A new coupled, one-dimensional biological-physical model for the upper ocean: Applications to the JGOFS Bermuda Atlantic Time-series study (BATS) site

Deep-Sea Research Part II: Topical Studies in Oceanography

Volumn 43, Issue 2-3, 1996, Pages 591-624

  Doney, Scott C ^a   Glover, David M ^b   Najjar, Raymond G ^c  

^a NATIONAL CENTER FOR ATMOSPHERIC RESEARCH   (United States)

^b WOODS HOLE OCEANOGRAPHIC INSTITUTION   (United States)

^c PENNSYLVANIA STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOGEOCHEMICAL CYCLE; BIOLOGICAL PRODUCTION; COUPLED BIOLOGICAL-PHYSICAL MODEL; HYDROGRAPHY; JGOFS; UPPER OCEAN;

SARGASSO SEA, BATS SITE;

EID: 0029752952     PISSN: 09670645     EISSN: None     Source Type: Journal    
DOI: 10.1016/0967-0645(95)00104-2     Document Type: Article

References (107)

1. Alldredge A. L. and M. W. Silver (1988) Characteristics, dynamics and significance of marine snow. Progress in Oceanography, 20, 41-82.
2. Alldredge A. L., T. C. Granata, C. G. Gotschalk and T. D. Dickey (1990) The physical strength of marine snow and its implications for particle disaggregation in the ocean. Limnology and Oceanography, 35, 1415-1428.
3. Altabet M. A. (1989) Particulate new nitrogen fluxes in the Sargasso Sea. Journal of Geophysical Research, 94, 12,771-12,779.
4. Andersen V. and P. Nival (1988) A pelagic ecosystem model simulating production and sedimentation of biogenic particles: role of salps and copepods. Marine Ecology Progress Series, 44, 37-50.
5. Baker K. S. and R. C. Smith (1982) Bio-optical classification and model of natural waters II. Limnology and Oceanography, 27, 500-509.
6. Baker K. S. and R. Frouin (1987) Relation between photosynthetically available radiation and total insulation at the ocean surface under clear skies. Limnology and Oceanography, 32, 1370-1377.
7. Banse K. (1990) New views on the degradation and disposition of organic particles collected by sediment traps in the open sea. Deep-Sea Research, 37, 1177-1195.
8. Biggs G. R., T. D. Jickells, A. H. Knap and R. Sherriff-Dow (1989) The significance of short-term wind induced mixing events for "new" primary production in sub-tropical gyres. Oceanologica Acta, 12, 437-442.
9. Bissett W. P., M. B. Meyers, J. J. Walsh and F. E. Muller-Karger (1994) The effects of temporal variability of mixed-layer depth on primary productivity around Bermuda. Journal Geophysical Research, 99, 7539-7553.
10. Broecker W. S. and T. H. Peng (1982) Tracers in the sea. Eldigio Press, Palisades, New York, 690 pp.
11. Buesseler K. O. (1991) Do upper-ocean sediment traps provide an accurate record of particle flux? Nature, 353, 420-423.
12. Buesseler K. O., A. F. Michaels, D. A. Siegel and A. H. Knap (1994) A three dimensional time-dependent approach to calibrating sediment trap fluxes. Global Biogeochemical Cycles, 8, 179-193.
13. Carlson C. A., H. W. Ducklow and A. F. Michaels (1994) Annual flux of dissolved organic carbon from the euphotic zone in the Northwestern Sargasso Sea. Nature, 371, 405-408.
14. Cho B. C. and F. Azam (1988) Major role of bacteria in biogeochemical fluxes in the ocean's interior. Nature, 332, 441-443.
15. Conover R. J. and M. E. Huntley (1980) General rules of grazing in pelagic ecosystems. In: Primary productivity in the sea, P. Falkowski, editor, Plenum Press, New York, pp. 461-486.
16. Cullen J. J. (1990) On models of growth and photosynthesis in phytoplankton. Deep-Sea Research, 37, 667-683.
17. Cullen J., X. Yang, H. L. MacIntyre, (1992) Nutrient limitation and marine photosynthesis. In: Primary productivity and biogeochemical cycles in the sea, P. G. Falkowski and A. D. Woodhead, editors, Plenum Press, New York, pp. 69-88.
18. Cullen J. J., R. J. Geider, J. Ishizaka, D. A. Kiefer, J. Marra, E. Sakshaug and J. A. Raven (1993) Towards a general description of phytoplankton growth for biogeochemical models. In: Towards a model of ocean biogeochemical processes, G. T. Evans and M. J. R. Fasham, editors, Springer-Verlag, Berlin, pp. 153-176.
19. Dobson F. W. and S. D. Smith (1988) Bulk models of solar radiation at sea. Quarterly Journal of the Royal Meteorological Society, 114, 165-182.
20. Doney S. C., R. G. Najjar and S. Stewart (1995) Photochemistry, mixing, and diurnal cycles in the upper ocean. Journal of Marine Research, 53, 341-369.
21. Ducklow H. W. (1983) Production and fate of bacteria in the oceans. Bioscience, 33, 494-501.
22. Dugdale R. C. and J. C. Goering (1967) Uptake of new and regenerated forms of nitrogen in primary productivity. Limnology and Oceanography, 12, 196-206.
23. Eppley R. W. (1972) Temperature and phytoplankton growth in the sea. Fishery Bulletin, 17, 15-24.
24. Eppley R. W. (1981) Relations between nutrient assimilation and growth in phytoplankton with a brief review of estimates of growth rate in the ocean. Physiological basis of phytoplankton ecology. Canadian Bulletin of Fisheries and Aquatics Sciences, 210, 251-263.
25. Eppley R. W. and B. J. Peterson (1979) Particulate organic matter flux and planktonic new production in the deep ocean. Nature, 282, 677-680.
26. Eriksen C. C. (1987) Observations of the seasonal cycle of upper ocean structure and the roles of advection and diapycnal mixing. Journal of Geophysical Research, 92, 5354-5368.
27. Esbensen S. K. and Y. Kushnir (1981) The heat budget of the global ocean: an atlas based on estimates from surface marine observations. Climatic Research Institute, Report 29, Oregon State University, OR, U.S.A.
28. Evans G. T. and J. S. Parslow (1985) A model of annual plankton cycles. Biological Oceanography, 3, 327-347.
29. Fasham M. J. R. (1995) Variations in the seasonal cycle of biological production in subarctic oceans: A model sensitivity analysis. Deep-Sea Research I, 42, 1111-1149.
30. Fasham M. J. R., H. W. Ducklow and S. M. McKelvie (1990) A nitrogen-based model of plankton dynamics in the oceanic mixed layer. Journal Marine Research, 48, 591-639.
31. Fasham M. J. R., J. L. Sarmiento, R. D. Slater, H. W. Ducklow and R. Williams (1993) Ecosystem behavior at Bermuda Station "S" and Ocean Weather Station "India": A general circulation and observational analysis. Global Biogeochemical Cycles, 7, 379-415.
32. Franks P. J. S., J. S. Wroblewski and G. R. Flierl (1986) Behavior of a simple plankton model with food-level acclamation by herbivores. Marine Biology, 91, 121-129.
33. Frost B. W. (1987) Grazing control of phytoplankton stock in the open subarctic Pacific Ocean: a model assessing the role of mesozooplankton, particularly the large calanoid copepods Neocalanus supp. Marine Ecology Progress Series, 39, 49-68.
34. Geider R. J. (1987) Light and temperature dependence of the carbon to chlorophyll a ratio in microalgae and cyanobacteria: implications for physiology and growth of phytoplankton. New Phytology, 106, 1-34.
35. Glover D. M. and P. G. Brewer (1988) Estimates of winter-time mixed layer nutrient concentrations in the North Atlantic. Deep-Sea Research, 3, 1525-1546.
36. Goldman J. C. (1987) Spatial and temporal discontinuities of biological processes in pelagic surface waters. In: Towards a theory on biological-physical interactions in the world ocean. B. J. Rothschild, editor, Kulwer, Boston.
37. Gregg M. C. (1987) Diapycnal mixing in the thermocline: a review. Journal of Geophysical Research, 92, 5249-5286.
38. Gregg M. C. and T. B. Sanford (1980) Signatures of mixing from the Bermuda slope, the Sargasso Sea and the Gulf Stream. Journal of Physical Oceanography, 10, 105-127.
39. Hurtt G. C. and R. A. Armstrong (1996) A pelagic ecosystem model calibrated with BATS data. Deep-Sea Research II, 43, 653-683.
40. Isemer H. and L. Hasse (1985) The bunker climate atlas of the North Atlantic Ocean, Volume 2. Air-sea interactions. Springer-Verlag, New York, 252 pp.
41. 3He in the Sargasso Sea. Journal of Marine Research, 38, 533-569.
42. Jenkins W. J. (1982) Oxygen utilization rates in the North Atlantic Subtropical Gyre and primary production in oligotrophic systems. Nature, 300, 246-248.
43. Jenkins W. J. (1988) Nitrate flux into the euphotic zone near Bermuda. Nature, 331, 521-523.
44. Jenkins W. J. and J. C. Goldman (1985) Seasonal oxygen cycling and primary production in the Sargasso Sea. Journal of Marine Research, 43, 465-491.
45. Jumars P. A. (1993) Concepts in biological oceanography: An interdisciplinary primer. Oxford University Press, New York, NY, 348 pp.
46. Karl D. M., G. A. Knauer and J. H. Martin (1988) Downward flux of particulate organic matter in the ocean: a particle decompostion paradox. Nature, 332, 438-441.
47. Kiefer D. A. (1993) Modelling growth and light absorption in the marine diatom Skeletonema Costatum. In: Towards a model of ocean biogeochemical processes, G. T. Evans and M. J. R. Fasham, editors, Springer-Verlag, Berlin, pp. 93-121.
48. Kiefer D. A. and J. N. Kremer (1981) Origins of vertical patterns of phytoplankton and nutrients in temperate open ocean: A stratigraphic hypothesis. Deep-Sea Research, 28, 1087-1105.
49. Kiefer D. A. and B. G. Mitchell (1983) A simple, steady state description of phytoplankton growth based on absorption cross section and quantum efficiency. Limnology and Oceanography, 28, 770-776.
50. Knap A., T. Ickells, A. Pszenny and J. Galloway (1986) Significance of atmospheric-derived fixed nitrogen on productivity of the Sargasso Sea, Nature, 320, 158-160.
51. Knap A. H., A. F. Michaels, R. L. Dow, R. J. Johnson, K. Gundersen, G. A. Knauer, S. E. Lohrenz, V. A. Asper, M. Tuel, H. Duddow, H. Quinby and P. Brewer (1991) U.S. JGOFS Bermuda Atlantic Time-series Study, Data Report for BATS 1-BATS 12, October 1988-September 1989. U.S. JGOFS Planning Office, Woods Hole, MA, U.S.A., 286 pp.
52. Knap A. H., A. F. Michaels, R. L. Dow, R. J. Johnson, K. Gundersen, J. C. Sorensen, A. R. Close, M. Hammer, G. A. Knauer, S. E. Lohrenz, V. A. Asper, M. Thel, H. Duddow, H. Quinby, P. Brewer and R. Bidigare (1992) U.S. JGOFS Bermuda Atlantic Time-series Study, Data Report for BATS 13-BATS 24, October 1989-September 1990. U.S. JGOFS Planning Office, Woods Hole, MA, U.S.A., 345 pp.
53. Knap A. H., A. F. Michaels, R. L. Dow, R. J. Johnson, K. Gundersen, J. C. Sorensen, A. R. Close, F. Howse, M. Hammer, N. Bates, G. A. Knauer, S. E. Lohrenz, V. A. Asper, M. Thel, H. Duddow and H. Quinby (1993) U.S. JGOFS Bermuda Atlantic Time-series Study, Data Report for BATS 25-BATS 36, October 1990-September 1991. U.S. JGOFS Planning Office, Woods Hole, MA, U.S.A., 339 pp.
54. Knap A. H., A. F. Michaels, R. L. Dow, R. J. Johnson, K. Gundersen, J. C. Sorensen, A. R. Close, F. Howse, N. Bates, M. Best, M. Hammer and A. P. Doyle (1994) U.S. JGOFS Bermuda Atlantic Time-series Study, Data Report for BATS 37-BATS 48, October 1991-September 1992. U.S. JGOFS Planning Office, Woods Hole, MA, U.S.A., 263 pp.
55. Large W. G. and G. B. Crawford (1995) Observations and simulations of upper ocean response to wind events during the Ocean Storms Experiment. Journal of Physical Oceanography, 25, 2831-2852.
56. Large W. G., J. C. McWilliams and P. P. Niiler (1986) Upper ocean thermal response to strong autumnal forcing in the Northeast Pacific. Journal of Physical Oceanography, 16, 1524-1550.
57. Large W. G., J. C. McWilliams and S. C. Doney (1994) Oceanic vertical mixing: A review and a model with a non-local boundary layer parameterization. Reviews of Geophysics, 32, 363-403.
58. Laws E. A. and T. T. Bannister (1980) Nutrient- and light-limited growth of Thalassiosira fluviatilis in continuous culture, with implications for phytoplankton growth in the ocean. Limnology and Oceanography, 25, 457-473.
59. Ledwell J. R., A. J. Wilson and C. S. Low (1993) Evidence for slow mixing across the pycnocline from an open-ocean tracer release experiment. Nature, 364, 701-703.
60. Leetmaa A. and A. F. Bunker (1978) Updated charts of the mean annual wind stress, convergences in the Ekman Layers, and Sverdrup transports in the North Atlantic. Journal of Marine Research, 36, 311-322.
61. Legendre L. and M. Gosselin (1989) New production and export of organic matter to the deep ocean: consequences of some recent discoveries. Limnology and Oceanography, 34, 1374-1380.
62. Lewis M. R., W. G. Harrison, N. S. Oakey, D. Herbert and T. Platt (1986) Vertical nitrate fluxes in the oligotrophic ocean. Science, 234, 870-873.
63. Lohrenz S. E., G. A. Knauer, V. L. Asper, M. Tuel, A. F. Michaels and A. H. Knap (1992) Seasonal variability in primary production and particle flux in the northwestern Sargasso Sea: U.S. JGOFS Bermuda Atlantic Time-series Study. Deep-Sea Research, 39, 1373-1391.
64. Longhurst A. G., A. Bedo, W. G. Harrison, E. J. H. Head, E. P. Home, B. Irwin and C. Morales (1989) NFLUX: a test of vertical nitrogen flux by diel migrant biota. Deep-Sea Research, 36, 1705-1719.
65. Malone T. C., S. E. Pike and D. J. Conley (1993) Transient variations in phytoplankton productivity at the JGOFS Bermuda time series station. Deep-Sea Research I, 40, 903-924.
66. Mann K. H. and J. R. N. Lazier (1991) Dynamics of marine ecosystems, biological-physical interactions in the oceans. Blackwell Scientific Publications, Boston, MA, 466 pp.
67. Marra J., R. R. Bidigare and T. D. Dickey (1990) Nutrients and mixing, chlorophyll and phytoplankton growth. Deep-Sea Research, 37, 127-143.
68. Martin J. H., G. A. Knauer, D. M. Karl and W. W. Broenkow (1987) VERTEX: carbon cycling in the northeast Pacific. Deep-Sea Research, 34, 267-285.
69. McClain C. R., W. E. Esaias, G. C. Feldman, J. Elrod, D. Endres, J. Firestone, M. Darzi, R. Evans and J. Brown (1990) Physical and biological processes in the North Atlantic during the fist GARP global experiment. Journal of Geophysical Research, 95, 18,027-18,048.
70. McWilliams J. C. (1983) On the mean dynamical balances of the Gulf Stream recirculation zone. Journal of Marine Research, 41, 427-460.
71. Menzel D. W and J. H. Ryther (1960) The annual cycle of primary production in the Sargasso Sea off Bermuda. Deep-Sea Research, 6, 351-367.
72. Menzel D. W and J. H. Ryther (1961) Annual variations in primary production in the Sargasso Sea off Bermuda. Deep-Sea Research, 7, 282-288.
73. Michaels A. F. and M. W. Silver (1988) Primary production, sinking fluxes and the microbial food web. Deep-Sea Research, 35, 473-490.
74. Michaels A. F., N. R. Bates, K. O. Buesseler, C. A. Carlson and A. H. Knap (1994a) Carbon cycle imbalances in the Sargasso Sea. Nature, 372, 537-540.
75. Michaels A. F., A. H. Knap, R. L. Dow, K. Gundersen, R. J. Johnson, J. C. Sorensen, A. Close, G. A. Knauer, S. E. Lohrenz, V. A. Asper, M. Tuel and B. Bidigare (1994b) Seasonal patterns of ocean biogeochemistry at the U.S. JGOFS Bermuda Atlantic Time-series Study site. Deep-Sea Research I, 41, 1013-1038.
76. Mitchell B. G., E. A. Brody, O. Holm-Hansen, C. McClain and J. Bishop (1991) Light limitation of phytoplankton biomass and macronutrient utilization. Limnology and Oceanography, 36, 1662-1677.
77. Morel A. (1988) Optical modeling of the upper ocean in relation to its biogenous matter content (Case I waters). Journal of Geophysical Research, 93, 10,749-10,768.
78. Musgrave D. L., J. Chou and W. J. Jenkins (1988) Application of a model of upper-ocean physics for studying seasonal cycles of oxygen. Journal of Geophysical Research, 93, 15,679-15,700.
79. Najjar R. G. (1992) Marine biogeochemistry. In: Climate system modeling, K. Trenberth, editor, Cambridge University Press, New York, pp. 241-280.
80. Najjar R. G., J. L. Sarmiento and J. R. Toggweiler (1992) Downward transport and fate of organic matter in the ocean: Simulations with a general circulation. Global Biogeochemical Cycles, 6, 45-76.
81. Paduan J. D. and R. A. Deszoeke (1986) Heat and energy balances in the upper ocean at 50°N, 140°W during November 1980 (STREX). Journal of Physical Oceanography, 16, 25-38.
82. Paulson C. A. and J. J. Simpson (1977) Irradiance measurements in the upper ocean. Journal of Physical Oceanography, 1, 952-956.
83. Peterson D. H., M. J. Perry, K. E. Bencala and M. C. Talbot (1987) Phytoplankton productivity in relation to light intensity: a simple equation. Estuarine, Coastal and Shelf Science, 24, 813-832.
84. Platt T., W. G. Harrison, M. R. Lewis, W. K. W. Li, S. Sathyendranath, R. E. Smith and A. F. Vezina (1989) Biological production in the oceans: the case for a consensus. Marine Ecology Progress Series, 52, 77-88.
85. Platt T., S. Sathyendranath, O. Ulloa, W. G. Harrison, N. Hoepffner and J. Goes (1992) Nutrient control of phytoplankton photosynthesis in the Western North Atlatic. Nature, 356, 229-231.
86. Prézelin B. B., M. M. Tilzer, O. Schofield and C. Haese (1991) The control of the production process of phytoplankton by the physical structure of the aquatic environment with special reference to its optical properties. Aquatic Science, 53, 136-186.
87. Price J. F., R. A. Weller and R. R. Schudlich (1987) Wind-driven ocean currents and Ekman transport. Science, 238, 1534-1538.
88. Reynolds C. S. (1984) The ecology of freshwater phytoplankton. Cambridge University Press, Cambridge, 384 pp.
89. Roman M. R., H. G. Dam, A. L. Gauzens and J. M. Napp (1993) Zooplankton biomass and grazing at the JGOFS Sargasso Sea time series station. Deep-Sea Research I, 40, 883-901.
90. Sakshaug E., K. Andresen and D. A. Kiefer (1989) A steady state description of growth and light absorption in the marine planktonic diatom Skeletonema costatum. Limnology and Oceanography, 34, 198-205.
91. Sambrotto R. N., G. Savidge, C. Robinson, P. Boyd, T. Takahshi, D. M. Karl, C. Langdon, D. Chipman, J. Marra and L. Codispoti (1993) Elevated consumption of carbon relative to nitrogen in the surface ocean. Nature, 363, 248-250.
92. Sarmiento J. L., R. D. Slater, M. J. R. Fasham, H. W. Ducklow, J. R. Toggweiler and G. T. Evans (1993) A seasonal three-dimensional ecosystem model of nitrogen cycling in the North Atlantic euphotic zone. Global Biogeochemical Cycles, 1, 415-450.
93. Siegel D. A., R. Iturriaga, R. R. Bidigare, R. C. Smith, H. Pak, T. D. Dickey, J. Marra and K. S. Baker (1990) Meridional variations of the spring-time phytoplankton community in the Sargasso Sea. Journal of Marine Research, 48, 379-412.
94. Silver M. W. and M. M. Gowing (1991) The "particle" flux: Origins and biological components. Progress in Oceanography, 26, 75-113.
95. Spitzer W. S. and W. J. Jenkins (1989) Rates of vertical mixing, gas exchange, and new production: estimates from seasonal gas cycles in the upper ocean near Bermuda. Journal of Marine Research, 47, 169-196.
96. Steele J. H. and E. M. Henderson (1992) the role of predation in plankton models. Journal of Plankton Research, 114, 157-172.
97. Stramska M. and T. D. Dickey (1994) Modeling phytoplankton dynamics in the northeast Atlantic during the initiation of the spring bloom. Journal of Geophysical Research, 99, 10,241-10,253.
98. Talley L. D. and M. R. Raymer (1982) Eighteen degree water variability. Journal of Marine Research, 40, 757-775.
99. Toggweiler J. R. (1993) Carbon overconsumption. Nature, 363, 210-211.
100. Toggweiler J. R., J. L. Sarmiento, R. Najjar and D. Papademetriou (1987) Models of chemical cycling in the oceans: a progress report. Ocean Tracers Laboratory Technical Report No. 4, Princeton University, Princeton, U.S.A.
101. Villareal T. A., M. A. Altabet and K. Culver-Rymsza (1993) Nitrogen transport by vertically migrating diatom mats in the North Pacific Ocean. Nature, 363, 709-712.
102. Wakeham S. G. and E. A. Canuel (1988) Organic geochemistry of particulate matter in the eastern tropical North Pacific Ocean: Implications for particle dynamics. Journal of Marine Research, 46, 183-213.
103. Ward B. B., K. A. Kilpatrick, E. H. Renger and R. W. Eppley (1989) Biological nitrogen cycling in the nitracline. Limnology and Oceanography, 34, 493-513.
104. Warren S. G., C. J. Halm, J. London, R. M. Chervin and R. L. Jenne (1988) Global distribution of total cloud and cloud type over the ocean. NCAR Technical Note, NCAR-TN 317.
105. Woods Hole Oceanographic Institution and Bermuda Biological Station for Research (1988) Station "S" off Bermuda, physical measurements 1954-1984. WHOI and BBSR Data Report, MA, U.S.A., 189 pp.
106. Wroblewski J. S. (1989) A model of the spring bloom in the North Atlantic and its impact on ocean optics. Limnology and Oceanography, 34, 1563-1571.
107. Wroblewski J. S., J. L. Sarmiento and G. R. Flieral (1988) An ocean basin scale model of plankton dynamics in the North Atlantic 1. Solutions for the climatological oceanographic conditions in May. Global Biogeochemical Cycles, 2, 199-218.