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Volume 15, issue 1
Biogeosciences, 15, 73–90, 2018
https://doi.org/10.5194/bg-15-73-2018
© Author(s) 2018. This work is distributed under
the Creative Commons Attribution 4.0 License.
https://doi.org/10.5194/bg-15-73-2018
© Author(s) 2018. This work is distributed under
the Creative Commons Attribution 4.0 License.
Biogeosciences, 15, 73–90, 2018
https://doi.org/10.5194/bg-15-73-2018
© Author(s) 2018. This work is distributed under
the Creative Commons Attribution 4.0 License.
https://doi.org/10.5194/bg-15-73-2018
© Author(s) 2018. This work is distributed under
the Creative Commons Attribution 4.0 License.
Research article 04 Jan 2018
Research article | 04 Jan 2018
Assimilating bio-optical glider data during a phytoplankton bloom in the southern Ross Sea
Daniel E. Kaufman et al.
Related authors
Erin Lynch, Daniel Kaufman, A. Surjalal Sharma, Eugenia Kalnay, and Kayo Ide
Nonlin. Processes Geophys., 23, 137–141, https://doi.org/10.5194/npg-23-137-2016, https://doi.org/10.5194/npg-23-137-2016, 2016
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In this article, bred vectors are computed from a single time series data using time-delay embedding, with a new technique, nearest-neighbor breeding. Since the dynamical properties of the nearest-neighbor bred vectors are shown to be similar to bred vectors computed using evolution equations, this provides a new and novel way to model and predict sudden transitions in systems represented by time series data alone.
Pierre St-Laurent, Marjorie A. M. Friedrichs, Raymond G. Najjar, Elizabeth H. Shadwick, Hanqin Tian, and Yuanzhi Yao
Biogeosciences, 17, 3779–3796, https://doi.org/10.5194/bg-17-3779-2020, https://doi.org/10.5194/bg-17-3779-2020, 2020
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Over the past century, estuaries have experienced global (atmospheric CO2 concentrations and temperature) and regional changes (river inputs, land use), but their relative impact remains poorly known. In the Chesapeake Bay, we find that global and regional changes have worked together to enhance how much atmospheric CO2 is taken up by the estuary. The increased uptake is roughly equally due to the global and regional changes, providing crucial perspective for managers of the bay's watershed.
Isaac D. Irby, Marjorie A. M. Friedrichs, Fei Da, and Kyle E. Hinson
Biogeosciences, 15, 2649–2668, https://doi.org/10.5194/bg-15-2649-2018, https://doi.org/10.5194/bg-15-2649-2018, 2018
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We use an estuarine-watershed modeling system of the Chesapeake Bay to examine the impact climate change may have on the ability of nutrient reduction regulations to increase dissolved oxygen. We find that climate change will move the onset of hypoxia ~7 days earlier, while also decreasing oxygen in the bay primarily due to increased temperature. While this effect is smaller than the increase in oxygen due to nutrient reduction, it is enough to limit the regulation's future effectiveness.
Julia M. Moriarty, Courtney K. Harris, Katja Fennel, Marjorie A. M. Friedrichs, Kehui Xu, and Christophe Rabouille
Biogeosciences, 14, 1919–1946, https://doi.org/10.5194/bg-14-1919-2017, https://doi.org/10.5194/bg-14-1919-2017, 2017
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In coastal aquatic environments, resuspension of sediment and organic material from the seabed into the overlying water can impact biogeochemistry. Here, we used a novel modeling approach to quantify this impact for the Rhône River delta. In the model, resuspension increased oxygen consumption during individual resuspension events, and when results were averaged over 2 months. This implies that observations and models that only represent calm conditions may underestimate net oxygen consumption.
Markus Schartau, Philip Wallhead, John Hemmings, Ulrike Löptien, Iris Kriest, Shubham Krishna, Ben A. Ward, Thomas Slawig, and Andreas Oschlies
Biogeosciences, 14, 1647–1701, https://doi.org/10.5194/bg-14-1647-2017, https://doi.org/10.5194/bg-14-1647-2017, 2017
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Plankton models have become an integral part in marine ecosystem and biogeochemical research. These models differ in complexity and in their number of parameters. How values are assigned to parameters is essential. An overview of major methodologies of parameter estimation is provided. Aspects of parameter identification in the literature are diverse. Individual findings could be better synthesized if notation and expertise of the different scientific communities would be reasonably merged.
Erin Lynch, Daniel Kaufman, A. Surjalal Sharma, Eugenia Kalnay, and Kayo Ide
Nonlin. Processes Geophys., 23, 137–141, https://doi.org/10.5194/npg-23-137-2016, https://doi.org/10.5194/npg-23-137-2016, 2016
Short summary
Short summary
In this article, bred vectors are computed from a single time series data using time-delay embedding, with a new technique, nearest-neighbor breeding. Since the dynamical properties of the nearest-neighbor bred vectors are shown to be similar to bred vectors computed using evolution equations, this provides a new and novel way to model and predict sudden transitions in systems represented by time series data alone.
Isaac D. Irby, Marjorie A. M. Friedrichs, Carl T. Friedrichs, Aaron J. Bever, Raleigh R. Hood, Lyon W. J. Lanerolle, Ming Li, Lewis Linker, Malcolm E. Scully, Kevin Sellner, Jian Shen, Jeremy Testa, Hao Wang, Ping Wang, and Meng Xia
Biogeosciences, 13, 2011–2028, https://doi.org/10.5194/bg-13-2011-2016, https://doi.org/10.5194/bg-13-2011-2016, 2016
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A comparison of eight hydrodynamic-oxygen models revealed that while models have difficulty resolving key drivers of dissolved oxygen (DO) variability, all models exhibit skill in reproducing the variability of DO itself. Further, simple oxygen models and complex biogeochemical models reproduced observed DO variability similarly well. Future advances in hypoxia simulations will depend more on the ability to reproduce the depth of the mixed layer than the degree of the vertical density gradient.
W. O. Smith Jr. and K. Donaldson
Biogeosciences, 12, 3567–3577, https://doi.org/10.5194/bg-12-3567-2015, https://doi.org/10.5194/bg-12-3567-2015, 2015
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A compilation of photosynthesis-irradiance measurements from the Ross Sea, Antarctica, was analyzed for spatial and temporal trends, as well as the oceanographic factors that control the responses. The maximum, chlorophyll-specific, irradiance-saturated rate averaged 1.07+/-0.060 ug C per ug Chl per hour. Spring rates were 59% greater than summer rates. Irradiance, CO2, and iron had significant effects on rates. The effects of time need to be incorporated into models of Antarctic production.
Y. Xiao and M. A. M. Friedrichs
Biogeosciences, 11, 3015–3030, https://doi.org/10.5194/bg-11-3015-2014, https://doi.org/10.5194/bg-11-3015-2014, 2014
J. Peloquin, C. Swan, N. Gruber, M. Vogt, H. Claustre, J. Ras, J. Uitz, R. Barlow, M. Behrenfeld, R. Bidigare, H. Dierssen, G. Ditullio, E. Fernandez, C. Gallienne, S. Gibb, R. Goericke, L. Harding, E. Head, P. Holligan, S. Hooker, D. Karl, M. Landry, R. Letelier, C. A. Llewellyn, M. Lomas, M. Lucas, A. Mannino, J.-C. Marty, B. G. Mitchell, F. Muller-Karger, N. Nelson, C. O'Brien, B. Prezelin, D. Repeta, W. O. Jr. Smith, D. Smythe-Wright, R. Stumpf, A. Subramaniam, K. Suzuki, C. Trees, M. Vernet, N. Wasmund, and S. Wright
Earth Syst. Sci. Data, 5, 109–123, https://doi.org/10.5194/essd-5-109-2013, https://doi.org/10.5194/essd-5-109-2013, 2013
Related subject area
Biogeochemistry: Modelling, Aquatic
Extreme event waves in marine ecosystems: an application to Mediterranean Sea surface chlorophyll
Use of optical absorption indices to assess seasonal variability of dissolved organic matter in Amazon floodplain lakes
The 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 model
One size fits all? Calibrating an ocean biogeochemistry model for different circulations
Assessing the temporal scale of deep-sea mining impacts on sediment biogeochemistry
Seasonal patterns of surface inorganic carbon system variables in the Gulf of Mexico inferred from a regional high-resolution ocean biogeochemical model
Oxygen dynamics and evaluation of the single-station diel oxygen model across contrasting geologies
Oceanic CO2 outgassing and biological production hotspots induced by pre-industrial river loads of nutrients and carbon in a global modeling approach
Global trends in marine nitrate N isotopes from observations and a neural network-based climatology
Merging bio-optical data from Biogeochemical-Argo floats and models in marine biogeochemistry
Model constraints on the anthropogenic carbon budget of the Arctic Ocean
Modeling oceanic nitrate and nitrite concentrations and isotopes using a 3-D inverse N cycle model
Biogeochemical response of the Mediterranean Sea to the transient SRES-A2 climate change scenario
Modelling the biogeochemical effects of heterotrophic and autotrophic N2 fixation in the Gulf of Aqaba (Israel), Red Sea
A perturbed biogeochemistry model ensemble evaluated against in situ and satellite observations
Diazotrophy as the main driver of the oligotrophy gradient in the western tropical South Pacific Ocean: results from a one-dimensional biogeochemical–physical coupled model
Causes of simulated long-term changes in phytoplankton biomass in the Baltic proper: a wavelet analysis
Modelling N2 fixation related to Trichodesmium sp.: driving processes and impacts on primary production in the tropical Pacific Ocean
Long-term response of oceanic carbon uptake to global warming via physical and biological pumps
Seasonal patterns in phytoplankton biomass across the northern and deep Gulf of Mexico: a numerical model study
Sea-surface dimethylsulfide (DMS) concentration from satellite data at global and regional scales
A new look at the multi-G model for organic carbon degradation in surface marine sediments for coupled benthic–pelagic simulations of the global ocean
Groundwater data improve modelling of headwater stream CO2 outgassing with a stable DIC isotope approach
The influence of the ocean circulation state on ocean carbon storage and CO2 drawdown potential in an Earth system model
Modelling potential production of macroalgae farms in UK and Dutch coastal waters
Primary production sensitivity to phytoplankton light attenuation parameter increases with transient forcing
On the long-range offshore transport of organic carbon from the Canary Upwelling System to the open North Atlantic
Improving the inverse modeling of a trace isotope: how precisely can radium-228 fluxes toward the ocean and submarine groundwater discharge be estimated?
Implications of sea-ice biogeochemistry for oceanic production and emissions of dimethyl sulfide in the Arctic
A numerical analysis of biogeochemical controls with physical modulation on hypoxia during summer in the Pearl River estuary
Potential sources of variability in mesocosm experiments on the response of phytoplankton to ocean acidification
A data–model synthesis to explain variability in calcification observed during a CO2 perturbation mesocosm experiment
Reviews and syntheses: parameter identification in marine planktonic ecosystem modelling
Manganese in the west Atlantic Ocean in the context of the first global ocean circulation model of manganese
Growth of the coccolithophore Emiliania huxleyi in light- and nutrient-limited batch reactors: relevance for the BIOSOPE deep ecological niche of coccolithophores
Biogeochemical fluxes and fate of diazotroph-derived nitrogen in the food web after a phosphate enrichment: modeling of the VAHINE mesocosms experiment
Marine regime shifts in ocean biogeochemical models: a case study in the Gulf of Alaska
Modeling pCO2 variability in the Gulf of Mexico
Seasonal variability of the oxygen minimum zone off Peru in a high-resolution regional coupled model
Ocean acidification over the next three centuries using a simple global climate carbon-cycle model: projections and sensitivities
Methane and sulfate dynamics in sediments from mangrove-dominated tropical coastal lagoons, Yucatán, Mexico
Transfer of radiocaesium from contaminated bottom sediments to marine organisms through benthic food chains in post-Fukushima and post-Chernobyl periods
A probabilistic assessment of calcium carbonate export and dissolution in the modern ocean
Potential environmental impact of tidal energy extraction in the Pentland Firth at large spatial scales: results of a biogeochemical model
Challenges in modeling spatiotemporally varying phytoplankton blooms in the Northwestern Arabian Sea and Gulf of Oman
Parameterization of biogeochemical sediment–water fluxes using in situ measurements and a diagenetic model
A latitudinally banded phytoplankton response to 21st century climate change in the Southern Ocean across the CMIP5 model suite
The mechanisms of North Atlantic CO2 uptake in a large Earth System Model ensemble
Capturing optically important constituents and properties in a marine biogeochemical and ecosystem model
Valeria Di Biagio, Gianpiero Cossarini, Stefano Salon, and Cosimo Solidoro
Biogeosciences, 17, 5967–5988, https://doi.org/10.5194/bg-17-5967-2020, https://doi.org/10.5194/bg-17-5967-2020, 2020
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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, https://doi.org/10.5194/bg-17-5355-2020, https://doi.org/10.5194/bg-17-5355-2020, 2020
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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, https://doi.org/10.5194/bg-17-5043-2020, https://doi.org/10.5194/bg-17-5043-2020, 2020
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, https://doi.org/10.5194/bg-17-3385-2020, https://doi.org/10.5194/bg-17-3385-2020, 2020
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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, https://doi.org/10.5194/bg-17-3057-2020, https://doi.org/10.5194/bg-17-3057-2020, 2020
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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, https://doi.org/10.5194/bg-17-2767-2020, https://doi.org/10.5194/bg-17-2767-2020, 2020
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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, https://doi.org/10.5194/bg-17-1685-2020, https://doi.org/10.5194/bg-17-1685-2020, 2020
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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, https://doi.org/10.5194/bg-17-305-2020, https://doi.org/10.5194/bg-17-305-2020, 2020
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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, https://doi.org/10.5194/bg-17-55-2020, https://doi.org/10.5194/bg-17-55-2020, 2020
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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, https://doi.org/10.5194/bg-16-2617-2019, https://doi.org/10.5194/bg-16-2617-2019, 2019
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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, https://doi.org/10.5194/bg-16-2527-2019, https://doi.org/10.5194/bg-16-2527-2019, 2019
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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, https://doi.org/10.5194/bg-16-2343-2019, https://doi.org/10.5194/bg-16-2343-2019, 2019
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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, https://doi.org/10.5194/bg-16-347-2019, https://doi.org/10.5194/bg-16-347-2019, 2019
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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, https://doi.org/10.5194/bg-16-135-2019, https://doi.org/10.5194/bg-16-135-2019, 2019
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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, https://doi.org/10.5194/bg-15-7379-2018, https://doi.org/10.5194/bg-15-7379-2018, 2018
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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, https://doi.org/10.5194/bg-15-6685-2018, https://doi.org/10.5194/bg-15-6685-2018, 2018
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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, https://doi.org/10.5194/bg-15-6573-2018, https://doi.org/10.5194/bg-15-6573-2018, 2018
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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, https://doi.org/10.5194/bg-15-5113-2018, https://doi.org/10.5194/bg-15-5113-2018, 2018
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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, https://doi.org/10.5194/bg-15-4333-2018, https://doi.org/10.5194/bg-15-4333-2018, 2018
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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, https://doi.org/10.5194/bg-15-4163-2018, https://doi.org/10.5194/bg-15-4163-2018, 2018
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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, https://doi.org/10.5194/bg-15-3561-2018, https://doi.org/10.5194/bg-15-3561-2018, 2018
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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, https://doi.org/10.5194/bg-15-3497-2018, https://doi.org/10.5194/bg-15-3497-2018, 2018
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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, https://doi.org/10.5194/bg-15-3391-2018, https://doi.org/10.5194/bg-15-3391-2018, 2018
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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, https://doi.org/10.5194/bg-15-3093-2018, https://doi.org/10.5194/bg-15-3093-2018, 2018
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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, https://doi.org/10.5194/bg-15-1367-2018, https://doi.org/10.5194/bg-15-1367-2018, 2018
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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, https://doi.org/10.5194/bg-15-1123-2018, https://doi.org/10.5194/bg-15-1123-2018, 2018
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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.
Karin F. Kvale and Katrin J. Meissner
Biogeosciences, 14, 4767–4780, https://doi.org/10.5194/bg-14-4767-2017, https://doi.org/10.5194/bg-14-4767-2017, 2017
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Climate models containing ocean biogeochemistry contain a lot of poorly constrained parameters, which makes model tuning difficult. For more than 20 years modellers have generally assumed phytoplankton light attenuation parameter value choice has an insignificant affect on model ocean primary production; thus, it is often overlooked for tuning. We show that an empirical range of light attenuation parameter values can affect primary production, with increasing sensitivity under climate change.
Elisa Lovecchio, Nicolas Gruber, Matthias Münnich, and Zouhair Lachkar
Biogeosciences, 14, 3337–3369, https://doi.org/10.5194/bg-14-3337-2017, https://doi.org/10.5194/bg-14-3337-2017, 2017
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We find that a big portion of the phytoplankton, zooplankton, and detrital organic matter produced near the northern African coast is laterally transported towards the open North Atlantic. This offshore flux sustains a relevant part of the biological activity in the open sea and reaches as far as the middle of the North Atlantic. Our results, obtained with a state-of-the-art model, highlight the fundamental role of the narrow but productive coastal ocean in sustaining global marine life.
Guillaume Le Gland, Laurent Mémery, Olivier Aumont, and Laure Resplandy
Biogeosciences, 14, 3171–3189, https://doi.org/10.5194/bg-14-3171-2017, https://doi.org/10.5194/bg-14-3171-2017, 2017
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In this study, we computed the fluxes of radium-228 from the continental shelf to the open ocean by fitting a numerical model to observations. After determining appropriate model parameters (cost function and number of source regions), we found a lower and more precise global flux than previous estimates: 8.01–8.49×1023 atoms yr−1. This result can be used to assess nutrient and trace element fluxes to the open ocean, but we cannot identify specific pathways like submarine groundwater discharge.
Hakase Hayashida, Nadja Steiner, Adam Monahan, Virginie Galindo, Martine Lizotte, and Maurice Levasseur
Biogeosciences, 14, 3129–3155, https://doi.org/10.5194/bg-14-3129-2017, https://doi.org/10.5194/bg-14-3129-2017, 2017
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In remote regions, cloud conditions may be strongly influenced by oceanic source of dimethylsulfide (DMS) produced by plankton and bacteria. In the Arctic, sea ice provides an additional source of these aerosols. The results of this study highlight the importance of taking into account both the sea-ice sulfur cycle and ecosystem in the flux estimates of oceanic DMS near the ice margins and identify key uncertainties in processes and rates that would be better constrained by new observations.
Bin Wang, Jiatang Hu, Shiyu Li, and Dehong Liu
Biogeosciences, 14, 2979–2999, https://doi.org/10.5194/bg-14-2979-2017, https://doi.org/10.5194/bg-14-2979-2017, 2017
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We proposed a novel method named the physical modulation method to quantify the contributions of boundary conditions, the source and sink processes occurring in local and adjacent waters to DO conditions. A mass balance analysis of DO based on the physical modulation method indicated that the DO conditions were mainly controlled by source and sink processes, among which the sediment oxygen demand and re-aeration were two main processes controlling the spatial extent and the duration of hypoxia.
Maria Moreno de Castro, Markus Schartau, and Kai Wirtz
Biogeosciences, 14, 1883–1901, https://doi.org/10.5194/bg-14-1883-2017, https://doi.org/10.5194/bg-14-1883-2017, 2017
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Observations from different mesocosms exposed to the same treatment level typically show variability that hinders the detection of potential treatments effects. To unearth relevant sources of variability, we developed and performed a data-based model analysis that simulates uncertainty propagation. With this method we investigate the divergence in the outcomes due to the amplification of differences in experimentally unresolved ecological factors within replicates of the same treatment level.
Shubham Krishna and Markus Schartau
Biogeosciences, 14, 1857–1882, https://doi.org/10.5194/bg-14-1857-2017, https://doi.org/10.5194/bg-14-1857-2017, 2017
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This study combines experimental data with results from numerical modelling. Data of an ocean acidification mesocosm experiment are used to constrain parameter values of a plankton model. Three different intensities of calcification are resolved with ensembles of optimised model results. Observed variability in data can be well explained by these ensemble model solutions. The simulated ocean acidification effect on calcification is small compared to the spread of the ensemble model solutions.
Markus Schartau, Philip Wallhead, John Hemmings, Ulrike Löptien, Iris Kriest, Shubham Krishna, Ben A. Ward, Thomas Slawig, and Andreas Oschlies
Biogeosciences, 14, 1647–1701, https://doi.org/10.5194/bg-14-1647-2017, https://doi.org/10.5194/bg-14-1647-2017, 2017
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Plankton models have become an integral part in marine ecosystem and biogeochemical research. These models differ in complexity and in their number of parameters. How values are assigned to parameters is essential. An overview of major methodologies of parameter estimation is provided. Aspects of parameter identification in the literature are diverse. Individual findings could be better synthesized if notation and expertise of the different scientific communities would be reasonably merged.
Marco van Hulten, Rob Middag, Jean-Claude Dutay, Hein de Baar, Matthieu Roy-Barman, Marion Gehlen, Alessandro Tagliabue, and Andreas Sterl
Biogeosciences, 14, 1123–1152, https://doi.org/10.5194/bg-14-1123-2017, https://doi.org/10.5194/bg-14-1123-2017, 2017
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We ran a global ocean model to understand manganese (Mn), a biologically essential element. Our model shows that (i) in the deep ocean, dissolved [Mn] is mostly homogeneous ~0.10—0.15 nM. The model reproduces this with a threshold on MnO2 of 25 pM, suggesting a minimal particle concentration is needed before aggregation and removal become efficient.
(ii) The observed distinct hydrothermal signals are produced by assuming both a strong source and a strong removal of Mn near hydrothermal vents.
Laura Perrin, Ian Probert, Gerald Langer, and Giovanni Aloisi
Biogeosciences, 13, 5983–6001, https://doi.org/10.5194/bg-13-5983-2016, https://doi.org/10.5194/bg-13-5983-2016, 2016
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Coccolithophores are calcifying marine algae that play an important role in the oceanic carbon cycle. Deep niches of coccolithophores exist in the ocean and are poorly understood. Laboratory cultures with the coccolithophore Emiliania huxleyi were carried out to reproduce the environmental conditions (light–nutrient limitation) of a deep niche in the South Pacific Ocean. Physiological modelling of experimental results allows us to estimate the growth rates of coccolithophores in this niche.
Audrey Gimenez, Melika Baklouti, Sophie Bonnet, and Thierry Moutin
Biogeosciences, 13, 5103–5120, https://doi.org/10.5194/bg-13-5103-2016, https://doi.org/10.5194/bg-13-5103-2016, 2016
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In the context of the VAHINE mesocosm experiment in the Nouméa lagoon (New Caledonia), a 1-D vertical biogeochemical mechanistic model was used together with the in situ experiment to complement our comprehension of the planktonic ecosystem dynamics and the main biogeochemical carbon, nitrogen and phosphate fluxes. The model also showed the fate of fixed N2 by providing, over time, the proportion of diazotroph-derived nitrogen (DDN) in each compartment (mineral and organic) of the model.
Claudie Beaulieu, Harriet Cole, Stephanie Henson, Andrew Yool, Thomas R. Anderson, Lee de Mora, Erik T. Buitenhuis, Momme Butenschön, Ian J. Totterdell, and J. Icarus Allen
Biogeosciences, 13, 4533–4553, https://doi.org/10.5194/bg-13-4533-2016, https://doi.org/10.5194/bg-13-4533-2016, 2016
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Regime shifts have been suggested in the late 1970s and late 1980s in the Gulf of Alaska with important consequences for fisheries. Here we investigate the ability of a suite of ocean biogeochemical models of varying complexity to simulate these regime shifts. Our results demonstrate that ocean models can successfully simulate regime shifts in the Gulf of Alaska region, thereby improving our understanding of how changes in physical conditions are propagated from lower to upper trophic levels.
Zuo Xue, Ruoying He, Katja Fennel, Wei-Jun Cai, Steven Lohrenz, Wei-Jen Huang, Hanqin Tian, Wei Ren, and Zhengchen Zang
Biogeosciences, 13, 4359–4377, https://doi.org/10.5194/bg-13-4359-2016, https://doi.org/10.5194/bg-13-4359-2016, 2016
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In this study we used a state-of-the-science coupled physical–biogeochemical model to simulate and examine temporal and spatial variability of sea surface CO2 concentration in the Gulf of Mexico. Our model revealed the Gulf was a net CO2 sink with a flux of 1.11 ± 0.84 × 1012 mol C yr−1. We also found that biological uptake was the primary driver making the Gulf an overall CO2 sink and that the carbon flux in the northern Gulf was very susceptible to changes in river inputs.
Oscar Vergara, Boris Dewitte, Ivonne Montes, Veronique Garçon, Marcel Ramos, Aurélien Paulmier, and Oscar Pizarro
Biogeosciences, 13, 4389–4410, https://doi.org/10.5194/bg-13-4389-2016, https://doi.org/10.5194/bg-13-4389-2016, 2016
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The Southeast Pacific hosts one of the most extensive oxygen minimum zone (OMZ), yet the dynamics behind it remain unveiled. We use a high-resolution coupled physical–biogeochemical model to document the seasonal cycle of dissolved oxygen within the OMZ in both the coastal zone and the offshore ocean. The OMZ seasonal variability is driven by the seasonal fluctuations of the dissolved oxygen eddy flux, with a peak in Austral winter (fall) at the northern (southern) boundary and near the coast.
Corinne A. Hartin, Benjamin Bond-Lamberty, Pralit Patel, and Anupriya Mundra
Biogeosciences, 13, 4329–4342, https://doi.org/10.5194/bg-13-4329-2016, https://doi.org/10.5194/bg-13-4329-2016, 2016
Pei-Chuan Chuang, Megan B. Young, Andrew W. Dale, Laurence G. Miller, Jorge A. Herrera-Silveira, and Adina Paytan
Biogeosciences, 13, 2981–3001, https://doi.org/10.5194/bg-13-2981-2016, https://doi.org/10.5194/bg-13-2981-2016, 2016
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A transport-reaction model was used to simulate porewater methane and sulfate concentrations. Model results and sediment slurry incubation experiments show high methane production rates supported by non-competitive substrates and ample dissolved and labile organic matter as well as methane from deeper sediment through bubbles dissolution and diffusion. The shallow methane production and accumulation depths in these sediments promote high methane fluxes to the water column and atmosphere.
Roman Bezhenar, Kyung Tae Jung, Vladimir Maderich, Stefan Willemsen, Govert de With, and Fangli Qiao
Biogeosciences, 13, 3021–3034, https://doi.org/10.5194/bg-13-3021-2016, https://doi.org/10.5194/bg-13-3021-2016, 2016
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Measurements after the Fukushima Dai-ichi accident show that elevated concentrations of Cs-137 still remain in sediments, benthic organisms, and demersal fishes in the coastal zone. The dynamic food chain model has been extended to include benthic organisms. We showed that the gradual decrease of activity in the demersal fish after the accident was caused by the transfer of activity from organic matter deposited on the bottom through the deposit-feeding invertebrates.
Gianna Battaglia, Marco Steinacher, and Fortunat Joos
Biogeosciences, 13, 2823–2848, https://doi.org/10.5194/bg-13-2823-2016, https://doi.org/10.5194/bg-13-2823-2016, 2016
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The marine cycle of calcium carbonate (CaCO3) influences the distribution of CO2 between atmosphere and ocean, and thereby climate. We constrain export of biogenic CaCO3 (globally: 0.72–1.05 Gt C yr−1) and dissolution within the water column (~ 80 %) in a novel Monte Carlo set-up with the Bern3D model based on alkalinity data. Whether CaCO3 dissolves in the upper ocean remains unresolved. We recommend using constant (saturation-independent) dissolution rates in Earth system models.
Johan van der Molen, Piet Ruardij, and Naomi Greenwood
Biogeosciences, 13, 2593–2609, https://doi.org/10.5194/bg-13-2593-2016, https://doi.org/10.5194/bg-13-2593-2016, 2016
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The potential large-scale (> 100 km) effects of marine renewable tidal energy generation in the Pentland Firth were studied using a 3-D hydrodynamics–biogeochemistry model. A realistic 800 MW scenario suggested minor effects on tides and biogeochemistry. A massive-expansion 8 GW scenario suggested effects over hundreds of kilometres away with changes of up to 10 % in tidal and ecosystem variables, the latter through clearer waters and increased primary production with associated increases in fauna.
S. Sedigh Marvasti, A. Gnanadesikan, A. A. Bidokhti, J. P. Dunne, and S. Ghader
Biogeosciences, 13, 1049–1069, https://doi.org/10.5194/bg-13-1049-2016, https://doi.org/10.5194/bg-13-1049-2016, 2016
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This study examines challenges in modeling phytoplankton blooms in Northwestern Arabian Sea and Gulf of Oman. Blooms in the region show strong modulation both by seasons and in the wintertime by eddies. However getting both of these correct is a challenge in a set of state-of-the-art global Earth System models. It is argued that maintaining a sharp pycnocline may be the key for preventing the wintertime bloom from being too strong and for allowing eddies to modulate upward mixing of nutrients.
A. Laurent, K. Fennel, R. Wilson, J. Lehrter, and R. Devereux
Biogeosciences, 13, 77–94, https://doi.org/10.5194/bg-13-77-2016, https://doi.org/10.5194/bg-13-77-2016, 2016
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In low oxygen environments, the lack of oxygen influences sediment biogeochemistry and in turn sediment-water fluxes. These nonlinear interactions are often missing from biogeochemical circulation models because sediment models are computationally expensive. A method for parameterizing realistic sediment-water fluxes is presented and applied to the Mississippi River Dead Zone where high primary production, stimulated by excess nutrient loads, promotes low bottom water conditions in summer.
S. Leung, A. Cabré, and I. Marinov
Biogeosciences, 12, 5715–5734, https://doi.org/10.5194/bg-12-5715-2015, https://doi.org/10.5194/bg-12-5715-2015, 2015
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Using the latest earth system models, we find that shifts in nutrient and light availability with future climate warming drive latitudinally banded changes in Southern Ocean phytoplankton distributions, which have the potential to significantly alter nutrient cycling as well as higher trophic level productivity throughout the global ocean. Spatial patterns in the modelled mechanisms driving these predicted phytoplankton trends qualitatively agree with recent observations.
P. R. Halloran, B. B. B. Booth, C. D. Jones, F. H. Lambert, D. J. McNeall, I. J. Totterdell, and C. Völker
Biogeosciences, 12, 4497–4508, https://doi.org/10.5194/bg-12-4497-2015, https://doi.org/10.5194/bg-12-4497-2015, 2015
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The oceans currently take up around a quarter of the carbon dioxide (CO2) emitted by human activity. While stored in the ocean, this CO2 is not causing global warming. Here we explore high latitude North Atlantic CO2 uptake across a set of climate model simulations, and find that the models show a peak in ocean CO2 uptake around the middle of the century after which time CO2 uptake begins to decline. We identify the causes of this long-term change and interannual variability in the models.
S. Dutkiewicz, A. E. Hickman, O. Jahn, W. W. Gregg, C. B. Mouw, and M. J. Follows
Biogeosciences, 12, 4447–4481, https://doi.org/10.5194/bg-12-4447-2015, https://doi.org/10.5194/bg-12-4447-2015, 2015
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A numerical model is presented that explicitly includes spectral
irradiance and optically important water constituents. The model captures 3-D
biogeochemical, ecosystem, and optical observations, including surface
reflectance analogous to ocean colour satellite observations. Sensitivity
experiments demonstrate the relative importance of each of the water
constituents, and the feedbacks between the light field, fitness of
phytoplankton types, and the biogeochemistry of the ocean.
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Jones, E. M., Baird, M. E., Mongin, M., Parslow, J., Skerratt, J., Lovell, J., Margvelashvili, N., Matear, R. J., Wild-Allen, K., Robson, B., Rizwi, F., Oke, P., King, E., Schroeder, T., Steven, A., and Taylor, J.: Use of remote-sensing reflectance to constrain a data assimilating marine biogeochemical model of the Great Barrier Reef, Biogeosciences, 13, 6441–6469, https://doi.org/10.5194/bg-13-6441-2016, 2016.
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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.
Computer simulations of the highly variable phytoplankton in the Ross Sea demonstrated how...
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