Estuary News

October 2021

Tracking Natural Nitrogen Removal

Nitrogen inputs to the San Francisco Bay are among the highest of estuaries worldwide, yet so far have not caused harmful impacts like extreme algal blooms, oxygen depletion, and fish kills. But resistance to this nutrient may not last. Ever since the Gold Rush, excess sediment from pulverized rock has been pouring into the Bay, clouding the water and keeping algae in check by blocking sunlight. Recently, however, that protective sediment has diminished in parts of the Bay, contributing to concerns over nutrient pollution. A new study on a natural nitrogen-removal process is key to predicting whether nitrogen will cause ill effects here, too.

The Bay’s nitrogen comes primarily from sewage and, for the most part, this nutrient is not removed by the region’s wastewater treatment plants. Nutrient treatment is quite costly and has not been necessary in the region so far. But it may be in the future, as the sediment suspended in the water goes down and the region’s population goes up.

“The big question is should we be limiting the nutrients allowed to be discharged into the Bay?” says Tom Mumley, a chemical engineer who is Assistant Executive Officer at the San Francisco Bay Water Board, which regulates water quality in the Bay. “We need data, we want to get the science right.”

The fate of nitrogen in the Bay is complex. As various organisms consume this nutrient, it can cycle through a wide range of chemical forms including ammonium and nitrate, and can also be  incorporated into protein and DNA. The new research focuses on microbes in Bay sediment that transform nitrate into nitrogen gas, a process called denitrification because the resulting gas rises to the surface and releases harmlessly into the atmosphere.

“Denitrification is a natural remedy to the problem,” says project team member Ken Czapla, a biogeochemist at Stanford. “The Bay is helping itself.” That said, denitrification is just one facet of the fate of nitrogen in the Bay. The new study — part of a larger San Francisco Estuary Institute (SFEI)-led effort called the San Francisco Bay Nutrient Management Strategy — will help show how this natural remedy fits into the big picture.

The project — which entails punching sediment cores from the Bay and then bringing them back to the lab for analysis — was all set to go at the end of 2019. Then Covid hit, disrupting the research team’s plans. Collaborators on project include Stanford microbial ecologist Chris Francis and University of Maryland biogeochemist Jeff Cornwell.

Social distancing on the barge. Photo: Ariella Chelsky

“Our first big hiccup was finding a boat for safely collecting samples,” says project lead Ariella Chelsky, an SFEI environmental scientist, explaining that their usual research vessels are mostly enclosed with tiny decks that don’t allow for social distancing. The team scrambled for a back-up boat, ultimately hiring a private barge. “It was mostly open deck and allowed us to social distance,” Chelsky recalls. “We were very excited when we found it.”

The researchers collected sediment cores in clear tubes at nine sites in the South Bay, which is particularly nitrogen-rich. So far, they’ve sampled these sites in the winter, spring, and summer, and they plan to collect the final samples this fall. The sites are dotted around the South Bay and range from channels to shoals, which could reveal differences in denitrification by location and sediment type. Similarly, quarterly sampling could reveal seasonal differences in denitrification.

The next hurdle was that the team was barred from the Stanford lab originally planned for analyzing the sediment cores. So Chelsky decided to repurpose an SFEI garage into a lab. “It worked out surprisingly well,” she says, adding that they left the door open as a Covid precaution.

Garage lab in action. Photo: Ariella Chelsky

Stanford’s Czapla took the impromptu lab in stride. “We just rigged together stuff and got creative,” he says, adding that his doctoral work in salt marshes had taught him to improvise with whatever’s at hand. The garage lab is good enough that the researchers plan to continue using it to analyze the final set of sediment cores they collect in November.

Besides determining denitrification rates in the sediment, the researchers want to identify the underlying reasons for differences in those rates. “What’s driving the patterns that we see?” Chelsky asks.

While the results aren’t in yet, Czapla outlines some likely drivers. For example, denitrification is likely to vary with sediment type. The process only occurs when oxygen is not available, and oxygen penetrates faster and deeper into coarse-grained sediments like sand than into fine-grained sediments like mud. Denitrification is also likely to vary seasonally. The rate depends on temperature, which swung from a winter low of about 56°F to a summer high of about 71°F during sample collection in the Bay.

Field data like those generated by Chelsky, Czapla, and colleagues will help regulators by showing what actually happens to nitrogen after it’s discharged into the Bay. In turn, this will let sanitary sewer services install costly nitrogen treatments only if they’re actually needed rather than out of an abundance of caution.

“We could go full-throttle and implement traditional nitrogen treatments, but that has about a $12 billion price tag systemwide,” says Lorien Fono, an environmental engineer who directs the Bay Area Clean Water Agencies, which was formed by the region’s five largest wastewater treatment agencies. “Real-life data will tell us where best to spend limited funds.” Other potential approaches for nitrogen control include nature-based solutions, such as creating wetlands to help absorb nutrients from wastewater treatment plant effluent.

Collecting sediment cores. Photo: Ariella Chelsky.

Getting an accurate handle on the fate of nitrogen in the Bay will be increasingly important with the projected influx of people to the area. The regional population was 7.7 million in 2020 and is expected to reach 10 million by 2050, according to Plan Bay Area, a government-led effort to guide the region’s future. “The nutrients are coming from humans,” Mumley points out. “Even if the Bay is okay today, what happens as the population grows?” Nitrogen in the Bay is increasing by about 2 percent a year.

Fono is happy that wastewater agencies and the Water Board are working together to address  nitrogen’s potential to become a problem in the Bay. “It’s special to the Bay Area.” More is accomplished here than in places where dischargers and regulators have adversarial relationships, she says. “We all want the same thing — we all want the health of the Bay.”

Related Estuary Stories

More Links

SF Bay Nutrient Management Strategy

Top Photo: Working in the garage lab. Photo: Ariella Chelsky.

About the author

Robin Meadows is an independent science journalist in the San Francisco Bay Area. She’s a water reporter at Maven's Notebook, a California water news site, and contributor to Chemical & Engineering News, Ka Pili Kai, KneeDeep Times, and Scientific American. Robin is also a Pulitzer Center grantee, an Institute for Journalism & Natural Resources fellow, a contributor to The Craft of Science Writing, a mentor with The Open Notebook, and a UC Santa Cruz Science Communication Program graduate. Find her on Tumblr and Twitter.

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