For more than a decade, biologists have been picking away at a mystery: What caused a years-long decline of smallmouth bass in Pennsylvania’s Susquehanna River starting more than a decade ago?Biologist Vicki Blazer sorts slides holding tissues of smallmouth bass from the Susquehanna River in Pennsylvania. At the USGS Leetown Science Center near Kearneysville, WV, she’s studying the effects of parasites, disease and contaminants on young fish. (Dave Harp)

Some think they may have finally cracked the case. The results of recently published research, lauded by some as “the smoking gun,” points to a virus once thought not to affect smallmouth bass. In a series of laboratory experiments, scientists from Michigan State University found that largemouth bass virus can indeed be fatal to young smallmouth bass.

Others are not ready to stamp “case closed” on the mysterious die-off, saying the full explanation is much more complicated.

Biologist Vicki Blazer of the U.S. Geological Survey Leetown Science Center is one of them. Blazer has been leading a long-term study of wild bass from the Susquehanna. Her team of federal and state researchers has been working on the premise that multiple infections of disease and parasites caused the widespread deaths of young smallmouth bass that was first observed in 2005.

Those infections, she argues, may have been triggered by a brew of chemicals polluting the Susquehanna that weakened fish immune systems.

“The bottom line was, from site to site, there was no one pathogen that we were finding,” Blazer said. “Most of the places that had mortality had multiple pathogens. That led us to think that something was going on to be immunosuppressing those fish and making them more susceptible to disease.”

That’s not to say that largemouth virus isn’t the cause of the fish kills.

“The research has shown that the largemouth bass virus is capable of killing smallmouth bass at water temperatures that continue to exist in the Susquehanna,” said Coja Yamashita, a fisheries biologist with the Pennsylvania Fish and Boat Commission who worked with the Michigan lab during the study. “The virus is one piece of the puzzle, just a much larger part than we originally thought.”

Yamashita said that while there’s no way to remove the virus from the river, educating anglers and boaters is needed to help stop its spread. The virus was most likely transported by boats and equipment from other waters into the Susquehanna.

“As far as what Vicki Blazer is doing, there’s no doubt that contaminants in the water aren’t helping the situation,” he said. “Identifying which toxins are the worst for fish health — that’s something we can do something about.”

A new technique to analyze the immune response in fish tissue is helping Blazer’s research.

Using the new process, Blazer’s team can expose the tissue of healthy, laboratory-raised fish to one stressor at a time — whether chemical, parasite or disease —and view the type of cells that it produces. Researchers compare the results with fish tissue collected in the wild to gauge the severity of the effects each stressor has on the ability to fight disease. The process may also reveal whether certain stressors play a larger role in immunosuppression.

“It is very complicated to understand these things in the wild,” Blazer said. “But until you start looking at them in the wild, we will never understand them.”

Young smallmouth bass in an experimental pond at Leetown Science Center are used to compare tissue samples with other smallmouth bass caught in the Susquehanna River that experienced unusually high mortality rates for a period of time. All fish are captured and humanely euthanized to look for pesticides, herbicides, parasites and diseases in the tissue of various organs under a microscope. (Dave Harp)

When the problem first became evident in 2005, young fish hatched in the spring were found dead and dying in July and August in the middle and lower sections of the river. The number of young that never grew to adulthood led to fewer fish being “recruited” into the population, said Geoff Smith, Susquehanna fisheries biologist for the Pennsylvania Fish and Boat Commission.

“This was not a typical crash,” Smith said. “Populations bounce back pretty quickly. What happened in 2005 was not a one-off thing. We were waiting until the next year for it to be all over with, but it [was not] over by 2006 or 2007.”

The affected area stretched nearly 100 miles from the confluence of the West and North branches to York Haven near the Maryland border. Deaths also occurred in the lower Juniata River, the Susquehanna’s largest tributary.

To stem the loss, the Pennsylvania Fish and Boat Commission allowed only catch-and-release fishing for smallmouth bass starting in 2011. The next year, the commission also banned fishing during the spawn, when female bass lay eggs and males guard the nest — to alleviate the stress of being hooked while reproducing.

The population began to rebound in 2016 but, as with the deaths, the cause is unclear. According to annual commission surveys, the prevalence of disease and parasite infections has declined in the last five years, and more fish are surviving past their first year. From 2005 to 2012, up to 70 percent of the fish surveyed were visibly sick, compared with up to 10 percent from 2013 to 2018.

Biologists sampling the river with electrofishing gear saw nearly four times as many adult smallmouth bass last year in the middle Susquehanna than in any one year since 2005.

The U.S. Environmental Protection agency gathered experts in 2015 to brainstorm theories on the possible causes of the population crash. Participants came from state and federal government, nonprofit organizations and academia. Using available data and research, the group narrowed down the likely causes to the presence of endocrine disruptors — many of which originate in pharmaceutical and health care products— and herbicides in the water, as well as pathogens and parasites.

Blazer led a group of researchers from 2007 to 2012 who examined Susquehanna smallmouth collected from four basins of the river. A paper compiling those data was published in April, about the same time as the Michigan State University study.

Research from the Blazer team established that the 2– to 3-month-old fish had been exposed to a plethora of substances, diseases and parasites. The diseases ranged from parasitic flat worms, commonly found in rivers, to multiple bacterial infections and largemouth bass virus. Few young fish were found with only one infection; in fact, many had three or more different infections.

Passive water monitors collected samples at the same time fish were collected in spring and early summer. Thirty-four chemicals were found in the water. Of those 34 chemicals, 32 were found in the tissues of fish. Some contained as many as 10 to 34 compounds.

Blazer still sounds surprised when she talks about the amount of contaminants picked up by these fish. “Remembering these fish are only 2– to 3 months old, they are accumulating contaminants very quickly,” she said. “Yet we don’t know, what is the level of a PCB or a pesticide that is going to cause disease?”

Blazer and her team found that the number of “co-infections” differed between sites on the river. Also, the fish with more diseases also had a greater number of chemicals in their tissue. For example, young-of-the-year from the Juniata River and lower and middle Susquehanna River had both more co-infections and more agricultural chemicals than those in the West Branch. Fish from the West Branch and its tributaries had some of the lowest rates of co-infections, skin lesions and infections, and there were fewer hormones and agricultural chemicals in their tissue.

The results of these tests were compared with those of fish collected from a test pond, where no disease has been reported. The fish collected in those waters had a much lower occurrence of disease and contaminants.

“Throughout this whole process, we’ve come at the problem with the assumption that this is the link, that there is some kind of immunosuppression,” said Smith, the Fish Commission biologist. “They didn’t have a way to test that, until now.”

According to Blazer, there are 400 different types of land-use attributes in the Susquehanna River valley. From the small river towns on the Juniata River to the cities of Harrisburg, York and Lancaster along the lower Susquehanna, stormwater runoff carries debris and chemicals into waterways.

Staff from the USGS are compiling and mapping the data on each of those land uses — including pesticide, herbicide and fertilizer use — to compare them with the results of water quality sampling that will take place every two weeks this summer. This information will be further combined with weather data, to examine the impacts of stormwater runoff, as well as new data gleaned from studies on stressors to young fishes’ immune systems.

The goal is to cross-reference what happens on the land with the presence of chemicals in both water and fish tissue.

Added to this round of research is the examination of nutrient levels in the water. An abundance of nutrients can affect which organisms thrive and which ones suffer, including algae and bacteria. Nutrients can also cause infections within the fish to grow faster, further degrading their tissue.

Nutrients, combined with warm summer weather and the relatively shallow waters of the river, create the perfect recipe for an explosion of some pathogens that could compromise fish health. In fact, in 2005, fish commission biologists first thought that the bass were dying from an outbreak of columnaris — a common infection fish contract when water is low and warm. That year the water was low enough to reach 85 degrees in the summer. It also followed two years of high rain — and increased runoff. Columnaris was found in the earlier study but never by itself.

Researchers will also explore whether young, contaminated fish are born from contaminated eggs or whether they acquire the contaminants from the water column. Some chemicals, like the herbicide atrazine, do not build up in fatty tissues like eggs. If a fish tests positive for atrazine, then it came from the water column.

But tracking the source of contaminants is still difficult; the pollutants may not originate in areas of the river where the fish are found. Adult bass tend to move long distances, Smith explained. A female who breeds in the river near Harrisburg could potentially carry her eggs to another river segment and bring the contaminants with them.

Blazer’s team is trying to pinpoint what management options could possibly relieve some of the stress on the fish. In looking at many risk factors at once, Blazer said, the possibility increases of learning which pollutants or diseases have the greatest impact on smallmouth bass — if any.

People get caught up in finding a single cause, Blazer said, but “from what our data tells us, there is not one cause. I just hope I get to finish this thing before I retire.”