Articles | Volume 15, issue 24
https://doi.org/10.5194/bg-15-7379-2018
© Author(s) 2018. This work is distributed under
the Creative Commons Attribution 4.0 License.
the Creative Commons Attribution 4.0 License.
https://doi.org/10.5194/bg-15-7379-2018
© Author(s) 2018. This work is distributed under
the Creative Commons Attribution 4.0 License.
the Creative Commons Attribution 4.0 License.
Research article
| 
14 Dec 2018
Research article |
| 14 Dec 2018
| 14 Dec 2018
Modelling the biogeochemical effects of heterotrophic and autotrophic N2 fixation in the Gulf of Aqaba (Israel), Red Sea
Angela M. Kuhn
CORRESPONDING AUTHOR
Department of Oceanography, Dalhousie University, Halifax, B3H 4R2,
Canada
current address: Scripps Institution of Oceanography, University of California San
Diego, La Jolla, 92093-0021, USA
Katja Fennel
Department of Oceanography, Dalhousie University, Halifax, B3H 4R2,
Canada
Ilana Berman-Frank
Mina and Everard Goodman Faculty of Life Sciences, Bar Ilan
University, Ramat Gan, 5290002, Israel
current address: Leon H. Charney School of Marine Sciences, University of Haifa, Mt.
Carmel, Haifa, 3498838, Israel
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EGUsphere, https://doi.org/10.5194/egusphere-2025-3361, https://doi.org/10.5194/egusphere-2025-3361, 2025
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Surface ocean alkalinity enhancement, through the release of alkaline materials, is a technology that could increase the storage of anthropogenic carbon in the ocean. Halifax Harbour (Canada) is a current test site for operational alkalinity addition. Here, we present a model of Halifax Harbour that simulates alkalinity addition at various locations of the harbour and quantifies the resulting net CO2 uptake. The model can be relocated to study alkalinity addition in other coastal systems.
Lina Garcia-Suarez, Katja Fennel, Neha Mehendale, Tronje Peer Kemena, and David Peter Keller
EGUsphere, https://doi.org/10.22541/essoar.173758192.24328151/v2, https://doi.org/10.22541/essoar.173758192.24328151/v2, 2025
This preprint is open for discussion and under review for Ocean Science (OS).
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This study shows that regional ocean warming can make the Gulf Stream appear to shift north, even when its path remains stable in a changing climate. Temperature-based proxies, like the Gulf Stream North Wall, overestimate changes in its position. Methods based on sea surface height provide a more accurate view. These results help improve how we track changes in ocean currents and avoid misinterpreting signs of climate-related shifts.
Gianpiero Cossarini, Andrew Moore, Stefano Ciavatta, and Katja Fennel
State Planet, 5-opsr, 12, https://doi.org/10.5194/sp-5-opsr-12-2025, https://doi.org/10.5194/sp-5-opsr-12-2025, 2025
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Marine biogeochemistry refers to the cycling of chemical elements resulting from physical transport, chemical reaction, uptake, and processing by living organisms. Biogeochemical models can have a wide range of complexity, from a single nutrient to fully explicit representations of multiple nutrients, trophic levels, and functional groups. Uncertainty sources are the lack of knowledge about the parameterizations, the initial and boundary conditions, and the lack of observations.
Tom Reich, Natalia Belkin, Guy Sisma-Ventura, Hagar Hauzer, Maxim Rubin-Blum, Ilana Berman-Frank, and Eyal Rahav
EGUsphere, https://doi.org/10.5194/egusphere-2025-1445, https://doi.org/10.5194/egusphere-2025-1445, 2025
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Dark carbon fixation by chemoautotrophs take a vital part in marine primary productivity. Measured rates can be seen all the way down to the dark layers of the ocean and integrated in our study site come close to the magnitude of photosynthesis. It can also explain about ~35 % of the missing organic carbon supply needed by deep microbial communities. By using oceanographic observations and analysis this paper highlights the significant of this overlooked parameter.
Kyoko Ohashi, Arnaud Laurent, Christoph Renkl, Jinyu Sheng, Katja Fennel, and Eric Oliver
Geosci. Model Dev., 17, 8697–8733, https://doi.org/10.5194/gmd-17-8697-2024, https://doi.org/10.5194/gmd-17-8697-2024, 2024
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We developed a modelling system of the northwest Atlantic Ocean that simulates the currents, temperature, salinity, and parts of the biochemical cycle of the ocean, as well as sea ice. The system combines advanced, open-source models and can be used to study, for example, the ocean capture of atmospheric carbon dioxide, which is a key process in the global climate. The system produces realistic results, and we use it to investigate the roles of tides and sea ice in the northwest Atlantic Ocean.
Nir Haim, Vika Grigorieva, Rotem Soffer, Boaz Mayzel, Timor Katz, Ronen Alkalay, Eli Biton, Ayah Lazar, Hezi Gildor, Ilana Berman-Frank, Yishai Weinstein, Barak Herut, and Yaron Toledo
Earth Syst. Sci. Data, 16, 2659–2668, https://doi.org/10.5194/essd-16-2659-2024, https://doi.org/10.5194/essd-16-2659-2024, 2024
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This paper outlines the process of creating an open-access surface wave dataset, drawing from deep-sea research station observations located 50 km off the coast of Israel. The discussion covers the wave monitoring procedure, from instrument configuration to wave field retrieval, and aspects of quality assurance. The dataset presented spans over 5 years, offering uncommon in situ wave measurements in the deep sea, and addresses the existing gap in wave information within the region.
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.
Robert W. Izett, Katja Fennel, Adam C. Stoer, and David P. Nicholson
Biogeosciences, 21, 13–47, https://doi.org/10.5194/bg-21-13-2024, https://doi.org/10.5194/bg-21-13-2024, 2024
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This paper provides an overview of the capacity to expand the global coverage of marine primary production estimates using autonomous ocean-going instruments, called Biogeochemical-Argo floats. We review existing approaches to quantifying primary production using floats, provide examples of the current implementation of the methods, and offer insights into how they can be better exploited. This paper is timely, given the ongoing expansion of the Biogeochemical-Argo array.
Li-Qing Jiang, Adam V. Subhas, Daniela Basso, Katja Fennel, and Jean-Pierre Gattuso
State Planet, 2-oae2023, 13, https://doi.org/10.5194/sp-2-oae2023-13-2023, https://doi.org/10.5194/sp-2-oae2023-13-2023, 2023
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This paper provides comprehensive guidelines for ocean alkalinity enhancement (OAE) researchers on archiving their metadata and data. It includes data standards for various OAE studies and a universal metadata template. Controlled vocabularies for terms like alkalinization methods are included. These guidelines also apply to ocean acidification data.
Katja Fennel, Matthew C. Long, Christopher Algar, Brendan Carter, David Keller, Arnaud Laurent, Jann Paul Mattern, Ruth Musgrave, Andreas Oschlies, Josiane Ostiguy, Jaime B. Palter, and Daniel B. Whitt
State Planet, 2-oae2023, 9, https://doi.org/10.5194/sp-2-oae2023-9-2023, https://doi.org/10.5194/sp-2-oae2023-9-2023, 2023
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This paper describes biogeochemical models and modelling techniques for applications related to ocean alkalinity enhancement (OAE) research. Many of the most pressing OAE-related research questions cannot be addressed by observation alone but will require a combination of skilful models and observations. We present illustrative examples with references to further information; describe limitations, caveats, and future research needs; and provide practical recommendations.
Stefania A. Ciliberti, Enrique Alvarez Fanjul, Jay Pearlman, Kirsten Wilmer-Becker, Pierre Bahurel, Fabrice Ardhuin, Alain Arnaud, Mike Bell, Segolene Berthou, Laurent Bertino, Arthur Capet, Eric Chassignet, Stefano Ciavatta, Mauro Cirano, Emanuela Clementi, Gianpiero Cossarini, Gianpaolo Coro, Stuart Corney, Fraser Davidson, Marie Drevillon, Yann Drillet, Renaud Dussurget, Ghada El Serafy, Katja Fennel, Marcos Garcia Sotillo, Patrick Heimbach, Fabrice Hernandez, Patrick Hogan, Ibrahim Hoteit, Sudheer Joseph, Simon Josey, Pierre-Yves Le Traon, Simone Libralato, Marco Mancini, Pascal Matte, Angelique Melet, Yasumasa Miyazawa, Andrew M. Moore, Antonio Novellino, Andrew Porter, Heather Regan, Laia Romero, Andreas Schiller, John Siddorn, Joanna Staneva, Cecile Thomas-Courcoux, Marina Tonani, Jose Maria Garcia-Valdecasas, Jennifer Veitch, Karina von Schuckmann, Liying Wan, John Wilkin, and Romane Zufic
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Zhibo Shao, Yangchun Xu, Hua Wang, Weicheng Luo, Lice Wang, Yuhong Huang, Nona Sheila R. Agawin, Ayaz Ahmed, Mar Benavides, Mikkel Bentzon-Tilia, Ilana Berman-Frank, Hugo Berthelot, Isabelle C. Biegala, Mariana B. Bif, Antonio Bode, Sophie Bonnet, Deborah A. Bronk, Mark V. Brown, Lisa Campbell, Douglas G. Capone, Edward J. Carpenter, Nicolas Cassar, Bonnie X. Chang, Dreux Chappell, Yuh-ling Lee Chen, Matthew J. Church, Francisco M. Cornejo-Castillo, Amália Maria Sacilotto Detoni, Scott C. Doney, Cecile Dupouy, Marta Estrada, Camila Fernandez, Bieito Fernández-Castro, Debany Fonseca-Batista, Rachel A. Foster, Ken Furuya, Nicole Garcia, Kanji Goto, Jesús Gago, Mary R. Gradoville, M. Robert Hamersley, Britt A. Henke, Cora Hörstmann, Amal Jayakumar, Zhibing Jiang, Shuh-Ji Kao, David M. Karl, Leila R. Kittu, Angela N. Knapp, Sanjeev Kumar, Julie LaRoche, Hongbin Liu, Jiaxing Liu, Caroline Lory, Carolin R. Löscher, Emilio Marañón, Lauren F. Messer, Matthew M. Mills, Wiebke Mohr, Pia H. Moisander, Claire Mahaffey, Robert Moore, Beatriz Mouriño-Carballido, Margaret R. Mulholland, Shin-ichiro Nakaoka, Joseph A. Needoba, Eric J. Raes, Eyal Rahav, Teodoro Ramírez-Cárdenas, Christian Furbo Reeder, Lasse Riemann, Virginie Riou, Julie C. Robidart, Vedula V. S. S. Sarma, Takuya Sato, Himanshu Saxena, Corday Selden, Justin R. Seymour, Dalin Shi, Takuhei Shiozaki, Arvind Singh, Rachel E. Sipler, Jun Sun, Koji Suzuki, Kazutaka Takahashi, Yehui Tan, Weiyi Tang, Jean-Éric Tremblay, Kendra Turk-Kubo, Zuozhu Wen, Angelicque E. White, Samuel T. Wilson, Takashi Yoshida, Jonathan P. Zehr, Run Zhang, Yao Zhang, and Ya-Wei Luo
Earth Syst. Sci. Data, 15, 3673–3709, https://doi.org/10.5194/essd-15-3673-2023, https://doi.org/10.5194/essd-15-3673-2023, 2023
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N2 fixation by marine diazotrophs is an important bioavailable N source to the global ocean. This updated global oceanic diazotroph database increases the number of in situ measurements of N2 fixation rates, diazotrophic cell abundances, and nifH gene copy abundances by 184 %, 86 %, and 809 %, respectively. Using the updated database, the global marine N2 fixation rate is estimated at 223 ± 30 Tg N yr−1, which triplicates that using the original database.
Benjamin Richaud, Katja Fennel, Eric C. J. Oliver, Michael D. DeGrandpre, Timothée Bourgeois, Xianmin Hu, and Youyu Lu
The Cryosphere, 17, 2665–2680, https://doi.org/10.5194/tc-17-2665-2023, https://doi.org/10.5194/tc-17-2665-2023, 2023
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Sea ice is a dynamic carbon reservoir. Its seasonal growth and melt modify the carbonate chemistry in the upper ocean, with consequences for the Arctic Ocean carbon sink. Yet, the importance of this process is poorly quantified. Using two independent approaches, this study provides new methods to evaluate the error in air–sea carbon flux estimates due to the lack of biogeochemistry in ice in earth system models. Those errors range from 5 % to 30 %, depending on the model and climate projection.
Arnaud Laurent, Haiyan Zhang, and Katja Fennel
Biogeosciences, 19, 5893–5910, https://doi.org/10.5194/bg-19-5893-2022, https://doi.org/10.5194/bg-19-5893-2022, 2022
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The Changjiang is the main terrestrial source of nutrients to the East China Sea (ECS). Nutrient delivery to the ECS has been increasing since the 1960s, resulting in low oxygen (hypoxia) during phytoplankton decomposition in summer. River phosphorus (P) has increased less than nitrogen, and therefore, despite the large nutrient delivery, phytoplankton growth can be limited by the lack of P. Here, we investigate this link between P limitation, phytoplankton production/decomposition, and hypoxia.
Krysten Rutherford, Katja Fennel, Dariia Atamanchuk, Douglas Wallace, and Helmuth Thomas
Biogeosciences, 18, 6271–6286, https://doi.org/10.5194/bg-18-6271-2021, https://doi.org/10.5194/bg-18-6271-2021, 2021
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Using a regional model of the northwestern North Atlantic shelves in combination with a surface water time series and repeat transect observations, we investigate surface CO2 variability on the Scotian Shelf. The study highlights a strong seasonal cycle in shelf-wide pCO2 and spatial variability throughout the summer months driven by physical events. The simulated net flux of CO2 on the Scotian Shelf is out of the ocean, deviating from the global air–sea CO2 flux trend in continental shelves.
Bin Wang, Katja Fennel, and Liuqian Yu
Ocean Sci., 17, 1141–1156, https://doi.org/10.5194/os-17-1141-2021, https://doi.org/10.5194/os-17-1141-2021, 2021
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We demonstrate that even sparse BGC-Argo profiles can substantially improve biogeochemical prediction via a priori model tuning. By assimilating satellite surface chlorophyll and physical observations, subsurface distributions of physical properties and nutrients were improved immediately. The improvement of subsurface chlorophyll was modest initially but was greatly enhanced after adjusting the parameterization for light attenuation through further a priori tuning.
Thomas S. Bianchi, Madhur Anand, Chris T. Bauch, Donald E. Canfield, Luc De Meester, Katja Fennel, Peter M. Groffman, Michael L. Pace, Mak Saito, and Myrna J. Simpson
Biogeosciences, 18, 3005–3013, https://doi.org/10.5194/bg-18-3005-2021, https://doi.org/10.5194/bg-18-3005-2021, 2021
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Better development of interdisciplinary ties between biology, geology, and chemistry advances biogeochemistry through (1) better integration of contemporary (or rapid) evolutionary adaptation to predict changing biogeochemical cycles and (2) universal integration of data from long-term monitoring sites in terrestrial, aquatic, and human systems that span broad geographical regions for use in modeling.
Arnaud Laurent, Katja Fennel, and Angela Kuhn
Biogeosciences, 18, 1803–1822, https://doi.org/10.5194/bg-18-1803-2021, https://doi.org/10.5194/bg-18-1803-2021, 2021
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CMIP5 and CMIP6 models, and a high-resolution regional model, were evaluated by comparing historical simulations with observations in the northwest North Atlantic, a climate-sensitive and biologically productive ocean margin region. Many of the CMIP models performed poorly for biological properties. There is no clear link between model resolution and skill in the global models, but there is an overall improvement in performance in CMIP6 from CMIP5. The regional model performed best.
Haiyan Zhang, Katja Fennel, Arnaud Laurent, and Changwei Bian
Biogeosciences, 17, 5745–5761, https://doi.org/10.5194/bg-17-5745-2020, https://doi.org/10.5194/bg-17-5745-2020, 2020
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In coastal seas, low oxygen, which is detrimental to coastal ecosystems, is increasingly caused by man-made nutrients from land. This is especially so near mouths of major rivers, including the Changjiang in the East China Sea. Here a simulation model is used to identify the main factors determining low-oxygen conditions in the region. High river discharge is identified as the prime cause, while wind and intrusions of open-ocean water modulate the severity and extent of low-oxygen conditions.
Christopher Gordon, Katja Fennel, Clark Richards, Lynn K. Shay, and Jodi K. Brewster
Biogeosciences, 17, 4119–4134, https://doi.org/10.5194/bg-17-4119-2020, https://doi.org/10.5194/bg-17-4119-2020, 2020
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We describe a method for correcting errors in oxygen optode measurements on autonomous platforms in the ocean. The errors result from the relatively slow response time of the sensor. The correction method includes an in situ determination of the effective response time and requires the time stamps of the individual measurements. It is highly relevant for the BGC-Argo program and also applicable to gliders. We also explore if diurnal changes in oxygen can be obtained from profiling floats.
Bin Wang, Katja Fennel, Liuqian Yu, and Christopher Gordon
Biogeosciences, 17, 4059–4074, https://doi.org/10.5194/bg-17-4059-2020, https://doi.org/10.5194/bg-17-4059-2020, 2020
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We assess trade-offs between different types of biological observations, specifically satellite ocean color and BGC-Argo profiles and the benefits of combining both for optimizing a biogeochemical model of the Gulf of Mexico. Using all available observations leads to significant improvements in observed and unobserved variables (including primary production and C export). Our results highlight the significant benefits of BGC-Argo measurements for biogeochemical model optimization and validation.
Fabian Große, Katja Fennel, Haiyan Zhang, and Arnaud Laurent
Biogeosciences, 17, 2701–2714, https://doi.org/10.5194/bg-17-2701-2020, https://doi.org/10.5194/bg-17-2701-2020, 2020
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In the East China Sea, hypoxia occurs frequently from spring to fall due to high primary production and subsequent decomposition of organic matter. Nitrogen inputs from the Changjiang and the open ocean have been suggested to contribute to hypoxia formation. We used a numerical modelling approach to quantify the relative contributions of these nitrogen sources. We found that the Changjiang dominates, which suggests that nitrogen management in the watershed would improve oxygen conditions.
Liuqian Yu, Katja Fennel, Bin Wang, Arnaud Laurent, Keith R. Thompson, and Lynn K. Shay
Ocean Sci., 15, 1801–1814, https://doi.org/10.5194/os-15-1801-2019, https://doi.org/10.5194/os-15-1801-2019, 2019
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We present a first direct comparison of nonidentical versus identical twin approaches for an ocean data assimilation system. We show that the identical twin approach overestimates the value of assimilating satellite observations and undervalues the benefit of assimilating temperature and salinity profiles. Misleading assessments such as undervaluing the impact of observational assets are problematic and can lead to misguided decisions on balancing investments among different observing assets.
Katja Fennel, Simone Alin, Leticia Barbero, Wiley Evans, Timothée Bourgeois, Sarah Cooley, John Dunne, Richard A. Feely, Jose Martin Hernandez-Ayon, Xinping Hu, Steven Lohrenz, Frank Muller-Karger, Raymond Najjar, Lisa Robbins, Elizabeth Shadwick, Samantha Siedlecki, Nadja Steiner, Adrienne Sutton, Daniela Turk, Penny Vlahos, and Zhaohui Aleck Wang
Biogeosciences, 16, 1281–1304, https://doi.org/10.5194/bg-16-1281-2019, https://doi.org/10.5194/bg-16-1281-2019, 2019
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We review and synthesize available information on coastal ocean carbon fluxes around North America (NA). There is overwhelming evidence, compiled and discussed here, that the NA coastal margins act as a sink. Our synthesis shows the great diversity in processes driving carbon fluxes in different coastal regions, highlights remaining gaps in observations and models, and discusses current and anticipated future trends with respect to carbon fluxes and acidification.
Krysten Rutherford and Katja Fennel
Ocean Sci., 14, 1207–1221, https://doi.org/10.5194/os-14-1207-2018, https://doi.org/10.5194/os-14-1207-2018, 2018
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Using a regional model of the northwestern North Atlantic shelves, we calculate transport timescales and pathways in order to understand the transport processes that underlie the rapid oxygen loss, air–sea CO2 flux, and supply of plankton seed populations on the Scotian Shelf. Study results highlight the limited connectivity between the Scotian Shelf and adjacent slope waters; instead, the dominant southwestward currents bring Grand Banks and Gulf of St. Lawrence waters to the Scotian Shelf.
Dina Spungin, Natalia Belkin, Rachel A. Foster, Marcus Stenegren, Andrea Caputo, Mireille Pujo-Pay, Nathalie Leblond, Cécile Dupouy, Sophie Bonnet, and Ilana Berman-Frank
Biogeosciences, 15, 3893–3908, https://doi.org/10.5194/bg-15-3893-2018, https://doi.org/10.5194/bg-15-3893-2018, 2018
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The way marine organisms die can determine the fate of organic matter (OM) in the ocean. We investigated whether a form of auto-induced programmed cell death (PCD) influenced phytoplankton mortality and fate of OM. Our results from high biomass blooms of the cyanobacterium Trichodesmium show evidence for PCD and high production of sticky carbon material termed transparent exopolymeric particles (TEP) that facilitates cellular aggregation and enhances the vertical flux of OM to depth.
Katja Fennel and Arnaud Laurent
Biogeosciences, 15, 3121–3131, https://doi.org/10.5194/bg-15-3121-2018, https://doi.org/10.5194/bg-15-3121-2018, 2018
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Increasing human-derived nutrient inputs to coastal oceans lead to spreading dead zones around the world. Here a biogeochemical model for the northern Gulf of Mexico, where nutrients from the Mississippi River create the largest dead zone in North American coastal waters, is used for the first time to show the effects of single and dual nutrient reductions of nitrogen (N) and phosphorus (P). Significant reductions in N or N&P load would be required to significantly reduce hypoxia in this system.
Jonathan Lemay, Helmuth Thomas, Susanne E. Craig, William J. Burt, Katja Fennel, and Blair J. W. Greenan
Biogeosciences, 15, 2111–2123, https://doi.org/10.5194/bg-15-2111-2018, https://doi.org/10.5194/bg-15-2111-2018, 2018
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We report a detailed mechanistic investigation of the impact of Hurricane Arthur on the CO2 cycling on the Scotian Shelf. We can show that in contrast to common thinking, the deepening of the surface during the summer months can lead to increased CO2 uptake as carbon-poor waters from subsurface water are brought up to the surface. Only during prolonged storm events is the deepening of the mixed layer strong enough to bring the (expected) carbon-rich water to the surface.
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.
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.
Dina Spungin, Ulrike Pfreundt, Hugo Berthelot, Sophie Bonnet, Dina AlRoumi, Frank Natale, Wolfgang R. Hess, Kay D. Bidle, and Ilana Berman-Frank
Biogeosciences, 13, 4187–4203, https://doi.org/10.5194/bg-13-4187-2016, https://doi.org/10.5194/bg-13-4187-2016, 2016
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The marine cyanobacterium Trichodesmium spp. forms massive blooms important to carbon and nitrogen cycling in the oceans that often collapse abruptly. We investigated a Trichodesmium bloom in the lagoon waters of New Caledonia to specifically elucidate the cellular processes mediating the bloom decline. We demonstrate physiological, biochemical, and genetic evidence for nutrient and oxidative stress that induced a genetically controlled programmed cell death (PCD) pathway leading to bloom demise.
Ulrike Pfreundt, Dina Spungin, Sophie Bonnet, Ilana Berman-Frank, and Wolfgang R. Hess
Biogeosciences, 13, 4135–4149, https://doi.org/10.5194/bg-13-4135-2016, https://doi.org/10.5194/bg-13-4135-2016, 2016
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The VAHINE experiment in the New Caledonia lagoon (SW Pacific) targeted the dynamics of nutrient pools and fluxes, N2 fixation, and the composition and productivity of the microbial communities. To connect this information to the actual activities of diverse microbial taxa, we present the analysis of the community-wide gene expression for 23 days. The results from this experiment provide insight into the microbial activities in a low-nutrient, low-chlorophyll ecosystem and within a mesocosm.
Ilana Berman-Frank, Dina Spungin, Eyal Rahav, France Van Wambeke, Kendra Turk-Kubo, and Thierry Moutin
Biogeosciences, 13, 3793–3805, https://doi.org/10.5194/bg-13-3793-2016, https://doi.org/10.5194/bg-13-3793-2016, 2016
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In the marine environment, sticky sugar-containing gels, termed transparent exopolymeric particles (TEP), are produced from biological sources and physical and chemical processes. These compounds are essential vectors enhancing downward flow of organic matter and its storage at depth. Spatial and temporal dynamics of TEPs were followed for 23 days during the VAHINE mesocosm experiment that investigated the fate of nitrogen and carbon derived from organisms fixing atmospheric N2 (diazotrophs).
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.
L. Yu, K. Fennel, A. Laurent, M. C. Murrell, and J. C. Lehrter
Biogeosciences, 12, 2063–2076, https://doi.org/10.5194/bg-12-2063-2015, https://doi.org/10.5194/bg-12-2063-2015, 2015
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Our study suggests that a combination of physical processes and sediment oxygen consumption determine the spatial extent and temporal dynamics of hypoxia on the Louisiana shelf. In summer, stratification isolates oxygen-rich surface waters from hypoxic bottom waters; oxygen outgasses to the atmosphere at this time. A large fraction of primary production occurs below the pycnocline in summer, but this primary production does not strongly affect the spatial extent of hypoxic bottom waters.
K.-K. Liu, C.-K. Kang, T. Kobari, H. Liu, C. Rabouille, and K. Fennel
Biogeosciences, 11, 7061–7075, https://doi.org/10.5194/bg-11-7061-2014, https://doi.org/10.5194/bg-11-7061-2014, 2014
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This paper provides background info on the East China Sea, Japan/East Sea and South China Sea and highlights major findings in the special issue on their biogeochemical conditions and ecosystem functions. The three seas are subject to strong impacts from human activities and/or climate forcing. Because these continental margins sustain arguably some of the most productive marine ecosystems in the world, changes in these stressed ecosystems may threaten the livelihood of a large human population.
Z. Xue, R. He, K. Fennel, W.-J. Cai, S. Lohrenz, and C. Hopkinson
Biogeosciences, 10, 7219–7234, https://doi.org/10.5194/bg-10-7219-2013, https://doi.org/10.5194/bg-10-7219-2013, 2013
E. Rahav, B. Herut, M. R. Mulholland, B. Voß, D. Stazic, C. Steglich, W. R. Hess, and I. Berman-Frank
Biogeosciences Discuss., https://doi.org/10.5194/bgd-10-10327-2013, https://doi.org/10.5194/bgd-10-10327-2013, 2013
Revised manuscript has not been submitted
E. Rahav, B. Herut, A. Levi, M. R. Mulholland, and I. Berman-Frank
Ocean Sci., 9, 489–498, https://doi.org/10.5194/os-9-489-2013, https://doi.org/10.5194/os-9-489-2013, 2013
W. J. Burt, H. Thomas, K. Fennel, and E. Horne
Biogeosciences, 10, 53–66, https://doi.org/10.5194/bg-10-53-2013, https://doi.org/10.5194/bg-10-53-2013, 2013
Related subject area
Biogeochemistry: Modelling, Aquatic
Acidification, warming, and nutrient management are projected to cause reductions in shell and tissue weights of oysters in a coastal plain estuary
Modeling the contribution of micronekton diel vertical migrations to carbon export in the mesopelagic zone
Mixing, spatial resolution and argon saturation in a suite of coupled general ocean circulation biogeochemical models off Mauritania
Optimisation of the World Ocean Model of Biogeochemistry and Trophic-dynamics (WOMBAT) using surrogate machine learning methods
Efficiency metrics for ocean alkalinity enhancements under responsive and prescribed atmospheric pCO2 conditions
Changes in Arctic Ocean plankton community structure and trophic dynamics on seasonal to interannual timescales
Global impact of benthic denitrification on marine N2 fixation and primary production simulated by a variable-stoichiometry Earth system model
Killing the predator: impacts of highest-predator mortality on the global-ocean ecosystem structure
Hydrodynamic and biochemical impacts on the development of hypoxia in the Louisiana–Texas shelf – Part 1: roles of nutrient limitation and plankton community
Validation of the coupled physical–biogeochemical ocean model NEMO–SCOBI for the North Sea–Baltic Sea system
Investigating ecosystem connections in the shelf sea environment using complex networks
Seasonal and interannual variability of the pelagic ecosystem and of the organic carbon budget in the Rhodes Gyre (eastern Mediterranean): influence of winter mixing
How much do bacterial growth properties and biodegradable dissolved organic matter control water quality at low flow?
Methane emissions from Arctic landscapes during 2000–2015: an analysis with land and lake biogeochemistry models
Including filter-feeding gelatinous macrozooplankton in a global marine biogeochemical model: model–data comparison and impact on the ocean carbon cycle
Riverine impact on future projections of marine primary production and carbon uptake
Subsurface oxygen maximum in oligotrophic marine ecosystems: mapping the interaction between physical and biogeochemical processes
Quantifying biological carbon pump pathways with a data-constrained mechanistic model ensemble approach
Assessing the spatial and temporal variability of methylmercury biogeochemistry and bioaccumulation in the Mediterranean Sea with a coupled 3D model
Hydrodynamic and biochemical impacts on the development of hypoxia in the Louisiana–Texas shelf – Part 2: statistical modeling and hypoxia prediction
Modelling the effects of benthic fauna on carbon, nitrogen and phosphorus dynamics in the Baltic Sea
Improved prediction of dimethyl sulfide (DMS) distributions in the northeast subarctic Pacific using machine-learning algorithms
Nutrient transport and transformation in macrotidal estuaries of the French Atlantic coast: a modeling approach using the Carbon-Generic Estuarine Model
A modelling study of temporal and spatial pCO2 variability on the biologically active and temperature-dominated Scotian Shelf
Modeling the marine chromium cycle: new constraints on global-scale processes
New insights into large-scale trends of apparent organic matter reactivity in marine sediments and patterns of benthic carbon transformation
Evaluation of ocean dimethylsulfide concentration and emission in CMIP6 models
Zooplankton mortality effects on the plankton community of the northern Humboldt Current System: sensitivity of a regional biogeochemical model
Multi-compartment kinetic–allometric (MCKA) model of radionuclide bioaccumulation in marine fish
Impact of bottom trawling on sediment biogeochemistry: a modelling approach
Cyanobacteria blooms in the Baltic Sea: a review of models and facts
Arctic Ocean acidification over the 21st century co-driven by anthropogenic carbon increases and freshening in the CMIP6 model ensemble
Modeling silicate–nitrate–ammonium co-limitation of algal growth and the importance of bacterial remineralization based on an experimental Arctic coastal spring bloom culture study
Role of jellyfish in the plankton ecosystem revealed using a global ocean biogeochemical model
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
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
Catherine R. Czajka, Marjorie A. M. Friedrichs, Emily B. Rivest, Pierre St-Laurent, Mark J. Brush, and Fei Da
Biogeosciences, 22, 3181–3206, https://doi.org/10.5194/bg-22-3181-2025, https://doi.org/10.5194/bg-22-3181-2025, 2025
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Under future acidification, warming, and nutrient management, substantial reductions in shell and tissue weights of Eastern oysters are projected for the Chesapeake Bay. Lower oyster growth rates will be largely driven by reduced calcium carbonate saturation states and reduced food availability. Oyster aquaculture practices in the region will likely be affected, with site selection becoming increasingly important as impacts will be highly spatially variable.
Hélène Thibault, Frédéric Ménard, Jeanne Abitbol-Spangaro, Jean-Christophe Poggiale, and Séverine Martini
Biogeosciences, 22, 2181–2200, https://doi.org/10.5194/bg-22-2181-2025, https://doi.org/10.5194/bg-22-2181-2025, 2025
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Micronekton significantly impact oceanic carbon transport yet are often overlooked. Using a trait-based model, we simulated their diel vertical migrations and carbon production, revealing size, taxonomy, light, and primary production as key factors. In temperate regions, micronekton greatly influenced the transport efficiency in summer. Future research must focus on micronekton metabolism and dynamics, considering global warming and their potential exploitation.
Heiner Dietze and Ulrike Löptien
Biogeosciences, 22, 1215–1236, https://doi.org/10.5194/bg-22-1215-2025, https://doi.org/10.5194/bg-22-1215-2025, 2025
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We introduce argon saturation as a prognostic variable in a suite of coupled general ocean circulation biogeochemical models off Mauritania. Our results indicate that the effect of increasing the spatial horizontal model resolutions from 12 km to 1.5 km leads to changes comparable to other infamous spurious effects of state-of-the-art numerical advection numerics.
Pearse James Buchanan, P. Jyoteeshkumar Reddy, Richard J. Matear, Matthew A. Chamberlain, Tyler Rohr, Dougal Squire, and Elizabeth H. Shadwick
EGUsphere, https://doi.org/10.5194/egusphere-2024-4026, https://doi.org/10.5194/egusphere-2024-4026, 2025
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We developed a cost-effective method to improve ocean models for studying the global carbon cycle. Using machine learning, we optimized parameters in the WOMBAT-lite model, enhancing its accuracy in predicting chlorophyll levels, air-sea carbon dioxide exchange, and phytoplankton nutrient use. This approach increases model reliability and offers a pathway for scientists to better understand and predict ocean changes, contributing to improved insights into Earth's climate system.
Michael D. Tyka
Biogeosciences, 22, 341–353, https://doi.org/10.5194/bg-22-341-2025, https://doi.org/10.5194/bg-22-341-2025, 2025
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Marine CO2 removal (mCDR) is a promising technology for removing legacy emissions from the atmosphere. Its indirect nature makes it difficult to assess experimentally; instead one relies heavily on simulation. Many past papers have treated the atmosphere as non-responsive to the intervention studied. We show that even under these simplified assumptions, the increase in ocean CO2 inventory is equal to the equivalent quantity of direct CO2 removals occurring over time, in a realistic atmosphere.
Gabriela Negrete-García, Jessica Y. Luo, Colleen M. Petrik, Manfredi Manizza, and Andrew D. Barton
Biogeosciences, 21, 4951–4973, https://doi.org/10.5194/bg-21-4951-2024, https://doi.org/10.5194/bg-21-4951-2024, 2024
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The Arctic Ocean experiences significant seasonal and year-to-year changes, impacting marine plankton populations. Using a plankton community model, we studied these effects on plankton communities and their influence on fish production. Our findings revealed earlier plankton blooms, shifts towards more carnivorous zooplankton, and increased fishery potential during summertime, especially in warmer years with less ice, highlighting the delicate balance of Arctic ecosystems.
Na Li, Christopher J. Somes, Angela Landolfi, Chia-Te Chien, Markus Pahlow, and Andreas Oschlies
Biogeosciences, 21, 4361–4380, https://doi.org/10.5194/bg-21-4361-2024, https://doi.org/10.5194/bg-21-4361-2024, 2024
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N is a crucial nutrient that limits phytoplankton growth in large ocean areas. The amount of oceanic N is governed by the balance of N2 fixation and denitrification. Here we incorporate benthic denitrification into an Earth system model with variable particulate stoichiometry. Our model compares better to the observed surface nutrient distributions, marine N2 fixation, and primary production. Benthic denitrification plays an important role in marine N and C cycling and hence the global climate.
David Talmy, Eric Carr, Harshana Rajakaruna, Selina Våge, and Anne Willem Omta
Biogeosciences, 21, 2493–2507, https://doi.org/10.5194/bg-21-2493-2024, https://doi.org/10.5194/bg-21-2493-2024, 2024
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The structure of plankton communities is central to global cycles of carbon, nitrogen, and other elements. This study explored the sensitivity of different assumptions about highest-predator mortality in ecosystem models with contrasting food web structures. In the context of environmental data, we find support for models assuming a density-dependent mortality of the highest predator, irrespective of assumed food web structure.
Yanda Ou and Z. George Xue
Biogeosciences, 21, 2385–2424, https://doi.org/10.5194/bg-21-2385-2024, https://doi.org/10.5194/bg-21-2385-2024, 2024
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Developed for the Gulf of Mexico (2006–2020), a 3D hydrodynamic–biogeochemical model validated against in situ data reveals the impact of nutrients and plankton diversity on dissolved oxygen dynamics. It highlights the role of physical processes, sediment oxygen consumption, and nutrient distribution in shaping bottom oxygen levels and hypoxia. The model underscores the importance of complex plankton interactions for understanding primary production and hypoxia evolution.
Itzel Ruvalcaba Baroni, Elin Almroth-Rosell, Lars Axell, Sam T. Fredriksson, Jenny Hieronymus, Magnus Hieronymus, Sandra-Esther Brunnabend, Matthias Gröger, Ivan Kuznetsov, Filippa Fransner, Robinson Hordoir, Saeed Falahat, and Lars Arneborg
Biogeosciences, 21, 2087–2132, https://doi.org/10.5194/bg-21-2087-2024, https://doi.org/10.5194/bg-21-2087-2024, 2024
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The health of the Baltic and North seas is threatened due to high anthropogenic pressure; thus, different methods to assess the status of these regions are urgently needed. Here, we validated a novel model simulating the ocean dynamics and biogeochemistry of the Baltic and North seas that can be used to create future climate and nutrient scenarios, contribute to European initiatives on de-eutrophication, and provide water quality advice and support on nutrient load reductions for both seas.
Ieuan Higgs, Jozef Skákala, Ross Bannister, Alberto Carrassi, and Stefano Ciavatta
Biogeosciences, 21, 731–746, https://doi.org/10.5194/bg-21-731-2024, https://doi.org/10.5194/bg-21-731-2024, 2024
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A complex network is a way of representing which parts of a system are connected to other parts. We have constructed a complex network based on an ecosystem–ocean model. From this, we can identify patterns in the structure and areas of similar behaviour. This can help to understand how natural, or human-made, changes will affect the shelf sea ecosystem, and it can be used in multiple future applications such as improving modelling, data assimilation, or machine learning.
Joelle Habib, Caroline Ulses, Claude Estournel, Milad Fakhri, Patrick Marsaleix, Mireille Pujo-Pay, Marine Fourrier, Laurent Coppola, Alexandre Mignot, Laurent Mortier, and Pascal Conan
Biogeosciences, 20, 3203–3228, https://doi.org/10.5194/bg-20-3203-2023, https://doi.org/10.5194/bg-20-3203-2023, 2023
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The Rhodes Gyre, eastern Mediterranean Sea, is the main Levantine Intermediate Water formation site. In this study, we use a 3D physical–biogeochemical model to investigate the seasonal and interannual variability of organic carbon dynamics in the gyre. Our results show its autotrophic nature and its high interannual variability, with enhanced primary production, downward exports, and onward exports to the surrounding regions during years marked by intense heat losses and deep mixed layers.
Masihullah Hasanyar, Thomas Romary, Shuaitao Wang, and Nicolas Flipo
Biogeosciences, 20, 1621–1633, https://doi.org/10.5194/bg-20-1621-2023, https://doi.org/10.5194/bg-20-1621-2023, 2023
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The results of this study indicate that biodegradable dissolved organic matter is responsible for oxygen depletion at low flow during summer seasons when heterotrophic bacterial activity is so intense. Therefore, the dissolved organic matter must be well measured in the water monitoring networks in order to have more accurate water quality models. It also advocates for high-frequency data collection for better quantification of the uncertainties related to organic matter.
Xiangyu Liu and Qianlai Zhuang
Biogeosciences, 20, 1181–1193, https://doi.org/10.5194/bg-20-1181-2023, https://doi.org/10.5194/bg-20-1181-2023, 2023
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We are among the first to quantify methane emissions from inland water system in the pan-Arctic. The total CH4 emissions are 36.46 Tg CH4 yr−1 during 2000–2015, of which wetlands and lakes were 21.69 Tg yr−1 and 14.76 Tg yr−1, respectively. By using two non-overlap area change datasets with land and lake models, our simulation avoids small lakes being counted twice as both lake and wetland, and it narrows the gap between two different methods used to quantify regional CH4 emissions.
Corentin Clerc, Laurent Bopp, Fabio Benedetti, Meike Vogt, and Olivier Aumont
Biogeosciences, 20, 869–895, https://doi.org/10.5194/bg-20-869-2023, https://doi.org/10.5194/bg-20-869-2023, 2023
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Gelatinous zooplankton play a key role in the ocean carbon cycle. In particular, pelagic tunicates, which feed on a wide size range of prey, produce rapidly sinking detritus. Thus, they efficiently transfer carbon from the surface to the depths. Consequently, we added these organisms to a marine biogeochemical model (PISCES-v2) and evaluated their impact on the global carbon cycle. We found that they contribute significantly to carbon export and that this contribution increases with depth.
Shuang Gao, Jörg Schwinger, Jerry Tjiputra, Ingo Bethke, Jens Hartmann, Emilio Mayorga, and Christoph Heinze
Biogeosciences, 20, 93–119, https://doi.org/10.5194/bg-20-93-2023, https://doi.org/10.5194/bg-20-93-2023, 2023
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We assess the impact of riverine nutrients and carbon (C) on projected marine primary production (PP) and C uptake using a fully coupled Earth system model. Riverine inputs alleviate nutrient limitation and thus lessen the projected PP decline by up to 0.7 Pg C yr−1 globally. The effect of increased riverine C may be larger than the effect of nutrient inputs in the future on the projected ocean C uptake, while in the historical period increased nutrient inputs are considered the largest driver.
Valeria Di Biagio, Stefano Salon, Laura Feudale, and Gianpiero Cossarini
Biogeosciences, 19, 5553–5574, https://doi.org/10.5194/bg-19-5553-2022, https://doi.org/10.5194/bg-19-5553-2022, 2022
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The amount of dissolved oxygen in the ocean is the result of interacting physical and biological processes. Oxygen vertical profiles show a subsurface maximum in a large part of the ocean. We used a numerical model to map this subsurface maximum in the Mediterranean Sea and to link local differences in its properties to the driving processes. This emerging feature can help the marine ecosystem functioning to be better understood, also under the impacts of climate change.
Michael R. Stukel, Moira Décima, and Michael R. Landry
Biogeosciences, 19, 3595–3624, https://doi.org/10.5194/bg-19-3595-2022, https://doi.org/10.5194/bg-19-3595-2022, 2022
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The biological carbon pump (BCP) transports carbon into the deep ocean, leading to long-term marine carbon sequestration. It is driven by many physical, chemical, and ecological processes. We developed a model of the BCP constrained using data from 11 cruises in 4 different ocean regions. Our results show that sinking particles and vertical mixing are more important than transport mediated by vertically migrating zooplankton. They also highlight the uncertainty in current estimates of the BCP.
Ginevra Rosati, Donata Canu, Paolo Lazzari, and Cosimo Solidoro
Biogeosciences, 19, 3663–3682, https://doi.org/10.5194/bg-19-3663-2022, https://doi.org/10.5194/bg-19-3663-2022, 2022
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Methylmercury (MeHg) is produced and bioaccumulated in marine food webs, posing concerns for human exposure through seafood consumption. We modeled and analyzed the fate of MeHg in the lower food web of the Mediterranean Sea. The modeled spatial–temporal distribution of plankton bioaccumulation differs from the distribution of MeHg in surface water. We also show that MeHg exposure concentrations in temperate waters can be lowered by winter convection, which is declining due to climate change.
Yanda Ou, Bin Li, and Z. George Xue
Biogeosciences, 19, 3575–3593, https://doi.org/10.5194/bg-19-3575-2022, https://doi.org/10.5194/bg-19-3575-2022, 2022
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Over the past decades, the Louisiana–Texas shelf has been suffering recurring hypoxia (dissolved oxygen < 2 mg L−1). We developed a novel prediction model using state-of-the-art statistical techniques based on physical and biogeochemical data provided by a numerical model. The model can capture both the magnitude and onset of the annual hypoxia events. This study also demonstrates that it is possible to use a global model forecast to predict regional ocean water quality.
Eva Ehrnsten, Oleg Pavlovitch Savchuk, and Bo Gustav Gustafsson
Biogeosciences, 19, 3337–3367, https://doi.org/10.5194/bg-19-3337-2022, https://doi.org/10.5194/bg-19-3337-2022, 2022
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We studied the effects of benthic fauna, animals living on or in the seafloor, on the biogeochemical cycles of carbon, nitrogen and phosphorus using a model of the Baltic Sea ecosystem. By eating and excreting, the animals transform a large part of organic matter sinking to the seafloor into inorganic forms, which fuel plankton blooms. Simultaneously, when they move around (bioturbate), phosphorus is bound in the sediments. This reduces nitrogen-fixing plankton blooms and oxygen depletion.
Brandon J. McNabb and Philippe D. Tortell
Biogeosciences, 19, 1705–1721, https://doi.org/10.5194/bg-19-1705-2022, https://doi.org/10.5194/bg-19-1705-2022, 2022
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The trace gas dimethyl sulfide (DMS) plays an important role in the ocean sulfur cycle and can also influence Earth’s climate. Our study used two statistical methods to predict surface ocean concentrations and rates of sea–air exchange of DMS in the northeast subarctic Pacific. Our results show improved predictive power over previous approaches and suggest that nutrient availability, light-dependent processes, and physical mixing may be important controls on DMS in this region.
Xi Wei, Josette Garnier, Vincent Thieu, Paul Passy, Romain Le Gendre, Gilles Billen, Maia Akopian, and Goulven Gildas Laruelle
Biogeosciences, 19, 931–955, https://doi.org/10.5194/bg-19-931-2022, https://doi.org/10.5194/bg-19-931-2022, 2022
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Estuaries are key reactive ecosystems along the land–ocean aquatic continuum and are often strongly impacted by anthropogenic activities. We calculated nutrient in and out fluxes by using a 1-D transient model for seven estuaries along the French Atlantic coast. Among these, large estuaries with high residence times showed higher retention rates than medium and small ones. All reveal coastal eutrophication due to the excess of diffused nitrogen from intensive agricultural river basins.
Krysten Rutherford, Katja Fennel, Dariia Atamanchuk, Douglas Wallace, and Helmuth Thomas
Biogeosciences, 18, 6271–6286, https://doi.org/10.5194/bg-18-6271-2021, https://doi.org/10.5194/bg-18-6271-2021, 2021
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Using a regional model of the northwestern North Atlantic shelves in combination with a surface water time series and repeat transect observations, we investigate surface CO2 variability on the Scotian Shelf. The study highlights a strong seasonal cycle in shelf-wide pCO2 and spatial variability throughout the summer months driven by physical events. The simulated net flux of CO2 on the Scotian Shelf is out of the ocean, deviating from the global air–sea CO2 flux trend in continental shelves.
Frerk Pöppelmeier, David J. Janssen, Samuel L. Jaccard, and Thomas F. Stocker
Biogeosciences, 18, 5447–5463, https://doi.org/10.5194/bg-18-5447-2021, https://doi.org/10.5194/bg-18-5447-2021, 2021
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Chromium (Cr) is a redox-sensitive element that holds promise as a tracer of ocean oxygenation and biological activity. We here implemented the oxidation states Cr(III) and Cr(VI) in the Bern3D model to investigate the processes that shape the global Cr distribution. We find a Cr ocean residence time of 5–8 kyr and that the benthic source dominates the tracer budget. Further, regional model–data mismatches suggest strong Cr removal in oxygen minimum zones and a spatially variable benthic source.
Felipe S. Freitas, Philip A. Pika, Sabine Kasten, Bo B. Jørgensen, Jens Rassmann, Christophe Rabouille, Shaun Thomas, Henrik Sass, Richard D. Pancost, and Sandra Arndt
Biogeosciences, 18, 4651–4679, https://doi.org/10.5194/bg-18-4651-2021, https://doi.org/10.5194/bg-18-4651-2021, 2021
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It remains challenging to fully understand what controls carbon burial in marine sediments globally. Thus, we use a model–data approach to identify patterns of organic matter reactivity at the seafloor across distinct environmental conditions. Our findings support the notion that organic matter reactivity is a dynamic ecosystem property and strongly influences biogeochemical cycling and exchange. Our results are essential to improve predictions of future changes in carbon cycling and climate.
Josué Bock, Martine Michou, Pierre Nabat, Manabu Abe, Jane P. Mulcahy, Dirk J. L. Olivié, Jörg Schwinger, Parvadha Suntharalingam, Jerry Tjiputra, Marco van Hulten, Michio Watanabe, Andrew Yool, and Roland Séférian
Biogeosciences, 18, 3823–3860, https://doi.org/10.5194/bg-18-3823-2021, https://doi.org/10.5194/bg-18-3823-2021, 2021
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In this study we analyse surface ocean dimethylsulfide (DMS) concentration and flux to the atmosphere from four CMIP6 Earth system models over the historical and ssp585 simulations.
Our analysis of contemporary (1980–2009) climatologies shows that models better reproduce observations in mid to high latitudes. The models disagree on the sign of the trend of the global DMS flux from 1980 onwards. The models agree on a positive trend of DMS over polar latitudes following sea-ice retreat dynamics.
Mariana Hill Cruz, Iris Kriest, Yonss Saranga José, Rainer Kiko, Helena Hauss, and Andreas Oschlies
Biogeosciences, 18, 2891–2916, https://doi.org/10.5194/bg-18-2891-2021, https://doi.org/10.5194/bg-18-2891-2021, 2021
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In this study we use a regional biogeochemical model of the eastern tropical South Pacific Ocean to implicitly simulate the effect that fluctuations in populations of small pelagic fish, such as anchovy and sardine, may have on the biogeochemistry of the northern Humboldt Current System. To do so, we vary the zooplankton mortality in the model, under the assumption that these fishes eat zooplankton. We also evaluate the model for the first time against mesozooplankton observations.
Roman Bezhenar, Kyeong Ok Kim, Vladimir Maderich, Govert de With, and Kyung Tae Jung
Biogeosciences, 18, 2591–2607, https://doi.org/10.5194/bg-18-2591-2021, https://doi.org/10.5194/bg-18-2591-2021, 2021
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A new approach to predicting the accumulation of radionuclides in fish was developed by taking into account heterogeneity of distribution of contamination in the organism and dependence of metabolic process rates on the fish mass. Predicted concentrations of radionuclides in fish agreed well with the laboratory and field measurements. The model with the defined generic parameters could be used in marine environments without local calibration, which is important for emergency decision support.
Emil De Borger, Justin Tiano, Ulrike Braeckman, Adriaan D. Rijnsdorp, and Karline Soetaert
Biogeosciences, 18, 2539–2557, https://doi.org/10.5194/bg-18-2539-2021, https://doi.org/10.5194/bg-18-2539-2021, 2021
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Bottom trawling alters benthic mineralization: the recycling of organic material (OM) to free nutrients. To better understand how this occurs, trawling events were added to a model of seafloor OM recycling. Results show that bottom trawling reduces OM and free nutrients in sediments through direct removal thereof and of fauna which transport OM to deeper sediment layers protected from fishing. Our results support temporospatial trawl restrictions to allow key sediment functions to recover.
Britta Munkes, Ulrike Löptien, and Heiner Dietze
Biogeosciences, 18, 2347–2378, https://doi.org/10.5194/bg-18-2347-2021, https://doi.org/10.5194/bg-18-2347-2021, 2021
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Cyanobacteria blooms can strongly aggravate eutrophication problems of water bodies. Their controls are, however, not comprehensively understood, which impedes effective management and protection plans. Here we review the current understanding of cyanobacteria blooms. Juxtaposition of respective field and laboratory studies with state-of-the-art mathematical models reveals substantial uncertainty associated with nutrient demands, grazing, and death of cyanobacteria.
Jens Terhaar, Olivier Torres, Timothée Bourgeois, and Lester Kwiatkowski
Biogeosciences, 18, 2221–2240, https://doi.org/10.5194/bg-18-2221-2021, https://doi.org/10.5194/bg-18-2221-2021, 2021
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The uptake of carbon, emitted as a result of human activities, results in ocean acidification. We analyse 21st-century projections of acidification in the Arctic Ocean, a region of particular vulnerability, using the latest generation of Earth system models. In this new generation of models there is a large decrease in the uncertainty associated with projections of Arctic Ocean acidification, with freshening playing a greater role in driving acidification than previously simulated.
Tobias R. Vonnahme, Martial Leroy, Silke Thoms, Dick van Oevelen, H. Rodger Harvey, Svein Kristiansen, Rolf Gradinger, Ulrike Dietrich, and Christoph Völker
Biogeosciences, 18, 1719–1747, https://doi.org/10.5194/bg-18-1719-2021, https://doi.org/10.5194/bg-18-1719-2021, 2021
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Diatoms are crucial for Arctic coastal spring blooms, and their growth is controlled by nutrients and light. At the end of the bloom, inorganic nitrogen or silicon can be limiting, but nitrogen can be regenerated by bacteria, extending the algal growth phase. Modeling these multi-nutrient dynamics and the role of bacteria is challenging yet crucial for accurate modeling. We recreated spring bloom dynamics in a cultivation experiment and developed a representative dynamic model.
Rebecca M. Wright, Corinne Le Quéré, Erik Buitenhuis, Sophie Pitois, and Mark J. Gibbons
Biogeosciences, 18, 1291–1320, https://doi.org/10.5194/bg-18-1291-2021, https://doi.org/10.5194/bg-18-1291-2021, 2021
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Jellyfish have been included in a global ocean biogeochemical model for the first time. The global mean jellyfish biomass in the model is within the observational range. Jellyfish are found to play an important role in the plankton ecosystem, influencing community structure, spatiotemporal dynamics and biomass. The model raises questions about the sensitivity of the zooplankton community to jellyfish mortality and the interactions between macrozooplankton and jellyfish.
Valeria Di Biagio, Gianpiero Cossarini, Stefano Salon, and Cosimo Solidoro
Biogeosciences, 17, 5967–5988, 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
Short summary
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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
Short summary
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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
Short summary
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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
Short summary
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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
Short summary
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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
Short summary
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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.
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
Short summary
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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
Short summary
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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.
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Short summary
Recent studies demonstrate that marine N2 fixation can be carried out without light. However, direct measurements of N2 fixation in dark environments are relatively scarce. This study uses a model that represents biogeochemical cycles at a deep-ocean location in the Gulf of Aqaba (Red Sea). Different model versions are used to test assumptions about N2 fixers. Relaxing light limitation for marine N2 fixers improved the similarity between model results and observations of deep nitrate and oxygen.
Recent studies demonstrate that marine N2 fixation can be carried out without light. However,...
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