, Volume 129, Issue 1, pp 69–90

Benthic fluxes in San Francisco Bay

  • Douglas E. Hammond
  • Christopher Fuller
  • Dana Harmon
  • Blayne Hartman
  • Michael Korosec
  • Laurence G. Miller
  • Rebecca Rea
  • Steven Warren
  • William Berelson
  • Stephen W. Hager


Measurements of benthic fluxes have been made on four occasions between February 1980 and February 1981 at a channel station and a shoal station in South San Francisco Bay, using in situ flux chambers. On each occasion replicate measurements of easily measured substances such as radon, oxygen, ammonia, and silica showed a variability (±1α) of 30% or more over distances of a few meters to tens of meters, presumably due to spatial heterogeneity in the benthic community. Fluxes of radon were greater at the shoal station than at the channel station because of greater macrofaunal irrigation at the former, but showed little seasonal variability at either station. At both stations fluxes of oxygen, carbon dioxide, ammonia, and silica were largest following the spring bloom. Fluxes measured during different seasons ranged over factors of 2–3, 3, 4–5, and 3–10 (respectively), due to variations in phytoplankton productivity and temperature. Fluxes of oxygen and carbon dioxide were greater at the shoal station than at the channel station because the net phytoplankton productivity is greater there and the organic matter produced must be rapidly incorporated in the sediment column. Fluxes of silica were greater at the shoal station, probably because of the greater irrigation rates there. N + N (nitrate + nitrite) fluxes were variable in magnitude and in sign. Phosphate fluxes were too small to measure accurately. Alkalinity fluxes were similar at the two stations and are attributed primarily to carbonate dissolution at the shoal station and to sulfate reduction at the channel station. The estimated average fluxes into South Bay, based on results from these two stations over the course of a year, are (in mmol m−2 d−1): O2 = −27 ± 6; TCO2 = 23 ± 6; Alkalinity = 9 ± 2; N + N = −0.3 ± 0.5; NH3 = 1.4 ± 0.2; PO4 = 0.1 ± 0.4; Si = 5.6 ± 1.1. These fluxes are comparable in magnitude to those in other temperate estuaries with similar productivity, although the seasonal variability is smaller, probably because the annual temperature range in San Francisco Bay is smaller.

Budgets constructed for South San Francisco Bay show that large fractions of the net annual productivity of carbon (about 90%) and silica (about 65%) are recycled by the benthos. Substantial rates of simultaneous nitrification and denitrification must occur in shoal areas, apparently resulting in conversion to N2 of 55% of the particulate nitrogen reaching the sediments. In shoal areas, benthic fluxes can replace the water column standing stocks of ammonia in 2–6 days and silica in 17–34 days, indicating the importance of benthic fluxes in the maintenance of productivity.

Pore water profiles of nutrients and Rn-222 show that macrofaunal irrigation is extremely important in transport of silica, ammonia, and alkalinity. Calculations of benthic fluxes from these profiles are less accurate, but yield results consistent with chamber measurements and indicate that most of the NH3, SiO2, and alkalinity fluxes are sustained by reactions occurring throughout the upper 20–40 cm of the sediment column. In contrast, O2, CO2, and N + N fluxes must be dominated by reactions occurring within the upper one cm of the sediment-water interface. While most data support the statements made above, a few flux measurements are contradictory and demonstrate the complexity of benthic exchange.


San Francisco Bay benthic fluxes nutrient cycling macrofaunal irrigation 


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  1. Aller, R. C., 1980. Quantifying solute distributions in the bioturbated zone of marine sediments by defining an average microenvironment. Geochim. Cosmochim. Acta 44: 1955–1965.Google Scholar
  2. Aller, R. C., 1982. The effects of macrobenthos on chemical properties of marine sediment and overlying water. In P. L. McCall & M. J. S. Tevesz (eds.), Animal-Sediment relations. Plenum, New York: 53–102.Google Scholar
  3. Aller, R. C., 1983. The importance of the diffusive permeability of animal burrow linings in determining marine sediment chemistry. J. Mar. Res. 41: 299–322.Google Scholar
  4. Aller, R. C., 1984. Solute transport in bioturbated sediments: model artifacts. Trans. Am. Geophys. Un. 65: 933.Google Scholar
  5. Aller, R. C. & J. Y. Yingst, 1978. Biogeochemistry of tube dwellings: A study of the sedentary polychaete Amphitrite ornata (Leidy). J. Mar. Res. 36: 201–254.Google Scholar
  6. Berner, R. A., 1980. Early diagenesis: A theoretical approach. Princeton Univ. Press, Princeton, N.J.: 241 pp.Google Scholar
  7. Boudreau, Bernard P., 1984. On the equivalence of nonlocal and radialdiffusion models for porewater irrigation. J. Mar. Res. 42: 731–735.Google Scholar
  8. Boynton, W. R., W. M. Kemp, C. G. Osborne, K. R. Kaumeyer & M. C. Jenkins, 1981. Influence of water circulation rate on in situ measurements of benthic community respiration. Mar. Biol. 65: 185–190.Google Scholar
  9. Broecker, W. S., 1965. The application of natural radon to problems in ocean circulation. In T. Ichiye (ed.), Symposium on Diffusion in Oceans and Fresh Waters. Lamont Geol. Obs., Palisades, N.Y.: 116–145.Google Scholar
  10. Callender, E. & D. E. Hammond, 1982. Nutrient exchange across the sediment-water interface in the Potomac River estuary. Estuar. Coast. Shelf Sci. 15: 395–413.Google Scholar
  11. Carpenter, J. H., 1965. The Chesapeake Bay Institute technique for the Winkler dissolved oxygen method. Limnol. Oceanogr. 10: 141–143.Google Scholar
  12. Christensen, J. P., A. H. Devol & H. Smethie, 1984. Biological enhancement of solute exchange between sediments and bottom water on the Washington continental shelf. Cont. Shelf Res. 3: 9–23.Google Scholar
  13. Claypool, G. E. & I. R. Kaplan, 1974. The origin and distribution of methane in marine sediments. In I. R. Kaplan (ed.), Natural Gases in Marine Sediments, Plenum, New York: 99–139.Google Scholar
  14. Cloern, J. E., 1982. Does the benthos control phytoplankton biomass in South San Francisco Bay? Mar. Ecol. Prog. Ser. 9: 191–202.Google Scholar
  15. Cloern, J. E., B. E. Cole, R. L. J. Wong & A. E. Alpine, 1985. Temporal dynamics of estuarine phytoplankton: A case study of San Francisco Bay. Hydrobiologia (this volume).Google Scholar
  16. Cole, B. E. & J. E. Cloern, 1984. Significance of biomass and light availability to phytoplankton productivity in San Francisco Bay. Mar. Ecol. Prog. Ser. 17: 15–24.Google Scholar
  17. Conomos, T. J., 1979. Properties and circulation of San Francisco Bay waters. In T. J. Conomos (ed.), San Francisco Bay: The Urbanized Estuary, Pacific Div. Am. Ass. Adv. Sci., San Francisco: 47–84.Google Scholar
  18. D'Elia, C. F., D. M. Nelson & W. R. Boynton, 1983. Chesapeake Bay nutrient and plankton dynamics: III. The annual cycle of dissolved silicon. Geochim. Cosmochim. Acta 47: 1945–1955.Google Scholar
  19. Emerson, S., R. Jahnke & D. Heggie, 1984. Sediment-water exchange in shallow water environments. J. Mar. Res. 42: 709–730.Google Scholar
  20. Froelich, P. N., G. P. Klinkhammer, M. L. Bender, N. A. Luedtke, G. R. Heath, D. Cullen, P. Dauphin, D. Hammond, B. Hartman & V. Maynard, 1979. Early oxidation of of organic matter in pelagic sediments of the eastern equatorial Atlantic: Suboxic diagenesis. Geochim. Cosmochim. Acta 43: 1075–1091.Google Scholar
  21. Fuller, C. C., 1982. The use of Pb-210, Th-234 and Cs-137 as tracers of sedimentary processes in San Francisco Bay, California. M.S. Thesis, Univ. So. Calif.: 251 pp.Google Scholar
  22. Gieskes, J. M. & W. C. Rogers, 1973. Alkalinity determination in interstitial waters of marine sediments. J. Sed. Petrol. 43: 272–277.Google Scholar
  23. Goldhaber, M. B., R. C. Aller, J. K. Cochran, J. K. Rosenfeld, C. S. Martens & R. A. Berner, 1977. Sulfate reduction, diffusion, and bioturbation in Long Island Sound sediments: Report of the FOAM Group. Am. J. Sci. 277: 193–237.Google Scholar
  24. Grundmanis, G. V. & J. W. Murray, 1977. Nitrification and denitrification in marine sediments from Puget Sound. Limnol. Oceanogr. 22: 804–813.Google Scholar
  25. Hammond, D. E. & C. Fuller, 1979. The use of radon-222 to estimate benthic exchange and atmospheric exchange rates in San Francisco Bay. In T. J. Conomos (ed.), San Francisco Bay: The Urbanized Estuary. Pacific Div. Am. Ass. Adv. Sci., San Francisco: 213–230.Google Scholar
  26. Hammond, D. E., H. J. Simpson & G. Mathieu, 1977. 222Radon distribution and transport across the sediment-water interface in the Hudson River Estuary. J. Geophys. Res. 82: 3913–3920.Google Scholar
  27. Harmon, D. D., P. V. Cascos & R. E. Smith, 1985. Nitrogen dynamics in a partially mixed estuary. Unpubl. ms.Google Scholar
  28. Hartman, B. & D. E. Hammond, 1984. Gas exchange rates across the sediment-water and air-water interface in South San Francisco Bay. J. Geophys. Res. 89: 3593–3603.Google Scholar
  29. Hartman, B. & D. E. Hammond, 1985. Gas exchange in San Francisco Bay. Hydrobiologia (this volume).Google Scholar
  30. Hargrave, B. T. & G. F. Connolly, 1978. A device to collect supernatant water for measurement of the flux of dissolved compounds across sediment surfaces. Limnol. Oceanogr. 23: 1005–1010.Google Scholar
  31. Hinga, K. R., J. M. Sieburth & G. R. Heath, 1979. The supply and use of organic material at the deep sea floor. J. Mar. Res. 37: 557–579.Google Scholar
  32. Howarth, R. W. & B. B. Jorgensen, 1984. Formation of 35S-labelled elemental sulfur and pyrite in coastal marine sediments (Limfjorden and Kysing Fjord, Denmark) during short-term 35SO2− reduction measurements. Geochim. Cosmochim. Acta 48: 1807–1818.Google Scholar
  33. Imboden, D. M., 1981. Tracers and mixing in the aquatic environment. Habilitation Thesis, Swiss Federal Institute of Technology, Dubendorf, Switzerland: 137 pp.Google Scholar
  34. Jannasch, H. J., C. O. Wixsen & C. D. Taylor, 1976. Undecompressed microbial populations from the Deep Sea. Appl. Environ. Microbiol. 32: 360–367.Google Scholar
  35. Jorgensen, B. B., 1977. The sulfur cycle of a coastal marine sediment (Limfjorden, Denmark). Limnol. Oceanogr. 22: 814–831.Google Scholar
  36. Jorgensen, B. B. & N. P. Revsbech, 1985. Diffusive boundary layers and the oxygen uptake of sediments and detritus. Limnol. Oceanogr. 30: 111–122.Google Scholar
  37. Katz, A. & S. Ben-Yaakov, 1980. Diffusion of seawater ions Part II. The role of activity coefficients and ion pairing. Mar. Chem. 8: 263–280.Google Scholar
  38. Keir, R. S., 1980. The dissolution kinetics of biogenic calcium carbonates in sea water. Geochim. Cosmochim. Acta 34: 241–252.Google Scholar
  39. Korosec, M., 1979. The effects of biological activity on transport of dissolved species across the sediment-water interface of San Francisco Bay. M.S. Thesis, Univ. So. Calif.: 91 pp.Google Scholar
  40. Lasaga, A. C., 1979. The treatment of multi-component diffusion and ion pairs in diagenetic fluxes. Am. J. Sci. 279: 324–346.Google Scholar
  41. Lerman, A., 1977. Migrational processes and chemical reactions in interstitial waters. In E. Goldberg, I. McCave, J. O'Brien & J. Steele (eds.), The Sea, v. 6: 695–738.Google Scholar
  42. Li, Y.-H. & S. Gregory, 1974. Diffusion of ions in sea water in deep sea sediment. Geochim. Cosmochim. Acta 38: 703–714.Google Scholar
  43. Lord, C. J.,III & T. M. Church, 1983. The geochemistry of salt marshes: Sedimentary ion diffusion, sulfate reduction, and pyritization. Geochim. Cosmochim. Acta 47: 1381–1391.Google Scholar
  44. Manheim, F. T., 1970. The diffusion of ions in unconsolidated sediments. Earth Planet. Sci. Lett. 9: 307–309.Google Scholar
  45. Martens, C. S., G. W. Kipphut & V. Klump, 1980. Sediment-water chemical exchange in the coastal zone traced by in situ radon-222 flux measurements. Science 208: 285–288.Google Scholar
  46. McCaffrey, R. J., A. C. Myers, E. Davey, G. Morrison, M. Bender, N. Luedtke, D. Cullen, P. Froelich & G. Klinkhammer, 1980. The relation between pore water chemistry and benthics of fluxes of nutrients and manganese in Narragansett Bay, Rhode Island. Limnol. Oceanogr. 25: 31–44.Google Scholar
  47. Morse, J. W., 1978. Dissolution kinetics of calcium carbonate in sea water: VI. The near equilibrium dissolution kinetics of calcium carbonate-rich deep sea sediments. Am. J. Sci. 278: 344–353.Google Scholar
  48. Nichols, F. H. & J. K. Thompson, 1985. Time scales of change in the San Francisco Bay benthos. Hydrobiologia (this volume).Google Scholar
  49. Nixon, S. W., 1981. Remineralization and nutrient cycling in coastal marine ecosystems. In B. J. Neilson & L. E. Cronin (eds.), Estuaries and Nutrients. The Humana Press: 112–138.Google Scholar
  50. Nixon, S. W., J. R. Kelly, B. N. Furnas, C. A. Oviatt & S. S. Hale, 1980. Phosphorus regeneration and the metabolism of coastal marine bottom communities. In K. R. Tenore & B. C. Coull (eds.), Marine Benthic Dynamics. Univ. South Carolina Press, Columbia, S.C.: 219–242.Google Scholar
  51. Nixon, S. W., C. A. Oviatt & S. S. Hale, 1976. Nitrogen regeneration and the metabolism of coastal marine bottom communities. In J. M. Anderson & A. Macfadyed (eds.), The Role of Terrestrial and Aquatic Organisms in Decomposition Processes, Proc. 17th Symposium British Ecological Soc., Blackwell Scient. Pub.: 269–283.Google Scholar
  52. Officer, C. B., R. B. Biggs, J. L. Taft, L. E. Cronin, M. A. Tyler & W. R. Boynton, 1984. Chesapeake Bay anoxia: Origin, development and significance. Science 223: 22–27.Google Scholar
  53. Pamatmat, M. M., 1971. Oxygen consumption by the seabed IV. Shipboard and laboratory experiments. Limnol. Oceanogr. 16: 536–550.Google Scholar
  54. Pamatmat, M. M. & K. Banse, 1969. Oxygen consumption by the seabed II. In situ measurement to a depth of 180 m. Limnol. Oceanogr. 14: 250–259.Google Scholar
  55. Peterson, D. H., 1979. Sources and sinks of biologically reactive substances (oxygen, carbon, nitrogen, and silica) in San Francisco Bay. In T. J. Conomos (ed.), San Francisco Bay: The Urbanized Estuary. Pacific Div. Am. Ass. Adv. Sci., San Francisco: 175–194.Google Scholar
  56. Peterson, D. H., R. E. Smith, S. W. Hager, D. D. Harmon, R. E. Herndon & L. E. Schemel, 1985. Interannual variability in dissolved inorganic nutrients in Northern San Francisco Bay Estuary. Hydrobiologia (this volume).Google Scholar
  57. Rea, R. L., 1981. The flux of dissolved silica from South San Francisco Bay sediments: Observations and models. M.S. Thesis, Univ. So. Calif.: 88 pp.Google Scholar
  58. Revsbech, N. P., J. Sorensen, T. H. Blackburn & J. P. Lomholt, 1980. Distribution of oxygen in marine sediments measured with microelectrodes. Limnol. Oceanogr. 25: 403–411.Google Scholar
  59. Riedl, R. J., N. Huang & R. Machan, 1972. The subtidal pump: A mechanism of interstitial water exchange by wave action. Mar. Biol. 13: 210–221.Google Scholar
  60. Santschi, P. H., P. Bower, U. P. Nyffeler, A. Azevedo & W. S. Broecker, 1983. Measurements of the resistance to chemical transport posed by the deep sea benthic boundary layer and their significance to benthic fluxes. Limnol. Oceanogr. 28: 899–912.Google Scholar
  61. Smith, K. L., 1978. Benthic community respiration in the N. W. Atlantic Ocean: In situ measurements from 40–5 200 m. Mar. Biol. 47: 337–347.Google Scholar
  62. Smith, K. L., C. H. Clifford, A. H. Eliason, B. Walden, G. T. Rowe & J. M. Teal, 1976. A free vehicle for measuring benthic community metabolism. Limnol. Oceanogr. 21: 164–170.Google Scholar
  63. Smith, K. L., G. A. White & M. B. Laver, 1979. Oxygen uptake and nutrient exchange of sediments measured in situ using a free vehicle grab respirometer. Deep-Sea Res. 26A: 337–346.Google Scholar
  64. Smith, R. L., R. E. Herndon & D. D. Harmon, 1979. Physical and chemical properties of San Francisco Bay waters, 1969–1976. U.S. Geological Survey Open File Rep.: 79–511.Google Scholar
  65. Spiker, E. C. & L. E. Schemel, 1979. Distribution and stable-isotope composition of carbon in San Francisco Bay. In T. J. Conomos (ed.), San Francisco Bay: The Urbanized Estuary. Pacific Div. Am. Ass. Adv. Sci., San Francisco: 195–212Google Scholar
  66. Vanderborght, J. P., R. Wollast & G. Billen, 1977. Kinetic models of diagenesis in disturbed sediments, Part 1: mass transfer properties and silicate diagenesis. Limnol. Oceanogr. 22: 787–793.Google Scholar
  67. Weiss, R. F., O. H. Kiersten & R. Ackerman, 1977. Free vehicle instrumentation for the in situ measurement of processes controlling the formation of deep-sea ferromanganese nodules. In Oceans '77 Conference Record, Marine Technol. Soc. 2-44D: 1–4.Google Scholar
  68. Zeitzschel, B., 1980. Sediment-water interactions in nutrient dynamics. In K. R. Tenore & B. C. Coull (eds.), Marine Benthic Dynamics, Univ. South Carolina Press, Columbia, S. C.: 195–218.Google Scholar

Copyright information

© Dr W. Junk Publishers 1985

Authors and Affiliations

  • Douglas E. Hammond
    • 1
  • Christopher Fuller
    • 1
  • Dana Harmon
    • 2
  • Blayne Hartman
    • 1
  • Michael Korosec
    • 1
  • Laurence G. Miller
    • 1
  • Rebecca Rea
    • 1
  • Steven Warren
    • 1
  • William Berelson
    • 1
  • Stephen W. Hager
    • 2
  1. 1.Department of Geological SciencesUniversity of Southern CaliforniaLos AngelesUSA
  2. 2.U.S. Geological SurveyMenlo ParkUSA

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