Articles | Volume 15, issue 20
Model description paper
20 Oct 2022
Model description paper | 20 Oct 2022
CANOPS-GRB v1.0: a new Earth system model for simulating the evolution of ocean–atmosphere chemistry over geologic timescales
Kazumi Ozaki et al.
No articles found.
Yoshiki Kanzaki, Shuang Zhang, Noah J. Planavsky, and Christopher T. Reinhard
Geosci. Model Dev., 15, 4959–4990,Short summary
Increasing carbon dioxide in the atmosphere is an urgent issue in the coming century. Enhanced rock weathering in soils can be one of the most efficient C capture strategies. On the basis as a weathering simulator, the newly developed SCEPTER model implements bio-mixing by fauna/humans and enables organic matter and crushed rocks/minerals at the soil surface with an option to track their particle size distributions. Those features can be useful for evaluating the carbon capture efficiency.
Sebastiaan J. van de Velde, Dominik Hülse, Christopher T. Reinhard, and Andy Ridgwell
Geosci. Model Dev., 14, 2713–2745,Short summary
Biogeochemical interactions between iron and sulfur are central to the long-term biogeochemical evolution of Earth’s oceans. Here, we introduce an iron–sulphur cycle in a model of Earth's oceans. Our analyses show that the results of the model are robust towards parameter choices and that simulated concentrations and reactions are comparable to those observed in ancient ocean analogues (anoxic lakes). Our model represents an important step forward in the study of iron–sulfur cycling.
Christopher T. Reinhard, Stephanie L. Olson, Sandra Kirtland Turner, Cecily Pälike, Yoshiki Kanzaki, and Andy Ridgwell
Geosci. Model Dev., 13, 5687–5706,Short summary
We provide documentation and testing of new developments for the oceanic and atmospheric methane cycles in the cGENIE Earth system model. The model is designed to explore Earth's methane cycle across a wide range of timescales and scenarios, in particular assessing the mean climate state and climate perturbations in Earth's deep past. We further document the impact of atmospheric oxygen levels and ocean chemistry on fluxes of methane to the atmosphere from the ocean biosphere.
Related subject area
BiogeosciencesLow sensitivity of three terrestrial biosphere models to soil texture over the South American tropicsFESDIA (v1.0): exploring temporal variations of sediment biogeochemistry under the influence of flood events using numerical modellingImpact of changes in climate and CO2 on the carbon storage potential of vegetation under limited water availability using SEIB-DGVM version 3.02FORCCHN V2.0: an individual-based model for predicting multiscale forest carbon dynamicsClimate and parameter sensitivity and induced uncertainties in carbon stock projections for European forests (using LPJ-GUESS 4.0)Use of genetic algorithms for ocean model parameter optimisation: a case study using PISCES-v2_RC for North Atlantic particulate organic carbonSurEau-Ecos v2.0: a trait-based plant hydraulics model for simulations of plant water status and drought-induced mortality at the ecosystem levelImproved representation of plant physiology in the JULES-vn5.6 land surface model: photosynthesis, stomatal conductance and thermal acclimationRepresentation of the phosphorus cycle in the Joint UK Land Environment Simulator (vn5.5_JULES-CNP)CLM5-FruitTree: a new sub-model for deciduous fruit trees in the Community Land Model (CLM5)The impact of hurricane disturbances on a tropical forest: implementing a palm plant functional type and hurricane disturbance module in ED2-HuDi V1.0A validation standard for area of habitat maps for terrestrial birds and mammalsUpscaling microbial stoichiometric adaptability in SOM turnover: The SESAM Soil Enzyme Steady Allocation Model (v3.0)Soil Cycles of Elements simulator for Predicting TERrestrial regulation of greenhouse gases: SCEPTER v0.9Using terrestrial laser scanning to constrain forest ecosystem structure and functions in the Ecosystem Demography model (ED2.2)A map of global peatland extent created using machine learning (Peat-ML)Implementation and evaluation of the unified stomatal optimization approach in the Functionally Assembled Terrestrial Ecosystem Simulator (FATES)Non-Redfield carbon model for the Baltic Sea (ERGOM version 1.2) – Implementation and Budget estimatesMatrix representation of lateral soil movements: scaling and calibrating CE-DYNAM (v2) at a continental levelECOSMO II(CHL): a marine biogeochemical model for the North Atlantic and the ArcticWater Ecosystems Tool (WET) 1.0 – a new generation of flexible aquatic ecosystem modelDevelopment of an open-source regional data assimilation system in PEcAn v. 1.7.2: application to carbon cycle reanalysis across the contiguous US using SIPNETPredicting global terrestrial biomes with the LeNet convolutional neural networkKGML-ag: a modeling framework of knowledge-guided machine learning to simulate agroecosystems: a case study of estimating N2O emission using data from mesocosm experimentsAssessing methane emissions for northern peatlands in ORCHIDEE-PEAT revision 7020A dynamic local-scale vegetation model for lycopsids (LYCOm v1.0)Modeling demographic-driven vegetation dynamics and ecosystem biogeochemical cycling in NASA GISS’s Earth system model (ModelE-BiomeE v.1.0)Soil-related developments of the Biome-BGCMuSo v6.2 terrestrial ecosystem modelGlobal evaluation of the Ecosystem Demography model (ED v3.0)A new snow module improves predictions of the isotope-enabled MAIDENiso forest growth modelCalibrating the soil organic carbon model Yasso20 with multiple datasetsThe PFLOTRAN Reaction SandboxA new approach to simulate peat accumulation, degradation and stability in a global land surface scheme (JULES vn5.8_accumulate_soil) for northern and temperate peatlandsDefinitions and methods to estimate regional land carbon fluxes for the second phase of the REgional Carbon Cycle Assessment and Processes Project (RECCAP-2)Locating trees to mitigate outdoor radiant load of humans in urban areas using a metaheuristic hill-climbing algorithm – introducing TreePlanter v1.0Sensitivity of asymmetric oxygen minimum zones to mixing intensity and stoichiometry in the tropical Pacific using a basin-scale model (OGCM-DMEC V1.4)The importance of turbulent ocean–sea ice nutrient exchanges for simulation of ice algal biomass and production with CICE6.1 and Icepack 1.2Modeling symbiotic biological nitrogen fixation in grain legumes globally with LPJ-GUESS (v4.0, r10285)Afforestation impact on soil temperature in regional climate model simulations over EuropeBioRT-Flux-PIHM v1.0: a biogeochemical reactive transport model at the watershed scaleModeling the short-term fire effects on vegetation dynamics and surface energy in southern Africa using the improved SSiB4/TRIFFID-Fire modelForest fluxes and mortality response to drought: model description (ORCHIDEE-CAN-NHA, r7236) and evaluation at the Caxiuanã drought experimentExplicit silicate cycling in the Kiel Marine Biogeochemistry Model version 3 (KMBM3) embedded in the UVic ESCM version 2.9Performance analysis of regional AquaCrop (v6.1) biomass and surface soil moisture simulations using satellite and in situ observationsOMEN-SED(-RCM) (v1.1): a pseudo-reactive continuum representation of organic matter degradation dynamics for OMEN-SEDTesting stomatal models at the stand level in deciduous angiosperm and evergreen gymnosperm forests using CliMA Land (v0.1)Comparing an exponential respiration model to alternative models for soil respiration components in a Canadian wildfire chronosequence (FireResp v1.0)Accounting for forest management in the estimation of forest carbon balance using the dynamic vegetation model LPJ-GUESS (v4.0, r9710): implementation and evaluation of simulations for EuropeFABM-NflexPD 1.0: assessing an instantaneous acclimation approach for modeling phytoplankton growthA model for marine sedimentary carbonate diagenesis and paleoclimate proxy signal tracking: IMP v1.0
Félicien Meunier, Wim Verbruggen, Hans Verbeeck, and Marc Peaucelle
Geosci. Model Dev., 15, 7573–7591,Short summary
Drought stress occurs in plants when water supply (i.e. root water uptake) is lower than the water demand (i.e. atmospheric demand). It is strongly related to soil properties and expected to increase in intensity and frequency in the tropics due to climate change. In this study, we show that contrary to the expectations, state-of-the-art terrestrial biosphere models are mostly insensitive to soil texture and hence probably inadequate to reproduce in silico the plant water status in drying soils.
Stanley I. Nmor, Eric Viollier, Lucie Pastor, Bruno Lansard, Christophe Rabouille, and Karline Soetaert
Geosci. Model Dev., 15, 7325–7351,Short summary
The coastal marine environment serves as a transition zone in the land–ocean continuum and is susceptible to episodic phenomena such as flash floods, which cause massive organic matter deposition. Here, we present a model of sediment early diagenesis that explicitly describes this type of deposition while also incorporating unique flood deposit characteristics. This model can be used to investigate the temporal evolution of marine sediments following abrupt changes in environmental conditions.
Shanlin Tong, Weiguang Wang, Jie Chen, Chong-Yu Xu, Hisashi Sato, and Guoqing Wang
Geosci. Model Dev., 15, 7075–7098,Short summary
Plant carbon storage potential is central to moderate atmospheric CO2 concentration buildup and mitigation of climate change. There is an ongoing debate about the main driver of carbon storage. To reconcile this discrepancy, we use SEIB-DGVM to investigate the trend and response mechanism of carbon stock fractions among water limitation regions. Results show that the impact of CO2 and temperature on carbon stock depends on water limitation, offering a new perspective on carbon–water coupling.
Jing Fang, Herman H. Shugart, Feng Liu, Xiaodong Yan, Yunkun Song, and Fucheng Lv
Geosci. Model Dev., 15, 6863–6872,Short summary
Our study provided a detailed description and a package of an individual tree-based carbon model, FORCCHN2. This model used non-structural carbohydrate (NSC) pools to couple tree growth and phenology. The model could reproduce daily carbon fluxes across Northern Hemisphere forests. Given the potential importance of the application of this model, there is substantial scope for using FORCCHN2 in fields as diverse as forest ecology, climate change, and carbon estimation.
Johannes Oberpriller, Christine Herschlein, Peter Anthoni, Almut Arneth, Andreas Krause, Anja Rammig, Mats Lindeskog, Stefan Olin, and Florian Hartig
Geosci. Model Dev., 15, 6495–6519,Short summary
Understanding uncertainties of projected ecosystem dynamics under environmental change is of immense value for research and climate change policy. Here, we analyzed these across European forests. We find that uncertainties are dominantly induced by parameters related to water, mortality, and climate, with an increasing importance of climate from north to south. These results highlight that climate not only contributes uncertainty but also modifies uncertainties in other ecosystem processes.
Marcus Falls, Raffaele Bernardello, Miguel Castrillo, Mario Acosta, Joan Llort, and Martí Galí
Geosci. Model Dev., 15, 5713–5737,Short summary
This paper describes and tests a method which uses a genetic algorithm (GA), a type of optimisation algorithm, on an ocean biogeochemical model. The aim is to produce a set of numerical parameters that best reflect the observed data of particulate organic carbon in a specific region of the ocean. We show that the GA can provide optimised model parameters in a robust and efficient manner and can also help detect model limitations, ultimately leading to a reduction in the model uncertainties.
Julien Ruffault, François Pimont, Hervé Cochard, Jean-Luc Dupuy, and Nicolas Martin-StPaul
Geosci. Model Dev., 15, 5593–5626,Short summary
A widespread increase in tree mortality has been observed around the globe, and this trend is likely to continue because of ongoing climate change. Here we present SurEau-Ecos, a trait-based plant hydraulic model to predict tree desiccation and mortality. SurEau-Ecos can help determine the areas and ecosystems that are most vulnerable to drying conditions.
Rebecca J. Oliver, Lina M. Mercado, Doug B. Clark, Chris Huntingford, Christopher M. Taylor, Pier Luigi Vidale, Patrick C. McGuire, Markus Todt, Sonja Folwell, Valiyaveetil Shamsudheen Semeena, and Belinda E. Medlyn
Geosci. Model Dev., 15, 5567–5592,Short summary
We introduce new representations of plant physiological processes into a land surface model. Including new biological understanding improves modelled carbon and water fluxes for the present in tropical and northern-latitude forests. Future climate simulations demonstrate the sensitivity of photosynthesis to temperature is important for modelling carbon cycle dynamics in a warming world. Accurate representation of these processes in models is necessary for robust predictions of climate change.
Mahdi André Nakhavali, Lina M. Mercado, Iain P. Hartley, Stephen Sitch, Fernanda V. Cunha, Raffaello di Ponzio, Laynara F. Lugli, Carlos A. Quesada, Kelly M. Andersen, Sarah E. Chadburn, Andy J. Wiltshire, Douglas B. Clark, Gyovanni Ribeiro, Lara Siebert, Anna C. M. Moraes, Jéssica Schmeisk Rosa, Rafael Assis, and José L. Camargo
Geosci. Model Dev., 15, 5241–5269,Short summary
In tropical ecosystems, the availability of rock-derived elements such as P can be very low. Thus, without a representation of P cycling, tropical forest responses to rising atmospheric CO2 conditions in areas such as Amazonia remain highly uncertain. We introduced P dynamics and its interactions with the N and P cycles into the JULES model. Our results highlight the potential for high P limitation and therefore lower CO2 fertilization capacity in the Amazon forest with low-fertility soils.
Olga Dombrowski, Cosimo Brogi, Harrie-Jan Hendricks Franssen, Damiano Zanotelli, and Heye Bogena
Geosci. Model Dev., 15, 5167–5193,Short summary
Soil carbon storage and food production of fruit orchards will be influenced by climate change. However, they lack representation in models that study such processes. We developed and tested a new sub-model, CLM5-FruitTree, that describes growth, biomass distribution, and management practices in orchards. The model satisfactorily predicted yield and exchange of carbon, energy, and water in an apple orchard and can be used to study land surface processes in fruit orchards at different scales.
Jiaying Zhang, Rafael L. Bras, Marcos Longo, and Tamara Heartsill Scalley
Geosci. Model Dev., 15, 5107–5126,Short summary
We implemented hurricane disturbance in a vegetation dynamics model and calibrated the model with observations of a tropical forest. We used the model to study forest recovery from hurricane disturbance and found that a single hurricane disturbance enhances AGB and BA in the long term compared with a no-hurricane situation. The model developed and results presented in this study can be utilized to understand the impact of hurricane disturbances on forest recovery under the changing climate.
Prabhat Raj Dahal, Maria Lumbierres, Stuart H. M. Butchart, Paul F. Donald, and Carlo Rondinini
Geosci. Model Dev., 15, 5093–5105,Short summary
This paper describes the validation of area of habitat (AOH) maps produced for terrestrial birds and mammals. The main objective was to assess the accuracy of the maps based on independent data. We used open access data from repositories, such as ebird and gbif to check if our maps were a better reflection of species' distribution than random. When points were not available we used logistic models to validate the AOH maps. The majority of AOH maps were found to have a high accuracy.
Thomas Wutzler, Lin Yu, Marion Schrumpf, and Sönke Zaehle
Soil microbes process soil organic matter and affect carbon storage and plant nutrition at ecosystem scale. We hypothesized that decadal dynamics is constrained by the ratios of elements in litter inputs, microbes and matter and that microbial community optimizes growth. This allowed the SESAM model to descibe decadal-term carbon sequestration in soils and other biogeochemical processes explicitly accounting for microbial processes but without its problematic fine-scale parameterization.
Yoshiki Kanzaki, Shuang Zhang, Noah J. Planavsky, and Christopher T. Reinhard
Geosci. Model Dev., 15, 4959–4990,Short summary
Increasing carbon dioxide in the atmosphere is an urgent issue in the coming century. Enhanced rock weathering in soils can be one of the most efficient C capture strategies. On the basis as a weathering simulator, the newly developed SCEPTER model implements bio-mixing by fauna/humans and enables organic matter and crushed rocks/minerals at the soil surface with an option to track their particle size distributions. Those features can be useful for evaluating the carbon capture efficiency.
Félicien Meunier, Sruthi M. Krishna Moorthy, Marc Peaucelle, Kim Calders, Louise Terryn, Wim Verbruggen, Chang Liu, Ninni Saarinen, Niall Origo, Joanne Nightingale, Mathias Disney, Yadvinder Malhi, and Hans Verbeeck
Geosci. Model Dev., 15, 4783–4803,Short summary
We integrated state-of-the-art observations of the structure of the vegetation in a temperate forest to constrain a vegetation model that aims to reproduce such an ecosystem in silico. We showed that the use of this information helps to constrain the model structure, its critical parameters, as well as its initial state. This research confirms the critical importance of the representation of the vegetation structure in vegetation models and proposes a method to overcome this challenge.
Joe R. Melton, Ed Chan, Koreen Millard, Matthew Fortier, R. Scott Winton, Javier M. Martín-López, Hinsby Cadillo-Quiroz, Darren Kidd, and Louis V. Verchot
Geosci. Model Dev., 15, 4709–4738,Short summary
Peat-ML is a high-resolution global peatland extent map generated using machine learning techniques. Peatlands are important in the global carbon and water cycles, but their extent is poorly known. We generated Peat-ML using drivers of peatland formation including climate, soil, geomorphology, and vegetation data, and we train the model with regional peatland maps. Our accuracy estimation approaches suggest Peat-ML is of similar or higher quality than other available peatland mapping products.
Qianyu Li, Shawn P. Serbin, Julien Lamour, Kenneth J. Davidson, Kim S. Ely, and Alistair Rogers
Geosci. Model Dev., 15, 4313–4329,Short summary
Stomatal conductance is the rate of water release from leaves’ pores. We implemented an optimal stomatal conductance model in a vegetation model. We then tested and compared it with the existing empirical model in terms of model responses to key environmental variables. We also evaluated the model with measurements at a tropical forest site. Our study suggests that the parameterization of conductance models and current model response to drought are the critical areas for improving models.
Thomas Neumann, Hagen Radtke, Bronwyn Cahill, and Martin Schmidt
Geosci. Model Dev. Discuss.,
Revised manuscript accepted for GMDShort summary
Marine ecosystem models usually are constrained by elements nitrogen and phosphorus, and consider carbon in organic matter in a fixed ratio. Recent observations show a substantial deviation from the simulated carbon cycle variables. In this study, we present a marine ecosystem model for the Baltic Sea which allows for a flexible uptake ratio for carbon, nitrogen, and phosphorus. With this extension, the model reflects much more reasonable variables of the marine carbon cycle.
Arthur Nicolaus Fendrich, Philippe Ciais, Emanuele Lugato, Marco Carozzi, Bertrand Guenet, Pasquale Borrelli, Victoria Naipal, Matthew McGrath, Philippe Martin, and Panos Panagos
Geosci. Model Dev. Discuss.,
Revised manuscript accepted for GMDShort summary
Currently, spatially explicit models for soil carbon stock can simulate the impacts of several changes. However, they do not incorporate the erosion, lateral transport and deposition (ETD) of soil material. The present work: i) developed ETD formulation; ii) illustrated model calibration and validation for Europe; iii) presented the results for a depositional site. We expect that our work advances ETD models' description and facilitates its reproduction and incorporation in land surface models.
Veli Çağlar Yumruktepe, Annette Samuelsen, and Ute Daewel
Geosci. Model Dev., 15, 3901–3921,Short summary
We describe the coupled bio-physical model ECOSMO II(CHL), which is used for regional configurations for the North Atlantic and the Arctic hind-casting and operational purposes. The model is consistent with the large-scale climatological nutrient settings and is capable of representing regional and seasonal changes, and model primary production agrees with previous measurements. For the users of this model, this paper provides the underlying science, model evaluation and its development.
Nicolas Azaña Schnedler-Meyer, Tobias Kuhlmann Andersen, Fenjuan Rose Schmidt Hu, Karsten Bolding, Anders Nielsen, and Dennis Trolle
Geosci. Model Dev., 15, 3861–3878,Short summary
We present the Water Ecosystems Tool (WET) – a new modular aquatic ecosystem model configurable to a wide array of physical setups, ecosystems and research questions based on the popular FABM–PCLake model. We aim for the model to become a community staple, thus helping to consolidate the state of the art under a few flexible models, with the aim of improving comparability across studies and preventing the
re-inventions of the wheelthat are common to our scientific modeling community.
Hamze Dokoohaki, Bailey D. Morrison, Ann Raiho, Shawn P. Serbin, Katie Zarada, Luke Dramko, and Michael Dietze
Geosci. Model Dev., 15, 3233–3252,Short summary
We present a new terrestrial carbon cycle data assimilation system, built on the PEcAn model–data eco-informatics system, and its application for the development of a proof-of-concept carbon
reanalysisproduct that harmonizes carbon pools (leaf, wood, soil) and fluxes (GPP, Ra, Rh, NEE) across the contiguous United States from 1986–2019. Here, we build on a decade of work on uncertainty propagation to generate the most complete and robust uncertainty accounting available to date.
Hisashi Sato and Takeshi Ise
Geosci. Model Dev., 15, 3121–3132,Short summary
Accurately predicting global coverage of terrestrial biome is one of the earliest ecological concerns, and many empirical schemes have been proposed to characterize their relationship. Here, we demonstrate an accurate and practical method to construct empirical models for operational biome mapping via a convolutional neural network (CNN) approach.
Licheng Liu, Shaoming Xu, Jinyun Tang, Kaiyu Guan, Timothy J. Griffis, Matthew D. Erickson, Alexander L. Frie, Xiaowei Jia, Taegon Kim, Lee T. Miller, Bin Peng, Shaowei Wu, Yufeng Yang, Wang Zhou, Vipin Kumar, and Zhenong Jin
Geosci. Model Dev., 15, 2839–2858,Short summary
By incorporating the domain knowledge into a machine learning model, KGML-ag overcomes the well-known limitations of process-based models due to insufficient representations and constraints, and unlocks the “black box” of machine learning models. Therefore, KGML-ag can outperform existing approaches on capturing the hot moment and complex dynamics of N2O flux. This study will be a critical reference for the new generation of modeling paradigm for biogeochemistry and other geoscience processes.
Elodie Salmon, Fabrice Jégou, Bertrand Guenet, Line Jourdain, Chunjing Qiu, Vladislav Bastrikov, Christophe Guimbaud, Dan Zhu, Philippe Ciais, Philippe Peylin, Sébastien Gogo, Fatima Laggoun-Défarge, Mika Aurela, M. Syndonia Bret-Harte, Jiquan Chen, Bogdan H. Chojnicki, Housen Chu, Colin W. Edgar, Eugenie S. Euskirchen, Lawrence B. Flanagan, Krzysztof Fortuniak, David Holl, Janina Klatt, Olaf Kolle, Natalia Kowalska, Lars Kutzbach, Annalea Lohila, Lutz Merbold, Włodzimierz Pawlak, Torsten Sachs, and Klaudia Ziemblińska
Geosci. Model Dev., 15, 2813–2838,Short summary
A methane model that features methane production and transport by plants, the ebullition process and diffusion in soil, oxidation to CO2, and CH4 fluxes to the atmosphere has been embedded in the ORCHIDEE-PEAT land surface model, which includes an explicit representation of northern peatlands. This model, ORCHIDEE-PCH4, was calibrated and evaluated on 14 peatland sites. Results show that the model is sensitive to temperature and substrate availability over the top 75 cm of soil depth.
Suman Halder, Susanne K. M. Arens, Kai Jensen, Tais W. Dahl, and Philipp Porada
Geosci. Model Dev., 15, 2325–2343,Short summary
A dynamic vegetation model, designed to estimate potential impacts of early vascular vegetation, namely, lycopsids, on the biogeochemical cycle at a local scale. Lycopsid Model (LYCOm) estimates the productivity and physiological properties of lycopsids across a broad climatic range along with natural selection, which is then utilized to adjudge their weathering potential. It lays the foundation for estimation of their impacts during their long evolutionary history starting from the Ordovician.
Ensheng Weng, Igor Aleinov, Ram Singh, Michael J. Puma, Sonali S. McDermid, Nancy Y. Kiang, Maxwell Kelley, Kevin Wilcox, Ray Dybzinski, Caroline E. Farrior, Stephen W. Pacala, and Benjamin I. Cook
Geosci. Model Dev. Discuss.,
Revised manuscript accepted for GMDShort summary
We developed a new demographic vegetation model to improve the representation of terrestrial vegetation dynamics and ecosystem biogeochemical cycles in an Earth system model. The individual-based competition for light and soil resources makes the modeling of eco-evolutionary optimality possible. This model will enable ModelE to simulate long-term biogeophysical and biogeochemical feedbacks between the climate system and land ecosystems at decadal to century temporal scales.
Dóra Hidy, Zoltán Barcza, Roland Hollós, Laura Dobor, Tamás Ács, Dóra Zacháry, Tibor Filep, László Pásztor, Dóra Incze, Márton Dencső, Eszter Tóth, Katarína Merganičová, Peter Thornton, Steven Running, and Nándor Fodor
Geosci. Model Dev., 15, 2157–2181,Short summary
Biogeochemical models used by the scientific community can support society in the quantification of the expected environmental impacts caused by global climate change. The Biome-BGCMuSo v6.2 biogeochemical model has been created by implementing a lot of developments related to soil hydrology as well as the soil carbon and nitrogen cycle and by integrating crop model components. Detailed descriptions of developments with case studies are presented in this paper.
Lei Ma, George Hurtt, Lesley Ott, Ritvik Sahajpal, Justin Fisk, Rachel Lamb, Hao Tang, Steve Flanagan, Louise Chini, Abhishek Chatterjee, and Joseph Sullivan
Geosci. Model Dev., 15, 1971–1994,Short summary
We present a global version of the Ecosystem Demography (ED) model which can track vegetation 3-D structure and scale up ecological processes from individual vegetation to ecosystem scale. Model evaluation against multiple benchmarking datasets demonstrated the model’s capability to simulate global vegetation dynamics across a range of temporal and spatial scales. With this version, ED has the potential to be linked with remote sensing observations to address key scientific questions.
Ignacio Hermoso de Mendoza, Etienne Boucher, Fabio Gennaretti, Aliénor Lavergne, Robert Field, and Laia Andreu-Hayles
Geosci. Model Dev., 15, 1931–1952,Short summary
We modify the numerical model of forest growth MAIDENiso by explicitly simulating snow. This allows us to use the model in boreal environments, where snow is dominant. We tested the performance of the model before and after adding snow, using it at two Canadian sites to simulate tree-ring isotopes and comparing with local observations. We found that modelling snow improves significantly the simulation of the hydrological cycle, the plausibility of the model and the simulated isotopes.
Toni Viskari, Janne Pusa, Istem Fer, Anna Repo, Julius Vira, and Jari Liski
Geosci. Model Dev., 15, 1735–1752,Short summary
We wanted to examine how the chosen measurement data and calibration process affect soil organic carbon model calibration. In our results we found that there is a benefit in using data from multiple litter-bag decomposition experiments simultaneously, even with the required assumptions. Additionally, due to the amount of noise and uncertainties in the system, more advanced calibration methods should be used to parameterize the models.
Glenn E. Hammond
Geosci. Model Dev., 15, 1659–1676,Short summary
This paper describes a simplified interface for implementing and testing new chemical reactions within the reactive transport simulator PFLOTRAN. The paper describes the interface, providing example code for the interface. The paper includes several chemical reactions implemented through the interface.
Sarah E. Chadburn, Eleanor J. Burke, Angela V. Gallego-Sala, Noah D. Smith, M. Syndonia Bret-Harte, Dan J. Charman, Julia Drewer, Colin W. Edgar, Eugenie S. Euskirchen, Krzysztof Fortuniak, Yao Gao, Mahdi Nakhavali, Włodzimierz Pawlak, Edward A. G. Schuur, and Sebastian Westermann
Geosci. Model Dev., 15, 1633–1657,Short summary
We present a new method to include peatlands in an Earth system model (ESM). Peatlands store huge amounts of carbon that accumulates very slowly but that can be rapidly destabilised, emitting greenhouse gases. Our model captures the dynamic nature of peat by simulating the change in surface height and physical properties of the soil as carbon is added or decomposed. Thus, we model, for the first time in an ESM, peat dynamics and its threshold behaviours that can lead to destabilisation.
Philippe Ciais, Ana Bastos, Frédéric Chevallier, Ronny Lauerwald, Ben Poulter, Josep G. Canadell, Gustaf Hugelius, Robert B. Jackson, Atul Jain, Matthew Jones, Masayuki Kondo, Ingrid T. Luijkx, Prabir K. Patra, Wouter Peters, Julia Pongratz, Ana Maria Roxana Petrescu, Shilong Piao, Chunjing Qiu, Celso Von Randow, Pierre Regnier, Marielle Saunois, Robert Scholes, Anatoly Shvidenko, Hanqin Tian, Hui Yang, Xuhui Wang, and Bo Zheng
Geosci. Model Dev., 15, 1289–1316,Short summary
The second phase of the Regional Carbon Cycle Assessment and Processes (RECCAP) will provide updated quantification and process understanding of CO2, CH4, and N2O emissions and sinks for ten regions of the globe. In this paper, we give definitions, review different methods, and make recommendations for estimating different components of the total land–atmosphere carbon exchange for each region in a consistent and complete approach.
Nils Wallenberg, Fredrik Lindberg, and David Rayner
Geosci. Model Dev., 15, 1107–1128,Short summary
Exposure to solar radiation on clear and warm days can lead to heat stress and thermal discomfort. This can be alleviated by planting trees providing shade in particularly warm areas. Here, we use a model to locate trees and optimize their blocking of solar radiation. Our results show that locations can differ depending, e.g., tree size (juvenile or mature) and number of trees that are positioned simultaneously. The model is available as a tool for accessibility by researchers and others.
Kai Wang, Xiujun Wang, Raghu Murtugudde, Dongxiao Zhang, and Rong-Hua Zhang
Geosci. Model Dev., 15, 1017–1035,Short summary
We use observational data of dissolved oxygen (DO) and organic nitrogen to calibrate a basin-scale model (OGCM-DEMC V1.4) and then evaluate model capacity for simulating mid-depth DO in the tropical Pacific. Sensitivity studies show that enhanced vertical mixing combined with reduced biological consumption performs well in reproducing asymmetric oxygen minimum zones (OMZs). We find that DO is more sensitive to biological processes in the upper OMZs but to physical processes in the lower OMZs.
Pedro Duarte, Philipp Assmy, Karley Campbell, and Arild Sundfjord
Geosci. Model Dev., 15, 841–857,Short summary
Sea ice modeling is an important part of Earth system models (ESMs). The results of ESMs are used by the Intergovernmental Panel on Climate Change in their reports. In this study we present an improvement to calculate the exchange of nutrients between the ocean and the sea ice. This nutrient exchange is an essential process to keep the ice-associated ecosystem functioning. We found out that previous calculation methods may underestimate the primary production of the ice-associated ecosystem.
Jianyong Ma, Stefan Olin, Peter Anthoni, Sam S. Rabin, Anita D. Bayer, Sylvia S. Nyawira, and Almut Arneth
Geosci. Model Dev., 15, 815–839,Short summary
The implementation of the biological N fixation process in LPJ-GUESS in this study provides an opportunity to quantify N fixation rates between legumes and to better estimate grain legume production on a global scale. It also helps to predict and detect the potential contribution of N-fixing plants as
green manureto reducing or removing the use of N fertilizer in global agricultural systems, considering different climate conditions, management practices, and land-use change scenarios.
Giannis Sofiadis, Eleni Katragkou, Edouard L. Davin, Diana Rechid, Nathalie de Noblet-Ducoudre, Marcus Breil, Rita M. Cardoso, Peter Hoffmann, Lisa Jach, Ronny Meier, Priscilla A. Mooney, Pedro M. M. Soares, Susanna Strada, Merja H. Tölle, and Kirsten Warrach Sagi
Geosci. Model Dev., 15, 595–616,Short summary
Afforestation is currently promoted as a greenhouse gas mitigation strategy. In our study, we examine the differences in soil temperature and moisture between grounds covered either by forests or grass. The main conclusion emerged is that forest-covered grounds are cooler but drier than open lands in summer. Therefore, afforestation disrupts the seasonal cycle of soil temperature, which in turn could trigger changes in crucial chemical processes such as soil carbon sequestration.
Wei Zhi, Yuning Shi, Hang Wen, Leila Saberi, Gene-Hua Crystal Ng, Kayalvizhi Sadayappan, Devon Kerins, Bryn Stewart, and Li Li
Geosci. Model Dev., 15, 315–333,Short summary
Watersheds are the fundamental Earth surface functioning unit that connects the land to aquatic systems. Here we present the recently developed BioRT-Flux-PIHM v1.0, a watershed-scale biogeochemical reactive transport model, to improve our ability to understand and predict solute export and water quality. The model has been verified against the benchmark code CrunchTope and has recently been applied to understand reactive transport processes in multiple watersheds of different conditions.
Huilin Huang, Yongkang Xue, Ye Liu, Fang Li, and Gregory S. Okin
Geosci. Model Dev., 14, 7639–7657,Short summary
This study applies a fire-coupled dynamic vegetation model to quantify fire impact at monthly to annual scales. We find fire reduces grass cover by 4–8 % annually for widespread areas in south African savanna and reduces tree cover by 1 % at the periphery of tropical Congolese rainforest. The grass cover reduction peaks at the beginning of the rainy season, which quickly diminishes before the next fire season. In contrast, the reduction of tree cover is irreversible within one growing season.
Yitong Yao, Emilie Joetzjer, Philippe Ciais, Nicolas Viovy, Fabio Cresto Aleina, Jerome Chave, Lawren Sack, Megan Bartlett, Patrick Meir, Rosie Fisher, and Sebastiaan Luyssaert
Geosci. Model Dev. Discuss.,
Revised manuscript accepted for GMDShort summary
To facilitate more mechanistic modeling of drought effects on forest dynamics, our study implements a hydraulic module to simulate the vertical water flow, change in water storage and percentage loss of stem conductance (PLC). With the relationship between PLC and tree mortality, our model can successfully reproduce the large biomass drop observed under throughfall exclusion. Our hydraulic module provides promising avenues benefiting the prediction for mortality under future drought events.
Karin Kvale, David P. Keller, Wolfgang Koeve, Katrin J. Meissner, Christopher J. Somes, Wanxuan Yao, and Andreas Oschlies
Geosci. Model Dev., 14, 7255–7285,Short summary
We present a new model of biological marine silicate cycling for the University of Victoria Earth System Climate Model (UVic ESCM). This new model adds diatoms, which are a key aspect of the biological carbon pump, to an existing ecosystem model. Our modifications change how the model responds to warming, with net primary production declining more strongly than in previous versions. Diatoms in particular are simulated to decline with climate warming due to their high nutrient requirements.
Shannon de Roos, Gabriëlle J. M. De Lannoy, and Dirk Raes
Geosci. Model Dev., 14, 7309–7328,Short summary
A spatially distributed version of the field-scale crop model AquaCrop v6.1 was developed for applications at various spatial scales. Multi-year 1 km simulations over central Europe were evaluated against biomass and surface soil moisture products derived from optical and microwave satellite missions, as well as in situ observations of soil moisture. The regional version of the AquaCrop model provides a suitable setup for subsequent satellite-based data assimilation.
Philip Pika, Dominik Hülse, and Sandra Arndt
Geosci. Model Dev., 14, 7155–7174,Short summary
OMEN-SED is a model for early diagenesis in marine sediments simulating organic matter (OM) degradation and nutrient dynamics. We replaced the original description with a more realistic one accounting for the widely observed decrease in OM reactivity. The new model reproduces pore water profiles and sediment–water interface fluxes across different environments. This functionality extends the model’s applicability to a broad range of environments and timescales while requiring fewer parameters.
Yujie Wang, Philipp Köhler, Liyin He, Russell Doughty, Renato K. Braghiere, Jeffrey D. Wood, and Christian Frankenberg
Geosci. Model Dev., 14, 6741–6763,Short summary
We present the first step in testing a new land model as part of a new Earth system model. Our model links plant hydraulics, stomatal optimization theory, and a comprehensive canopy radiation scheme. We compared model-predicted carbon and water fluxes to flux tower observations and model-predicted sun-induced chlorophyll fluorescence to satellite retrievals. Our model quantitatively predicted the carbon and water fluxes as well as the canopy fluorescence yield.
John Zobitz, Heidi Aaltonen, Xuan Zhou, Frank Berninger, Jukka Pumpanen, and Kajar Köster
Geosci. Model Dev., 14, 6605–6622,Short summary
Forest fires heavily affect carbon stocks and fluxes of carbon in high-latitude forests. Long-term trends in soil respiration following forest fires are associated with recovery of aboveground biomass. We evaluated models for soil autotrophic and heterotrophic respiration with data from a chronosequence of stand-replacing forest fires in northern Canada. The best model that reproduced expected patterns in soil respiration components takes into account soil microbe carbon as a model variable.
Mats Lindeskog, Benjamin Smith, Fredrik Lagergren, Ekaterina Sycheva, Andrej Ficko, Hans Pretzsch, and Anja Rammig
Geosci. Model Dev., 14, 6071–6112,Short summary
Forests play an important role in the global carbon cycle and for carbon storage. In Europe, forests are intensively managed. To understand how management influences carbon storage in European forests, we implement detailed forest management into the dynamic vegetation model LPJ-GUESS. We test the model by comparing model output to typical forestry measures, such as growing stock and harvest data, for different countries in Europe.
Onur Kerimoglu, Prima Anugerahanti, and Sherwood Lan Smith
Geosci. Model Dev., 14, 6025–6047,Short summary
In large-scale models, variations in cellular composition of phytoplankton are often insufficiently represented. Detailed modeling approaches exist, but they require additional state variables that increase the computational costs. In this study, we test an instantaneous acclimation model in a spatially explicit setup and show that its behavior is mostly similar to that of a variant with an additional state variable but different from that of a fixed composition variant.
Yoshiki Kanzaki, Dominik Hülse, Sandra Kirtland Turner, and Andy Ridgwell
Geosci. Model Dev., 14, 5999–6023,Short summary
Sedimentary carbonate plays a central role in regulating Earth’s carbon cycle and climate, and also serves as an archive of paleoenvironments, hosting various trace elements/isotopes. To help obtain
trueenvironmental changes from carbonate records over diagenetic distortion, IMP has been newly developed and has the capability to simulate the diagenesis of multiple carbonate particles and implement different styles of particle mixing by benthos using an adapted transition matrix method.
Alcott, L. J., Mills, B. J. W., and Poulton, S. W.: Stepwise Earth oxygenation is an inherent property of global biogeochemical cycling, Science, 366, 1333–1337, https://doi.org/10.1126/science.aax6459, 2019.
Algeo, T. J. and Ingall, E.: Sedimentary Corg:P ratios, paleocean ventilation, and Phanerozoic atmospheric pO2, Palaeogeogr. Palaeocl., 256, 130–155, https://doi.org/10.1016/j.palaeo.2007.02.029, 2007.
Anderson, L. D., Delaney, M. L., and Faul, K. L.: Carbon to phosphorus ratios in sediments: Implications for nutrient cycling, Global Biogeochem. Cycles, 15, 65–79, https://doi.org/10.1029/2000GB001270, 2001.
Archer, D., Kheshgi, H., and Maier-Reimer, E.: Dynamics of fossil fuel CO2 neutralization by marine CaCO3, Global Biogeochem. Cycles, 12, 259–276, https://doi.org/10.1029/98GB00744, 1998.
Archer, D. E., Eshel, G., Winguth, A., Broecker, W., Pierrehumbert, R., Tobis, M., and Jacob, R.: Atmospheric pCO2 sensitivity to the biological pump in the ocean, Global Biogeochem. Cycles, 14, 1219–1230, https://doi.org/10.1029/1999GB001216, 2000.
Archer, D. E., Morford, J. L., and Emerson, S. R.: A model of suboxic sedimentary diagenesis suitable for automatic tuning and gridded global domains, Global Biogeochem. Cycles, 16, 17-11–17-21, https://doi.org/10.1029/2000gb001288, 2002.
Armstrong, R. A., Lee, C., Hedges, J. I., Honjo, S., and Wakeham, S. G.: A new, mechanistic model for organic carbon fluxes in the ocean based on the quantitative association of POC with ballast minerals, Deep-Sea Res. Pt. II, 49, 219–236, https://doi.org/10.1016/S0967-0645(01)00101-1, 2001.
Arndt, S., Regnier, P., Goddéris, Y., and Donnadieu, Y.: GEOCLIM reloaded (v 1.0): a new coupled earth system model for past climate change, Geosci. Model Dev., 4, 451–481, https://doi.org/10.5194/gmd-4-451-2011, 2011.
Baturin, G. N.: Issue of the relationship between primary productivity of organic carbon in ocean and phosphate accumulation (Holocene-Late Jurassic), Lithol. Min. Resour., 42, 318–348, https://doi.org/10.1134/s0024490207040025, 2007.
Beal, E. J., Claire, M. W., and House, C. H.: High rates of anaerobic methanotrophy at low sulfate concentrations with implications for past and present methane levels, Geobiology, 9, 131–139, https://doi.org/10.1111/j.1472-4669.2010.00267.x, 2011.
Belcher, C. M. and McElwain, J. C.: Limits for combustion in low O2 redefine paleoatmospheric predictions for the Mesozoic, Science, 321, 1197–1200, https://doi.org/10.1126/science.1160978, 2008.
Bellefroid, E. J., Hood, A. v. S., Hoffman, P. F., Thomas, M. D., Reinhard, C. T., and Planavsky, N. J.: Constraints on Paleoproterozoic atmospheric oxygen levels, P. Natl Acad. Sci. USA, 115, 8104–8109, https://doi.org/10.1073/pnas.1806216115, 2018.
Benitez-Nelson, C. R.: The biogeochemical cycling of phosphorus in marine systems, Earth-Sci. Rev., 51, 109–135, https://doi.org/10.1016/S0012-8252(00)00018-0, 2000.
Berelson, W. M.: Particle settling rates increase with depth in the ocean, Deep-Sea Res. Pt. II, 49, 237–251, https://doi.org/10.1016/S0967-0645(01)00102-3, 2001a.
Berelson, W. M.: The Flux of Particulate Organic Carbon Into the Ocean Interior: A Comparison of Four U.S. JGOFS Regional Studies, Oceanography, 14, 59–67, 2001b.
Berelson, W. M., Balch, W. M., Najjar, R., Feely, R. A., Sabine, C., and Lee, K.: Relating estimates of CaCO3 production, export, and dissolution in the water column to measurements of CaCO3 rain into sediment traps and dissolution on the sea floor: A revised global carbonate budget, Global Biogeochem. Cycles, 21, GB1024, https://doi.org/10.1029/2006GB002803, 2007.
Bergman, N. M., Lenton, T. M., and Watson, A. J.: COPSE: A new model of biogeochemical cycling over Phanerozoic time, Am. J. Sci., 304, 397–437, https://doi.org/10.2475/ajs.304.5.397, 2004.
Berner, R. A.: Early diagenesis: A theoretical approach, Princeton University Press, Princeton, 256 pp., ISBN 0-691-08258-8, 1980.
Berner, R. A.: Burial of organic carbon and pyrite sulfur in the modern ocean; its geochemical and environmental significance, Am. J. Sci., 282, 451–473, https://doi.org/10.2475/ajs.282.4.451, 1982.
Berner, R. A.: Biogeochemical cycles of carbon and sulfur and their effect on atmospheric oxygen over phanerozoic time, Palaeogeogr. Palaeocl., 75, 97–122, https://doi.org/10.1016/0031-0182(89)90186-7, 1989.
Berner, R. A.: The Phanerozoic Carbon Cycle: CO2 and O2, Oxford University Press, ISBN 0-19-517333-3, 2004a.
Berner, R. A.: A model for calcium, magnesium and sulfate in seawater over Phanerozoic time, Am. J. Sci., 304, 438–453, https://doi.org/10.2475/ajs.304.5.438, 2004b.
Berner, R. A.: GEOCARBSULF: A combined model for Phanerozoic atmospheric O2 and CO2, Geochim. Cosmochim. Ac., 70, 5653–5664, https://doi.org/10.1016/j.gca.2005.11.032, 2006.
Berner, R. A.: Phanerozoic atmospheric oxygen: New results using the GEOCARBSULF model, Am. J. Sci., 309, 603–606, https://doi.org/10.2475/07.2009.03, 2009.
Berner, R. A. and Canfield, D. E.: A new model for atmospheric oxygen over Phanerozoic time, Am. J. Sci., 289, 333–361, https://doi.org/10.2475/ajs.289.4.333, 1989.
Berner, R. A. and Westrich, J. T.: Bioturbation and the early diagenesis of carbon and sulfur, Am. J. Sci., 285, 193–206, https://doi.org/10.2475/ajs.285.3.193, 1985.
Betts, J. N. and Holland, H. D.: The oxygen content of ocean bottom waters, the burial efficiency of organic carbon, and the regulation of atmospheric oxygen, Palaeogeogr. Palaeocl., 97, 5–18, https://doi.org/10.1016/0031-0182(91)90178-T, 1991.
Bohlen, L., Dale, A. W., and Wallmann, K.: Simple transfer functions for calculating benthic fixed nitrogen losses and regeneration ratios in global biogeochemical models, Global Biogeochem. Cycles, 26, GB3029, https://doi.org/10.1029/2011gb004198, 2012.
Bolton, E. W., Berner, R. A., and Petsch, S. T.: The Weathering of Sedimentary Organic Matter as a Control on Atmospheric O2: II. Theoretical Modeling, Am. J. Sci., 306, 575–615, https://doi.org/10.2475/08.2006.01, 2006.
Bottrell, S. H. and Newton, R. J.: Reconstruction of changes in global sulfur cycling from marine sulfate isotopes, Earth-Sci. Rev., 75, 59–83, https://doi.org/10.1016/j.earscirev.2005.10.004, 2006.
Boudreau, B. P.: A method-of-lines code for carbon and nutrient diagenesis in aquatic sediments, Comput. Geosci., 22, 479–496, https://doi.org/10.1016/0098-3004(95)00115-8, 1996.
Bowles, M. W., Mogollón, J. M., Kasten, S., Zabel, M., and Hinrichs, K.-U.: Global rates of marine sulfate reduction and implications for sub–sea-floor metabolic activities, Science, 344, 889–891, https://doi.org/10.1126/science.1249213, 2014.
Bradley, J. A., Arndt, S., Amend, J. P., Burwicz, E., Dale, A. W., Egger, M., and LaRowe, D. E.: Widespread energy limitation to life in global subseafloor sediments, Sci. Adv., 6, eaba0697, https://doi.org/10.1126/sciadv.aba0697, 2020.
Brandes, J. A. and Devol, A. H.: A global marine-fixed nitrogen isotopic budget: Implications for Holocene nitrogen cycling, Global Biogeochem. Cycles, 16, GB001856, https://doi.org/10.1029/2001gb001856, 2002.
Broecker, W. S. and Peng, T.-H.: Tracers in the sea, Eldigio Pr, New York, 690 pp., ISBN 9993186724, 1982.
Burdige, D. J.: Burial of terrestrial organic matter in marine sediments: A re-assessment, Global Biogeochem. Cycles, 19, GB4011, https://doi.org/10.1029/2004gb002368, 2005.
Burdige, D. J.: Preservation of Organic Matter in Marine Sediments: Controls, Mechanisms, and an Imbalance in Sediment Organic Carbon Budgets?, Chem. Rev., 107, 467–485, https://doi.org/10.1021/cr050347q, 2007.
Canfield, D. E.: Sulfate reduction and oxic respiration in marine sediments: implications for organic carbon preservation in euxinic environments, Deep-Sea Res. Pt. A., 36, 121–138, https://doi.org/10.1016/0198-0149(89)90022-8, 1989.
Canfield, D. E.: Sulfate reduction in deep-sea sediments, Am. J. Sci., 291, 177–188, https://doi.org/10.2475/ajs.291.2.177, 1991.
Canfield, D. E.: Organic Matter Oxidation in Marine Sediments, in: Interactions of C, N, P and S Biogeochemical Cycles and Global Change, edited by: Wollast, R., Mackenzie, F. T., and Chou, L., Springer Berlin Heidelberg, Berlin, 333–363, ISBN 978-3-642-76066-2, 1993.
Canfield, D. E.: The evolution of the Earth surface sulfur reservoir, Am. J. Sci., 304, 839–861, https://doi.org/10.2475/ajs.304.10.839, 2004.
Canfield, D. E. and Farquhar, J.: Animal evolution, bioturbation, and the sulfate concentration of the oceans, P. Natl Acad. Sci. USA, 106, 8123–8127, https://doi.org/10.1073/pnas.0902037106, 2009.
Canfield, D. E., Zhang, S., Frank, A. B., Wang, X., Wang, H., Su, J., Ye, Y., and Frei, R.: Highly fractionated chromium isotopes in Mesoproterozoic-aged shales and atmospheric oxygen, Nat. Commun., 9, 2871, https://doi.org/10.1038/s41467-018-05263-9, 2018.
Carr, M.-E., Friedrichs, M. A. M., Schmeltz, M., Noguchi Aita, M., Antoine, D., Arrigo, K. R., Asanuma, I., Aumont, O., Barber, R., Behrenfeld, M., Bidigare, R., Buitenhuis, E. T., Campbell, J., Ciotti, A., Dierssen, H., Dowell, M., Dunne, J., Esaias, W., Gentili, B., Gregg, W., Groom, S., Hoepffner, N., Ishizaka, J., Kameda, T., Le Quéré, C., Lohrenz, S., Marra, J., Mélin, F., Moore, K., Morel, A., Reddy, T. E., Ryan, J., Scardi, M., Smyth, T., Turpie, K., Tilstone, G., Waters, K., and Yamanaka, Y.: A comparison of global estimates of marine primary production from ocean color, Deep-Sea Res. Pt. II, 53, 741–770, https://doi.org/10.1016/j.dsr2.2006.01.028, 2006.
Catling, D. C. and Kasting, J. F.: Atmospheric Evolution on Inhabited and Lifeless Worlds, Cambridge University Press, ISBN 978-0-521-84412-3, 2017.
Catling, D. C. and Zahnle, K. J.: The Archean atmosphere, Sci. Adv., 6, eaax1420, https://doi.org/10.1126/sciadv.aax1420, 2020.
Cha, H. J., Lee, C. B., Kim, B. S., Choi, M. S., and Ruttenberg, K. C.: Early diagenetic redistribution and burial of phosphorus in the sediments of the southwestern East Sea (Japan Sea), Marine Geol., 216, 127–143, https://doi.org/10.1016/j.margeo.2005.02.001, 2005.
Claire, M. W., Catling, D. C., and Zahnle, K. J.: Biogeochemical modelling of the rise in atmospheric oxygen, Geobiology, 4, 239–269, https://doi.org/10.1111/j.1472-4669.2006.00084.x, 2006.
Cole, D. B., Reinhard, C. T., Wang, X., Gueguen, B., Halverson, G. P., Gibson, T., Hodgskiss, M. S. W., McKenzie, N. R., Lyons, T. W., and Planavsky, N. J.: A shale-hosted Cr isotope record of low atmospheric oxygen during the Proterozoic, Geology, 44, 555–558, https://doi.org/10.1130/g37787.1, 2016.
Cole, D. B., Ozaki, K., and Reinhard, C. T.: Atmospheric Oxygen Abundance, Marine Nutrient Availability, and Organic Carbon Fluxes to the Seafloor, Global Biogeochem. Cycles, 36, e2021GB007052, https://doi.org/10.1029/2021GB007052, 2022.
Colman, A. S. and Holland, H. D.: The global diagenetic flux of phosphorus from marine sediments to the oceans: redox sensitivity and the control of atmosphreic oxygen levels, in: Marine authigenesis: from global to microbial, edited by: Glenn, C. R., Prevot-Lucas, L., and Lucas, J., SEPM (Society for Sedimentary Geology), 53–75, ISBN 1-56576-064-6, 2000.
Compton, J., Mallinson, D., Glenn, C. R., Filippelli, G., Follmi, K., Shields, G. A., and Zanin, Y.: Variations in the global phosphorus cycle, in: Marine authigenesis: from global to microbial, edited by: Glenn, C. R., Prevot-Lucas, L., and Lucas, J., SEPM (Society for Sedimentary Geology), 21–33, 2000.
Crichton, K. A., Wilson, J. D., Ridgwell, A., and Pearson, P. N.: Calibration of temperature-dependent ocean microbial processes in the cGENIE.muffin (v0.9.13) Earth system model, Geosci. Model Dev., 14, 125–149, https://doi.org/10.5194/gmd-14-125-2021, 2021.
Crockford, P. W., Hayles, J. A., Bao, H., Planavsky, N. J., Bekker, A., Fralick, P. W., Halverson, G. P., Bui, T. H., Peng, Y., and Wing, B. A.: Triple oxygen isotope evidence for limited mid-Proterozoic primary productivity, Nature, 559, 613–616, https://doi.org/10.1038/s41586-018-0349-y, 2018.
Daines, S. J., Mills, B. J. W., and Lenton, T. M.: Atmospheric oxygen regulation at low Proterozoic levels by incomplete oxidative weathering of sedimentary organic carbon, Nat. Commun., 8, 14379, https://doi.org/10.1038/ncomms14379, 2017.
Dale, A. W., Meyers, S. R., Aguilera, D. R., Arndt, S., and Wallmann, K.: Controls on organic carbon and molybdenum accumulation in Cretaceous marine sediments from the Cenomanian–Turonian interval including Oceanic Anoxic Event 2, Chem. Geol., 324–325, 28–45, https://doi.org/10.1016/j.chemgeo.2011.10.004, 2012.
Delaney, M. L.: Phosphorus accumulation in marine sediments and the oceanic phosphorus cycle, Global Biogeochem. Cycles, 12, 563–572, https://doi.org/10.1029/98gb02263, 1998.
Dellwig, O., Leipe, T., März, C., Glockzin, M., Pollehne, F., Schnetger, B., Yakushev, E. V., Böttcher, M. E., and Brumsack, H.-J.: A new particulate Mn–Fe–P-shuttle at the redoxcline of anoxic basins, Geochim. Cosmochim. Ac., 74, 7100–7115, https://doi.org/10.1016/j.gca.2010.09.017, 2010.
Derry, L. A.: Causes and consequences of mid-Proterozoic anoxia, Geophys. Res. Lett., 42, 2015GL065333, https://doi.org/10.1002/2015gl065333, 2015.
Des Marais, D. J., Harwit, M. O., Jucks, K. W., Kasting, J. F., Lin, D. N., Lunine, J. I., Schneider, J., Seager, S., Traub, W. A., and Woolf, N. J.: Remote Sensing of Planetary Properties and Biosignatures on Extrasolar Terrestrial Planets, Astrobiology, 2, 153–181, https://doi.org/10.1089/15311070260192246, 2002.
Deutsch, C., Sarmiento, J. L., Sigman, D. M., Gruber, N., and Dunne, J. P.: Spatial coupling of nitrogen inputs and losses in the ocean, Nature, 445, 163, https://doi.org/10.1038/nature05392, 2007.
Devol, A. and Christensen, J. P.: Benthic fluxes and nitrogen cycling in sediments of the continental margin of the eastern North Pacific, J. Marine Res., 51, 345–372, 1993.
Devol, A. H.: Denitrification, Anammox, and N2 Production in Marine Sediments, Ann. Rev. Mar. Sci., 7, 403–423, https://doi.org/10.1146/annurev-marine-010213-135040, 2015.
DeVries, T., Deutsch, C., Primeau, F., Chang, B., and Devol, A.: Global rates of water-column denitrification derived from nitrogen gas measurements, Nat. Geosci., 5, 547, https://doi.org/10.1038/ngeo1515, 2012.
DeVries, T., Deutsch, C., Rafter, P. A., and Primeau, F.: Marine denitrification rates determined from a global 3-D inverse model, Biogeosciences, 10, 2481–2496, https://doi.org/10.5194/bg-10-2481-2013, 2013.
Doney, S. C., Lindsay, K., Caldeira, K., Campin, J. M., Drange, H., Dutay, J. C., Follows, M., Gao, Y., Gnanadesikan, A., Gruber, N., Ishida, A., Joos, F., Madec, G., Maier-Reimer, E., Marshall, J. C., Matear, R. J., Monfray, P., Mouchet, A., Najjar, R., Orr, J. C., Plattner, G. K., Sarmiento, J., Schlitzer, R., Slater, R., Totterdell, I. J., Weirig, M. F., Yamanaka, Y., and Yool, A.: Evaluating global ocean carbon models: The importance of realistic physics, Global Biogeochem. Cycles, 18, GB3017, https://doi.org/10.1029/2003gb002150, 2004.
Donis, D., McGinnis, D. F., Holtappels, M., Felden, J., and Wenzhofer, F.: Assessing benthic oxygen fluxes in oligotrophic deep sea sediments (HAUSGARTEN observatory), Deep-Sea Res. Pt. I, 111, 1–10, https://doi.org/10.1016/j.dsr.2015.11.007, 2016.
Duce, R. A., LaRoche, J., Altieri, K., Arrigo, K. R., Baker, A. R., Capone, D. G., Cornell, S., Dentener, F., Galloway, J., Ganeshram, R. S., Geider, R. J., Jickells, T., Kuypers, M. M., Langlois, R., Liss, P. S., Liu, S. M., Middelburg, J. J., Moore, C. M., Nickovic, S., Oschlies, A., Pedersen, T., Prospero, J., Schlitzer, R., Seitzinger, S., Sorensen, L. L., Uematsu, M., Ulloa, O., Voss, M., Ward, B., and Zamora, L.: Impacts of Atmospheric Anthropogenic Nitrogen on the Open Ocean, Science, 320, 893–897, https://doi.org/10.1126/science.1150369, 2008.
Dunne, J. P., Sarmiento, J. L., and Gnanadesikan, A.: A synthesis of global particle export from the surface ocean and cycling through the ocean interior and on the seafloor, Global Biogeochem. Cycles, 21, GB4006, https://doi.org/10.1029/2006gb002907, 2007.
Eguchi, J., Seales, J., and Dasgupta, R.: Great Oxidation and Lomagundi events linked by deep cycling and enhanced degassing of carbon, Nat. Geosci., 13, 71–76, https://doi.org/10.1038/s41561-019-0492-6, 2020.
Etheridge, D. M., Steele, L. P., Francey, R. J., and Langenfelds, R. L.: Atmospheric methane between 1000 A.D. and present: Evidence of anthropogenic emissions and climatic variability, J. Geophys. Res., 103, 15979–15993, https://doi.org/10.1029/98JD00923, 1998.
Eugster, O. and Gruber, N.: A probabilistic estimate of global marine N-fixation and denitrification, Global Biogeochem. Cycles, 26, GB4013, https://doi.org/10.1029/2012gb004300, 2012.
Fakhraee, M., Planavsky, N. J., and Reinhard, C. T.: The role of environmental factors in the long-term evolution of the marine biological pump, Nat. Geosci., 13, 812–816, https://doi.org/10.1038/s41561-020-00660-6, 2020.
Fiebig, J., Woodland, A. B., D'Alessandro, W., and Püttmann, W.: Excess methane in continental hydrothermal emissions is abiogenic, Geology, 37, 495–498, https://doi.org/10.1130/g25598a.1, 2009.
Filippelli, G. M.: Carbon and phosphorus cycling in anoxic sediments of the Saanich Inlet, British Columbia, Marine Geol., 174, 307–321, https://doi.org/10.1016/S0025-3227(00)00157-2, 2001.
Föllmi, K. B.: The phosphorus cycle, phosphogenesis and marine phosphate-rich deposits, Earth-Sci. Rev., 40, 55–124, https://doi.org/10.1016/0012-8252(95)00049-6, 1996.
Fowler, D., Coyle, M., Skiba, U., Sutton, M. A., Cape, J. N., Reis, S., Sheppard, L. J., Jenkins, A., Grizzetti, B., Galloway, J. N., Vitousek, P., Leach, A., Bouwman, A. F., Butterbach-Bahl, K., Dentener, F., Stevenson, D., Amann, M., and Voss, M.: The global nitrogen cycle in the twenty-first century, Phil. Trans. R. Soc. B, 368, 20130164, https://doi.org/10.1098/rstb.2013.0164, 2013.
Francois, R., Honjo, S., Krishfield, R., and Manganini, S.: Factors controlling the flux of organic carbon to the bathypelagic zone of the ocean, Global Biogeochem. Cycles, 16, 1087, https://doi.org/10.1029/2001gb001722, 2002.
Froelich, P. N., Klinkhammer, G. P., Bender, M. L., Luedtke, N. A., Heath, G. R., Cullen, D., Dauphin, P., Hammond, D., Hartman, B., and Maynard, V.: Early oxidation of organic matter in pelagic sediments of the eastern equatorial Atlantic: suboxic diagenesis, Geochim. Cosmochim. Ac., 43, 1075–1090, https://doi.org/10.1016/0016-7037(79)90095-4, 1979.
Galbraith, E. D. and Martiny, A. C.: A simple nutrient-dependence mechanism for predicting the stoichiometry of marine ecosystems, P. Natl Acad. Sci. USA, 112, 8199–8204, https://doi.org/10.1073/pnas.1423917112, 2015.
Galloway, J. N., Dentener, F. J., Capone, D. G., Boyer, E. W., Howarth, R. W., Seitzinger, S. P., Asner, G. P., Cleveland, C. C., Green, P. A., Holland, E. A., Karl, D. M., Michaels, A. F., Porter, J. H., Townsend, A. R., and Vöosmarty, C. J.: Nitrogen Cycles: Past, Present, and Future, Biogeochemistry, 70, 153–226, https://doi.org/10.1007/s10533-004-0370-0, 2004.
Garcia, H. E. and Gordon, L. I.: Oxygen solubility in seawater: Better fitting equations, Limnol. Oceanogr., 37, 1307–1312, https://doi.org/10.4319/lo.19188.8.131.527, 1992.
Garrels, R. M. and Lerman, A.: Phanerozoic cycles of sedimentary carbon and sulfur, P. Natl Acad. Sci. USA, 78, 4652–4656, 1981.
Garrels, R. M. and Perry, J. E. A.: Cycling of carbon, sulfur, and oxygen through geologic time, The Sea, Wiley-Interscience, New York, edited by: Goldberg, E. D., 303–336, ISBN 067401734X, 1974.
Goldblatt, C., Lenton, T. M., and Watson, A. J.: Bistability of atmospheric oxygen and the Great Oxidation, Nature, 443, 683–686, 2006.
Graham, W. F. and Duce, R. A.: Atmospheric pathways of the phosphorus cycle, Geochim. Cosmochim. Ac., 43, 1195–1208, https://doi.org/10.1016/0016-7037(79)90112-1, 1979.
Großkopf, T., Mohr, W., Baustian, T., Schunck, H., Gill, D., Kuypers, M. M. M., Lavik, G., Schmitz, R. A., Wallace, D. W. R., and LaRoche, J.: Doubling of marine dinitrogen-fixation rates based on direct measurements, Nature, 488, 361, https://doi.org/10.1038/nature11338, 2012.
Gruber, N.: Chapter 1 – The Marine Nitrogen Cycle: Overview and Challenges, in: Nitrogen in the Marine Environment, 2nd edn., Academic Press, San Diego, 1–50, https://doi.org/10.1016/B978-0-12-372522-6.00001-3, 2008.
Gruber, N. and Sarmiento, J. L.: Global patterns of marine nitrogen fixation and denitrification, Global Biogeochem. Cycles, 11, 235–266, https://doi.org/10.1029/97gb00077, 1997.
Gruber, N. and Sarmiento, J. L.: Biogeochemical/physical interactions in elemental cycles, in: THE SEA: Biological-Physical Interactions in the Oceans, edited by: Robinson, A. R., McCarthy, J. J., and Rothschild, B. J., John Wiley and Sons, New York, 337–399, 2002.
Guidry, M. W., Mackenzie, F. T., and Arvidson, R. S.: Role of tectonics in phosphorus distribution and cycling, in: Marine Authigenesis: From Global to Microbial, edited by: Glenn, C. R., Prevot-Lucas, L., and Lucas, J., SEPM, 35–51, 2000.
Gundersen, J. K. and Jorgensen, B. B.: Microstructure of diffusive boundary layers and the oxygen uptake of the sea floor, Nature, 345, 604, https://doi.org/10.1038/345604a0, 1990.
Halevy, I., Peters, S. E., and Fischer, W. W.: Sulfate Burial Constraints on the Phanerozoic Sulfur Cycle, Science, 337, 331–334, https://doi.org/10.1126/science.1220224, 2012.
Handoh, I. C. and Lenton, T. M.: Periodic mid-Cretaceous oceanic anoxic events linked by oscillations of the phosphorus and oxygen biogeochemical cycles, Global Biogeochem. Cycles, 17, 1092, https://doi.org/10.1029/2003gb002039, 2003.
Hartnett, H. E. and Devol, A. H.: Role of a strong oxygen-deficient zone in the preservation and degradation of organic matter: a carbon budget for the continental margins of northwest Mexico and Washington State, Geochim. Cosmochim. Ac., 67, 247–264, https://doi.org/10.1016/S0016-7037(02)01076-1, 2003.
Hartnett, H. E., Keil, R. G., Hedges, J. I., and Devol, A. H.: Influence of oxygen exposure time on organic carbon preservation in continental margin sediments, Nature, 391, 572–575, 1998.
Hayes, C. T., Costa, K. M., Anderson, R. F., Calvo, E., Chase, Z., Demina, L. L., Dutay, J.-C., German, C. R., Heimbürger-Boavida, L.-E., Jaccard, S. L., Jacobel, A., Kohfeld, K. E., Kravchishina, M. D., Lippold, J., Mekik, F., Missiaen, L., Pavia, F. J., Paytan, A., Pedrosa-Pamies, R., Petrova, M. V., Rahman, S., Robinson, L. F., Roy-Barman, M., Sanchez-Vidal, A., Shiller, A., Tagliabue, A., Tessin, A. C., van Hulten, M., and Zhang, J.: Global Ocean Sediment Composition and Burial Flux in the Deep Sea, Global Biogeochem. Cycles, 35, e2020GB006769, https://doi.org/10.1029/2020GB006769, 2021.
Hayes, J. M. and Waldbauer, J. R.: The carbon cycle and associated redox processes through time, Phil. Trans. R. Soc. B, 361, 931–950, https://doi.org/10.1098/rstb.2006.1840, 2006.
Hedges, J. I., Hu, F. S., Devol, A. H., Hartnett, H. E., Tsamakis, E., and Keil, R. G.: Sedimentary organic matter preservation; a test for selective degradation under oxic conditions, Am. J. Sci., 299, 529–555, https://doi.org/10.2475/ajs.299.7-9.529, 1999.
Heinze, C., Kriest, I., and Maier-Reimer, E.: Age offsets among different biogenic and lithogenic components of sediment cores revealed by numerical modeling, Paleoceanography, 24, PA4214, https://doi.org/10.1029/2008pa001662, 2009.
Henrichs, S. M. and Reeburgh, W. S.: Anaerobic mineralization of marine sediment organic matter: Rates and the role of anaerobic processes in the oceanic carbon economy, Geomicrobiol. J., 5, 191–237, https://doi.org/10.1080/01490458709385971, 1987.
Hensen, C., Landenberger, H., Zabel, M., and Schulz, H. D.: Quantification of diffusive benthic fluxes of nitrate, phosphate, and silicate in the southern Atlantic Ocean, Global Biogeochem. Cycles, 12, 193–210, https://doi.org/10.1029/97gb02731, 1998.
Hitchcock, D. R. and Lovelock, J. E.: Life detection by atmospheric analysis, Icarus, 7, 149–159, https://doi.org/10.1016/0019-1035(67)90059-0, 1967.
Holland, H. D.: The Chemistry of the Atmosphere and Oceans, John Wiley & Sons, New York, ISBN 0471035092, 1978.
Holser, W. T., Maynard, J. B., and Cruikshank, K. M.: Modelling the natural cycle of sulphur through Phanerozoic time, in: Evolution of the Global Biogeochemical Sulphur Cycle, edited by: Brimblecombe, P., and Lein, A. Y., John Wiley & Sons Ltd, New York, 21–56, 1989.
Honjo, S.: Material fluxes and modes of sedimentation in the mesopelagic and bathypelagic zones, J. Marine Res., 38, 53–97, 1980.
Honjo, S. and Manganini, S. J.: Annual biogenic particle fluxes to the interior of the North Atlantic Ocean; studied at 34∘ N 21∘ W and 48∘ N 21∘ W, Deep-Sea Res. Pt. II, 40, 587–607, https://doi.org/10.1016/0967-0645(93)90034-K, 1993.
Hotinski, R. M., Kump, L. R., and Najjar, R. G.: Opening Pandora's Box: The impact of open system modeling on interpretations of anoxia, Paleoceanography, 15, 267–279, https://doi.org/10.1029/1999pa000408, 2000.
Hyacinthe, C., Anschutz, P., Carbonel, P., Jouanneau, J. M., and Jorissen, F. J.: Early diagenetic processes in the muddy sediments of the Bay of Biscay, Marine Geol., 177, 111–128, https://doi.org/10.1016/S0025-3227(01)00127-X, 2001.
Ingall, E. and Jahnke, R.: Evidence for enhanced phosphorus regeneration from marine sediments overlain by oxygen depleted waters, Geochim. Cosmochim. Ac., 58, 2571–2575, https://doi.org/10.1016/0016-7037(94)90033-7, 1994.
Ingall, E. and Jahnke, R.: Influence of water-column anoxia on the elemental fractionation of carbon and phosphorus during sediment diagenesis, Marine Geol., 139, 219–229, https://doi.org/10.1016/S0025-3227(96)00112-0, 1997.
Ingall, E. D. and Cappellen, P. V.: Relation between sedimentation rate and burial of organic phosphorus and organic carbon in marine sediments, Geochim. Cosmochim. Ac., 54, 373–386, https://doi.org/10.1016/0016-7037(90)90326-G, 1990.
Ingall, E. D., Bustin, R. M., and Van Cappellen, P.: Influence of water column anoxia on the burial and preservation of carbon and phosphorus in marine shales, Geochim. Cosmochim. Ac., 57, 303–316, https://doi.org/10.1016/0016-7037(93)90433-W, 1993.
Ittekkot, V.: The abiotically driven biological pump in the ocean and short-term fluctuations in atmospheric CO2 contents, Global Planet. Change, 8, 17–25, https://doi.org/10.1016/0921-8181(93)90060-2, 1993.
Jahnke, R. A.: The global ocean flux of particulate organic carbon: Areal distribution and magnitude, Global Biogeochem. Cycles, 10, 71–88, https://doi.org/10.1029/95GB03525, 1996.
Joos, F., Sarmiento, J. L., and Siegenthaler, U.: Estimates of the effect of Southern Ocean iron fertilization on atmospheric CO2 concentrations, Nature, 349, 772–775, https://doi.org/10.1038/349772a0, 1991.
Jørgensen, B. B.: Mineralization of organic matter in the sea bed—the role of sulphate reduction, Nature, 296, 643, https://doi.org/10.1038/296643a0, 1982.
Jørgensen, B. B. and Kasten, S.: Sulfur cycling and methane oxidation, in: Marine Geochemistry, edited by: Schulz, H. D. and Zabel, M., Springer Berlin Heidelberg, 271–309, https://doi.org/10.1007/3-540-32144-6_8, 2006.
Kagoshima, T., Sano, Y., Takahata, N., Maruoka, T., Fischer, T. P., and Hattori, K.: Sulphur geodynamic cycle, Sci. Rep.-UK, 5, 8330, https://doi.org/10.1038/srep08330, 2015.
Karl, D., Michaels, A., Bergman, B., Capone, D., Carpenter, E., Letelier, R., Lipschultz, F., Paerl, H., Sigman, D., and Stal, L.: Dinitrogen fixation in the world's oceans, in: The Nitrogen Cycle at Regional to Global Scales, edited by: Boyer, E. W., and Howarth, R. W., Springer Netherlands, Dordrecht, 47–98, https://doi.org/10.1007/978-94-017-3405-9_2, 2002.
Karl, D. M., Beversdorf, L., Björkman, K. M., Church, M. J., Martinez, A., and Delong, E. F.: Aerobic production of methane in the sea, Nat. Geosci., 1, 473–478, https://doi.org/10.1038/ngeo234, 2008.
Karthäuser, C., Ahmerkamp, S., Marchant, H. K., Bristow, L. A., Hauss, H., Iversen, M. H., Kiko, R., Maerz, J., Lavik, G., and Kuypers, M. M. M.: Small sinking particles control anammox rates in the Peruvian oxygen minimum zone, Nat. Commun., 12, 3235, https://doi.org/10.1038/s41467-021-23340-4, 2021.
Kashiyama, Y., Ozaki, K., and Tajika, E.: Impact of the Evolution of Carbonate Ballasts on Marine Biogeochemistry in the Mesozoic and Associated Changes in Energy Delivery to Subsurface Waters, Paleontol. Res., 15, 89–99, https://doi.org/10.2517/1342-8144-15.2.089, 2011.
Katsev, S. and Crowe, S. A.: Organic carbon burial efficiencies in sediments: The power law of mineralization revisited, Geology, 43, 607–610, https://doi.org/10.1130/g36626.1, 2015.
Key, R. M., Olsen, A., van Heuven, S., Lauvset, S. K., Velo, A., Lin, X., Schirnick, C., Kozyr, A., Tanhua, T., Hoppema, M., Jutterström, S., Steinfeldt, R., Jeansson, E., Ishii, M., Perez, F. F., and Suzuki, T.: Global Ocean Data Analysis Project, Version 2 (GLODAPv2), https://doi.org/10.3334/CDIAC/OTG. NDP093_GLODAPv2, 2015.
Kharecha, P., Kasting, J., and Siefert, J.: A coupled atmosphere–ecosystem model of the early Archean Earth, Geobiology, 3, 53–76, https://doi.org/10.1111/j.1472-4669.2005.00049.x, 2005.
Klaas, C. and Archer, D. E.: Association of sinking organic matter with various types of mineral ballast in the deep sea: Implications for the rain ratio, Global Biogeochem. Cycles, 16, 63-61–63-14, https://doi.org/10.1029/2001gb001765, 2002.
Knox, F. and McElroy, M. B.: Changes in atmospheric CO2: Influence of the marine biota at high latitude, J. Geophys. Res., 89, 4629–4637, https://doi.org/10.1029/JD089iD03p04629, 1984.
Krissansen-Totton, J., Garland, R., Irwin, P., and Catling, D. C.: Detectability of Biosignatures in Anoxic Atmospheres with the James Webb Space Telescope: A TRAPPIST-1e Case Study, The Astronom. J., 156, 114, https://doi.org/10.3847/1538-3881/aad564, 2018.
Kump, L. R.: Chemical stability of the atmosphere and ocean, Palaeogeogr. Palaeocl., 75, 123–136, https://doi.org/10.1016/0031-0182(89)90187-9, 1989.
Kump, L. R.: The rise of atmospheric oxygen, Nature, 451, 277–278, https://doi.org/10.1038/nature06587, 2008.
Kuypers, M. M. M., Lavik, G., Woebken, D., Schmid, M., Fuchs, B. M., Amann, R., Jørgensen, B. B., and Jetten, M. S. M.: Massive nitrogen loss from the Benguela upwelling system through anaerobic ammonium oxidation, P. Natl. Acad. Sci. USA, 102, 6478–6483, https://doi.org/10.1073/pnas.0502088102, 2005.
Kuznetsov, I., Neumann, T., and Burchard, H.: Model study on the ecosystem impact of a variable ratio for cyanobacteria in the Baltic Proper, Ecol. Model., 219, 107–114, https://doi.org/10.1016/j.ecolmodel.2008.08.002, 2008.
Laakso, T. A. and Schrag, D. P.: Regulation of atmospheric oxygen during the Proterozoic, Earth Planet. Sc. Lett., 388, 81–91, https://doi.org/10.1016/j.epsl.2013.11.049, 2014.
Larsson, U., Hajdu, S., Walve, J., and Elmgren, R.: Baltic Sea nitrogen fixation estimated from the summer increase in upper mixed layer total nitrogen, Limnol. Oceanogr., 46, 811–820, https://doi.org/10.4319/lo.2001.46.4.0811, 2001.
Lasaga, A. C.: A new approach to isotopic modeling of the variation of atmospheric oxygen through the Phanerozoic, Am. J. Sci., 289, 411–435, https://doi.org/10.2475/ajs.289.4.411, 1989.
Lasaga, A. C. and Ohmoto, H.: The oxygen geochemical cycle: dynamics and stability, Geochim. Cosmochim. Ac., 66, 361–381, https://doi.org/10.1016/S0016-7037(01)00685-8, 2002.
Laws, E. A., Falkowski, P. G., Smith, W. O., Ducklow, H., and McCarthy, J. J.: Temperature effects on export production in the open ocean, Global Biogeochem. Cycles, 14, 1231–1246, https://doi.org/10.1029/1999gb001229, 2000.
Ledwell, J. R., Watson, A. J., and Law, C. S.: Mixing of a tracer in the pycnocline, J. Geophys. Res., 103, 21499–21529, https://doi.org/10.1029/98JC01738, 1998.
Lenton, T. M.: Fire Feedbacks on Atmospheric Oxygen, in: Fire Phenomena and the Earth System, edited by: Belcher, C. M., 289–308, https://doi.org/10.1002/9781118529539.ch15, 2013.
Lenton, T. M.: On the use of models in understanding the rise of complex life, Interface Focus, 10, 20200018, https://doi.org/10.1098/rsfs.2020.0018, 2020.
Lenton, T. M. and Watson, A. J.: Redfield revisited: 1. Regulation of nitrate, phosphate, and oxygen in the ocean, Global Biogeochem. Cycles, 14, 225–248, https://doi.org/10.1029/1999gb900065, 2000a.
Lenton, T. M. and Watson, A. J.: Redfield revisited: 2. What regulates the oxygen content of the atmosphere?, Global Biogeochem. Cycles, 14, 249–268, https://doi.org/10.1029/1999gb900076, 2000b.
Lenton, T. M., Daines, S. J., and Mills, B. J. W.: COPSE reloaded: An improved model of biogeochemical cycling over Phanerozoic time, Earth-Sci. Rev., 178, 1–28, https://doi.org/10.1016/j.earscirev.2017.12.004, 2018.
Lenton, T. M., Dahl, T. W., Daines, S. J., Mills, B. J. W., Ozaki, K., Saltzman, M. R., and Porada, P.: Earliest land plants created modern levels of atmospheric oxygen, P. Natl Acad. Sci. USA, 113, 9704–9709, https://doi.org/10.1073/pnas.1604787113, 2016.
Lin, S. and Morse, J. W.: Sulfate reduction and iron sulfide mineral formation in Gulf of Mexico anoxic sediments, Am. J. Sci., 291, 55–89, https://doi.org/10.2475/ajs.291.1.55, 1991.
Liss, P. S. and Slater, P. G.: Flux of Gases across the Air-Sea Interface, Nature, 247, 181–184, 1974.
Lord, N. S., Ridgwell, A., Thorne, M. C., and Lunt, D. J.: An impulse response function for the “long tail” of excess atmospheric CO2 in an Earth system model, Global Biogeochem. Cycles, 30, 2–17, https://doi.org/10.1002/2014GB005074, 2016.
Lovelock, J. E.: A Physical Basis for Life Detection Experiments, Nature, 207, 568–570, https://doi.org/10.1038/207568a0, 1965.
Lovelock, J. E.: Gaia as seen through the atmosphere, Atmos. Environ., 6, 579–580, https://doi.org/10.1016/0004-6981(72)90076-5, 1972.
Lovelock, J. E.: Thermodynamics and the recognition of alien biospheres, P. Roy. Soc. Lond. B, 189, 167–181, https://doi.org/10.1098/rspb.1975.0051, 1975.
Lumpkin, R. and Speer, K.: Global Ocean Meridional Overturning, J. Phys. Oceanogr., 37, 2550–2562, https://doi.org/10.1175/jpo3130.1, 2007.
Luo, Y.-W., Doney, S. C., Anderson, L. A., Benavides, M., Berman-Frank, I., Bode, A., Bonnet, S., Boström, K. H., Böttjer, D., Capone, D. G., Carpenter, E. J., Chen, Y. L., Church, M. J., Dore, J. E., Falcón, L. I., Fernández, A., Foster, R. A., Furuya, K., Gómez, F., Gundersen, K., Hynes, A. M., Karl, D. M., Kitajima, S., Langlois, R. J., LaRoche, J., Letelier, R. M., Marañón, E., McGillicuddy Jr., D. J., Moisander, P. H., Moore, C. M., Mouriño-Carballido, B., Mulholland, M. R., Needoba, J. A., Orcutt, K. M., Poulton, A. J., Rahav, E., Raimbault, P., Rees, A. P., Riemann, L., Shiozaki, T., Subramaniam, A., Tyrrell, T., Turk-Kubo, K. A., Varela, M., Villareal, T. A., Webb, E. A., White, A. E., Wu, J., and Zehr, J. P.: Database of diazotrophs in global ocean: abundance, biomass and nitrogen fixation rates, Earth Syst. Sci. Data, 4, 47–73, https://doi.org/10.5194/essd-4-47-2012, 2012.
Lutz, M., Dunbar, R., and Caldeira, K.: Regional variability in the vertical flux of particulate organic carbon in the ocean interior, Global Biogeochem. Cycles, 16, 11-11–11-18, https://doi.org/10.1029/2000gb001383, 2002.
Lyons, T. W. and Gill, B. C.: Ancient Sulfur Cycling and Oxygenation of the Early Biosphere, Elements, 6, 93–99, https://doi.org/10.2113/gselements.6.2.93, 2010.
Lyons, T. W., Reinhard, C. T., and Planavsky, N. J.: The rise of oxygen in Earth's early ocean and atmosphere, Nature, 506, 307–315, https://doi.org/10.1038/nature13068, 2014.
Mackenzie, F. T., Ver, L. M., Sabine, C., Lane, M., and Lerman, A.: C, N, P, S Global Biogeochemical Cycles and Modeling of Global Change, in: Interactions of C, N, P and S Biogeochemical Cycles and Global Change, edited by: Wollast, R., Mackenzie, F. T., and Chou, L., Springer Berlin Heidelberg, Berlin, Heidelberg, 1–61, 1993.
Maier-Reimer, E.: Geochemical cycles in an ocean general circulation model. Preindustrial tracer distributions, Global Biogeochem. Cycles, 7, 645–677, https://doi.org/10.1029/93gb01355, 1993.
Markovic, S., Paytan, A., and Wortmann, U. G.: Pleistocene sediment offloading and the global sulfur cycle, Biogeosciences, 12, 3043–3060, https://doi.org/10.5194/bg-12-3043-2015, 2015.
Martin, J. H., Knauer, G. A., Karl, D. M., and Broenkow, W. W.: VERTEX: carbon cycling in the northeast Pacific, Deep-Sea Res. Pt. A, 34, 267–285, https://doi.org/10.1016/0198-0149(87)90086-0, 1987.
Martin, W. R. and Sayles, F. L.: The Recycling of Biogenic Material at the Sea Floor, in: Treatise on Geochemistry (Second Edition), edited by: Turekian, K. K., Elsevier, Oxford, 33–59, https://doi.org/10.1016/B978-0-08-095975-7.00702-6, 2014.
Mayor, M. and Queloz, D.: A Jupiter-mass companion to a solar-type star, Nature, 378, 355–359, https://doi.org/10.1038/378355a0, 1995.
McManus, J., Berelson, W. M., Coale, K. H., Johnson, K. S., and Kilgore, T. E.: Phosphorus regeneration in continental margin sediments, Geochim. Cosmochim. Ac., 61, 2891–2907, https://doi.org/10.1016/S0016-7037(97)00138-5, 1997.
McManus, J., Berelson, W. M., Klinkhammer, G. P., Hammond, D. E., and Holm, C.: Authigenic uranium: Relationship to oxygen penetration depth and organic carbon rain, Geochim. Cosmochim. Ac., 69, 95–108, https://doi.org/10.1016/j.gca.2004.06.023, 2005.
Meadows, V. S.: Reflections on O2 as a Biosignature in Exoplanetary Atmospheres, Astrobiology, 17, 1022–1052, https://doi.org/10.1089/ast.2016.1578, 2017.
Meadows, V. S., Reinhard, C. T., Arney, G. N., Parenteau, M. N., Schwieterman, E. W., Domagal-Goldman, S. D., Lincowski, A. P., Stapelfeldt, K. R., Rauer, H., DasSarma, S., Hegde, S., Narita, N., Deitrick, R., Lustig-Yaeger, J., Lyons, T. W., Siegler, N., and Grenfell, J. L.: Exoplanet Biosignatures: Understanding Oxygen as a Biosignature in the Context of Its Environment, Astrobiology, 18, 630–662, https://doi.org/10.1089/ast.2017.1727, 2018.
Middelburg, J. J., Soetaert, K., Herman, P. M. J., and Heip, C. H. R.: Denitrification in marine sediments: A model study, Global Biogeochem. Cycles, 10, 661–673, https://doi.org/10.1029/96gb02562, 1996.
Middelburg, J. J., Soetaert, K., and Herman, P. M. J.: Empirical relationships for use in global diagenetic models, Deep-Sea Res. Pt. I, 44, 327–344, https://doi.org/10.1016/S0967-0637(96)00101-X, 1997.
Millero, F. J.: The oxidation of H2S in Black Sea waters, Deep-Sea Res. Pt. A, 38, S1139–S1150, https://doi.org/10.1016/S0198-0149(10)80028-7, 1991.
Millero, F. J.: Chemical Oceanography, 3rd edn., Taylor & Francis Group CRC Press, Boca Raton, 496 pp., 2006.
Millero, F. J., Plese, T., and Fernandez, M.: The dissociation of hydrogen-sulfide in seawater, Limnol. Oceanogr., 33, 269–274, 1988.
Morford, J. L. and Emerson, S.: The geochemistry of redox sensitive trace metals in sediments, Geochim. Cosmochim. Ac., 63, 1735–1750, https://doi.org/10.1016/S0016-7037(99)00126-X, 1999.
Muller-Karger, F. E., Varela, R., Thunell, R., Luerssen, R., Hu, C., and Walsh, J. J.: The importance of continental margins in the global carbon cycle, Geophys. Res. Lett., 32, L01602, https://doi.org/10.1029/2004gl021346, 2005.
National Academies of Sciences, E. and Medicine: An Astrobiology Strategy for the Search for Life in the Universe, The National Academies Press, Washington, D.C., 188 pp., https://doi.org/10.17226/25252, 2019.
Nierop, K. G. J., Reichart, G.-J., Veld, H., and Sinninghe Damsté, J. S.: The influence of oxygen exposure time on the composition of macromolecular organic matter as revealed by surface sediments on the Murray Ridge (Arabian Sea), Geochim. Cosmochim. Ac., 206, 40–56, https://doi.org/10.1016/j.gca.2017.02.032, 2017.
Oguz, T., Ducklow, H. W., and Malanotte-Rizzoli, P.: Modeling distinct vertical biogeochemical structure of the Black Sea: Dynamical coupling of the oxic, suboxic, and anoxic layers, Global Biogeochem. Cycles, 14, 1331–1352, https://doi.org/10.1029/1999GB001253, 2000.
Oguz, T., Murray, J. W., and Callahan, A. E.: Modeling redox cycling across the suboxic–anoxic interface zone in the Black Sea, Deep-Sea Res. Pt. I, 48, 761–787, https://doi.org/10.1016/S0967-0637(00)00054-6, 2001.
Olsen, A., Key, R. M., van Heuven, S., Lauvset, S. K., Velo, A., Lin, X., Schirnick, C., Kozyr, A., Tanhua, T., Hoppema, M., Jutterström, S., Steinfeldt, R., Jeansson, E., Ishii, M., Pérez, F. F., and Suzuki, T.: The Global Ocean Data Analysis Project version 2 (GLODAPv2) – an internally consistent data product for the world ocean, Earth Syst. Sci. Data, 8, 297–323, https://doi.org/10.5194/essd-8-297-2016, 2016.
Olsen, A., Lange, N., Key, R. M., Tanhua, T., Álvarez, M., Becker, S., Bittig, H. C., Carter, B. R., Cotrim da Cunha, L., Feely, R. A., van Heuven, S. M. A. C., Hoppema, M., Ishii, M., Jeansson, E., Jones, S. D., Jutterström, S., Karlsen, M. K., Kozyr, A., Lauvset, S. K., Lo Monaco, C., Murata, A., Pérez, F. F., Pfeil, B., Schirnick, C., Steinfeldt, R., Suzuki, T., Telszewski, M., Tilbrook, B., Velo, A., and Wanninkhof, R.: Global Ocean Data Analysis Project version 2.2019 (GLODAPv2.2019) (NCEI Accession 0186803), version 2.2019, NOAA National Centers for Environmental Information [data set], https://doi.org/10.25921/xnme-wr20, 2019.
Olson, S. L., Reinhard, C. T., and Lyons, T. W.: Limited role for methane in the mid-Proterozoic greenhouse, P. Natl Acad. Sci. USA, 113, 11447–11452, https://doi.org/10.1073/pnas.1608549113, 2016.
Oschlies, A., Schulz, K. G., Riebesell, U., and Schmittner, A.: Simulated 21st century's increase in oceanic suboxia by CO2-enhanced biotic carbon export, Global Biogeochem. Cycles, 22, GB4008, https://doi.org/10.1029/2007gb003147, 2008.
Ozaki, K.: kazumi-ozaki/CANOPS-GRBv1: CANOPS-GRBv1 (Version v1), Zenodo [code], https://doi.org/10.5281/zenodo.5893804, 2022.
Ozaki, K. and Reinhard, C. T.: The future lifespan of Earth's oxygenated atmosphere, Nat. Geosci., 14, 138–142, https://doi.org/10.1038/s41561-021-00693-5, 2021.
Ozaki, K. and Tajika, E.: Biogeochemical effects of atmospheric oxygen concentration, phosphorus weathering, and sea-level stand on oceanic redox chemistry: Implications for greenhouse climates, Earth Planet. Sc. Lett., 373, 129–139, https://doi.org/10.1016/j.epsl.2013.04.029, 2013.
Ozaki, K., Tajima, S., and Tajika, E.: Conditions required for oceanic anoxia/euxinia: Constraints from a one-dimensional ocean biogeochemical cycle model, Earth Planet. Sc. Lett., 304, 270–279, https://doi.org/10.1016/j.epsl.2011.02.011, 2011.
Ozaki, K., Tajika, E., Hong, P. K., Nakagawa, Y., and Reinhard, C. T.: Effects of primitive photosynthesis on Earth's early climate system, Nat. Geosci., 11, 55–59, https://doi.org/10.1038/s41561-017-0031-2, 2018.
Ozaki, K., Reinhard, C. T., and Tajika, E.: A sluggish mid-Proterozoic biosphere and its effect on Earth's redox balance, Geobiology, 17, 3–11, https://doi.org/10.1111/gbi.12317, 2019a.
Ozaki, K., Thompson, K. J., Simister, R. L., Crowe, S. A., and Reinhard, C. T.: Anoxygenic photosynthesis and the delayed oxygenation of Earth's atmosphere, Nat. Commun., 10, 3026, https://doi.org/10.1038/s41467-019-10872-z, 2019b.
Pallud, C. and Van Cappellen, P.: Kinetics of microbial sulfate reduction in estuarine sediments, Geochim. Cosmochim. Ac., 70, 1148–1162, https://doi.org/10.1016/j.gca.2005.11.002, 2006.
Papadomanolaki, N. M., Lenstra, W. K., Wolthers, M., and Slomp, C. P.: Enhanced phosphorus recycling during past oceanic anoxia amplified by low rates of apatite authigenesis, Sci, Adv,, 8, eabn2370, https://doi.org/10.1126/sciadv.abn2370, 2022.
Petsch, S. T. and Berner, R. A.: Coupling the geochemical cycles of C, P, Fe, and S; the effect on atmospheric O2 and the isotopic records of carbon and sulfur, Am. J. Sci., 298, 246–262, https://doi.org/10.2475/ajs.298.3.246, 1998.
Petsch, S. T., Eglinton, T. I., and Edwards, K. J.: 14C-Dead Living Biomass: Evidence for Microbial Assimilation of Ancient Organic Carbon During Shale Weathering, Science, 292, 1127–1131, https://doi.org/10.1126/science.1058332, 2001.
Pfeifer, K., Hensen, C., Adler, M., Wenzhfer, F., Weber, B., and Schulz, H. D.: Modeling of subsurface calcite dissolution, including the respiration and reoxidation processes of marine sediments in the region of equatorial upwelling off Gabon, Geochim. Cosmochim. Ac., 66, 4247–4259, https://doi.org/10.1016/S0016-7037(02)01073-6, 2002.
Planavsky, N. J., Cole, D. B., Reinhard, C. T., Diamond, C., Love, G. D., Luo, G., Zhang, S., Konhauser, K. O., and Lyons, T. W.: No evidence for high atmospheric oxygen levels 1,400 million years ago, P. Natl Acad. Sci. USA, 113, E2550–E2551, https://doi.org/10.1073/pnas.1601925113, 2016.
Planavsky, N. J., Cole, D. B., Isson, T. T., Reinhard, C. T., Crockford, P. W., Sheldon, N. D., and Lyons, T. W.: A case for low atmospheric oxygen levels during Earth's middle history, Emerging Topics in Life Sciences, 2, 149–159, https://doi.org/10.1042/etls20170161, 2018.
Prentice, I. C., Farquhar, G. D., Fasham, M. J. R., Goulden, M. L., Heimann, M., Jaramillo, V. J., Kheshgi, H. S., Le Quere, C., Scholes, R. J., and Wallace, D. W. R.: The carbon cycle and atmospheric carbon dioxide, in: Climate Change 2001: the Scientific Basis, edited by: Houghton, J. T., Ding, Y., Griggs, D. J., Noguer, N., van der Linden, P. J., Xiaosu, D., Maskell, K., and Johnson, C. A., Cambridge University Press, New York, 2001.
Quigg, A., Finkel, Z. V., Irwin, A. J., Rosenthal, Y., Ho, T.-Y., Reinfelder, J. R., Schofield, O., Morel, F. M. M., and Falkowski, P. G.: The evolutionary inheritance of elemental stoichiometry in marine phytoplankton, Nature, 425, 291–294, https://doi.org/10.1038/nature01953, 2003.
Raiswell, R. and Canfield, D. E.: The Iron Biogeochemical Cycle Past and Present, Geochemical Perspectives, 1, 1–2, 2012.
Raynaud, D., Jouzel, J., Barnola, J. M., Chappellaz, J., Delmas, R. J., and Lorius, C.: The Ice Record of Greenhouse Gases, Science, 259, 926–934, https://doi.org/10.1126/science.259.5097.926, 1993.
Redfield, A. C., Ketchum, B. H., and Richards, F. A.: The influence of organisms on the composition of sea-water, in: The Sea, edited by: Hill, M. N., Interscience Publishers, New York, 26–77, 1963.
Reimers, C. E., Jahnke, R. A., and McCorkle, D. C.: Carbon fluxes and burial rates over the continental slope and rise off central California with implications for the global carbon cycle, Global Biogeochem. Cycles, 6, 199–224, https://doi.org/10.1029/92gb00105, 1992.
Reinhard, C. T., Olson, S. L., Schwieterman, E. W., and Lyons, T. W.: False Negatives for Remote Life Detection on Ocean-Bearing Planets: Lessons from the Early Earth, Astrobiology, 17, 287–297, https://doi.org/10.1089/ast.2016.1598, 2017a.
Reinhard, C. T., Planavsky, N. J., Gill, B. C., Ozaki, K., Robbins, L. J., Lyons, T. W., Fischer, W. W., Wang, C., Cole, D. B., and Konhauser, K. O.: Evolution of the global phosphorus cycle, Nature, 541, 386–389, https://doi.org/10.1038/nature20772, 2017b.
Reinhard, C. T., Olson, S. L., Kirtland Turner, S., Pälike, C., Kanzaki, Y., and Ridgwell, A.: Oceanic and atmospheric methane cycling in the cGENIE Earth system model – release v0.9.14, Geosci. Model Dev., 13, 5687–5706, https://doi.org/10.5194/gmd-13-5687-2020, 2020.
Ridgwell, A. and Hargreaves, J. C.: Regulation of atmospheric CO2 by deep-sea sediments in an Earth system model, Global Biogeochem. Cycles, 21, GB2008, https://doi.org/10.1029/2006gb002764, 2007.
Romaniello, S. J. and Derry, L. A.: An intermediate-complexity model for simulating marine biogeochemistry in deep time: Validation against the modern global ocean, Geochem. Geophys. Geosyst., 11, Q08001, https://doi.org/10.1029/2009gc002711, 2010.
Rowe, G. T., Morse, J., Nunnally, C., and Boland, G. S.: Sediment community oxygen consumption in the deep Gulf of Mexico, Deep-Sea Res. Pt. II, 55, 2686–2691, https://doi.org/10.1016/j.dsr2.2008.07.018, 2008.
Ruttenberg, K. C.: Reassessment of the oceanic residence time of phosphorus, Chem. Geol., 107, 405–409, https://doi.org/10.1016/0009-2541(93)90220-D, 1993.
Ruttenberg, K. C.: The Global Phosphorus Cycle, in: Treatise on Geochemistry, edited by: Turekian, K. K., Pergamon, Oxford, 585–643, https://doi.org/10.1016/B0-08-043751-6/08153-6, 2003.
Sachs, O., Sauter, E. J., Schlüter, M., Rutgers van der Loeff, M. M., Jerosch, K., and Holby, O.: Benthic organic carbon flux and oxygen penetration reflect different plankton provinces in the Southern Ocean, Deep-Sea Res. Pt. I, 56, 1319–1335, https://doi.org/10.1016/j.dsr.2009.02.003, 2009.
Sagan, C., Thompson, W. R., Carlson, R., Gurnett, D., and Hord, C.: A search for life on Earth from the Galileo spacecraft, Nature, 365, 715–721, 1993.
Sarmiento, J. L. and Gruber, N.: Ocean biogeochemical dynamics, Princeton University Press, ISBN 0-691-01707-7, 2006.
Sarmiento, J. L. and Toggweiler, J. R.: A new model for the role of the oceans in determining atmospheric , Nature, 308, 621–624, https://doi.org/10.1038/308621a0, 1984.
Schenau, S. J. and De Lange, G. J.: Phosphorus regeneration vs. burial in sediments of the Arabian Sea, Marine Chem., 75, 201–217, https://doi.org/10.1016/S0304-4203(01)00037-8, 2001.
Schlesinger, W. H. and Bernhardt, E. S.: The Global Cycles of Sulfur and Mercury, in: Biogeochemistry, 3rd edn., Academic Press, Boston, 469–486, https://doi.org/10.1016/B978-0-12-385874-0.00013-3, 2013.
Schwieterman, E. W., Kiang, N. Y., Parenteau, M. N., Harman, C. E., DasSarma, S., Fischer, T. M., Arney, G. N., Hartnett, H. E., Reinhard, C. T., Olson, S. L., Meadows, V. S., Cockell, C. S., Walker, S. I., Grenfell, J. L., Hegde, S., Rugheimer, S., Hu, R., and Lyons, T. W.: Exoplanet Biosignatures: A Review of Remotely Detectable Signs of Life, Astrobiology, 18, 663–708, https://doi.org/10.1089/ast.2017.1729, 2018.
Shaffer, G.: Phosphate pumps and shuttles in the Black Sea, Nature, 321, 515–517, https://doi.org/10.1038/321515a0, 1986.
Shaffer, G. and Sarmiento, J. L.: Biogeochemical cycling in the global ocean: 1. A new, analytical model with continuous vertical resolution and high-latitude dynamics, J. Geophys. Res., 100, 2659–2672, https://doi.org/10.1029/94JC01167, 1995.
Shaffer, G., Malskær Olsen, S., and Pepke Pedersen, J. O.: Presentation, calibration and validation of the low-order, DCESS Earth System Model (Version 1), Geosci. Model Dev., 1, 17–51, https://doi.org/10.5194/gmd-1-17-2008, 2008.
Sharoni, S. and Halevy, I.: Geologic controls on phytoplankton elemental composition, P. Natl Acad. Sci. USA, 119, e2113263118, https://doi.org/10.1073/pnas.2113263118, 2022.
Siegenthaler, U. and Wenk, T.: Rapid atmospheric CO2 variations and ocean circulation, Nature, 308, 624–626, https://doi.org/10.1038/308624a0, 1984.
Sleep, N. H.: Dioxygen over geological time, in: Metal ions in biological systems, edited by: Sigel, A., Sigel, H., and Sigel, R. K. O., Taylor & Francis Group, Boca Raton, 49–73, 2005.
Slomp, C. P. and Van Cappellen, P.: The global marine phosphorus cycle: sensitivity to oceanic circulation, Biogeosciences, 4, 155–171, https://doi.org/10.5194/bg-4-155-2007, 2007.
Slomp, C. P., Thomson, J., and de Lange, G. J.: Enhanced regeneration of phosphorus during formation of the most recent eastern Mediterranean sapropel (S1), Geochim. Cosmochim. Ac., 66, 1171–1184, https://doi.org/10.1016/S0016-7037(01)00848-1, 2002.
Sloyan, B. M.: Spatial variability of mixing in the Southern Ocean, Geophys. Res. Lett., 32, L18603, https://doi.org/10.1029/2005gl023568, 2005.
Soulet, G., Hilton, R. G., Garnett, M. H., Roylands, T., Klotz, S., Croissant, T., Dellinger, M., and Le Bouteiller, C.: Temperature control on CO2 emissions from the weathering of sedimentary rocks, Nat. Geosci., 14, 665–671, https://doi.org/10.1038/s41561-021-00805-1, 2021.
Southam, J. R., Peterson, W. H., and Brass, G. W.: Dynamics of anoxia, Palaeogeogr. Palaeocl., 40, 183–198, https://doi.org/10.1016/0031-0182(82)90089-X, 1982.
Steefel, C. I. and MacQuarrie, K. T. B.: Approaches to modeling of reactive transport in porous media, Rev. Miner. Geochem., 34, 85–129, 1996.
Suess, E.: Particulate organic carbon flux in the oceans – surface productivity and oxygen utilization, Nature, 288, 260–263, https://doi.org/10.1038/288260a0, 1980.
Tang, D., Shi, X., Wang, X., and Jiang, G.: Extremely low oxygen concentration in mid-Proterozoic shallow seawaters, Precambrian Res., 276, 145–157, https://doi.org/10.1016/j.precamres.2016.02.005, 2016.
Tarhan, L. G., Droser, M. L., Planavsky, N. J., and Johnston, D. T.: Protracted development of bioturbation through the early Palaeozoic Era, Nat. Geosci., 8, 865, https://doi.org/10.1038/ngeo2537, 2015.
Tarpgaard, I. H., Røy, H., and Jørgensen, B. B.: Concurrent low- and high-affinity sulfate reduction kinetics in marine sediment, Geochim. Cosmochim. Ac., 75, 2997–3010, https://doi.org/10.1016/j.gca.2011.03.028, 2011.
The LUVOIR Team: Mission Concept Study Final Report, in: arXiv e-prints, https://doi.org/10.48550/arXiv.1912.06219, 2019.
Tostevin, R., Turchyn, A. V., Farquhar, J., Johnston, D. T., Eldridge, D. L., Bishop, J. K. B., and McIlvin, M.: Multiple sulfur isotope constraints on the modern sulfur cycle, Earth Planet. Sc. Lett., 396, 14–21, https://doi.org/10.1016/j.epsl.2014.03.057, 2014.
Tromp, T. K., Van Cappellen, P., and Key, R. M.: A global model for the early diagenesis of organic carbon and organic phosphorus in marine sediments, Geochim. Cosmochim. Ac., 59, 1259–1284, https://doi.org/10.1016/0016-7037(95)00042-X, 1995.
Tsunogai, S. and Noriki, S.: Particulate fluxes of carbonate and organic carbon in the ocean. Is the marine biological activity working as a sink of the atmospheric carbon?, Tellus B, 43, 265–266, https://doi.org/10.3402/tellusb.v43i2.15272, 1991.
Turchyn, A. V. and Schrag, D. P.: Oxygen Isotope Constraints on the Sulfur Cycle over the Past 10 Million Years, Science, 303, 2004–2007, https://doi.org/10.1126/science.1092296, 2004.
Turchyn, A. V. and Schrag, D. P.: Cenozoic evolution of the sulfur cycle: Insight from oxygen isotopes in marine sulfate, Earth Planet. Sc. Lett., 241, 763–779, https://doi.org/10.1016/j.epsl.2005.11.007, 2006.
Turnewitsch, R. and Pohl, C.: An estimate of the efficiency of the iron- and manganese-driven dissolved inorganic phosphorus trap at an oxic/euxinic water column redoxcline, Global Biogeochem. Cycles, 24, GB4025, https://doi.org/10.1029/2010gb003820, 2010.
Tyrrell, T.: The relative influences of nitrogen and phosphorus on oceanic primary production, Nature, 400, 525–531, https://doi.org/10.1038/22941, 1999.
Van Cappellen, P. and Ingall, E. D.: Benthic phosphorus regeneration, net primary production, and ocean anoxia: A model of the coupled marine biogeochemical cycles of carbon and phosphorus, Paleoceanography, 9, 677–692, https://doi.org/10.1029/94PA01455, 1994.
Van Cappellen, P. and Ingall, E. D.: Redox Stabilization of the Atmosphere and Oceans by Phosphorus-Limited Marine Productivity, Science, 271, 493–496, https://doi.org/10.1126/science.271.5248.493, 1996.
Van Cappellen, P. and Wang, Y.: Cycling of iron and manganese in surface sediments; a general theory for the coupled transport and reaction of carbon, oxygen, nitrogen, sulfur, iron, and manganese, Am. J. Sci., 296, 197–243, https://doi.org/10.2475/ajs.296.3.197, 1996.
van de Velde, S. J., Hülse, D., Reinhard, C. T., and Ridgwell, A.: Iron and sulfur cycling in the cGENIE.muffin Earth system model (v0.9.21), Geosci. Model Dev., 14, 2713–2745, https://doi.org/10.5194/gmd-14-2713-2021, 2021.
Volk, T. and Hoffert, M. I.: Ocean carbon pumps: Analysis of relative strengths and efficiencies in ocean-driven atmospheric CO2 changes, in: The Carbon Cycle and Atmospheric CO2: Natural Variations Archean to Present, edited by: Sundquist, E. T. and Broecker, W. S., 99–110, https://doi.org/10.1029/GM032p0099, 1985.
Walker, J. C. G.: Evolution of the atmosphere, Macmillan, New York, 318 pp., ISBN 0-02-854390-4, 1977.
Walker, J. C. G. and Brimblecombe, P.: Iron and sulfur in the pre-biologic ocean, Precambrian Res., 28, 205–222, https://doi.org/10.1016/0301-9268(85)90031-2, 1985.
Wallmann, K.: Feedbacks between oceanic redox states and marine productivity: A model perspective focused on benthic phosphorus cycling, Global Biogeochem. Cycles, 17, 1084, https://doi.org/10.1029/2002gb001968, 2003.
Wallmann, K.: Phosphorus imbalance in the global ocean?, Global Biogeochem. Cycles, 24, GB4030, https://doi.org/10.1029/2009gb003643, 2010.
Wang, W.-L., Moore, J. K., Martiny, A. C., and Primeau, F. W.: Convergent estimates of marine nitrogen fixation, Nature, 566, 205–211, https://doi.org/10.1038/s41586-019-0911-2, 2019.
WebBook, N. C.: NIST Chemistry WebBook, https://doi.org/10.18434/T4D303, 2022.
Westrich, J. T. and Berner, R. A.: The role of sedimentary organic matter in bacterial sulfate reduction: The G model tested, Limnol. Oceanogr., 29, 236–249, https://doi.org/10.4319/lo.1984.29.2.0236, 1984.
Wheat, C. G., Feely, R. A., and Mottl, M. J.: Phosphate removal by oceanic hydrothermal processes: An update of the phosphorus budget in the oceans, Geochim. Cosmochim. Ac., 60, 3593–3608, https://doi.org/10.1016/0016-7037(96)00189-5, 1996.
Wheat, C. G., McManus, J., Mottl, M. J., and Giambalvo, E.: Oceanic phosphorus imbalance: Magnitude of the mid-ocean ridge flank hydrothermal sink, Geophys. Res. Lett., 30, 1895, https://doi.org/10.1029/2003GL017318, 2003.
Woodward, F. I.: Global primary production, Current Biology, 17, R269–R273, https://doi.org/10.1016/j.cub.2007.01.054, 2007.
Wortmann, U. G. and Paytan, A.: Rapid Variability of Seawater Chemistry Over the Past 130 Million Years, Science, 337, 334–336, https://doi.org/10.1126/science.1220656, 2012.
Yakushev, E. V. and Neretin, L. N.: One-dimensional modeling of nitrogen and sulfur cycles in the aphotic zones of the Black and Arabian Seas, Global Biogeochem. Cycles, 11, 401–414, https://doi.org/10.1029/97GB00782, 1997.
Yakushev, E. V., Pollehne, F., Jost, G., Kuznetsov, I., Schneider, B., and Umlauf, L.: Analysis of the water column oxic/anoxic interface in the Black and Baltic seas with a numerical model, Marine Chem., 107, 388–410, https://doi.org/10.1016/j.marchem.2007.06.003, 2007.
Yamanaka, Y. and Tajika, E.: The role of the vertical fluxes of particulate organic matter and calcite in the oceanic carbon cycle: Studies using an ocean biogeochemical general circulation model, Global Biogeochem. Cycles, 10, 361–382, https://doi.org/10.1029/96gb00634, 1996.
Yao, W. and Millero, F.: The chemistry of the anoxic waters in the Framvaren Fjord, Norway, Aquatic Geochemistry, 1, 53–88, https://doi.org/10.1007/bf01025231, 1995.
Yaroshevsky, A. A.: Abundances of chemical elements in the Earth's crust, Geochem. Int., 44, 48–55, https://doi.org/10.1134/s001670290601006x, 2006.
Zabel, M., Dahmke, A., and Schulz, H. D.: Regional distribution of diffusive phosphate and silicate fluxes through the sediment–water interface: the eastern South Atlantic, Deep-Sea Res. Pt. I, 45, 277–300, https://doi.org/10.1016/S0967-0637(97)00073-3, 1998.
Zhang, S., Wang, X., Wang, H., Bjerrum, C. J., Hammarlund, E. U., Dahl, T. W., and Canfield, D. E.: Reply to Planavsky et al.: Strong evidence for high atmospheric oxygen levels 1,400 million years ago, P. Natl Acad. Sci. USA, 113, E2552–E2553, https://doi.org/10.1073/pnas.1603982113, 2016.
Zhao, M., Zhang, S., Tarhan, L. G., Reinhard, C. T., and Planavsky, N.: The role of calcium in regulating marine phosphorus burial and atmospheric oxygenation, Nat. Commun., 11, 2232, https://doi.org/10.1038/s41467-020-15673-3, 2020.
A new biogeochemical model (CANOPS-GRB v1.0) for assessing the redox stability and dynamics of the ocean–atmosphere system on geologic timescales has been developed. In this paper, we present a full description of the model and its performance. CANOPS-GRB is a useful tool for understanding the factors regulating atmospheric O2 level and has the potential to greatly refine our current understanding of Earth's oxygenation history.
A new biogeochemical model (CANOPS-GRB v1.0) for assessing the redox stability and dynamics of...