Two years after bacteria caused Gaithersburg to shut down its biodiesel pumps, the city is using the fuel again.

Gaithersburg refilled its biodiesel fuel tank at the Public Works Department pumping station in May after stopping the biofuel program in November 2008 when a bacterial buildup in the fuel tank began clogging the filters on the city’s trucks, haulers and street sweepers.

For the past two years, the department has been researching how to improve biodiesel storage and maintenance for the vehicles that use the fuel, said Jim Arnoult, the city’s public works director.

The city’s new biodiesel blend, called B5, is 95 percent petrodiesel and 5 percent soy-based fuel.

By using a biofuel made only from petrodiesel and soybeans, instituting annual $900 tank cleanings and adding a biocide — a chemical that will kill the bacterial buildup caused by the fuel — to the tanks, the city hopes to avoid any further problems with the fuel, said Mark Scafide, the city’s biodiesel project manager.

“We just felt like it was a good and environmentally friendly thing to do,” Arnoult said of the city’s desire to restart the program.

About 15 public-works vehicles, including dump trucks, are using the biodiesel as part of a trial program, Scafide said. Smaller pickup trucks and other vehicles that had problems with biofuel in 2006 and 2007 will be run on regular diesel, he said.

If the trial goes well, the city hopes to move to a blend of biodiesel called B20, which is 20 percent plant-based fuel. B20 was used in the original program, Scafide said.

“That is important,” he said. “That will help to reduce our use of foreign oil by 20 percent.”

He would not say how much the new program will cost but said that the most recent fuel deliveries came in at $3.08 a gallon for regular diesel and $3.19 a gallon for B5.

The city is also saving money by transitioning its police cruisers from using a premium blend to a less expensive, 87 octane fuel, Scafide said.

“Then again, all fuel prices are going up this year,” he said.

The city passed a budget this month that included a $200,000 contingency fund to cover increasing energy bills.