Bibliography - John P Dunne

1. Adcroft, Alistair, Robert W Hallberg, John P Dunne, Bonita L Samuels, J Galt, C Barker, and D Payton, in press: Simulations of underwater plumes of dissolved oil in the Gulf of Mexico. Geophysical Research Letters. 8/10.
   [ Abstract ]

   A simple model of the temperature-dependent biological decay of dissolved oil is embedded in an ocean climate circulation model and used to simulate underwater plumes of dissolved and suspended oil originating from a point source in the northern Gulf of Mexico. Plumes at different source depths are considered and the behavior at each depth is found to be determined by the combination of sheared current strength and vertical profile of decay rate. An upper bound on the supply rate of dissolved and suspended oil is estimated for the interior water column from contemporary analysis of the Deepwater Horizon blowout. For all plume scenarios, toxic levels of dissolved oil are found to remain confined to the northern Gulf of Mexico, and abate within a few weeks after the spill stops. An estimate of oxygen consumption due to microbial oxidation of oil suggests that the presence of oil alone will not lead to hypoxia, but a deep plume of oil and methane (which dissolves readily in water) does lead to localized regions of persistent hypoxia and anoxia in the vicinity of the source.

2. Galbraith, E D., Anand Gnanadesikan, John P Dunne, and M R Hiscock, March 2010: Regional impacts of iron-light colimitation in a global biogeochemical model. Biogeosciences, 7(3), 1043-1064.
   [ Abstract PDF ]

   Laboratory and field studies have revealed that iron has multiple roles in phytoplankton physiology, with particular importance for light-harvesting cellular machinery. However, although iron-limitation is explicitly included in numerous biogeochemical/ecosystem models, its implementation varies, and its effect on the efficiency of light harvesting is often ignored. Given the complexity of the ocean environment, it is difficult to predict the consequences of applying different iron limitation schemes. Here we explore the interaction of iron and nutrient cycles in an ocean general circulation model using a new, streamlined model of ocean biogeochemistry. Building on previously published parameterizations of photoadaptation and export production, the Biogeochemistry with Light Iron Nutrients and Gasses (BLING) model is constructed with only three explicit tracers but including macronutrient and micronutrient limitation, light limitation, and an implicit treatment of community structure. The structural simplicity of this computationally inexpensive model allows us to clearly isolate the global effect that iron availability has on maximum light-saturated photosynthesis rates vs. the effect iron has on photosynthetic efficiency. We find that the effect on light-saturated photosynthesis rates is dominant, negating the importance of photosynthetic efficiency in most regions, especially the cold waters of the Southern Ocean. The primary exceptions to this occur in iron-rich regions of the Northern Hemisphere, where high light-saturated photosynthesis rates allow photosynthetic efficiency to play a more important role. In other words, the ability to efficiently harvest photons has little effect in regions where light-saturated growth rates are low. Additionally, we speculate that the small phytoplankton cells dominating iron-limited regions tend to have relatively high photosynthetic efficiency, due to reduced packaging effects. If this speculation is correct, it would imply that natural communities of iron-stressed phytoplankton may tend to harvest photons more efficiently than would be inferred from iron limitation experiments with larger phytoplankton. We suggest that iron limitation of photosynthetic efficiency has a relatively small impact on global biogeochemistry, though it is expected to impact the seasonal cycle of plankton as well as the vertical structure of primary production.

3. Henson, S A., Jorge L Sarmiento, John P Dunne, L Bopp, I Lima, S C Doney, Jasmin John, and C Beaulieu, February 2010: Detection of anthropogenic climate change in satellite records of ocean chlorophyll and productivity. Biogeosciences, 7(2), 621-640.
   [ Abstract PDF ]

   Global climate change is predicted to alter the ocean's biological productivity. But how will we recognise the impacts of climate change on ocean productivity? The most comprehensive information available on its global distribution comes from satellite ocean colour data. Now that over ten years of satellite-derived chlorophyll and productivity data have accumulated, can we begin to detect and attribute climate change-driven trends in productivity? Here we compare recent trends in satellite ocean colour data to longer-term time series from three biogeochemical models (GFDL, IPSL and NCAR). We find that detection of climate change-driven trends in the satellite data is confounded by the relatively short time series and large interannual and decadal variability in productivity. Thus, recent observed changes in chlorophyll, primary production and the size of the oligotrophic gyres cannot be unequivocally attributed to the impact of global climate change. Instead, our analyses suggest that a time series of similar to 40 years length is needed to distinguish a global warming trend from natural variability. In some regions, notably equatorial regions, detection times are predicted to be shorter (similar to 20-30 years). Analysis of modelled chlorophyll and primary production from 2001-2100 suggests that, on average, the climate change-driven trend will not be unambiguously separable from decadal variability until similar to 2055. Because the magnitude of natural variability in chlorophyll and primary production is larger than, or similar to, the global warming trend, a consistent, decades-long data record must be established if the impact of climate change on ocean productivity is to be definitively detected.

4. Saba, V S., and John P Dunne, in press: Challenges of modeling depth-integrated marine primary productivity over multiple decades: A case study at BATS and HOT. Global Biogeochemical Cycles. 4/10.
   [ Abstract ]

   The performance of 36 models (22 ocean color models and 14 biogeochemical ocean circulation models; BOGCMs) that estimate depth-integrated marine net primary productivity (NPP) was assessed by comparing their output to in situ 14C data at the Bermuda Atlantic Timeseries Study (BATS) and the Hawaii Ocean Time-series (HOT) over nearly two decades. Specifically, skill was assessed based on the models’ ability to estimate the observed mean, variability, and trends of NPP. At both sites, more than 90% of the models underestimated mean NPP, with the average bias of the BOGCMs being nearly twice that of the ocean color models. However, the difference in overall skill between the best BOGCM and the best ocean color model at each site was not significant. Between 1989 and 2007, in situ NPP at BATS and HOT increased by an average of nearly 2% per year and was positively correlated to the North Pacific Gyre Oscillation index. The majority of ocean color models produced in situ NPP trends that were closer to the observed trends when chlorophyll-a was derived from high-performance liquid chromatography (HPLC), rather than fluorometric or SeaWiFS data. However, this was a function of time such that average trend magnitude was more accurately estimated over longer time periods. Among BOGCMs, only two individual models successfully produced an increasing NPP trend (one model at each site). We caution against the use of models to assess multiannual changes in NPP over short time periods. Ocean color model estimates of NPP trends could improve if more high quality HPLC chlorophyll-a time series were available.

5. Stock, Charles A., and John P Dunne, January 2010: Controls on the ratio of mesozooplankton production to primary production in marine ecosystems. Deep-Sea Research, Part I, 57(1), doi:10.1016/j.dsr.2009.10.006.
   [ Abstract ]

   An ecosystem model was used to (1) determine the extent to which global trends in the ratio of mesozooplankton production to primary production (referred to herein as the “z-ratio”) can be explained by nutrient enrichment, temperature, and euphotic zone depth, and (2) quantitatively diagnose the mechanisms driving these trends. Equilibrium model solutions were calibrated to observed and empirically derived patterns in phytoplankton biomass and growth rates, mesozooplankton biomass and growth rates, and the fraction of phytoplankton that are large (>5 μm ESD). This constrained several otherwise highly uncertain model parameters. Most notably, half-saturation constants for zooplankton feeding were constrained by the biomass and growth rates of their prey populations, and low zooplankton basal metabolic rates were required to match observations from oligotrophic ecosystems. Calibrated model solutions had no major biases and produced median z-ratios and ranges consistent with estimates. However, much of the variability around the median values in the calibration dataset (72 points) could not be explained. Model results were then compared with an extended global compilation of z-ratio estimates (>10 000 points). This revealed a modest yet significant (r=0.40) increasing trend in z-ratios from values 0.01–0.04 to 0.1–0.2 with increasing primary productivity, with the transition from low to high z-ratios occurring at lower primary productivity in cold-water ecosystems. Two mechanisms, both linked to increasing phytoplankton biomass, were responsible: (1) zooplankton gross growth efficiencies increased as their ingestion rates became much greater than basal metabolic rates and (2) the trophic distance between primary producers and mesozooplankton shortened as primary production shifted toward large phytoplankton. Mechanism (1) was most important during the transition from low to moderate productivity ecosystems and mechanism (2) was responsible for a relatively abrupt transition to values >0.1 in high productivity ecosystems. Substantial z-ratio variations overlying these mean trends remained unexplained by these mechanisms. Potential sources of this variability include zooplankton patchiness, unresolved effects of advection and unsteady dynamics, unresolved shifts in mesozooplankton sizes and species, and unresolved aspects of zooplankton bioenergetics. Comparison of the modeled z-ratio patterns and mechanisms diagnosed herein with those obtained using models with expanded biological dynamics embedded in global circulation models will help further elucidate the causes of this variation.

6. Christensen, V, John P Dunne, and Jorge L Sarmiento, et al., September 2009: Database-driven models of the world's Large Marine Ecosystems. Ecological Modelling, 220(17), doi:10.1016/j.ecolmodel.2009.04.041.
   [ Abstract ]

   We present a new methodology for database-driven ecosystem model generation and apply the methodology to the world's 66 currently defined Large Marine Ecosystems. The method relies on a large number of spatial and temporal databases, including FishBase, SeaLifeBase, as well as several other databases developed notably as part of the Sea Around Us project. The models are formulated using the freely available Ecopath with Ecosim (EwE) modeling approach and software. We tune the models by fitting to available time series data, but recognize that the models represent only a first-generation of database-driven ecosystem models. We use the models to obtain a first estimate of fish biomass in the world's LMEs. The biggest hurdles at present to further model development and validation are insufficient time series trend information, and data on spatial fishing effort.

7. Friedrichs, M A., and John P Dunne, et al., February 2009: Assessing the uncertainties of model estimates of primary productivity in the tropical Pacific Ocean. Journal of Marine Systems, 76(1-2), doi:10.1016/j.jmarsys.2008.05.010.
   [ Abstract ]

   Depth-integrated primary productivity (PP) estimates obtained from satellite ocean color-based models (SatPPMs) and those generated from biogeochemical ocean general circulation models (BOGCMs) represent a key resource for biogeochemical and ecological studies at global as well as regional scales. Calibration and validation of these PP models are not straightforward, however, and comparative studies show large differences between model estimates. The goal of this paper is to compare PP estimates obtained from 30 different models (21 SatPPMs and 9 BOGCMs) to a tropical Paci fic PP database consisting of ~1000 ¹⁴C measurements spanning more than a decade (1983–1996). Primary findings include: skill varied significantly between models, but performance was not a function of model complexity or type (i.e. SatPPM vs. BOGCM); nearly all models underestimated the observed variance of PP, specifically yielding too few low PP (<0.2 g Cm^-2 d^-1) values; more than half of the total root-mean-squared model–data differences associated with the satellite-based PP models might be accounted for by uncertainties in the input variables and/or the PP data; and the tropical Pacific database captures a broad scale shift from low biomass normalized productivity in the 1980s to higher biomass-normalized productivity in the 1990s, which was not successfully captured by any of the models. This latter result suggests that interdecadal and global changes will be a significant challenge for both SatPPMs and BOGCMs. Finally, average root-mean-squared differences between in situ PP data on the equator at 140°W and PP estimates from the satellite-based productivity models were 58% lower than analogous values computed in a previous PP model comparison 6 years ago. The success of these types of comparison exercises is illustrated by the continual modification and improvement of the participating models and the resulting increase in model skill.

8. Henson, S A., John P Dunne, and Jorge L Sarmiento, April 2009: Decadal variability in North Atlantic phytoplankton blooms. Journal of Geophysical Research, 114, C04013, doi:10.1029/2008JC005139.
   [ Abstract ]

   The interannual to decadal variability in the timing and magnitude of the North Atlantic phytoplankton bloom is examined using a combination of satellite data and output from an ocean biogeochemistry general circulation model. The timing of the bloom as estimated from satellite chlorophyll data is used as a novel metric for validating the model's skill. Maps of bloom timing reveal that the subtropical bloom begins in winter and progresses northward starting in May in subpolar regions. A transition zone, which experiences substantial interannual variability in bloom timing, separates the two regions. Time series of the modeled decadal (1959–2004) variability in bloom timing show no long‐term trend toward earlier or delayed blooms in any of the three regions considered here. However, the timing of the subpolar bloom does show distinct decadal‐scale periodicity, which is found to be correlated with the North Atlantic Oscillation (NAO) index. The mechanism underpinning the relationship is identified as anomalous wind‐driven mixing conditions associated with the NAO. In positive NAO phases, stronger westerly winds result in deeper mixed layers, delaying the start of the subpolar spring bloom by 2–3 weeks. The subpolar region also expands during positive phases, pushing the transition zone further south in the central North Atlantic. The magnitude of the bloom is found to be only weakly dependent on bloom timing, but is more strongly correlated with mixed layer depth. The extensive interannual variability in the timing of the bloom, particularly in the transition region, is expected to strongly impact the availability of food to higher trophic levels.

9. Henson, S A., D Raitsos, John P Dunne, and A McQuatters-Gollop, November 2009: Decadal variability in biogeochemical models: Comparison with a 50-year ocean colour dataset. Geophysical Research Letters, 36(L21601), doi:10.1029/2009GL040874.
   [ Abstract ]

   Assessing the skill of biogeochemical models to hindcast past variability is challenging, yet vital in order to assess their ability to predict biogeochemical change. However, the validation of decadal variability is limited by the sparsity of consistent, long-term biological datasets. The Phytoplankton Colour Index (PCI) product from the Continuous Plankton Recorder survey, which has been sampling the North Atlantic since 1948, is an example of such a dataset. Converting the PCI to chlorophyll values using SeaWiFS data allows a direct comparison with model output. Here we validate decadal variability in chlorophyll from the GFDL TOPAZ model. The model demonstrates skill at reproducing interannual variability, but cannot simulate the regime shifts evident in the PCI data. Comparison of the model output, data and climate indices highlights under-represented processes that it may be necessary to include in future biogeochemical models in order to accurately simulate decadal variability in ocean ecosystems.

10. Rodgers, K B., Robert M Key, Anand Gnanadesikan, Jorge L Sarmiento, John P Dunne, and A R Jacobson, et al., September 2009: Using altimetry to help explain patchy changes in hydrographic carbon measurements. Journal of Geophysical Research, C09013, doi:10.1029/2008JC005183.
    [ Abstract ]

    Here we use observations and ocean models to identify mechanisms driving large seasonal to interannual variations in dissolved inorganic carbon (DIC) and dissolved oxygen (O₂) in the upper ocean. We begin with observations linking variations in upper ocean DIC and O₂ inventories with changes in the physical state of the ocean. Models are subsequently used to address the extent to which the relationships derived from short-timescale (6 months to 2 years) repeat measurements are representative of variations over larger spatial and temporal scales. The main new result is that convergence and divergence (column stretching) attributed to baroclinic Rossby waves can make a first-order contribution to DIC and O₂ variability in the upper ocean. This results in a close correspondence between natural variations in DIC and O₂ column inventory variations and sea surface height (SSH) variations over much of the ocean. Oceanic Rossby wave activity is an intrinsic part of the natural variability in the climate system and is elevated even in the absence of significant interannual variability in climate mode indices. The close correspondence between SSH and both DIC and O₂ column inventories for many regions suggests that SSH changes (inferred from satellite altimetry) may prove useful in reducing uncertainty in separating natural and anthropogenic DIC signals (using measurements from Climate Variability and Predictability's CO₂/Repeat Hydrography program). Correction: 10.1029/2009JC005835

11. Anderson, Whit G., Anand Gnanadesikan, Robert W Hallberg, John P Dunne, and Bonita L Samuels, June 2007: Impact of ocean color on the maintenance of the Pacific Cold Tongue. Geophysical Research Letters, 34, L11609, doi:10.1029/2007GL030100.
    [ Abstract ]

    The impact of the penetration length scale of shortwave radiation into the surface ocean is investigated with a fully coupled ocean, atmosphere, land and ice model. Oceanic shortwave radiation penetration is assumed to depend on the chlorophyll concentration. As chlorophyll concentrations increase the distribution of shortwave heating becomes shallower. This change in heat distribution impacts mixed-layer depth. This study shows that removing all chlorophyll from the ocean results in a system that tends strongly towards an El Niño state—suggesting that chlorophyll is implicated in maintenance of the Pacific cold tongue. The regions most responsible for this response are located off-equator and correspond to the oligotrophic gyres. Results from a suite of surface chlorophyll perturbation experiments suggest a potential positive feedback between chlorophyll concentration and a non-local coupled response in the fully coupled ocean-atmosphere system.

12. Deutsch, Curtis A., Jorge L Sarmiento, D M Sigman, N Gruber, and John P Dunne, 2007: Spatial coupling of nitrogen inputs and losses in the ocean. Nature, 445(7124), doi:10.1038/nature05392.
    [ Abstract ]

    Nitrogen fixation is crucial for maintaining biological productivity in the oceans, because it replaces the biologically available nitrogen that is lost through denitrification. But, owing to its temporal and spatial variability, the global distribution of marine nitrogen fixation is difficult to determine from direct shipboard measurements. This uncertainty limits our understanding of the factors that influence nitrogen fixation, which may include iron, nitrogen-to-phosphorus ratios, and physical conditions such as temperature. Here we determine nitrogen fixation rates in the world's oceans through their impact on nitrate and phosphate concentrations in surface waters, using an ocean circulation model. Our results indicate that nitrogen fixation rates are highest in the Pacific Ocean, where water column denitrification rates are high but the rate of atmospheric iron deposition is low. We conclude that oceanic nitrogen fixation is closely tied to the generation of nitrogen-deficient waters in denitrification zones, supporting the view that nitrogen fixation stabilizes the oceanic inventory of fixed nitrogen over time.

13. Dunne, John P., Jorge L Sarmiento, and Anand Gnanadesikan, 2007: A synthesis of global particle export from the surface ocean and cycling through the ocean interior and on the seafloor. Global Biogeochemical Cycles, 21, GB4006, doi:10.1029/2006GB002907.
    [ Abstract ]

    We present a new synthesis of the oceanic cycles of organic carbon, silicon, and calcium carbonate. Our calculations are based on a series of algorithms starting with satellite-based primary production and continuing with conversion of primary production to sinking particle flux, penetration of particle flux to the deep sea, and accumulation in sediments. Regional and global budgets from this synthesis highlight the potential importance of shelves and near-shelf regions for carbon burial. While a high degree of uncertainty remains, this analysis suggests that shelves, less than 50 m water depths accounting for 2% of the total ocean area, may account for 48% of the global flux of organic carbon to the seafloor. Our estimates of organic carbon and nitrogen flux are in generally good agreement with previous work while our estimates for CaCO₃ and SiO₂ fluxes are lower than recent work. Interannual variability in particle export fluxes is found to be relatively small compared to intra-annual variability over large domains with the single exception of the dominating role of El Niño-Southern Oscillation variability in the central tropical Pacific. Comparison with available sediment-based syntheses of benthic remineralization and burial support the recent theory of mineral protection of organic carbon flux through the deep ocean, pointing to lithogenic material as an important carrier phase of organic carbon to the deep seafloor. This work suggests that models which exclude the role of lithogenic material would underestimate the penetration of POC to the deep seafloor by approximately 16–51% globally, and by a much larger fraction in areas with low productivity. Interestingly, atmospheric dust can only account for 31% of the total lithogenic flux and 42% of the lithogenically associated POC flux, implying that a majority of this material is riverine or directly erosional in origin.

14. Friedrichs, M A., J A Dusenberry, L A Anderson, R A Armstrong, F Chai, J R Christian, S C Doney, John P Dunne, M Fujii, R Hood, D J McGillicuddy, Jr, J K Moore, M Schartau, Y H Spitz, and J D Wiggert, 2007: Assessment of skill and portability in regional marine biogeochemical models: Role of multiple planktonic groups. Journal of Geophysical Research, 112, C08001, doi:10.1029/2006JC003852.
    [ Abstract ]

    Application of biogeochemical models to the study of marine ecosystems is pervasive, yet objective quantification of these models' performance is rare. Here, 12 lower trophic level models of varying complexity are objectively assessed in two distinct regions (equatorial Pacific and Arabian Sea). Each model was run within an identical one-dimensional physical framework. A consistent variational adjoint implementation assimilating chlorophyll-a, nitrate, export, and primary productivity was applied and the same metrics were used to assess model skill. Experiments were performed in which data were assimilated from each site individually and from both sites simultaneously. A cross-validation experiment was also conducted whereby data were assimilated from one site and the resulting optimal parameters were used to generate a simulation for the second site. When a single pelagic regime is considered, the simplest models fit the data as well as those with multiple phytoplankton functional groups. However, those with multiple phytoplankton functional groups produced lower misfits when the models are required to simulate both regimes using identical parameter values. The cross-validation experiments revealed that as long as only a few key biogeochemical parameters were optimized, the models with greater phytoplankton complexity were generally more portable. Furthermore, models with multiple zooplankton compartments did not necessarily outperform models with single zooplankton compartments, even when zooplankton biomass data are assimilated. Finally, even when different models produced similar least squares model-data misfits, they often did so via very different element flow pathways, highlighting the need for more comprehensive data sets that uniquely constrain these pathways.

15. Delworth, Thomas L., Anthony J Broccoli, Anthony Rosati, Ronald J Stouffer, Ventakramani Balaji, J A Beesley, W F Cooke, Keith W Dixon, John P Dunne, Krista A Dunne, J W Durachta, Kirsten L Findell, Paul Ginoux, Anand Gnanadesikan, C Tony Gordon, Stephen Griffies, Rich Gudgel, Matthew J Harrison, Isaac Held, Richard S Hemler, Larry Horowitz, Stephen A Klein, Thomas R Knutson, P J Kushner, A R Langenhorst, H C Lee, Shian-Jiann Lin, Jian Lu, S Malyshev, P C D Milly, V Ramaswamy, J L Russell, M Daniel Schwarzkopf, Elena Shevliakova, Joseph J Sirutis, Michael J Spelman, William F Stern, Michael Winton, Andrew T Wittenberg, Bruce Wyman, Fanrong Zeng, and Rong Zhang, 2006: GFDL's CM2 Global Coupled Climate Models. Part I: Formulation and Simulation Characteristics. Journal of Climate, 19(5), doi:10.1175/JCLI3629.1.
    [ Abstract ]

    The formulation and simulation characteristics of two new global coupled climate models developed at NOAA's Geophysical Fluid Dynamics Laboratory (GFDL) are described. The models were designed to simulate atmospheric and oceanic climate and variability from the diurnal time scale through multicentury climate change, given our computational constraints. In particular, an important goal was to use the same model for both experimental seasonal to interannual forecasting and the study of multicentury global climate change, and this goal has been achieved. Two versions of the coupled model are described, called CM2.0 and CM2.1. The versions differ primarily in the dynamical core used in the atmospheric component, along with the cloud tuning and some details of the land and ocean components. For both coupled models, the resolution of the land and atmospheric components is 2° latitude × 2.5° longitude; the atmospheric model has 24 vertical levels. The ocean resolution is 1° in latitude and longitude, with meridional resolution equatorward of 30° becoming progressively finer, such that the meridional resolution is 1/3° at the equator. There are 50 vertical levels in the ocean, with 22 evenly spaced levels within the top 220 m. The ocean component has poles over North America and Eurasia to avoid polar filtering. Neither coupled model employs flux adjustments. The control simulations have stable, realistic climates when integrated over multiple centuries. Both models have simulations of ENSO that are substantially improved relative to previous GFDL coupled models. The CM2.0 model has been further evaluated as an ENSO forecast model and has good skill (CM2.1 has not been evaluated as an ENSO forecast model). Generally reduced temperature and salinity biases exist in CM2.1 relative to CM2.0. These reductions are associated with 1) improved simulations of surface wind stress in CM2.1 and associated changes in oceanic gyre circulations; 2) changes in cloud tuning and the land model, both of which act to increase the net surface shortwave radiation in CM2.1, thereby reducing an overall cold bias present in CM2.0; and 3) a reduction of ocean lateral viscosity in the extratropics in CM2.1, which reduces sea ice biases in the North Atlantic. Both models have been used to conduct a suite of climate change simulations for the 2007 Intergovernmental Panel on Climate Change (IPCC) assessment report and are able to simulate the main features of the observed warming of the twentieth century. The climate sensitivities of the CM2.0 and CM2.1 models are 2.9 and 3.4 K, respectively. These sensitivities are defined by coupling the atmospheric components of CM2.0 and CM2.1 to a slab ocean model and allowing the model to come into equilibrium with a doubling of atmospheric CO2. The output from a suite of integrations conducted with these models is freely available online (see http://nomads.gfdl.noaa.gov/). Manuscript received 8 December 2004, in final form 18 March 2005

16. Gnanadesikan, Anand, Keith W Dixon, Stephen Griffies, Ventakramani Balaji, M Barreiro, J A Beesley, W F Cooke, Thomas L Delworth, R Gerdes, Matthew J Harrison, Isaac Held, William J Hurlin, H C Lee, Z Liang, G Nong, Ronald C Pacanowski, Anthony Rosati, J L Russell, Bonita L Samuels, Qian Song, Michael J Spelman, Ronald J Stouffer, C Sweeney, Gabriel A Vecchi, Michael Winton, Andrew T Wittenberg, Fanrong Zeng, Rong Zhang, and John P Dunne, 2006: GFDL's CM2 Global Coupled Climate Models. Part II: The baseline ocean simulation. Journal of Climate, 19(5), doi:10.1175/JCLI3630.1.
    [ Abstract ]

    The current generation of coupled climate models run at the Geophysical Fluid Dynamics Laboratory (GFDL) as part of the Climate Change Science Program contains ocean components that differ in almost every respect from those contained in previous generations of GFDL climate models. This paper summarizes the new physical features of the models and examines the simulations that they produce. Of the two new coupled climate model versions 2.1 (CM2.1) and 2.0 (CM2.0), the CM2.1 model represents a major improvement over CM2.0 in most of the major oceanic features examined, with strikingly lower drifts in hydrographic fields such as temperature and salinity, more realistic ventilation of the deep ocean, and currents that are closer to their observed values. Regional analysis of the differences between the models highlights the importance of wind stress in determining the circulation, particularly in the Southern Ocean. At present, major errors in both models are associated with Northern Hemisphere Mode Waters and outflows from overflows, particularly the Mediterranean Sea and Red Sea.

17. Jin, X, N Gruber, John P Dunne, Jorge L Sarmiento, and R A Armstrong, 2006: Diagnosing the contribution of phytoplankton functional groups to the production and export of particulate organic carbon, CaCO3, and opal from global nutrient and alkalinity distributions. Global Biogeochemical Cycles, 20, GB2015, doi:10.1029/2005GB002532.
    [ Abstract ]

    We diagnose the contribution of four main phytoplankton functional groups to the production and export of particulate organic carbon (POC), CaCO3, and opal by combining in a restoring approach global oceanic observations of nitrate, silicic acid, and alkalinity with a simple size-dependent ecological/biogeochemical model. In order to determine the robustness of our results, we employ three different variants of the ocean general circulation model (OGCM) required to transport and mix the nutrients and alkalinity into the upper ocean. In our standard model, the global export of CaCO3 is diagnosed as 1.1 PgC yr−1 (range of sensitivity cases 0.8 to 1.2 PgC yr−1) and that of opal as 180 Tmol Si yr−1 (range 160 to 180 Tmol Si yr−1). CaCO3 export is found to have three maxima at approximately 40¡ÆS, the equator, and around 40¡ÆN. In contrast, the opal export is dominated by the Southern Ocean with a single maximum at around 60¡ÆS. The molar export ratio of inorganic to organic carbon is diagnosed in our standard model to be about 0.09 (range 0.07 to 0.10) and found to be remarkably uniform spatially. The molar export ratio of opal to organic nitrogen varies substantially from values around 2 to 3 in the Southern Ocean south of 45¡ÆS to values below 0.5 throughout most of the rest of the ocean, except for the North Pacific. Irrespective of which OGCM is used, large phytoplankton dominate the export of POC, with diatoms alone accounting for 40% of this export, while the contribution of coccolithophorids is only about 10%. Small phytoplankton dominate net primary production (NPP) with a fraction of ¡­70%. Diatoms and coccolithophorids account for about 15% and less than 2% of NPP, respectively. These diagnosed contributions of the main phytoplankton functional groups to NPP are also robust across all OGCMs investigated. Correlation and regression analyses reveal that the variations in the relative contributions of diatoms and coccolithophorids to NPP can be predicted reasonably well on the basis of a few key parameters.

18. Dunne, John P., R A Armstrong, Anand Gnanadesikan, and Jorge L Sarmiento, 2005: Empirical and mechanistic models for the particle export ratio. Global Biogeochemical Cycles, 19, GB4026, doi:10.1029/2004GB002390.
    [ Abstract ]

    We present new empirical and mechanistic models for predicting the export of organic carbon out of the surface ocean by sinking particles. To calibrate these models, we have compiled a synthesis of field observations related to ecosystem size structure, primary production and particle export from around the globe. The empirical model captures 61% of the observed variance in the ratio of particle export to primary production (the pe ratio) using sea-surface temperature and chlorophyll concentrations (or primary productivity) as predictor variables. To describe the mechanisms responsible for pe-ratio variability, we present size-based formulations of phytoplankton grazing and sinking particle export, combining them into an alternative, mechanistic model. The formulation of grazing dynamics, using simple power laws as closure terms for small and large phytoplankton, reproduces 74% of the observed variability in phytoplankton community composition wherein large phytoplankton augment small ones as production increases. The formulation for sinking particle export partitions a temperature-dependent fraction of small and large phytoplankton grazing into sinking detritus. The mechanistic model also captures 61% of the observed variance in pe ratio, with large phytoplankton in high biomass and relatively cold regions leading to more efficient export. In this model, variability in primary productivity results in a biomass-modulated switch between small and large phytoplankton pathways.

19. Griffies, Stephen, Anand Gnanadesikan, Keith W Dixon, John P Dunne, R Gerdes, Matthew J Harrison, Anthony Rosati, J L Russell, Bonita L Samuels, Michael J Spelman, Michael Winton, and Rong Zhang, 2005: Formulation of an ocean model for global climate simulations. Ocean Science, 1, 45-79.
    [ Abstract PDF ]

    This paper summarizes the formulation of the ocean component to the Geophysical Fluid Dynamics Laboratory's (GFDL) climate model used for the 4th IPCC Assessment (AR4) of global climate change. In particular, it reviews the numerical schemes and physical parameterizations that make up an ocean climate model and how these schemes are pieced together for use in a state-of-the-art climate model. Features of the model described here include the following: (1) tripolar grid to resolve the Arctic Ocean without polar filtering, (2) partial bottom step representation of topography to better represent topographically influenced advective and wave processes, (3) more accurate equation of state, (4) three-dimensional flux limited tracer advection to reduce overshoots and undershoots, (5) incorporation of regional climatological variability in shortwave penetration, (6) neutral physics parameterization for representation of the pathways of tracer transport, (7) staggered time stepping for tracer conservation and numerical efficiency, (8) anisotropic horizontal viscosities for representation of equatorial currents, (9) parameterization of exchange with marginal seas, (10) incorporation of a free surface that accomodates a dynamic ice model and wave propagation, (11) transport of water across the ocean free surface to eliminate unphysical "virtual tracer flux" methods, (12) parameterization of tidal mixing on continental shelves. We also present preliminary analyses of two particularly important sensitivities isolated during the development process, namely the details of how parameterized subgridscale eddies transport momentum and tracers.

20. Gnanadesikan, Anand, John P Dunne, Robert M Key, K Matsumoto, Jorge L Sarmiento, Richard D Slater, and P S Swathi, 2004: Oceanic ventilation and biogeochemical cycling: Understanding the physical mechanisms that produce realistic distributions of tracers and productivity. Global Biogeochemical Cycles, 18(4), GB4010, doi:10.1029/2003GB002097.
    [ Abstract ]

    Differing models of the ocean circulation support different rates of ventilation, which in turn produce different distributions of radiocarbon, oxygen, and export production. We examine these fields within a suite of general circulation models run to examine the sensitivity of the circulation to the parameterization of subgridscale mixing and surface forcing. We find that different models can explain relatively high fractions of the spatial variance in some fields such as radiocarbon, and that newer estimates of the rate of biological cycling are in better agreement with the models than previously published estimates. We consider how different models achieve such agreement and show that they can accomplish this in different ways. For example, models with high vertical diffusion move young surface waters into the Southern Ocean, while models with high winds move more young North Atlantic water into this region. The dependence on parameter values is not simple. Changes in the vertical diffusion coefficient, for example, can produce major changes in advective fluxes. In the coarse-resolution models studied here, lateral diffusion plays a major role in the tracer budget of the deep ocean, a somewhat worrisome fact as it is poorly constrained both observationally and theoretically.

21. Sarmiento, Jorge L., N Gruber, M Brzezinski, and John P Dunne, 2004: High-latitude controls of thermocline nutrients and low latitude biological productivity. Nature, 427, 56-60.
    [ Abstract PDF ]

    The ocean's biological pump strips nutrients out of the surface waters and exports them into the thermocline and deep waters. If there were no return path of nutrients from deep waters, the biological pump would eventually deplete the surface waters and thermocline of nutrients; surface biological productivity would plummet. Here we make use of the combined distributions of silicic acid and nitrate to trace the main nutrient return path from deep waters by upwelling in the Southern Ocean and subsequent entrainment into subantarctic mode water. We show that the subantarctic mode water, which spreads throughout the entire Southern Hemisphere and North Atlantic Ocean, is the main source of nutrients for the thermocline. We also find that an additional return path exists in the northwest corner of the Pacific Ocean, where enhanced vertical mixing, perhaps driven by tides, brings abyssal nutrients to the surface and supplies them to the thermocline of the North Pacific. Our analysis has important implications for our understanding of large-scale controls on the nature and magnitude of low-latitude biological productivity and its sensitivity to climate change.

22. Dunne, John P., A H Devol, and S Emerson, 2002: The Oceanic Remote Chemical/Optical Analyzer (ORCA)--An autonomous moored profiler. Journal of Atmospheric and Oceanic Technology, 19(10), 1709-1721.
    [ Abstract PDF ]

    An autonomous, moored profiler [the Oceanic Remote Chemical/Optical Analyzer (ORCA)] was developed to sense a variety of chemical and optical properties in the upper water column. It is presently used to monitor water quality parameters in South Puget Sound--a largely undeveloped area subject to extensive future urbanization. ORCA has three main components: 1) a three-point moored Autonomous Temperature Line Acquisition System (ATLAS) toroidal float; 2) a profiling assembly on the float with computer, winch, cellular system, meteorological sensors (wind, temperature, humidity, irradiance), solar panels, and batteries; and 3) an underwater sensor package consisting of a Seabird CTD profiler, YSI dissolved oxygen electrode, Wetlabs transmissometer, and Wetlabs chlorophyll fluorometer. At regular sampling intervals, ORCA profiles the water column using the winch and pressure information from the CTD. The data are recorded on the computer and transmitted to the lab automatically via cellular communications. Data are presented from a 1-day deployment in May 2000 and from a long-term, 7-month deployment. The dataset reveals the combination of intermittent stratification mixing and strong seasonal forcing in this estuarine system.

23. Sarmiento, Jorge L., John P Dunne, Anand Gnanadesikan, Robert M Key, K Matsumoto, and Richard D Slater, 2002: A new estimate of the CaCO3 to organic carbon export ratio. Global Biogeochemical Cycles, 16(4), doi:10.1029/2002GB001919.
    [ Abstract ]

    We use an ocean biogeochemical-transport box model of the top 100 m of the water column to estimate the CaCO3 to organic carbon export ratio from observations of the vertical gradients of potential alkalinity and nitrate. We find a global average molar export ratio of 0.06 ± 0.03. This is substantially smaller than earlier estimates of 0.25 on which a majority of ocean biogeochemical models had based their parameterization of CaCO3 production. Contrary to the pattern of coccolithophore blooms determined from satellite observations, which show high latitude predominance, we find maximum export ratios in the equatorial region and generally smaller ratios in the subtropical and subpolar gyres. Our results suggest a dominant contribution to global calcification by low-latitude nonbloom forming coccolithophores or other organisms such as foraminifera and pteropods.

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