scholarly journals Calibration of temperature-dependent ocean microbial processes in the cGENIE.muffin (v0.9.13) Earth system model

2021 ◽  
Vol 14 (1) ◽  
pp. 125-149
Author(s):  
Katherine A. Crichton ◽  
Jamie D. Wilson ◽  
Andy Ridgwell ◽  
Paul N. Pearson
Keyword(s):  
Organic Matter ◽  
Carbon Cycling ◽  
System Model ◽  
Earth System ◽  
Temperature Dependent ◽  
Poc Export ◽  
Dependent Processes ◽  
Global Carbon ◽  
Atmospheric Pco2

Abstract. Temperature is a master parameter in the marine carbon cycle, exerting a critical control on the rate of biological transformation of a variety of solid and dissolved reactants and substrates. Although in the construction of numerical models of marine carbon cycling, temperature has been long recognised as a key parameter in the production and export of organic matter at the ocean surface, its role in the ocean interior is much less frequently accounted for. There, bacteria (primarily) transform sinking particulate organic matter (POM) into its dissolved constituents and consume dissolved oxygen (and/or other electron acceptors such as sulfate). The nutrients and carbon thereby released then become available for transport back to the surface, influencing biological productivity and atmospheric pCO2, respectively. Given the substantial changes in ocean temperature occurring in the past, as well as in light of current anthropogenic warming, appropriately accounting for the role of temperature in marine carbon cycling may be critical to correctly projecting changes in ocean deoxygenation and the strength of feedbacks on atmospheric pCO2. Here we extend and calibrate a temperature-dependent representation of marine carbon cycling in the cGENIE.muffin Earth system model, intended for both past and future climate applications. In this, we combine a temperature-dependent remineralisation scheme for sinking organic matter with a biological export production scheme that also includes a dependence on ambient seawater temperature. Via a parameter ensemble, we jointly calibrate the two parameterisations by statistically contrasting model-projected fields of nutrients, oxygen, and the stable carbon isotopic signature (δ13C) of dissolved inorganic carbon in the ocean with modern observations. We additionally explore the role of temperature in the creation and recycling of dissolved organic matter (DOM) and hence its impact on global carbon cycle dynamics. We find that for the present day, the temperature-dependent version shows a fit to the data that is as good as or better than the existing tuned non-temperature-dependent version of the cGENIE.muffin. The main impact of accounting for temperature-dependent remineralisation of POM is in driving higher rates of remineralisation in warmer waters, in turn driving a more rapid return of nutrients to the surface and thereby stimulating organic matter production. As a result, more POM is exported below 80 m but on average reaches shallower depths in middle- and low-latitude warmer waters compared to the standard model. Conversely, at higher latitudes, colder water temperature reduces the rate of nutrient resupply to the surface and POM reaches greater depth on average as a result of slower subsurface rates of remineralisation. Further adding temperature-dependent DOM processes changes this overall picture only a little, with a slight weakening of export production at higher latitudes. As an illustrative application of the new model configuration and calibration, we take the example of historical warming and briefly assess the implications for global carbon cycling of accounting for a more complete set of temperature-dependent processes in the ocean. We find that between the pre-industrial era (ca. 1700) and the present (year 2010), in response to a simulated air temperature increase of 0.9 ∘C and an associated projected mean ocean warming of 0.12 ∘C (0.6 ∘C in surface waters and 0.02 ∘C in deep waters), a reduction in particulate organic carbon (POC) export at 80 m of just 0.3 % occurs (or 0.7 % including a temperature-dependent DOM response). However, due to this increased recycling nearer the surface, the efficiency of the transfer of carbon away from the surface (at 80 m) to the deep ocean (at 1040 m) is reduced by 5 %. In contrast, with no assumed temperature-dependent processes impacting production or remineralisation of either POM or DOM, global POC export at 80 m falls by 2.9 % between the pre-industrial era and the present day as a consequence of ocean stratification and reduced nutrient resupply to the surface. Our analysis suggests that increased temperature-dependent nutrient recycling in the upper ocean has offset much of the stratification-induced restriction in its physical transport.

scholarly journals Calibration of key temperature-dependent ocean microbial processes in the cGENIE.muffin Earth system model

2020 ◽  
Author(s):  
Katherine Anne Crichton ◽  
Jamie Devereux Wilson ◽  
Andy Ridgwell ◽  
Paul N. Pearson
Keyword(s):  
Organic Matter ◽  
Carbon Cycling ◽  
Surface Waters ◽  
Numerical Models ◽  
Nutrient Supply ◽  
Earth System Model ◽  
System Model ◽  
Earth System ◽  
Temperature Dependent ◽  
Poc Export

Abstract. Temperature is a master parameter in the marine carbon cycle, exerting a critical control on the rate of biological transformation of a variety of solid and dissolved reactants and substrates. Although in the construction of numerical models of marine carbon cycling, temperature has been long-recognised as a key parameter in the production and export of organic matter at the ocean surface, it is much less commonly taken into account in the ocean interior. There, bacteria (primarily) transform sinking particulate organic matter into its dissolved constituents and thereby consume dissolved oxygen (and/or other electron acceptors such as sulphate) and release nutrients, which are then available for transport back to the surface. Here we present and calibrate a more complete temperature-dependent representation of marine carbon cycling in the cGENIE.muffin Earth system model, intended for both past and future climate applications. In this, we combine a temperature-dependent remineralisation scheme for sinking organic matter with a biological export production scheme that also includes a temperature-dependent limitation on nutrient uptake in surface waters (and hence phytoplankton growth). Via a parameter ensemble, we jointly calibrate the two parameterisations by statistically contrasting model projected fields of nutrients, oxygen, and the stable carbon isotopic signature (δ13C) of dissolved inorganic carbon in the ocean, with modern observations. We find that for the present-day, the temperature-dependent version shows as-good-as or better fit to data than the existing tuned non-temperature dependent version of the cGENIE.muffin. The main impact of adding temperature-dependent remineralisation is in driving higher rates of remineralisation in warmer waters and hence a more rapid return of nutrients to the surface there – stimulating organic matter production. As a result, more organic matter is exported below 80 m in mid and low latitude warmer waters as compared to the standard model. Conversely, at higher latitudes, colder water temperature reduces the rate of nutrient supply to the surface as a result of slower in-situ rates of remineralisation. We also assess the implications of including a more complete set of temperature-dependent parameterisations by analysing a series of historical transient experiments. We find that between the pre-industrial and the present day, in response to a simulated air temperature increase of 0.9 °C and ocean warming of 0.12 °C (0.6 °C in surface waters and 0.02 °C in deep waters), a reduction in POC export at 80 m of just 0.3 % occurs. In contrast, with no assumed temperature-dependent biological processes, global POC export at 80 m falls by 2.9 % between the pre-industrial and present day as a consequence of ocean stratification and reduced nutrient supply to the surface. This suggests that increased nutrient recycling in warmer conditions offsets some of the stratification-induced surface nutrient limitation in a warmer world, and that less carbon (and nutrients) then reaches the inner and deep ocean. This extension to the cGENIE.muffin Earth system model provides it with additional capabilities in addressing marine carbon cycling in warmer past and future worlds.

scholarly journals MESMO 3: Flexible phytoplankton stoichiometry and refractory DOM

2021 ◽  
Author(s):  
Katsumi Matsumoto ◽  
Tatsuro Tanioka ◽  
Jacob Zahn
Keyword(s):  
Organic Matter ◽  
Earth System Model ◽  
System Model ◽  
Earth System ◽  
Temperature Dependent ◽  
Potential Growth ◽  
The Past ◽  
Phosphate Nitrate ◽  
Residual Nitrate ◽  
Environmental Dependence

Abstract. We describe the third version of Minnesota Earth System Model for Ocean biogeochemistry (MESMO 3), an earth system model of intermediate complexity, with a dynamical ocean, a dynamic-thermodynamic sea ice, and an energy moisture balanced atmosphere. A major feature of Version 3 is the flexible C : N : P ratio for the three phytoplankton functional types represented in the model. The flexible stoichiometry is based on the power law formulation with environmental dependence on phosphate, nitrate, temperature, and light. Other new features include nitrogen fixation, water column denitrification, oxygen and temperature-dependent organic matter remineralization, and CaCO3 production based on the concept of the residual nitrate potential growth. Also, we describe the semi-labile and refractory dissolved organic pools of C, N, P, and Fe that can be enabled in MEMSO 3 as an optional feature. The refractory dissolved organic matter can be degraded by photodegradation at the surface and hydrothermal vent degradation at the bottom. These improvements provide a basis for using MESMO 3 in further investigations of the global marine carbon cycle to changes in the environmental conditions of the past, present, and future.

scholarly journals MESMO 3: Flexible phytoplankton stoichiometry and refractory dissolved organic matter

2021 ◽  
Vol 14 (4) ◽  
pp. 2265-2288
Author(s):  
Katsumi Matsumoto ◽  
Tatsuro Tanioka ◽  
Jacob Zahn
Keyword(s):  
Organic Matter ◽  
Dissolved Organic Matter ◽  
Earth System Model ◽  
System Model ◽  
Earth System ◽  
Temperature Dependent ◽  
Potential Growth ◽  
Phosphate Nitrate ◽  
Residual Nitrate ◽  
Environmental Dependence

Abstract. We describe the third version of Minnesota Earth System Model for Ocean biogeochemistry (MESMO 3), an Earth system model of intermediate complexity, with a dynamical ocean, dynamic–thermodynamic sea ice, and an energy–moisture-balanced atmosphere. A major feature of version 3 is the flexible C:N:P ratio for the three phytoplankton functional types represented in the model. The flexible stoichiometry is based on the power law formulation with environmental dependence on phosphate, nitrate, temperature, and light. Other new features include nitrogen fixation, water column denitrification, oxygen and temperature-dependent organic matter remineralization, and CaCO3 production based on the concept of the residual nitrate potential growth. In addition, we describe the semi-labile and refractory dissolved organic pools of C, N, P, and Fe that can be enabled in MESMO 3 as an optional feature. The refractory dissolved organic matter can be degraded by photodegradation at the surface and hydrothermal vent degradation at the bottom. These improvements provide a basis for using MESMO 3 in further investigations of the global marine carbon cycle to changes in the environmental conditions of the past, present, and future.

scholarly journals High and specific diversity of protists in the deep-sea basins dominated by diplonemids, kinetoplastids, ciliates and foraminiferans

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Alexandra Schoenle ◽  
Manon Hohlfeld ◽  
Karoline Hermanns ◽  
Frédéric Mahé ◽  
Colomban de Vargas ◽  
...  
Keyword(s):  
Carbon Cycling ◽  
Deep Sea ◽  
Trophic Levels ◽  
Earth System ◽  
Parasitic Species ◽  
Unicellular Eukaryotes ◽  
The Earth ◽  
Dna Metabarcoding ◽  
Global Carbon ◽  
Pelagic Communities

AbstractHeterotrophic protists (unicellular eukaryotes) form a major link from bacteria and algae to higher trophic levels in the sunlit ocean. Their role on the deep seafloor, however, is only fragmentarily understood, despite their potential key function for global carbon cycling. Using the approach of combined DNA metabarcoding and cultivation-based surveys of 11 deep-sea regions, we show that protist communities, mostly overlooked in current deep-sea foodweb models, are highly specific, locally diverse and have little overlap to pelagic communities. Besides traditionally considered foraminiferans, tiny protists including diplonemids, kinetoplastids and ciliates were genetically highly diverse considerably exceeding the diversity of metazoans. Deep-sea protists, including many parasitic species, represent thus one of the most diverse biodiversity compartments of the Earth system, forming an essential link to metazoans.

scholarly journals Presentation, calibration and validation of the low-order, DCESS Earth System Model (Version 1)

2008 ◽  
Vol 1 (1) ◽  
pp. 17-51 ◽  
Author(s):  
G. Shaffer ◽  
S. Malskær Olsen ◽  
J. O. Pepke Pedersen
Keyword(s):  
Organic Matter ◽  
Organic Carbon ◽  
Dissolved Oxygen ◽  
Inorganic Carbon ◽  
Dissolved Inorganic Carbon ◽  
System Model ◽  
Earth System ◽  
Weathering Rates ◽  
Ocean Sediment ◽  
System Data

Abstract. A new, low-order Earth System Model is described, calibrated and tested against Earth system data. The model features modules for the atmosphere, ocean, ocean sediment, land biosphere and lithosphere and has been designed to simulate global change on time scales of years to millions of years. The atmosphere module considers radiation balance, meridional transport of heat and water vapor between low-mid latitude and high latitude zones, heat and gas exchange with the ocean and sea ice and snow cover. Gases considered are carbon dioxide and methane for all three carbon isotopes, nitrous oxide and oxygen. The ocean module has 100 m vertical resolution, carbonate chemistry and prescribed circulation and mixing. Ocean biogeochemical tracers are phosphate, dissolved oxygen, dissolved inorganic carbon for all three carbon isotopes and alkalinity. Biogenic production of particulate organic matter in the ocean surface layer depends on phosphate availability but with lower efficiency in the high latitude zone, as determined by model fit to ocean data. The calcite to organic carbon rain ratio depends on surface layer temperature. The semi-analytical, ocean sediment module considers calcium carbonate dissolution and oxic and anoxic organic matter remineralisation. The sediment is composed of calcite, non-calcite mineral and reactive organic matter. Sediment porosity profiles are related to sediment composition and a bioturbated layer of 0.1 m thickness is assumed. A sediment segment is ascribed to each ocean layer and segment area stems from observed ocean depth distributions. Sediment burial is calculated from sedimentation velocities at the base of the bioturbated layer. Bioturbation rates and oxic and anoxic remineralisation rates depend on organic carbon rain rates and dissolved oxygen concentrations. The land biosphere module considers leaves, wood, litter and soil. Net primary production depends on atmospheric carbon dioxide concentration and remineralization rates in the litter and soil are related to mean atmospheric temperatures. Methane production is a small fraction of the soil remineralization. The lithosphere module considers outgassing, weathering of carbonate and silicate rocks and weathering of rocks containing old organic carbon and phosphorus. Weathering rates are related to mean atmospheric temperatures. A pre-industrial, steady state calibration to Earth system data is carried out. Ocean observations of temperature, carbon 14, phosphate, dissolved oxygen, dissolved inorganic carbon and alkalinity constrain air-sea exchange and ocean circulation, mixing and biogeochemical parameters. Observed calcite and organic carbon distributions and inventories in the ocean sediment help constrain sediment module parameters. Carbon isotopic data and carbonate vs. silicate weathering fractions are used to estimate initial lithosphere outgassing and rock weathering rates. Model performance is tested by simulating atmospheric greenhouse gas increases, global warming and model tracer evolution for the period 1765 to 2000, as forced by prescribed anthropogenic greenhouse gas inputs and other anthropogenic and natural forcing. Long term, transient model behavior is studied with a set of 100 000 year simulations, forced by a slow, 5000 Gt C input of CO2 to the atmosphere, and with a 1.5 million year simulation, forced by a doubling of lithosphere CO2 outgassing.

The role of land surface dynamics in glacial inception: a study with the UVic Earth System Model

2003 ◽  
Vol 21 (7-8) ◽  
pp. 515-537 ◽  
Author(s):  
K. J. Meissner ◽  
A. J. Weaver ◽  
H. D. Matthews ◽  
P. M. Cox
Keyword(s):  
Land Surface ◽  
Earth System Model ◽  
System Model ◽  
Earth System ◽  
Surface Dynamics

Indian Summer Monsoon as simulated by the regional earth system model RegCM-ES: the role of local air–sea interaction

2019 ◽  
Vol 53 (1-2) ◽  
pp. 759-778 ◽  
Author(s):  
Fabio Di Sante ◽  
Erika Coppola ◽  
Riccardo Farneti ◽  
Filippo Giorgi
Keyword(s):  
Summer Monsoon ◽  
Indian Summer Monsoon ◽  
Earth System Model ◽  
System Model ◽  
Earth System

scholarly journals OMEN-SED 0.9: A novel, numerically efficient organic matter sediment diagenesis module for coupling to Earth system models

2018 ◽  
Author(s):  
Dominik Hülse ◽  
Sandra Arndt ◽  
Stuart Daines ◽  
Pierre Regnier ◽  
Andy Ridgwell
Keyword(s):  
Organic Matter ◽  
Marine Sediments ◽  
Earth System Model ◽  
System Model ◽  
Earth System ◽  
Model Framework ◽  
System Models ◽  
Wide Range ◽  
Earth System Models ◽  
Sediment Model

Abstract. We present the first version of OMEN-SED (Organic Matter ENabled SEDiment model), a new, one-dimensional analytical early diagenetic model resolving organic matter cycling and associated biogeochemical dynamics in marine sediments designed to be coupled to Earth system models. OMEN-SED explicitly describes organic matter (OM) cycling as well as associated dynamics of the most important terminal electron acceptors (i.e. O2, NO3, SO4) and methane (CH4), related reduced substances (NH4, H2S), macronutrients (PO4) and associated pore water quantities (ALK, DIC). Its reaction network accounts for the most important primary and secondary redox reactions, equilibrium reactions, mineral dissolution and precipitation, as well as adsorption and desorption processes associated with OM dynamics that affect the dissolved and solid species explicitly resolved in the model. To represent a redox-dependent sedimentary P cycle we also include a representation of the formation and burial of Fe-bound P and authigenic Ca-P minerals. Thus, OMEN-SED is able to capture the main features of diagenetic dynamics in marine sediments and, therefore, offers similar predictive abilities than a complex, numerical diagenetic model. Yet, its computational efficiency allows its coupling to global Earth system models and therefore the investigation of coupled global biogeochemical dynamics over a wide range of climate relevant timescales. This paper provides a detailed description of the new sediment model, an extensive sensitivity analysis, as well as an evaluation of OMEN-SED's performance through comprehensive comparisons with observations and results from a more complex numerical model. We find solid phase and dissolved pore water profiles for different ocean depths are reproduced with good accuracy and simulated terminal electron acceptor fluxes fall well within the range of globally observed fluxes. Finally, we illustrate its application in an Earth system model framework by coupling OMEN-SED to the Earth system model cGENIE and tune the OM degradation rate constants to optimise the fit of simulated benthic OM contents to global observations. We find simulated sediment characteristics of the coupled model framework, such as OM degradation rates, oxygen penetration depths and sediment-water interface fluxes are generally in good agreement with observations and in line with what one would expect on a global scale. Coupled to an Earth system model, OMEN-SED is thus a powerful tool that will not only help elucidate the role of benthic-pelagic exchange processes in the evolution and, in particular, the termination of a wide range of climate events, but will also allow a direct comparison of model output with the sedimentary record – the most important climate archive on Earth.

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