Articles | Volume 13, issue 23
https://doi.org/10.5194/bg-13-6441-2016
© Author(s) 2016. This work is distributed under
the Creative Commons Attribution 3.0 License.
the Creative Commons Attribution 3.0 License.
https://doi.org/10.5194/bg-13-6441-2016
© Author(s) 2016. This work is distributed under
the Creative Commons Attribution 3.0 License.
the Creative Commons Attribution 3.0 License.
Research article
| Highlight paper
| 
07 Dec 2016
Research article | Highlight paper |
| 07 Dec 2016
Use of remote-sensing reflectance to constrain a data assimilating marine biogeochemical model of the Great Barrier Reef
Emlyn M. Jones
CORRESPONDING AUTHOR
CSIRO Oceans and Atmosphere, Hobart, 7000, Australia
Mark E. Baird
CSIRO Oceans and Atmosphere, Hobart, 7000, Australia
Mathieu Mongin
CSIRO Oceans and Atmosphere, Hobart, 7000, Australia
John Parslow
CSIRO Oceans and Atmosphere, Hobart, 7000, Australia
Jenny Skerratt
CSIRO Oceans and Atmosphere, Hobart, 7000, Australia
Jenny Lovell
CSIRO Oceans and Atmosphere, Hobart, 7000, Australia
Nugzar Margvelashvili
CSIRO Oceans and Atmosphere, Hobart, 7000, Australia
Richard J. Matear
CSIRO Oceans and Atmosphere, Hobart, 7000, Australia
Karen Wild-Allen
CSIRO Oceans and Atmosphere, Hobart, 7000, Australia
Barbara Robson
CSIRO Land and Water, Canberra, 2601, Australia
Farhan Rizwi
CSIRO Oceans and Atmosphere, Hobart, 7000, Australia
Peter Oke
CSIRO Oceans and Atmosphere, Hobart, 7000, Australia
Edward King
CSIRO Oceans and Atmosphere, Hobart, 7000, Australia
Thomas Schroeder
CSIRO Oceans and Atmosphere, Brisbane, 4102, Australia
Andy Steven
CSIRO Oceans and Atmosphere, Brisbane, 4102, Australia
John Taylor
CSIRO Data61, Canberra, 2601, Australia
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Earth Syst. Sci. Data, 16, 2113–2122, https://doi.org/10.5194/essd-16-2113-2024, https://doi.org/10.5194/essd-16-2113-2024, 2024
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Modeling the ocean's carbon and oxygen cycles accurately is challenging. Parameter optimization improves the fit to observed tracers but can introduce artifacts in the biological pump. Organic-matter production and subsurface remineralization rates adjust to compensate for circulation biases, changing the pathways and timescales with which nutrients return to the surface. Circulation biases can thus strongly alter the system’s response to ecological change, even when parameters are optimized.
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Hakase Hayashida, Meibing Jin, Nadja S. Steiner, Neil C. Swart, Eiji Watanabe, Russell Fiedler, Andrew McC. Hogg, Andrew E. Kiss, Richard J. Matear, and Peter G. Strutton
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Geosci. Model Dev., 12, 1491–1523, https://doi.org/10.5194/gmd-12-1491-2019, https://doi.org/10.5194/gmd-12-1491-2019, 2019
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Oceanic sediment cores are commonly used to understand past climates. The composition of the sediments changes with the ocean above it. An understanding of oceanographic conditions that existed many thousands of years ago, in some cases many millions of years ago, can therefore be extracted from sediment cores. We simulate two chemical signatures (13C and 15N) of sediment cores in a model. This study assesses the model before it is applied to reinterpret the sedimentary record.
Andrew Lenton, Richard J. Matear, David P. Keller, Vivian Scott, and Naomi E. Vaughan
Earth Syst. Dynam., 9, 339–357, https://doi.org/10.5194/esd-9-339-2018, https://doi.org/10.5194/esd-9-339-2018, 2018
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Artificial ocean alkalinization (AOA) is capable of reducing atmospheric carbon dioxide concentrations and surface warming while also addressing ocean acidification. We simulate the Earth system response to a fixed addition of AOA under low and high emissions. We explore the regional and global response to AOA. A key finding is that AOA is much more effective at reducing warming and ocean acidification under low emissions, despite lower carbon uptake.
Richard J. Matear and Andrew Lenton
Biogeosciences, 15, 1721–1732, https://doi.org/10.5194/bg-15-1721-2018, https://doi.org/10.5194/bg-15-1721-2018, 2018
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We show climate–carbon feedbacks accelerate and enhance ocean acidification. Such an acceleration of ocean acidification may further undermine the ability of marine biota to adapt to the changing environment. Our study also identifies the need to use Earth system models to make future ocean acidification projections (relevance to AR6) and the need to reduce the uncertainty in the climate–carbon feedbacks.
Mabel Costa Calim, Paulo Nobre, Peter Oke, Andreas Schiller, Leo San Pedro Siqueira, and Guilherme Pimenta Castelão
Geosci. Model Dev. Discuss., https://doi.org/10.5194/gmd-2018-5, https://doi.org/10.5194/gmd-2018-5, 2018
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A new tool inspired on tides is introduced. The Spectral Taylor Diagram designed for evaluating and monitoring models performance in frequency domain calculates the degree of correspondence between simulated and observed fields for a given frequency (or a band of frequencies). It's a powerful tool to detect co-oscillating patterns in multi scale analysis, without using filtering techniques.
Rachel M. Law, Tilo Ziehn, Richard J. Matear, Andrew Lenton, Matthew A. Chamberlain, Lauren E. Stevens, Ying-Ping Wang, Jhan Srbinovsky, Daohua Bi, Hailin Yan, and Peter F. Vohralik
Geosci. Model Dev., 10, 2567–2590, https://doi.org/10.5194/gmd-10-2567-2017, https://doi.org/10.5194/gmd-10-2567-2017, 2017
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The paper describes a version of the Australian Community Climate and Earth System Simulator that has been enabled to simulate the carbon cycle, which is designated ACCESS-ESM1. The model performance for pre-industrial conditions is assessed and land and ocean carbon fluxes are found to be simulated realistically.
Tilo Ziehn, Andrew Lenton, Rachel M. Law, Richard J. Matear, and Matthew A. Chamberlain
Geosci. Model Dev., 10, 2591–2614, https://doi.org/10.5194/gmd-10-2591-2017, https://doi.org/10.5194/gmd-10-2591-2017, 2017
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Our work presents the evaluation of the Australian Community Climate and Earth System Simulator (ACCESS-ESM1) over the historical period (1850–2005). The main focus is on climate and carbon related variables. Globally integrated land–atmosphere and ocean–atmosphere fluxes and flux patterns are well reproduced and show good agreement with most recent observations. This makes ACCESS-ESM1 a useful tool to explore the change in land and oceanic carbon uptake in the future.
James C. Orr, Raymond G. Najjar, Olivier Aumont, Laurent Bopp, John L. Bullister, Gokhan Danabasoglu, Scott C. Doney, John P. Dunne, Jean-Claude Dutay, Heather Graven, Stephen M. Griffies, Jasmin G. John, Fortunat Joos, Ingeborg Levin, Keith Lindsay, Richard J. Matear, Galen A. McKinley, Anne Mouchet, Andreas Oschlies, Anastasia Romanou, Reiner Schlitzer, Alessandro Tagliabue, Toste Tanhua, and Andrew Yool
Geosci. Model Dev., 10, 2169–2199, https://doi.org/10.5194/gmd-10-2169-2017, https://doi.org/10.5194/gmd-10-2169-2017, 2017
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The Ocean Model Intercomparison Project (OMIP) is a model comparison effort under Phase 6 of the Coupled Model Intercomparison Project (CMIP6). Its physical component is described elsewhere in this special issue. Here we describe its ocean biogeochemical component (OMIP-BGC), detailing simulation protocols and analysis diagnostics. Simulations focus on ocean carbon, other biogeochemical tracers, air-sea exchange of CO2 and related gases, and chemical tracers used to evaluate modeled circulation.
Pearse J. Buchanan, Richard J. Matear, Andrew Lenton, Steven J. Phipps, Zanna Chase, and David M. Etheridge
Clim. Past, 12, 2271–2295, https://doi.org/10.5194/cp-12-2271-2016, https://doi.org/10.5194/cp-12-2271-2016, 2016
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We quantify the contributions of physical and biogeochemical changes in the ocean to enhancing ocean carbon storage at the Last Glacial Maximum. We find that simulated circulation and surface conditions cannot explain changes in carbon storage or other major biogeochemical fields that existed during the glacial climate. Key modifications to the functioning of the biological pump are therefore required to explain the glacial climate and improve model–proxy agreement for all fields.
Colette Kerry, Brian Powell, Moninya Roughan, and Peter Oke
Geosci. Model Dev., 9, 3779–3801, https://doi.org/10.5194/gmd-9-3779-2016, https://doi.org/10.5194/gmd-9-3779-2016, 2016
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Ocean circulation drives weather and climate and supports marine ecosystems, so providing accurate predictions is important. The ocean circulation is complex, 3-D and highly variable, and its prediction requires advanced numerical models combined with real-time measurements. Focusing on the dynamic East Austr. Current, we use novel mathematical techniques to combine an ocean model with measurements to better estimate the circulation. This is an important step towards improving ocean forecasts.
Peter R. Oke, Roger Proctor, Uwe Rosebrock, Richard Brinkman, Madeleine L. Cahill, Ian Coghlan, Prasanth Divakaran, Justin Freeman, Charitha Pattiaratchi, Moninya Roughan, Paul A. Sandery, Amandine Schaeffer, and Sarath Wijeratne
Geosci. Model Dev., 9, 3297–3307, https://doi.org/10.5194/gmd-9-3297-2016, https://doi.org/10.5194/gmd-9-3297-2016, 2016
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The Marine Virtual Laboratory (MARVL) is designed to help ocean modellers hit the ground running. Usually, setting up an ocean model involves a handful of technical steps that time and effort. MARVL provides a user-friendly interface that allows users to choose what options they want for their model, including the region, time period, and input data sets. The user then hits "go", and MARVL does the rest – delivering a "take-away bundle" that contains all the files needed to run the model.
Oscar Serrano, Paul S. Lavery, Carlos M. Duarte, Gary A. Kendrick, Antoni Calafat, Paul H. York, Andy Steven, and Peter I. Macreadie
Biogeosciences, 13, 4915–4926, https://doi.org/10.5194/bg-13-4915-2016, https://doi.org/10.5194/bg-13-4915-2016, 2016
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We explored the relationship between organic carbon and mud (i.e. silt and clay) contents in seagrass ecosystems to address whether mud can be used to predict soil C content, thereby enabling robust scaling up exercises at a low cost as part of blue carbon stock assessments. We show that mud is not a universal proxy for blue carbon content in seagrass ecosystems, but it can be used to estimate soil Corg content when low biomass seagrass species (i.e. Zostera, Halodule and Halophila) are present.
Oscar Serrano, Aurora M. Ricart, Paul S. Lavery, Miguel Angel Mateo, Ariane Arias-Ortiz, Pere Masque, Mohammad Rozaimi, Andy Steven, and Carlos M. Duarte
Biogeosciences, 13, 4581–4594, https://doi.org/10.5194/bg-13-4581-2016, https://doi.org/10.5194/bg-13-4581-2016, 2016
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The recent focus on carbon (C) trading has intensified interest in "Blue Carbon" – C sequestered by coastal vegetation. However, the factors influencing C storage are poorly understood. The patterns found in this study support that C storage in Posidonia seagrass soils is influenced by interactions of biological, chemical and physical factors within the meadow. We conclude that there is a need to improve global estimates accounting for biogeochemical factors driving variability within habitats.
Amandine Schaeffer, Moninya Roughan, Emlyn M. Jones, and Dana White
Biogeosciences, 13, 1967–1975, https://doi.org/10.5194/bg-13-1967-2016, https://doi.org/10.5194/bg-13-1967-2016, 2016
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The water properties of the coastal ocean such as temperature, salt, oxygen, or chlorophyll content vary spatially, and estimates need to be made regarding the scales of variability. Here, we use statistical techniques to determine the spatial variability of ocean properties from high-resolution measurements by gliders. We show that biological activity is patchy compared to the distribution of physical characteristics, and that the size and shape of this is determined by coastal ocean processes.
Andrew Lenton, Bronte Tilbrook, Richard J. Matear, Tristan P. Sasse, and Yukihiro Nojiri
Biogeosciences, 13, 1753–1765, https://doi.org/10.5194/bg-13-1753-2016, https://doi.org/10.5194/bg-13-1753-2016, 2016
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We reconstruct the observed variability and mean state in pH and aragonite saturation state around Australia at high spatial resolution and reconstruct the changes that have occurred in the Australian region over the last 140 years. We find that large changes in aragonite saturation state and pH have very different spatial patterns, which suggests that the biological responses to ocean acidification are likely to be non-uniform and dependent on the relative sensitivity of organisms to change.
Paulina Cetina-Heredia, Erik van Sebille, Richard Matear, and Moninya Roughan
Biogeosciences Discuss., https://doi.org/10.5194/bg-2016-53, https://doi.org/10.5194/bg-2016-53, 2016
Revised manuscript not accepted
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Characterizing phytoplankton growth influences fisheries and climate. We use a lagrangian approach to identify phytoplankton blooms in the Great Australian Bight (GAB), and associate them with nitrate sources. We find that 88 % of the nitrate utilized in blooms is originated between the GAB and the SubAntarctic Front. Large nitrate concentrations are supplied at depth but do not reach the euphotic zone often. As a result, 55 % of blooms utilize nitrate supplied in the top 100 m.
X. Zhang, P. R. Oke, M. Feng, M. A. Chamberlain, J. A. Church, D. Monselesan, C. Sun, R. J. Matear, A. Schiller, and R. Fiedler
Geosci. Model Dev. Discuss., https://doi.org/10.5194/gmd-2016-17, https://doi.org/10.5194/gmd-2016-17, 2016
Revised manuscript not accepted
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Eddy-resolving global ocean models are highly desired, but expensive to run, and also subject to many problems including drift. Here we modified a near-global eddy-resolving OGCM for climate studies with some novel strategies. We demonstrated that the historical experiment driven by Japanese atmospheric reanalysis product, didn't have significant drifts, and also provided an eddy-resolving simulation of the global ocean over 1979–2014. Our experiences can be helpful to other modelling groups.
B. Nechad, K. Ruddick, T. Schroeder, K. Oubelkheir, D. Blondeau-Patissier, N. Cherukuru, V. Brando, A. Dekker, L. Clementson, A. C. Banks, S. Maritorena, P. J. Werdell, C. Sá, V. Brotas, I. Caballero de Frutos, Y.-H. Ahn, S. Salama, G. Tilstone, V. Martinez-Vicente, D. Foley, M. McKibben, J. Nahorniak, T. Peterson, A. Siliò-Calzada, R. Röttgers, Z. Lee, M. Peters, and C. Brockmann
Earth Syst. Sci. Data, 7, 319–348, https://doi.org/10.5194/essd-7-319-2015, https://doi.org/10.5194/essd-7-319-2015, 2015
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The CoastColour Round Robin (CCRR) project (European Space Agency) was designed to set up the first database for remote-sensing algorithm testing and accuracy assessment of water quality parameter retrieval in coastal waters, from satellite imagery. This paper analyses the CCRR database, which includes in situ bio-geochemical and optical measurements in various water types, match-up reflectance products from the MEdium Resolution Imaging Spectrometer (MERIS), and radiative transfer simulations.
T. P. Sasse, B. I. McNeil, R. J. Matear, and A. Lenton
Biogeosciences, 12, 6017–6031, https://doi.org/10.5194/bg-12-6017-2015, https://doi.org/10.5194/bg-12-6017-2015, 2015
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Our results show that accounting for oceanic CO2 seasonality is crucial to projecting the future onset of critical ocean acidification levels (i.e. aragonite undersaturation). In particular, seasonality will bring forward the initial onset of month-long undersaturation by a global average of 17 years. Importantly, widespread undersaturation is projected to occur once atmospheric CO2 reaches 496ppm in the North Pacific and 511ppm in the Southern Ocean, independent of emissions scenario.
I. Mazarrasa, N. Marbà, C. E. Lovelock, O. Serrano, P. S. Lavery, J. W. Fourqurean, H. Kennedy, M. A. Mateo, D. Krause-Jensen, A. D. L. Steven, and C. M. Duarte
Biogeosciences, 12, 4993–5003, https://doi.org/10.5194/bg-12-4993-2015, https://doi.org/10.5194/bg-12-4993-2015, 2015
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There has been growing interest in quantifying the capacity of seagrass ecosystems to act as carbon sinks as a natural way of offsetting anthropogenic carbon emissions to the atmosphere. However, most of the efforts have focused on the organic fraction and ignored the inorganic carbon pool. This study offers the first global assessment of PIC stocks and accumulation rates in seagrass sediments, identifying these ecosystems as important contributors to carbonate dynamics in coastal areas.
P. G. Strutton, V. J. Coles, R. R. Hood, R. J. Matear, M. J. McPhaden, and H. E. Phillips
Biogeosciences, 12, 2367–2382, https://doi.org/10.5194/bg-12-2367-2015, https://doi.org/10.5194/bg-12-2367-2015, 2015
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In 2010, a first-of-its-kind deployment of biological sensors on a mooring in the central Indian Ocean revealed interesting variability in chlorophyll (a proxy for ocean productivity) at timescales of about 2 weeks. Using the mooring data with satellite observations and a biogeochemical model, it was determined that local wind mixing and entrainment, rather than mixed Rossby gravity waves, were likely responsible for much of the observed variability.
R. J. Matear, A. Lenton, D. Etheridge, and S. J. Phipps
Clim. Past Discuss., https://doi.org/10.5194/cpd-11-1093-2015, https://doi.org/10.5194/cpd-11-1093-2015, 2015
Revised manuscript has not been submitted
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Global climate models provide an important tool for simulating the earth's climate. Here we present a simulation of the climate of the Last Glacial Maximum, which was obtained by setting atmospheric greenhouse gas concentrations and the earth's orbital parameters to the 21 000 years before present values. We simulate an ocean behaviour that agrees with paleoclimate reconstructions supporting our ability to model the climate system and use the model to explore the impacts on the carbon cycle.
R. J. Matear and A. Lenton
Biogeosciences, 11, 3965–3983, https://doi.org/10.5194/bg-11-3965-2014, https://doi.org/10.5194/bg-11-3965-2014, 2014
O. Duteil, W. Koeve, A. Oschlies, D. Bianchi, E. Galbraith, I. Kriest, and R. Matear
Biogeosciences, 10, 7723–7738, https://doi.org/10.5194/bg-10-7723-2013, https://doi.org/10.5194/bg-10-7723-2013, 2013
A. Lenton, B. Tilbrook, R. M. Law, D. Bakker, S. C. Doney, N. Gruber, M. Ishii, M. Hoppema, N. S. Lovenduski, R. J. Matear, B. I. McNeil, N. Metzl, S. E. Mikaloff Fletcher, P. M. S. Monteiro, C. Rödenbeck, C. Sweeney, and T. Takahashi
Biogeosciences, 10, 4037–4054, https://doi.org/10.5194/bg-10-4037-2013, https://doi.org/10.5194/bg-10-4037-2013, 2013
P. R. Oke, D. A. Griffin, A. Schiller, R. J. Matear, R. Fiedler, J. Mansbridge, A. Lenton, M. Cahill, M. A. Chamberlain, and K. Ridgway
Geosci. Model Dev., 6, 591–615, https://doi.org/10.5194/gmd-6-591-2013, https://doi.org/10.5194/gmd-6-591-2013, 2013
B. I. McNeil and R. J. Matear
Biogeosciences, 10, 2219–2228, https://doi.org/10.5194/bg-10-2219-2013, https://doi.org/10.5194/bg-10-2219-2013, 2013
Related subject area
Biogeochemistry: Coastal Ocean
Ocean alkalinity enhancement (OAE) does not cause cellular stress in a phytoplankton community of the subtropical Atlantic Ocean
Reviews and syntheses: On increasing hypoxia in eastern boundary upwelling systems – zooplankton under metabolic stress
Technical note: Testing a new approach for the determination of N2 fixation rates by coupling a membrane equilibrator to a mass spectrometer for long-term observations
Long-term variations in pH in coastal waters along the Korean Peninsula
The effect of carbonate mineral additions on biogeochemical conditions in surface sediments and benthic–pelagic exchange fluxes
Evaluating ocean alkalinity enhancement as a carbon dioxide removal strategy in the North Sea
Assessing the impacts of simulated ocean alkalinity enhancement on viability and growth of nearshore species of phytoplankton
Responses of microbial metabolic rates to non-equilibrated silicate- versus calcium-based ocean alkalinity enhancement
High metabolic zinc demand within native Amundsen and Ross sea phytoplankton communities determined by stable isotope uptake rate measurements
The influence of zooplankton and oxygen on the particulate organic carbon flux in the Benguela Upwelling System
Reviews and syntheses: Biological indicators of low-oxygen stress in marine water-breathing animals
Temperature-enhanced effects of iron on Southern Ocean phytoplankton
Riverine nutrient impact on global ocean nitrogen cycle feedbacks and marine primary production in an Earth system model
Effects of Submarine Groundwater on Nutrient Concentration and Primary Production in a Deep Bay of the Japan Sea
The Northeast Greenland Shelf as a potential late-summer CO2 source to the atmosphere
Spring-neap tidal cycles modulate the strength of the carbon source at the estuary-coast interface
Technical note: Ocean Alkalinity Enhancement Pelagic Impact Intercomparison Project (OAEPIIP)
Estimates of carbon sequestration potential in an expanding Arctic fjord (Hornsund, Svalbard) affected by dark plumes of glacial meltwater
An assessment of ocean alkalinity enhancement using aqueous hydroxides: kinetics, efficiency, and precipitation thresholds
Dissolved nitric oxide in the lower Elbe Estuary and the Port of Hamburg area
The bacteria-protist link as a main route of dissolved organic matter across contrasting productivity areas in the Patagonian Shelf
Variable contribution of wastewater treatment plant effluents to downstream nitrous oxide concentrations and emissions
Depositional controls and budget of organic carbon burial in fine-grained sediments of the North Sea – the Helgoland Mud Area as a test field
Improved understanding of eutrophication trends, indicators and problem areas using machine learning
Distribution of nutrients and dissolved organic matter in a eutrophic equatorial estuary: the Johor River and the East Johor Strait
Amplified bottom water acidification rates on the Bering Sea shelf from 1970–2022
Investigating the effect of silicate- and calcium-based ocean alkalinity enhancement on diatom silicification
Ocean alkalinity enhancement using sodium carbonate salts does not lead to measurable changes in Fe dynamics in a mesocosm experiment
Quantification and mitigation of bottom-trawling impacts on sedimentary organic carbon stocks in the North Sea
Influence of ocean alkalinity enhancement with olivine or steel slag on a coastal plankton community in Tasmania
Multi-model comparison of trends and controls of near-bed oxygen concentration on the northwest European continental shelf under climate change
Picoplanktonic methane production in eutrophic surface waters
Vertical mixing alleviates autumnal oxygen deficiency in the central North Sea
Hypoxia also occurs in small highly turbid estuaries: the example of the Charente (Bay of Biscay)
Seasonality and response of ocean acidification and hypoxia to major environmental anomalies in the southern Salish Sea, North America (2014–2018)
Oceanographic processes driving low-oxygen conditions inside Patagonian fjords
Above- and belowground plant mercury dynamics in a salt marsh estuary in Massachusetts, USA
Variability and drivers of carbonate chemistry at shellfish aquaculture sites in the Salish Sea, British Columbia
Unusual Hemiaulus bloom influences ocean productivity in Northeastern US Shelf waters
Insights into carbonate environmental conditions in the Chukchi Sea
UAV approaches for improved mapping of vegetation cover and estimation of carbon storage of small saltmarshes: examples from Loch Fleet, northeast Scotland
Iron “ore” nothing: benthic iron fluxes from the oxygen-deficient Santa Barbara Basin enhance phytoplankton productivity in surface waters
Marine anoxia initiates giant sulfur-oxidizing bacterial mat proliferation and associated changes in benthic nitrogen, sulfur, and iron cycling in the Santa Barbara Basin, California Borderland
Uncertainty in the evolution of northwestern North Atlantic circulation leads to diverging biogeochemical projections
The additionality problem of ocean alkalinity enhancement
Short-term variation in pH in seawaters around coastal areas of Japan: characteristics and forcings
Revisiting the applicability and constraints of molybdenum- and uranium-based paleo redox proxies: comparing two contrasting sill fjords
Influence of a small submarine canyon on biogenic matter export flux in the lower St. Lawrence Estuary, eastern Canada
Single-celled bioturbators: benthic foraminifera mediate oxygen penetration and prokaryotic diversity in intertidal sediment
Assessing impacts of coastal warming, acidification, and deoxygenation on Pacific oyster (Crassostrea gigas) farming: a case study in the Hinase area, Okayama Prefecture, and Shizugawa Bay, Miyagi Prefecture, Japan
Librada Ramírez, Leonardo J. Pozzo-Pirotta, Aja Trebec, Víctor Manzanares-Vázquez, José L. Díez, Javier Arístegui, Ulf Riebesell, Stephen D. Archer, and María Segovia
Biogeosciences, 22, 1865–1886, https://doi.org/10.5194/bg-22-1865-2025, https://doi.org/10.5194/bg-22-1865-2025, 2025
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We studied the potential effects of increasing ocean alkalinity on a natural plankton community in subtropical waters of the Atlantic near Gran Canaria, Spain. Alkalinity is the capacity of water to resist acidification, and plankton are usually microscopic plants (phytoplankton) and animals (zooplankton), often less than 2.5 cm in length. This study suggests that increasing ocean alkalinity did not have a significant negative impact on the plankton community studied.
Leissing Frederick, Mauricio A. Urbina, and Ruben Escribano
Biogeosciences, 22, 1839–1852, https://doi.org/10.5194/bg-22-1839-2025, https://doi.org/10.5194/bg-22-1839-2025, 2025
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Evidence shows that due to global warming, zooplankton inhabiting the coastal upwelling zone are exposed to increasing hypoxia affecting their physiology, metabolism, and population dynamics. The adaptive responses of zooplankton to cope with mild/severe hypoxia may depend on trade-offs with other metabolic/energy demands, implying less energy for growth, feeding, and reproduction, with ecological consequences for the zooplankton population and the marine food web.
Sören Iwe, Oliver Schmale, and Bernd Schneider
Biogeosciences, 22, 1767–1779, https://doi.org/10.5194/bg-22-1767-2025, https://doi.org/10.5194/bg-22-1767-2025, 2025
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We present a novel method for quantifying N2 fixation by cyanobacteria, which is crucial in Baltic Sea eutrophication. Our Gas Equilibrium – Membrane-Inlet Mass Spectrometer (GE-MIMS), designed for operation on voluntary observing ships (VOSs), enables large-scale monitoring of surface water N2 depletion caused by N2 fixation. Laboratory tests confirm the device’s accuracy and precision, ensuring that it can complement current methods and contribute valuable data for better understanding N2 fixation in the Baltic Sea.
Yong-Woo Lee, Mi-Ok Park, Seong-Gil Kim, Tae-Hoon Kim, Yong Hwa Oh, Sang Heon Lee, and DongJoo Joung
Biogeosciences, 22, 675–690, https://doi.org/10.5194/bg-22-675-2025, https://doi.org/10.5194/bg-22-675-2025, 2025
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Long-term pH variation in coastal waters along the Korean Peninsula was assessed for the first time, and it exhibited no significant pH change over an 11-year period. This contrasts with the ongoing pH decline in open oceans and other coastal areas. Analysis of environmental data showed that pH is mainly controlled by dissolved oxygen in bottom waters. This suggests that ocean warming could cause a pH decline in Korean coastal waters, affecting many fish and seaweed aquaculture operations.
Kadir Biçe, Tristen Myers Stewart, George G. Waldbusser, and Christof Meile
Biogeosciences, 22, 641–657, https://doi.org/10.5194/bg-22-641-2025, https://doi.org/10.5194/bg-22-641-2025, 2025
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We studied the effect of addition of carbonate minerals on coastal sediments. We carried out laboratory experiments to quantify the dissolution kinetics and integrated these observations into a numerical model that describes biogeochemical cycling in surficial sediments. Using the model, we demonstrate the buffering effect of the mineral additions and their duration. We quantify the effect under different environmental conditions and assess the potential for increased atmospheric CO2 uptake.
Feifei Liu, Ute Daewel, Jan Kossack, Kubilay Timur Demir, Helmuth Thomas, and Corinna Schrum
EGUsphere, https://doi.org/10.5194/egusphere-2025-81, https://doi.org/10.5194/egusphere-2025-81, 2025
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Ocean Alkalinity Enhancement boosts oceanic CO₂ absorption, offering a climate solution. Using a regional model, we examined OAE in the North Sea, revealing that shallow coastal areas achieve higher CO₂ uptake than offshore, where alkalinity is more susceptible to deep-ocean loss. Long-term carbon storage is limited, and pH shifts vary by location. Our findings guide OAE deployment to optimize carbon removal while minimizing ecological effects, supporting global climate mitigation efforts.
Jessica L. Oberlander, Mackenzie E. Burke, Cat A. London, and Hugh L. MacIntyre
Biogeosciences, 22, 499–512, https://doi.org/10.5194/bg-22-499-2025, https://doi.org/10.5194/bg-22-499-2025, 2025
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Ocean alkalinity enhancement (OAE) is a promising negative emission technology that results in the net sequestration of atmospheric carbon. In this paper, we assess the potential impact of OAE on phytoplankton through an analysis of prior studies and the effects of simulated OAE on photosynthetic competence. Our findings suggest that there may be little if any significant impact on most phytoplankton studied to date if OAE is conducted in well-flushed, nearshore environments.
Laura Marín-Samper, Javier Arístegui, Nauzet Hernández-Hernández, and Ulf Riebesell
Biogeosciences, 21, 5707–5724, https://doi.org/10.5194/bg-21-5707-2024, https://doi.org/10.5194/bg-21-5707-2024, 2024
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This study exposed a natural community to two non-CO2-equilibrated ocean alkalinity enhancement (OAE) deployments using different minerals. Adding alkalinity in this manner decreases dissolved CO2, essential for photosynthesis. While photosynthesis was not suppressed, bloom formation was mildly delayed, potentially impacting marine food webs. The study emphasizes the need for further research on OAE without prior equilibration and on its ecological implications.
Riss M. Kell, Rebecca J. Chmiel, Deepa Rao, Dawn M. Moran, Matthew R. McIlvin, Tristan J. Horner, Nicole L. Schanke, Ichiko Sugiyama, Robert B. Dunbar, Giacomo R. DiTullio, and Mak A. Saito
Biogeosciences, 21, 5685–5706, https://doi.org/10.5194/bg-21-5685-2024, https://doi.org/10.5194/bg-21-5685-2024, 2024
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Despite interest in modeling the biogeochemical uptake and cycling of the trace metal zinc (Zn), measurements of Zn uptake in natural marine phytoplankton communities have not been conducted previously. To fill this gap, we employed a stable isotope uptake rate measurement method to quantify Zn uptake into natural phytoplankton assemblages within the Southern Ocean. Zn demand was high and rapid enough to depress the inventory of Zn available to phytoplankton on seasonal timescales.
Luisa Chiara Meiritz, Tim Rixen, Anja Karin van der Plas, Tarron Lamont, and Niko Lahajnar
Biogeosciences, 21, 5261–5276, https://doi.org/10.5194/bg-21-5261-2024, https://doi.org/10.5194/bg-21-5261-2024, 2024
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Moored and drifting sediment trap experiments in the northern (nBUS) and southern (sBUS) Benguela Upwelling System showed that active carbon fluxes by vertically migrating zooplankton were about 3 times higher in the sBUS than in the nBUS. Despite these large variabilities, the mean passive particulate organic carbon (POC) fluxes were almost equal in the two subsystems. The more intense near-bottom oxygen minimum layer seems to lead to higher POC fluxes and accumulation rates in the nBUS.
Michael R. Roman, Andrew H. Altieri, Denise Breitburg, Erica M. Ferrer, Natalya D. Gallo, Shin-ichi Ito, Karin Limburg, Kenneth Rose, Moriaki Yasuhara, and Lisa A. Levin
Biogeosciences, 21, 4975–5004, https://doi.org/10.5194/bg-21-4975-2024, https://doi.org/10.5194/bg-21-4975-2024, 2024
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Oxygen-depleted ocean waters have increased worldwide. In order to improve our understanding of the impacts of this oxygen loss on marine life it is essential that we develop reliable indicators that track the negative impacts of low oxygen. We review various indicators of low-oxygen stress for marine animals including their use, research needs, and application to confront the challenges of ocean oxygen loss.
Charlotte Eich, Mathijs van Manen, J. Scott P. McCain, Loay J. Jabre, Willem H. van de Poll, Jinyoung Jung, Sven B. E. H. Pont, Hung-An Tian, Indah Ardiningsih, Gert-Jan Reichart, Erin M. Bertrand, Corina P. D. Brussaard, and Rob Middag
Biogeosciences, 21, 4637–4663, https://doi.org/10.5194/bg-21-4637-2024, https://doi.org/10.5194/bg-21-4637-2024, 2024
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Phytoplankton growth in the Southern Ocean (SO) is often limited by low iron (Fe) concentrations. Sea surface warming impacts Fe availability and can affect phytoplankton growth. We used shipboard Fe clean incubations to test how changes in Fe and temperature affect SO phytoplankton. Their abundances usually increased with Fe addition and temperature increase, with Fe being the major factor. These findings imply potential shifts in ecosystem structure, impacting food webs and elemental cycling.
Miriam Tivig, David P. Keller, and Andreas Oschlies
Biogeosciences, 21, 4469–4493, https://doi.org/10.5194/bg-21-4469-2024, https://doi.org/10.5194/bg-21-4469-2024, 2024
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Marine biological production is highly dependent on the availability of nitrogen and phosphorus. Rivers are the main source of phosphorus to the oceans but poorly represented in global model oceans. We include dissolved nitrogen and phosphorus from river export in a global model ocean and find that the addition of riverine phosphorus affects marine biology on millennial timescales more than riverine nitrogen alone. Globally, riverine phosphorus input increases primary production rates.
Menghong Dong, Xinyu Guo, Takuya Matsuura, Taichi Tebakari, and Jing Zhang
EGUsphere, https://doi.org/10.5194/egusphere-2024-2581, https://doi.org/10.5194/egusphere-2024-2581, 2024
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Submarine groundwater discharge (SGD), a common coastal hydrological process that involves submarine inflow of groundwater into the sea, is associated with a large nutrient load. To clarify the distribution of SGD-derived nutrients after release at the bottom of the sea and their contribution to phytoplankton growth in the marine ecosystem, we modeled the SGD process in Toyama Bay using a specialized computer code that can distinguish SGD-derived nutrients from nutrients from other sources.
Esdoorn Willcox, Marcos Lemes, Thomas Juul-Pedersen, Mikael Kristian Sejr, Johnna Marchiano Holding, and Søren Rysgaard
Biogeosciences, 21, 4037–4050, https://doi.org/10.5194/bg-21-4037-2024, https://doi.org/10.5194/bg-21-4037-2024, 2024
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In this work, we measured the chemistry of seawater from samples obtained from different depths and locations off the east coast of the Northeast Greenland National Park to determine what is influencing concentrations of dissolved CO2. Historically, the region has always been thought to take up CO2 from the atmosphere, but we show that it is possible for the region to become a source in late summer. We discuss the variables that may be related to such changes.
Vlad A. Macovei, Louise C. V. Rewrie, Rüdiger Röttgers, and Yoana G. Voynova
EGUsphere, https://doi.org/10.5194/egusphere-2024-2643, https://doi.org/10.5194/egusphere-2024-2643, 2024
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A commercial vessel equipped with scientific instruments regularly travelled between two large macro-tidal estuaries. We found that biogeochemical variability in the outer estuaries is driven by the 14-day spring-neap tidal cycle, with strong effects on dissolved inorganic and organic carbon concentrations and distribution. Since this land-sea interface effect increases the strength of the carbon source to the atmosphere by 74 % during spring tide, it should be accounted for in regional models.
Lennart Thomas Bach, Aaron James Ferderer, Julie LaRoche, and Kai Georg Schulz
Biogeosciences, 21, 3665–3676, https://doi.org/10.5194/bg-21-3665-2024, https://doi.org/10.5194/bg-21-3665-2024, 2024
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Ocean alkalinity enhancement (OAE) is an emerging marine CO2 removal method, but its environmental effects are insufficiently understood. The OAE Pelagic Impact Intercomparison Project (OAEPIIP) provides funding for a standardized and globally replicated microcosm experiment to study the effects of OAE on plankton communities. Here, we provide a detailed manual for the OAEPIIP experiment. We expect OAEPIIP to help build scientific consensus on the effects of OAE on plankton.
Marlena Szeligowska, Déborah Benkort, Anna Przyborska, Mateusz Moskalik, Bernabé Moreno, Emilia Trudnowska, and Katarzyna Błachowiak-Samołyk
Biogeosciences, 21, 3617–3639, https://doi.org/10.5194/bg-21-3617-2024, https://doi.org/10.5194/bg-21-3617-2024, 2024
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The European Arctic is experiencing rapid regional warming, causing glaciers that terminate in the sea to retreat onto land. Due to this process, the area of a well-studied fjord, Hornsund, has increased by around 100 km2 (40%) since 1976. Combining satellite and in situ data with a mathematical model, we estimated that, despite some negative consequences of glacial meltwater release, such emerging coastal waters could mitigate climate change by increasing carbon uptake and storage by sediments.
Mallory C. Ringham, Nathan Hirtle, Cody Shaw, Xi Lu, Julian Herndon, Brendan R. Carter, and Matthew D. Eisaman
Biogeosciences, 21, 3551–3570, https://doi.org/10.5194/bg-21-3551-2024, https://doi.org/10.5194/bg-21-3551-2024, 2024
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Ocean alkalinity enhancement leverages the large surface area and carbon storage capacity of the oceans to store atmospheric CO2 as dissolved bicarbonate. We monitored CO2 uptake in seawater treated with NaOH to establish operational boundaries for carbon removal experiments. Results show that CO2 equilibration occurred on the order of weeks to months, was consistent with values expected from equilibration calculations, and was limited by mineral precipitation at high pH and CaCO3 saturation.
Riel Carlo O. Ingeniero, Gesa Schulz, and Hermann W. Bange
Biogeosciences, 21, 3425–3440, https://doi.org/10.5194/bg-21-3425-2024, https://doi.org/10.5194/bg-21-3425-2024, 2024
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Our research is the first to measure dissolved NO concentrations in temperate estuarine waters, providing insights into its distribution under varying conditions and enhancing our understanding of its production processes. Dissolved NO was supersaturated in the Elbe Estuary, indicating that it is a source of atmospheric NO. The observed distribution of dissolved NO most likely resulted from nitrification.
Celeste López-Abbate, John E. Garzón-Cardona, Ricardo Silva, Juan-Carlos Molinero, Laura A. Ruiz-Etcheverry, Ana M. Martínez, Azul S. Gilabert, and Rubén J. Lara
EGUsphere, https://doi.org/10.5194/egusphere-2024-1860, https://doi.org/10.5194/egusphere-2024-1860, 2024
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This study examines how microbial community structure, growth, and grazing impact the DOM pool in the Patagonian Shelf. Despite higher phytoplankton biomass, faster-growing bacteria were selectively grazed by protists leading to DOM accumulation, likely due to a reduction in DOM-consuming bacteria and the addition of egestion compounds. Experimental data showed that while bacteria remained as the primarily shapers of DOM quality, grazing pressure impacted on DOM accumulation.
Weiyi Tang, Jeff Talbott, Timothy Jones, and Bess B. Ward
Biogeosciences, 21, 3239–3250, https://doi.org/10.5194/bg-21-3239-2024, https://doi.org/10.5194/bg-21-3239-2024, 2024
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Wastewater treatment plants (WWTPs) are known to be hotspots of greenhouse gas emissions. However, the impact of WWTPs on the emission of the greenhouse gas N2O in downstream aquatic environments is less constrained. We found spatially and temporally variable but overall higher N2O concentrations and fluxes in waters downstream of WWTPs, pointing to the need for efficient N2O removal in addition to the treatment of nitrogen in WWTPs.
Daniel Müller, Bo Liu, Walter Geibert, Moritz Holtappels, Lasse Sander, Elda Miramontes, Heidi Taubner, Susann Henkel, Kai-Uwe Hinrichs, Denise Bethke, Ingrid Dohrmann, and Sabine Kasten
EGUsphere, https://doi.org/10.5194/egusphere-2024-1632, https://doi.org/10.5194/egusphere-2024-1632, 2024
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Coastal and shelf sediments are the most important sinks for organic carbon (OC) on Earth. We produced a new high-resolution sediment and pore-water dataset from the Helgoland Mud Area (HMA), North Sea, to determine, which depositional factors control the preservation of OC. The burial efficiency is highest in an area of high sedimentation and terrigenous OC. The HMA covers 0.09 % of the North Sea, but accounts for 0.76 % of its OC accumulation, highlighting the importance of the depocentre.
Deep S. Banerjee and Jozef Skakala
EGUsphere, https://doi.org/10.22541/essoar.171405637.76928549/v1, https://doi.org/10.22541/essoar.171405637.76928549/v1, 2024
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Nitrate is a crucial nutrient in oceans. Excess nutrients can trigger uncontrolled algae growth (eutrophication), damaging marine ecosystems. We used a machine learning tool to generate a skilled, gap-free, bi-decadal surface nitrate dataset from sparse observations. This dataset reveals areas on the North West European Shelf at risk of eutrophication, bi-decadal trends in coastal nitrate, and an impact of winter nitrate on spring phytoplankton blooms.
Amanda Y. L. Cheong, Kogila Vani Annammala, Ee Ling Yong, Yongli Zhou, Robert S. Nichols, and Patrick Martin
Biogeosciences, 21, 2955–2971, https://doi.org/10.5194/bg-21-2955-2024, https://doi.org/10.5194/bg-21-2955-2024, 2024
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We measured nutrients and dissolved organic matter for 1 year in a eutrophic tropical estuary to understand their sources and cycling. Our data show that the dissolved organic matter originates partly from land and partly from microbial processes in the water. Internal recycling is likely important for maintaining high nutrient concentrations, and we found that there is often excess nitrogen compared to silicon and phosphorus. Our data help to explain how eutrophication persists in this system.
Darren Pilcher, Jessica Cross, Natalie Monacci, Linquan Mu, Kelly Kearney, Albert Hermann, and Wei Cheng
EGUsphere, https://doi.org/10.5194/egusphere-2024-1096, https://doi.org/10.5194/egusphere-2024-1096, 2024
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The Bering Sea shelf is a highly productive marine ecosystem that is vulnerable to ocean acidification. We use a computational model to simulate the carbon cycle and acidification rates from 1970–2022. The results suggest that bottom water acidification rates are more than twice as great as surface rates. Bottom waters are also naturally more acidic, thus these waters will pass key thresholds known to negatively impact marine organisms, such as red king crab, much sooner than surface waters.
Aaron Ferderer, Kai G. Schulz, Ulf Riebesell, Kirralee G. Baker, Zanna Chase, and Lennart T. Bach
Biogeosciences, 21, 2777–2794, https://doi.org/10.5194/bg-21-2777-2024, https://doi.org/10.5194/bg-21-2777-2024, 2024
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Ocean alkalinity enhancement (OAE) is a promising method of atmospheric carbon removal; however, its ecological impacts remain largely unknown. We assessed the effects of simulated silicate- and calcium-based mineral OAE on diatom silicification. We found that increased silicate concentrations from silicate-based OAE increased diatom silicification. In contrast, the enhancement of alkalinity had no effect on community silicification and minimal effects on the silicification of different genera.
David González-Santana, María Segovia, Melchor González-Dávila, Librada Ramírez, Aridane G. González, Leonardo J. Pozzo-Pirotta, Veronica Arnone, Victor Vázquez, Ulf Riebesell, and J. Magdalena Santana-Casiano
Biogeosciences, 21, 2705–2715, https://doi.org/10.5194/bg-21-2705-2024, https://doi.org/10.5194/bg-21-2705-2024, 2024
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In a recent experiment off the coast of Gran Canaria (Spain), scientists explored a method called ocean alkalinization enhancement (OAE), where carbonate minerals were added to seawater. This process changed the levels of certain ions in the water, affecting its pH and buffering capacity. The researchers were particularly interested in how this could impact the levels of essential trace metals in the water.
Lucas Porz, Wenyan Zhang, Nils Christiansen, Jan Kossack, Ute Daewel, and Corinna Schrum
Biogeosciences, 21, 2547–2570, https://doi.org/10.5194/bg-21-2547-2024, https://doi.org/10.5194/bg-21-2547-2024, 2024
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Seafloor sediments store a large amount of carbon, helping to naturally regulate Earth's climate. If disturbed, some sediment particles can turn into CO2, but this effect is not well understood. Using computer simulations, we found that bottom-contacting fishing gears release about 1 million tons of CO2 per year in the North Sea, one of the most heavily fished regions globally. We show how protecting certain areas could reduce these emissions while also benefitting seafloor-living animals.
Jiaying A. Guo, Robert F. Strzepek, Kerrie M. Swadling, Ashley T. Townsend, and Lennart T. Bach
Biogeosciences, 21, 2335–2354, https://doi.org/10.5194/bg-21-2335-2024, https://doi.org/10.5194/bg-21-2335-2024, 2024
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Ocean alkalinity enhancement aims to increase atmospheric CO2 sequestration by adding alkaline materials to the ocean. We assessed the environmental effects of olivine and steel slag powder on coastal plankton. Overall, slag is more efficient than olivine in releasing total alkalinity and, thus, in its ability to sequester CO2. Slag also had less environmental effect on the enclosed plankton communities when considering its higher CO2 removal potential based on this 3-week experiment.
Giovanni Galli, Sarah Wakelin, James Harle, Jason Holt, and Yuri Artioli
Biogeosciences, 21, 2143–2158, https://doi.org/10.5194/bg-21-2143-2024, https://doi.org/10.5194/bg-21-2143-2024, 2024
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This work shows that, under a high-emission scenario, oxygen concentration in deep water of parts of the North Sea and Celtic Sea can become critically low (hypoxia) towards the end of this century. The extent and frequency of hypoxia depends on the intensity of climate change projected by different climate models. This is the result of a complex combination of factors like warming, increase in stratification, changes in the currents and changes in biological processes.
Sandy E. Tenorio and Laura Farías
Biogeosciences, 21, 2029–2050, https://doi.org/10.5194/bg-21-2029-2024, https://doi.org/10.5194/bg-21-2029-2024, 2024
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Time series studies show that CH4 is highly dynamic on the coastal ocean surface and planktonic communities are linked to CH4 accumulation, as found in coastal upwelling off Chile. We have identified the crucial role of picoplankton (> 3 µm) in CH4 recycling, especially with the addition of methylated substrates (trimethylamine and methylphosphonic acid) during upwelling and non-upwelling periods. These insights improve understanding of surface ocean CH4 recycling, aiding CH4 emission estimates.
Charlotte A. J. Williams, Tom Hull, Jan Kaiser, Claire Mahaffey, Naomi Greenwood, Matthew Toberman, and Matthew R. Palmer
Biogeosciences, 21, 1961–1971, https://doi.org/10.5194/bg-21-1961-2024, https://doi.org/10.5194/bg-21-1961-2024, 2024
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Oxygen (O2) is a key indicator of ocean health. The risk of O2 loss in the productive coastal/continental slope regions is increasing. Autonomous underwater vehicles equipped with O2 optodes provide lots of data but have problems resolving strong vertical O2 changes. Here we show how to overcome this and calculate how much O2 is supplied to the low-O2 bottom waters via mixing. Bursts in mixing supply nearly all of the O2 to bottom waters in autumn, stopping them reaching ecologically low levels.
Sabine Schmidt and Ibrahima Iris Diallo
Biogeosciences, 21, 1785–1800, https://doi.org/10.5194/bg-21-1785-2024, https://doi.org/10.5194/bg-21-1785-2024, 2024
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Along the French coast facing the Bay of Biscay, the large Gironde and Loire estuaries suffer from hypoxia. This prompted a study of the small Charente estuary located between them. This work reveals a minimum oxygen zone in the Charente estuary, which extends for about 25 km. Temperature is the main factor controlling the hypoxia. This calls for the monitoring of small turbid macrotidal estuaries that are vulnerable to hypoxia, a risk expected to increase with global warming.
Simone R. Alin, Jan A. Newton, Richard A. Feely, Samantha Siedlecki, and Dana Greeley
Biogeosciences, 21, 1639–1673, https://doi.org/10.5194/bg-21-1639-2024, https://doi.org/10.5194/bg-21-1639-2024, 2024
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We provide a new multi-stressor data product that allows us to characterize the seasonality of temperature, O2, and CO2 in the southern Salish Sea and delivers insights into the impacts of major marine heatwave and precipitation anomalies on regional ocean acidification and hypoxia. We also describe the present-day frequencies of temperature, O2, and ocean acidification conditions that cross thresholds of sensitive regional species that are economically or ecologically important.
Pamela Linford, Iván Pérez-Santos, Paulina Montero, Patricio A. Díaz, Claudia Aracena, Elías Pinilla, Facundo Barrera, Manuel Castillo, Aida Alvera-Azcárate, Mónica Alvarado, Gabriel Soto, Cécile Pujol, Camila Schwerter, Sara Arenas-Uribe, Pilar Navarro, Guido Mancilla-Gutiérrez, Robinson Altamirano, Javiera San Martín, and Camila Soto-Riquelme
Biogeosciences, 21, 1433–1459, https://doi.org/10.5194/bg-21-1433-2024, https://doi.org/10.5194/bg-21-1433-2024, 2024
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The Patagonian fjords comprise a world region where low-oxygen water and hypoxia conditions are observed. An in situ dataset was used to quantify the mechanism involved in the presence of these conditions in northern Patagonian fjords. Water mass analysis confirmed the contribution of Equatorial Subsurface Water in the advection of the low-oxygen water, and hypoxic conditions occurred when the community respiration rate exceeded the gross primary production.
Ting Wang, Buyun Du, Inke Forbrich, Jun Zhou, Joshua Polen, Elsie M. Sunderland, Prentiss H. Balcom, Celia Chen, and Daniel Obrist
Biogeosciences, 21, 1461–1476, https://doi.org/10.5194/bg-21-1461-2024, https://doi.org/10.5194/bg-21-1461-2024, 2024
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The strong seasonal increases of Hg in aboveground biomass during the growing season and the lack of changes observed after senescence in this salt marsh ecosystem suggest physiologically controlled Hg uptake pathways. The Hg sources found in marsh aboveground tissues originate from a mix of sources, unlike terrestrial ecosystems, where atmospheric GEM is the main source. Belowground plant tissues mostly take up Hg from soils. Overall, the salt marsh currently serves as a small net Hg sink.
Eleanor Simpson, Debby Ianson, Karen E. Kohfeld, Ana C. Franco, Paul A. Covert, Marty Davelaar, and Yves Perreault
Biogeosciences, 21, 1323–1353, https://doi.org/10.5194/bg-21-1323-2024, https://doi.org/10.5194/bg-21-1323-2024, 2024
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Shellfish aquaculture operates in nearshore areas where data on ocean acidification parameters are limited. We show daily and seasonal variability in pH and saturation states of calcium carbonate at nearshore aquaculture sites in British Columbia, Canada, and determine the contributing drivers of this variability. We find that nearshore locations have greater variability than open waters and that the uptake of carbon by phytoplankton is the major driver of pH and saturation state variability.
S. Alejandra Castillo Cieza, Rachel H. R. Stanley, Pierre Marrec, Diana N. Fontaine, E. Taylor Crockford, Dennis J. McGillicuddy Jr., Arshia Mehta, Susanne Menden-Deuer, Emily E. Peacock, Tatiana A. Rynearson, Zoe O. Sandwith, Weifeng Zhang, and Heidi M. Sosik
Biogeosciences, 21, 1235–1257, https://doi.org/10.5194/bg-21-1235-2024, https://doi.org/10.5194/bg-21-1235-2024, 2024
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The coastal ocean in the northeastern USA provides many services, including fisheries and habitats for threatened species. In summer 2019, a bloom occurred of a large unusual phytoplankton, the diatom Hemiaulus, with nitrogen-fixing symbionts. This led to vast changes in productivity and grazing rates in the ecosystem. This work shows that the emergence of one species can have profound effects on ecosystem function. Such changes may become more prevalent as the ocean warms due to climate change.
Claudine Hauri, Brita Irving, Sam Dupont, Rémi Pagés, Donna D. W. Hauser, and Seth L. Danielson
Biogeosciences, 21, 1135–1159, https://doi.org/10.5194/bg-21-1135-2024, https://doi.org/10.5194/bg-21-1135-2024, 2024
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Arctic marine ecosystems are highly susceptible to impacts of climate change and ocean acidification. We present pH and pCO2 time series (2016–2020) from the Chukchi Ecosystem Observatory and analyze the drivers of the current conditions to get a better understanding of how climate change and ocean acidification could affect the ecological niches of organisms.
William Hiles, Lucy C. Miller, Craig Smeaton, and William E. N. Austin
Biogeosciences, 21, 929–948, https://doi.org/10.5194/bg-21-929-2024, https://doi.org/10.5194/bg-21-929-2024, 2024
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Saltmarsh soils may help to limit the rate of climate change by storing carbon. To understand their impacts, they must be accurately mapped. We use drone data to estimate the size of three saltmarshes in NE Scotland. We find that drone imagery, combined with tidal data, can reliably inform our understanding of saltmarsh size. When compared with previous work using vegetation communities, we find that our most reliable new estimates of stored carbon are 15–20 % smaller than previously estimated.
De'Marcus Robinson, Anh L. D. Pham, David J. Yousavich, Felix Janssen, Frank Wenzhöfer, Eleanor C. Arrington, Kelsey M. Gosselin, Marco Sandoval-Belmar, Matthew Mar, David L. Valentine, Daniele Bianchi, and Tina Treude
Biogeosciences, 21, 773–788, https://doi.org/10.5194/bg-21-773-2024, https://doi.org/10.5194/bg-21-773-2024, 2024
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The present study suggests that high release of ferrous iron from the seafloor of the oxygen-deficient Santa Barabara Basin (California) supports surface primary productivity, creating positive feedback on seafloor iron release by enhancing low-oxygen conditions in the basin.
David J. Yousavich, De'Marcus Robinson, Xuefeng Peng, Sebastian J. E. Krause, Frank Wenzhöfer, Felix Janssen, Na Liu, Jonathan Tarn, Franklin Kinnaman, David L. Valentine, and Tina Treude
Biogeosciences, 21, 789–809, https://doi.org/10.5194/bg-21-789-2024, https://doi.org/10.5194/bg-21-789-2024, 2024
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Declining oxygen (O2) concentrations in coastal oceans can threaten people’s ways of life and food supplies. Here, we investigate how mats of bacteria that proliferate on the seafloor of the Santa Barbara Basin sustain and potentially worsen these O2 depletion events through their unique chemoautotrophic metabolism. Our study shows how changes in seafloor microbiology and geochemistry brought on by declining O2 concentrations can help these mats grow as well as how that growth affects the basin.
Krysten Rutherford, Katja Fennel, Lina Garcia Suarez, and Jasmin G. John
Biogeosciences, 21, 301–314, https://doi.org/10.5194/bg-21-301-2024, https://doi.org/10.5194/bg-21-301-2024, 2024
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We downscaled two mid-century (~2075) ocean model projections to a high-resolution regional ocean model of the northwest North Atlantic (NA) shelf. In one projection, the NA shelf break current practically disappears; in the other it remains almost unchanged. This leads to a wide range of possible future shelf properties. More accurate projections of coastal circulation features would narrow the range of possible outcomes of biogeochemical projections for shelf regions.
Lennart Thomas Bach
Biogeosciences, 21, 261–277, https://doi.org/10.5194/bg-21-261-2024, https://doi.org/10.5194/bg-21-261-2024, 2024
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Ocean alkalinity enhancement (OAE) is a widely considered marine carbon dioxide removal method. OAE aims to accelerate chemical rock weathering, which is a natural process that slowly sequesters atmospheric carbon dioxide. This study shows that the addition of anthropogenic alkalinity via OAE can reduce the natural release of alkalinity and, therefore, reduce the efficiency of OAE for climate mitigation. However, the additionality problem could be mitigated via a variety of activities.
Tsuneo Ono, Daisuke Muraoka, Masahiro Hayashi, Makiko Yorifuji, Akihiro Dazai, Shigeyuki Omoto, Takehiro Tanaka, Tomohiro Okamura, Goh Onitsuka, Kenji Sudo, Masahiko Fujii, Ryuji Hamanoue, and Masahide Wakita
Biogeosciences, 21, 177–199, https://doi.org/10.5194/bg-21-177-2024, https://doi.org/10.5194/bg-21-177-2024, 2024
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We carried out parallel year-round observations of pH and related parameters in five stations around the Japan coast. It was found that short-term acidified situations with Omega_ar less than 1.5 occurred at four of five stations. Most of such short-term acidified events were related to the short-term low salinity event, and the extent of short-term pH drawdown at high freshwater input was positively correlated with the nutrient concentration of the main rivers that flow into the coastal area.
K. Mareike Paul, Martijn Hermans, Sami A. Jokinen, Inda Brinkmann, Helena L. Filipsson, and Tom Jilbert
Biogeosciences, 20, 5003–5028, https://doi.org/10.5194/bg-20-5003-2023, https://doi.org/10.5194/bg-20-5003-2023, 2023
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Seawater naturally contains trace metals such as Mo and U, which accumulate under low oxygen conditions on the seafloor. Previous studies have used sediment Mo and U contents as an archive of changing oxygen concentrations in coastal waters. Here we show that in fjords the use of Mo and U for this purpose may be impaired by additional processes. Our findings have implications for the reliable use of Mo and U to reconstruct oxygen changes in fjords.
Hannah Sharpe, Michel Gosselin, Catherine Lalande, Alexandre Normandeau, Jean-Carlos Montero-Serrano, Khouloud Baccara, Daniel Bourgault, Owen Sherwood, and Audrey Limoges
Biogeosciences, 20, 4981–5001, https://doi.org/10.5194/bg-20-4981-2023, https://doi.org/10.5194/bg-20-4981-2023, 2023
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We studied the impact of submarine canyon processes within the Pointe-des-Monts system on biogenic matter export and phytoplankton assemblages. Using data from three oceanographic moorings, we show that the canyon experienced two low-amplitude sediment remobilization events in 2020–2021 that led to enhanced particle fluxes in the deep-water column layer > 2.6 km offshore. Sinking phytoplankton fluxes were lower near the canyon compared to background values from the lower St. Lawrence Estuary.
Dewi Langlet, Florian Mermillod-Blondin, Noémie Deldicq, Arthur Bauville, Gwendoline Duong, Lara Konecny, Mylène Hugoni, Lionel Denis, and Vincent M. P. Bouchet
Biogeosciences, 20, 4875–4891, https://doi.org/10.5194/bg-20-4875-2023, https://doi.org/10.5194/bg-20-4875-2023, 2023
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Benthic foraminifera are single-cell marine organisms which can move in the sediment column. They were previously reported to horizontally and vertically transport sediment particles, yet the impact of their motion on the dissolved fluxes remains unknown. Using microprofiling, we show here that foraminiferal burrow formation increases the oxygen penetration depth in the sediment, leading to a change in the structure of the prokaryotic community.
Masahiko Fujii, Ryuji Hamanoue, Lawrence Patrick Cases Bernardo, Tsuneo Ono, Akihiro Dazai, Shigeyuki Oomoto, Masahide Wakita, and Takehiro Tanaka
Biogeosciences, 20, 4527–4549, https://doi.org/10.5194/bg-20-4527-2023, https://doi.org/10.5194/bg-20-4527-2023, 2023
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This is the first study of the current and future impacts of climate change on Pacific oyster farming in Japan. Future coastal warming and acidification may affect oyster larvae as a result of longer exposure to lower-pH waters. A prolonged spawning period may harm oyster processing by shortening the shipping period and reducing oyster quality. To minimize impacts on Pacific oyster farming, in addition to mitigation measures, local adaptation measures may be required.
Cited articles
Ariathurai, R. and Krone, R. B.: Finite element model for cohesive sediment transport, J. Hydr. Eng. Div.-ASCE, 104, 323–328, 1976.
Atkinson, M. J. and Smith, S. V.: C : N : P ratios of benthic marine plants, Limnol. Oceanogr., 28, 568–574, 1983.
Baird, M. E.: Limits to prediction in a size-resolved pelagic ecosystem model, J. Plankton Res., 32, 1131–1146, 2010.
Baird, M. E., Ralph, P. J., Wild-Allen, K., Rizwi, F., and Steven, A. D. L.: A dynamic model of the cellular carbon to chlorophyll ratio applied to a batch culture and a continental shelf ecosystem, Limnol. Oceanogr., 58, 1215–1226, 2013.
Baird, M. E., Cherukuru, N., Jones, E., Margvelashvili, N., Mongin, M., Oubelkheir, K., Ralph, P. J., Rizwi, F., Robson, B. J., Schroeder, T., Skerratt, J., Steven, A. D. L., and Wild-Allen, K. A.: Remote-sensing reflectance and true colour produced by a coupled hydrodynamic, optical, sediment, biogeochemical model of the Great Barrier Reef, Australia: comparison with satellite data, Env. Model. Softw., 78, 79–96, 2016a.
Baird, M. E., Adams, M. P., Babcock, R. C., Oubelkheir, K., Mongin, M., Wild-Allen, K. A., Skerratt, J., Robson, B. J., Petrou, K., Ralph, P. J., O'Brien, K. R., Carter, A. B., Jarvis, J. C., and Rasheed, M. A.: A biophysical representation of seagrass growth for application in a complex shallow-water biogeochemical model, Ecol. Modell., 325, 13–27, 2016b.
Blondeau-Patissier, D., Brando, V. E., Oubelkheir, K., Dekker, A. G., Clementson, L. A., and Daniel, P.: Bio-optical variability of the absorption and scattering properties of the Queensland inshore and reef waters, Australia, J. Geophys. Res.-Oceans, 114, https://doi.org/10.1029/2008JC005039, 2009.
Brando, V. E., Schroeder, T., King, E., and Dyce, P.: Reef Rescue Marine Monitoring Program: Using remote sensing for GBR-wide water quality, Final Report for 2012/13 Activities, CSIRO Report to the Great Barrier Reef Marine Park Authority, 213 pp., 2015.
Carmillet, V., Brankart, J. M., Brasseur, P., Drange, H., Evensen, G., and Verron, J.: A singular evolutive extended Kalman filter to assimilate ocean color data in a coupled physical–biochemical model of the North Atlantic Ocean, Ocean Modell., 3, 167–192, 2001.
Ciavatta, S., Torres, R., Martinez-Vicente, V., Smyth, T., Dall'Olmo, G., Polimene, L., and Allen, J. I.: Assimilation of remotely-sensed optical properties to improve marine biogeochemistry modelling, Prog. Oceanogr., 127, 74–95, 2014.
Ciavatta, S., Kay, S., Saux-Picart, S., Butenschön, M., and Allen, J. I.: Decadal reanalysis of biogeochemical indicators and fluxes in the North West European shelf-sea ecosystem, J. Geophys. Res.-Oceans., 121, 1824–1845, 2016.
Collier, C. J., Waycott, M., and McKenzie, L. J.: Light thresholds derived from seagrass loss in the coastal zone of the northern Great Barrier Reef, Australia, Ecol. Indic., 23, 211–219, 2012.
Cummings, J. A.: Operational multivariate ocean data assimilation, Q. J. Roy. Meteorol. Soc., 131, 3583–3604, 2005.
De'ath, G., Fabricius, K. E., Sweatman, H., and Puotinen, M.: The 27–year decline of coral cover on the Great Barrier Reef and its causes, P. Natl. Acad. Sci. USA, 109, 17995–17999, 2012.
Dee, D. P., Uppala, S. M., Simmons, A. J., Berrisford, P., Poli, P., Kobayashi, S., and Bechtold, P.: The ERA-Interim reanalysis: Configuration and performance of the data assimilation system, Q. J. Roy. Meteorol. Soc., 137, 553–597, 2011.
Derber, J. C. and Wu, W. S.: The use of TOVS cloud-cleared radiances in the NCEP SSI analysis system, Mon.Weather Rev., 126, 2287–2299, 1998.
Dowd, M., Jones, E., and Parslow, J.: A statistical overview and perspectives on data assimilation for marine biogeochemical models, Environmetrics, 25, 203–213, 2014.
Dutkiewicz, S., Hickman, A. E., Jahn, O., Gregg, W. W., Mouw, C. B., and Follows, M. J.: Capturing optically important constituents and properties in a marine biogeochemical and ecosystem model, Biogeosciences, 12, 4447–4481, https://doi.org/10.5194/bg-12-4447-2015, 2015.
Egbert, G. D. and Erofeeva, S. Y.: Efficient inverse modeling of barotropic ocean tides, J. Atmos. Ocean. Technol., 19, 183–204, 2002.
Ford, D. and Barciela, R.: Forecasting Research Technical Report No: 609, Marine biogeochemical data assimilation–literature review and scoping report, 46 pp., 2015.
Ford, D. A., Edwards, K. P., Lea, D., Barciela, R. M., Martin, M. J., and Demaria, J.: Assimilating GlobColour ocean colour data into a pre-operational physical-biogeochemical model, Ocean Sci., 8, 751–771, https://doi.org/10.5194/os-8-751-2012, 2012.
Fujii, M., Boss, E., and Chai, F.: The value of adding optics to ecosystem models: a case study, Biogeosciences, 4, 817–835, https://doi.org/10.5194/bg-4-817-2007, 2007.
Furnas, M.: Catchments and corals: terrestrial runoff to the Great Barrier Reef, Australian Institute of Marine Science, Queensland, 334 pp., 2003.
Garnier, F., Brankart, J. M., Brasseur, P., and Cosme, E.: Stochastic parameterizations of biogeochemical uncertainties in a 1∕4° NEMO/PISCES model for probabilistic comparisons with ocean color data, J. Mar. Syst., 155, 59–72, 2016.
Gaspari, G. and Cohn, S. E.: Construction of correlation functions in two and three dimensions, Q. J. Roy. Meteorol. Soc., 125, 723–757, 1999.
Gehlen, M., Barciela, R., Bertino, L., Brasseur, P., Butenschön, M., Chai, F., Crise, A., Drillet, Y., Ford, D., Lavoie, D., and Lehodey, P.: Building the capacity for forecasting marine biogeochemistry and ecosystems: recent advances and future developments, J. Operat. Oceanogr., 8, s168–s187, 2015.
Gillibrand, P. A. and Herzfeld, M.: A mass-conserving advection scheme for offline simulation of scalar transport in coastal ocean models, Ocean Modell., 101, 1–16, 2016.
Goyens, C., Jamet, C., and Schroeder, T.: Evaluation of four atmospheric correction algorithms for MODIS-Aqua images over contrasted coastal watersm, Remote Sens. Environ., 131, 63–75, 2013.
Gregg, W. W.: Assimilation of SeaWiFS ocean chlorophyll data into a three-dimensional global ocean model, J. Mar. Syst., 69, 205–225, 2008.
Herzfeld, M.: An alternative coordinate system for solving finite difference ocean models, Ocean Modell., 14, 174–196, 2006.
Herzfeld, M.: Methods for freshwater riverine input into regional ocean models, Ocean Modell., 90, 1–15, 2015.
Herzfeld, M. and Gillibrand, P. A.: Active open boundary forcing using dual relaxation time-scales in downscaled ocean models, Ocean Modell., 89, 71–83, 2015.
Herzfeld, M., Andrewartha, J., Baird, M., Brinkman, R., Furnas, M., Gillibrand, P., Hemer, M., Joehnk, K., Jones, E., McKinnon, D., Margvelashvili, N., Mongin, M., Oke, P., Rizwi, F., Robson, B., Seaton, S., Skerratt, J., Tonin, H., Wild-Allen, K.: eReefs Marine Modelling: Final Report, Jan. 2016, CSIRO, Hobart, 497 pp., 2016.
Hu, J., Fennel, K., Mattern, J. P., and Wilkin, J.: Data assimilation with a local Ensemble Kalman Filter applied to a three-dimensional biological model of the Middle Atlantic Bight, J. Mar. Syst., 94, 145–156, 2012.
King, E. A., Schroeder, T., Brando, V. E., and Suber, K.: A pre-operational System for Satellite Monitoring of the Great Barrier Reef Marine Water Quality, Tech. rep., CSIRO Report, 56 pp., 2014.
Lee, Z., Carder, K. L., and Arnone, R. A.: Deriving inherent optical properties from water color: a multiband quasi-analytical algorithm for optically deep waters, Appl. Opt., 41, 5755–5772, 2002.
Lynch, T. P., Morello, E. B., Evans, K., Richardson, A. J., Rochester, W., Steinberg, C. R., and Sherrington, R.: IMOS National Reference Stations: a continental-wide physical, chemical and biological coastal observing system, PloS one, 9, e113652, https://doi.org/10.1371/journal.pone.0113652, 2014.
Madsen, O. S.: Spectral wave-current bottom boundary layer flows, in Coastal Engineering 1994 Proceedings, 24 th International Conference Coastal Engineering Research Council/ASCE, 384–398, 1994.
Margvelashvili, N.: Stretched Eulerian coordinate model of coastal sediment transport, Comput. Geosci., 35, 1167–1176, 2009.
Margvelashvili, N., Saint-Cast, F., and Condie, S.: Numerical modelling of the suspended sediment transport in Torres Strait, Cont. Shelf Res., 28, 2241–2256, 2008.
Margvelashvili, N. Y., Herzfeld, M., Rizwi, F., Mongin, M., Baird, M. E., Jones, E., and Schroeder, T.: Emulator-assisted data assimilation in complex models, Ocean Dynam., 66, 1109–1124, 2016.
Mongin, M., Baird, M. E., Tilbrook, B., Matear, R. J., Lenton, A., Herzfeld, M., Wild-Allen, K. A., Skerratt, J., Margvelashvili, N., Robson, B. J., Duarte, C. M., Gustafsson, M. S. M., Ralph, P. J., and Steven, A. D. L.: The exposure of the Great Barrier Reef to ocean acidification, Nat. Commun., 7, 10732, https://doi.org/10.1038/ncomms10732, 2016.
Moore, T. S., Campbell, J. W., and Dowell, M. D.: A class-based approach to characterizing and mapping the uncertainty of the MODIS ocean chlorophyll product, Remote Sens. Environ., 113, 2424–2430, 2009.
Morel, A., Antoine, D., and Gentili, B.: Bidirectional reflectance of oceanic waters: accounting for Raman emission and varying particle scattering phase function, Appl. Opt., 41, 6289–6306, 2002.
Morello, E. B., Plagányi, É. E., Babcock, R. C., Sweatman, H., Hillary, R., and Punt, A. E.: Model to manage and reduce crown-of-thorns starfish outbreaks, Mar. Ecol.-Prog. Ser., 512, 167–183, 2014.
Natvik, L. J. and Evensen, G.: Assimilation of ocean colour data into a biochemical model of the North Atlantic: Part 1. Data assimilation experiments, J. Mar. Syst., 40, 127–153, 2003.
Odermatt, D., Gitelson, A., Brando, V. E., and Schaepman, M.: Review of constituent retrieval in optically deep and complex waters from satellite imagery, Remote Sens, Environ., 118, 116–126, 2012.
Oke, P. R. and Sakov, P.: Representation error of oceanic observations for data assimilation, J. Atmos. Ocean. Technol. 25, 1004–1017, 2008a.
Oke, P. R., Brassington, G. B., Griffin, D. A., and Schiller, A.: The Bluelink ocean data assimilation system (BODAS), Ocean Modell., 21, 46–70, 2008b.
Parslow, J. S., Cressie, N., Campbell, E., Jones. E. M., and Murray, L.: Bayesian learning and predictability in a stochastic nonlinear dynamical model, Ecol. Appl., 23, 679–698, 2013.
Qin, Y., Brando, V. E., Dekker, A. G., and Blondeau-Patissier, D.: Validity of SeaDAS water constituents retrieval algorithms in Australian tropical coastal waters, Geophys. Res. Lett., 34, https://doi.org/10.1029/2007GL030599, 2007.
Redfield, A. C.: The influence of organisms on the composition of sea-water, The Sea, 26–77, 1963.
Ridgway, K. R., Dunn, J. R., and Wilkin, J. L.: Ocean interpolation by four-dimensional weighted least squares-application to the waters around Australasia, J. Atmos. Ocean. Technol., 19, 1357–1375, 2002.
Robson, B. J., Baird, M., and Wild-Allen, K.: A physiological model for the marine cyanobacteria, Trichodesmium, in: MODSIM2013, 20th International Congress on Modelling and Simulation. Modelling and Simulation Society of Australia and New Zealand, ISBN (978-0), 2013.
Rolfe, J. and Gregg, D.: Factors affecting adoption of improved management practices in the pastoral industry in Great Barrier Reef catchments, J. Environ. Manage., 157, 182–193, 2015.
Sakov, P. and Oke, P. R.: A deterministic formulation of the ensemble Kalman filter: an alternative to ensemble square root filters, Tellus A, 60, 361–371, 2008.
Sakov, P. and Bertino, L.: Relation between two common localisation methods for the EnKF, Comput. Geosci., 15, 225–237, 2011.
Sarmiento, J. L and Gruber, N.: Ocean Biogeochemical Dynamics, Princeton University Press, ISBN: 9780691017075, 528,2006
Schaeffer, A., Roughan, M., Jones, E. M., and White, D.: Physical and biogeochemical spatial scales of variability in the East Australian Current separation from shelf glider measurements, Biogeosciences, 13, 1967–1975, https://doi.org/10.5194/bg-13-1967-2016, 2016.
Schiller, A., Herzfeld, M., Brinkman, R., and Stuart, G.: Monitoring, predicting, and managing one of the seven natural wonders of the world, B. Am. Meteorol. Soc., 95, 23–30, 2014.
Schroeder, T., Behnert, I., Schaale, M., Fischer, J., and Doerffer, R.: Atmospheric correction algorithm for MERIS above case-2 waters, Int. J. Remote Sens., 28, 1469–1486, 2007.
Schroeder, T., Devlin, M. J., Brando, V. E., Dekker, A. G., Brodie, J. E., Clementson, L. A., and McKinna, L.: Inter-annual variability of wet season freshwater plume extent into the Great Barrier Reef lagoon based on satellite coastal ocean colour observations, Mar. Pollut. Bull., 65, 210–223, 2012.
Schroeder, T., Lovell, J., King, E., Clementson, L., and Scott, R.: IMOS Ocean Colour Validation Report 2015–16, 2016.
Shulman, I., Frolov, S., Anderson, S., Penta, B., Gould, R., Sakalaukus, P., and Ladner, S.: Impact of bio-optical data assimilation on short-term coupled physical, bio-optical model predictions, J. Geophys. Res.-Oceans, 118, 2215–2230, 2013.
Skerratt, J., Wild-Allen, K., Rizwi, F., Whitehead, J., and Coughanowr, C.: Use of a high resolution 3-D fully coupled hydrodynamic, sediment and biogeochemical model to understand estuarine nutrient dynamics under various water quality scenarios, Ocean Coast. Manage., 83, 52–66, 2013.
Thompson, A., Costello, P., Davidson, J., Logan, M., Schaffelke, B., Uthicke, S., and Takahashi, M.: Reef rescue marine monitoring program. Report of AIMS Activities–Inshore coral reef monitoring, 128 pp., 2011.
Thompson, A., Schroeder, T., Brando, V. E., and Schaffelke, B.: Coral community responses to declining water quality: Whitsunday Islands, Great Barrier Reef, Australia, Coral Reefs, 33, 923–938, 2014.
Willmott, C. J., Ackleson, S. G., Davis, R. E., Feddema, J. J., Klink, K. M., Legates, D. R., ODonnell, J., and Rowe, C. M.: Statistics for the evaluation of model performance, J. Geophys. Res., 90, 8995–9005, 1985.
Short summary
Marine biogeochemical models are often used to understand water quality, nutrient and blue-carbon dynamics at scales that range from estuaries and bays, through to the global ocean. We introduce a new methodology allowing for the assimilation of observed remote sensing reflectances, avoiding the need to use empirically derived chlorophyll-a concentrations. This method opens up the possibility to assimilate of reflectances from a variety of missions and potentially non-satellite platforms.
Marine biogeochemical models are often used to understand water quality, nutrient and...
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