulates readily and quickly. In agricultural areas, runoff from fertilizers rich in nitrogen (N) content pollutes the nearby waters. In urban environments, human waste that enters the water ways is the leading cause for N-overload. Nitrogen enriched waters, also called eutrophic waters, can cause phytoplankton overgrowth such that it can be stimulated to nuisance levels. Phytoplankton are small organisms that reside in the sunlit surface water. They comprise the link between sunlight energy and the aquatic food web. Under a nutrient rich environment, such as eutrophic waters, phytoplankton undergo rapid growth and accumulate to high densities. These large amounts of phytoplankton can cause clouding and coloring of the water. With their abundance come serious consequences for the rest of the ecosystem. Phytoplankton cloud the surface of the water such that it becomes difficult to allow light to permeate the surface, which in turn reduces the oxygen that phytoplankton can provide to the rest of the aquatic ecosystem. Oysters are a key species in aquatic systems. Their method of food intake is through filter feeding. Oysters suck in water and filter out phytoplankton to swallow. The water is then spit back out. Through doing this, oysters clean the water around them. This concept powers oyster restoration as a method that may improve overall water quality. Due to over-harvesting, pollution, and disease, oyster populations have greatly declined over the years. In response to this, oyster restoration projects have been implemented across the country to restore their ecological role.

Oyster restoration has been proposed to help clean up the Hudson-Raritan estuary. We are studying the effects of oyster restoration in Jamaica Bay, New York City (see Figure 1). Jamaica Bay is a great body of water to study because of its surrounding environment. It derives its nitrogen enrichment through all the combined sewer outfalls, landfills, water pollution treatment plants, and the nearby John F. Kennedy International Airport (in gray on the north eastern side of the Bay). We sample at four locations across an eutrophication gradient. These locations include: Spring Creek, Wildlife Refuge, Motts Basin, and Floyd Bennett Field. Sediment samples are taken bi-monthly from July 2010 to the present for four oyster treatments: control, low, medium, and high. These treatments vary in the density of oysters, with the control containing no oysters and high containing a greater density of oysters. These oysters sit inside a bag which is wired on top of a box filled with sediment (see Fig. 2). These boxes are then tied to a rope and lowered into the bay. During the time they sit in the water, the oysters filter the water, consume the phytoplankton, and deposit nitrogen enriched waste into the sediment. Research will measure how oysters assimilate and excrete nitrogen, and how nitrogen is processed by sediment microbes through analysis of field data from Jamaica Bay, NYC. In Dr. Timothy Hoelleins lab, I focused on the oyster aspect of the project. In lab, I worked on data analysis often with my research-mates and Dr. Hoellein. When I did field work in New York, I worked alongside the New York team comprised of Dr. Zarnoch and his graduate students. Completing the fieldwork under the hot sun from sunrise to sunset with a team of scientists was incredibly rewarding because I learned leadership and cooperation skills.

At the lab bench, I worked on data analysis for the remainder of my time. There is a tool that measures sediment quality. This is called the carbon to nitrogen (C:N) ratio. Normally, sediment contains a high amount of carbon. This then means that the amount of nitrogen is the determining factor of the quality of the sediment. A low C:N ratio (meaning that there is a high amount of nitrogen) reveals good sediment quality whereas a high C:N ratio describes poorer sediment quality. The first prediction that can be drawn is that among the four treatments of oyster density, high oyster density should create a higher organic matter and nitrogen content in the sediment, resulting in low C:N ratio. From this, we can see whether oysters really have an effect in influencing sediment and water quality. This semester, however, I am undertaking a side project to look at the molecular side of oyster restoration. I work alongside Monica Micek, the graduate student, and with another undergraduate student. In this lab, Ive learned greater responsibility by working under the head of the Biology department and with new people. In this case, we are looking at two genes that are present in denitrifying bacteria that should be present in the sediment samples. Denitrifying bacteria are involved in the process of converting forms of nitrogen to be accessible to other life forms. The two genes involved in this process are the nirS and nirK genes. Through identifying the presence of these genes, we can detect the existence of denitrifying bacteria. These genes code for nitrite reductases (enzymes involved in nitrite reduction) and can identify microorganisms that are capable of NO2- reduction to N2O or N2 gas. Denitrifying bacteria contain structurally different but functionally equivalent enzymes that catalyze nitrite reduction. A cytochrome cd1-containing nitrite reductase encoded by the nirS, and a copper nitrite reductase encoded by nirK.

To do this, I am working under Dr. Domenic Castignetti. I have taken the sediment samples that we have collected over months and extracted the DNA. The DNA will then be examined through polymerase chain reaction (PCR) and gel electrophoresis. PCR is a molecular technique that amplifies a targeted piece of DNA. Gel electrophoresis then uses those PCR products and separates them based on size and charge. Since previous research has already identified these two genes, which are conserved among bacteria, we can detect the presence of either gene in Jamaica Bay bacteria because the nirK and nirS gene are different sizes. Since they are different sizes, the gel should show two distinct bands in different positions which we can then identify as nirK or nirS. Through examining the microbial community in the sediment, we may be able to see how the oyster treatments interact with denitrifying bacteria in N removal. As a result, the nirK and nirS genes are useful targets for PCR primers to detect communities of denitrifying bacteria in Jamaican Bay sediment samples. Thus, isolated genomic DNA and the gene of interest were amplified via PCR. The PCR products were analyzed through gel electrophoresis and compared to known bacterial controls in order to see what kind of microbial community is interacting with the oyster treatments. Other methodologies might expand on this research. This form of water treatment directly concerns public health departments. As clean water provides citizens with fewer waterborne diseases, the success of methods such as oyster restoration is invaluable. When I was in India, I volunteered at a medical lab which studied the effects of water pollution in children and diseases with hopes to implement a vaccination program to reduce the risk of contracting waterborne diseases. In America, health officials can expand on oyster restoration by seeing if these kinds of methods really have a positive effect on health.

Although Jamaica Bay is polluted and is already surrounded with many sewer outfalls and landfills, oyster restoration may be able to work in other less eutrophic waters. If public health research can utilize the same theory behind improving water quality, they may be able to help communities struggling with clean water and its related diseases. If indeed oyster restoration works, in theory, it should improve water quality by making the water clear and clean. This allows for improved commercial and recreational fishing. Research for tourism should benefit from oyster restoration seeing as quality of water impacts fishing, boating, and ecotourism. If tourism is improved based on water quality, then the overall economy will be improved as well. Overall, oyster restoration efforts are valuable to different areas of related research: public health, economy, tourism, etc. Through research, I have been able to learn how to work with a team of scientists. I gained analytical, working, and presenting skills that I would have not been able to acquire elsewhere. I learned the basics of research in Dr. Hoelleins lab. As I progressed, I was able to develop my own research protocol for a new side project. To be able to do this under the supervision of Dr. Castignetti has given me an opportunity to learn how to be responsible for myself and my research. I have gained valuable leadership skills as I have had to teach the undergraduate student who works with me what the project entails. These skills are invaluable as they can help students progress through their future, whether it be in a graduate school, medical school, or any other career path.

Fig. 1: Map of Jamaica Bay, NYC.

Fig. 2: Oyster treatment boxes.