Articles | Volume 10, issue 6
© Author(s) 2013. This work is distributed under
the Creative Commons Attribution 3.0 License.
the Creative Commons Attribution 3.0 License.
© Author(s) 2013. This work is distributed under
the Creative Commons Attribution 3.0 License.
the Creative Commons Attribution 3.0 License.
A model for variable phytoplankton stoichiometry based on cell protein regulation
J. A. Bonachela
Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey, 08544, USA
S. D. Allison
Department of Ecology and Evolutionary Biology & Department of Earth System Science, University of California, Irvine, California, 92697, USA
A. C. Martiny
Department of Ecology and Evolutionary Biology & Department of Earth System Science, University of California, Irvine, California, 92697, USA
S. A. Levin
Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey, 08544, USA
No articles found.
Elizabeth S. Duan, Luciana Chavez Rodriguez, Nicole Hemming-Schroeder, Baptiste Wijas, Habacuc Flores-Moreno, Alexander W. Cheesman, Lucas A. Cernusak, Michael J. Liddell, Paul Eggleton, Amy E. Zanne, and Steven D. Allison
Understanding the link between climate and carbon fluxes is crucial in predicting how climate change will impact carbon sinks. We estimated CO2 fluxes from deadwood in tropical Australia using wood microclimate variables (wood moisture content and temperature). Our model predicted that the majority of deadwood carbon is released as CO2, except when termite activity is detected. Future models should also incorporate wood traits, like species and chemical composition, to better predict fluxes.
Hua W. Xie, Adriana L. Romero-Olivares, Michele Guindani, and Steven D. Allison
Biogeosciences, 17, 4043–4057,Short summary
Soil biogeochemical models (SBMs) are needed to predict future soil CO2 emissions levels, but we presently lack statistically rigorous frameworks for assessing the predictive utility of SBMs. In this study, we demonstrate one possible approach to evaluating SBMs by comparing the fits of two models to soil CO2 respiration data with recently developed Bayesian statistical goodness-of-fit metrics. Our results demonstrate that our approach is a viable one for continued development and refinement.
K. E. O. Todd-Brown, J. T. Randerson, F. Hopkins, V. Arora, T. Hajima, C. Jones, E. Shevliakova, J. Tjiputra, E. Volodin, T. Wu, Q. Zhang, and S. D. Allison
Biogeosciences, 11, 2341–2356,
A. E. Zimmerman, A. C. Martiny, M. W. Lomas, and S. D. Allison
Biogeosciences, 11, 1599–1611,
K. E. O. Todd-Brown, J. T. Randerson, W. M. Post, F. M. Hoffman, C. Tarnocai, E. A. G. Schuur, and S. D. Allison
Biogeosciences, 10, 1717–1736,
Related subject area
Biogeochemistry: Modelling, AquaticSeasonal and interannual variability of the pelagic ecosystem and of the organic carbon budget in the Rhodes Gyre (eastern Mediterranean): influence of winter mixingHow much do bacterial growth properties and biodegradable dissolved organic matter control water quality at low flow?Methane emissions from Arctic landscapes during 2000–2015: an analysis with land and lake biogeochemistry modelsIncluding filter-feeding gelatinous macrozooplankton in a global marine biogeochemical model: model–data comparison and impact on the ocean carbon cycleRiverine impact on future projections of marine primary production and carbon uptakeSubsurface oxygen maximum in oligotrophic marine ecosystems: mapping the interaction between physical and biogeochemical processesQuantifying biological carbon pump pathways with a data-constrained mechanistic model ensemble approachAssessing the spatial and temporal variability of methylmercury biogeochemistry and bioaccumulation in the Mediterranean Sea with a coupled 3D modelHydrodynamic and biochemical impacts on the development of hypoxia in the Louisiana–Texas shelf – Part 2: statistical modeling and hypoxia predictionModelling the effects of benthic fauna on carbon, nitrogen and phosphorus dynamics in the Baltic SeaImproved prediction of dimethyl sulfide (DMS) distributions in the northeast subarctic Pacific using machine-learning algorithmsNutrient transport and transformation in macrotidal estuaries of the French Atlantic coast: a modeling approach using the Carbon-Generic Estuarine ModelA modelling study of temporal and spatial pCO2 variability on the biologically active and temperature-dominated Scotian ShelfModeling the marine chromium cycle: new constraints on global-scale processesNew insights into large-scale trends of apparent organic matter reactivity in marine sediments and patterns of benthic carbon transformationEvaluation of ocean dimethylsulfide concentration and emission in CMIP6 modelsZooplankton mortality effects on the plankton community of the northern Humboldt Current System: sensitivity of a regional biogeochemical modelMulti-compartment kinetic–allometric (MCKA) model of radionuclide bioaccumulation in marine fishImpact of bottom trawling on sediment biogeochemistry: a modelling approachCyanobacteria blooms in the Baltic Sea: a review of models and factsArctic Ocean acidification over the 21st century co-driven by anthropogenic carbon increases and freshening in the CMIP6 model ensembleModeling silicate–nitrate–ammonium co-limitation of algal growth and the importance of bacterial remineralization based on an experimental Arctic coastal spring bloom culture studyRole of jellyfish in the plankton ecosystem revealed using a global ocean biogeochemical modelExtreme event waves in marine ecosystems: an application to Mediterranean Sea surface chlorophyllUse of optical absorption indices to assess seasonal variability of dissolved organic matter in Amazon floodplain lakesThe role of sediment-induced light attenuation on primary production during Hurricane Gustav (2008)Quantifying spatiotemporal variability in zooplankton dynamics in the Gulf of Mexico with a physical–biogeochemical modelOne size fits all? Calibrating an ocean biogeochemistry model for different circulationsAssessing the temporal scale of deep-sea mining impacts on sediment biogeochemistrySeasonal patterns of surface inorganic carbon system variables in the Gulf of Mexico inferred from a regional high-resolution ocean biogeochemical modelOxygen dynamics and evaluation of the single-station diel oxygen model across contrasting geologiesOceanic CO2 outgassing and biological production hotspots induced by pre-industrial river loads of nutrients and carbon in a global modeling approachGlobal trends in marine nitrate N isotopes from observations and a neural network-based climatologyMerging bio-optical data from Biogeochemical-Argo floats and models in marine biogeochemistryModel constraints on the anthropogenic carbon budget of the Arctic OceanModeling oceanic nitrate and nitrite concentrations and isotopes using a 3-D inverse N cycle modelBiogeochemical response of the Mediterranean Sea to the transient SRES-A2 climate change scenarioModelling the biogeochemical effects of heterotrophic and autotrophic N2 fixation in the Gulf of Aqaba (Israel), Red SeaA perturbed biogeochemistry model ensemble evaluated against in situ and satellite observationsDiazotrophy as the main driver of the oligotrophy gradient in the western tropical South Pacific Ocean: results from a one-dimensional biogeochemical–physical coupled modelCauses of simulated long-term changes in phytoplankton biomass in the Baltic proper: a wavelet analysisModelling N2 fixation related to Trichodesmium sp.: driving processes and impacts on primary production in the tropical Pacific OceanLong-term response of oceanic carbon uptake to global warming via physical and biological pumpsSeasonal patterns in phytoplankton biomass across the northern and deep Gulf of Mexico: a numerical model studySea-surface dimethylsulfide (DMS) concentration from satellite data at global and regional scalesA new look at the multi-G model for organic carbon degradation in surface marine sediments for coupled benthic–pelagic simulations of the global oceanGroundwater data improve modelling of headwater stream CO2 outgassing with a stable DIC isotope approachThe influence of the ocean circulation state on ocean carbon storage and CO2 drawdown potential in an Earth system modelModelling potential production of macroalgae farms in UK and Dutch coastal watersAssimilating bio-optical glider data during a phytoplankton bloom in the southern Ross Sea
Joelle Habib, Caroline Ulses, Claude Estournel, Milad Fakhri, Patrick Marsaleix, Mireille Pujo-Pay, Marine Fourrier, Laurent Coppola, Alexandre Mignot, Laurent Mortier, and Pascal Conan
Biogeosciences, 20, 3203–3228,Short summary
The Rhodes Gyre, eastern Mediterranean Sea, is the main Levantine Intermediate Water formation site. In this study, we use a 3D physical–biogeochemical model to investigate the seasonal and interannual variability of organic carbon dynamics in the gyre. Our results show its autotrophic nature and its high interannual variability, with enhanced primary production, downward exports, and onward exports to the surrounding regions during years marked by intense heat losses and deep mixed layers.
Masihullah Hasanyar, Thomas Romary, Shuaitao Wang, and Nicolas Flipo
Biogeosciences, 20, 1621–1633,Short summary
The results of this study indicate that biodegradable dissolved organic matter is responsible for oxygen depletion at low flow during summer seasons when heterotrophic bacterial activity is so intense. Therefore, the dissolved organic matter must be well measured in the water monitoring networks in order to have more accurate water quality models. It also advocates for high-frequency data collection for better quantification of the uncertainties related to organic matter.
Xiangyu Liu and Qianlai Zhuang
Biogeosciences, 20, 1181–1193,Short summary
We are among the first to quantify methane emissions from inland water system in the pan-Arctic. The total CH4 emissions are 36.46 Tg CH4 yr−1 during 2000–2015, of which wetlands and lakes were 21.69 Tg yr−1 and 14.76 Tg yr−1, respectively. By using two non-overlap area change datasets with land and lake models, our simulation avoids small lakes being counted twice as both lake and wetland, and it narrows the gap between two different methods used to quantify regional CH4 emissions.
Corentin Clerc, Laurent Bopp, Fabio Benedetti, Meike Vogt, and Olivier Aumont
Biogeosciences, 20, 869–895,Short summary
Gelatinous zooplankton play a key role in the ocean carbon cycle. In particular, pelagic tunicates, which feed on a wide size range of prey, produce rapidly sinking detritus. Thus, they efficiently transfer carbon from the surface to the depths. Consequently, we added these organisms to a marine biogeochemical model (PISCES-v2) and evaluated their impact on the global carbon cycle. We found that they contribute significantly to carbon export and that this contribution increases with depth.
Shuang Gao, Jörg Schwinger, Jerry Tjiputra, Ingo Bethke, Jens Hartmann, Emilio Mayorga, and Christoph Heinze
Biogeosciences, 20, 93–119,Short summary
We assess the impact of riverine nutrients and carbon (C) on projected marine primary production (PP) and C uptake using a fully coupled Earth system model. Riverine inputs alleviate nutrient limitation and thus lessen the projected PP decline by up to 0.7 Pg C yr−1 globally. The effect of increased riverine C may be larger than the effect of nutrient inputs in the future on the projected ocean C uptake, while in the historical period increased nutrient inputs are considered the largest driver.
Valeria Di Biagio, Stefano Salon, Laura Feudale, and Gianpiero Cossarini
Biogeosciences, 19, 5553–5574,Short summary
The amount of dissolved oxygen in the ocean is the result of interacting physical and biological processes. Oxygen vertical profiles show a subsurface maximum in a large part of the ocean. We used a numerical model to map this subsurface maximum in the Mediterranean Sea and to link local differences in its properties to the driving processes. This emerging feature can help the marine ecosystem functioning to be better understood, also under the impacts of climate change.
Michael R. Stukel, Moira Décima, and Michael R. Landry
Biogeosciences, 19, 3595–3624,Short summary
The biological carbon pump (BCP) transports carbon into the deep ocean, leading to long-term marine carbon sequestration. It is driven by many physical, chemical, and ecological processes. We developed a model of the BCP constrained using data from 11 cruises in 4 different ocean regions. Our results show that sinking particles and vertical mixing are more important than transport mediated by vertically migrating zooplankton. They also highlight the uncertainty in current estimates of the BCP.
Ginevra Rosati, Donata Canu, Paolo Lazzari, and Cosimo Solidoro
Biogeosciences, 19, 3663–3682,Short summary
Methylmercury (MeHg) is produced and bioaccumulated in marine food webs, posing concerns for human exposure through seafood consumption. We modeled and analyzed the fate of MeHg in the lower food web of the Mediterranean Sea. The modeled spatial–temporal distribution of plankton bioaccumulation differs from the distribution of MeHg in surface water. We also show that MeHg exposure concentrations in temperate waters can be lowered by winter convection, which is declining due to climate change.
Yanda Ou, Bin Li, and Z. George Xue
Biogeosciences, 19, 3575–3593,Short summary
Over the past decades, the Louisiana–Texas shelf has been suffering recurring hypoxia (dissolved oxygen < 2 mg L−1). We developed a novel prediction model using state-of-the-art statistical techniques based on physical and biogeochemical data provided by a numerical model. The model can capture both the magnitude and onset of the annual hypoxia events. This study also demonstrates that it is possible to use a global model forecast to predict regional ocean water quality.
Eva Ehrnsten, Oleg Pavlovitch Savchuk, and Bo Gustav Gustafsson
Biogeosciences, 19, 3337–3367,Short summary
We studied the effects of benthic fauna, animals living on or in the seafloor, on the biogeochemical cycles of carbon, nitrogen and phosphorus using a model of the Baltic Sea ecosystem. By eating and excreting, the animals transform a large part of organic matter sinking to the seafloor into inorganic forms, which fuel plankton blooms. Simultaneously, when they move around (bioturbate), phosphorus is bound in the sediments. This reduces nitrogen-fixing plankton blooms and oxygen depletion.
Brandon J. McNabb and Philippe D. Tortell
Biogeosciences, 19, 1705–1721,Short summary
The trace gas dimethyl sulfide (DMS) plays an important role in the ocean sulfur cycle and can also influence Earth’s climate. Our study used two statistical methods to predict surface ocean concentrations and rates of sea–air exchange of DMS in the northeast subarctic Pacific. Our results show improved predictive power over previous approaches and suggest that nutrient availability, light-dependent processes, and physical mixing may be important controls on DMS in this region.
Xi Wei, Josette Garnier, Vincent Thieu, Paul Passy, Romain Le Gendre, Gilles Billen, Maia Akopian, and Goulven Gildas Laruelle
Biogeosciences, 19, 931–955,Short summary
Estuaries are key reactive ecosystems along the land–ocean aquatic continuum and are often strongly impacted by anthropogenic activities. We calculated nutrient in and out fluxes by using a 1-D transient model for seven estuaries along the French Atlantic coast. Among these, large estuaries with high residence times showed higher retention rates than medium and small ones. All reveal coastal eutrophication due to the excess of diffused nitrogen from intensive agricultural river basins.
Krysten Rutherford, Katja Fennel, Dariia Atamanchuk, Douglas Wallace, and Helmuth Thomas
Biogeosciences, 18, 6271–6286,Short summary
Using a regional model of the northwestern North Atlantic shelves in combination with a surface water time series and repeat transect observations, we investigate surface CO2 variability on the Scotian Shelf. The study highlights a strong seasonal cycle in shelf-wide pCO2 and spatial variability throughout the summer months driven by physical events. The simulated net flux of CO2 on the Scotian Shelf is out of the ocean, deviating from the global air–sea CO2 flux trend in continental shelves.
Frerk Pöppelmeier, David J. Janssen, Samuel L. Jaccard, and Thomas F. Stocker
Biogeosciences, 18, 5447–5463,Short summary
Chromium (Cr) is a redox-sensitive element that holds promise as a tracer of ocean oxygenation and biological activity. We here implemented the oxidation states Cr(III) and Cr(VI) in the Bern3D model to investigate the processes that shape the global Cr distribution. We find a Cr ocean residence time of 5–8 kyr and that the benthic source dominates the tracer budget. Further, regional model–data mismatches suggest strong Cr removal in oxygen minimum zones and a spatially variable benthic source.
Felipe S. Freitas, Philip A. Pika, Sabine Kasten, Bo B. Jørgensen, Jens Rassmann, Christophe Rabouille, Shaun Thomas, Henrik Sass, Richard D. Pancost, and Sandra Arndt
Biogeosciences, 18, 4651–4679,Short summary
It remains challenging to fully understand what controls carbon burial in marine sediments globally. Thus, we use a model–data approach to identify patterns of organic matter reactivity at the seafloor across distinct environmental conditions. Our findings support the notion that organic matter reactivity is a dynamic ecosystem property and strongly influences biogeochemical cycling and exchange. Our results are essential to improve predictions of future changes in carbon cycling and climate.
Josué Bock, Martine Michou, Pierre Nabat, Manabu Abe, Jane P. Mulcahy, Dirk J. L. Olivié, Jörg Schwinger, Parvadha Suntharalingam, Jerry Tjiputra, Marco van Hulten, Michio Watanabe, Andrew Yool, and Roland Séférian
Biogeosciences, 18, 3823–3860,Short summary
In this study we analyse surface ocean dimethylsulfide (DMS) concentration and flux to the atmosphere from four CMIP6 Earth system models over the historical and ssp585 simulations. Our analysis of contemporary (1980–2009) climatologies shows that models better reproduce observations in mid to high latitudes. The models disagree on the sign of the trend of the global DMS flux from 1980 onwards. The models agree on a positive trend of DMS over polar latitudes following sea-ice retreat dynamics.
Mariana Hill Cruz, Iris Kriest, Yonss Saranga José, Rainer Kiko, Helena Hauss, and Andreas Oschlies
Biogeosciences, 18, 2891–2916,Short summary
In this study we use a regional biogeochemical model of the eastern tropical South Pacific Ocean to implicitly simulate the effect that fluctuations in populations of small pelagic fish, such as anchovy and sardine, may have on the biogeochemistry of the northern Humboldt Current System. To do so, we vary the zooplankton mortality in the model, under the assumption that these fishes eat zooplankton. We also evaluate the model for the first time against mesozooplankton observations.
Roman Bezhenar, Kyeong Ok Kim, Vladimir Maderich, Govert de With, and Kyung Tae Jung
Biogeosciences, 18, 2591–2607,Short summary
A new approach to predicting the accumulation of radionuclides in fish was developed by taking into account heterogeneity of distribution of contamination in the organism and dependence of metabolic process rates on the fish mass. Predicted concentrations of radionuclides in fish agreed well with the laboratory and field measurements. The model with the defined generic parameters could be used in marine environments without local calibration, which is important for emergency decision support.
Emil De Borger, Justin Tiano, Ulrike Braeckman, Adriaan D. Rijnsdorp, and Karline Soetaert
Biogeosciences, 18, 2539–2557,Short summary
Bottom trawling alters benthic mineralization: the recycling of organic material (OM) to free nutrients. To better understand how this occurs, trawling events were added to a model of seafloor OM recycling. Results show that bottom trawling reduces OM and free nutrients in sediments through direct removal thereof and of fauna which transport OM to deeper sediment layers protected from fishing. Our results support temporospatial trawl restrictions to allow key sediment functions to recover.
Britta Munkes, Ulrike Löptien, and Heiner Dietze
Biogeosciences, 18, 2347–2378,Short summary
Cyanobacteria blooms can strongly aggravate eutrophication problems of water bodies. Their controls are, however, not comprehensively understood, which impedes effective management and protection plans. Here we review the current understanding of cyanobacteria blooms. Juxtaposition of respective field and laboratory studies with state-of-the-art mathematical models reveals substantial uncertainty associated with nutrient demands, grazing, and death of cyanobacteria.
Jens Terhaar, Olivier Torres, Timothée Bourgeois, and Lester Kwiatkowski
Biogeosciences, 18, 2221–2240,Short summary
The uptake of carbon, emitted as a result of human activities, results in ocean acidification. We analyse 21st-century projections of acidification in the Arctic Ocean, a region of particular vulnerability, using the latest generation of Earth system models. In this new generation of models there is a large decrease in the uncertainty associated with projections of Arctic Ocean acidification, with freshening playing a greater role in driving acidification than previously simulated.
Tobias R. Vonnahme, Martial Leroy, Silke Thoms, Dick van Oevelen, H. Rodger Harvey, Svein Kristiansen, Rolf Gradinger, Ulrike Dietrich, and Christoph Völker
Biogeosciences, 18, 1719–1747,Short summary
Diatoms are crucial for Arctic coastal spring blooms, and their growth is controlled by nutrients and light. At the end of the bloom, inorganic nitrogen or silicon can be limiting, but nitrogen can be regenerated by bacteria, extending the algal growth phase. Modeling these multi-nutrient dynamics and the role of bacteria is challenging yet crucial for accurate modeling. We recreated spring bloom dynamics in a cultivation experiment and developed a representative dynamic model.
Rebecca M. Wright, Corinne Le Quéré, Erik Buitenhuis, Sophie Pitois, and Mark J. Gibbons
Biogeosciences, 18, 1291–1320,Short summary
Jellyfish have been included in a global ocean biogeochemical model for the first time. The global mean jellyfish biomass in the model is within the observational range. Jellyfish are found to play an important role in the plankton ecosystem, influencing community structure, spatiotemporal dynamics and biomass. The model raises questions about the sensitivity of the zooplankton community to jellyfish mortality and the interactions between macrozooplankton and jellyfish.
Valeria Di Biagio, Gianpiero Cossarini, Stefano Salon, and Cosimo Solidoro
Biogeosciences, 17, 5967–5988,Short summary
Events that influence the functioning of the Earth’s ecosystems are of interest in relation to a changing climate. We propose a method to identify and characterise
wavesof extreme events affecting marine ecosystems for multi-week periods over wide areas. Our method can be applied to suitable ecosystem variables and has been used to describe different kinds of extreme event waves of phytoplankton chlorophyll in the Mediterranean Sea, by analysing the output from a high-resolution model.
Maria Paula da Silva, Lino A. Sander de Carvalho, Evlyn Novo, Daniel S. F. Jorge, and Claudio C. F. Barbosa
Biogeosciences, 17, 5355–5364,Short summary
In this study, we analyze the seasonal changes in the dissolved organic matter (DOM) quality (based on its optical properties) in four Amazon floodplain lakes. DOM plays a fundamental role in surface water chemistry, controlling metal bioavailability and mobility, and nutrient cycling. The model proposed in our paper highlights the potential to study DOM quality at a wider spatial scale, which may help to better understand the persistence and fate of DOM in the ecosystem.
Zhengchen Zang, Z. George Xue, Kehui Xu, Samuel J. Bentley, Qin Chen, Eurico J. D'Sa, Le Zhang, and Yanda Ou
Biogeosciences, 17, 5043–5055,
Taylor A. Shropshire, Steven L. Morey, Eric P. Chassignet, Alexandra Bozec, Victoria J. Coles, Michael R. Landry, Rasmus Swalethorp, Glenn Zapfe, and Michael R. Stukel
Biogeosciences, 17, 3385–3407,Short summary
Zooplankton are the smallest animals in the ocean and important food for fish. Despite their importance, zooplankton have been relatively undersampled. To better understand the zooplankton community in the Gulf of Mexico (GoM), we developed a model to simulate their dynamics. We found that heterotrophic protists are important for supporting mesozooplankton, which are the primary prey of larval fish. The model developed in this study has the potential to improve fisheries management in the GoM.
Iris Kriest, Paul Kähler, Wolfgang Koeve, Karin Kvale, Volkmar Sauerland, and Andreas Oschlies
Biogeosciences, 17, 3057–3082,Short summary
Constants of global biogeochemical ocean models are often tuned
by handto match observations of nutrients or oxygen. We investigate the effect of this tuning by optimising six constants of a global biogeochemical model, simulated in five different offline circulations. Optimal values for three constants adjust to distinct features of the circulation applied and can afterwards be swapped among the circulations, without losing too much of the model's fit to observed quantities.
Laura Haffert, Matthias Haeckel, Henko de Stigter, and Felix Janssen
Biogeosciences, 17, 2767–2789,Short summary
Deep-sea mining for polymetallic nodules is expected to have severe environmental impacts. Through prognostic modelling, this study aims to provide a holistic assessment of the biogeochemical recovery after a disturbance event. It was found that the recovery strongly depends on the impact type; e.g. complete removal of the surface sediment reduces seafloor nutrient fluxes over centuries.
Fabian A. Gomez, Rik Wanninkhof, Leticia Barbero, Sang-Ki Lee, and Frank J. Hernandez Jr.
Biogeosciences, 17, 1685–1700,Short summary
We use a numerical model to infer annual changes of surface carbon chemistry in the Gulf of Mexico (GoM). The main seasonality drivers of partial pressure of carbon dioxide and aragonite saturation state from the model are temperature and river runoff. The GoM basin is a carbon sink in winter–spring and carbon source in summer–fall, but uptake prevails near the Mississippi Delta year-round due to high biological production. Our model results show good correspondence with observational studies.
Simon J. Parker
Biogeosciences, 17, 305–315,Short summary
Dissolved oxygen (DO) models typically assume constant ecosystem respiration over the course of a single day. Using a data-driven approach, this research examines this assumption in four streams across two (hydro-)geological types (Chalk and Greensand). Despite hydrogeological equivalence in terms of baseflow index for each hydrogeological pairing, model suitability differed within, rather than across, geology types. This corresponded with associated differences in timings of DO minima.
Fabrice Lacroix, Tatiana Ilyina, and Jens Hartmann
Biogeosciences, 17, 55–88,Short summary
Contributions of rivers to the oceanic cycling of carbon have been poorly represented in global models until now. Here, we assess the long–term implications of preindustrial riverine loads in the ocean in a novel framework which estimates the loads through a hierarchy of weathering and land–ocean export models. We investigate their impacts for the oceanic biological production and air–sea carbon flux. Finally, we assess the potential incorporation of the framework in an Earth system model.
Patrick A. Rafter, Aaron Bagnell, Dario Marconi, and Timothy DeVries
Biogeosciences, 16, 2617–2633,Short summary
The N isotopic composition of nitrate (
nitrate δ15N) is a useful tracer of ocean N cycling and many other ocean processes. Here, we use a global compilation of marine nitrate δ15N as an input, training, and validating dataset for an artificial neural network (a.k.a.,
machine learning) and examine basin-scale trends in marine nitrate δ15N from the surface to the seafloor.
Elena Terzić, Paolo Lazzari, Emanuele Organelli, Cosimo Solidoro, Stefano Salon, Fabrizio D'Ortenzio, and Pascal Conan
Biogeosciences, 16, 2527–2542,Short summary
Measuring ecosystem properties in the ocean is a hard business. Recent availability of data from Biogeochemical-Argo floats can help make this task easier. Numerical models can integrate these new data in a coherent picture and can be used to investigate the functioning of ecosystem processes. Our new approach merges experimental information and model capabilities to quantitatively demonstrate the importance of light and water vertical mixing for algae dynamics in the Mediterranean Sea.
Jens Terhaar, James C. Orr, Marion Gehlen, Christian Ethé, and Laurent Bopp
Biogeosciences, 16, 2343–2367,Short summary
A budget of anthropogenic carbon in the Arctic Ocean, the main driver of open-ocean acidification, was constructed for the first time using a high-resolution ocean model. The budget reveals that anthropogenic carbon enters the Arctic Ocean mainly by lateral transport; the air–sea flux plays a minor role. Coarser-resolution versions of the same model, typical of earth system models, store less anthropogenic carbon in the Arctic Ocean and thus underestimate ocean acidification in the Arctic Ocean.
Taylor S. Martin, François Primeau, and Karen L. Casciotti
Biogeosciences, 16, 347–367,Short summary
Nitrite is a key intermediate in many nitrogen (N) cycling processes in the ocean, particularly in areas with low oxygen that are hotspots for N loss. We have created a 3-D global N cycle model with nitrite as a tracer. Stable isotopes of N are also included in the model and we are able to model the isotope fractionation associated with each N cycling process. Our model accurately represents N concentrations and isotope distributions in the ocean.
Camille Richon, Jean-Claude Dutay, Laurent Bopp, Briac Le Vu, James C. Orr, Samuel Somot, and François Dulac
Biogeosciences, 16, 135–165,Short summary
We evaluate the effects of climate change and biogeochemical forcing evolution on the nutrient and plankton cycles of the Mediterranean Sea for the first time. We use a high-resolution coupled physical and biogeochemical model and perform 120-year transient simulations. The results indicate that changes in external nutrient fluxes and climate change may have synergistic or antagonistic effects on nutrient concentrations, depending on the region and the scenario.
Angela M. Kuhn, Katja Fennel, and Ilana Berman-Frank
Biogeosciences, 15, 7379–7401,Short summary
Recent studies demonstrate that marine N2 fixation can be carried out without light. However, direct measurements of N2 fixation in dark environments are relatively scarce. This study uses a model that represents biogeochemical cycles at a deep-ocean location in the Gulf of Aqaba (Red Sea). Different model versions are used to test assumptions about N2 fixers. Relaxing light limitation for marine N2 fixers improved the similarity between model results and observations of deep nitrate and oxygen.
Prima Anugerahanti, Shovonlal Roy, and Keith Haines
Biogeosciences, 15, 6685–6711,Short summary
Minor changes in the biogeochemical model equations lead to major dynamical changes. We assessed this structural sensitivity for the MEDUSA biogeochemical model on chlorophyll and nitrogen concentrations at five oceanographic stations over 10 years, using 1-D ensembles generated by combining different process equations. The ensemble performed better than the default model in most of the stations, suggesting that our approach is useful for generating a probabilistic biogeochemical ensemble model.
Audrey Gimenez, Melika Baklouti, Thibaut Wagener, and Thierry Moutin
Biogeosciences, 15, 6573–6589,Short summary
During the OUTPACE cruise conducted in the oligotrophic to ultra-oligotrophic region of the western tropical South Pacific, two contrasted regions were sampled in terms of N2 fixation rates, primary production rates and nutrient availability. The aim of this work was to investigate the role of N2 fixation in the differences observed between the two contrasted areas by comparing two simulations only differing by the presence or not of N2 fixers using a 1-D biogeochemical–physical coupled model.
Jenny Hieronymus, Kari Eilola, Magnus Hieronymus, H. E. Markus Meier, Sofia Saraiva, and Bengt Karlson
Biogeosciences, 15, 5113–5129,Short summary
This paper investigates how phytoplankton concentrations in the Baltic Sea co-vary with nutrient concentrations and other key variables on inter-annual timescales in a model integration over the years 1850–2008. The study area is not only affected by climate change; it has also been subjected to greatly increased nutrient loads due to extensive use of agricultural fertilizers. The results indicate the largest inter-annual coherence of phytoplankton with the limiting nutrient.
Cyril Dutheil, Olivier Aumont, Thomas Gorguès, Anne Lorrain, Sophie Bonnet, Martine Rodier, Cécile Dupouy, Takuhei Shiozaki, and Christophe Menkes
Biogeosciences, 15, 4333–4352,Short summary
N2 fixation is recognized as one of the major sources of nitrogen in the ocean. Thus, N2 fixation sustains a significant part of the primary production (PP) by supplying the most common limiting nutrient for phytoplankton growth. From numerical simulations, the local maximums of Trichodesmium biomass in the Pacific are found around islands, explained by the iron fluxes from island sediments. We assessed that 15 % of the PP may be due to Trichodesmium in the low-nutrient, low-chlorophyll areas.
Akitomo Yamamoto, Ayako Abe-Ouchi, and Yasuhiro Yamanaka
Biogeosciences, 15, 4163–4180,Short summary
Millennial-scale changes in oceanic CO2 uptake due to global warming are simulated by a GCM and offline biogeochemical model. Sensitivity studies show that decreases in oceanic CO2 uptake are mainly caused by a weaker biological pump and seawater warming. Enhanced CO2 uptake due to weaker equatorial upwelling cancels out reduced CO2 uptake due to weaker AMOC and AABW formation. Thus, circulation change plays only a small direct role in reduction of CO2 uptake due to global warming.
Fabian A. Gomez, Sang-Ki Lee, Yanyun Liu, Frank J. Hernandez Jr., Frank E. Muller-Karger, and John T. Lamkin
Biogeosciences, 15, 3561–3576,Short summary
Seasonal patterns in nanophytoplankton and diatom biomass in the Gulf of Mexico were examined with an ocean–biogeochemical model. We found silica limitation of model diatom growth in the deep GoM and Mississippi delta. Zooplankton grazing and both transport and vertical mixing of biomass substantially influence the model phytoplankton biomass seasonality. We stress the need for integrated analyses of biologically and physically driven biomass fluxes to describe phytoplankton seasonal changes.
Martí Galí, Maurice Levasseur, Emmanuel Devred, Rafel Simó, and Marcel Babin
Biogeosciences, 15, 3497–3519,Short summary
We developed a new algorithm to estimate the sea-surface concentration of dimethylsulfide (DMS) using satellite data. DMS is a gas produced by marine plankton that, once emitted to the atmosphere, plays a key climatic role by seeding cloud formation. We used the algorithm to produce global DMS maps and also regional DMS time series. The latter suggest that DMS can vary largely from one year to another, which should be taken into account in atmospheric studies.
Konstantin Stolpovsky, Andrew W. Dale, and Klaus Wallmann
Biogeosciences, 15, 3391–3407,Short summary
The paper describes a new way to parameterize G-type models in marine sediments using data about reactivity of organic carbon sinking to the seafloor.
Anne Marx, Marcus Conrad, Vadym Aizinger, Alexander Prechtel, Robert van Geldern, and Johannes A. C. Barth
Biogeosciences, 15, 3093–3106,Short summary
CO2 outgassing from small streams causes one of the main uncertainties in global carbon budgets. These are caused by variable flow conditions, changing stream surface areas, and groundwater seeps. Here we used groundwater data to improve a novel stable carbon isotope modelling approach. We found that CO2 outgassing contributed more than three-fourths of annual stream inorganic carbon loss in a small, silicate catchment. We underline the potential of this approach for global applications.
Malin Ödalen, Jonas Nycander, Kevin I. C. Oliver, Laurent Brodeau, and Andy Ridgwell
Biogeosciences, 15, 1367–1393,Short summary
We conclude that different initial states for an ocean model result in different capacities for ocean carbon storage due to differences in the ocean circulation state and the origin of the carbon in the initial ocean carbon reservoir. This could explain why it is difficult to achieve comparable responses of the ocean carbon system in model inter-comparison studies in which the initial states vary between models. We show that this effect of the initial state is quantifiable.
Johan van der Molen, Piet Ruardij, Karen Mooney, Philip Kerrison, Nessa E. O'Connor, Emma Gorman, Klaas Timmermans, Serena Wright, Maeve Kelly, Adam D. Hughes, and Elisa Capuzzo
Biogeosciences, 15, 1123–1147,Short summary
Macroalgae farming may provide biofuel. Modelled macroalgae production is given for four sites in UK and Dutch waters. Macroalgae growth depended on nutrient concentrations and light levels. Macroalgae carbohydrate content, important for biofuel use, was lower for high nutrient concentrations. The hypothetical large-scale farm off the UK north Norfolk coast gave high, stable yields of macroalgae from year to year with substantial carbohydrate content.
Daniel E. Kaufman, Marjorie A. M. Friedrichs, John C. P. Hemmings, and Walker O. Smith Jr.
Biogeosciences, 15, 73–90,Short summary
Computer simulations of the highly variable phytoplankton in the Ross Sea demonstrated how incorporating data from different sources (satellite, ship, or glider) results in different system interpretations. For example, simulations assimilating satellite-based data produced lower carbon export estimates. Combining observations with models in this remote, harsh, and biologically variable environment should include consideration of the potential impacts of data frequency, duration, and coverage.
Ågren, G. I.: The \chemC:N:P stoichiometry of autotrophs – theory and observations, Ecol. Lett., 7, 185–191, 2004.
Alon, U.: An Introduction to Systems Biology: Design Principles of Biological Circuits, Chapman & Hall/CRC Press, Boca Raton, FL, 2007.
Aksnes, D. L. and Egge, J. K.: A theoretical model for nutrient uptake in phytoplankton, Mar. Ecol. Prog. Ser., 70, 65–72, 1991.
Armstrong, R. A.: Nutrient uptake rate as a function of cell size and surface transporter density: a Michaelis-like approximation to the model of Pasciak and Gavis, Deep-Sea Res. Pt. I, 55, 1311–1317, 2008.
Bonachela, J. A., Raghib, M., and Levin, S. A.: Dynamic model of flexible phytoplankton nutrient uptake, Proc. Natl. Acad. Sci. USA, 108, 20633–20638, 2011.
Bougaran, G., Bernard, O., and Sciandra, A.: Modeling continuous cultures of microalgae colimited by nitrogen and phosphorus, J. Theor. Biol., 265, 443–454, 2010.
Caperon, J.: Time lag in population growth response of Isochrysis galbana to a variable environment, Ecology, 50, 188–192, 1969.
Droop, M. R.: Vitamin B12 and marine ecology IV: the kinetics of uptake, growth and inhibition in Monochrysis lutheri, J. Mar. Biol. Assoc. UK, 48, 689–733, 1968.
Dyhrman, S. T. and Palenik, B.: A single-cell immunoassay for phosphate stress in the dinoflagellate Prorocentrum minimum (Dinophyceae), J. Phycol., 37, 400–410, 2001.
Elrifi, I. R. and Turpin, D. H.: Steady state luxury consumption and the concept of optimum nutrient ratios: a study with phosphate and nitrate limited Selenastrum minutum (Chlorophyta), J. Phycol., 21, 592–602, 1985.
Fiksen, Ø., Follows, M. J., and Aksnes, D. L.: Trait-based models of nutrient uptake in microbes extend the Michaelis-Menten framework, Limnol. Oceanogr., 58, 193–202, 2013.
Flynn, K. J.: Use, abuse, misconceptions and insights from quota models – the Droop Cell Quota Model 40 years on, Oceanogr. Mar. Biol., 46, 1–23, 2008.
Flynn, K. J., Raven, J. A., Rees, T. A. V., Finkel, Z. V., Quigg, A., and Beardall, J.: Is the growth rate hypothesis applicable to microalgae?, J. Phycol., 46, 1–12, 2010.
Geider, R. J. and La Roche, J.: Redfield revisited: variability of C:N:P in marine microalgae and its biochemical basis, Eur. J. Phycol., 37, 1–17, 2002.
Geider, R. J., MacIntyre, H. L., and Kana, T. M.: A dynamic regulatory model of phytoplanktonic acclimation to light, nutrients, and temperature, Limnol. Oceanogr., 43, 679–694, 1998.
Goldman, J. C., McCarthy, J. J., and Peavey, D. G.: Growth rate influence on the chemical composition of phytoplankton in oceanic waters, Nature, 279, 210–215, 1979.
Gotham, I. J. and Rhee, G. Y.: Comparative kinetic studies of nitrate-limited growth and nitrate uptake in phytoplankton in continuous culture, J. Phycol., 17, 309–314, 1981a.
Gotham, I. J. and Rhee, G. Y.: Comparative kinetic studies of phosphate-limited growth and phosphate uptake in phytoplankton in continuous culture, J. Phycol., 17, 257–265, 1981b.
Göthlich, L. and Oschlies, A.: Phytoplankton niche generation by interspecific stoichiometric variation, Global Biogeochem. Cy., 26, GB2010, 1–8, 2012.
Hall, S. R., Smith, V. H., Lytle, D. A., and Leibold, M. A.: Constraints on primary producer N:P stoichiometry along N:P supply ratio gradients, Ecology, 86, 1894–1904, 2005.
Healey, F. P.: Interacting Effects of light and nutrient limitation on the growth rate of Synechococcus linearis (Cyanophyceae), J. Phycol., 21, 134–146, 1985.
Healey, F. P. and Hendzel, L. L.: Indicators of phosphorus and nitrogen deficiency in five algae in culture, J. Fish. Res. Board Can., 36, 1364–1369, 1979.
Hense, I. and Beckmann, A.: Towards a model of cyanobacteria life cycle-effects of growing and resting stages on bloom formation of N2-fixing species, Ecol. Model., 195, 205–218, 2006.
Ikeya, T., Ohki, K., Takahashi, M., and Fujita, Y.: Study on phosphate uptake of the marine cyanophyte Synechococcus sp. NIBB 1071 in relation to oligotrophic environments in the open ocean, Mar. Biol., 129, 195–202, 1997.
Klausmeier, C. A., Litchman, E., Daufresne, T., and Levin, S. A.: Optimal nitrogen-to-phosphorus stoichiometry of phytoplankton, Nature, 429, 171–174, 2004a.
Klausmeier, C. A., Litchman, E., and Levin, S. A.: Phytoplankton growth and stoichiometry under multiple nutrient limitation, Limnol. Oceanogr., 49, 1463–1470, 2004b.
Klausmeier, C. A., Litchman, E., and Levin, S. A.: A model of flexible uptake of two essential resources, J. Theor. Biol., 246, 278–289, 2007.
Kunikane, S., Kaneko, M., and Maehara, R.: Growth and nutrient uptake of green alga, Scenedesmus dimorphus, under a wide range of nitrogen/phosphorus ratio – I Experimental study, Water Res., 18, 1299–1311, 1984.
Legović, T. and Cruzado, A.: A model of phytoplankton growth on multiple nutrients based on the Michaelis–Menten–Monod uptake, Droop's growth and Liebig's law, Ecol. Model., 99, 19–31, 1997.
Martiny, A. C., Pham, C. T. A., Primeau, F. P., Vrugt J. A., Moore, J. K., Levin, S. A., and Lomas, M. W.: Strong latitudinal patterns in the elemental ratios of marine plankton and organic matter, Nature Geoscience, 6, 279–283, 2013.
McCarthy, J. J. and Goldman, J. C.: Nitrogenous nutrition of marine phytoplankton in nutrient-depleted waters, Science, 203, 670–672, 1979.
Mierle, G.: Kinetics of phosphate transport by Synechococcus leopoliensis (Cyanophyta): evidence for diffusion limitation of phosphate uptake, J. Phycol., 21, 177–181, 1985.
Morel, F. M. M.: Kinetics of nutrient uptake and growth in phytoplankton, J. Phycol., 23, 137–150, 1987.
Pahlow, M. and Oschlies, A.: Chain model of phytoplankton P, N and light co-limitation, Mar. Ecol.-Prog. Ser., 376, 69–83, 2009.
Pasciak, W. J. and Gavis, J.: Transport limitation of nutrient uptake in phytoplankton, Limnol. Oceanogr., 19, 881–888, 1974.
Rhee, G. Y.: A continuous culture study of phosphate uptake, growth rate and polyphosphate in Scenedesmus Sp., J. Phycol., 9, 495–506, 1973.
Rhee, G. Y.: Effects of N:P atomic ratios and nitrate limitation on algal growth, cell compositions, and nitrate uptake, Limnol. Oceanogr., 23, 10–25, 1978.
Rhee, G. Y. and Gotham, I. J.: Optimum N:P ratios and coexistence of planktonic algae, J. Phycol., 16, 486–489, 1980.
Riegman, R. and Mur, L. R.: Regulation of phosphate uptake kinetics in Oscillatoria agardhii, Arch. Microbiol., 139, 28–32, 1984.
Roelke, D. L., Eldridge, P. M., and Cifuentes, L. A.: A model of phytoplankton competition for limiting and nonlimiting nutrient: implications for development of estuarine and nearshore management schemes, Estuaries, 22, 92–104, 1999.
Saito, M. A., Goepfert, T. J., and Ritt, J. T.: Some thoughts on the concept of colimitation: three definitions and the importance of bioavailability, Limnol. Oceanogr., 53, 276–290, 2008.
Smith, S. L. and Yamanaka, Y.: Optimization-based model of multinutrient uptake kinetics, Limnol. Oceanogr., 52, 1545–1558, 2007.
Song, B. and Ward, B. B.: Molecular cloning and characterization of high affinity nitrate transporters in marine phytoplankton, J. Phycol., 43, 542–552, 2007.
Sterner, R. W. and Elser, J. J.: Ecological Stoichiometry: The Biology of Elements from Molecules to the Biosphere, Princeton University Press, Princeton, NJ, 2002.
Terry, K. L.: Nitrate and phosphate uptake interactions in a marine prymnesiophyte, J. Phycol., 18, 79–86, 1982.
Terry, K., Laws, E. A., and Burns, D. J.: Growth rate variation in the N:P requirement ratio of phytoplankton, J. Phycol., 21, 323–329, 1985.
Tilman, D.: Resource Competition and Community Structure, Princeton University Press, Princeton, NJ, 1982.