Articles | Volume 15, issue 11
https://doi.org/10.5194/essd-15-5039-2023
© Author(s) 2023. This work is distributed under
the Creative Commons Attribution 4.0 License.
the Creative Commons Attribution 4.0 License.
https://doi.org/10.5194/essd-15-5039-2023
© Author(s) 2023. This work is distributed under
the Creative Commons Attribution 4.0 License.
the Creative Commons Attribution 4.0 License.
Data description paper
| 
16 Nov 2023
Data description paper |
| 16 Nov 2023
| 16 Nov 2023
Database of nitrification and nitrifiers in the global ocean
Department of Geosciences, Princeton University, Princeton, NJ 08544, USA
Bess B. Ward
Department of Geosciences, Princeton University, Princeton, NJ 08544, USA
Michael Beman
Life and Environmental Sciences, University of California, Merced, CA, USA
Laura Bristow
Department of Marine Sciences, University of Gothenburg, Gothenburg, Sweden
Darren Clark
Somerset Scientific Services, Westpark 26, Chelston, Wellington, Somerset TA21 9AD, UK
Sarah Fawcett
Department of Oceanography, University of Cape Town, Rondebosch 7701, South Africa
Claudia Frey
Department of Environmental Science, University of Basel, Basel, Switzerland
François Fripiat
Department of Geosciences, Environment and Society, Université Libre de Bruxelles, Brussels, Belgium
Gerhard J. Herndl
Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
Mhlangabezi Mdutyana
Department of Oceanography, University of Cape Town, Rondebosch 7701, South Africa
Fabien Paulot
Geophysical Fluid Dynamics Laboratory, National Oceanic and Atmospheric Administration, Princeton, NJ, USA
Xuefeng Peng
School of Earth, Ocean and Environment, University of South Carolina, Columbia, SC 29208, USA
Alyson E. Santoro
Department of Ecology, Evolution and Marine Biology, University of California, Santa Barbara, CA, USA
Takuhei Shiozaki
Atmosphere and Ocean Research Institute, The University of Tokyo, Chiba, Japan
Eva Sintes
Instituto Español de Oceanografía-CSIC, Centro Oceanográfico de Baleares, Palma de Mallorca, Spain
Charles Stock
Geophysical Fluid Dynamics Laboratory, National Oceanic and Atmospheric Administration, Princeton, NJ, USA
Department of Global Ecology, Carnegie Institution for Science, Stanford, CA, USA
Xianhui S. Wan
Department of Geosciences, Princeton University, Princeton, NJ 08544, USA
Min N. Xu
State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou 570228, China
Yao Zhang
State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen 361101, China
Related authors
Weiyi Tang, Jeff Talbott, Timothy Jones, and Bess B. Ward
EGUsphere, https://doi.org/10.5194/egusphere-2024-638, https://doi.org/10.5194/egusphere-2024-638, 2024
Short summary
Short summary
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 treating nitrogen in WWTPs.
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
Short summary
Short summary
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.
Fabien Paulot, Gabrielle Pétron, Andrew M. Crotwell, and Matteo B. Bertagni
Atmos. Chem. Phys., 24, 4217–4229, https://doi.org/10.5194/acp-24-4217-2024, https://doi.org/10.5194/acp-24-4217-2024, 2024
Short summary
Short summary
New data from the National Oceanic and Atmospheric Administration show that hydrogen (H2) concentrations increased from 2010 to 2019, which is consistent with the simulated increase in H2 photochemical production (mainly from methane). But this cannot be reconciled with the expected decrease (increase) in H2 anthropogenic emissions (soil deposition) in the same period. This shows gaps in our knowledge of the H2 biogeochemical cycle that must be resolved to quantify the impact of higher H2 usage.
Weiyi Tang, Jeff Talbott, Timothy Jones, and Bess B. Ward
EGUsphere, https://doi.org/10.5194/egusphere-2024-638, https://doi.org/10.5194/egusphere-2024-638, 2024
Short summary
Short summary
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 treating nitrogen in WWTPs.
Andrew C. Ross, Charles A. Stock, Vimal Koul, Thomas L. Delworth, Feiyu Lu, Andrew Wittenberg, and Michael A. Alexander
EGUsphere, https://doi.org/10.5194/egusphere-2024-394, https://doi.org/10.5194/egusphere-2024-394, 2024
Short summary
Short summary
In this paper, we use a high resolution regional ocean model to downscale seasonal ocean forecasts from GFDL’s SPEAR model. We find that the downscaled model has significantly higher prediction skill in many cases.
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
Short summary
Short summary
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.
Paul R. Bierman, Andrew J. Christ, Catherine M. Collins, Halley M. Mastro, Juliana Souza, Pierre-Henri Blard, Stefanie Brachfeld, Zoe R. Courville, Tammy M. Rittenour, Elizabeth K. Thomas, Jean-Louis Tison, and Francois Fripiat
EGUsphere, https://doi.org/10.5194/egusphere-2023-2922, https://doi.org/10.5194/egusphere-2023-2922, 2024
Short summary
Short summary
In 1966, the US Army drilled through the Greenland Ice Sheet at Camp Century, Greenland; they recovered 3.44 meters of frozen sediment. Here, we decipher the material’s history. Water, flowing during a warm interglacial when the ice sheet melted from northwest Greenland, deposited the upper material which contains fossil plant and insect parts. The lower material, separated by more than a meter of ice with some sediment, is till, deposited by the ice sheet during a prior cold period.
Mak A. Saito, Jaclyn K. Saunders, Matthew R. McIlvin, Erin M. Bertrand, John A. Breier, Margaret Mars Brisbin, Sophie M. Colston, Jaimee R. Compton, Tim J. Griffin, W. Judson Hervey, Robert L. Hettich, Pratik D. Jagtap, Michael Janech, Rod Johnson, Rick Keil, Hugo Kleikamp, Dagmar Leary, Lennart Martens, J. Scott P. McCain, Eli Moore, Subina Mehta, Dawn M. Moran, Jaqui Neibauer, Benjamin A. Neely, Michael V. Jakuba, Jim Johnson, Megan Duffy, Gerhard J. Herndl, Richard Giannone, Ryan Mueller, Brook L. Nunn, Martin Pabst, Samantha Peters, Andrew Rajczewski, Elden Rowland, Brian Searle, Tim Van Den Bossche, Gary J. Vora, Jacob R. Waldbauer, Haiyan Zheng, and Zihao Zhao
EGUsphere, https://doi.org/10.5194/egusphere-2023-3148, https://doi.org/10.5194/egusphere-2023-3148, 2024
Short summary
Short summary
The ability to assess the functional capabilities of microbes in the environment is of increasing interest. Metaproteomics, the ability to measure proteins across microbial populations, has been increasing in capability and popularity in recent years. Here, an international team of scientists conducted an intercomparison study using samples collected from the North Atlantic Ocean and observed consistency in the peptides and proteins identified, their functions, and taxonomic origins.
Sarah Wauthy, Jean-Louis Tison, Mana Inoue, Saïda El Amri, Sainan Sun, François Fripiat, Philippe Claeys, and Frank Pattyn
Earth Syst. Sci. Data, 16, 35–58, https://doi.org/10.5194/essd-16-35-2024, https://doi.org/10.5194/essd-16-35-2024, 2024
Short summary
Short summary
The datasets presented are the density, water isotopes, ions, and conductivity measurements, as well as age models and surface mass balance (SMB) from the top 120 m of two ice cores drilled on adjacent ice rises in Dronning Maud Land, dating from the late 18th century. They offer many development possibilities for the interpretation of paleo-profiles and for addressing the mechanisms behind the spatial and temporal variability of SMB and proxies observed at the regional scale in East Antarctica.
Katja Frieler, Jan Volkholz, Stefan Lange, Jacob Schewe, Matthias Mengel, María del Rocío Rivas López, Christian Otto, Christopher P. O. Reyer, Dirk Nikolaus Karger, Johanna T. Malle, Simon Treu, Christoph Menz, Julia L. Blanchard, Cheryl S. Harrison, Colleen M. Petrik, Tyler D. Eddy, Kelly Ortega-Cisneros, Camilla Novaglio, Yannick Rousseau, Reg A. Watson, Charles Stock, Xiao Liu, Ryan Heneghan, Derek Tittensor, Olivier Maury, Matthias Büchner, Thomas Vogt, Tingting Wang, Fubao Sun, Inga J. Sauer, Johannes Koch, Inne Vanderkelen, Jonas Jägermeyr, Christoph Müller, Sam Rabin, Jochen Klar, Iliusi D. Vega del Valle, Gitta Lasslop, Sarah Chadburn, Eleanor Burke, Angela Gallego-Sala, Noah Smith, Jinfeng Chang, Stijn Hantson, Chantelle Burton, Anne Gädeke, Fang Li, Simon N. Gosling, Hannes Müller Schmied, Fred Hattermann, Jida Wang, Fangfang Yao, Thomas Hickler, Rafael Marcé, Don Pierson, Wim Thiery, Daniel Mercado-Bettín, Robert Ladwig, Ana Isabel Ayala-Zamora, Matthew Forrest, and Michel Bechtold
Geosci. Model Dev., 17, 1–51, https://doi.org/10.5194/gmd-17-1-2024, https://doi.org/10.5194/gmd-17-1-2024, 2024
Short summary
Short summary
Our paper provides an overview of all observational climate-related and socioeconomic forcing data used as input for the impact model evaluation and impact attribution experiments within the third round of the Inter-Sectoral Impact Model Intercomparison Project. The experiments are designed to test our understanding of observed changes in natural and human systems and to quantify to what degree these changes have already been induced by climate change.
Mathilde Dugenne, Marco Corrales-Ugalde, Jessica Luo, Rainer Kiko, Todd O'Brien, Jean-Olivier Irisson, Fabien Lombard, Lars Stemmann, Charles Stock, Clarissa R. Anderson, Marcel Babin, Nagib Bhairy, Sophie Bonnet, Francois Carlotti, Astrid Cornils, E. Taylor Crockford, Patrick Daniel, Corinne Desnos, Laetitia Drago, Amanda Elineau, Alexis Fischer, Nina Grandrémy, Pierre-Luc Grondin, Lionel Guidi, Cecile Guieu, Helena Hauss, Kendra Hayashi, Jenny A. Huggett, Laetitia Jalabert, Lee Karp-Boss, Kasia M. Kenitz, Raphael M. Kudela, Magali Lescot, Claudie Marec, Andrew McDonnell, Zoe Mériguet, Barbara Niehoff, Margaux Noyon, Thelma Panaïotis, Emily Peacock, Marc Picheral, Emilie Riquier, Collin Roesler, Jean-Baptiste Romagnan, Heidi M. Sosik, Gretchen Spencer, Jan Taucher, Chloé Tilliette, and Marion Vilain
Earth Syst. Sci. Data Discuss., https://doi.org/10.5194/essd-2023-479, https://doi.org/10.5194/essd-2023-479, 2023
Revised manuscript accepted for ESSD
Short summary
Short summary
Plankton and particles influence carbon cycling and energy flow in marine ecosystems. We used three types of novel plankton imaging systems to obtain size measurements from a range of plankton and particle sizes and across all major oceans. Data were compiled and cross-calibrated from many thousands of images, showing seasonal and spatial changes in particle size structure in different ocean basins. These datasets form the first release of the Pelagic Size Structure database (PSSdb).
Andrew C. Ross, Charles A. Stock, Alistair Adcroft, Enrique Curchitser, Robert Hallberg, Matthew J. Harrison, Katherine Hedstrom, Niki Zadeh, Michael Alexander, Wenhao Chen, Elizabeth J. Drenkard, Hubert du Pontavice, Raphael Dussin, Fabian Gomez, Jasmin G. John, Dujuan Kang, Diane Lavoie, Laure Resplandy, Alizée Roobaert, Vincent Saba, Sang-Ik Shin, Samantha Siedlecki, and James Simkins
Geosci. Model Dev., 16, 6943–6985, https://doi.org/10.5194/gmd-16-6943-2023, https://doi.org/10.5194/gmd-16-6943-2023, 2023
Short summary
Short summary
We evaluate a model for northwest Atlantic Ocean dynamics and biogeochemistry that balances high resolution with computational economy by building on the new regional features in the MOM6 ocean model and COBALT biogeochemical model. We test the model's ability to simulate impactful historical variability and find that the model simulates the mean state and variability of most features well, which suggests the model can provide information to inform living-marine-resource applications.
Colette L. Kelly, Nicole M. Travis, Pascale A. Baya, Claudia Frey, Xin Sun, Bess B. Ward, and Karen L. Casciotti
EGUsphere, https://doi.org/10.5194/egusphere-2023-2642, https://doi.org/10.5194/egusphere-2023-2642, 2023
Short summary
Short summary
We investigated the origins of nitrous oxide, a potent greenhouse gas, in low oxygen ocean regions. Our findings shed light on the microbial processes behind nitrous oxide production, including “hybrid” nitrous oxide generation by ammonia-oxidizing archaea, one of the most abundant organisms in the ocean. We also observed a strong link between nitrous oxide production and oxygen levels. These results set up potential feedbacks between oxygen depletion and greenhouse gas cycling in the oceans.
Colleen L. Hoffman, Patrick J. Monreal, Justine B. Albers, Alastair J. M. Lough, Alyson E. Santoro, Travis Mellett, Kristen N. Buck, Alessandro Tagliabue, Maeve C. Lohan, Joseph A. Resing, and Randelle M. Bundy
EGUsphere, https://doi.org/10.1101/2023.01.05.522639, https://doi.org/10.1101/2023.01.05.522639, 2023
Short summary
Short summary
Hydrothermally-derived iron can be transported thousands of kilometers away from deep-sea vents, representing a significant flux of vital micronutrients to the ocean. However, the mechanisms that support the stabilization and transport of dissolved iron remain elusive. Using electrochemical methods, advanced mass spectrometry techniques, and genomic tools we demonstrate that strong microbially-produced ligands appear to exert an important control on plume iron biogeochemistry and dissemination.
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
Short summary
Short summary
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.
Xuefeng Peng, David J. Yousavich, Annie Bourbonnais, Frank Wenzhoefer, Felix Janssen, Tina Treude, and David L. Valentine
EGUsphere, https://doi.org/10.5194/egusphere-2023-1498, https://doi.org/10.5194/egusphere-2023-1498, 2023
Short summary
Short summary
Biologically available (fixed) nitrogen (N) is a limiting nutrient for life in the ocean. Under low oxygen conditions, fixed N is either removed via denitrification or retained via dissimilatory nitrate reduction to ammonia (DNRA). Using in-situ incubations in the Santa Barbara Basin which undergoes seasonal anoxia, we found that benthic denitrification was the dominant nitrate reduction process, while nitrate availability and organic matter content control the relative importance of DNRA.
John C. Tracey, Andrew R. Babbin, Elizabeth Wallace, Xin Sun, Katherine L. DuRussel, Claudia Frey, Donald E. Martocello III, Tyler Tamasi, Sergey Oleynik, and Bess B. Ward
Biogeosciences, 20, 2499–2523, https://doi.org/10.5194/bg-20-2499-2023, https://doi.org/10.5194/bg-20-2499-2023, 2023
Short summary
Short summary
Nitrogen (N) is essential for life; thus, its availability plays a key role in determining marine productivity. Using incubations of seawater spiked with a rare form of N measurable on a mass spectrometer, we quantified microbial pathways that determine marine N availability. The results show that pathways that recycle N have higher rates than those that result in its loss from biomass and present new evidence for anaerobic nitrite oxidation, a process long thought to be strictly aerobic.
Fabian A. Gomez, Sang-Ki Lee, Charles A. Stock, Andrew C. Ross, Laure Resplandy, Samantha A. Siedlecki, Filippos Tagklis, and Joseph E. Salisbury
Earth Syst. Sci. Data, 15, 2223–2234, https://doi.org/10.5194/essd-15-2223-2023, https://doi.org/10.5194/essd-15-2223-2023, 2023
Short summary
Short summary
We present a river chemistry and discharge dataset for 140 rivers in the United States, which integrates information from the Water Quality Database of the US Geological Survey (USGS), the USGS’s Surface-Water Monthly Statistics for the Nation, and the U.S. Army Corps of Engineers. This dataset includes dissolved inorganic carbon and alkalinity, two key properties to characterize the carbonate system, as well as nutrient concentrations, such as nitrate, phosphate, and silica.
Alban Planchat, Lester Kwiatkowski, Laurent Bopp, Olivier Torres, James R. Christian, Momme Butenschön, Tomas Lovato, Roland Séférian, Matthew A. Chamberlain, Olivier Aumont, Michio Watanabe, Akitomo Yamamoto, Andrew Yool, Tatiana Ilyina, Hiroyuki Tsujino, Kristen M. Krumhardt, Jörg Schwinger, Jerry Tjiputra, John P. Dunne, and Charles Stock
Biogeosciences, 20, 1195–1257, https://doi.org/10.5194/bg-20-1195-2023, https://doi.org/10.5194/bg-20-1195-2023, 2023
Short summary
Short summary
Ocean alkalinity is critical to the uptake of atmospheric carbon and acidification in surface waters. We review the representation of alkalinity and the associated calcium carbonate cycle in Earth system models. While many parameterizations remain present in the latest generation of models, there is a general improvement in the simulated alkalinity distribution. This improvement is related to an increase in the export of biotic calcium carbonate, which closer resembles observations.
Minjin Lee, Charles A. Stock, John P. Dunne, and Elena Shevliakova
Geosci. Model Dev. Discuss., https://doi.org/10.5194/gmd-2022-236, https://doi.org/10.5194/gmd-2022-236, 2023
Revised manuscript accepted for GMD
Short summary
Short summary
Modeling global freshwater solid and nutrient loads, in both magnitude and form, is imperative for understanding emerging eutrophication problems. Such efforts, however, have been challenged by the difficulty of balancing details of freshwater biogeochemical processes with limited knowledge, input and validation datasets. Here we develop a global freshwater model that resolves intertwined algae, solid, and nutrient dynamics and provide performance assessment against measurement-based estimates.
Emily J. Zakem, Barbara Bayer, Wei Qin, Alyson E. Santoro, Yao Zhang, and Naomi M. Levine
Biogeosciences, 19, 5401–5418, https://doi.org/10.5194/bg-19-5401-2022, https://doi.org/10.5194/bg-19-5401-2022, 2022
Short summary
Short summary
We use a microbial ecosystem model to quantitatively explain the mechanisms controlling observed relative abundances and nitrification rates of ammonia- and nitrite-oxidizing microorganisms in the ocean. We also estimate how much global carbon fixation can be associated with chemoautotrophic nitrification. Our results improve our understanding of the controls on nitrification, laying the groundwork for more accurate predictions in global climate models.
Johannes Quaas, Hailing Jia, Chris Smith, Anna Lea Albright, Wenche Aas, Nicolas Bellouin, Olivier Boucher, Marie Doutriaux-Boucher, Piers M. Forster, Daniel Grosvenor, Stuart Jenkins, Zbigniew Klimont, Norman G. Loeb, Xiaoyan Ma, Vaishali Naik, Fabien Paulot, Philip Stier, Martin Wild, Gunnar Myhre, and Michael Schulz
Atmos. Chem. Phys., 22, 12221–12239, https://doi.org/10.5194/acp-22-12221-2022, https://doi.org/10.5194/acp-22-12221-2022, 2022
Short summary
Short summary
Pollution particles cool climate and offset part of the global warming. However, they are washed out by rain and thus their effect responds quickly to changes in emissions. We show multiple datasets to demonstrate that aerosol emissions and their concentrations declined in many regions influenced by human emissions, as did the effects on clouds. Consequently, the cooling impact on the Earth energy budget became smaller. This change in trend implies a relative warming.
Xiaofeng Dai, Mingming Chen, Xianhui Wan, Ehui Tan, Jialing Zeng, Nengwang Chen, Shuh-Ji Kao, and Yao Zhang
Biogeosciences, 19, 3757–3773, https://doi.org/10.5194/bg-19-3757-2022, https://doi.org/10.5194/bg-19-3757-2022, 2022
Short summary
Short summary
This study revealed the distinct distribution patterns of six key microbial functional genes and transcripts related to N2O sources and sinks in four estuaries spanning the Chinese coastline, which were significantly constrained by nitrogen and oxygen concentrations, salinity, temperature, and pH. The community structure of the nosZ clade II was distinctly different from those in the soil and marine OMZs. Denitrification may principally control the N2O emissions patterns across the estuaries.
Mhlangabezi Mdutyana, Tanya Marshall, Xin Sun, Jessica M. Burger, Sandy J. Thomalla, Bess B. Ward, and Sarah E. Fawcett
Biogeosciences, 19, 3425–3444, https://doi.org/10.5194/bg-19-3425-2022, https://doi.org/10.5194/bg-19-3425-2022, 2022
Short summary
Short summary
Nitrite-oxidizing bacteria in the winter Southern Ocean show a high affinity for nitrite but require a minimum (i.e., "threshold") concentration before they increase their rates of nitrite oxidation significantly. The classic Michaelis–Menten model thus cannot be used to derive the kinetic parameters, so a modified equation was employed that also yields the threshold nitrite concentration. Dissolved iron availability may play an important role in limiting nitrite oxidation.
Shantelle Smith, Katye E. Altieri, Mhlangabezi Mdutyana, David R. Walker, Ruan G. Parrott, Sedick Gallie, Kurt A. M. Spence, Jessica M. Burger, and Sarah E. Fawcett
Biogeosciences, 19, 715–741, https://doi.org/10.5194/bg-19-715-2022, https://doi.org/10.5194/bg-19-715-2022, 2022
Short summary
Short summary
Ammonium is a crucial yet poorly understood component of the Southern Ocean nitrogen cycle. We attribute our finding of consistently high ammonium concentrations in the winter mixed layer to limited ammonium consumption and sustained ammonium production, conditions under which the Southern Ocean becomes a source of carbon dioxide to the atmosphere. From similar data collected over an annual cycle, we propose a seasonal cycle for ammonium in shallow polar waters – a first for the Southern Ocean.
Sebastian Landwehr, Michele Volpi, F. Alexander Haumann, Charlotte M. Robinson, Iris Thurnherr, Valerio Ferracci, Andrea Baccarini, Jenny Thomas, Irina Gorodetskaya, Christian Tatzelt, Silvia Henning, Rob L. Modini, Heather J. Forrer, Yajuan Lin, Nicolas Cassar, Rafel Simó, Christel Hassler, Alireza Moallemi, Sarah E. Fawcett, Neil Harris, Ruth Airs, Marzieh H. Derkani, Alberto Alberello, Alessandro Toffoli, Gang Chen, Pablo Rodríguez-Ros, Marina Zamanillo, Pau Cortés-Greus, Lei Xue, Conor G. Bolas, Katherine C. Leonard, Fernando Perez-Cruz, David Walton, and Julia Schmale
Earth Syst. Dynam., 12, 1295–1369, https://doi.org/10.5194/esd-12-1295-2021, https://doi.org/10.5194/esd-12-1295-2021, 2021
Short summary
Short summary
The Antarctic Circumnavigation Expedition surveyed a large number of variables describing the dynamic state of ocean and atmosphere, freshwater cycle, atmospheric chemistry, ocean biogeochemistry, and microbiology in the Southern Ocean. To reduce the dimensionality of the dataset, we apply a sparse principal component analysis and identify temporal patterns from diurnal to seasonal cycles, as well as geographical gradients and
hotspotsof interaction. Code and data are open access.
Raquel F. Flynn, Thomas G. Bornman, Jessica M. Burger, Shantelle Smith, Kurt A. M. Spence, and Sarah E. Fawcett
Biogeosciences, 18, 6031–6059, https://doi.org/10.5194/bg-18-6031-2021, https://doi.org/10.5194/bg-18-6031-2021, 2021
Short summary
Short summary
Biological activity in the shallow Weddell Sea affects the biogeochemistry of recently formed deep waters. To investigate the drivers of carbon and nutrient export, we measured rates of primary production and nitrogen uptake, characterized the phytoplankton community, and estimated nutrient depletion ratios across the under-sampled western Weddell Sea in mid-summer. Carbon export was highest at the ice shelves and was determined by a combination of physical, chemical, and biological factors.
Kai G. Schulz, Eric P. Achterberg, Javier Arístegui, Lennart T. Bach, Isabel Baños, Tim Boxhammer, Dirk Erler, Maricarmen Igarza, Verena Kalter, Andrea Ludwig, Carolin Löscher, Jana Meyer, Judith Meyer, Fabrizio Minutolo, Elisabeth von der Esch, Bess B. Ward, and Ulf Riebesell
Biogeosciences, 18, 4305–4320, https://doi.org/10.5194/bg-18-4305-2021, https://doi.org/10.5194/bg-18-4305-2021, 2021
Short summary
Short summary
Upwelling of nutrient-rich deep waters to the surface make eastern boundary upwelling systems hot spots of marine productivity. This leads to subsurface oxygen depletion and the transformation of bioavailable nitrogen into inert N2. Here we quantify nitrogen loss processes following a simulated deep water upwelling. Denitrification was the dominant process, and budget calculations suggest that a significant portion of nitrogen that could be exported to depth is already lost in the surface ocean.
Alexander Braun, Marina Spona-Friedl, Maria Avramov, Martin Elsner, Federico Baltar, Thomas Reinthaler, Gerhard J. Herndl, and Christian Griebler
Biogeosciences, 18, 3689–3700, https://doi.org/10.5194/bg-18-3689-2021, https://doi.org/10.5194/bg-18-3689-2021, 2021
Short summary
Short summary
It is known that CO2 fixation by photoautotrophic organisms is the major sink from the atmosphere. While biologists are aware that CO2 fixation also occurs in heterotrophic organisms, this route of inorganic carbon, and its quantitative role, is hardly recognized in biogeochemistry. We demonstrate that a considerable amount of CO2 is fixed annually through anaplerotic reactions in heterotrophic organisms, and a significant quantity of inorganic carbon is temporally sequestered in biomass.
Siqi Wu, Moge Du, Xianhui Sean Wan, Corday Selden, Mar Benavides, Sophie Bonnet, Robert Hamersley, Carolin R. Löscher, Margaret R. Mulholland, Xiuli Yan, and Shuh-Ji Kao
Biogeosciences Discuss., https://doi.org/10.5194/bg-2021-104, https://doi.org/10.5194/bg-2021-104, 2021
Preprint withdrawn
Short summary
Short summary
Nitrogen (N2) fixation is one of the most important nutrient sources to the ocean. Here, we report N2 fixation in the deep, dark ocean in the South China Sea via a highly sensitive new method and elaborate controls, showing the overlooked importance of N2 fixation in the deep ocean. By global data compilation, we also provide an easy measured basic parameter to estimate deep N2 fixation. Our study may help to expand the area limit of N2 fixation studies and better constrain global N2 fixation.
Gillian Thornhill, William Collins, Dirk Olivié, Ragnhild B. Skeie, Alex Archibald, Susanne Bauer, Ramiro Checa-Garcia, Stephanie Fiedler, Gerd Folberth, Ada Gjermundsen, Larry Horowitz, Jean-Francois Lamarque, Martine Michou, Jane Mulcahy, Pierre Nabat, Vaishali Naik, Fiona M. O'Connor, Fabien Paulot, Michael Schulz, Catherine E. Scott, Roland Séférian, Chris Smith, Toshihiko Takemura, Simone Tilmes, Kostas Tsigaridis, and James Weber
Atmos. Chem. Phys., 21, 1105–1126, https://doi.org/10.5194/acp-21-1105-2021, https://doi.org/10.5194/acp-21-1105-2021, 2021
Short summary
Short summary
We find that increased temperatures affect aerosols and reactive gases by changing natural emissions and their rates of removal from the atmosphere. Changing the composition of these species in the atmosphere affects the radiative budget of the climate system and therefore amplifies or dampens the climate response of climate models of the Earth system. This study found that the largest effect is a dampening of climate change as warmer temperatures increase the emissions of cooling aerosols.
Amal Jayakumar and Bess B. Ward
Biogeosciences, 17, 5953–5966, https://doi.org/10.5194/bg-17-5953-2020, https://doi.org/10.5194/bg-17-5953-2020, 2020
Short summary
Short summary
Diversity and community composition of nitrogen-fixing microbes in the three main oxygen minimum zones of the world ocean were investigated using nifH clone libraries. Representatives of three main clusters of nifH genes were detected. Sequences were most diverse in the surface waters. The most abundant OTUs were affiliated with Alpha- and Gammaproteobacteria. The sequences were biogeographically distinct and the dominance of a few OTUs was commonly observed in OMZs in this (and other) studies.
Samuel T. Wilson, Alia N. Al-Haj, Annie Bourbonnais, Claudia Frey, Robinson W. Fulweiler, John D. Kessler, Hannah K. Marchant, Jana Milucka, Nicholas E. Ray, Parvadha Suntharalingam, Brett F. Thornton, Robert C. Upstill-Goddard, Thomas S. Weber, Damian L. Arévalo-Martínez, Hermann W. Bange, Heather M. Benway, Daniele Bianchi, Alberto V. Borges, Bonnie X. Chang, Patrick M. Crill, Daniela A. del Valle, Laura Farías, Samantha B. Joye, Annette Kock, Jabrane Labidi, Cara C. Manning, John W. Pohlman, Gregor Rehder, Katy J. Sparrow, Philippe D. Tortell, Tina Treude, David L. Valentine, Bess B. Ward, Simon Yang, and Leonid N. Yurganov
Biogeosciences, 17, 5809–5828, https://doi.org/10.5194/bg-17-5809-2020, https://doi.org/10.5194/bg-17-5809-2020, 2020
Short summary
Short summary
The oceans are a net source of the major greenhouse gases; however there has been little coordination of oceanic methane and nitrous oxide measurements. The scientific community has recently embarked on a series of capacity-building exercises to improve the interoperability of dissolved methane and nitrous oxide measurements. This paper derives from a workshop which discussed the challenges and opportunities for oceanic methane and nitrous oxide research in the near future.
Claudine Hauri, Cristina Schultz, Katherine Hedstrom, Seth Danielson, Brita Irving, Scott C. Doney, Raphael Dussin, Enrique N. Curchitser, David F. Hill, and Charles A. Stock
Biogeosciences, 17, 3837–3857, https://doi.org/10.5194/bg-17-3837-2020, https://doi.org/10.5194/bg-17-3837-2020, 2020
Short summary
Short summary
The coastal ecosystem of the Gulf of Alaska (GOA) is especially vulnerable to the effects of ocean acidification and climate change. To improve our conceptual understanding of the system, we developed a new regional biogeochemical model setup for the GOA. Model output suggests that bottom water is seasonally high in CO2 between June and January. Such extensive periods of reoccurring high CO2 may be harmful to ocean acidification-sensitive organisms.
Lester Kwiatkowski, Olivier Torres, Laurent Bopp, Olivier Aumont, Matthew Chamberlain, James R. Christian, John P. Dunne, Marion Gehlen, Tatiana Ilyina, Jasmin G. John, Andrew Lenton, Hongmei Li, Nicole S. Lovenduski, James C. Orr, Julien Palmieri, Yeray Santana-Falcón, Jörg Schwinger, Roland Séférian, Charles A. Stock, Alessandro Tagliabue, Yohei Takano, Jerry Tjiputra, Katsuya Toyama, Hiroyuki Tsujino, Michio Watanabe, Akitomo Yamamoto, Andrew Yool, and Tilo Ziehn
Biogeosciences, 17, 3439–3470, https://doi.org/10.5194/bg-17-3439-2020, https://doi.org/10.5194/bg-17-3439-2020, 2020
Short summary
Short summary
We assess 21st century projections of marine biogeochemistry in the CMIP6 Earth system models. These models represent the most up-to-date understanding of climate change. The models generally project greater surface ocean warming, acidification, subsurface deoxygenation, and euphotic nitrate reductions but lesser primary production declines than the previous generation of models. This has major implications for the impact of anthropogenic climate change on marine ecosystems.
Mirjana Najdek, Marino Korlević, Paolo Paliaga, Marsej Markovski, Ingrid Ivančić, Ljiljana Iveša, Igor Felja, and Gerhard J. Herndl
Biogeosciences, 17, 3299–3315, https://doi.org/10.5194/bg-17-3299-2020, https://doi.org/10.5194/bg-17-3299-2020, 2020
Short summary
Short summary
The response of Cymodocea nodosa to environmental changes was reported during a 15-month period. The meadow decline was triggered in spring by the simultaneous reduction of available light in the water column and the creation of anoxic conditions in the rooted area. This disturbance was critical for the plant since it took place during its recruitment phase when metabolic needs are maximal and stored reserves minimal. The loss of such habitat-forming seagrass is a major environmental concern.
Claudia Frey, Hermann W. Bange, Eric P. Achterberg, Amal Jayakumar, Carolin R. Löscher, Damian L. Arévalo-Martínez, Elizabeth León-Palmero, Mingshuang Sun, Xin Sun, Ruifang C. Xie, Sergey Oleynik, and Bess B. Ward
Biogeosciences, 17, 2263–2287, https://doi.org/10.5194/bg-17-2263-2020, https://doi.org/10.5194/bg-17-2263-2020, 2020
Short summary
Short summary
The production of N2O via nitrification and denitrification associated with low-O2 waters is a major source of oceanic N2O. We investigated the regulation and dynamics of these processes with respect to O2 and organic matter inputs. The transcription of the key nitrification gene amoA rapidly responded to changes in O2 and strongly correlated with N2O production rates. N2O production by denitrification was clearly stimulated by organic carbon, implying that its supply controls N2O production.
Le Kuai, Kevin W. Bowman, Kazuyuki Miyazaki, Makoto Deushi, Laura Revell, Eugene Rozanov, Fabien Paulot, Sarah Strode, Andrew Conley, Jean-François Lamarque, Patrick Jöckel, David A. Plummer, Luke D. Oman, Helen Worden, Susan Kulawik, David Paynter, Andrea Stenke, and Markus Kunze
Atmos. Chem. Phys., 20, 281–301, https://doi.org/10.5194/acp-20-281-2020, https://doi.org/10.5194/acp-20-281-2020, 2020
Short summary
Short summary
The tropospheric ozone increase from pre-industrial to the present day leads to a radiative forcing. The top-of-atmosphere outgoing fluxes at the ozone band are controlled by ozone, water vapor, and temperature. We demonstrate a method to attribute the models’ flux biases to these key players using satellite-constrained instantaneous radiative kernels. The largest spread between models is found in the tropics, mainly driven by ozone and then water vapor.
Li Ma, Hua Lin, Xiabing Xie, Minhan Dai, and Yao Zhang
Biogeosciences, 16, 4765–4781, https://doi.org/10.5194/bg-16-4765-2019, https://doi.org/10.5194/bg-16-4765-2019, 2019
Short summary
Short summary
The major microbial process producing N2O in estuarine ecosystems remains controversial. Combining the concentrations and isotopic compositions of N2O, distributions and transcript levels of ammonia-oxidizing bacterial and archaeal amoA and denitrifier nirS genes, and in situ incubation estimates of nitrification rates and N2O production rates, we clarified that ammonia-oxidizing bacteria contributed the major part in N2O production in the upper Pearl River estuary despite their low abundance.
Adeline N. Y. Cojean, Jakob Zopfi, Alan Gerster, Claudia Frey, Fabio Lepori, and Moritz F. Lehmann
Biogeosciences, 16, 4705–4718, https://doi.org/10.5194/bg-16-4705-2019, https://doi.org/10.5194/bg-16-4705-2019, 2019
Short summary
Short summary
Our results demonstrate the importance of oxygen in regulating the fate of nitrogen (N) in the sediments of Lake Lugano south basin, Switzerland. Hence, our study suggests that, by changing oxygen concentration in bottom waters, the seasonal water column turnover may significantly regulate the partitioning between N removal and N recycling in surface sediments, and it is likely that a similar pattern can be expected in a wide range of environments.
Federico Baltar and Gerhard J. Herndl
Biogeosciences, 16, 3793–3799, https://doi.org/10.5194/bg-16-3793-2019, https://doi.org/10.5194/bg-16-3793-2019, 2019
Short summary
Short summary
Around half of the global primary production (PP) is produced in the ocean. Here we quantified how much oceanic PP estimates would increase if we included the dark DIC fixation rates (which are usually excluded in the carbon-14 method) into the PP estimation. We found that the inclusion of dark DIC fixation would increase PP estimates by 5–22 %. This represents ca. 1.2 to 11 Pg C yr−1 of newly synthesized organic carbon available for the marine food web.
Fabien Paulot, Sergey Malyshev, Tran Nguyen, John D. Crounse, Elena Shevliakova, and Larry W. Horowitz
Atmos. Chem. Phys., 18, 17963–17978, https://doi.org/10.5194/acp-18-17963-2018, https://doi.org/10.5194/acp-18-17963-2018, 2018
Qixing Ji, Claudia Frey, Xin Sun, Melanie Jackson, Yea-Shine Lee, Amal Jayakumar, Jeffrey C. Cornwell, and Bess B. Ward
Biogeosciences, 15, 6127–6138, https://doi.org/10.5194/bg-15-6127-2018, https://doi.org/10.5194/bg-15-6127-2018, 2018
Short summary
Short summary
Nitrous oxide (N2O) is a strong greenhouse gas and ozone-depletion agent. Intense N2O effluxes had been observed from nutrient-rich estuaries with human impacts, such as the Chesapeake Bay. We report that increased nitrogen availability and low-oxygen conditions stimulate N2O production. Thus, controlling the nutrient input to the bay will decrease nitrogen availability and alleviate eutrophication, leading to water column reoxygenation, and subsequently will mitigate N2O emission.
Samuel T. Wilson, Hermann W. Bange, Damian L. Arévalo-Martínez, Jonathan Barnes, Alberto V. Borges, Ian Brown, John L. Bullister, Macarena Burgos, David W. Capelle, Michael Casso, Mercedes de la Paz, Laura Farías, Lindsay Fenwick, Sara Ferrón, Gerardo Garcia, Michael Glockzin, David M. Karl, Annette Kock, Sarah Laperriere, Cliff S. Law, Cara C. Manning, Andrew Marriner, Jukka-Pekka Myllykangas, John W. Pohlman, Andrew P. Rees, Alyson E. Santoro, Philippe D. Tortell, Robert C. Upstill-Goddard, David P. Wisegarver, Gui-Ling Zhang, and Gregor Rehder
Biogeosciences, 15, 5891–5907, https://doi.org/10.5194/bg-15-5891-2018, https://doi.org/10.5194/bg-15-5891-2018, 2018
Short summary
Short summary
To determine the variability between independent measurements of dissolved methane and nitrous oxide, seawater samples were analyzed by multiple laboratories. The results revealed the influences of the different parts of the analytical process, from the initial sample collection to the calculation of the final concentrations. Recommendations are made to improve dissolved methane and nitrous oxide measurements to help preclude future analytical discrepancies between laboratories.
Fabien Paulot, David Paynter, Paul Ginoux, Vaishali Naik, and Larry W. Horowitz
Atmos. Chem. Phys., 18, 13265–13281, https://doi.org/10.5194/acp-18-13265-2018, https://doi.org/10.5194/acp-18-13265-2018, 2018
Short summary
Short summary
Observations show that the sunlight reflected to space by particles has decreased over the US and Europe, increased over India, and not changed over China from 2001 to 2015. These changes are attributed to different types of particles, namely sulfate over the US and Europe, and black carbon, sulfate, and nitrate over China and India. Our results suggest that the recent shift in human emissions from the US and Europe to Asia has altered their impact on the Earth's outgoing energy.
Lei Hou, Xiabing Xie, Xianhui Wan, Shuh-Ji Kao, Nianzhi Jiao, and Yao Zhang
Biogeosciences, 15, 5169–5187, https://doi.org/10.5194/bg-15-5169-2018, https://doi.org/10.5194/bg-15-5169-2018, 2018
Short summary
Short summary
The niche differentiation of ammonia and nitrite oxidizers is controversial because they display disparate patterns in different environments. Combining molecular and nitrification rate analyses, our study clarified that water mass mixing and the substrate availability primarily regulated the niche differentiation of nitrifier populations along a salinity gradient. The nitrifier populations may have specific adaptations to different substrate conditions through their ecological strategies.
Jordan L. Schnell, Vaishali Naik, Larry W. Horowitz, Fabien Paulot, Jingqiu Mao, Paul Ginoux, Ming Zhao, and Kirpa Ram
Atmos. Chem. Phys., 18, 10157–10175, https://doi.org/10.5194/acp-18-10157-2018, https://doi.org/10.5194/acp-18-10157-2018, 2018
Short summary
Short summary
We evaluate the ability of a developmental version of the NOAA GFDL Atmospheric Model, version 4 to simulate observed wintertime pollution and its relationship to weather over Northern India, one of the most densely populated and polluted regions in world. We also compare two emission inventories and find that the newest version dramatically improves our simulation. Observed and modeled pollution is the highest within the Indo-Gangetic Plain, where it is closely related to near-surface weather.
Derek P. Tittensor, Tyler D. Eddy, Heike K. Lotze, Eric D. Galbraith, William Cheung, Manuel Barange, Julia L. Blanchard, Laurent Bopp, Andrea Bryndum-Buchholz, Matthias Büchner, Catherine Bulman, David A. Carozza, Villy Christensen, Marta Coll, John P. Dunne, Jose A. Fernandes, Elizabeth A. Fulton, Alistair J. Hobday, Veronika Huber, Simon Jennings, Miranda Jones, Patrick Lehodey, Jason S. Link, Steve Mackinson, Olivier Maury, Susa Niiranen, Ricardo Oliveros-Ramos, Tilla Roy, Jacob Schewe, Yunne-Jai Shin, Tiago Silva, Charles A. Stock, Jeroen Steenbeek, Philip J. Underwood, Jan Volkholz, James R. Watson, and Nicola D. Walker
Geosci. Model Dev., 11, 1421–1442, https://doi.org/10.5194/gmd-11-1421-2018, https://doi.org/10.5194/gmd-11-1421-2018, 2018
Short summary
Short summary
Model intercomparison studies in the climate and Earth sciences communities have been crucial for strengthening future projections. Given the speed and magnitude of anthropogenic change in the marine environment, the time is ripe for similar comparisons among models of fisheries and marine ecosystems. We describe the Fisheries and Marine Ecosystem Model Intercomparison Project, which brings together the marine ecosystem modelling community to inform long-term projections of marine ecosystems.
Jingyi Li, Jingqiu Mao, Arlene M. Fiore, Ronald C. Cohen, John D. Crounse, Alex P. Teng, Paul O. Wennberg, Ben H. Lee, Felipe D. Lopez-Hilfiker, Joel A. Thornton, Jeff Peischl, Ilana B. Pollack, Thomas B. Ryerson, Patrick Veres, James M. Roberts, J. Andrew Neuman, John B. Nowak, Glenn M. Wolfe, Thomas F. Hanisco, Alan Fried, Hanwant B. Singh, Jack Dibb, Fabien Paulot, and Larry W. Horowitz
Atmos. Chem. Phys., 18, 2341–2361, https://doi.org/10.5194/acp-18-2341-2018, https://doi.org/10.5194/acp-18-2341-2018, 2018
Short summary
Short summary
We present the first comprehensive model evaluation of summertime reactive oxidized nitrogen using a high-resolution chemistry–climate model with up-to-date isoprene oxidation chemistry, along with a series of observations from aircraft campaigns and ground measurement networks from 2004 to 2013 over the Southeast US. We investigate the impact of NOx emission reductions on changes in reactive nitrogen speciation and export efficiency as well as ozone in the past and future decade.
Giuliana Turi, Michael Alexander, Nicole S. Lovenduski, Antonietta Capotondi, James Scott, Charles Stock, John Dunne, Jasmin John, and Michael Jacox
Ocean Sci., 14, 69–86, https://doi.org/10.5194/os-14-69-2018, https://doi.org/10.5194/os-14-69-2018, 2018
Short summary
Short summary
A high-resolution global model was used to study the influence of El Niño/La Niña events on the California Current System (CalCS). The mean surface oxygen (O2) response extends well offshore, where the pH response occurs within ~ 100 km of the coast. The surface O2 (pH) is primarily driven by temperature (upwelling) changes. Below 100 m, anomalously low O2 and low pH occurred during La Niña events near the coast, potentially stressing the ecosystem, but there are large variations between events.
Lin Zhang, Youfan Chen, Yuanhong Zhao, Daven K. Henze, Liye Zhu, Yu Song, Fabien Paulot, Xuejun Liu, Yuepeng Pan, Yi Lin, and Binxiang Huang
Atmos. Chem. Phys., 18, 339–355, https://doi.org/10.5194/acp-18-339-2018, https://doi.org/10.5194/acp-18-339-2018, 2018
Short summary
Short summary
Substantial differences exist in current estimates of agricultural ammonia emissions in China, hindering understanding of their environmental consequences. This study applies both bottom-up and top-down methods to better quantify agricultural ammonia sources in China using observations from satellite and surface networks interpreted by a chemical transport model. Our estimate of annual Chinese anthropogenic ammonia emission is 11.7 tg (teragram) for 2008 with a strong seasonality peak in summer.
Yangyang Lu, Zuozhu Wen, Dalin Shi, Mingming Chen, Yao Zhang, Sophie Bonnet, Yuhang Li, Jiwei Tian, and Shuh-Ji Kao
Biogeosciences, 15, 1–12, https://doi.org/10.5194/bg-15-1-2018, https://doi.org/10.5194/bg-15-1-2018, 2018
Short summary
Short summary
We investigated the light response of field Trichodesmium N2 fixation and net dissolved nitrogen release behavior. Our results suggest that N2 fixation was a function of light intensity, and the light requirement of Trichodesmium nitrogen fixation was high relative to its photosynthetic light demand. Meanwhile, light is a crucial parameter driving the physiological state of Trichodesmium, which subsequently determined the C / N metabolism and net dissolved nitrogen release.
Angela N. Knapp, Sarah E. Fawcett, Alfredo Martínez-Garcia, Nathalie Leblond, Thierry Moutin, and Sophie Bonnet
Biogeosciences, 13, 4645–4657, https://doi.org/10.5194/bg-13-4645-2016, https://doi.org/10.5194/bg-13-4645-2016, 2016
Short summary
Short summary
The goal of this manuscript was to track the fate of newly fixed nitrogen (N) in large volume mesocosms in the coastal waters of New Caledonia. We used a N isotope ("δ15N") budget and found a shift in the δ15N of sinking particulate N over the 23-day experiment, indicating that nitrate supported export production at the beginning of the experiment, but that nitrogen fixation supported export at the end. We infer that nitrogen fixation supported export production by a release of dissolved N.
Sophie Bonnet, Hugo Berthelot, Kendra Turk-Kubo, Sarah Fawcett, Eyal Rahav, Stéphane L'Helguen, and Ilana Berman-Frank
Biogeosciences, 13, 2653–2673, https://doi.org/10.5194/bg-13-2653-2016, https://doi.org/10.5194/bg-13-2653-2016, 2016
Short summary
Short summary
N2 fixation rates were measured daily in ~ 50 m3 mesocosms deployed in New Caledonia to investigate the high-frequency dynamics of diazotrophy and the fate of diazotroph-derived nitrogen (DDN) oligotrophic ecosystems. ~ 10 % of UCYN-C from the water column were exported daily to the traps, representing as much as 22.4 ± 5.5 % of the total POC exported at the height of the UCYN-C bloom. 16 ± 6 % of the DDN was released to the dissolved pool and 21 ± 4 % was transferred to non-diazotrophic plankton.
F. Paulot, P. Ginoux, W. F. Cooke, L. J. Donner, S. Fan, M.-Y. Lin, J. Mao, V. Naik, and L. W. Horowitz
Atmos. Chem. Phys., 16, 1459–1477, https://doi.org/10.5194/acp-16-1459-2016, https://doi.org/10.5194/acp-16-1459-2016, 2016
Short summary
Short summary
We characterize the sensitivity of NO3 optical depth (OD) to both the sources of its precursors (NH3 and HNO3) and to its surface sinks. Uncertainties in the heterogeneous chemistry of HNO3 and the near-surface volatilization of NH4NO3 can cause up to 25 % difference in the global NO3 OD. Simulated NO3 OD increases little (< 30 %) in response to changes in emissions (2010 to 2050). Better constraints on the tropical flux of NH3 into the free troposphere are needed to improve estimates of NO3 OD.
H.-M. Lee, F. Paulot, D. K. Henze, K. Travis, D. J. Jacob, L. H. Pardo, and B. A. Schichtel
Atmos. Chem. Phys., 16, 525–540, https://doi.org/10.5194/acp-16-525-2016, https://doi.org/10.5194/acp-16-525-2016, 2016
Short summary
Short summary
Sources of nitrogen deposition (Ndep) in Federal Class I areas in the US are investigated, identifying unique features in contributions from different species, sectors and locations. Ndep in many parks is impacted by emissions several hundred km away; the role of oxidized vs reduced sources varies regionally. Emissions reductions in the western US most effectively reduce the extent of areas in critical load exceedance, while reductions in the east most effectively reduce exceedance magnitudes.
T. Shiozaki, S. Takeda, S. Itoh, T. Kodama, X. Liu, F. Hashihama, and K. Furuya
Biogeosciences, 12, 6931–6943, https://doi.org/10.5194/bg-12-6931-2015, https://doi.org/10.5194/bg-12-6931-2015, 2015
Short summary
Short summary
The high abundance of Trichodesmium and active nitrogen fixation in the Kuroshio were not explained by the nutrient (nitrate, phosphate, and iron) distribution. We observed a Trichodesmium bloom and high nitrogen fixation near islands situated along the Kuroshio. Numerical particle-tracking experiments simulated the transportation of water around the Ryukyu Islands to the Kuroshio. Our results indicate that Trichodesmium growing around the Ryukyu Islands could be advected into the Kuroshio.
L. Zhu, D. Henze, J. Bash, G.-R. Jeong, K. Cady-Pereira, M. Shephard, M. Luo, F. Paulot, and S. Capps
Atmos. Chem. Phys., 15, 12823–12843, https://doi.org/10.5194/acp-15-12823-2015, https://doi.org/10.5194/acp-15-12823-2015, 2015
Short summary
Short summary
We implement new diurnal variation scheme for ammonia livestock emissions and bidirectional exchange scheme and its adjoint in the GEOS-Chem global chemical transport model. Updated diurnal variability improves modeled-to-hourly in situ measurements comparison. The ammonium soil pool in the bidirectional exchange model largely extends the ammonia lifetime in the atmosphere. Large model biases remain as livestock emissions are still underestimated.
W. W. Hu, P. Campuzano-Jost, B. B. Palm, D. A. Day, A. M. Ortega, P. L. Hayes, J. E. Krechmer, Q. Chen, M. Kuwata, Y. J. Liu, S. S. de Sá, K. McKinney, S. T. Martin, M. Hu, S. H. Budisulistiorini, M. Riva, J. D. Surratt, J. M. St. Clair, G. Isaacman-Van Wertz, L. D. Yee, A. H. Goldstein, S. Carbone, J. Brito, P. Artaxo, J. A. de Gouw, A. Koss, A. Wisthaler, T. Mikoviny, T. Karl, L. Kaser, W. Jud, A. Hansel, K. S. Docherty, M. L. Alexander, N. H. Robinson, H. Coe, J. D. Allan, M. R. Canagaratna, F. Paulot, and J. L. Jimenez
Atmos. Chem. Phys., 15, 11807–11833, https://doi.org/10.5194/acp-15-11807-2015, https://doi.org/10.5194/acp-15-11807-2015, 2015
Short summary
Short summary
This work summarized all the studies reporting isoprene epoxydiols-derived secondary organic aerosol (IEPOX-SOA) measured globally by aerosol mass spectrometer and compare them with modeled gas-phase IEPOX, with results suggestive of the importance of IEPOX-SOA for regional and global OA budgets. A real-time tracer of IEPOX-SOA is thoroughly evaluated for the first time by combing multiple field and chamber studies. A quick and easy empirical method on IEPOX-SOA estimation is also presented.
Y. Zhao, L. Zhang, Y. Pan, Y. Wang, F. Paulot, and D. K. Henze
Atmos. Chem. Phys., 15, 10905–10924, https://doi.org/10.5194/acp-15-10905-2015, https://doi.org/10.5194/acp-15-10905-2015, 2015
Short summary
Short summary
Rapid Asian industrialization has led to increased atmospheric nitrogen deposition downwind. This work analyzes the sources and processes controlling atmospheric nitrogen deposition to the northwestern Pacific. Both nitrogen emissions and meteorology, largely controlled by the East Asian Monsoon, determine the seasonality of nitrogen deposition. Ascribing deposition over the marginal seas to nitrogen sources from different regions and sectors shows important contribution from fertilizer use.
T. Shiozaki, T. Nagata, M. Ijichi, and K. Furuya
Biogeosciences, 12, 4751–4764, https://doi.org/10.5194/bg-12-4751-2015, https://doi.org/10.5194/bg-12-4751-2015, 2015
Short summary
Short summary
We found that nitrogen fixation can proceed at high rates, depending on the season, in the temperate coastal region of the northwestern North Pacific. nifH sequences were omnipresent and recovered throughout the year. UCYN-A was a major diazotroph during summer, whereas Trichodesmium was abundant during fall, despite low temperatures. The Cluster III diazotrophs, putative anaerobic bacteria, were found at the surface throughout the year.
C. A. Stock, J. P. Dunne, and J. G. John
Biogeosciences, 11, 7125–7135, https://doi.org/10.5194/bg-11-7125-2014, https://doi.org/10.5194/bg-11-7125-2014, 2014
Short summary
Short summary
Climate change projections suggest large regional ocean productivity shifts for mesozooplankton, an important food resource for fish, which are amplified relative to changes in phytoplankton production. Amplification is attributed to changes in planktonic food web dynamics under global warming. Results have implications for regional economies and food security. Improved understanding of the response of plankton food webs to climate change is essential to refine amplification estimates.
N. Jiao, Y. Zhang, K. Zhou, Q. Li, M. Dai, J. Liu, J. Guo, and B. Huang
Biogeosciences, 11, 2465–2475, https://doi.org/10.5194/bg-11-2465-2014, https://doi.org/10.5194/bg-11-2465-2014, 2014
Y. Zhang, X. Xie, N. Jiao, S. S.-Y. Hsiao, and S.-J. Kao
Biogeosciences, 11, 2131–2145, https://doi.org/10.5194/bg-11-2131-2014, https://doi.org/10.5194/bg-11-2131-2014, 2014
S. S.-Y. Hsiao, T.-C. Hsu, J.-w. Liu, X. Xie, Y. Zhang, J. Lin, H. Wang, J.-Y. T. Yang, S.-C. Hsu, M. Dai, and S.-J. Kao
Biogeosciences, 11, 2083–2098, https://doi.org/10.5194/bg-11-2083-2014, https://doi.org/10.5194/bg-11-2083-2014, 2014
E. V. Fischer, D. J. Jacob, R. M. Yantosca, M. P. Sulprizio, D. B. Millet, J. Mao, F. Paulot, H. B. Singh, A. Roiger, L. Ries, R.W. Talbot, K. Dzepina, and S. Pandey Deolal
Atmos. Chem. Phys., 14, 2679–2698, https://doi.org/10.5194/acp-14-2679-2014, https://doi.org/10.5194/acp-14-2679-2014, 2014
A. E. Santoro, C. M. Sakamoto, J. M. Smith, J. N. Plant, A. L. Gehman, A. Z. Worden, K. S. Johnson, C. A. Francis, and K. L. Casciotti
Biogeosciences, 10, 7395–7410, https://doi.org/10.5194/bg-10-7395-2013, https://doi.org/10.5194/bg-10-7395-2013, 2013
Y. Xie, F. Paulot, W. P. L. Carter, C. G. Nolte, D. J. Luecken, W. T. Hutzell, P. O. Wennberg, R. C. Cohen, and R. W. Pinder
Atmos. Chem. Phys., 13, 8439–8455, https://doi.org/10.5194/acp-13-8439-2013, https://doi.org/10.5194/acp-13-8439-2013, 2013
Related subject area
Domain: ESSD – Ocean | Subject: Chemical oceanography
Updated climatological mean ΔfCO2 and net sea–air CO2 flux over the global open ocean regions
The annual update GLODAPv2.2023: the global interior ocean biogeochemical data product
Synthesis Product for Ocean Time Series (SPOTS) – a ship-based biogeochemical pilot
French coastal network for carbonate system monitoring: the CocoriCO2 dataset
A global database of dissolved organic matter (DOM) concentration measurements in coastal waters (CoastDOM v1)
A decade-long cruise time series (2008–2018) of physical and biogeochemical conditions in the southern Salish Sea, North America
A regional pCO2 climatology of the Baltic Sea from in situ pCO2 observations and a model-based extrapolation approach
A 12-year-long (2010–2021) hydrological and biogeochemical dataset in the Sicily Channel (Mediterranean Sea)
A decade of marine inorganic carbon chemistry observations in the northern Gulf of Alaska – insights into an environment in transition
A novel sea surface pCO2-product for the global coastal ocean resolving trends over 1982–2020
A high-resolution synthesis dataset for multistressor analyses along the US West Coast
CMEMS-LSCE: a global, 0.25°, monthly reconstruction of the surface ocean carbonate system
A synthesis of ocean total alkalinity and dissolved inorganic carbon measurements from 1993 to 2022: the SNAPO-CO2-v1 dataset
A year of transient tracers (chlorofluorocarbon 12 and sulfur hexafluoride), noble gases (helium and neon), and tritium in the Arctic Ocean from the MOSAiC expedition (2019–2020)
GOBAI-O2: temporally and spatially resolved fields of ocean interior dissolved oxygen over nearly 2 decades
Spatiotemporal variability in pH and carbonate parameters on the Canadian Atlantic continental shelf between 2014 and 2022
Barium in seawater: dissolved distribution, relationship to silicon, and barite saturation state determined using machine learning
Global oceanic diazotroph database version 2 and elevated estimate of global oceanic N2 fixation
High-frequency, year-round time series of the carbonate chemistry in a high-Arctic fjord (Svalbard)
OceanSODA-UNEXE: a multi-year gridded Amazon and Congo River outflow surface ocean carbonate system dataset
Evaluating the transport of surface seawater from 1956 to 2021 using 137Cs deposited in the global ocean as a chemical tracer
Spatial reconstruction of long-term (2003–2020) sea surface pCO2 in the South China Sea using a machine-learning-based regression method aided by empirical orthogonal function analysis
OceanSODA-MDB: a standardised surface ocean carbonate system dataset for model–data intercomparisons
Hyperspectral reflectance dataset of pristine, weathered, and biofouled plastics
A database of marine macronutrient, temperature and salinity measurements made around the highly productive island of South Georgia, the Scotia Sea and the Antarctic Peninsula between 1980 and 2009
GLODAPv2.2022: the latest version of the global interior ocean biogeochemical data product
Oil slicks in the Gulf of Guinea – 10 years of Envisat Advanced Synthetic Aperture Radar observations
Amanda R. Fay, David R. Munro, Galen A. McKinley, Denis Pierrot, Stewart C. Sutherland, Colm Sweeney, and Rik Wanninkhof
Earth Syst. Sci. Data, 16, 2123–2139, https://doi.org/10.5194/essd-16-2123-2024, https://doi.org/10.5194/essd-16-2123-2024, 2024
Short summary
Short summary
Presented here is a near-global monthly climatological estimate of the difference between atmosphere and ocean carbon dioxide concentrations. The ocean's ability to take up carbon, both now and in the future, is defined by this difference in concentrations. With over 30 million measurements of surface ocean carbon over the last 40 years and utilization of an extrapolation technique, a mean estimate of surface ocean ΔfCO2 is presented.
Siv K. Lauvset, Nico Lange, Toste Tanhua, Henry C. Bittig, Are Olsen, Alex Kozyr, Marta Álvarez, Kumiko Azetsu-Scott, Peter J. Brown, Brendan R. Carter, Leticia Cotrim da Cunha, Mario Hoppema, Matthew P. Humphreys, Masao Ishii, Emil Jeansson, Akihiko Murata, Jens Daniel Müller, Fiz F. Pérez, Carsten Schirnick, Reiner Steinfeldt, Toru Suzuki, Adam Ulfsbo, Anton Velo, Ryan J. Woosley, and Robert M. Key
Earth Syst. Sci. Data, 16, 2047–2072, https://doi.org/10.5194/essd-16-2047-2024, https://doi.org/10.5194/essd-16-2047-2024, 2024
Short summary
Short summary
GLODAP is a data product for ocean inorganic carbon and related biogeochemical variables measured by the chemical analysis of water bottle samples from scientific cruises. GLODAPv2.2023 is the fifth update of GLODAPv2 from 2016. The data that are included have been subjected to extensive quality controlling, including systematic evaluation of measurement biases. This version contains data from 1108 hydrographic cruises covering the world's oceans from 1972 to 2021.
Nico Lange, Björn Fiedler, Marta Álvarez, Alice Benoit-Cattin, Heather Benway, Pier Luigi Buttigieg, Laurent Coppola, Kim Currie, Susana Flecha, Dana S. Gerlach, Makio Honda, I. Emma Huertas, Siv K. Lauvset, Frank Muller-Karger, Arne Körtzinger, Kevin M. O'Brien, Sólveig R. Ólafsdóttir, Fernando C. Pacheco, Digna Rueda-Roa, Ingunn Skjelvan, Masahide Wakita, Angelicque White, and Toste Tanhua
Earth Syst. Sci. Data, 16, 1901–1931, https://doi.org/10.5194/essd-16-1901-2024, https://doi.org/10.5194/essd-16-1901-2024, 2024
Short summary
Short summary
The Synthesis Product for Ocean Time Series (SPOTS) is a novel achievement expanding and complementing the biogeochemical data landscape by providing consistent and high-quality biogeochemical time-series data from 12 ship-based fixed time-series programs. SPOTS covers multiple unique marine environments and time-series ranges, including data from 1983 to 2021. All in all, it facilitates a variety of applications that benefit from the collective value of biogeochemical time-series observations.
Sébastien Petton, Fabrice Pernet, Valérian Le Roy, Matthias Huber, Sophie Martin, Éric Macé, Yann Bozec, Stéphane Loisel, Peggy Rimmelin-Maury, Émilie Grossteffan, Michel Repecaud, Loïc Quemener, Michael Retho, Soazig Manac'h, Mathias Papin, Philippe Pineau, Thomas Lacoue-Labarthe, Jonathan Deborde, Louis Costes, Pierre Polsenaere, Loïc Rigouin, Jérémy Benhamou, Laure Gouriou, Joséphine Lequeux, Nathalie Labourdette, Nicolas Savoye, Grégory Messiaen, Elodie Foucault, Vincent Ouisse, Marion Richard, Franck Lagarde, Florian Voron, Valentin Kempf, Sébastien Mas, Léa Giannecchini, Francesca Vidussi, Behzad Mostajir, Yann Leredde, Samir Alliouane, Jean-Pierre Gattuso, and Frédéric Gazeau
Earth Syst. Sci. Data, 16, 1667–1688, https://doi.org/10.5194/essd-16-1667-2024, https://doi.org/10.5194/essd-16-1667-2024, 2024
Short summary
Short summary
Our research highlights the concerning impact of rising carbon dioxide levels on coastal areas. To better understand these changes, we've established an observation network in France. By deploying pH sensors and other monitoring equipment at key coastal sites, we're gaining valuable insights into how various factors, such as freshwater inputs, tides, temperature, and biological processes, influence ocean pH.
Christian Lønborg, Cátia Carreira, Gwenaël Abril, Susana Agustí, Valentina Amaral, Agneta Andersson, Javier Arístegui, Punyasloke Bhadury, Mariana B. Bif, Alberto V. Borges, Steven Bouillon, Maria Ll. Calleja, Luiz C. Cotovicz Jr., Stefano Cozzi, Maryló Doval, Carlos M. Duarte, Bradley Eyre, Cédric G. Fichot, E. Elena García-Martín, Alexandra Garzon-Garcia, Michele Giani, Rafael Gonçalves-Araujo, Renee Gruber, Dennis A. Hansell, Fuminori Hashihama, Ding He, Johnna M. Holding, William R. Hunter, J. Severino P. Ibánhez, Valeria Ibello, Shan Jiang, Guebuem Kim, Katja Klun, Piotr Kowalczuk, Atsushi Kubo, Choon-Weng Lee, Cláudia B. Lopes, Federica Maggioni, Paolo Magni, Celia Marrase, Patrick Martin, S. Leigh McCallister, Roisin McCallum, Patricia M. Medeiros, Xosé Anxelu G. Morán, Frank E. Muller-Karger, Allison Myers-Pigg, Marit Norli, Joanne M. Oakes, Helena Osterholz, Hyekyung Park, Maria Lund Paulsen, Judith A. Rosentreter, Jeff D. Ross, Digna Rueda-Roa, Chiara Santinelli, Yuan Shen, Eva Teira, Tinkara Tinta, Guenther Uher, Masahide Wakita, Nicholas Ward, Kenta Watanabe, Yu Xin, Youhei Yamashita, Liyang Yang, Jacob Yeo, Huamao Yuan, Qiang Zheng, and Xosé Antón Álvarez-Salgado
Earth Syst. Sci. Data, 16, 1107–1119, https://doi.org/10.5194/essd-16-1107-2024, https://doi.org/10.5194/essd-16-1107-2024, 2024
Short summary
Short summary
In this paper, we present the first edition of a global database compiling previously published and unpublished measurements of dissolved organic matter (DOM) collected in coastal waters (CoastDOM v1). Overall, the CoastDOM v1 dataset will be useful to identify global spatial and temporal patterns and to facilitate reuse in studies aimed at better characterizing local biogeochemical processes and identifying a baseline for modelling future changes in coastal waters.
Simone R. Alin, Jan A. Newton, Richard A. Feely, Dana Greeley, Beth Curry, Julian Herndon, and Mark Warner
Earth Syst. Sci. Data, 16, 837–865, https://doi.org/10.5194/essd-16-837-2024, https://doi.org/10.5194/essd-16-837-2024, 2024
Short summary
Short summary
The Salish cruise data product provides 2008–2018 oceanographic data from the southern Salish Sea and nearby coastal sampling stations. Temperature, salinity, oxygen, nutrient, and dissolved inorganic carbon measurements from 715 oceanographic profiles will facilitate further study of ocean acidification, hypoxia, and marine heatwave impacts in this region. Three subsets of the compiled datasets from 35 cruises are available with consistent formatting and multiple commonly used units.
Henry C. Bittig, Erik Jacobs, Thomas Neumann, and Gregor Rehder
Earth Syst. Sci. Data, 16, 753–773, https://doi.org/10.5194/essd-16-753-2024, https://doi.org/10.5194/essd-16-753-2024, 2024
Short summary
Short summary
We present a pCO2 climatology of the Baltic Sea using a new approach to extrapolate from individual observations to the entire Baltic Sea. The extrapolation approach uses (a) a model to inform on how data at one location are connected to data at other locations, together with (b) very accurate pCO2 observations from 2003 to 2021 as the base data. The climatology can be used e.g. to assess uptake and release of CO2 or to identify extreme events.
Francesco Placenti, Marco Torri, Katrin Schroeder, Mireno Borghini, Gabriella Cerrati, Angela Cuttitta, Vincenzo Tancredi, Carmelo Buscaino, and Bernardo Patti
Earth Syst. Sci. Data, 16, 743–752, https://doi.org/10.5194/essd-16-743-2024, https://doi.org/10.5194/essd-16-743-2024, 2024
Short summary
Short summary
Oceanographic surveys were conducted in the Strait of Sicily between 2010 and 2021. This paper provides a description of the time series of nutrients and hydrological data collected in this zone. The dataset fills an important gap in field observations of a crucial area where exchanges with the Mediterranean sub-basin take place, providing support for studies aimed at describing ongoing processes and at realizing reliable projections of the effects of these processes in the near future.
Natalie M. Monacci, Jessica N. Cross, Wiley Evans, Jeremy T. Mathis, and Hongjie Wang
Earth Syst. Sci. Data, 16, 647–665, https://doi.org/10.5194/essd-16-647-2024, https://doi.org/10.5194/essd-16-647-2024, 2024
Short summary
Short summary
As carbon dioxide is released into the air through human-generated activity, about one third dissolves into the surface water of oceans, lowering pH and increasing acidity. This is known as ocean acidification. We merged 10 years of ocean carbon data and made them publicly available for adaptation planning during a time of change. The data confirmed that Alaska is already experiencing the effects of ocean acidification due to naturally cold water, high productivity, and circulation patterns.
Alizée Roobaert, Pierre Regnier, Peter Landschützer, and Goulven G. Laruelle
Earth Syst. Sci. Data, 16, 421–441, https://doi.org/10.5194/essd-16-421-2024, https://doi.org/10.5194/essd-16-421-2024, 2024
Short summary
Short summary
The quantification of the coastal air–sea CO2 exchange (FCO2) has improved in recent years, but its multiannual variability remains unclear. This study, based on interpolated observations, reconstructs the longest global time series of coastal FCO2 (1982–2020). Results show the coastal ocean acts as a CO2 sink, with increasing intensity over time. This new coastal FCO2-product allows establishing regional carbon budgets and provides new constraints for closing the global carbon cycle.
Esther G. Kennedy, Meghan Zulian, Sara L. Hamilton, Tessa M. Hill, Manuel Delgado, Carina R. Fish, Brian Gaylord, Kristy J. Kroeker, Hannah M. Palmer, Aurora M. Ricart, Eric Sanford, Ana K. Spalding, Melissa Ward, Guadalupe Carrasco, Meredith Elliott, Genece V. Grisby, Evan Harris, Jaime Jahncke, Catherine N. Rocheleau, Sebastian Westerink, and Maddie I. Wilmot
Earth Syst. Sci. Data, 16, 219–243, https://doi.org/10.5194/essd-16-219-2024, https://doi.org/10.5194/essd-16-219-2024, 2024
Short summary
Short summary
We present a new synthesis of oceanographic observations along the US West Coast that has been optimized for multiparameter investigations of coastal warming, deoxygenation, and acidification risk. This synthesis includes both previously published and new observations, all of which have been consistently formatted and quality-controlled to facilitate high-resolution investigations of climate risks and consequences across a wide range of spatial and temporal scales.
Thi-Tuyet-Trang Chau, Marion Gehlen, Nicolas Metzl, and Frédéric Chevallier
Earth Syst. Sci. Data, 16, 121–160, https://doi.org/10.5194/essd-16-121-2024, https://doi.org/10.5194/essd-16-121-2024, 2024
Short summary
Short summary
CMEMS-LSCE leads as the first global observation-based reconstructions of six carbonate system variables for the years 1985–2021 at monthly and 0.25° resolutions. The high-resolution reconstructions outperform their 1° counterpart in reproducing horizontal and temporal gradients of observations over various oceanic regions to nearshore time series stations. New datasets can be exploited in numerous studies, including monitoring changes in ocean carbon uptake and ocean acidification.
Nicolas Metzl, Jonathan Fin, Claire Lo Monaco, Claude Mignon, Samir Alliouane, David Antoine, Guillaume Bourdin, Jacqueline Boutin, Yann Bozec, Pascal Conan, Laurent Coppola, Frédéric Diaz, Eric Douville, Xavier Durrieu de Madron, Jean-Pierre Gattuso, Frédéric Gazeau, Melek Golbol, Bruno Lansard, Dominique Lefèvre, Nathalie Lefèvre, Fabien Lombard, Férial Louanchi, Liliane Merlivat, Léa Olivier, Anne Petrenko, Sébastien Petton, Mireille Pujo-Pay, Christophe Rabouille, Gilles Reverdin, Céline Ridame, Aline Tribollet, Vincenzo Vellucci, Thibaut Wagener, and Cathy Wimart-Rousseau
Earth Syst. Sci. Data, 16, 89–120, https://doi.org/10.5194/essd-16-89-2024, https://doi.org/10.5194/essd-16-89-2024, 2024
Short summary
Short summary
This work presents a synthesis of 44 000 total alkalinity and dissolved inorganic carbon observations obtained between 1993 and 2022 in the Global Ocean and the Mediterranean Sea at the surface and in the water column. Seawater samples were measured using the same method and calibrated with international Certified Reference Material. We describe the data assemblage, quality control and some potential uses of this dataset.
Céline Heuzé, Oliver Huhn, Maren Walter, Natalia Sukhikh, Salar Karam, Wiebke Körtke, Myriel Vredenborg, Klaus Bulsiewicz, Jürgen Sültenfuß, Ying-Chih Fang, Christian Mertens, Benjamin Rabe, Sandra Tippenhauer, Jacob Allerholt, Hailun He, David Kuhlmey, Ivan Kuznetsov, and Maria Mallet
Earth Syst. Sci. Data, 15, 5517–5534, https://doi.org/10.5194/essd-15-5517-2023, https://doi.org/10.5194/essd-15-5517-2023, 2023
Short summary
Short summary
Gases dissolved in the ocean water not used by the ecosystem (or "passive tracers") are invaluable to track water over long distances and investigate the processes that modify its properties. Unfortunately, especially so in the ice-covered Arctic Ocean, such gas measurements are sparse. We here present a data set of several passive tracers (anthropogenic gases, noble gases and their isotopes) collected over the full ocean depth, weekly, during the 1-year drift in the Arctic during MOSAiC.
Jonathan D. Sharp, Andrea J. Fassbender, Brendan R. Carter, Gregory C. Johnson, Cristina Schultz, and John P. Dunne
Earth Syst. Sci. Data, 15, 4481–4518, https://doi.org/10.5194/essd-15-4481-2023, https://doi.org/10.5194/essd-15-4481-2023, 2023
Short summary
Short summary
Dissolved oxygen content is a critical metric of ocean health. Recently, expanding fleets of autonomous platforms that measure oxygen in the ocean have produced a wealth of new data. We leverage machine learning to take advantage of this growing global dataset, producing a gridded data product of ocean interior dissolved oxygen at monthly resolution over nearly 2 decades. This work provides novel information for investigations of spatial, seasonal, and interannual variability in ocean oxygen.
Olivia Gibb, Frédéric Cyr, Kumiko Azetsu-Scott, Joël Chassé, Darlene Childs, Carrie-Ellen Gabriel, Peter S. Galbraith, Gary Maillet, Pierre Pepin, Stephen Punshon, and Michel Starr
Earth Syst. Sci. Data, 15, 4127–4162, https://doi.org/10.5194/essd-15-4127-2023, https://doi.org/10.5194/essd-15-4127-2023, 2023
Short summary
Short summary
The ocean absorbs large quantities of carbon dioxide (CO2) released into the atmosphere as a result of the burning of fossil fuels. This, in turn, causes ocean acidification, which poses a major threat to global ocean ecosystems. In this study, we compiled 9 years (2014–2022) of ocean carbonate data (i.e., ocean acidification parameters) collected in Atlantic Canada as part of the Atlantic Zone Monitoring Program.
Öykü Z. Mete, Adam V. Subhas, Heather H. Kim, Ann G. Dunlea, Laura M. Whitmore, Alan M. Shiller, Melissa Gilbert, William D. Leavitt, and Tristan J. Horner
Earth Syst. Sci. Data, 15, 4023–4045, https://doi.org/10.5194/essd-15-4023-2023, https://doi.org/10.5194/essd-15-4023-2023, 2023
Short summary
Short summary
We present results from a machine learning model that accurately predicts dissolved barium concentrations for the global ocean. Our results reveal that the whole-ocean barium inventory is significantly lower than previously thought and that the deep ocean below 1000 m is at equilibrium with respect to barite. The model output can be used for a number of applications, including intercomparison, interpolation, and identification of regions warranting additional investigation.
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
Short summary
Short summary
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.
Jean-Pierre Gattuso, Samir Alliouane, and Philipp Fischer
Earth Syst. Sci. Data, 15, 2809–2825, https://doi.org/10.5194/essd-15-2809-2023, https://doi.org/10.5194/essd-15-2809-2023, 2023
Short summary
Short summary
The Arctic Ocean is subject to high rates of ocean warming and acidification, with critical implications for marine organisms, ecosystems and the services they provide. We report here on the first high-frequency (1 h), multi-year (5 years) dataset of the carbonate system at a coastal site in a high-Arctic fjord (Kongsfjorden, Svalbard). This site is a significant sink for CO2 every month of the year (9 to 17 mol m-2 yr-1). The saturation state of aragonite can be as low as 1.3.
Richard P. Sims, Thomas M. Holding, Peter E. Land, Jean-Francois Piolle, Hannah L. Green, and Jamie D. Shutler
Earth Syst. Sci. Data, 15, 2499–2516, https://doi.org/10.5194/essd-15-2499-2023, https://doi.org/10.5194/essd-15-2499-2023, 2023
Short summary
Short summary
The flow of carbon between the land and ocean is poorly quantified with existing measurements. It is not clear how seasonality and long-term variability impact this flow of carbon. Here, we demonstrate how satellite observations can be used to create decadal time series of the inorganic carbonate system in the Amazon and Congo River outflows.
Yayoi Inomata and Michio Aoyama
Earth Syst. Sci. Data, 15, 1969–2007, https://doi.org/10.5194/essd-15-1969-2023, https://doi.org/10.5194/essd-15-1969-2023, 2023
Short summary
Short summary
The behavior of 137Cs in surface seawater in the global ocean was analyzed by using the HAMGlobal2021 database. Approximately 32 % of 137Cs existed in the surface seawater in 1970. The 137Cs released into the North Pacific Ocean by large-scale nuclear weapons tests was transported to the Indian Ocean and then the Atlantic Ocean on a 4–5 decadal timescale, whereas 137Cs released from nuclear reprocessing plants was transported northward to the Arctic Ocean on a decadal scale.
Zhixuan Wang, Guizhi Wang, Xianghui Guo, Yan Bai, Yi Xu, and Minhan Dai
Earth Syst. Sci. Data, 15, 1711–1731, https://doi.org/10.5194/essd-15-1711-2023, https://doi.org/10.5194/essd-15-1711-2023, 2023
Short summary
Short summary
We reconstructed monthly sea surface pCO2 data with a high spatial resolution in the South China Sea (SCS) from 2003 to 2020. We validate our reconstruction with three independent testing datasets and present a new method to assess the uncertainty of the data. The results strongly suggest that our reconstruction effectively captures the main features of the spatiotemporal patterns of pCO2 in the SCS. Using this dataset, we found that the SCS is overall a weak source of atmospheric CO2.
Peter Edward Land, Helen S. Findlay, Jamie D. Shutler, Jean-Francois Piolle, Richard Sims, Hannah Green, Vassilis Kitidis, Alexander Polukhin, and Irina I. Pipko
Earth Syst. Sci. Data, 15, 921–947, https://doi.org/10.5194/essd-15-921-2023, https://doi.org/10.5194/essd-15-921-2023, 2023
Short summary
Short summary
Measurements of the ocean’s carbonate system (e.g. CO2 and pH) have increased greatly in recent years, resulting in a need to combine these data with satellite measurements and model results, so they can be used to test predictions of how the ocean reacts to changes such as absorption of the CO2 emitted by humans. We show a method of combining data into regions of interest (100 km circles over a 10 d period) and apply it globally to produce a harmonised and easy-to-use data archive.
Giulia Leone, Ana I. Catarino, Liesbeth De Keukelaere, Mattias Bossaer, Els Knaeps, and Gert Everaert
Earth Syst. Sci. Data, 15, 745–752, https://doi.org/10.5194/essd-15-745-2023, https://doi.org/10.5194/essd-15-745-2023, 2023
Short summary
Short summary
This paper illustrates a dataset of hyperspectral reflectance measurements of macroplastics. Plastic samples consisted of pristine, artificially weathered, and biofouled plastic items and field plastic debris. Samples were measured in dry conditions and a subset of plastics in wet and submerged conditions. This dataset can be used to better understand plastic optical features when exposed to natural agents and to support the development of algorithms for monitoring environmental plastics.
Michael J. Whitehouse, Katharine R. Hendry, Geraint A. Tarling, Sally E. Thorpe, and Petra ten Hoopen
Earth Syst. Sci. Data, 15, 211–224, https://doi.org/10.5194/essd-15-211-2023, https://doi.org/10.5194/essd-15-211-2023, 2023
Short summary
Short summary
We present a database of Southern Ocean macronutrient, temperature and salinity measurements collected on 20 oceanographic cruises between 1980 and 2009. Vertical profiles and underway surface measurements were collected year-round as part of an integrated ecosystem study. Our data provide a novel view of biogeochemical cycling in biologically productive regions across a critical period in recent climate history and will contribute to a better understanding of the drivers of primary production.
Siv K. Lauvset, Nico Lange, Toste Tanhua, Henry C. Bittig, Are Olsen, Alex Kozyr, Simone Alin, Marta Álvarez, Kumiko Azetsu-Scott, Leticia Barbero, Susan Becker, Peter J. Brown, Brendan R. Carter, Leticia Cotrim da Cunha, Richard A. Feely, Mario Hoppema, Matthew P. Humphreys, Masao Ishii, Emil Jeansson, Li-Qing Jiang, Steve D. Jones, Claire Lo Monaco, Akihiko Murata, Jens Daniel Müller, Fiz F. Pérez, Benjamin Pfeil, Carsten Schirnick, Reiner Steinfeldt, Toru Suzuki, Bronte Tilbrook, Adam Ulfsbo, Anton Velo, Ryan J. Woosley, and Robert M. Key
Earth Syst. Sci. Data, 14, 5543–5572, https://doi.org/10.5194/essd-14-5543-2022, https://doi.org/10.5194/essd-14-5543-2022, 2022
Short summary
Short summary
GLODAP is a data product for ocean inorganic carbon and related biogeochemical variables measured by the chemical analysis of water bottle samples from scientific cruises. GLODAPv2.2022 is the fourth update of GLODAPv2 from 2016. The data that are included have been subjected to extensive quality controlling, including systematic evaluation of measurement biases. This version contains data from 1085 hydrographic cruises covering the world's oceans from 1972 to 2021.
Zhour Najoui, Nellya Amoussou, Serge Riazanoff, Guillaume Aurel, and Frédéric Frappart
Earth Syst. Sci. Data, 14, 4569–4588, https://doi.org/10.5194/essd-14-4569-2022, https://doi.org/10.5194/essd-14-4569-2022, 2022
Short summary
Short summary
Oil spills could have serious repercussions for both the marine environment and ecosystem. The Gulf of Guinea is a very active area with respect to maritime traffic as well as oil and gas exploitation (platforms). As a result, the region is subject to a large number of oil pollution events. This study aims to detect oil slicks in the Gulf of Guinea and analyse their spatial and temporal distribution using satellite data.
Cited articles
Agogue, H., Brink, M., Dinasquet, J., and Herndl, G. J.: Major gradients in putatively nitrifying and non-nitrifying Archaea in the deep North Atlantic, Nature, 456, 788–791, https://doi.org/10.1038/nature07535, 2008.
Alonso-Saez, L., Waller, A. S., Mende, D. R., Bakker, K., Farnelid, H., Yager, P. L., Lovejoy, C., Tremblay, J. E., Potvin, M., Heinrich, F., Estrada, M., Riemann, L., Bork, P., Pedros-Alio, C., and Bertilsson, S.: Role for urea in nitrification by polar marine Archaea, P. Natl. Acad. Sci. USA, 109, 17989–17994, https://doi.org/10.1073/pnas.1201914109, 2012.
Alves, R. J. E., Minh, B. Q., Urich, T., von Haeseler, A., and Schleper, C.: Unifying the global phylogeny and environmental distribution of ammonia-oxidising archaea based on amoA genes, Nat. Commun., 9, 1517, https://doi.org/10.1038/s41467-018-03861-1, 2018.
Babbin, A. R., Peters, B. D., Mordy, C. W., Widner, B., Casciotti, K. L., and Ward, B. B.: Multiple metabolisms constrain the anaerobic nitrite budget in the Eastern Tropical South Pacific, Global Biogeochem. Cy., 31, 258–271, https://doi.org/10.1002/2016GB005407, 2017.
Babbin, A. R., Buchwald, C., Morel, F. M. M., Wankel, S. D., and Ward, B. B.: Nitrite oxidation exceeds reduction and fixed nitrogen loss in anoxic Pacific waters, Mar. Chem., 224, 103814, https://doi.org/10.1016/j.marchem.2020.103814, 2020.
Baer, S. E., Connelly, T. L., Sipler, R. E., Yager, P. L., and Bronk, D. A.: Effect of temperature on rates of ammonium uptake and nitrification in the western coastal Arctic during winter, spring, and summer, Global Biogeochem. Cy., 28, 1455–1466, 2014.
Baer, S. E., Sipler, R. E., Roberts, Q. N., Yager, P. L., Frischer, M. E., and Bronk, D. A.: Seasonal nitrogen uptake and regeneration in the western coastal Arctic, Limnol. Oceanogr., 62, 2463–2479, https://doi.org/10.1002/lno.10580, 2017.
Bayer, B., McBeain, K., Carlson, C. A., and Santoro, A. E.: Carbon content, carbon fixation yield and dissolved organic carbon release from diverse marine nitrifiers, Limnol. Oceanogr., 68, 84–96, https://doi.org/10.1002/lno.12252, 2022.
Beman, J., Popp, B. N., and Alford, S. E.: Quantification of ammonia oxidation rates and ammonia-oxidizing archaea and bacteria at high resolution in the Gulf of California and eastern tropical North Pacific Ocean, Limnol. Oceanogr., 57, 711–726, https://doi.org/10.4319/lo.2012.57.3.0711, 2012.
Beman, J. M., Popp, B. N., and Francis, C. A.: Molecular and biogeochemical evidence for ammonia oxidation by marine Crenarchaeota in the Gulf of California, ISME J., 2, 429–441, https://doi.org/10.1038/ismej.2007.118, 2008.
Beman, J. M., Chow, C., King, A. L., Feng, Y. Y., Furhman, J. A., Andersson, A., Bates, N. R., Popp, B., and Hutchins, D. A.: Global declines in oceanic nitrification rates as a consequence of ocean acidification, P. Natl. Acad. Sci. USA, 108, 208–213, 2011.
Beman, J. M., Leilei Shih, J., and Popp, B. N.: Nitrite oxidation in the upper water column and oxygen minimum zone of the eastern tropical North Pacific Ocean, ISME J., 7, 2192–2205, https://doi.org/10.1038/ismej.2013.96, 2013.
Beman, J. M., Vargas, S. M., Wilson, J. M., Perez-Coronel, E., Karolewski, J. S., Vazquez, S., Yu, A., Cairo, A. E., White, M. E., Koester, I., and Aluwihare, L. I.: Substantial oxygen consumption by aerobic nitrite oxidation in oceanic oxygen minimum zones, Nat. Commun., 12, 7043, https://doi.org/10.1038/s41467-021-27381-7, 2021.
Berthelot, H., Duhamel, S., L'Helguen, S., Maguer, J.-F., Wang, S., Cetinić, I., and Cassar, N.: NanoSIMS single cell analyses reveal the contrasting nitrogen sources for small phytoplankton, ISME J., 13, 651–662, https://doi.org/10.1038/s41396-018-0285-8, 2018.
Bianchi, M., Feliatra, F., Tréguer, P., Vincendeau, M.-A., and Morvan, J.: Nitrification rates, ammonium and nitrate distribution in upper layers of the water column and in sediments of the Indian sector of the Southern Ocean, Deep-Sea Res. Pt. II, 44, 1017–1032, https://doi.org/10.1016/S0967-0645(96)00109-9, 1997.
Breider, F., Yoshikawa, C., Makabe, A., Toyoda, S., Wakita, M., Matsui, Y., Kawagucci, S., Fujiki, T., Harada, N., and Yoshida, N.: Response of N2O production rate to ocean acidification in the western North Pacific, Nat. Clim. Change, 9, 954–958, https://doi.org/10.1038/s41558-019-0605-7, 2019.
Breitburg, D., Levin, L. A., Oschlies, A., Grégoire, M., Chavez, F. P., Conley, D. J., Garçon, V., Gilbert, D., Gutiérrez, D., Isensee, K., Jacinto, G. S., Limburg, K. E., Montes, I., Naqvi, S. W. A., Pitcher, G. C., Rabalais, N. N., Roman, M. R., Rose, K. A., Seibel, B. A., Telszewski, M., Yasuhara, M., and Zhang, J.: Declining oxygen in the global ocean and coastal waters, Science, 359, eaam7240, https://doi.org/10.1126/science.aam7240, 2018.
Bristow, L. A., Sarode, N., Cartee, J., Caro-Quintero, A., Thamdrup, B., and Stewart, F. J.: Biogeochemical and metagenomic analysis of nitrite accumulation in the Gulf of Mexico hypoxic zone, Limnol. Oceanogr., 60, 1733–1750, https://doi.org/10.1002/lno.10130, 2015.
Bristow, L. A., Dalsgaard, T., Tiano, L., Mills, D. B., Bertagnolli, A. D., Wright, J. J., Hallam, S. J., Ulloa, O., Canfield, D. E., Revsbech, N. P., and Thamdrup, B.: Ammonium and nitrite oxidation at nanomolar oxygen concentrations in oxygen minimum zone waters, P. Natl. Acad. Sci. USA, 113, 10601–10606, https://doi.org/10.1073/pnas.1600359113, 2016a.
Bristow, L. A., Callbeck, C. M., Larsen, M., Altabet, M. A., Dekaezemacker, J., Forth, M., Gauns, M., Glud, R. N., Kuypers, M. M. M., Lavik, G., Milucka, J., Naqvi, S. W. A., Pratihary, A., Revsbech, N. P., Thamdrup, B., Treusch, A. H., and Canfield, D. E.: N2 production rates limited by nitrite availability in the Bay of Bengal oxygen minimum zone, Nat. Geosci., 10, 24–29, https://doi.org/10.1038/ngeo2847, 2016b.
Buchanan, P. J., Sun, X., Weissman, J., and Zakem, E.: Oxygen intrusions sustain aerobic nitrite oxidation in anoxic marine zones, bioRxiv, https://doi.org/10.1101/2023.02.22.529547, 2023.
Buitenhuis, E. T., Vogt, M., Moriarty, R., Bednaršek, N., Doney, S. C., Leblanc, K., Le Quéré, C., Luo, Y.-W., O'Brien, C., O'Brien, T., Peloquin, J., Schiebel, R., and Swan, C.: MAREDAT: towards a world atlas of MARine Ecosystem DATa, Earth Syst. Sci. Data, 5, 227–239, https://doi.org/10.5194/essd-5-227-2013, 2013.
Busecke, J. J., Resplandy, L., Ditkovsky, S. J., and John, J. G.: Diverging fates of the Pacific Ocean oxygen minimum zone and its core in a warming world, AGU Advances, 3, e2021AV000470, https://doi.org/10.1029/2021AV000470, 2022.
Bustin, S. A., Benes, V., Garson, J. A., Hellemans, J., Huggett, J., Kubista, M., Mueller, R., Nolan, T., Pfaffl, M. W., Shipley, G. L., Vandesompele, J., and Wittwer, C. T.: The MIQE guidelines: minimum information for publication of quantitative real-time PCR experiments, Clin. Chem., 55, 611–622, https://doi.org/10.1373/clinchem.2008.112797, 2009.
Cavagna, A. J., Fripiat, F., Elskens, M., Mangion, P., Chirurgien, L., Closset, I., Lasbleiz, M., Florez-Leiva, L., Cardinal, D., Leblanc, K., Fernandez, C., Lefèvre, D., Oriol, L., Blain, S., Quéguiner, B., and Dehairs, F.: Production regime and associated N cycling in the vicinity of Kerguelen Island, Southern Ocean, Biogeosciences, 12, 6515–6528, https://doi.org/10.5194/bg-12-6515-2015, 2015.
Clark, D. R., Rees, A. P., and Joint, I.: A method for the determination of nitrification rates in oligotrophic marine seawater by gas chromatography/mass spectrometry, Mar. Chem., 103, 84–96, https://doi.org/10.1016/j.marchem.2006.06.005, 2007.
Clark, D. R., Rees, A. P., and Joint, I.: Ammonium regeneration and nitrification rates in the oligotrophic Atlantic Ocean: Implications for new production estimates, Limnol. Oceanogr., 53, 52–62, https://doi.org/10.4319/lo.2008.53.1.0052, 2008.
Clark, D. R., Miller, P. I., Malcolm, E., Woodward, S., and Rees, A. P.: Inorganic nitrogen assimilation and regeneration in the coastal upwelling region of the Iberian Peninsula, Limnol. Oceanogr., 56, 1689–1702, https://doi.org/10.4319/lo.2011.56.5.1689, 2011.
Clark, D. R., Brown, I. J., Rees, A. P., Somerfield, P. J., and Miller, P. I.: The influence of ocean acidification on nitrogen regeneration and nitrous oxide production in the northwest European shelf sea, Biogeosciences, 11, 4985–5005, https://doi.org/10.5194/bg-11-4985-2014, 2014.
Clark, D. R., Widdicombe, C. E., Rees, A. P., and Woodward, E. M. S.: The significance of nitrogen regeneration for new production within a filament of the Mauritanian upwelling system, Biogeosciences, 13, 2873–2888, https://doi.org/10.5194/bg-13-2873-2016, 2016.
Clark, D. R., Rees, A. P., Ferrera, C. M., Al-Moosawi, L., Somerfield, P. J., Harris, C., Quartly, G. D., Goult, S., Tarran, G., and Lessin, G.: Nitrite regeneration in the oligotrophic Atlantic Ocean, Biogeosciences, 19, 1355–1376, https://doi.org/10.5194/bg-19-1355-2022, 2022.
Daims, H., Lebedeva, E. V., Pjevac, P., Han, P., Herbold, C., Albertsen, M., Jehmlich, N., Palatinszky, M., Vierheilig, J., Bulaev, A., Kirkegaard, R. H., von Bergen, M., Rattei, T., Bendinger, B., Nielsen, P. H., and Wagner, M.: Complete nitrification by Nitrospira bacteria, Nature, 528, 504–509, https://doi.org/10.1038/nature16461, 2015.
Daims, H., Lucker, S., and Wagner, M.: A New Perspective on Microbes Formerly Known as Nitrite-Oxidizing Bacteria, Trends Microbiol., 24, 699–712, https://doi.org/10.1016/j.tim.2016.05.004, 2016.
Dalsgaard, T., Thamdrup, B., Farías, L., and Revsbech, N.P.: Anammox and denitrification in the oxygen minimum zone of the eastern South Pacific, Limnol. Oceanogr., 57, 1331–1346, 2012.
Damashek, J., Tolar, B. B., Liu, Q., Okotie-Oyekan, A. O., Wallsgrove, N. J., Popp, B. N., and Hollibaugh, J. T.: Microbial oxidation of nitrogen supplied as selected organic nitrogen compounds in the South Atlantic Bight, Limnol. Oceanogr., 64, 982–995, https://doi.org/10.1002/lno.11089, 2018.
Diaz, F. and Raimbault, P.: Nitrogen regeneration and dissolved organic nitrogen release during spring in a NW Mediterranean coastal zone (Gulf of Lions): implications for the estimation of new production, Mar. Ecol. Prog. Ser., 197, 51–65, 2000.
Dore, J. E. and Karl, D. M.: Nitrification in the euphotic zone as a source for nitrite, nitrate, and nitrous oxide at Station ALOHA, Limnol. Oceanogr., 41, 1619–1628, https://doi.org/10.4319/lo.1996.41.8.1619, 1996.
Emerson, K., Russo, R. C., Lund, R. E., and Thurston, R. V.: Aqueous ammonia equilibrium calculations – effect of ph and temperature, J. Fish. Res. Board Can., 32, 2379–2383, https://doi.org/10.1139/f75-274, 1975.
Eppley, R. W. and Peterson, B. J.: Particulate organic matter flux and planktonic new production in the deep ocean, Nature, 282, 677–680, 1979.
Falkowski, F. G.: Evolutionof the nitrogen cycle and its influence on biological sequestion of CO2 in the ocean, Nature, 387, 272–285, 1997.
Fawcett, S. E., Lomas, M. W., Casey, J. R., Ward, B. B., and Sigman, D. M.: Assimilation of upwelled nitrate by small eukaryotes in the Sargasso Sea, Nat. Geosci., 4, 717–722, https://doi.org/10.1038/ngeo1265, 2011.
Fernández, C., Farías, L., and Alcaman, M. E.: Primary production and nitrogen regeneration processes in surface waters of the Peruvian upwelling system, Prog. Oceanogr., 83, 159–168, https://doi.org/10.1016/j.pocean.2009.07.010, 2009.
Flynn, R. F., Bornman, T. G., Burger, J. M., Smith, S., Spence, K. A. M., and Fawcett, S. E.: Summertime productivity and carbon export potential in the Weddell Sea, with a focus on the waters adjacent to Larsen C Ice Shelf, Biogeosciences, 18, 6031–6059, https://doi.org/10.5194/bg-18-6031-2021, 2021.
Francis, C. A., Roberts, K. J., Beman, J. M., Santoro, A. E., and Oakley, B. B.: Ubiquity and diversity of ammonia-oxidizing archaea in water columns and sediments of the ocean, P. Natl. Acad. Sci. USA, 102, 14683–14688, https://doi.org/10.1073/pnas.0506625102, 2005.
Freing, A., Wallace, D. W. R., and Bange, H. W.: Global oceanic production of nitrous oxide, Philos. T. Roy. Soc. B, 367, 1245–1255, https://doi.org/10.1098/rstb.2011.0360, 2012.
Frey, C., Bange, H. W., Achterberg, E. P., Jayakumar, A., Löscher, C. R., Arévalo-Martínez, D. L., León-Palmero, E., Sun, M., Sun, X., Xie, R. C., Oleynik, S., and Ward, B. B.: Regulation of nitrous oxide production in low-oxygen waters off the coast of Peru, Biogeosciences, 17, 2263–2287, https://doi.org/10.5194/bg-17-2263-2020, 2020.
Frey, C., Sun, X., Szemberski, L., Casciotti, K. L., Garcia-Robledo, E., Jayakumar, A., Kelly, C. L., Lehmann, M. F., and Ward, B. B.: Kinetics of nitrous oxide production from ammonia oxidation in the Eastern Tropical North Pacific, Limnol. Oceanogr., 68, 424–438, https://doi.org/10.1002/lno.12283, 2022.
Füssel, J., Lam, P., Lavik, G., Jensen, M. M., Holtappels, M., Günter, M., and Kuypers, M. M.: Nitrite oxidation in the Namibian oxygen minimum zone. ISME J., 6, 1200–1209, https://doi.org/10.1038/ismej.2011.178, 2012.
Ganesh, S., Bristow, L. A., Larsen, M., Sarode, N., Thamdrup, B., and Stewart, F. J.: Size-fraction partitioning of community gene transcription and nitrogen metabolism in a marine oxygen minimum zone, ISME J., 9, 2682–2696, https://doi.org/10.1038/ismej.2015.44, 2015.
Garcia, H. E., Weathers, K. W., Paver, C. R., Smolyar, I., Boyer, T. P., Locarnini, M. M., Zweng, M. M., Mishonov, A. V., Baranova, O. K., Seidov, D., and Reagan, J. R.: World Ocean Atlas 2018. Vol. 4: Dissolved inorganic nutrients (phosphate, nitrate and nitrate+ nitrite, silicate), https://www.ncei.noaa.gov/sites/default/files/2022-06/woa18_vol4.pdf (last access: 14 November 2023), 2019.
Garcia-Robledo, E., Paulmier, A., Borisov, S. M., and Revsbech, N. P.: Sampling in low oxygen aquatic environments: The deviation from anoxic conditions, Limnol. Oceanogr.-Methods, 19, 733–740, https://doi.org/10.1002/lom3.10457, 2021.
Glover, D. M., Jenkins, W. J., and Doney, S. C.: Modeling methods for marine science, Cambridge University Press, https://doi.org/10.1017/CBO9780511975721, 2011.
Graham, D. W., Knapp, C. W., Van Vleck, E. S., Bloor, K., Lane, T. B., and Graham, C. E.: Experimental demonstration of chaotic instability in biological nitrification, ISME J., 1, 385–393, https://doi.org/10.1038/ismej.2007.45, 2007.
Granger, J. and Sigman, D. M.: Removal of nitrite with sulfamic acid for nitrate N and O isotope analysis with the denitrifier method, Rapid Commun. Mass Spectrom., 23, 3753–3762, https://doi.org/10.1002/rcm.4307, 2009.
Grundle, D. S., Juniper, S. K., and Giesbrecht, K. E.: Euphotic zone nitrification in the NE subarctic Pacific: Implications for measurements of new production, Mar. Chem., 155, 113–123, https://doi.org/10.1016/j.marchem.2013.06.004, 2013.
Hiraoka, S., Ijichi, M., Takeshima, H., Kumagai, Y., Yang, C.C., Makabe-Kobayashi, Y., Fukuda, H., Yoshizawa, S., Iwasaki, W., Kogure, K., and Shiozaki, T.: Probe capture enrichment sequencing of amoA genes discloses diverse ammonia-oxidizing archaeal and bacterial populations, bioRxiv, 2023-04, https://doi.org/10.1101/2023.04.10.536224, 2023.
Hollibaugh, J. T., Gifford, S. M., Moran, M. A., Ross, M. J., Sharma, S., and Tolar, B. B.: Seasonal variation in the metratranscriptomes of a Thaumarchaeota population from SE USA coastal waters, ISME J., 8, 685–698, 2014.
Horak, R. E., Qin, W., Schauer, A. J., Armbrust, E. V., Ingalls, A. E., Moffett, J. W., Stahl, D. A., and Devol, A. H.: Ammonia oxidation kinetics and temperature sensitivity of a natural marine community dominated by Archaea, ISME J., 7, 2023–2033, https://doi.org/10.1038/ismej.2013.75, 2013.
Horak, R. E. A., Qin, W., Bertagnolli, A. D., Nelson, A., Heal, K. R., Han, H., Heller, M., Schauer, A. J., Jeffrey, W. H., Armbrust, E. V., Moffett, J. W., Ingalls, A. E., Stahl, D. A., and Devol, A. H.: Relative impacts of light, temperature, and reactive oxygen on thaumarchaeal ammonia oxidation in the North Pacific Ocean, Limnol. Oceanogr., 63, 741–757, https://doi.org/10.1002/lno.10665, 2018.
Hornek, R., Pommerening-Röser, A., Koops, H.-P., Farnleitner, A. H., Kreuzinger, N., Kirschner, A., and Mach, R. L.: Primers containing universal bases reduce multiple amoA gene specific DGGE band patterns when analysing the diversity of beta-ammonia oxidizers in the environment, J. Microbiol. Meth., 66, 147–155, https://doi.org/10.1016/j.mimet.2005.11.001, 2006.
Hsiao, S. S.-Y., Hsu, T.-C., Liu, J.-w., Xie, X., Zhang, Y., Lin, J., Wang, H., Yang, J.-Y. T., Hsu, S.-C., Dai, M., and Kao, S.-J.: Nitrification and its oxygen consumption along the turbid Chang Jiang River plume, Biogeosciences, 11, 2083–2098, https://doi.org/10.5194/bg-11-2083-2014, 2014.
Ji, Q., Buitenhuis, E., Suntharalingam, P., Sarmiento, J. L., and Ward, B. B.: Global Nitrous Oxide Production Determined by Oxygen Sensitivity of Nitrification and Denitrification, Global Biogeochem. Cy., 32, 1790–1802, https://doi.org/10.1029/2018gb005887, 2018.
Kalvelage, T., Jensen, M. M., Contreras, S., Revsbech, N. P., Lam, P., Gunter, M., LaRoche, J., Lavik, G., and Kuypers, M. M.: Oxygen sensitivity of anammox and coupled N-cycle processes in oxygen minimum zones, PloS one, 6, e29299, https://doi.org/10.1371/journal.pone.0029299, 2011.
Kalvelage, T., Lavik, G., Lam, P., Contreras, S., Arteaga, L., Löscher, C. R., Oschlies, A., Paulmier, A., Stramma, L., and Kuypers, M. M. M.: Nitrogen cycling driven by organic matter export in the South Pacific oxygen minimum zone, Nat. Geosci., 6, 228, https://doi.org/10.1038/ngeo1739, 2013.
Kanda, J., Laws, E. A., Saino, T., and Hattori, A.: An evaluation of isotope dilution effect from conventional data sets of 15N uptake experiments, J. Plankton Res., 9, 79–90, https://doi.org/10.1093/plankt/9.1.79, 1987.
Kitzinger, K., Padilla, C. C., Marchant, H. K., Hach, P. F., Herbold, C. W., Kidane, A. T., Könneke, M., Littmann, S., Mooshammer, M., Niggemann, J., Petrov, S., Richter, A., Stewart, F. J., Wagner, M., Kuypers, M. M. M., and Bristow, L. A.: Cyanate and urea are substrates for nitrification by Thaumarchaeota in the marine environment, Nat. Microbiol., 4, 234–243, https://doi.org/10.1038/s41564-018-0316-2, 2018.
Kitzinger, K., Marchant, H. K., Bristow, L. A., Herbold, C. W., Padilla, C. C., Kidane, A. T., Littmann, S., Daims, H., Pjevac, P., Stewart, F. J., and Wagner, M.: Single cell analyses reveal contrasting life strategies of the two main nitrifiers in the ocean, Nat. Commun., 11, 767, https://doi.org/10.1038/s41467-020-14542-3, 2020.
Khachikyan, A., Milucka, J., Littmann, S., Ahmerkamp, S., Meador, T., Könneke, M., Burg, T., and Kuypers, M. M.: Direct cell mass measurements expand the role of small microorganisms in nature, Appl. Environ. Microb., 85, e00493-19, https://doi.org/10.1128/AEM.00493-19, 2019.
Kraft, B., Jehmlich, N., Larsen, M., Bristow Laura, A., Könneke, M., Thamdrup, B., and Canfield Donald, E.: Oxygen and nitrogen production by an ammonia-oxidizing archaeon, Science, 375, 97–100, https://doi.org/10.1126/science.abe6733, 2022.
Lam, P., Lavika, G., Jensena, M. M., van de Vossenbergb, J., Schmidb, M., and Woebkena, D.: Revising the nitrogen cycle in the Peruvian oxygen minimum zone, P. Natl. Acad. Sci. USA, 106, 4752–4757, https://doi.org/10.1073/pnas.0812444106, 2009.
Laperriere, S. M., Morando, M., Capone, D. G., Gunderson, T., Smith, J. M., and Santoro, A. E.: Nitrification and nitrous oxide dynamics in the Southern California Bight, Limnol. Oceanogr., 66, 1099–1112, https://doi.org/10.1002/lno.11667, 2020.
Li, G., Cheng, L., Zhu, J., Trenberth, K. E., Mann, M. E., and Abraham, J. P.: Increasing ocean stratification over the past half-century, Nat. Clim. Change, 10, 1116–1123, https://doi.org/10.1038/s41558-020-00918-2, 2020.
Lin, Y., Gifford, S., Ducklow, H., Schofield, O., and Cassar, N.: Towards quantitative microbiome community profiling using internal standards, Appl. Environ. Microb., 85, e02634-18, https://doi.org/10.1128/AEM.02634-18, 2019.
Lipschultz, F.: Isotope tracer methods for studies of the marine nitrogen cycle, Nitrogen in the Marine Environment, 2, 1345–1384, https://doi.org/10.1016/B978-0-12-372522-6.00031-1, 2008.
Lipschultz, F., Wofsy, S. C., and Fox, L. E.: Nitrogen metabolism of the eutrophic Delaware River ecosystem1, Limnol. Oceanogr., 31, https://doi.org/10.4319/lo.1986.31.4.0701, 701–716, 1986.
Liu, H., Zhou, P., Cheung, S., Lu, Y., Liu, H., and Jing, H.: Distribution and Oxidation Rates of Ammonia-Oxidizing Archaea Influenced by the Coastal Upwelling off Eastern Hainan Island, Microorganisms, 10, 952, https://doi.org/10.3390/microorganisms10050952, 2022.
Liu, Q., Tolar, B. B., Ross, M. J., Cheek, J. B., Sweeney, C. M., Wallsgrove, N. J., Popp, B. N., and Hollibaugh, J. T.: Light and temperature control the seasonal distribution of thaumarchaeota in the South Atlantic bight, ISME J., 12, 1473–1485, https://doi.org/10.1038/s41396-018-0066-4, 2018.
Lomas, M. W. and Lipschultz, F.: Forming the primary nitrite maximum: Nitrifiers or phytoplankton?, Limnol. Oceanogr., 51, 2453–2467, https://doi.org/10.4319/lo.2006.51.5.2453, 2006.
McCarthy, J. J., Garside, C., and Nevins, J. L.: Nitrogen dynamics during the Arabian Sea Northeast Monsoon, Deep-Sea Res. Pt. II, 46, 1623–1664, https://doi.org/10.1016/S0967-0645(99)00038-7, 1999.
McIlvin, M. R. and Altabet, M. A.: Chemical Conversion of Nitrate and Nitrite to Nitrous Oxide for Nitrogen and Oxygen Isotopic Analysis in Freshwater and Seawater, Anal. Chem., 77, 5589–5595, https://doi.org/10.1021/ac050528s, 2005.
Mdutyana, M., Thomalla, S. J., Philibert, R., Ward, B. B., and Fawcett, S. E.: The Seasonal Cycle of Nitrogen Uptake and Nitrification in the Atlantic Sector of the Southern Ocean, Global Biogeochem. Cy., 34, e2019GB006363, https://doi.org/10.1029/2019gb006363, 2020.
Mdutyana, M., Marshall, T., Sun, X., Burger, J. M., Thomalla, S. J., Ward, B. B., and Fawcett, S. E.: Controls on nitrite oxidation in the upper Southern Ocean: insights from winter kinetics experiments in the Indian sector, Biogeosciences, 19, 3425–3444, https://doi.org/10.5194/bg-19-3425-2022, 2022a.
Mdutyana, M., Sun, X., Burger, J. M., Flynn, R. F., Smith, S., Horsten, N. R., Roychoudhury, A. N., Planquette, H., Bucciarelli, E., Thomalla, S. J., Ward, B. B., and Fawcett, S. E.: The kinetics of ammonium uptake and oxidation across the Southern Ocean, Limnol. Oceanogr., 67, 973–991, https://doi.org/10.1002/lno.12050, 2022b.
Merbt, S. N., Stahl, D. A., Casamayor, E. O., Marti, E., Nicol, G. W., and Prosser, J. I.: Differential photoinhibition of bacterial and archaeal ammonia oxidation, FEMS Microbiol. Lett., 327, 41–46, https://doi.org/10.1111/j.1574-6968.2011.02457.x, 2012.
Meredith, M., Sommerkorn, M., Cassotta, S., Derksen, C., Ekaykin, A., Hollowed, A., Kofinas, G., Mackintosh, A., Melbourne-Thomas, J., Muelbert, M., Ottersen, G., Pritchard, H., and Schuur, E. A. G.: Polar Regions, Chapter 3, IPCC Special Report on the Ocean and Cryosphere in a Changing Climate, https://doi.org/10.1017/9781009157964.005, 2019.
Middelburg, J. J.: Chemoautotrophy in the ocean, Geophys. Res. Lett., 38, L24604, https://doi.org/10.1029/2011gl049725, 2011.
Mincer, T. J., Church, M. J., Taylor, L. T., Preston, C., Karl, D. M., and DeLong, E. F.: Quantitative distribution of presumptive archaeal and bacterial nitrifiers in Monterey Bay and the North Pacific Subtropical Gyre, Environ. Microbiol., 9, 1162–1175, https://doi.org/10.1111/j.1462-2920.2007.01239.x, 2007.
Mosier, A. C. and Francis, C. A.: Determining the distribution of marine and coastal ammonia-oxidizing archaea and bacteria using a quantitative approach, Method. Enzymol., 486, 205–221, 2012.
Newell, S. E., Fawcett, S. E., and Ward, B. B.: Depth distribution of ammonia oxidation rates and ammonia-oxidizer community composition in the Sargasso Sea, Limnol. Oceanogr, 58, 1491–1500, 2013.
Olson, R.: 15N tracer studies of the primary nitrite maximum, J. Mar. Res., 39, 203–226, 1981a.
Olson, R.: Differential photoinhibition of marine nitrifying bacteria: a possible mechanism for the formation of the primary nitrite maximum, J. Mar. Res., 39, 227–238, 1981b.
Pachiadaki, M. G., Sintes, E., Bergauer, K., Brown, J. M., Record, N. R., Swan, B. K., Mathyer, M. E., Hallam, S. J., Lopez-Garcia, P., Takaki, Y., Nunoura, T., Woyke, T., Herndl, G. J., and Stepanauskas, R.: Major role of nitrite-oxidizing bacteria in dark ocean carbon fixation, Science, 358, 1046–1051, https://doi.org/10.1126/science.aan8260, 2017.
Peng, X., Jayakumar, A., and Ward, B. B.: Community composition of ammonia-oxidizing archaea from surface and anoxic depths of oceanic oxygen minimum zones, Front. Microbiol., 4, 177, https://doi.org/10.3389/fmicb.2013.00177, 2013.
Peng, X., Fuchsman, C. A., Jayakumar, A., Oleynik, S., Martens-Habbena, W., Devol, A. H., and Ward, B. B.: Ammonia and nitrite oxidation in the Eastern Tropical North Pacific, Global Biogeochem. Cy., 29, 2034–2049, https://doi.org/10.1002/2015GB005278, 2015.
Peng, X., Fuchsman, C. A., Jayakumar, A., Warner, M. J., Devol, A. H., and Ward, B. B.: Revisiting nitrification in the Eastern Tropical South Pacific: A focus on controls, J. Geophys. Res.-Oceans, 121, 1667–1684, https://doi.org/10.1002/2015jc011455, 2016.
Peng, X., Fawcett, S. E., van Oostende, N., Wolf, M. J., Marconi, D., Sigman, D. M., and Ward, B. B.: Nitrogen uptake and nitrification in the subarctic North Atlantic Ocean, Limnol. Oceanogr., 63, 1462–1487, https://doi.org/10.1002/lno.10784, 2018.
Pester, M., Maixner, F., Berry, D., Rattei, T., Koch, H., Lucker, S., Nowka, B., Richter, A., Spieck, E., Lebedeva, E., Loy, A., Wagner, M., and Daims, H.: NxrB encoding the beta subunit of nitrite oxidoreductase as functional and phylogenetic marker for nitrite-oxidizing Nitrospira, Environ. Microbiol., 16, 3055–3071, https://doi.org/10.1111/1462-2920.12300, 2014.
Raes, E. J., van de Kamp, J., Bodrossy, L., Fong, A. A., Riekenberg, J., Holmes, B. H., Erler, D. V., Eyre, B. D., Weil, S.-S., and Waite, A. M.: N2 Fixation and New Insights Into Nitrification From the Ice-Edge to the Equator in the South Pacific Ocean, Front. Mar. Sci., 7, 389, https://doi.org/10.3389/fmars.2020.00389, 2020.
Raimbault, P., Slawyk, G., Boudjellal, B., Coatanoan, C., Conan, P., Coste, B., Garcia, N., Moutin, T., and Pujo-Pay, M.: Carbon and nitrogen uptake and export in the equatorial Pacific at 150∘ W: Evidence of an efficient regenerated production cycle, J. Geophys. Res.-Oceans, 104, 3341–3356, https://doi.org/10.1029/1998jc900004, 1999.
Rotthauwe, J. H., Witzel, K. P., and Liesack, W.: The ammonia monooxygenase structural gene amoA as a functional marker: molecular fine-scale analysis of natural ammonia-oxidizing populations, Appl. Environ. Microbiol., 63, 4704–4712, 1997.
Saito, M. A., McIlvin, M. R., Moran, D. M., Santoro, A. E., Dupont, C. L., Rafter, P. A., Saunders, J. K., Kaul, D., Lamborg, C. H., Westley, M., and Valois, F.: Abundant nitrite-oxidizing metalloenzymes in the mesopelagic zone of the tropical Pacific Ocean, Nat. Geosci., 13, 355–362, 2020.
Santoro, A. E., Casciotti, K. L., and Francis, C. A.: Activity, abundance and diversity of nitrifying archaea and bacteria in the central California Current, Environ. Microbiol., 12, 1989–2006, https://doi.org/10.1111/j.1462-2920.2010.02205.x, 2010.
Santoro, A. E., Sakamoto, C. M., Smith, J. M., Plant, J. N., Gehman, A. L., Worden, A. Z., Johnson, K. S., Francis, C. A., and Casciotti, K. L.: Measurements of nitrite production in and around the primary nitrite maximum in the central California Current, Biogeosciences, 10, 7395–7410, https://doi.org/10.5194/bg-10-7395-2013, 2013.
Santoro, A. E., Saito, M. A., Goepfert, T. J., Lamborg, C. H., Dupont, C. L., and DiTullio, G. R.: Thaumarchaeal ecotype distributions across the equatorial Pacific Ocean and their potential roles in nitrification and sinking flux attenuation, Limnol. Oceanogr., 62, 1984–2003, https://doi.org/10.1002/lno.10547, 2017.
Santoro, A. E., Buchwald, C., Knapp, A. N., Berelson, W. M., Capone, D. G., and Casciotti, K. L.: Nitrification and Nitrous Oxide Production in the Offshore Waters of the Eastern Tropical South Pacific, Global Biogeochem. Cy., 35, e2020GB006716, https://doi.org/10.1029/2020gb006716, 2021.
Satinsky, B. M., Gifford, S. M., Crump, B. C., and Moran, M. A.: Use of internal standards for quantitative metatranscriptome and metagenome analysis, Meth. Enzymol., 531, 237–250, 2013.
Schleper, C. and Nicol, G. W.: Ammonia-oxidising archaea–physiology, ecology and evolution, Adv. Microb. Physiol., 57, 1–41, https://doi.org/10.1016/B978-0-12-381045-8.00001-1, 2010.
Shafiee, R. T., Snow, J. T., Zhang, Q., and Rickaby, R. E. M.: Iron requirements and uptake strategies of the globally abundant marine ammonia-oxidising archaeon, Nitrosopumilus maritimus SCM1, ISME J., 13, 2295–2305, https://doi.org/10.1038/s41396-019-0434-8, 2019.
Shafiee, R. T., Diver, P. J., Snow, J. T., Zhang, Q., and Rickaby, R. E.: Marine ammonia-oxidising archaea and bacteria occupy distinct iron and copper niches, ISME Communications, 1, 1, https://doi.org/10.1038/s43705-021-00001-7, 2021.
Shiozaki, T., Ijichi, M., Fujiwara, A., Makabe, A., Nishino, S., Yoshikawa, C., and Harada, N.: Factors Regulating Nitrification in the Arctic Ocean: Potential Impact of Sea Ice Reduction and Ocean Acidification, Global Biogeochemi. Cy., 33, 1085–1099, https://doi.org/10.1029/2018gb006068, 2019.
Shiozaki, T., Ijichi, M., Isobe, K., Hashihama, F., Nakamura, K.-i., Ehama, M., Hayashizaki, K.-i., Takahashi, K., Hamasaki, K., and Furuya, K.: Nitrification and its influence on biogeochemical cycles from the equatorial Pacific to the Arctic Ocean, ISME J., 10, 2184–2197, https://doi.org/10.1038/ismej.2016.18, 2016.
Shiozaki, T., Hashihama, F., Endo, H., Ijichi, M., Takeda, N., Makabe, A., Fujiwara, A., Nishino, S., and Harada, N.: Assimilation and oxidation of urea-derived nitrogen in the summer Arctic Ocean, Limnol. Oceanogr., 66, 4159–4170, https://doi.org/10.1002/lno.11950, 2021.
Sigman, D. M., Casciotti, K. L., Andreani, M., Barford, C., Galanter, M., and Böhlke, J. K.: A Bacterial Method for the Nitrogen Isotopic Analysis of Nitrate in Seawater and Freshwater, Anal. Chem., 73, 4145–4153, https://doi.org/10.1021/ac010088e, 2001.
Sintes, E., Bergauer, K., De Corte, D., Yokokawa, T., and Herndl, G. J.: Archaeal amoA gene diversity points to distinct biogeography of ammonia-oxidizing Crenarchaeota in the ocean, Environ. Microbiol., 15, 1647–1658, https://doi.org/10.1111/j.1462-2920.2012.02801.x, 2013.
Sintes, E., De Corte, D., Haberleitner, E., and Herndl, G. J.: Geographic Distribution of Archaeal Ammonia Oxidizing Ecotypes in the Atlantic Ocean, Front. Microbiol., 7, 77, https://doi.org/10.3389/fmicb.2016.00077, 2016.
Smith, J. M., Chavez, F. P., and Francis, C. A.: Ammonium uptake by phytoplankton regulates nitrification in the sunlit ocean, PloS one, 9, e108173, https://doi.org/10.1371/journal.pone.0108173, 2014.
Smith, S., Altieri, K. E., Mdutyana, M., Walker, D. R., Parrott, R. G., Gallie, S., Spence, K. A. M., Burger, J. M., and Fawcett, S. E.: Biogeochemical controls on ammonium accumulation in the surface layer of the Southern Ocean, Biogeosciences, 19, 715–741, https://doi.org/10.5194/bg-19-715-2022, 2022.
Sun, X., Ji, Q., Jayakumar, A., and Ward, B. B.: Dependence of nitrite oxidation on nitrite and oxygen in low-oxygen seawater, Geophys. Res. Lett., 44, 7883–7891, https://doi.org/10.1002/2017GL074355, 2017.
Sun, X., Kop, L. F. M., Lau, M. C. Y., Frank, J., Jayakumar, A., Lücker, S., and Ward, B. B.: Uncultured Nitrospina-like species are major nitrite oxidizing bacteria in oxygen minimum zones, ISME J., 13, 2391–2402, https://doi.org/10.1038/s41396-019-0443-7, 2019.
Sun, X., Frey, C., Garcia-Robledo, E., Jayakumar, A., and Ward, B. B.: Microbial niche differentiation explains nitrite oxidation in marine oxygen minimum zones, ISME J., 15, 1317–1329, https://doi.org/10.1038/s41396-020-00852-3, 2021.
Sun, X., Frey, C., and Ward, B. B.: Nitrite oxidation across the full oxygen spectrum in the ocean, Global Biogeochem. Cy., 37, 2022GB007548, https://doi.org/10.1029/2022GB007548, 2023.
Sutka, R. L., Ostrom, N. E., Ostrom, P. H., and Phanikumar, M. S.: Stable nitrogen isotope dynamics of dissolved nitrate in a transect from the north Pacific subtropical gyre to the eastern tropical north Pacific, Geochim. Cosmochim. Ac., 68, 517–527, https://doi.org/10.1016/S0016-7037(03)00483-6, 2004.
Suzuki, I., Dular, U., and Kwok, S.: Ammonia or ammonium ion as substrate for oxidation by Nitrosomonas europaea cells and extracts, J. Bacteriol., 120, 556–558, https://doi.org/10.1128/jb.120.1.556-558.1974, 1974.
Tang, W., Ward, B., Beman, M., Bristow, L., Clark, D., Fawcett, S., Frey, C., Fripiat, F., Herndl, G., Mdutyana, M., Paulot, F., Peng, X., Santoro, A., Shiozaki, T., Sintes, E., Stock, C., Sun, X., Wan, X., Xu, M., and Zhang, Y.: Database of nitrification and nitrifiers in the global ocean, Zenodo [data set], https://doi.org/10.5281/zenodo.8355912, 2023.
Tolar, B. B., King, G. M., and Hollibaugh, J. T.: An analysis of Thaumarchaeota populations from the Northern Gulf of Mexico, Front. Microbiol., 4, 72, https://doi.org/10.3389/fmicb.2013.00072, 2013.
Tolar, B. B., Ross, M. J., Wallsgrove, N. J., Liu, Q., Aluwihare, L. I., Popp, B. N., and Hollibaugh, J. T.: Contribution of ammonia oxidation to chemoautotrophy in Antarctic coastal waters, ISME J., 10, 2605–2619, https://doi.org/10.1038/ismej.2016.61, 2016.
Tolar, B. B., Wallsgrove, N. J., Popp, B. N., and Hollibaugh, J. T.: Oxidation of urea-derived nitrogen by thaumarchaeota-dominated marine nitrifying communities, Environ. Microbiol., 19, 4838–4850, https://doi.org/10.1111/1462-2920.13457, 2017.
Tolar, B. B., Reji, L., Smith, J. M., Blum, M., Pennington, J. T., Chavez, F. P., and Francis, C. A.: Time series assessment of Thaumarchaeota ecotypes in Monterey Bay reveals the importance of water column position in predicting distribution–environment relationships, Limnol. Oceanogr., 65, 2041–2055, https://doi.org/10.1002/lno.11436, 2020.
Tracey, J. C., Babbin, A. R., Wallace, E., Sun, X., DuRussel, K. L., Frey, C., Martocello III, D. E., Tamasi, T., Oleynik, S., and Ward, B. B.: All about nitrite: exploring nitrite sources and sinks in the eastern tropical North Pacific oxygen minimum zone, Biogeosciences, 20, 2499–2523, https://doi.org/10.5194/bg-20-2499-2023, 2023.
van de Leemput, I. A., Veraart, A. J., Dakos, V., de Klein, J. J., Strous, M., and Scheffer, M.: Predicting microbial nitrogen pathways from basic principles, Environ. Microbiol., 13, 1477–1487, 2011.
van Kessel, M. A. H. J., Speth, D. R., Albertsen, M., Nielsen, P. H., Op den Camp, H. J. M., Kartal, B., Jetten, M. S. M., and Lücker, S.: Complete nitrification by a single microorganism, Nature, 528, 555–559, https://doi.org/10.1038/nature16459, 2015.
Wallschuss, S., Mdutyana, M., Parrott, R. G., Forrer, H. J., Roman, R., Walker, D. R., Ansorge, I. J., and Fawcett, S. E.: The influence of Agulhas leakage on primary production and nitrogen cycling in the southeastern Atlantic Ocean, J. Geophys. Res.-Oceans, 127, e2022JC018971, https://doi.org/10.1029/2022JC018971, 2022.
Wan, X. S., Sheng, H.-X., Dai, M., Zhang, Y., Shi, D., Trull, T. W., Zhu, Y., Lomas, M. W., and Kao, S.-J.: Ambient nitrate switches the ammonium consumption pathway in the euphotic ocean, Nat. Commun., 9, 915, https://doi.org/10.1038/s41467-018-03363-0, 2018.
Wan, X. S., Sheng, H.-X., Dai, M., Church, M. J., Zou, W., Li, X., Hutchins, D. A., Ward, B. B., and Kao, S.-J.: Phytoplankton-nitrifier interactions control the geographic distribution of nitrite in the upper ocean, Global Biogeochem. Cy., 35, e2021GB007072, https://doi.org/10.1029/2021GB007072, 2021.
Wan, X. S., Sheng, H.-X., Dai, M., Casciotti, K. L., Church, M. J., Zou, W., Liu, L., Shen, H., Zhou, K., Ward, B. B., and Kao, S.-J.: Epipelagic nitrous oxide production offsets carbon sequestration by the biological pump, Nat. Geosci., 16, 29–36, https://doi.org/10.1038/s41561-022-01090-2, 2022.
Ward, B. B.: Nitrogen transformations in the Southern California Bight, Deep-Sea Res. Pt. I, 34, 785–805, https://doi.org/10.1016/0198-0149(87)90037-9, 1987.
Ward, B. B.: Measurement and distribution of nitrification rates in the oceans, in: Methods in enzymology, Elsevier, 307–323, https://doi.org/10.1016/B978-0-12-381294-0.00013-4, 2011a.
Ward, B. B.: Nitrification in the Ocean, in: Nitrification, 323–345, https://doi.org/10.1128/9781555817145.ch13, 2011b.
Ward, B. B.: Temporal variability in nitrification rates and related biogeochemical factors in Monterey Bay, California, USA, Mar. Ecol. Prog. Ser., 292, 97–109, 2005.
Ward, B. B.: Nitrification in Marine Systems, in: Nitrogen in the Marine Environment, 2 ed., edited by: Capone, D. G., Bronk, D. A., Mulholland, M. R., and Carpenter, E. J., Elsevier, 199–262, https://doi.org/10.1016/B978-0-12-372522-6.00005-0, 2008.
Ward, B. B. and Zafiriou, O. C.: Nitrification and nitric oxide in the oxygen minimum of the eastern tropical North Pacific, Deep-Sea Res. Pt. I, 35, 1127–1142, https://doi.org/10.1016/0198-0149(88)90005-2, 1988.
Ward, B. B., Olson, R. J., and Perry, M. J.: Microbial nitrification rates in the primary nitrite maximum off southern California, Deep-Sea Res. Pt. I, 29, 247–255, https://doi.org/10.1016/0198-0149(82)90112-1, 1982.
Ward, B. B., Talbot, M. C., and Perry, M. J.: Contributions of phytoplankton and nitrifying bacteria to ammonium and nitrite dynamics in coastal waters, Cont. Shelf Res., 3, 383–398, https://doi.org/10.1016/0278-4343(84)90018-9, 1984.
Ward B. B, Kilpatrick, K. A., Renger, E. H., and Eppley, R. W.: Biological nitrogen cycling in the nitracline, Limnol. Oceanogr.. 34, 493–513, https://doi.org/10.4319/lo.1989.34.3.0493, 1989a.
Ward, B. B., Glover, H. E., and Lipschultz, F.: Chemoautotrophic activity and nitrification in the oxygen minimum zone off Peru, Deep-Sea Res. Pt. I, 36, 1031–1051, https://doi.org/10.1016/0198-0149(89)90076-9, 1989b.
Weigand, M. A., Foriel, J., Barnett, B., Oleynik, S., and Sigman, D. M.: Updates to instrumentation and protocols for isotopic analysis of nitrate by the denitrifier method, Rapid Commun. Mass Spectrom., 30, 1365–1383, 2016.
Wilkinson, M. D., Dumontier, M., Aalbersberg, I. J., Appleton, G., Axton, M., Baak, A., Blomberg, N., Boiten, J.-W., da Silva Santos, L. B., Bourne, P. E., Bouwman, J., Brookes, A. J., Clark, T., Crosas, M., Dillo, I., Dumon, O., Edmunds, S., Evelo, C. T., Finkers, R., Gonzalez-Beltran, A., Gray, A. J. G., Groth, P., Goble, C., Grethe, J. S., Heringa, J., 't Hoen, P. A. C., Hooft, R., Kuhn, T., Kok, R., Kok, J., Lusher, S. J., Martone, M. E., Mons, A., Packer, A. L., Persson, B., Rocca-Serra, P., Roos, M., van Schaik, R., Sansone, S.-A., Schultes, E., Sengstag, T., Slater, T., Strawn, G., Swertz, M. A., Thompson, M., van der Lei, J., van Mulligen, E., Velterop, J., Waagmeester, A., Wittenburg, P., Wolstencroft, K., Zhao, J., and Mons, B.: The FAIR Guiding Principles for scientific data management and stewardship, Sci. Data, 3, 160018, https://doi.org/10.1038/sdata.2016.18, 2016.
Wuchter, C., Abbas, B., Coolen, M. J., Herfort, L., van Bleijswijk, J., Timmers, P., Strous, M., Teira, E., Herndl, G. J., Middelburg, J. J., Schouten, S., and Sinninghe Damste, J. S.: Archaeal nitrification in the ocean, P. Natl. Acad. Sci. USA, 103, 12317–12322, https://doi.org/10.1073/pnas.0600756103, 2006.
Xia, F., Wang, J. G., Zhu, T., Zou, B., Rhee, S. K., and Quan, Z. X.: Ubiquity and diversity of complete ammonia oxidizers (comammox), Appl. Environ. Microb., 84, e01390-18, https://doi.org/10.1128/AEM.01390-18, 2018.
Xu, M. N., Zhang, W., Zhu, Y., Liu, L., Zheng, Z., Wan, X. S., Qian, W., Dai, M., Gan, J., and Hutchins, D. A.: Enhanced ammonia oxidation caused by lateral Kuroshio intrusion in the boundary zone of the northern South China Sea, Geophys. Res. Lett., 45, 6585–6593, https://doi.org/10.1029/2018GL077896, 2018.
Xu, M. N., Li, X., Shi, D., Zhang, Y., Dai, M., Huang, T., Glibert, P. M., and Kao, S. J.: Coupled effect of substrate and light on assimilation and oxidation of regenerated nitrogen in the euphotic ocean, Limnol. Oceanogr., 64, 1270–1283, https://doi.org/10.1002/lno.11114, 2019.
Yool, A., Martin, A. P., Fernández, C., and Clark, D. R.: The significance of nitrification for oceanic new production, Nature, 447, 999–1002, 2007.
Zakem, E. J., Al-Haj, A., Church, M. J., van Dijken, G. L., Dutkiewicz, S., Foster, S. Q., Fulweiler, R. W., Mills, M. M., and Follows, M. J.: Ecological control of nitrite in the upper ocean, Nat. Commun., 9, 1206, https://doi.org/10.1038/s41467-018-03553-w, 2018.
Zakem, E. J., Bayer, B., Qin, W., Santoro, A. E., Zhang, Y., and Levine, N. M.: Controls on the relative abundances and rates of nitrifying microorganisms in the ocean, Biogeosciences, 19, 5401–5418, https://doi.org/10.5194/bg-19-5401-2022, 2022.
Zhang, Y., Qin, W., Hou, L., Zakem, E. J., Wan, X., Zhao, Z., Liu, L., Hunt, K. A., Jiao, N., Kao, S. J., Tang, K., Xie, X., Shen, J., Li, Y., Chen, M., Dai, X., Liu, C., Deng, W., Dai, M., Ingalls, A. E., Stahl, D. A., and Herndl, G. J.: Nitrifier adaptation to low energy flux controls inventory of reduced nitrogen in the dark ocean, P. Natl. Acad. Sci. USA, 117, 4823–4830, https://doi.org/10.1073/pnas.1912367117, 2020.
Zheng, Z. Z., Wan, X. H., Xu, M. N., Hsiao, S. S. Y., Zhang, Y., Zheng, L. W., Wu, Y. H., Zou, W. B., and Kao, S. J.: Effects of temperature and particles on nitrification in a eutrophic coastal bay in southern China, J. Geophys. Res.-Biogeo., 122, 2325–2337, https://doi.org/10.1002/2017jg003871, 2017.
Zheng, Z.-Z., Zheng, L.-W., Xu, M. N., Tan, E., Hutchins, D. A., Deng, W., Zhang, Y., Shi, D., Dai, M., and Kao, S.-J.: Substrate regulation leads to differential responses of microbial ammonia-oxidizing communities to ocean warming, Nat. Commun., 11, 3511, https://doi.org/10.1038/s41467-020-17366-3, 2020.
Short summary
Nitrification and nitrifiers play an important role in marine nitrogen and carbon cycles by converting ammonium to nitrite and nitrate. Nitrification could affect microbial community structure, marine productivity, and the production of nitrous oxide – a powerful greenhouse gas. We introduce the newly constructed database of nitrification and nitrifiers in the marine water column and guide future research efforts in field observations and model development of nitrification.
Nitrification and nitrifiers play an important role in marine nitrogen and carbon cycles by...
Altmetrics
Final-revised paper
Preprint