The spill-plagued Clear Horizons manure processing plant near Waunakee is now facing nearly 90 alleged air pollution violations on top of a slate of water pollution problems regulators want a judge to remedy.

The plant’s electrical generators are belching excessive amounts of toxic formaldehyde and acid-rain inducing sulfur dioxide, according to a notice of violations dated Wednesday and released Friday by the state Department of Natural Resources.

Operators also have failed to promptly notify the state about excessive emissions, didn’t sufficiently test generator exhaust, neglected to seek air pollution permits for other machinery and didn’t comply with requirements for annual reports in 2011, 2012 and 2013, the DNR said.

The air pollution problems come on the heels of three spills of more than 400,000 gallons of dairy manure over the past 12 months and findings that the biodigester isn’t removing enough nutrients from manure that is spread on farm fields.

State regulators this month asked the state Department of Justice to take court action against Clear Horizons related to the alleged water pollution violations at the plant, which was built in 2010 for $12 million including tax subsidies. The plant is designed to generate sustainable energy while keeping manure-borne nutrients from fouling the lakes.

The state can levy fines of up to $1,000 a day for violations, or close the plant .

The Milwaukee-based company will have an opportunity to respond to the air pollution notice and make changes before the DNR will consider sending the allegations to DOJ for enforcement action.

Jim Ditter, CEO of Clear Horizons owner PPC Partners, couldn’t be reached Friday.

After the DNR referred the water violations for enforcement, Ditter said the company was confident in the steps it has taken to bring the plant into compliance, but he declined to provide details.

The Clear Horizons facility at 6321 Cuba Valley Road in the town of Vienna has three, 1.25-million-gallon tanks that hold manure piped in from three dairy farms. Gases from the manure are collected and burned in generators to create electricity, which is sold to a power company.

The plant was designed to extract most of the phosphorus from the manure before sending it back to the farms to be spread on fields.

Phosphorus runoff from farm fields is the major cause of foul-smelling weed and algae growth in Dane County’s lakes. Manure runoff and spills can also deliver harmful bacteria to surface water.

DNR officials weren’t available to discuss the new air pollution allegations.

The notice of violations alleges that the plant exceeded limits for hydrogen sulfide in the gas it collected from manure 43 times in 2013. Burning hydrogen sulfide produces sulfur dioxide, which causes acid rain.

The plant’s 2013 air monitoring report shows hydrogen sulfide concentrations were within limits in only six or seven of 50 tests. In 17 tests, the concentration was nearly 38,000 parts per million, which is more than 100 times the allowed maximum.

The notice also alleges Clear Horizons failed to:

• Report the excess emissions and corrective steps on the next business day.

• Test generator engines for excess formaldehyde exhaust.

• Seek an emissions permit for fiber drying and ammonia condensing equipment, despite being told to do so during a June 27, 2012, inspection.

• Pay annual fees and comply with the law requiring annual air emission reporting.

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