Stable isotopes reduce parameter uncertainty of an estuarine carbon cycling model

Alpine, 1992, Trophic interactions and direct physical effects control phytoplankton biomass and production in an estuary, Limnol. Oceanogr., 37, 946, 10.4319/lo.1992.37.5.0946 Arhonditsis, 2006, Evaluation of the current state of mechastic aquatic biogeochemical modeling: citation analysis and future perspectives, Environ. Sci. Technol., 40, 6547, 10.1021/es061030q Arhonditsis, 2008, Addressing equifinality and uncertainty in eutrophication models, Water Resour. Res., 44, W01420, 10.1029/2007WR005862 Atkins, 2013, Carbon dioxide dynamics driven by groundwater discharge in a coastal floodplain creek, J. Hydrol., 30, 10.1016/j.jhydrol.2013.04.008 Bennett, 2013, Characterising performance of environmental models, Environ. Model. Soft, 40, 1, 10.1016/j.envsoft.2012.09.011 BMT-WBM, 2014 Bruce, 2014, Hydrodynamic controls on oxygen dynamics in a riverine salt wedge estuary, the Yarra River estuary, Australia, Hydrol. Earth Syst. Sci., 18, 1397, 10.5194/hess-18-1397-2014 Bruggeman, 2014, A general framework for aquatic biogeochemical models, Environ. Model. Soft, 61, 249, 10.1016/j.envsoft.2014.04.002 Butler, 1998 Cai, 2011, Estuarine and coastal ocean carbon paradox: CO2 sinks or sites of terresterial carbon incineration, Annu. Rev. Mar. Sci., 3, 123, 10.1146/annurev-marine-120709-142723 Clark, 2005, Why environmental scientists are becoming Bayesians, Ecol. Lett., 8, 2, 10.1111/j.1461-0248.2004.00702.x Cloern, 2014, Phytoplankton primary production in the world's estuarine-coastal ecosystems, Biogeosciences, 11, 2477, 10.5194/bg-11-2477-2014 Dang, 2014, Perspectives on the microbial carbon pump with special reference to microbial respiration and ecosystem efficiency in large estuarine systems, Biogeosciences, 11, 3887, 10.5194/bg-11-3887-2014 Eyre, 1997, Importance of marine inputs to the sediment and nutrient load of coastal-plan estuaries: a case study of pumicestone passage, south-eastern Queensland, Australia, Mar. Freshwater Res., 48, 277, 10.1071/MF96071 Eyre, 1998, Transport, retention and transformation of material in Australian Estuaries, Estuaries, 21A, 540, 10.2307/1353293 Eyre, 2000, A regional evaluation of nutrient transformation and phytoplankton growth in nine river dominated sub-tropical East Australian estuaries, Mar. Ecol. Prog. Ser., 205, 61, 10.3354/meps205061 Eyre, 2006, Impact of a flood event on benthic and pelagic coupling in a sub-tropical east Australian estuary (Brunswick), Estuar. Coast. Shelf S, 66, 111, 10.1016/j.ecss.2005.08.008 Eyre, 2011, Metabolism of different benthic habitats and their contribution to the carbon budget of a shallow oligotrophic subtropical coastal system, Biogeochemistry, 103, 87, 10.1007/s10533-010-9424-7 Eyre, 2011 Fasham, 1990, A nitrogen-based model of plankton dynamic in the ocean mixed layer, J. Mar. Res., 48, 591, 10.1357/002224090784984678 Fasham, 2003 Ferguson, 2010, Carbon and nitrogen cycling in a shallow productive sub-tropical coastal embayment (Western Moreton Bay, Australia): the importance of pelagic-benthic coupling, Ecosystem, 13, 1127, 10.1007/s10021-010-9378-6 Fontana, 2009, Assimilation of SeaWiFS chlorophyll data into a 3D-coupled physical-biogeochemical model applied to a freshwater-influenced coastal zone, Cont. Shelf Res., 29, 1397, 10.1016/j.csr.2009.03.005 Fry, 2006, xii+308 Gal, 2009, Implementation of ecological modeling as an effective management and investigation tool: Lake Kinneret as a case study, Ecol. Model, 220, 1697, 10.1016/j.ecolmodel.2009.04.010 Gal, 2014, Novel approaches to address challenges in modelling aquatic ecosystems, Environ. Model. Soft, 61, 246, 10.1016/j.envsoft.2014.08.008 Geweke, 1992, Evaluating the accuracy of sampling based approaches to the calculation of posterior moments, 169 Grabe, 2010 Haario, 2006, DRAM: efficient adaptive MCMC, Stat. Comput., 16, 339, 10.1007/s11222-006-9438-0 Hamilton, 1992, Stable carbon and nitrogen isotopes in algae and detritus from the Orinoco River floodplain, Venezuela, Geochim. Cosmochim. Ac, 56, 4237, 10.1016/0016-7037(92)90264-J Harmon, 1997, A Markov chain Monte Carlo method for estimation and assimilation into models, Ecol. Model, 101, 41, 10.1016/S0304-3800(97)01947-9 Healthy Waterways, 2014 Hipsey, 2014, 22 Hofmann, 2000 Hullar, 1996, Microbial utilization of estuarine dissolved organic carbon: a stable isotope tracer approach tested by mass balance, App. Environ. Microbiol., 62, 2489, 10.1128/AEM.62.7.2489-2493.1996 Inoue, 1985, Carbon isotopic fractination during the CO2 exchange process between air and sea water under equilibrium and kinetic conditions, Geochim. Cosmochim. Ac, 49, 2453, 10.1016/0016-7037(85)90245-5 Johnson, 1982, Carbon dioxide hydration and dehydration kinetics in seawater, Limnol. Oceanogr., 27, 849, 10.4319/lo.1982.27.5.0849 Keeling, 2004 Kelley, 1990, Variations in sedimentary carbon remineralization rates in the White Oak River estuary, North Carolina, Linol. Oceanogr., 35, 372 Laws, 1995, Dependence on phytoplankton carbon isotopic composition on growth rate and [CO2]aq: theoretical considerations and experimental results, Geochim. Cosmochim. Ac, 59, 1131, 10.1016/0016-7037(95)00030-4 Londry, 2003, Stable carbon isotope fractionation by sulfate-reducing bacteria, Appl. Environ. Microbiol., 69, 2942, 10.1128/AEM.69.5.2942-2949.2003 Macklin, 2014, Estuarine canal estate waters: hotspots of CO2 outgassing driven by enhanced groundwater discharge?, Mar. Chem., 167, 82, 10.1016/j.marchem.2014.08.002 Maher, 2011, Insights into estuarine benthic dissolved organic carbon (DOC) dynamics using δ13C-DOC values, phospholipid fatty acids and dissolved organic nutrient fluxes, Geochim. Cosmochim. Ac, 75, 1889, 10.1016/j.gca.2011.01.007 Maher, 2012, Carbon budget for three autrotrophic Australian estuaries: Implications for global estimates of the coastal air-water CO2 flux, Glob. Biogeochem. Cy, 26, GB1032, 10.1029/2011GB004075 Maher, 2013, Groundwater-derived dissolved inorganic and organic carbon exports from a mangrove tidal creek: the missing mangrove carbon sink?, Limnol. Oceanogr., 58, 475, 10.4319/lo.2013.58.2.0475 Maher, 2015, Methane and carbon dioxide dynamics in a subtropical estuary over a diel cycle: Insights from automated in situ radioactive and stable isotope measurements, Mar. Chem., 168, 69, 10.1016/j.marchem.2014.10.017 Mahlstein, 2011, Ocean heat transport as a cause for model uncertainty in projected arctic warming, J. Clim., 24, 1451, 10.1175/2010JCLI3713.1 Makings, 2014, Importance of budgets for estimating the input of groundwater-derived nutrients to an eutrophic tidal river and estuary, Estuar. Coast. Shelf. S, 143, 65, 10.1016/j.ecss.2014.02.003 Matson, 1990, Stable carbon isotopes and the C: N ratio in the estuaries of the pamlico and neuse Rivers, North Carolina, Limnol. Oceanogr., 35, 1290, 10.4319/lo.1990.35.6.1290 McDonald, 2012, 1-D test-bed calibration of a 3-D Lake Superior biogeochemical model, Ecol. Model, 225, 115, 10.1016/j.ecolmodel.2011.11.021 Mead, 2010, Surface water metabolism potential in a tropical estuary, Hilo Bay, Hawai'i, USA, during storm and non-storm conditions, Estuaries Coasts, 33, 1099, 10.1007/s12237-010-9317-y Missaghi, 2010, Evaluation and application of a three-dimensional water quality model in a shallow lake with complex morphometry, Ecol. Model, 221, 1512, 10.1016/j.ecolmodel.2010.02.006 Moriasi, 2007, Model evaluation guidelines for systematic quantification of accuracy in watershed simulations, Trans. ASABE, 50, 885, 10.13031/2013.23153 Murray, 1995, Phytoplankton exudation: exploitation of the microbial loop s a defence against algal viruses, J. Plankton Res., 17, 1079, 10.1093/plankt/17.5.1079 Murray, 2015, Bayesian state-space modelling on high-performance hardware using LibBi, J. Stat. Softw., 67 Oakes, 2010, Stable isotopes trace estuarine transformations of carbon and nitrogen from primary- and secondary-treated paper and pulp mill effluent, Environ. Sci. Technol., 44, 7411, 10.1021/es101789v O'Leary, 1992, Physical and chemical basis of carbon isotope fractionation in plants, Plant Cell Environ., 15, 1099, 10.1111/j.1365-3040.1992.tb01660.x Otero, 2000, Allocation of particulate organic carbon from different sources in two constrasting estuaries of southeastern U.S.A. Limnol, Oceanogr, 45, 1753 Parslow, 2013, Bayesian learning and predictability in a stochastic nonlinear dynamical model, Ecol. Appl., 23, 679, 10.1890/12-0312.1 Petrone, 2009, Bioavailability and composition of dissolved organic carbon and nitrogen in a near coastal catchment of south-western Australia, Biogeochemistry, 92, 27, 10.1007/s10533-008-9238-z Pierrot, 2009, Recommendations for autonomous underway pCO2 measuring systems and data-reduction routines, Deep-Sea Res. II, 56, 512, 10.1016/j.dsr2.2008.12.005 Raymond, 2001, DOC cycling in a temperate estuary: a mass balance approach using natural 14C and 13C isotopes, Limnol. Oceanogr., 46, 655, 10.4319/lo.2001.46.3.0655 Reda, 2008 Reignier, 2004, On the mixing processes in estuaries: the fractional freshwater method revisited, Estuaries, 27, 571, 10.1007/BF02907645 Reynolds, 2006 Robson, 2014, When do aquatic systems models provide useful predictions, what is changing, and what is next?, Environ. Model. Soft, 61, 287, 10.1016/j.envsoft.2014.01.009 Robson, 2008, Ten steps applied to development and evaluation of process-based biogeochemical models of estuaries, Environ. Model. Soft, 23, 369, 10.1016/j.envsoft.2007.05.019 Rödenbeck, 2013, Global surface-ocean pCO2 and sea-air CO2 flux variability from an observation-driven ocean mixed-layer scheme, Ocean. Sci., 9, 193, 10.5194/os-9-193-2013 Saeck, 2013, Changes to chronic nitrogen loading from sewage discharges modify standing stocks of coastal phytoplankton, Mar. Pollut. Bull., 71, 159, 10.1016/j.marpolbul.2013.03.020 Santos, 2012, The “salt wedge pump”: convection-driven pore-water exchange as a source of dissolved organic and inorganic carbon and nitrogen to an estuary, Limnol. Oceanogr., 57, 1415, 10.4319/lo.2012.57.5.1415 Santos, 2012, Coupling automated radon and carbon dioxide measurements in coastal waters, Environ. Sci. Technol., 46, 7685, 10.1021/es301961b Skerratt, 2013, Use of a high resolution 3D fully coupled hydrodynamic, sediment and biogeochemical model to understand estuarine nutrient dynamics under various water quality scenarios, Ocean. Coast. Manage., 83, 52, 10.1016/j.ocecoaman.2013.05.005 Smith, 2006, Responses of estuarine and coastal marine phytoplankton to nitrogen and phosphorus enrichment, Limnol. Oceanogr., 51, 377, 10.4319/lo.2006.51.1_part_2.0377 St-Jean, 2003, Automated quantitative and isotopic (C-13) analysis of dissolved inorganic carbon and dissolved organic carbon in continuous-flow using a total organic carbon analyser, Rapid Comm. Mass Spectrom., 17, 419, 10.1002/rcm.926 Tans, 1993, Oceanic 13C/12C observations: a new window on ocean CO2 uptake, Glob. Biogeochem. Cy, 7, 353, 10.1029/93GB00053 Volta, 2014, C-gem (v 1.0): a new, cost-efficient biogeochemical model for estuaries and its application to a funnel-shaped system, Geosci. Model Dev., 7, 1271, 10.5194/gmd-7-1271-2014 Wanninkhof, 1985, Kinetic fractination of the carbon isotopes 13C and 12C during transfer of CO2 from air to seawater, Tellus, 37B, 128, 10.1111/j.1600-0889.1985.tb00061.x Wanninkhof, 1992, Relationship between wind speed and gas exchange over the ocean, J. Geophys. Res., 97, 7373, 10.1029/92JC00188 Ward, 2010, Parameter optimisation techniques and the problem of under determination in marine biogeochemical models, J. Mar. Syst., 81, 34, 10.1016/j.jmarsys.2009.12.005 Weiss, 1974, Carbon dioxide in water and seawater: the solubility of a non-ideal gas, Mar. Chem., 2, 203, 10.1016/0304-4203(74)90015-2 Yoshioka, 1997, Phytoplankton carbon isotope fractination: equations accounting for CO2-concentrating mechanisms, J. Plankton Res., 19, 1455, 10.1093/plankt/19.10.1455 Zhang, 1995, Carbon isotope fractination during gas-water exchange and dissolution of CO2, Geochim. Cosmochim. Ac, 59, 107, 10.1016/0016-7037(95)91550-D Zhang, 1997, The total organic carbon export rate based on 13C and 12C of DIC budgets in the equatorial Pacific region, Deep-Sea Res. II, 44, 2163, 10.1016/S0967-0645(97)00032-5 Zhang, 2009, A Bayesian hierarchical framework for calibrating aquatic biogeochemical models, Ecol. Model, 220, 2142, 10.1016/j.ecolmodel.2009.05.023