Tracking invasives, CSI style
LANSING – Great Lakes researchers from Notre Dame, Central Michigan and Michigan State universities are using new environmental DNA techniques to track down and control the spread of invasive species.
Their techniques are like what you see on CSI television dramas where scientists analyze DNA left at the crime scene and use it to prosecute the culprits.
Well, not quite. Fiction is faster, the scientists say.
“What it does, though, is it makes you jealous of how they’re able to solve crimes in an hour, because it doesn’t happen that way,” said Christopher Jerde, a professor at Notre Dame, which is creating a basin-wide surveillance program. “That would be nice.”
The scientists are searching for invaders’ eDNA with techniques that may be a boon for understanding how they enter the Great Lakes basin.
For instance, researchers collect water samples for DNA analysis at streams and tributaries leading into the lakes, especially areas they believe Asian carp may be poised to invade.
When evidence of alien carp was found beyond the Chicago Area Waterway System’s electric barrier in an earlier study, it signaled a larger issue: “The problem is nobody’s really looking for these things in other places,” Jerde said.
“What eDNA has done is spur at least some coordination to start getting serious in the Great Lakes basin,” he said. ‘We need to be looking for invasive species, not just haphazardly but going out there, bringing tools that are sensitive, getting early detection of these invaders, because if you ever want a chance at preventing an invasion or controlling an invasion, you got to get them at low abundance.”
The good news is that after almost a thousand samples there were no positive tests of bighead or silver carp in southern Lake Michigan, other than the canal system, he said.
Lake Erie sampling, however, did disclose such evidence.
“But it’s not that surprising,” Jerde said. “We got some detection for bighead and silver in Sandusky Bay, but not a lot.”
At least three bighead carp were caught in Lake Erie, Jerde said.
In another study, Central Michigan researchers are searching for invasive pathways into Lake Erie from the Erie Canal corridor that spans New York between Whitehall in the east to Buffalo in the west. They’re cataloguing nonnative species in the Mohawk-Hudson River and Lake Champlain basins that have potential to spread into the corridor.
One priority is to examine the range of snakehead, a voracious and highly competitive fish that could have dramatic effects on the Lake Erie ecosystem and even the Great Lakes at large, said Central Michigan biology Prof. Andrew Mahon, the study’s principal investigator.
Another goal is examining the genetic technology itself by analyzing and comparing its use across other species, such as Asian clam and the aquatic plant hydrilla.
“We know the eDNA works really well with fish, we’ve shown that with our Asian carp work,” said Mahon. “We know that if we go out and do ballast water surveys and try to compare that to the genetics, the genetics tends to work really well.
Many of these studies, which are funded through the Great Lakes Restoration Initiative, aim to refine existing environmental DNA technology so new techniques and applications can be developed.
Traditionally, scientists examine environmental DNA by taking water samples back to a lab. All living things – people and fish included – give off DNA to the surrounding environment in shed skin cells.
The analysis works like this:
First, scientists filter a water sample and pull out the DNA from everything they find, including bacteria, other fish and possibly the target species.
Then they identify a region of the DNA that is specific to the organism they’re looking for. They amplify it by making lots of copies and then load the DNA into a special gel with a florescent dye.
Scientists can then send the DNA into a sequencer that reveals all the chemical building blocks of that DNA. Those blocks can then be matched with the DNA of the target organism.
Jerde said, “We joke that we often wish we could just plug something into our iPhones and drop it into the water and say ‘Yeah, there’s an app for that,’ that tells you there’s a species there.'”
Researchers may be five years away from just that kind of technology, he said. In fact, some studies funded by the initiative may help real researchers rival their fictional television counterparts.
Notre Dame biologist Scott Egan is leading another study to make the technology portable and relatively real-time.
And Syed Hashsham, a civil and environmental engineering professor at MSU, is conducting a similar study.
Portability is important because it let scientists conduct field tests without hauling thousands of gallons of water back to a laboratory, Hashsham said.
“You could take a lot) of water, concentrate it and send it to some centralized facility for analysis, but then it becomes an issue of how many locations you want to analyze, how do you transport that concentrated water and other things,” he said.
The device his team is developing for the field is made to eliminate a lot of these and other processes, he said.
All those measures save time, which is vital in the race against invasive species, he said. “If we catch them early, only then do the control mechanisms have any hope of eliminating them or controlling them.”