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U.S. Geological Survey Open-File Report 2009-1286

Prepared in cooperation with the California Bay-Delta Authority and San Francisco State University

Benthic Flux of Nutrients and Trace Metals in the Northern Component of San Francisco Bay, California

By James S. Kuwabara, Brent R. Topping, Francis Parchaso, Anita C. Engelstad and Valerie E. Greene

Executive Summary

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Two sets of sampling trips were coordinated in late summer 2008 (weeks of July 8 and August 6) to sample the interstitial and overlying bottom waters at 10 shallow locations (9 sites <3 meters in depth) within the northern component of the San Francisco Bay/Delta (herein referred to as North Bay). The work was performed to better understand sources of biologically reactive solutes (namely, dissolved macronutrients and trace metals) that may affect the base of the food web in this part of the estuary. A nonmetallic pore-water profiler was used to obtain the first centimeter-scale estimates of the vertical solute-concentration gradients for diffusive-flux determinations. This study, performed in collaboration with scientists from San Francisco State University’s Romberg Tiburon Center for Environmental Studies, provides information to assist in developing and refining management strategies for the Bay/Delta system and supports efforts to monitor changes in food-web structure associated with regional habitat modifications directed by the California Bay-Delta Authority.

On July 7, 2008, and August 5, 2008, pore-water profilers were successfully deployed at six North Bay sites per trip to measure the concentration gradient of dissolved macronutrients and trace metals near the sediment-water interface. Only two of the sites (433 and SSB009 within Honker Bay) were sampled in both series of profiler deployments. At each sampling site, profilers were deployed in triplicate, while discrete samples and dataloggers were used to collect ancillary data from both the water column and benthos to help interpret diffusive-flux measurements.

Benthic flux of dissolved (0.2-micron filtered) inorganic phosphate (that is, soluble reactive phosphorus (SRP)) ranged from negligible levels (-0.003±0.005 millimole per square meter per day (mmole m-2d-1) at Site 4.1 outside Honker Bay) to 0.060±0.006 mmole m-2d-1 near the northern coast of Brown’s Island. Except for the elevated flux at Browns Island, the benthic flux of soluble reactive phosphorus (SRP) was consistently: (1) lower than previously reported for South Bay sites, (2) an order of magnitude lower than oligotrophic Coeur d’Alene Lake, (3) two orders of magnitude lower than determined for eutrophic Upper Klamath Lake, and (4) an order of magnitude or more lower than the estimated summer riverine inputs for SRP (900 to 1,300 kilograms of phosphorous per day (kg-P d-1)).

In contrast to fluxes reported for the South Bay, nitrate fluxes were consistently negative (that is, drawn from the water column into the sediment), except for one site with statistically insignificant nitrate fluxes (Site 409 within Suisun Bay). The most negative nitrate flux (-7.3±0.1 mmole m-2d-1) was observed within Grizzly Bay (Site 416). Observed nitrate fluxes bracketed the estimated summer fluvial flux of nitrate (3,500 to 5,000 kg-N d-1). With the exception of the two Grizzly Bay sites (416 and 417), the consistently positive benthic flux of ammonia generally counteracted the negative flux of nitrate to yield a net balance of dissolved inorganic nitrogen. Ammonia benthic fluxes extrapolated for Suisun Bay ranged from 320 kg-N d-1 (Site SSB009 near the entrance to Honker Bay) to 1,900 kg-N d-1 (Montezuma Island). These values represent a significant ammonia source to the water column relative to summer riverine inputs (approximately 400 to 600 kg-N d-1).

Dissolved silica also displayed a consistently positive benthic flux, except for Site 409 within Suisun Bay, which showed insignificant fluxes (also insignificant for nitrate and SRP). As with the nitrate fluxes, Grizzly Bay and Browns Island sites yielded the highest dissolved silica fluxes (1.3±1.2 to 2.5±0.6 mmole m-2d-1, respectively). These initial diffusive-flux estimates are greater than those measured in the South Bay using core-incubation experiments, which include bioturbation and bioirrigation effects, but they are nevertheless probably one to two orders of magnitude below summer riverine inputs.

In summary, riverine sources of SRP and silicate appear to overwhelm diffusive benthic fluxes. This is not true for the nitrogen species. Internal cycling of nitrate and ammonia in the Delta and Suisun Bay should not be disregarded, because the magnitude and direction of benthic sources and sinks for nitrogen species represent significant transport processes for these solutes. This finding may have particular relevance in this region of the estuary, where water-column clarity is gradually increasing and nitrogen-to-phosphorus molar ratios were consistently lower than the Redfield Ratio of 16.

Water-column concentrations for dissolved trace elements (for example, Cu, Ni, Co, Cd and Pb) were consistent with those reported by the San Francisco Estuarine Institute’s (SFEI) Regional Monitoring Program (SFEI 2009) at nearby stations. Diffusive fluxes for all trace metals, extrapolated over the Suisun Bay area, were insignificant compared to fluvial-flux estimates.

The diffusive-flux measurements reported herein serve as conservative (under-) estimates of benthic flux, because solute transport across the sediment-water interface can be enhanced by other processes, including bioturbation, bioirrigation, groundwater advection, and wind resuspension. They do, however, provide lower bounds to indicate the potential importance of this internal solute source.

Potential Management Implications: In support of the mission of the California Bay-Delta Authority (CALFED) “to improve California’s water supply and the ecological health of the San Francisco Bay/Sacramento-San Joaquin River Delta,” CALFED’s Food Web Project is administered by San Francisco State University’s Romberg Tiburon Center for Environmental Studies. They employ diverse yet complementary research approaches to quantitatively understand the processes that regulate pelagic and benthic food webs in the estuary. Availability of biologically reactive solutes (that is, both nutrients and toxic substances) may have pronounced effects at the base of the food web in structure and abundance. In North Bay, it is reasonable to initially assume that the major source of these biologically reactive solutes is advective transport from the Sacramento and San Joaquin Rivers. However, recent studies in freshwater, estuarine, and coastal environments indicate that the remobilization of particle-bound solutes, accumulated in bed material, may represent a significant water-column source relative to fluvial transport. This work provides: (1) initial determinations of the benthic flux of dissolved macronutrients and trace metals at hydrodynamically contrasting sites within North Bay, in the vicinity of ongoing and proposed CALFED restoration projects, and (2) a research approach to effectively screen areas where benthic sources of nutrients and toxic substances may be of concern. Results presented herein indicate the presence of significant benthic nutrient sources, particularly in Grizzly Bay and in the vicinity of Browns Island. Deployment of the pore-water profilers may serve as a cost-effective approach to help locate areas (“hot spots”) of particular concern and subsequent emphasis for restoration activities within and adjacent to the estuary.

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Suggested citation:

Kuwabara, J.S., Topping, B.R., Parchaso, F., Engelstad, A.C. and Greene, V.E., 2009, Benthic flux of nutrients and trace metals in the northern component of San Francisco Bay, California: U.S. Geological Survey Open-File Report 2009-1286, 26 p.


Executive Summary



Results and Discussion



References Cited

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