At first glance, there’s nothing even remotely intimidating about the QuantStudio 3. It presents as a humble white cube, easily mistaken for a stocky old school photo printer with a display that looks surprisingly like the screen on the seatback in front of you on your last flight. Its only off-putting trait may be its inability to recognize a caret (the ^ character above the 6 on your standard QWERTY keyboard) when you’re trying to enter the local wifi password.
But fire it up and the QuantStudio 3 can deliver you to the very foundation of life on Earth. That’s when it becomes intimidating, at least for the non-geneticists among us.
The QuantStudio is a real-time quantitative PCR (qPCR) system, a thermocycler used to create a polymerase chain reaction to amplify segments of DNA for analysis. You may recall the concept from the days when you needed a negative COVID-19 PCR test to return to work or school. That’s not what Save the Sound is using its qPCR system for, though there are considerable public and environmental health implications.
The last piece of equipment in a new countertop assembly line added this winter to the John and Daria Barry Foundation Water Quality Lab in Save the Sound’s Larchmont office, the qPCR system will take the lab team’s analytical capabilities to the next level.
“We’ve been able to quantify the presence of fecal indicator bacteria. Now, when we identify a hotspot, we can go figure out the source,” said Elena Colón, Save the Sound’s lab manager. “We can determine whether the DNA numbers suggest that it most likely came from a bird or a pig or if it’s canine. Or is it human?”
That’s a critical part of the ongoing work of restoring and protecting water quality. First, you need to know whether and where a problem exists; after that, you need to know what the problem is in order to address it.
“Understanding whether the source is human would be the biggest priority for us,” said Peter Linderoth, director of science and watersheds for Save the Sound’s Healthy Waters Institute. “If the source is goose or dog, it creates different sets of potential solutions. But if there are high concentrations of human markers in streams flowing through communities, that’s more an indicator of sewage, which is the type of pollution we’re most interested in stopping. The pathogens found in human waste are the ones most likely to make us sick.”
Save the Sound staff and volunteers collect more than 750 water samples every summer from locations around western Long Island Sound, from Greenwich, CT through Westchester County, NY and into Queens. Staff then analyze those samples in the lab for the presence of pathogen indicator bacteria (Enterococcus in marine waters, E. coli in freshwater). Starting this spring, there will be a second set of samples collected at each site. When we determine high levels of bacteria are present in a site’s first sample, we’ll run the second sample through a complex sequence of stops along that freshly stocked countertop in the lab.
At the first stops, the water sample is filtered through a vacuum pump and DNA is extracted. That DNA sample is put into a tube with tiny silica beads and placed into another machine—a bead beater, which does exactly what it sounds like. Eventually, lab staff places the extracted DNA into the thermocycler, which confirms the presence of a DNA from a specific species. In this case, Colón is looking for HF 183/BacR287—the DNA marker for human-associated bacteria.
This process of molecular source tracking is only one of the opportunities all this new equipment presents. The thermocycler can also identify the presence or absence of other species through environmental DNA (eDNA) analysis.
“Let’s say our Ecological Restoration team wants to know whether river herring have been swimming through or living in a section of a river,” said Colón. “We will be able to detect and quantify species of interest using a non-invasive and highly sensitive method of species detection.”
Save the Sound uses this information to drive action. Say the sample confirms the presence of river herring species in the water below a dam; we may prioritize removing that barrier to help the herring migrate further upstream to ancestral spawning grounds.
This expanded analytical capacity will help write a new chapter for Save the Sound’s water quality and restoration work across the region.
Save the Sound works across the Long Island Sound region to protect the Sound and its rivers, fight climate change, save endangered lands, and work with nature to restore ecosystems. More info at savethesound.org. ■
