The role of sediment in nitrogen cycling and hypoxia (fact sheet)

A woman wearing blue gloves standing on a boat sorting through sediment in a collection box. Water and clouds in the background.
Collecting sediment samples from Puget Sound. Photo: WA Department of Ecology (CC BY-NC 2.0)

How do marine sediments affect oxygen and nutrient levels in the water?

Nitrogen and phosphorus enter marine sediments either by diffusion from the water column or as part of organic particles that settle on the surface. Once nitrogen is in the sediment it can either be buried, be converted to nitrogen gas by bacteria (a process known as denitrification) or re-enter the water column. Similarly, phosphorus can be buried in the sediments, absorb onto iron oxides, or diffuse back out into the water column. By measuring the mass balance of nutrients entering and leaving the sediment, researchers can estimate some biological and biochemical processes happening in the sediments without measuring them directly.

What happens to carbon and nutrients once they enter the sediment?

In the top few millimeters of sediment, organic matter is broken down by aerobic bacteria, a process that consumes oxygen. Deeper down, it is decomposed by anaerobic bacteria using a suite of nitrogen, manganese, iron, and sulfur-containing compounds. If these compounds are later brought back up to the surface of the sediment, for example by animals digging burrows, they can become reoxidized, again consuming oxygen in the water.

The breakdown of organic matter by both aerobic and anaerobic bacteria produces dissolved inorganic carbon – essentially, carbon dioxide. This means that the amount of dissolved inorganic carbon entering the water from the sediments is a measure of the breakdown of organic matter. Overall, researchers expect that the amount of oxygen entering the sediments should be roughly equal to the amount of carbon coming out.

How much oxygen is taken up by sediments in Puget Sound?

The first measurements of oxygen consumption by the seabed in Puget Sound were made about half a century ago, mostly in the Main Basin. Since then, there has been scattered work on nutrient and oxygen exchange between the water and sediments, mostly from shallow inlets, but there is no comprehensive picture or even a sense of the average.

“This is a significant gap in the understanding of how the sediments affect water quality in Puget Sound,” says David Shull, an oceanographer at Western Washington University in Bellingham. Shull spoke at a workshop on oxygen and nutrient exchange in Puget Sound sediments.

To fill in some of the picture, Shull and his collaborators conducted a large-scale survey in April and May of 2018, collecting sediment cores to measure dissolved oxygen, dissolved inorganic carbon, pH, various forms of nitrogen, phosphorus, and silica at 40 locations throughout the Salish Sea.

On average, oxygen consumption by the sediments was greater than carbon released by the sediments, the researchers found – an unexpected result. This pattern was particularly pronounced at sites where the release of carbon is relatively low.

It may be that some of the oxygen consumption by the sediment reflects re-oxidizing of older compounds; essentially, there is a time lag that decouples organic matter breakdown from oxygen consumption. In support of this, higher dissolved oxygen consumption is also correlated with higher hydrogen ion production (re-oxidation of stored compounds produces hydrogen ions).

The researchers also found little relationship between the amount of organic matter being broken down in the sediment and the amount of nitrogen released into the water. At most sites, the amount of nitrogen entering the water was less than would be expected based on the amount of organic material being broken down in the sediment, suggesting that some process going on in the sediment inhibits release of nitrogen into the water.

They found a similar pattern for phosphorus: in general, phosphorus that enters the sediment stays there.            

How does oxygen consumption by sediments vary in different areas?

In the 2018 survey, oxygen consumption rates tended to be lower in deep areas of the Main Basin and Hood Canal. Oxygen consumption was higher in some shallow embayments such as Budd Inlet, near Lopez Island, and Bellingham Bay. But some shallow embayments, such as Commencement Bay near Tacoma, exhibited lower oxygen consumption.

Similarly, some sites with high oxygen consumption also have high rates of carbon dioxide leaving the sediment. But some, such as Budd Inlet, show high oxygen consumption but relatively low rates of dissolved inorganic carbon production.

Generally, Puget Sound sediments release ammonium and take up nitrate. But the movements of different forms of nitrogen vary greatly from one site to the next, as does the rate of denitrification. It’s not yet clear what is driving all these differences from place to place.

How does oxygen consumption by sediments relate to overall oxygen consumption in Puget Sound?

Understanding how sediment processes relate to the overall balance of oxygen in Puget Sound requires understanding oxygen consumption in the water column. Measuring the oxygen consumption rate, also called the respiration rate, is relatively straightforward with techniques that have been standard for a century: collect a water sample, and track how fast the oxygen is consumed. But this information is lacking, especially for the Main Basin of Puget Sound.

Based on measurements from water samples collected in summer, “about 10% of the oxygen consumption in the Whidbey Basin is from the sediments, and about 20% of oxygen consumption in the South Sound and Hood Canal are due to sediment processes,” Shull reports. In general, the deeper the water, the less the role of the sediments will be.

Preliminary calculations also suggest that nitrogen burial and denitrification have similar impacts on the nitrogen levels in the water column. These factors appear to be especially important in Hood Canal, due to the long residence time of water in that fjord.

What are the dynamics of sediment oxygen and nutrient flow in Bellingham Bay?

Shull has also coordinated hydrographic surveys to measure nutrients in Bellingham Bay for the last 15 years. His team conducted a more in-depth study of 25 sites throughout the bay in June 2017, and tracked nutrient exchange with the sediments over the course of a year at one of the sites.

Nearly 95% of the nitrogen supplied to Bellingham Bay is from deep marine water flowing into the bay. About 4% comes from the Nooksack River, and less than 2% is from a wastewater treatment plant near the shore of the bay.

About 11% of the nitrogen input to Bellingham Bay is lost due to denitrification, the team calculated. The bay has relatively rates of denitrification than compared to other sites in Puget Sound.

What are the remaining gaps in understanding oxygen and nutrient dynamics in Puget Sound sediments?

Scientists say more studies are needed to understand how sediment oxygen and nutrient dynamics vary seasonally, especially in deep basins.

Studies also need to sample Puget Sound sediments much more broadly and densely. “Sediment cores show high variability even among replicants and if you think about it, these sediment cores are eight centimeters in diameter,” Shull says. “And we're drawing conclusions about the Main Basin of Puget Sound based on tiny sections of the sediment.”

Existing data suggest that the sulfur cycle may strongly influence dissolved oxygen uptake by sediments, but sulfur dynamics in Puget Sound are not well understood.

There’s also a need to continue to understand the drivers behind the spatial variation in sediment dynamics. It may also be useful to measure sediment dynamics in areas that are known to become seasonally hypoxic.

How are these processes being incorporated into models?

Researchers are starting to incorporate sediment dynamics in ocean modeling, such as the Live Ocean Model  of Pacific Northwest coastal waters. Currently, the model is primarily set up to reflect sediment dynamics in the waters of the continental shelf and may need to be further calibrated to better reflect processes in the inland waters of the Salish Sea, says Parker MacCready of the University of Washington, who also spoke at the workshop. For example, “It's possible that there's more burial of organic matter inside the Salish Sea, because there's just less wave resuspension,” he says.

The Salish Sea Model also captures sediment dynamics, based on a widely used module that is also used in Chesapeake Bay and EPA water quality modeling. Modelers are working to improve the module by validating it against observational data and exploring how sediment dynamics may change in response to changing levels of nutrients, says Puget Sound Institute researcher Stefano Mazzilli, another workshop speaker.

The current iteration of the Salish Sea Model shows higher sediment oxygen demand in shallow embayments and lower demand in deeper basins, consistent with the data Shull’s team recently collected. “I was somewhat relieved to see” those results, says Tarang Khangaonkar of the University of Washington’s Salish Sea Modeling Center, a participant at the workshop.

Funding for this fact sheet was provided by King County as part of a series of online workshops addressing scientific uncertainities around nutrient pollution and hypoxia. 

About the Author: 
Sarah DeWeerdt is a Seattle-based freelance science writer specializing in biology, medicine, and the environment. Her work has appeared in publications including Nature, Conservation, and Nautilus.