Mentor(s)

Jeffrey Markert, Biology, Providence College, Bryan Clark, U.S. Environmental Protection Agency

Project Location

Providence College

Project Description

Coastal and marine ecosystems face a number of well documented challenges. Habitat loss, chemical pollution, climate change, and over-harvesting can damage local biological communities. Introduced species pose another kind of threat. When introduced species become invasive, this threat may manifest as novel diseases, parasites, predators, or competitors that disrupt local biological communities.

To manage these threats, careful monitoring is essential. Ideally, researchers and resource managers would have easy access to current census information for both local and introduced organisms. In practice, such surveys are resource intensive. One way to reduce this cost and effort is by using environmental DNA (eDNA) methods which are especially well suited to detecting creatures that live in water because shed bits of DNA are evenly mixed within the local aquatic or marine environment.

We collaborate with researchers at other academic institutions and federal conservation agencies. In the last research cycle, our team successfully used quantitative PCR on eDNA samples to estimate the census size of several individual local species.

Success with the qPCR method shows that we can reliably isolate high quality DNA from water samples. However the qPCR approach has limitations – we can only detect one species at a time, and we have to know in advance which creatures we are looking for.

Going forward, we are expanding our work by using metabarcoding methods which will allow us to detect DNA from a whole community by analyzing a single water sample. These sophisticated techniques combine careful sampling, high throughput sequencing technology, and bioinformatics tools to monitor the abundance of creatures within a habitat. This will allow us to detect creatures we might not expect to see. It’s an important tool for recognizing the presence of invasive species, rare species, and for recognizing range expansions and contractions in response to climate change.

In the medium- to long-term, these tools will be used to test hypotheses about the effects of pollution, climate change, and other anthropogenic forces on local ecological communities.

Our goals for the Summer 2023 research season are to collect water samples from several coastal field sites for eDNA analysis, to isolate DNA from these samples, and to use qPCR and metabarcoding methods to better understand the current composition of natural communities along the shores of Narragansett bay. We are especially interested in economically valuable fish species and invasive invertebrates.

Specific tasks include field work to collect samples, laboratory tasks to isolate and sequence DNA, and computer based analyses. In addition, compiling and interpreting information so that it can be shared with the scientific community and the public is an important component of any research project.

This project involves lab, field and computational work

Required/Preferred skills

Research students in our group typically have an interest in evolution or conservation biology. They are expected to have excellent organizational and record keeping skills. They should also have an interest in learning new and challenging techniques. Experience with the R programming language (or an interest in learning it) is advantageous. A car is not required, but a valid driver’s license will be helpful. We are planning an exciting summer that will include a mix of careful field work, advanced laboratory techniques, sophisticated data analyses, and networking with other researchers.

Will the project require transportation to field sites? No

Is this project open to Surf Flex? Yes

In which core facilities might student conduct research? RI Genomics & Sequencing Center @ URI

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