Why are the bats dying?

Thousands of sick and dying bats are being found in caves in New York, Vermont and Massachusetts. These are mostly Myotis lucifungus (the fairly common little brown bat) but at least three other species, including the endangered Myotis sodalis (Indiana bat) are affected as well.

But why?

So far, nobody knows. Bacteria, viruses and toxins have been tested for, and researchers thing an infectious disease of some kind is the most likely cause, but positive results remain elusive. according to Beth Buckles, assistant professor of biomedical sciences in Cornell's College of Veterinary Medicine,

"We have some good leads. We are continuing to look for infectious causes and are developing protocols to assess the bats' metabolic states. They may not have enough fat to make it through the winter"

Many of the sick bats have a white fungus growing on their faces, are very thin, and tend to hang out around the cave entrances, which is what sick bats are prone to do. People who find sick bats are encouraged to avoid handling it (a good idea generally with bats), but to call their state Department of Environmental Conservation.

[source]