A panel of independent scientists has affirmed in a new report that ammonia from urban wastewater is a "likely" contributor to environmental shifts in the Sacramento-San Joaquin Delta.

But the panel, assembled by the CalFed Bay Delta Authority, says more research is needed to determine where ammonia fits among numerous threats to the estuary.

The Bee reported last year on emerging research suggesting that ammonia from treated urban sewage, discharged continuously into Central Valley rivers, may disrupt the Delta food chain. The Sacramento metro area's wastewater, treated by the Sacramento Regional County Sanitation District, is the largest source of ammonia in the Delta.

But the research has been hotly disputed by the sanitation district and others. So CalFed agreed to host an independent review of existing science.

That review, released last week, raises more questions than it answers. But significantly, the four scientists on the panel conclude the subject merits further study as a potentially significant factor in the degradation of Delta.

Increased ammonia "likely has led to major modification" of the estuary to favor foods less nutritious to fish as well as toxic algae blooms, the panelists state.

Numerous Delta fish species have been in a death spiral since about 2001. Leading the pack are the Delta smelt, longfin smelt, threadfin shad and striped bass. A more charismatic victim is the Central Valley fall-run chinook salmon, whose collapse caused fishing bans this year and last.

Declines in the smelt species triggered new rules that cut water exports from the Delta, aggravating drought conditions in some parts of the state. Those exports are one suspect in the Delta's decline, along with water pollution and foreign species.

State and federal agencies have spent millions of dollars researching the problem but have not found a smoking gun. They believe many factors are at work, and it now seems they must add ammonia to that list.

The chief concern is not whether ammonia kills fish. Instead, the volume of ammonia may have grown so large from urbanization that it is upsetting the natural food chain.

"We now have better reason to believe that it (ammonia) is perhaps an important suspect, but we still don't know exactly its role among the huge number of suspects we have here," said Anke Mueller-Solger, a CalFed lead scientist investigating the species' declines.

Ammonia is a natural byproduct of human urine and feces. In the sewage treatment process, it typically gets converted into an ionized form called ammonium. But this isn't removed by so-called "secondary" sewage treatment systems like Sacramento's.

Many other sewage treatment entities have upgraded to more advanced "tertiary" systems that do remove ammonium. But the Sacramento district maintains this higher level of treatment would cost as much as $1 billion. It is reluctant to impose that cost on ratepayers without proof that ammonia harms the Delta.

The district manages the sewage of about 1.4 million people in the capital metro area and discharges treated wastewater into the Sacramento River near Freeport.

"Overall, they're saying it's a possibility that ammonia has played a role in the shift in the ecosystem over time," said Stan Dean, district chief of policy and planning. "But they don't go so far as to specify any shifts, how they work their way up or down the food chain, whether they're good or they're bad."

The panel does not point a finger at any ammonia source. Instead, it says many sources should be investigated, including ammonia that may come from farms and wetlands.

Sacramento's ammonia discharge set a new record last year, averaging 30,780 pounds daily. It is one component of a much larger wastewater volume it pumps continuously into the Sacramento River.

The agency has an expansion plan pending before the Central Valley Regional Water Quality Control Board to handle population growth. Board officials have been keenly interested in the ammonia problem as a factor to consider in reviewing the expansion.

Call The Bee's Matt Weiser, (916) 321-1264.