CAPITAL REGION — Zebra mussels arrived in the United States 20 years ago and quickly spread throughout the country. By 1989, they had made their way to New York; a year later, they were already causing problems.

Considered an invasive species, the tiny mollusk is notorious for clogging the intake pipes of power plants, and damaging boats and harbors. The only way to get rid of them was by using highly toxic, polluting pesticides.

But that’s about to change.

A New York State Museum researcher has created a non-toxic alternative pesticide, using a natural bacterium that zebra mussels can feed on in small quantities, but will kill them if they eat too much of it.

“Anything that kills a pest is considered a pesticide,” said Dr. Daniel Molloy, director of the Museum’s Field Research Laboratory in Cambridge. “This is not a chemical pesticide. This is a biological pesticide.”

The pesticide, which also kills the invasive quagga mussel, a relative of the zebra mussel, is likely to be available next year. Though it was invented and patented by the New York State Museum, it will be sold by the Museum’s commercial partner, Marrone Organic Innovations, based in Davis, Calif. Earlier this year the company received a $500,000 National Science Foundation grant to commercialize the pesticide, and the New York State Museum received $275,000.

“[Zebra and quagga mussels] are a very big problem,” said Pam Marrone, founder and CEO of Marrone Organic Innovations. “They increase costs dramatically. You can use chlorine to take care of them, but chlorine is [toxic].” She said the biopesticide will not harm the environment, because using it does not pose the same types of risks as using toxic chemicals.

In the 1980s, Molloy helped develop a biological pesticide that was used to kill black flies. Previously, he said, black flies in the Adirondacks were killed by spraying a chemical pesticide out of airplanes. A decade later, the state Department of Environmental Conservation approached Molloy and asked if he would be interested in trying to develop a non-chemical pesticide for zebra mussels.

Molloy knew little about mussels or clams — “I said, ‘I’ve never worked on mussels or clams before,’ ” he recalled — but was willing to give it a try. In 1991, a group of power companies provided the start-up money for the project, a $700,000 six-year grant.

The project was almost canceled several years later.

Molloy had looked at more than 700 strains of soil bacteria, hoping to find a strain that would kill zebra mussels, but his efforts were fruitless. He told the power companies he wasn’t sure he should continue, but they told him to keep working. It was good advice. Within two months, he found the strain of bacteria that worked: Pseudomonas fluorescens.

Zebra mussels feed on Pseudomonas fluorescens as a matter of course, but a larger-than-usual amount of the bacteria, which is naturally present in lake water, can kill them.

“It’s a question of dose,” Molloy said. “If you go to a pipe, and add a million times more [Pseudomonas fluorescens], and create artificially high densities of bacteria, they will feed on it until they die.”

Denise Meyer, the New York State Museum’s chief scientist, developed the culturing methods to grow Pseudomonas fluorescens so that it would be as effective as possible. Scientist Mike Gaylo developed the protocol for treating zebra and quagga mussels with Pseudomonas fluorescens.

Power companies, in particular, were interested in Molloy’s project.

Although hot water can kill zebra mussels — “If you’re up above 85 degrees, you’re in the lethal zone,” said Molloy — most power plants are unable to circulate hot water throughout their pipes, and it would be expensive to retrofit the plants so that they could do that.

“Most infrastructures rely on a broad spectrum of chemicals to clean out the pipes,” Molloy said. “It’s very effective, but it’s highly risky.”

Molloy said the biopesticide could also be in other contained places, such as fish hatcheries, but right now there is no way to use it in a large open water body. “That’s still unexplored,” he said, adding that it would be possible to seal in a marina and flood it with the biopesticide to kill the mussels.

Early next year, the U.S. Bureau of Reclamation will demonstrate the use of Pseudomonas fluorescens at Davis Dam, on the lower Colorado River in Bullhead City, Ariz. “They want to know if [Pseudomonas fluorescens] can be used in a dam to kill quagga mussels,” Molloy said.

Zebra mussels are native to Russia, but came to the U.S. by way of Europe. They were first discovered in the Great Lakes. Locally, Ballston and Saratoga lakes are infested with zebra mussels, as are Lake George, Lake Champlain, Lake Ontario and Lake Erie.