State officials issued a second set of alleged violations Tuesday against a manure processing plant that spilled more than 400,000 gallons of animal waste when pipes burst on three occasions since November.

The Wisconsin Department of Natural Resources told the Clear Horizons biodigester it must increase staffing at the plant near Waunakee and provide better explanations for the spills and for the plant’s worsening record for reducing phosphorus from manure that is spread as fertilizer on farm fields.

The troubled Clear Horizons biodigester generates electricity by burning methane that bubbles up from nearly 4 million gallons of animal waste stored at the site. The manure is also processed to reduce nutrients that run off farm fields and foul lakes with unnatural tangles of rank-smelling vegetation.

The plant’s state permit requires that 60 percent of phosphorus be removed from the manure. Clear Horizons averaged 63 percent in 2011, 56 percent in 2012 and 44 percent last year, company reports indicate.

The company said it is considering new equipment that could do a better job of reducing phosphorus, according to a DNR document released Tuesday.

Permit violations can bring fines of up to $10,000 per day, but the DNR is trying to negotiate a settlement that would lead to improved performance.

“Everybody who is concerned about water quality in Dane County sees this (biodigester) as a real vital piece of that effort and wants this concept to work,” said DNR spokesman Bob Manwell.

The facility’s woes began to come to light in November, when a section of curved pipe near a pump house burst and 380,000 gallons of manure poured out.

Some reached Six Mile Creek, more than a mile away. Another pipe failure in the same spot let loose 22,000 gallons in January. Unlike the first spill, employees were on duty to stop the flow of manure.

A consultant recommended alarms and automatic shutoff valves, but the company hasn’t announced any such changes.

On Jan. 29 the DNR alleged that the two spills, the company’s record on phosphorus, and other problems were in violation of the permit. On March 12, a day after the DNR and the company met to discuss the allegations, a different pipe ruptured and released about 35,000 gallons.

The second violation notice covers that spill and a new phosphorus report covering 2013.

Jim Ditter, CEO of Clear Horizons owner PPC Partners, didn’t respond to requests for comment.

The $12 million plant was built in 2010 with government subsidies.

Dane County officials say that because it serves three nearby farms, it is the state’s first community biodigester.

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