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The question of what limits primary productivity and phytoplankton biomass in natural waters has occupied oceanographers and limnologists for more than a century. The earliest oceanographers recognized that this issue is key to understanding the regulation of both aquatic food chains and biogeochemical cycles (reviewed by Mills, 1989). Traditionally, phytoplankton ecologists have been imbued with the concepts of the light, nitrogen and temperature limitation as they relate to the critical depth model (Sverdrup, 1953), Michaelis-Menten kinetics (Dugdale, 1967), and thermodynamic constraints on growth (Eppley, 1972), respectively. The recent suggestion that a micronutrient, such as iron, limits phytoplankton biomass or production in vast portions of the world’s oceans (Martin, 1991) has been met with some skepticism (e.g., Banse, 1990). To a large extent the difficulty in determining what limits primary production stems both from methodological deficiencies and semantic confusion. The identification of limiting factors has been based on primarily three techniques: correlative inference, experimental manipulation, and simulation modeling. Here we examine the concepts of limiting factors and explore the possibility of using in vivo chlorophyll fluorescence (a biophysical signal), in conjunction with molecular markers, to identify or diagnose factors limiting phytoplankton growth and production in the ocean.