Bibliography - John Dunne

1. Friedrichs, M A., and John 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.

2. Henson, S A., John 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.

3. Stock, Charles A., and John Dunne, in press: Controls on the ratio of mesozooplankton production to primary production in marine ecosystems. Deep-Sea Research, Part I. 2/09.
4. Anderson, Whit G., Anand Gnanadesikan, Robert W Hallberg, John 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.

5. Deutsch, Curtis A., Jorge L Sarmiento, D M Sigman, N Gruber, and John 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.

6. Dunne, John, 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.

7. Friedrichs, M A., J A Dusenberry, L A Anderson, R A Armstrong, F Chai, J R Christian, S C Doney, John 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.

8. Delworth, Thomas L., Anthony J Broccoli, Anthony Rosati, Ronald J Stouffer, Ventakramani Balaji, J A Beesley, W F Cooke, Keith W Dixon, John 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

9. 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, G A Vecchi, Michael Winton, Andrew T Wittenberg, Fanrong Zeng, Rong Zhang, and John 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.

10. Jin, X, N Gruber, John 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.

11. Dunne, John, 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.

12. Griffies, Stephen, Anand Gnanadesikan, Keith W Dixon, John 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.

13. Gnanadesikan, Anand, John 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.

14. Sarmiento, Jorge L., N Gruber, M Brzezinski, and John 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.

15. Dunne, John, 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.

16. Sarmiento, Jorge L., John 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:10.1029/2002/GB001919.
    [ 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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