Water Quality Monitoring Turns to DNA Tracking Instead of Sample Collecting

Science undergraduates will research new DNA-based ways to monitor water quality and aquatic life in Pittsburgh this summer without ever touching a fish.

A $24,750 grant from the EQT Foundation will support Dr. Brady Porter, associate professor of biology, and his student researchers in lab-intensive work called DNA meta-barcoding, which will determine what regions of fish DNA are common across local species but also can identify specific fish.

By collecting water samples that contain the environmental DNA (eDNA) shed by fish and mussels in the Allegheny, Monongahela and Ohio rivers, and comparing it against the meta-barcode results, Porter and his team will then be able to put together a picture of all aquatic life in the water. This will include endangered and threatened species as well as invasive species and others new to a location.

The presence or absence of certain fish and mussels has long been used to indicate water quality. Standard methods for large rivers rely on labor-intensive processes—trawling for fish and electroshocking fish to stun them so they can be caught. Scuba-diving surveys often are done in the murky, commercial and recreational waters for freshwater mussels. But both methods can be hazardous to the surveyors and the aquatic life, Porter explained.

By combining two cutting-edge methods that rely instead on DNA information, water quality surveys could be conducted at the molecular level—with greater safety for humans and wildlife, more accuracy and lower cost, Porter said.

Essentially, Porter and his team will map out the DNA region of Pennsylvania’s 130 species of fishes and 50 species of mussels to determine the best diagnostic DNA sequences regions.

“These DNA barcode sequences can identify organisms to the species level, much like a traditional bar code can identify a specific item in a store,” explained Porter, a member of the committee that evaluates the threatened and endangered status of fish statewide.

Then, using a second DNA-related process, they will focus on eDNA in water samples to determine what species are living alongside each other. While most eDNA studies are designed to detect only one or two specifically targeted species at a time, Porter and his lab will couple eDNA with DNA meta-barcoding to reveal all the species of fishes and mussel in specific waters.

Instead of focusing only on the indicator species for water quality, this new method will give an overview of the aquatic community—including newly introduced species that otherwise, would not be detected. The team can compare DNA sequence results to traditional surveys to validate the new survey method.

“We will develop this rapid, non-invasive molecular method to detect the presence or absence of a wide number of fish and mussel species without ever having to collect them directly,” Porter said. “This will provide an alternative where it’s difficult to sample with traditional methods.”