Tomales Bay, California

Sediment Nutrient Fluxes
========================
 
Stations (STA) numbers represent distance in Km from the
mouth of the bay.

Dome fluxes were measured at stations near
station 6, 10, and 16, at water depths between 2.5 and 4.0 m.

    STA 6: lat=  38 11' 25" N  
           lon= 122 55' 50" W
           estuary depth = 6m
    STA 10: lat=  38 09' 45" N  
            lon= 122 54' 45" W
           estuary depth = 5m
    STA 16: lat=  38 07' 00" N
            lon= 122 52' 15" W
           estuary depth = 3m

METHODOLOGY
===========

Domes were emplaced and sampled according to the procedures described in
Dollar et al. (1991) (see reference in LMER/BRIE publications list).
Incubations were typically 20-26 hours. For the analytical measurement
methods, see references in Smith et al. (1991). TA and DIC data are
corrected for nutrient fluxes. Rates reported in micromoles per square meter
per day (microequivalents, in the case of alkalinity).

ORIGINATORS:
=============
1) Dr. Stephen V. Smith
   University of Hawaii, 
   School of Ocean and Earth Science and Technology

2) Dr. James T. Hollibaugh
   San Francisco State University, Tiburon Center

PROJECTS: Land Margin Ecosystems Research (LMER),
          Biogeochemical Reactions in Estuaries (BRIE)

GENERAL COMMENT REGARDING THE PROJECT:
======================================
Tomales Bay was chosen as an LMER study site in 1989 because its simple
geometry, small surrounding watershed, and readily defined characteristics
of freshwater flow and internal water circulation make the site especially
tractable for the analysis of how a whole system receives, processes, and
exports materials. In this system freshwater (hydrological) transport
dominates material inputs, and the hydrological cycle shows several
characteristic time scales of variation. This program was named "BRIE." The
name is, at once, an acronym for "Biogeochemical Reactions in Estuaries" and
acknowledgment that dairy farming is a traditional livelihood for the
region.

Between 1985 and 1996, investigators from the University of Hawaii's School
of Ocean and Earth Science and Technology (SOEST), San Francisco State
University's Tiburon Center, and other institutions studied characteristics
of material transport from the land to the bay, internal cycling within the
bay, and burial and transport from the bay.

The group began a time series analysis of seasonal and interannual
variations in this system in 1987. In order to define these variations,
field trips occurred at two-month intervals, with some intermediate sampling
and automated continuous recording of environmental variables in this
system.

The program was divided into six component projects:

1. Analysis of non-conservative nutrient fluxes. This component focused on
sources and sinks of major forms of C, N and P in the bay.

2. Sedimentation analysis. We measured sediment input and accumulation, in
order to quantify loading of land-derived organic matter.

3. Circulation analysis. These studies focused on water circulation,
currents, and exchange of materials between the bay and ocean.

4. Nutrient cycling through major biotic components. We compared component
nutrient fluxes with baywide calculations based on stoichiometric
considerations. The studies considered major plants (phytoplankton,
eelgrass, benthic microalgae); and both planktonic and benthic microbial
processes.

5. Sites and controls of the processes of denitrification and nitrogen
fixation.

6. Modeling land and marine contributions to nutrient fluxes.

DATA SETS COLLECTED:
Tomales Bay and Lagunitas Creek water temperature.

Tomales Bay dissolved load water composition.

Tomales Bay particulate load composition.

Lagunitas Creek and Walker Creek water composition data

Tomales Bay water column biotic variables.

Tomales Bay sediment nutrient fluxes.

Tomales Bay meteorological data.

Watershed rainfall and water storage
gunitas Creek near Point Reyes Station stream flow.

Lagunitas Creek at Samuel P Taylor Park stream flow.

Walker Creek near Marshall stream flow.
 
Walker Creek near Tomales stream flow. NOTE: This gauge is no longer in
service, but the historical data are useful.

PUBLISHED LITERATURE:
Funding by NSF for biogeochemical research in Tomales Bay, California, began
in 1985. From 1989 until 1995 a project entitled "Biogeochemical Reactions
in Estuaries" (BRIE) was conducted as a continuation and expansion of the
initial funding under NSF's Land-Margin Ecosystems Research (LMER) program.
Publications marked with "*" have derived some or all of their support from
NSF-LMER funding. Other funding and support have included NSF other than
LMER, National Oceanographic and Atmospheric Administration (NOAA), United
States Department of Agriculture (USDA), United States Geological Survey
(USGS), United States Department of Energy (USDOE), Marin Municipal Water
District (MMWD), North Marin Water District (NMWD), plus miscellaneous other
sources.

Boynton, W., J.T. Hollibaugh, D. Jay, M. Kemp, J. Kremer, C. Simenstad, S.V.
Smith and I. Valiela. 1992. Understanding changes in coastal ecosystems: the
Land Margin Ecosystems Program. Eos 73: 481, 484-485.

* Chambers, R. M., J. W. Fourqurean, J. T. Hollibaugh, and S. M. Vink. 1995.
Importance of terrestrially-derived particulate phosphorus to phosphorus
dynamics in a West Coast Estuary. Estuaries 18: 518-526.

* Chambers, R. M., J. T. Hollibaugh, and S. Vink. 1994. Sulfate reduction
and sediment metabolism in Tomales Bay, California. Biogeochemistry 25:
1-18.

* Chambers, R. M., S. V. Smith, and J. T. Hollibaugh. 1994. An
ecosystem-level context for tidal exchange studies in salt marshes of
Tomales Bay, California, USA. pp. 265-276 In W. J. Mitsch (ed.) Global
Wetlands, Old World and New, Elsevier, NY.

* Christensen, S. J. 1995. Benthic flux and pore water models of the upper
sediments of Tomales Bay, California. MS thesis, U. Hawaii, 96 pp.

Cole, B. E., S. W. Hager and J. T. Hollibaugh. 1990. Hydrographic,
biological and nutrient properties of Tomales Bay, California, March 1985 to
May 1986. U.S. Geological Survey Open File Report 90-178.

* Dollar, S. J., S. V. Smith, S. M. Vink, S. Obrebski, and J. T. Hollibaugh.
1991. Annual cycle of benthic nutrient fluxes in Tomales Bay, California,
and contribution of the benthos to total ecosystem metabolism. Marine
Ecology--Progress Series 79: 115-125.

* Fischer, D. T. 1993. Modeling surface water runoff in the Tomales Bay
watershed, Marin County, California. Undergraduate thesis in Geography,
Middlebury College, Middlebury, VT, 21 pp.

* Fischer, D. T., S. V. Smith, and R. R. Churchill. 1996. Simulation of a
century of rainfall and runoff across the Tomales watershed. Journal of
Hydrology 186:253-273.

* Fourqurean, J. W., T. O. Moore, B. Fry, and J. T. Hollibaugh. Submitted.
Spatial and temporal variation in C:N:P ratios, (15N, and morphology of
eelgrass (Zostera marina L.) as indicators of ecosystem processes, Tomales
Bay, California, USA. Marine Ecology-Progress Series.

* Fourqurean, J. W., K. L. Webb, J. T. Hollibaugh, and S. V. Smith. 1997.
Plankton community respiration, Tomales Bay, California. Estuarine, Coastal
and Shelf Science 44: 493-505.

* Freifelder, R. R., S. V. Smith, and R. H. Bennett. submitted. Cows,
humans, and hydrology in the nitrogen dynamics of a grazed rural watershed.
Journal of Environmental Management.

Friedman, C. S., T. McDowell, J. M. Groff, J. T. Hollibaugh, D. Manzer and
R. P. Hedrick. 1988. Presence of Bonamia ostreae among populations of the
European flat oyster, Ostrea edulis Linne, in Tomales Bay, California, USA.
Journal of Shellfish Research 8: 1033-1037.

Gordon, D. C., P. R. Boudreau, K. H. Mann, J.-E. Ong, W. Silvert, S. V.
Smith, G. Wattayakorn, F. Wulff, and T. Yanagi.1996. LOICZ Biogeochemical
Modelling Guidelines. LOICZ Reports and Studies No. 5, 96 pp.

* Harvey, J. W., R. M. Chambers, and J. R. Hoelscher. in press.
Microzonation of pore water fluxes and solute chemistry in intertidal
wetland sediments. Estuaries.

* Hearn, C. J., and J. L. Largier. In press. The summer buoyancy dynamics of
a shallow mediterranean estuary and some effects of changing bathymetry;
Tomales Bay, California. Estuarine, Coastal and Shelf Science.

* Hearn, C. J., J. L. Largier, S. V. Smith, J. Plant, and J. Rooney. in
press. Effects of changing bathymetry on the summer buoyancy dynamics of a
shallow mediterranean estuary: Tomales Bay, California. 7th Internat. Conf.
on the Physics of Estuaries and Coastal Seas, Woods Hole.

* Hollibaugh, J. T. 1994. Relationship between thymidine metabolism,
bacterioplankton community metabolic capabilities and sources of organic
matter used for growth. Microbial Ecology 28: 117-131.

* Hollibaugh, J.T. 1993. Consistent patterns of thymidine metabolism by
bacterioplankton communities: A clue to community composition and to the
carbon sources used for growth? In: C. Pedros-Alios and R. Guerrero, [Eds]:
Proceedings of the Sixth International Symposium on Microbial Ecology,
Barcelona Spain, 7-11 September, 1992. pp. 471-474.

Hollibaugh, J. T., R. W. Buddemeier, and S. V. Smith. 1991. Contributions of
colloidal and high molecular weight dissolved material to alkalinity and
nutrient concentrations in shallow marine and estuarine systems. Marine
Chemistry 33: 1-27.

Hollibaugh, J. T. et al. 1988. Tomales Bay, California: a 'macrocosm' for
examining biogeochemical coupling at the land-sea interface. Eos 36:
843-845.

* Hollibaugh, J. T. and P. S. Wong. 1992. Ethanol-extractable substrate
pools and the incorporation of thymidine, L-leucine and other substrates by
bacterioplankton. Canadian Journal of Microbiology 38: 605-613.

* Hopkins, T. E. 1993. The physiological ecology of bat rays, Myliobatis
californica, in Tomales Bay, California. PhD dissertation in Ecology, U.
Ca., Davis. 104 pp.

* Joye, S. B. 1993. Spatial and temporal patterns of nitrogen fixation and
denitrification in the intertidal and subtidal sediments of a
Mediterranean-type estuary: Tomales Bay, California. Ph.D. thesis, UNC
Chapel Hill, 227 pp.

* Joye, S.B., and J.T. Hollibaugh. 1995. Sulfide inhibition of nitrification
influences nitrogen regeneration in sediments. Science 270: 623-625.

* Joye, S. B., M. L. Mazzotta, and J. T. Hollibaugh. In press. Community
metabolism in microbial mats: the role of iron and manganese reduction.
Applied and Environmental Microbiology.

* Joye, S. B., and H. W. Paerl. 1993. Nitrogen fixation and denitrification
in the intertidal and subtidal environments of Tomales Bay, California. pp.
633-653 In: R. S. Oremland (ed.) The Biogeochemistry of Global Change:
Radiatively Active Trace Gases. Chapman and Hall, NY.

* Joye, S. B., and H. W. Paerl. 1993. Contemporaneous nitrogen fixation and
denitrification in marine microbial mats: rapid response to runoff events.
Marine Ecology--Progress Series 94: 267-274.

* Joye, S.B. and H. W. Paerl. 1994. Nitrogen cycling in marine microbial
mats: rates and patterns of denitrification nitrogen fixation. Marine
Biology 119: 285-295.

* Joye, S. B., and H. W. Paerl. submitted. Nitrogen and carbon fixation
rates in benthic intertidal communities in Tomales Bay, California, effects
of terrestrial organic loading. Environmental Biology.

* Joye, S. B., S. V. Smith, J. T. Hollibaugh, H. W. Paerl.1996. Estimating
denitrification rates in estuarine sediments: a comparison of stoichiometric
and acetylene based methods. Biogeochemistry 33: 197-215.

Kimmerer, W. J. 1993. Distribution patterns of zooplankton in Tomales Bay,
California. Estuaries 16: 264-272.

* Kimmerer, W. J., S. V. Smith, and J. T. Hollibaugh. 1993. A simple
heuristic model of nutrient cycling in an estuary. Estuarine, Coastal and
Shelf Science 37: 145-159.

* Largier, J. L., and C. J. Hearn. in press. Seasonal occurrences of
hypersalinity and inverse structures in low-inflow estuaries. 7th
International Conference on the Physics of Estuaries and Coastal Seas, Woods
Hole.

* Largier, J. L., C. J. Hearn, and D. Chadwick. in press. Density structures
in "low inflow estuaries." Proc. 7th Internat. Conf. on the Physics of
Estuaries and Coastal Seas.

* Largier, J.L., J.T. Hollibaugh, and S.V. Smith. In press. Seasonally
hypersaline estuaries in mediterranean-climate regions. Estuaries.

* Murray, A.M. 1994. Community Fingerprint Analysis: A Molecular Method for
Studying Marine Bacterioplankton Biodiversity. M.S. thesis, Dept. Biology,
San Francisco State University. 93 pp.

* Murray, A. M., J. T. Hollibaugh, and C. Orrego. In press. Comparison of
the phylogenetic compositions of bacterioplankton in two California
estuaries by denaturing gradient gel electrophoresis of 16S rRNA gene
fragments. Applied and Environmental Microbiology 62:

Oberdorfer, J. A., M. A. Valentino, and S. V. Smith. 1990. Groundwater
contribution to the nutrient budget of Tomales Bay, California.
Biogeochemistry 10: 199-216.

* Paerl, H. W. 1992. Epi- and endobiotic interactions of cyanobacteria. In:
W. Reisser (ed.) Algae and Symbioses. Biopress Limited, Bristol, England.
pp. 537-566.

* Paerl, H. W. 1993. Interaction of nitrogen and carbon cycles in the marine
environment. pp. 343-381 In: T. Ford (ed.) Aquatic microbiology: An
ecological approach. Blackwell Scientific, Oxford.

* Paerl, H. W., B. M. Bebout, S. B. Joye, D. J. DeMarias. 1993. Microscale
characterization of dissolved organic matter production and uptake in marine
microbial mat communities. Limnology and Oceanography 38: 1150-1161.

* Paerl, H.W., S. B. Joye, M. Fitzpatrick. 1993. Evaluation of nutrient
limitation of CO2 and N2 fixation in marine microbial mats. Marine
Ecology--Progress Series 101: 297-306.

* Peak, S. 1994. The effect of changing bathymetry on salinities and
flushing times in Tomales Bay, California: 1861-1994, Honours thesis,
University of New South Wales, Australian Defence Force Academy, ACT,
Australia, 174 pp.

* Plant, J. N. 1995. Effects of land use change on Tomales Bay, California:
new ideas from old tracers. M.S. thesis in Oceanography, U. Hawaii, 103 pp.

* Popp, B. N., F. J. Sansone, T. M. Rust, D. A. Merritt. 1995. Determination
of concentration and carbon isotopic composition of dissolved methane in
sediments and nearshore waters. Analytical Chemistry 34: 405-411.

* Rooney, J. J. 1995. Determination of sedimentation rates in Tomales Bay,
California using a geographic information system. MS thesis, U. Hawaii, 95
pp.

* Rust, T. M. 1993. The relative importance of processes controlling the
distribution of methane in Tomales Bay, California. MS thesis, U. Hawaii, 76
pp.

* Sansone, F. J., J. T. Hollibaugh, S. M. Vink, R. M. Chambers, S. B. Joye,
B. N. Popp. 1994. Diver- operated piston corer for nearshore use. Estuaries
17: 716-720.

* Sansone, F. J., T. M. Rust, and S. V. Smith. submitted. Summer and winter
methane budgets for an estuary with low organic input: Tomales Bay,
California. Estuaries.

Smith, S. V. 1991. Stoichiometry of C:N:P fluxes in shallow-water marine
ecosystems. Chapter 13 in Proceedings of the Third Cary Conference:
Comparative analyses of ecosystems: patterns, mechanisms and theories, p.
259-286.

* Smith, S. V. 1995. Net carbon metabolism of oceanic margins and estuaries:
estimates of steady-state conditions, and speculations about anthropogenic
perturbations of that steady state. p. 246-250 In: G. M. Woodwell (ed.)
Biotic Feedbacks in the Global Climate System: Will the Warming Speed the
Warming? Oxford U.

Smith, S. V. 1995. Reflections on the measurement and significance of carbon
metabolism on coral reefs. Working paper for SCOR WG 104; on the WWW Home
Page for that working group; also put out as an Open File Report of the
Kansas Geological Survey.

* Smith, S. V., and M. J. Atkinson. 1994. Mass balance of nutrient fluxes in
coastal lagoons. p. 133-155 In B. Kjerfve (ed.) Coastal Lagoon Processes,
Elsevier.

* Smith, S. V., R. M. Chambers, and J. T. Hollibaugh. 1996. Dissolved and
particulate nutrient transport through a coastal watershed-estuary system.
Journal of Hydrology 176: 181-203.

Smith, S. V., and J. T. Hollibaugh. 1989. Carbon-controlled nitrogen cycling
in a marine 'macrocosm': an ecosystem-scale model for managing cultural
eutrophication. Marine Ecology--Progress Series 52: 103- 109.

* Smith, S. V., and J. T. Hollibaugh. 1993. Coastal metabolism and the
oceanic organic carbon balance. Reviews of Geophysics 31: 75-89.

* Smith, S. V., and J. T. Hollibaugh. In press. Annual cycle and interannual
variability of net and gross ecosystem metabolism in a temperate climate
embayment. Ecological Monographs.

* Smith, S. V., J. T. Hollibaugh, S. J. Dollar, and S. Vink. 1989. Tomales
Bay, California: a case for carbon-controlled nitrogen cycling. Limnology
and Oceanography 34: 37-52.

* Smith, S. V., J. T. Hollibaugh, S. J. Dollar, and S. Vink. 1991. Tomales
Bay metabolism: C-N-P stoichiometry and ecosystem heterotrophy at the
land-sea interface. Estuarine, Coastal and Shelf Science 33: 223-257.

Smith, S. V., and F. T. Mackenzie. 1987. The ocean as a net heterotrophic
system: Implications from the carbon biogeochemical cycle. Global
Biogeochemical Cycles 1: 187-198.

* Smith, S. V., and F. T. Mackenzie. 1991. Comments on the role of oceanic
biota as a sink for anthropogenic CO2 emissions. Global Biogeochemical
Cycles 5: 189-190.

Smith, S. V., W. J. Wiebe, J. T. Hollibaugh, S. J. Dollar, S. W. Hager, B.
E. Cole, G. W. Tribble, and P. A. Wheeler. 1987. Stoichiometry of C, N. P,
and Si fluxes in a temperate-climate embayment. Journal of Marine Research
45: 427-460.

* Snidvongs, A. 1993. Geochemistry of organic particulates in shallow water
continental shelf environments. PhD Dissertation, U. Hawaii, 201 pp.

* Vink, S. 1994. Sedimentary phosphorus cycling in Tomales Bay, California.
PhD Dissertation, U. Hawaii, 169 pp.

* Vink, S., R. M. chambers, and S. V. Smith. 1997. Distribution of
phosphorus in sediments from Tomales Bay, California. Marine Geology 139:
157-179.

Walsh, T. W. 1989. Total dissolved nitrogen in seawater: a new
high-temperature combustion method and comparison with photo-oxidation.
Marine Chemistry 26: 295-311.

* Walsh, T. W., S. V. Smith, and S. Vink. 1991. Review of particulate C:N:P
methods used by UH/HIMB Analytical Services. pp. 91-96 In: D. C. Hurd and D.
W. Spencer (eds.) Geophys. Monogr. 63, Marine Particles: Analysis and
Characterization.