Nestled between the land and sea, salt marshes are coastal ecosystems that harbor immense biodiversity. While traditional methods like traps, pots, and plankton nets are commonly used to quantify this diversity, they often introduce fishing biases that disproportionately detect the presence of certain species. To avoid these incidences, DNA-based approaches like environmental DNA (eDNA) are laying the groundwork for more comprehensive biodiversity assessments. Specifically, a molecular technique known as eDNA metabarcoding can characterize entire species compositions from environmental samples. In my research, I collected aquatic samples from the Jacques Cousteau National Estuarine Research Reserve (JCNERR) in New Jersey to assess the fish diversity within the marsh. In pursuit of this endeavor, I applied three specific methods which were outlined by the National Estuarine Research Reserves (NERRs). Their “Recommended Methods for eDNA Water Sampling in Estuarine Systems” offers a standardized approach for sample collection and processing which was referenced throughout this study.
Sunset overlooking the salt marsh from the Rutgers University Marine Field Station.
The goals of this project encompassed the following aims:
- To estimate the temporal scale of an eDNA signal across four distinct tidal phases- incoming, high, outgoing, and low tides (Method 1).
- To characterize the diversity of fish species occupying marsh pools during the low tide period (Method 2).
- To compare the species coverage from traditional plankton netting to eDNA metabarcoding at incoming tide (Method 3).
After a successful fieldwork season, my next step will be to process the collected environmental samples at the Rutgers University eDNA Laboratory. Each sample will undergo DNA extraction, amplification (polymerase chain reaction), and sequencing in accordance with an established protocol. Subsequently, the data will be processed bioinformatically to identify the resulting sequences taxonomically.
With sincere thanks to the eDNA Collaborative, I am honored to have been awarded this microgrant which has provided me the opportunity to participate in the Physalia course, Summer School in Bioinformatics. This workshop was an essential first step in learning the foundations of bioinformatic analysis and getting practical, hands-on experience with Next Generation Sequencing biology. I am very grateful to have acquired these critical skills and to now apply them to my research initiatives!