The dramatic declines are due to a fungus that attacks the bats during their winter hibernation in caves and abandoned mines. The outbreak is called white-nose syndrome for a white fuzz the fungus produces on the nose, ears and wing membranes of infected bats.
"It's definitely worsening," said MacKenzie Hall, a Conserve Wildlife Foundation biologist who runs the summer bat count for the state.
At several summer roost sites in Mahwah, for instance, populations dropped by 47 percent to 100 percent from the historical average. One site that used to have 139 bats had none this year.
New Jersey officials have estimated an overall 90 percent decline in the state's hibernating bat population.
Last winter, when Mick Valent, principal zoologist with the state's Endangered and Non-game Species Program, visited Morris County's Hibernia Mine, he found only about 1,700 bats alive, in a hibernation spot that historically housed 30,000.
"Some scientists are projecting the likelihood of the complete loss of a functioning population of little brown bats within the next 16 to 20 years," said Jeremy Coleman, the U.S. Fish and Wildlife Service's national white-nose syndrome coordinator. "This is unprecedented. We've never seen a decline in a species equal to this aside from those caused by human intervention, such as with the American bison."
The declines in New Jersey mirror death rates elsewhere.
The fungus has killed more than a million bats of six different species in 12 states and two Canadian provinces, and some experts believe the number is far higher, as much as 1.5 million dead. The fungus was first discovered in a cave near Albany, N.Y., in 2007 and now has spread as far west as Oklahoma.
"It's spreading across the country faster than scientists thought," said DeeAnn Reeder, a Bucknell University biologist who is studying the outbreak. "We're all behind."
The little brown bat species is the hardest hit in New Jersey and elsewhere.
The widespread loss of bats has potential ramifications for humans, since bats consume huge quantities of bugs, including insects that damage crops or carry West Nile and other potentially fatal diseases.
Scientists think humans who visit caves may inadvertently spread the fungus from cave to cave. To try and halt the spread, government agencies across the country have been closing access to caves and abandoned mines.
"People are getting desperate to do something," Reeder said.
In New Jersey, the Conserve Wildlife Foundation has teamed with owners of 15 forest areas in the northwestern part of the state, including one site in West Milford, to create more habitat for bats.
One endangered species, the Indiana bat, roosts in summer under the loose bark of dead trees and switches roosts every few days. "A lot of New Jersey woodlands are under management, so the dead and dying trees are the first to get cut down," Hall said.
The owners of the forested areas in the program will girdle some trees to kill them so they provide more roost sites, or attach cedar shakes and other items to tree trunks to create roost spots, Hall said.
Reeder said she has little faith in finding a treatment option, such as a chemical, that could be successfully applied in the caves. The caves that bats use for hibernation also contain many other living organisms that could be harmed by whatever might kill off the fungus.
Another option might be to raise bats in captivity in an artificial chamber where scientists could control temperature, moisture and other factors. "But that option is labor-intensive and possibly not a good long-term fix," Coleman said.
Some bat species, such as the big brown bat, are less vulnerable to the fungus, perhaps because of their hibernation behavior, said Bucknell's Reeder.
Unlike little brown bats, big brown bats go into hibernation later and emerge earlier, providing less time for the fungus to grow. In addition, big brown bats tend to hibernate in the coldest parts of caves, where it is too cold for the fungus to thrive, Reeder said.
If researchers can somehow lower the temperature of a cave using tubes that force cold air in, it could improve survival chances for little brown bats, Reeder theorizes. "But I'm not sure whether that would be a good option or even possible," she said.
European bats have managed to survive despite the presence of white-nose syndrome there for three decades.
Experts think human spelunkers somehow transported the fungus from a European cave to one in North America by carrying the fungus spores on their clothing. The result has been something similar to what occurred when European explorers arrived in America and spread smallpox to Native American tribes that had no resistance to the disease.
"No one has seen anything like this," Reeder said. "This fungus has found the Achilles heel of bats. They have no immune system to combat a cold-loving fungus when they are hibernating in the cold of caves and mines.
"You can go into a cave and see a thousand bats completely affected by the fungus," Reeder said. "And meanwhile you're crawling on bat carcasses, and the smell is overwhelming. It's incredibly depressing."
"The little brown bat is the most common bat in North America. Their disappearance would be similar to suddenly losing gray squirrels or robins," he said.