Microbial activity is a fundamental component of oceanic nutrient cycles. Photosynthetic microbes, collectively termed phytoplankton, are responsible for the vast majority of primary production in marine waters. The availability of nutrients in the upper ocean frequently limits the activity and abundance of these organisms. Experimental data have revealed two broad regimes of phytoplankton nutrient limitation in the modern upper ocean. Nitrogen availability tends to limit productivity throughout much of the surface low-latitude ocean, where the supply of nutrients from the subsurface is relatively slow. In contrast, iron often limits productivity where subsurface nutrient supply is enhanced, including within the main oceanic upwelling regions of the Southern Ocean and the eastern equatorial Pacific. Phosphorus, vitamins and micronutrients other than iron may also (co-)limit marine phytoplankton. The spatial patterns and importance of co-limitation, however, remain unclear. Variability in the stoichiometries of nutrient supply and biological demand are key determinants of oceanic nutrient limitation. Deciphering the mechanisms that underpin this variability, and the consequences for marine microbes, will be a challenge. But such knowledge will be crucial for accurately predicting the consequences of ongoing anthropogenic perturbations to oceanic nutrient biogeochemistry

Increasing quantities of atmospheric anthropogenic fixed nitrogen entering the open ocean could account for up to about a third of the ocean's external (nonrecycled) nitrogen supply and up to approximately 3% of the annual new marine biological production, approximately 0.3 petagram of carbon per year. This input could account for the production of up to approximately 1.6 teragrams of nitrous oxide (N2O) per year. Although approximately 10% of the ocean's drawdown of atmospheric anthropogenic carbon dioxide may result from this atmospheric nitrogen fertilization, leading to a decrease in radiative forcing, up to about two-thirds of this amount may be offset by the increase in N2O emissions. The effects of increasing atmospheric nitrogen deposition are expected to continue to grow in the future.

A new regulatory model can describe acclimation of phytoplankton growth rate (p), chlorophyll a : carbon ratio and nitrogen: carbon ratio to irradiance, temperature and nutrient availability. The model uses three indices of phytoplankton biomass-phytoplankton carbon (C), phytoplankton nitrogen (N), and chlorophyll a (Chl). The model links the light-saturated rate of photosynthesis to N: C, requires that Chl a synthesis be coupled to nitrogen assimilation, and includes several regulatory features. These include feedback inhibition of the nitrogen assimilation rate by increases in the N: C ratio, as well as regulation of Chl a synthesis by the balance between light absorption and photosynthetic carbon fixation. The model treats respiration as the sum of the maintenance metabolic requirement and the cost of biosynthesis. In addition, the model can account for accumulation and mobilization of energy reserves (i.e. variability of N: C) and photoacclimation (i.e. variability of Chl : N and Chl : C) in response to variations in irradiance and nutrient availability. The assumptions of the model are shown to be in agreement with experimental observations and the model output compares favorably with data for cultures in balanced and unbalanced growth.

The role of iron in enhancing phytoplankton productivity in high nutrient, low chlorophyll oceanic regions was demonstrated first through iron-addition bioassay experiments and subsequently confirmed by large-scale iron fertilization experiments. Iron supply has been hypothesized to limit nitrogen fixation and hence oceanic primary productivity on geological timescales, providing an alternative to phosphorus as the ultimate limiting nutrient. Oceanographic observations have been interpreted both to confirm and refute this hypothesis, but direct experimental evidence is lacking. We conducted experiments to test this hypothesis during the Meteor 55 cruise to the tropical North Atlantic. This region is rich in diazotrophs and strongly impacted by Saharan dust input. Here we show that community primary productivity was nitrogen-limited, and that nitrogen fixation was co-limited by iron and phosphorus. Saharan dust addition stimulated nitrogen fixation, presumably by supplying both iron and phosphorus. Our results support the hypothesis that aeolian mineral dust deposition promotes nitrogen fixation in the eastern tropical North Atlantic.

The photosynthesis-irradiance response (PE) curve, in which mass-specific photosynthetic rates are plotted versus irradiance, is commonly used to characterize photoacclimation. The interpretation of PE curves depends critically on the currency in which mass is expressed. Normalizing the light-limited rate to chl a yields the chl a -specific initial slope ( ␣ chl ). This is proportional to the light absorption coefficient (a chl ), the proportionality factor being the photon efficiency of photosynthesis ( m ). Thus, ␣ chl is the product of a chl and m . In microalgae ␣ chl typically shows little ( Ͻ 20%) phenotypic variability because declines of m under conditions of high-light stress are accompanied by increases of a chl . The variation of ␣ chl among species is dominated by changes in a chl due to differences in pigment complement and pigment packaging. In contrast to the microalgae, ␣ chl declines as irradiance increases in the cyanobacteria where phycobiliproteins dominate light absorption because of plasticity in the phycobiliprotein:chl a ratio. By definition, light-saturated photosynthesis (P m ) is limited by a factor other than the rate of light absorption. Normalizing P m to organic carbon concentration to obtain P m C allows a direct comparison with growth rates. Within species, P m C is independent of growth irradiance. Among species, P m C covaries with the resource-saturated growth rate. The chl a :C ratio is a key physiological variable because the appropriate currencies for normalizing light-limited and light-saturated photosynthetic rates are, respectively, chl a and carbon. Typically, chl a :C is reduced to about 40% of its maximum value at an irradiance that supports 50% of the species-specific maximum growth rate and light-harvesting accessory pigments show similar or greater declines. In the steady state, this down-regulation of pigment content prevents microalgae and cyanobacteria from maximizing photosynthetic rates throughout the light-limited region for growth. The reason for down-regulation of light harvesting, and therefore loss of potential photosynthetic gain at moderately limiting irradiances, is unknown. However, it is clear that maximizing the rate of photosynthetic carbon assimilation is not the only criterion governing photoacclimation.

The effects of nitrate, phosphate, and iron starvation and resupply on photosynthetic pigments, selected photosynthetic proteins, and photosystem II (PSII) photochemistry were examined in the diatom Phaeodactylum tricornutum Bohlin (CCMP 1327). Although cell chlorophyll a (chl a) content decreased in nutrient‐starved cells, the ratios of light‐harvesting accessory pigments (chl c and fucoxanthin) to chl a were unaffected by nutrient starvation. The chl a‐specific light absorpition coefficient (a*) and the functional absorption cross‐section of PSII (σ) increased during nutrient starvation, consistent with reduction of intracellular self‐shading (i.e. a reduction of the “package effect”) as cells became chlorotic. The light‐harvesting complex proteins remained a constant proportion of total cell protein during nutrient starvation, indicating that chlorosis mirrored a general reduction in cell protein content. The ratio of the xanthophylls cycle pigments diatoxanthin and diadinoxanthin to chl a increased during nutrient starvation. These pigments are thought to play a photo‐protective role by increasing dissipation of excitation energy in the pigment bed upstream from the reaction centers. Despite the increase in diatoxanthin and diadinoxanthin, the efficiency of PSII photochemistry, as measured by the ration of variable to maximum fluorescence (Fv/Fm) of dark‐adapted cells, declined markedly under nitrate and iron starvation and moderately under phosphate starvation. Parallel to changes in Fv/Fm were decreases in abundance of the reaction center protein D1 consistent with damage of PSII reaction centers in nutrient‐starved cells. The relative abundance of the carboxylating enzyme, ribulose bisphosphate carboxylase/oxygenase (RUBISCO), decreased in response to nitrate and iron starvation but not phosphate starvation. Most marked was the decline in the abundance of the small subunit of RUBISCO in nitrate‐starved cells. The changes in pigment content and fluorescence characteristics were typically reversed within 24 h of resupply of the limiting nutrient.

Fast repetition rate (FRR) fluorescence can provide highly resolved estimates of light absorption by photosystem II (PSII), a variable that is critical to bio-optical determinations of phytoplankton productivity. We compared estimates of chlorophyll a-specific light absorption by PSII, a chl PSII , using both biophysical (FRR) and optical (chlorophyll a-specific light absorption coefficient, a chl ) techniques on cultures of phytoplankton from diverse taxa. Biophysical determinations of a chl PSII were obtained from the product of the effective light absorption cross-section of PSII (σ PSII ), measured by FRR fluorescence, and the ratio of PSII reaction centers to chlorophyll a (n PSII ), measured by oxygen flash yields. Both parameters were highly variable between individual taxa. In mixtures of algae, the estimates of σ PSII were largely determined by the taxon that dominated fluorescence intensity. Independent optical estimates of a chl PSII were obtained by weighting the light absorption spectra of photosynthetic pigments by the fluorescence excitation spectra. The biophysical and optical estimates of a chl PSII were highly correlated (r 2 = 0.94) with a slope that was not significantly different from 1 and an intercept of 0. Estimates of productivity using biophysical or optical absorption measurements should therefore be comparable when the latter are adjusted to account for the proportion of light provided for photochemistry into both photosystem I and II. Finally, we show how simultaneous measurements of σ PSII and a chl PSII can be used to derive n PSII where flash-yield measurements are impractical, as is almost universally the case in field measurements.

Iron supply has been suggested to influence phytoplankton biomass, growth rate and species composition, as well as primary productivity in both high and low NO3 (-) surface waters. Recent investigations in the equatorial Pacific suggest that no single factor regulates primary productivity. Rather, an interplay of bottom-up (i.e., ecophysiological) and top-down (i.e., ecological) factors appear to control species composition and growth rates. One goal of biological oceanography is to isolate the effects of single factors from this multiplicity of interactions, and to identify the factors with a disproportionate impact. Unfortunately, our tools, with several notable exceptions, have been largely inadequate to the task. In particular, the standard technique of nutrient addition bioassays cannot be undertaken without introducing artifacts. These so-called 'bottle effects' include reducing turbulence, isolating the enclosed sample from nutrient resupply and grazing, trapping the isolated sample at a fixed position within the water column and thus removing it from vertical movement through a light gradient, and exposing the sample to potentially stimulatory or inhibitory substances on the enclosure walls. The problem faced by all users of enrichment experiments is to separate the effects of controlled nutrient additions from uncontrolled changes in other environmental and ecological factors. To overcome these limitations, oceanographers have sought physiological or molecular indices to diagnose nutrient limitation in natural samples. These indices are often based on reductions in the abundance of photosynthetic and other catalysts, or on changes in the efficiency of these catalysts. Reductions in photosynthetic efficiency often accompany nutrient limitation either because of accumulation of damage, or impairment of the ability to synthesize fully functional macromolecular assemblages. Many catalysts involved in electron transfer and reductive biosyntheses contain iron, and the abundances of most of these catalysts decline under iron-limited conditions. Reductions of ferredoxin or cytochrome f content, nitrate assimilation rates, and dinitrogen fixation rates are amongst the diagnostics that have been used to infer iron limitation in some marine systems. An alternative approach to diagnosing iron-limitation uses molecules whose abundance increases in response to iron-limitation. These include cell surface iron-transport proteins, and the electron transfer protein flavodoxin which replaces the Fe-S protein ferredoxin in many Fe-deficient algae and cyanobacteria.