Articles | Volume 17, issue 2
https://doi.org/10.5194/essd-17-393-2025
© Author(s) 2025. 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-17-393-2025
© Author(s) 2025. This work is distributed under
the Creative Commons Attribution 4.0 License.
the Creative Commons Attribution 4.0 License.
Data description paper
| 
04 Feb 2025
Data description paper |
| 04 Feb 2025
| 04 Feb 2025
Global biogeography of N2-fixing microbes: nifH amplicon database and analytics workflow
Michael Morando
Ocean Sciences Department, University of California, Santa Cruz, Santa Cruz, CA 95064, United States
Jonathan D. Magasin
Ocean Sciences Department, University of California, Santa Cruz, Santa Cruz, CA 95064, United States
Shunyan Cheung
Ocean Sciences Department, University of California, Santa Cruz, Santa Cruz, CA 95064, United States
Institute of Marine Biology and Center of Excellence for the Oceans, National Taiwan Ocean University, Keelung 20224, Taiwan
Matthew M. Mills
Earth System Science, Stanford University, Stanford, CA 94305, United States
Jonathan P. Zehr
Ocean Sciences Department, University of California, Santa Cruz, Santa Cruz, CA 95064, United States
Kendra A. Turk-Kubo
CORRESPONDING AUTHOR
Ocean Sciences Department, University of California, Santa Cruz, Santa Cruz, CA 95064, United States
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Zhibo Shao, Yangchun Xu, Hua Wang, Weicheng Luo, Lice Wang, Yuhong Huang, Nona Sheila R. Agawin, Ayaz Ahmed, Mar Benavides, Mikkel Bentzon-Tilia, Ilana Berman-Frank, Hugo Berthelot, Isabelle C. Biegala, Mariana B. Bif, Antonio Bode, Sophie Bonnet, Deborah A. Bronk, Mark V. Brown, Lisa Campbell, Douglas G. Capone, Edward J. Carpenter, Nicolas Cassar, Bonnie X. Chang, Dreux Chappell, Yuh-ling Lee Chen, Matthew J. Church, Francisco M. Cornejo-Castillo, Amália Maria Sacilotto Detoni, Scott C. Doney, Cecile Dupouy, Marta Estrada, Camila Fernandez, Bieito Fernández-Castro, Debany Fonseca-Batista, Rachel A. Foster, Ken Furuya, Nicole Garcia, Kanji Goto, Jesús Gago, Mary R. Gradoville, M. Robert Hamersley, Britt A. Henke, Cora Hörstmann, Amal Jayakumar, Zhibing Jiang, Shuh-Ji Kao, David M. Karl, Leila R. Kittu, Angela N. Knapp, Sanjeev Kumar, Julie LaRoche, Hongbin Liu, Jiaxing Liu, Caroline Lory, Carolin R. Löscher, Emilio Marañón, Lauren F. Messer, Matthew M. Mills, Wiebke Mohr, Pia H. Moisander, Claire Mahaffey, Robert Moore, Beatriz Mouriño-Carballido, Margaret R. Mulholland, Shin-ichiro Nakaoka, Joseph A. Needoba, Eric J. Raes, Eyal Rahav, Teodoro Ramírez-Cárdenas, Christian Furbo Reeder, Lasse Riemann, Virginie Riou, Julie C. Robidart, Vedula V. S. S. Sarma, Takuya Sato, Himanshu Saxena, Corday Selden, Justin R. Seymour, Dalin Shi, Takuhei Shiozaki, Arvind Singh, Rachel E. Sipler, Jun Sun, Koji Suzuki, Kazutaka Takahashi, Yehui Tan, Weiyi Tang, Jean-Éric Tremblay, Kendra Turk-Kubo, Zuozhu Wen, Angelicque E. White, Samuel T. Wilson, Takashi Yoshida, Jonathan P. Zehr, Run Zhang, Yao Zhang, and Ya-Wei Luo
Earth Syst. Sci. Data, 15, 3673–3709, https://doi.org/10.5194/essd-15-3673-2023, https://doi.org/10.5194/essd-15-3673-2023, 2023
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N2 fixation by marine diazotrophs is an important bioavailable N source to the global ocean. This updated global oceanic diazotroph database increases the number of in situ measurements of N2 fixation rates, diazotrophic cell abundances, and nifH gene copy abundances by 184 %, 86 %, and 809 %, respectively. Using the updated database, the global marine N2 fixation rate is estimated at 223 ± 30 Tg N yr−1, which triplicates that using the original database.
Yanhong Lu, Shunyan Cheung, Ling Chen, Shuh-Ji Kao, Xiaomin Xia, Jianping Gan, Minhan Dai, and Hongbin Liu
Biogeosciences, 17, 6017–6032, https://doi.org/10.5194/bg-17-6017-2020, https://doi.org/10.5194/bg-17-6017-2020, 2020
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Through a comprehensive investigation, we observed differential niche partitioning among diverse ammonia-oxidizing archaea (AOA) sublineages in a typical subtropical estuary. Distinct AOA communities observed at DNA and RNA levels suggested that a strong divergence in ammonia-oxidizing activity among different AOA groups occurs. Our result highlights the importance of identifying major ammonia oxidizers at RNA level in future studies.
Karine Leblanc, Véronique Cornet, Mathieu Caffin, Martine Rodier, Anne Desnues, Hugo Berthelot, Kendra Turk-Kubo, and Jules Heliou
Biogeosciences, 13, 5205–5219, https://doi.org/10.5194/bg-13-5205-2016, https://doi.org/10.5194/bg-13-5205-2016, 2016
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
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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.
K. A. Turk-Kubo, I. E. Frank, M. E. Hogan, A. Desnues, S. Bonnet, and J. P. Zehr
Biogeosciences, 12, 7435–7452, https://doi.org/10.5194/bg-12-7435-2015, https://doi.org/10.5194/bg-12-7435-2015, 2015
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-A shift from diatom-associated diazotrophs (DDAs) to unicellular cyanobacterial group C (UCYN-C) in response to DIP fertilization was captured in a large-scale mesocosm experiment in the Noumea lagoon (NL), a low-nutrient low-chlorophyll coastal environment. -First report of in situ net growth and mortality rates for unicellular diazotrophs UCYN-A2, and UCYN-C. -First quantitative abundance data for diazotrophs in NL indicate that DDAs and UCYN-A1/A2 may be important N2 fixers in this region.
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Earth Syst. Sci. Data, 16, 5681–5701, https://doi.org/10.5194/essd-16-5681-2024, https://doi.org/10.5194/essd-16-5681-2024, 2024
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Earth Syst. Sci. Data Discuss., https://doi.org/10.5194/essd-2024-342, https://doi.org/10.5194/essd-2024-342, 2024
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Earth Syst. Sci. Data, 16, 3851–3871, https://doi.org/10.5194/essd-16-3851-2024, https://doi.org/10.5194/essd-16-3851-2024, 2024
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We build a compilation of early-life dispersal traits for coastal fish species. The database contains over 110 000 entries collected from 1993 to 2021 in the western Mediterranean. All observations are harmonized to provide information on dates and locations of spawning and settlement, along with pelagic larval durations. When applicable, missing data are reconstructed from dynamic energy budget theory. Statistical analyses reveal sampling biases across taxa, space and time.
Yan Yang, Patrick Brockmann, Carolina Galdino, Uwe Schindler, and Frédéric Gazeau
Earth Syst. Sci. Data, 16, 3771–3780, https://doi.org/10.5194/essd-16-3771-2024, https://doi.org/10.5194/essd-16-3771-2024, 2024
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Jaime Pitarch and Vittorio Ernesto Brando
Earth Syst. Sci. Data Discuss., https://doi.org/10.5194/essd-2024-295, https://doi.org/10.5194/essd-2024-295, 2024
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This research presents a comprehensive synthetic dataset in the optical domain, created thanks to a large mining of available bio-optical data. Utilizing the Hydrolight radiative transfer model, the dataset provides detailed light fields from ultraviolet to visible light, aiding in the development of satellite algorithms. The dataset will significantly enhance research on light behavior in water and supporting future hyperspectral missions. It has been made publicly available on Zenodo.
Thomas M. Jordan, Giorgio Dall'Olmo, Gavin Tilstone, Robert J. W. Brewin, Francesco Nencioli, Ruth Airs, Crystal S. Thomas, and Louise Schlüter
Earth Syst. Sci. Data Discuss., https://doi.org/10.5194/essd-2024-267, https://doi.org/10.5194/essd-2024-267, 2024
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We present a compilation of water optical properties and phytoplankton pigments from the surface of the Atlantic Ocean collected during nine cruises between 2009–2019. We derive continuous Chlorophyll a concentrations (a biomass proxy) from water absorption. We then illustrate geographical variations and relationships for water optical properties, Chlorophyll a, and the other pigments. The dataset will be useful to researchers in ocean optics, remote-sensing, ecology, and biogeochemistry.
Mathilde Dugenne, Marco Corrales-Ugalde, Jessica Y. Luo, Rainer Kiko, Todd D. 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, 16, 2971–2999, https://doi.org/10.5194/essd-16-2971-2024, https://doi.org/10.5194/essd-16-2971-2024, 2024
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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).
Nina Grandremy, Paul Bourriau, Edwin Daché, Marie-Madeleine Danielou, Mathieu Doray, Christine Dupuy, Bertrand Forest, Laetitia Jalabert, Martin Huret, Sophie Le Mestre, Antoine Nowaczyk, Pierre Petitgas, Philippe Pineau, Justin Rouxel, Morgan Tardivel, and Jean-Baptiste Romagnan
Earth Syst. Sci. Data, 16, 1265–1282, https://doi.org/10.5194/essd-16-1265-2024, https://doi.org/10.5194/essd-16-1265-2024, 2024
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We present two space- and time-resolved zooplankton datasets originating from samples collected in the Bay of Biscay in spring over the 2004–2019 period and imaged with the interoperable imaging systems ZooScan and ZooCAM. These datasets are suited for long-term size-based or combined size- and taxonomy-based ecological studies of zooplankton. The set of sorted images are provided along with a set of morphological descriptors that are useful when machine learning is applied to plankton studies.
Dieter Piepenburg, Thomas Brey, Katharina Teschke, Jennifer Dannheim, Paul Kloss, Marianne Rehage, Miriam L. S. Hansen, and Casper Kraan
Earth Syst. Sci. Data, 16, 1177–1184, https://doi.org/10.5194/essd-16-1177-2024, https://doi.org/10.5194/essd-16-1177-2024, 2024
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Research on ecological footprints of climate change and human impacts in Arctic seas is still hampered by problems in accessing sound data, which is unevenly distributed among regions and faunal groups. To address this issue, we present the PAN-Arctic data collection of benthic BIOtas (PANABIO). It provides open access to valuable biodiversity information by integrating data from various sources and of various formats and offers versatile exploration tools for data filtering and mapping.
Andrea J. McEvoy, Angus Atkinson, Ruth L. Airs, Rachel Brittain, Ian Brown, Elaine S. Fileman, Helen S. Findlay, Caroline L. McNeill, Clare Ostle, Tim J. Smyth, Paul J. Somerfield, Karen Tait, Glen A. Tarran, Simon Thomas, Claire E. Widdicombe, E. Malcolm S. Woodward, Amanda Beesley, David V. P. Conway, James Fishwick, Hannah Haines, Carolyn Harris, Roger Harris, Pierre Hélaouët, David Johns, Penelope K. Lindeque, Thomas Mesher, Abigail McQuatters-Gollop, Joana Nunes, Frances Perry, Ana M. Queiros, Andrew Rees, Saskia Rühl, David Sims, Ricardo Torres, and Stephen Widdicombe
Earth Syst. Sci. Data, 15, 5701–5737, https://doi.org/10.5194/essd-15-5701-2023, https://doi.org/10.5194/essd-15-5701-2023, 2023
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Western Channel Observatory is an oceanographic time series and biodiversity reference site within 40 km of Plymouth (UK), sampled since 1903. Differing levels of reporting and formatting hamper the use of the valuable individual datasets. We provide the first summary database as monthly averages where comparisons can be made of the physical, chemical and biological data. We describe the database, illustrate its utility to examine seasonality and longer-term trends, and summarize previous work.
Zhongkun Hong, Di Long, Xingdong Li, Yiming Wang, Jianmin Zhang, Mohamed A. Hamouda, and Mohamed M. Mohamed
Earth Syst. Sci. Data, 15, 5281–5300, https://doi.org/10.5194/essd-15-5281-2023, https://doi.org/10.5194/essd-15-5281-2023, 2023
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Changes in ocean chlorophyll-a (Chl-a) concentration are related to ecosystem balance. Here, we present high-quality gap-filled Chl-a data in open oceans, reflecting the distribution and changes in global Chl-a concentration. Our findings highlight the efficacy of reconstructing missing satellite observations using convolutional neural networks. This dataset and model are valuable for research in ocean color remote sensing, offering data support and methodological references for related studies.
Thomas J. Ryan-Keogh, Sandy J. Thomalla, Nicolette Chang, and Tumelo Moalusi
Earth Syst. Sci. Data, 15, 4829–4848, https://doi.org/10.5194/essd-15-4829-2023, https://doi.org/10.5194/essd-15-4829-2023, 2023
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Oceanic productivity has been highlighted as an important environmental indicator of climate change in comparison to other existing metrics. However, the availability of these data to assess trends and trajectories is plagued with issues, such as application to only a single satellite reducing the time period for assessment. We have applied multiple algorithms to the longest ocean colour record to provide a record for assessing climate-change-driven trends.
Raed Halawi Ghosn, Émilie Poisson-Caillault, Guillaume Charria, Armel Bonnat, Michel Repecaud, Jean-Valery Facq, Loïc Quéméner, Vincent Duquesne, Camille Blondel, and Alain Lefebvre
Earth Syst. Sci. Data, 15, 4205–4218, https://doi.org/10.5194/essd-15-4205-2023, https://doi.org/10.5194/essd-15-4205-2023, 2023
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This article describes a long-term (2004–2022) dataset from an in situ instrumented station located in the eastern English Channel and belonging to the COAST-HF network (ILICO). It provides high temporal resolution (sub-hourly) oceanographic and meteorological measurements. The MAREL Carnot dataset can be used to conduct research in marine ecology, oceanography, and data science. It was utilized to characterize recurrent, rare, and extreme events in the coastal area.
Shungudzemwoyo P. Garaba, Michelle Albinus, Guido Bonthond, Sabine Flöder, Mario L. M. Miranda, Sven Rohde, Joanne Y. L. Yong, and Jochen Wollschläger
Earth Syst. Sci. Data, 15, 4163–4179, https://doi.org/10.5194/essd-15-4163-2023, https://doi.org/10.5194/essd-15-4163-2023, 2023
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These high-quality data document a harmful algal bloom dominated by Nodularia spumigena, a cyanobacterium that has been recurring in waters around the world, using advanced water observation technologies. We also showcase the benefits of experiments of opportunity and the issues with obtaining synoptic spatio-temporal data for monitoring water quality. The dataset can be leveraged to gain more knowledge on related blooms, develop detection algorithms and optimize future monitoring efforts.
Fabrice Stephenson, Tom Brough, Drew Lohrer, Daniel Leduc, Shane Geange, Owen Anderson, David Bowden, Malcolm R. Clark, Niki Davey, Enrique Pardo, Dennis P. Gordon, Brittany Finucci, Michelle Kelly, Diana Macpherson, Lisa McCartain, Sadie Mills, Kate Neill, Wendy Nelson, Rachael Peart, Matthew H. Pinkerton, Geoffrey B. Read, Jodie Robertson, Ashley Rowden, Kareen Schnabel, Andrew Stewart, Carl Struthers, Leigh Tait, Di Tracey, Shaun Weston, and Carolyn Lundquist
Earth Syst. Sci. Data, 15, 3931–3939, https://doi.org/10.5194/essd-15-3931-2023, https://doi.org/10.5194/essd-15-3931-2023, 2023
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Understanding the distribution of species that live at the seafloor is critical to the management of the marine environment but is lacking in many areas. Here, we showcase an atlas of seafloor biodiversity that describes the distribution of approximately 600 organisms throughout New Zealand’s vast marine realm. Each layer in the open-access atlas has been evaluated by leading experts and provides a key resource for the sustainable use of New Zealand's marine environment.
Hubert Loisel, Daniel Schaffer Ferreira Jorge, Rick A. Reynolds, and Dariusz Stramski
Earth Syst. Sci. Data, 15, 3711–3731, https://doi.org/10.5194/essd-15-3711-2023, https://doi.org/10.5194/essd-15-3711-2023, 2023
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Studies of light fields in aquatic environments require data from radiative transfer simulations that are free of measurement errors. In contrast to previously published synthetic optical databases, the present database was created by simulations covering a broad range of seawater optical properties that exhibit probability distributions consistent with a global ocean dominated by open-ocean pelagic environments. This database is intended to support ocean color science and applications.
Philippe Massicotte, Marcel Babin, Frank Fell, Vincent Fournier-Sicre, and David Doxaran
Earth Syst. Sci. Data, 15, 3529–3545, https://doi.org/10.5194/essd-15-3529-2023, https://doi.org/10.5194/essd-15-3529-2023, 2023
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The COASTlOOC oceanographic expeditions in 1997 and 1998 studied the relationship between seawater properties and biology and chemistry across the European coasts. The team collected data from 379 stations using ships and helicopters to support the development of ocean color remote-sensing algorithms. This unique and consistent dataset is still used today by researchers.
Valentin Siebert, Brivaëla Moriceau, Lukas Fröhlich, Bernd R. Schöne, Erwan Amice, Beatriz Beker, Kevin Bihannic, Isabelle Bihannic, Gaspard Delebecq, Jérémy Devesa, Morgane Gallinari, Yoan Germain, Émilie Grossteffan, Klaus Peter Jochum, Thierry Le Bec, Manon Le Goff, Céline Liorzou, Aude Leynaert, Claudie Marec, Marc Picheral, Peggy Rimmelin-Maury, Marie-Laure Rouget, Matthieu Waeles, and Julien Thébault
Earth Syst. Sci. Data, 15, 3263–3281, https://doi.org/10.5194/essd-15-3263-2023, https://doi.org/10.5194/essd-15-3263-2023, 2023
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This article presents an overview of the results of biological, chemical and physical parameters measured at high temporal resolution (sampling once and twice per week) during environmental monitoring that took place in 2021 in the Bay of Brest. We strongly believe that this dataset could be very useful for other scientists performing sclerochronological investigations, studying biogeochemical cycles or conducting various ecological research projects.
Sofie Vranken, Marine Robuchon, Stefanie Dekeyzer, Ignacio Bárbara, Inka Bartsch, Aurélie Blanfuné, Charles-François Boudouresque, Wim Decock, Christophe Destombe, Bruno de Reviers, Pilar Díaz-Tapia, Anne Herbst, Romain Julliard, Rolf Karez, Priit Kersen, Stacy A. Krueger-Hadfield, Ralph Kuhlenkamp, Akira F. Peters, Viviana Peña, Cristina Piñeiro-Corbeira, Fabio Rindi, Florence Rousseau, Jan Rueness, Hendrik Schubert, Kjersti Sjøtun, Marta Sansón, Dan Smale, Thierry Thibaut, Myriam Valero, Leen Vandepitte, Bart Vanhoorne, Alba Vergés, Marc Verlaque, Christophe Vieira, Line Le Gall, Frederik Leliaert, and Olivier De Clerck
Earth Syst. Sci. Data, 15, 2711–2754, https://doi.org/10.5194/essd-15-2711-2023, https://doi.org/10.5194/essd-15-2711-2023, 2023
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We present AlgaeTraits, a high-quality seaweed trait database. The data are structured within the framework of WoRMS and are supported by an expert editor community. With 45 175 trait records for 21 prioritised biological and ecological traits, and a taxonomic coverage of 1 745 European species, AlgaeTraits significantly advances previous efforts to provide standardised seaweed trait data. AlgaeTraits will serve as a foundation for future research on diversity and evolution of seaweeds.
Alain Lefebvre and David Devreker
Earth Syst. Sci. Data, 15, 1077–1092, https://doi.org/10.5194/essd-15-1077-2023, https://doi.org/10.5194/essd-15-1077-2023, 2023
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The Suivi Regional des Nutriments (SRN) data set includes long-term time series on marine phytoplankton and physicochemical measures in the eastern English Channel and the Southern Bight of the North Sea. These data sets should be useful for comparing contrasted coastal marine ecosystems to further knowledge about the direct and indirect effects of human pressures and environmental changes on ecosystem structure and function, including eutrophication and harmful algal bloom issues.
Jacopo Pulcinella, Enrico Nicola Armelloni, Carmen Ferrà, Giuseppe Scarcella, and Anna Nora Tassetti
Earth Syst. Sci. Data, 15, 809–820, https://doi.org/10.5194/essd-15-809-2023, https://doi.org/10.5194/essd-15-809-2023, 2023
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Deep-sea fishery in the Mediterranean Sea was historically driven by the commercial profitability of deepwater red shrimps. Understanding spatiotemporal dynamics of fishing is key to comprehensively evaluate the status of these resources and prevent stock collapse. The observed monthly fishing effort and frequency dataset released by the automatic identification system (AIS) may help researchers as well as those involved in fishery management and in the update of existing management plans.
Simone Strydom, Roisin McCallum, Anna Lafratta, Chanelle L. Webster, Caitlyn M. O'Dea, Nicole E. Said, Natasha Dunham, Karina Inostroza, Cristian Salinas, Samuel Billinghurst, Charlie M. Phelps, Connor Campbell, Connor Gorham, Rachele Bernasconi, Anna M. Frouws, Axel Werner, Federico Vitelli, Viena Puigcorbé, Alexandra D'Cruz, Kathryn M. McMahon, Jack Robinson, Megan J. Huggett, Sian McNamara, Glenn A. Hyndes, and Oscar Serrano
Earth Syst. Sci. Data, 15, 511–519, https://doi.org/10.5194/essd-15-511-2023, https://doi.org/10.5194/essd-15-511-2023, 2023
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Seagrasses are important underwater plants that provide valuable ecosystem services to humans, including mitigating climate change. Understanding the natural history of seagrass meadows across different types of environments is crucial to conserving seagrasses in the global ocean. This dataset contains data extracted from peer-reviewed publications and highlights which seagrasses have been studied and in which locations and is useful for pointing out which need further investigation.
Flavienne Bruyant, Rémi Amiraux, Marie-Pier Amyot, Philippe Archambault, Lise Artigue, Lucas Barbedo de Freitas, Guislain Bécu, Simon Bélanger, Pascaline Bourgain, Annick Bricaud, Etienne Brouard, Camille Brunet, Tonya Burgers, Danielle Caleb, Katrine Chalut, Hervé Claustre, Véronique Cornet-Barthaux, Pierre Coupel, Marine Cusa, Fanny Cusset, Laeticia Dadaglio, Marty Davelaar, Gabrièle Deslongchamps, Céline Dimier, Julie Dinasquet, Dany Dumont, Brent Else, Igor Eulaers, Joannie Ferland, Gabrielle Filteau, Marie-Hélène Forget, Jérome Fort, Louis Fortier, Martí Galí, Morgane Gallinari, Svend-Erik Garbus, Nicole Garcia, Catherine Gérikas Ribeiro, Colline Gombault, Priscilla Gourvil, Clémence Goyens, Cindy Grant, Pierre-Luc Grondin, Pascal Guillot, Sandrine Hillion, Rachel Hussherr, Fabien Joux, Hannah Joy-Warren, Gabriel Joyal, David Kieber, Augustin Lafond, José Lagunas, Patrick Lajeunesse, Catherine Lalande, Jade Larivière, Florence Le Gall, Karine Leblanc, Mathieu Leblanc, Justine Legras, Keith Lévesque, Kate-M. Lewis, Edouard Leymarie, Aude Leynaert, Thomas Linkowski, Martine Lizotte, Adriana Lopes dos Santos, Claudie Marec, Dominique Marie, Guillaume Massé, Philippe Massicotte, Atsushi Matsuoka, Lisa A. Miller, Sharif Mirshak, Nathalie Morata, Brivaela Moriceau, Philippe-Israël Morin, Simon Morisset, Anders Mosbech, Alfonso Mucci, Gabrielle Nadaï, Christian Nozais, Ingrid Obernosterer, Thimoté Paire, Christos Panagiotopoulos, Marie Parenteau, Noémie Pelletier, Marc Picheral, Bernard Quéguiner, Patrick Raimbault, Joséphine Ras, Eric Rehm, Llúcia Ribot Lacosta, Jean-François Rontani, Blanche Saint-Béat, Julie Sansoulet, Noé Sardet, Catherine Schmechtig, Antoine Sciandra, Richard Sempéré, Caroline Sévigny, Jordan Toullec, Margot Tragin, Jean-Éric Tremblay, Annie-Pier Trottier, Daniel Vaulot, Anda Vladoiu, Lei Xue, Gustavo Yunda-Guarin, and Marcel Babin
Earth Syst. Sci. Data, 14, 4607–4642, https://doi.org/10.5194/essd-14-4607-2022, https://doi.org/10.5194/essd-14-4607-2022, 2022
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This paper presents a dataset acquired during a research cruise held in Baffin Bay in 2016. We observed that the disappearance of sea ice in the Arctic Ocean increases both the length and spatial extent of the phytoplankton growth season. In the future, this will impact the food webs on which the local populations depend for their food supply and fisheries. This dataset will provide insight into quantifying these impacts and help the decision-making process for policymakers.
Rainer Kiko, Marc Picheral, David Antoine, Marcel Babin, Léo Berline, Tristan Biard, Emmanuel Boss, Peter Brandt, Francois Carlotti, Svenja Christiansen, Laurent Coppola, Leandro de la Cruz, Emilie Diamond-Riquier, Xavier Durrieu de Madron, Amanda Elineau, Gabriel Gorsky, Lionel Guidi, Helena Hauss, Jean-Olivier Irisson, Lee Karp-Boss, Johannes Karstensen, Dong-gyun Kim, Rachel M. Lekanoff, Fabien Lombard, Rubens M. Lopes, Claudie Marec, Andrew M. P. McDonnell, Daniela Niemeyer, Margaux Noyon, Stephanie H. O'Daly, Mark D. Ohman, Jessica L. Pretty, Andreas Rogge, Sarah Searson, Masashi Shibata, Yuji Tanaka, Toste Tanhua, Jan Taucher, Emilia Trudnowska, Jessica S. Turner, Anya Waite, and Lars Stemmann
Earth Syst. Sci. Data, 14, 4315–4337, https://doi.org/10.5194/essd-14-4315-2022, https://doi.org/10.5194/essd-14-4315-2022, 2022
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The term
marine particlescomprises detrital aggregates; fecal pellets; bacterioplankton, phytoplankton and zooplankton; and even fish. Here, we present a global dataset that contains 8805 vertical particle size distribution profiles obtained with Underwater Vision Profiler 5 (UVP5) camera systems. These data are valuable to the scientific community, as they can be used to constrain important biogeochemical processes in the ocean, such as the flux of carbon to the deep sea.
Autun Purser, Laura Hehemann, Lilian Boehringer, Ellen Werner, Santiago E. A. Pineda-Metz, Lucie Vignes, Axel Nordhausen, Moritz Holtappels, and Frank Wenzhoefer
Earth Syst. Sci. Data, 14, 3635–3648, https://doi.org/10.5194/essd-14-3635-2022, https://doi.org/10.5194/essd-14-3635-2022, 2022
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Within this paper we present the seafloor images, maps and acoustic camera data collected by a towed underwater research platform deployed in 20 locations across the eastern Weddell Sea, Antarctica, during the PS124 COSMUS expedition with the research icebreaker RV Polarstern in 2021. The 20 deployments highlight the great variability in seafloor structure and faunal communities present. Of key interest was the discovery of the largest fish nesting colony discovered globally to date.
Cited articles
Amir, A., McDonald, D., Navas-Molina, J. A., Kopylova, E., Morton, J. T., Zech Xu, Z., Kightley, E. P., Thompson, L. R., Hyde, E. R., Gonzalez, A., and Knight, R.: Deblur rapidly resolves single-nucleotide community sequence patterns, mSystems, 2, e00191–16, https://doi.org/10.1128/msystems.00191-16, 2017.
Angel, R., Nepel, M., Panholzl, C., Schmidt, H., Herbold, C. W., Eichorst, S. A., and Woebken, D.: Evaluation of primers targeting the diazotroph functional gene and development of NifMAP – a bioinformatics pipeline for analyzing nifH amplicon data, Front. Microbiol., 9, 703, https://doi.org/10.3389/fmicb.2018.00703, 2018.
Ashkezari, M. D., Hagen, N. R., Denholtz, M., Neang, A., Burns, T. C., Morales, R. L., Lee, C. P., Hill, C. N., and Armbrust, E. V.: Simons Collaborative Marine Atlas Project (Simons CMAP): an open-source portal to share, visualize, and analyze ocean data, Limnol. Oceanogr.-Meth., 19, 488–496, https://doi.org/10.1002/lom3.10439, 2021.
Benavides, M., Conradt, L., Bonnet, S., Berman-Frank, I., Barrillon, S., Petrenko, A., and Dogliolii, A.: Fine-scale sampling unveils diazotroph patchiness in the South Pacific Ocean, ISME Communications, 1, 3, https://doi.org/10.1038/s43705-021-00006-2, 2021.
Bentzon-Tilia, M., Traving, S. J., Mantikci, M., Knudsen-Leerbeck, H., Hansen, J. L. S., Markager, S., and Riemann, L.: Significant N2 fixation by heterotrophs, photoheterotrophs and heterocystous cyanobacteria in two temperate estuaries, ISME J., 9, 273–285, https://doi.org/10.1038/ismej.2014.119, 2015.
Blais, M., Tremblay, J. É., Jungblut, A. D., Gagnon, J., Martin, J., Thaler, M., and Lovejoy, C.: Nitrogen fixation and identification of potential diazotrophs in the Canadian Arctic, Global Biogeochem. Cy., 26, GB3022, https://doi.org/10.1029/2011gb004096, 2012.
Bostrom, K. H., Riemann, L., Kuhl, M., and Hagstrom, A.: Isolation and gene quantification of heterotrophic N2-fixing bacterioplankton in the Baltic Sea, Environ. Microbiol., 9, 152–164, https://doi.org/10.1111/j.1462-2920.2006.01124.x, 2007.
Cabello, A. M., Turk-Kubo, K. A., Hayashi, K., Jacobs, L., Kudela, R. M., and Zehr, J. P.: Unexpected presence of the nitrogen-fixing symbiotic cyanobacterium UCYN-A in Monterey Bay, California, J. Phycol., 56, 1521–1533, https://doi.org/10.1111/jpy.13045, 2020.
Callahan, B. J., McMurdie, P. J., Rosen, M. J., Han, A. W., Johnson, A. J., and Holmes, S. P.: DADA2: high-resolution sample inference from Illumina amplicon data, Nat. Methods, 13, 581–583, https://doi.org/10.1038/nmeth.3869, 2016.
Callahan, B. J., McMurdie, P. J., and Holmes, S. P.: Exact sequence variants should replace operational taxonomic units in marker-gene data analysis, ISME J., 11, 12, 2639–2643, https://doi.org/10.1038/ismej.2017.119, 2017.
Capone, D. G., Burns, J. A., Montoya, J. P., Subramaniam, A., Mahaffey, C., Gunderson, T., Michaels, A. F., and Carpenter, E. J.: Nitrogen fixation by Trichodesmium spp.: an important source of new nitrogen to the tropical and subtropical North Atlantic Ocean, Global Biogeochem. Cy., 19, GB2024, https://doi.org/10.1029/2004GB002331, 2005.
Carpenter, E. J. and Capone, D. G. (Eds.): Nitrogen in the marine environment (First edition), Academic Press, New York, ISBN 012160280X, 1983.
Carpenter, E. J. and Foster, R. A.: Marine symbioses, in: Cyanobacteria in symbiosis, edited by: Rai, A. N., Bergman, B., and Rasmussen, U., Kluwer Academic Publishers, the Netherlands, 11–17, https://doi.org/10.1007/0-306-48005-0, 2002.
Cheung, S., Xia, X., Guo, C., and Liu, H.: Diazotroph community structure in the deep oxygen minimum zone of the Costa Rica Dome, J. Plankton Res., 38, 380–391, https://doi.org/10.1093/plankt/fbw003, 2016.
Cheung, S., Zehr, J. P., Xia, X., Tsurumoto, C., Endo, H., Nakaoka, S. I., Mak, W., Suzuki, K., and Liu, H.: Gamma4: a genetically versatile Gammaproteobacterial nifH phylotype that is widely distributed in the North Pacific Ocean, Environ. Microbiol., 23, 4246–4259, https://doi.org/10.1111/1462-2920.15604, 2021.
Coale, T. H., Loconte, V., Turk-Kubo, K. A., Vanslembrouck, B., Mak, W. K. E., Cheung, S., Ekman, A., Chen, J. H., Hagino, K., Takano, Y., Nishimura, T., Adachi, M., Le Gros, M., Larabell, C., and Zehr, J. P.: Nitrogen-fixing organelle in a marine alga, Science, 384, 217–222, https://doi.org/10.1126/science.adk1075, 2024.
Delmont, T. O., Quince, C., Shaiber, A., Esen, Ö. C., Lee, S. T., Rappé, M. S., MacLellan, S. L., Lücker, S., and Eren, A. M.: Nitrogen-fixing populations of Planctomycetes and Proteobacteria are abundant in surface ocean metagenomes, Nat. Microbiol., 3, 804–813, https://doi.org/10.1038/s41564-018-0176-9, 2018.
Delmont, T. O., Karlusich, J. J. P., Veseli, I., Fuessel, J., Eren, A. M., Foster, R. A., Bowler, C., Wincker, P., and Pelletier, E.: Heterotrophic bacterial diazotrophs are more abundant than their cyanobacterial counterparts in metagenomes covering most of the sunlit ocean, ISME J., 16, 927–936, https://doi.org/10.1038/s41564-018-0176-9, 2022.
Ding, C., Wu, C., Li, L., Pujari, L., Zhang, G., and Sun, J.: Comparison of diazotrophic composition and distribution in the South China Sea and the Western Pacific Ocean, Biology (Basel), 10, 555, https://doi.org/10.3390/biology10060555, 2021.
Edgar, R.: UCHIME2: improved chimera prediction for amplicon sequencing, bioRxiv, https://doi.org/10.1101/074252, 2016a.
Edgar, R.: UNOISE2: improved error-correction for Illumina 16S and ITS amplicon sequencing, bioRxiv, https://doi.org/10.1101/081257, 2016b.
Eren, A. M., Vineis, J. H., Morrison, H. G., and Sogin, M. L.: A filtering method to generate high quality short reads using Illumina paired-end technology, PLOS ONE, 8, e66643, https://doi.org/10.1371/journal.pone.0066643, 2013.
Eren, A. M., Morrison, H. G., Lescault, P. J., Reveillaud, J., Vineis, J. H., and Sogin, M. L.: Minimum entropy decomposition: unsupervised oligotyping for sensitive partitioning of high-throughput marker gene sequences, ISME J., 9, 968–979, https://doi.org/10.1038/ismej.2014.195, 2014.
Falcón, L., Cipriano, F., Chistoserdov, A., and Carpenter, E.: Diversity of diazotrophic unicellular cyanobacteria in the tropical North Atlantic Ocean, Appl. Environ. Microb., 68, 5760–5764, https://doi.org/10.1128/AEM.68.11.5760-5764.2002, 2002.
Falcón, L., Carpenter, E., Cipriano, F., Bergman, B., and Capone, D.: N2 fixation by unicellular bacterioplankton from the Atlantic and Pacific Oceans: phylogeny and in situ rates, Appl. Environ. Microb., 70, 765–770, https://doi.org/10.1128/AEM.70.2.765-770.2004, 2004.
Farnelid, H., Oberg, T., and Riemann, L.: Identity and dynamics of putative N2-fixing picoplankton in the Baltic Sea proper suggest complex patterns of regulation, Env. Microbiol. Rep., 1, 145–154, https://doi.org/10.1111/j.1758-2229.2009.00021.x, 2009.
Farnelid, H., Andersson, A. F., Bertilsson, S., Al-Soud, W. A., Hansen, L. H., Sørensen, S., Steward, G. F., Hagström, A., and Riemann, L.: Nitrogenase gene amplicons from global marine surface waters are dominated by genes of non-cyanobacteria, PLOS ONE, 6, e19223, https://doi.org/10.1371/journal.pone.0019223, 2011.
Farnelid, H., Turk-Kubo, K., Ploug, H., Ossolinski, J. E., Collins, J. R., Van Mooy, B. A. S., and Zehr, J. P.: Diverse diazotrophs are present on sinking particles in the North Pacific Subtropical Gyre, ISME J., 13, 170–182, https://doi.org/10.1038/s41396-018-0259-x, 2019.
Fernandez, C., Farias, L., and Ulloa, O.: Nitrogen fixation in denitrified marine waters, PLOS ONE, 6, e20539, https://doi.org/10.1371/journal.pone.0020539, 2011.
Fernández-Méndez, M., Turk-Kubo, K. A., Buttigieg, P. L., Rapp, J. Z., Krumpen, T., Zehr, J. P., and Boetius, A.: Diazotroph diversity in the sea ice, melt ponds, and durface waters of the Eurasian basin of the Central Arctic Ocean, Front. Microbiol., 7, 1–18, https://doi.org/10.3389/fmicb.2016.01884, 2016.
Frank, I. E., Turk-Kubo, K. A., and Zehr, J. P.: Rapid annotation of nifH gene sequences using classification and regression trees facilitates environmental functional gene analysis, Env. Microbiol. Rep., 8, 905–916, https://doi.org/10.1111/1758-2229.12455, 2016.
Gaby, J. C. and Buckley, D. H.: A global census of nitrogenase diversity, Environ. Microbiol., 13, 1790–1799, https://doi.org/10.1111/j.1462-2920.2011.02488.x, 2011.
Gérikas Ribeiro, C., Lopes dos Santos, A., Marie, D., Pereira Brandini, F., and Vaulot, D.: Small eukaryotic phytoplankton communities in tropical waters off Brazil are dominated by symbioses between Haptophyta and nitrogen-fixing cyanobacteria, ISME J., 12, 1360–1374, https://doi.org/10.1038/s41396-018-0050-z, 2018.
Goto, M., Ando, S., Hachisuka, Y., and Yoneyama, T.: Contamination of diverse nifH and nifH-like DNA into commercial PCR primers, FEMS Microbiol. Lett., 246, 33–38, https://doi.org/10.1016/j.femsle.2005.03.042, 2005.
Gradoville, M. R., Bombar, D., Crump, B. C., Letelier, R. M., Zehr, J. P., and White, A. E.: Diversity and activity of nitrogen-fixing communities across ocean basins, Limnol. Oceanogr., 62, 1895–1909, https://doi.org/10.1002/lno.10542, 2017.
Gradoville, M. R., Farnelid, H., White, A. E., Turk-Kubo, K. A., Stewart, B., Ribalet, F., Ferrón, S., Pinedo-Gonzalez, P., Armbrust, E. V., Karl, D. M., John, S., and Zehr, J. P.: Latitudinal constraints on the abundance and activity of the cyanobacterium UCYN-A and other marine diazotrophs in the North Pacific, Limnol. Oceanogr., 65, 1858–1875, https://doi.org/10.1002/lno.11423, 2020.
Green, S. J., Venkatramanan, R., and Naqib, A.: Deconstructing the polymerase chain reaction: understanding and correcting bias associated with primer degeneracies and primer-template mismatches, PLOS ONE, 10, e0128122, https://doi.org/10.1371/journal.pone.0128122, 2015.
Hallstrøm, S., Benavides, M., Salamon, E. R., Arístegui, J., and Riemann, L.: Activity and distribution of diazotrophic communities across the Cape Verde Frontal Zone in the Northeast Atlantic Ocean, Biogeochemistry, 160, 49–67, https://doi.org/10.1007/s10533-022-00940-w, 2022a.
Hallstrøm, S., Benavides, M., Salamon, E. R., Evans, C. W., Potts, L. J., Granger, J., Tobias, C. R., Moisander, P. H., and Riemann, L.: Pelagic N2 fixation dominated by sediment diazotrophic communities in a shallow temperate estuary, Limnol. Oceanogr., 67, 364–378, https://doi.org/10.1002/lno.11997, 2022b.
Halm, H., Lam, P., Ferdelman, T. G., Lavik, G., Dittmar, T., LaRoche, J., D'Hondt, S., and Kuypers, M. M.: Heterotrophic organisms dominate nitrogen fixation in the South Pacific Gyre, ISME J., 6, 1238–1249, https://doi.org/10.1038/ismej.2011.182, 2012.
Harding, K., Turk-Kubo, K. A., Sipler, R. E., Mills, M. M., Bronk, D. A., and Zehr, J. P.: Symbiotic unicellular cyanobacteria fix nitrogen in the Arctic Ocean, P. Natl. Acad. Sci. USA, 115, 13371–13375, https://doi.org/10.1073/pnas.1813658115, 2018.
Heller, P., Tripp, H. J., Turk-Kubo, K., and Zehr, J. P.: ARBitrator: a software pipeline for on-demand retrieval of auto-curated nifH sequences from GenBank, Bioinformatics, 30, 2883–2890, https://doi.org/10.1093/bioinformatics/btu417, 2014.
Jickells, T., Buitenhuis, E., Altieri, K., Baker, A., Capone, D., Duce, R., Dentener, F., Fennel, K., Kanakidou, M., and LaRoche, J.: A reevaluation of the magnitude and impacts of anthropogenic atmospheric nitrogen inputs on the ocean, Global Biogeochem. Cy., 31, 289–305, https://doi.org/10.1002/2016GB005586, 2017.
Langlois, R., Großkopf, T., Mills, M., Takeda, S., and LaRoche, J.: Widespread distribution and expression of Gamma A (UMB), an uncultured, diazotrophic, γ-proteobacterial nifH phylotype, PLOS ONE, 10, e0128912, https://doi.org/10.1371/journal.pone.0128912, 2015.
Langlois, R. J., LaRoche, J., and Raab, P. A.: Diazotrophic diversity and distribution in the tropical and subtropical Atlantic Ocean, Appl. Environ. Microb., 71, 7910–7919, https://doi.org/10.1128/AEM.71.12.7910-7919.2005, 2005.
Li, Y. Y., Chen, X. H., Xie, Z. X., Li, D. X., Wu, P. F., Kong, L. F., Lin, L., Kao, S. J., and Wang, D. Z.: Bacterial diversity and nitrogen utilization strategies in the upper layer of the Northwestern Pacific Ocean, Front. Microbiol., 9, https://doi.org/10.3389/fmicb.2018.00797, 2018.
Liu, J., Zhou, L., Li, J., Lin, Y., Ke, Z., Zhao, C., Liu, H., Jiang, X., He, Y., and Tan, Y.: Effect of mesoscale eddies on diazotroph community structure and nitrogen fixation rates in the South China Sea, Regional Studies in Marine Science, 35, 101106, https://doi.org/10.1016/j.rsma.2020.101106, 2020.
Löscher, C. R., Großkopf, T., Desai, F. D., Gill, D., Schunck, H., Croot, P. L., Schlosser, C., Neulinger, S. C., Pinnow, N., and Lavik, G.: Facets of diazotrophy in the oxygen minimum zone waters off Peru, ISME J., 8, 2180–2192, https://doi.org/10.1038/ismej.2014.71, 2014.
Luo, Y.-W., Doney, S. C., Anderson, L. A., Benavides, M., Berman-Frank, I., Bode, A., Bonnet, S., Boström, K. H., Böttjer, D., Capone, D. G., Carpenter, E. J., Chen, Y. L., Church, M. J., Dore, J. E., Falcón, L. I., Fernández, A., Foster, R. A., Furuya, K., Gómez, F., Gundersen, K., Hynes, A. M., Karl, D. M., Kitajima, S., Langlois, R. J., LaRoche, J., Letelier, R. M., Marañón, E., McGillicuddy Jr., D. J., Moisander, P. H., Moore, C. M., Mouriño-Carballido, B., Mulholland, M. R., Needoba, J. A., Orcutt, K. M., Poulton, A. J., Rahav, E., Raimbault, P., Rees, A. P., Riemann, L., Shiozaki, T., Subramaniam, A., Tyrrell, T., Turk-Kubo, K. A., Varela, M., Villareal, T. A., Webb, E. A., White, A. E., Wu, J., and Zehr, J. P.: Database of diazotrophs in global ocean: abundance, biomass and nitrogen fixation rates, Earth Syst. Sci. Data, 4, 47–73, https://doi.org/10.5194/essd-4-47-2012, 2012.
Manley, L. J., Ma, D., and Levine, S. S.: Monitoring error rates In Illumina sequencing, J. Biomol. Tech., 27, 4, 125–128, https://doi.org/10.7171/jbt.16-2704-002, 2016.
Martin, M.: Cutadapt removes adapter sequences from high-throughput sequencing reads, EMBnet.journal, 17, 10–12, https://doi.org/10.14806/ej.17.1.200, 2011.
Messer, L. F., Mahaffey, C., Robinson, C. M., Jeffries, T. C., Baker, K. G., Isaksson, J. B., Ostrowski, M., Doblin, M. A., Brown, M. V., and Seymour, J. R.: High levels of heterogeneity in diazotroph diversity and activity within a putative hotspot for marine nitrogen fixation, ISME J., 10, 1499–1513, https://doi.org/10.1038/ismej.2015.205, 2015.
Mistry, J., Chuguransky, S., Williams, L., Qureshi, M., Salazar, G. A., Sonnhammer, E. L. L., Tosatto, S. C. E., Paladin, L., Raj, S., Richardson, L. J., Finn, R. D., and Bateman, A.: Pfam: The protein families database in 2021, Nucleic Acids Res., 49, D412–D419, https://doi.org/10.1093/nar/gkaa913, 2021.
Moisander, P. H., Beinart, R. A., Voss, M., and Zehr, J. P.: Diversity and abundance of diazotrophic microorganisms in the South China Sea during intermonsoon, ISME J., 2, 954–967, https://doi.org/10.1038/ismej.2008.51, 2008.
Moisander, P. H., Serros, T., Paerl, R. W., Beinart, R. A., and Zehr, J. P.: Gammaproteobacterial diazotrophs and nifH gene expression in surface waters of the South Pacific Ocean, ISME J., 8, 1962–1973, https://doi.org/10.1038/ismej.2014.49, 2014.
Moisander, P. H., Benavides, M., Bonnet, S., Berman-Frank, I., White, A. E., and Riemann, L.: Chasing after non-cyanobacterial nitrogen fixation in marine pelagic environments, Front. Microbiol., 8, 1736, https://doi.org/10.3389/fmicb.2017.01736, 2017.
Moonsamy, P. V., Williams, T., Bonella, P., Holcomb, C. L., Hoglund, B. N., Hillman, G., Goodridge, D., Turenchalk, G. S., Blake, L. A., Daigle, D. A., Simen, B. B., Hamilton, A., May, A. P., and Erlich, H. A.: High throughput HLA genotyping using 454 sequencing and the Fluidigm Access Array System for simplified amplicon library preparation, Tissue Antigens, 81, 141–149, https://doi.org/10.1111/tan.12071, 2013.
Morando, M., Magasin, J. D., Cheung, S., Mills, M. M., Zehr, J. P., and Turk-Kubo, K. A.: DADA2 nifH pipeline in Global biogeography of N2-fixing microbes: nifH amplicon database and analytics workflow, GitHub [code], https://github.com/jdmagasin/nifH_amplicons_DADA2 (last access: 21 January 2025), 2024a.
Morando, M., Magasin, J. D., Cheung, S., Mills, M. M., Zehr, J. P., and Turk-Kubo, K. A.: nifH ASV database in Global biogeography of N2-fixing microbes: nifH amplicon database and analytics workflow, Figshare [data set], https://doi.org/10.6084/m9.figshare.23795943.v2, 2024b.
Morando, M., Magasin, J. D., Cheung, S., Mills, M. M., Zehr, J. P., and Turk-Kubo, K. A.: nifH ASV workflow in Global biogeography of N2-fixing microbes: nifH amplicon database and analytics workflow, GitHub [code], https://github.com/jdmagasin/nifH-ASV-workflow (last access: 21 January 2025), 2024c.
Mulholland, M. R., Bernhardt, P. W., Widner, B. N., Selden, C. R., Chappell, P. D., Clayton, S., Mannino, A., and Hyde, K.: High rates of N2 fixation in temperate, western North Atlantic coastal waters expand the realm of marine diazotrophy, Global Biogeochem. Cy., 33, 826–840, https://doi.org/10.1029/2018gb006130, 2019.
Pierella Karlusich, J. J., Pelletier, E., Lombard, F., Carsique, M., Dvorak, E., Colin, S., Picheral, M., Cornejo-Castillo, F. M., Acinas, S. G., Pepperkok, R., Karsenti, E., de Vargas, C., Wincker, P., Bowler, C., and Foster, R. A.: Global distribution patterns of marine nitrogen-fixers by imaging and molecular methods, Nat. Commun., 12, 1–18, https://doi.org/10.1038/s41467-021-24299-y, 2021.
Quince, C., Lanzén, A., Curtis, T. P., Davenport, R. J., Hall, N., Head, I. M., Read, L. F., and Sloan, W. T.: Accurate determination of microbial diversity from 454 pyrosequencing data, Nat. Methods, 6, 639–641, https://doi.org/10.1038/nmeth.1361, 2009.
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. Marine Sci., 7, 1–20, https://doi.org/10.3389/fmars.2020.00389, 2020.
Rahav, E., Giannetto, M., and Bar-Zeev, E.: Contribution of mono and polysaccharides to heterotrophic N2 fixation at the eastern Mediterranean coastline, Sci. Rep.-UK, 6, 27858, https://doi.org/10.1038/srep27858, 2016.
Rho, M., Tang, H., and Ye, Y.: FragGeneScan: predicting genes in short and error-prone reads, Nucleic Acids Res., 38, e191, https://doi.org/10.1093/nar/gkq747, 2010.
Rognes, T., Flouri, T., Nichols, B., Quince, C., and Mahe, F.: VSEARCH: a versatile open source tool for metagenomics, PeerJ, 4, e2584, https://doi.org/10.7717/peerj.2584, 2016.
Sato, T., Shiozaki, T., Taniuchi, Y., Kasai, H., and Takahashi, K.: Nitrogen fixation and diazotroph community in the subarctic Sea of Japan and Sea of Okhotsk, J. Geophys. Res.-Oceans, 126, e2020JC017071, https://doi.org/10.1029/2020JC017071, 2021.
Schlessman, J. L., Woo, D., Joshua-Tor, L., Howard, J. B., and Rees, D. C.: Conformational variability in structures of the nitrogenase iron proteins from Azotobacter vinelandii and Clostridium pasteurianum, J. Mol. Biol., 280, 669–685, https://doi.org/10.1006/jmbi.1998.1898, 1998.
Selden, C. R., Chappell, P. D., Clayton, S., Macías-Tapia, A., Bernhardt, P. W., and Mulholland, M. R.: A coastal N2 fixation hotspot at the Cape Hatteras front: elucidating spatial heterogeneity in diazotroph activity via supervised machine learning, Limnol. Oceanogr., 66, 1832–1849, https://doi.org/10.1002/lno.11727, 2021.
Shao, Z. and Luo, Y.-W.: Controlling factors on the global distribution of a representative marine non-cyanobacterial diazotroph phylotype (Gamma A), Biogeosciences, 19, 2939–2952, https://doi.org/10.5194/bg-19-2939-2022, 2022.
Shao, Z., Xu, Y., Wang, H., Luo, W., Wang, L., Huang, Y., Agawin, N. S. R., Ahmed, A., Benavides, M., Bentzon-Tilia, M., Berman-Frank, I., Berthelot, H., Biegala, I. C., Bif, M. B., Bode, A., Bonnet, S., Bronk, D. A., Brown, M. V., Campbell, L., Capone, D. G., Carpenter, E. J., Cassar, N., Chang, B. X., Chappell, D., Chen, Y.-L., Church, M. J., Cornejo-Castillo, F. M., Detoni, A. M. S., Doney, S. C., Dupouy, C., Estrada, M., Fernandez, C., Fernández-Castro, B., Fonseca-Batista, D., Foster, R. A., Furuya, K., Garcia, N., Goto, K., Gago, J., Gradoville, M. R., Hamersley, M. R., Henke, B. A., Hörstmann, C., Jayakumar, A., Jiang, Z., Kao, S.-J., Karl, D. M., Kittu, L. R., Knapp, A. N., Kumar, S., LaRoche, J., Liu, H., Liu, J., Lory, C., Löscher, C. R., Marañón, E., Messer, L. F., Mills, M. M., Mohr, W., Moisander, P. H., Mahaffey, C., Moore, R., Mouriño-Carballido, B., Mulholland, M. R., Nakaoka, S., Needoba, J. A., Raes, E. J., Rahav, E., Ramírez-Cárdenas, T., Reeder, C. F., Riemann, L., Riou, V., Robidart, J. C., Sarma, V. V. S. S., Sato, T., Saxena, H., Selden, C., Seymour, J. R., Shi, D., Shiozaki, T., Singh, A., Sipler, R. E., Sun, J., Suzuki, K., Takahashi, K., Tan, Y., Tang, W., Tremblay, J.-É., Turk-Kubo, K., Wen, Z., White, A. E., Wilson, S. T., Yoshida, T., Zehr, J. P., Zhang, R., Zhang, Y., and Luo, Y.-W.: Global oceanic diazotroph database version 2 and elevated estimate of global oceanic N2 fixation, Earth Syst. Sci. Data, 15, 3673–3709, https://doi.org/10.5194/essd-15-3673-2023, 2023.
Shilova, I., Mills, M., Robidart, J., Turk-Kubo, K., Björkman, K., Kolber, Z., Rapp, I., van Dijken, G., Church, M., and Arrigo, K.: Differential effects of nitrate, ammonium, and urea as N sources for microbial communities in the North Pacific Ocean, Limnol. Oceanogr., 62, 2550–2574, https://doi.org/10.1002/lno.10590, 2017.
Shiozaki, T., Bombar, D., Riemann, L., Hashihama, F., Takeda, S., Yamaguchi, T., Ehama, M., Hamasaki, K., and Furuya, K.: Basin scale variability of active diazotrophs and nitrogen fixation in the North Pacific, from the tropics to the subarctic Bering Sea, Global Biogeochem. Cy., 31, 996–1009, https://doi.org/10.1002/2017gb005681, 2017.
Shiozaki, T., Bombar, D., Riemann, L., Sato, M., Hashihama, F., Kodama, T., Tanita, I., Takeda, S., Saito, H., Hamasaki, K., and Furuya, K.: Linkage between dinitrogen fixation and primary production in the oligotrophic South Pacific Ocean, Global Biogeochem. Cy., 32, 1028–1044, https://doi.org/10.1029/2017GB005869, 2018a.
Shiozaki, T., Fujiwara, A., Ijichi, M., Harada, N., Nishino, S., Nishi, S., Nagata, T., and Hamasaki, K.: Diazotroph community structure and the role of nitrogen fixation in the nitrogen cycle in the Chukchi Sea (western Arctic Ocean), Limnol. Oceanogr., 63, 2191–2205, https://doi.org/10.1002/lno.10933, 2018b.
Shiozaki, T., Fujiwara, A., Inomura, K., Hirose, Y., Hashihama, F., and Harada, N.: Biological nitrogen fixation detected under Antarctic sea ice, Nat. Geosci., 13, 729–732, https://doi.org/10.1038/s41561-020-00651-7, 2020.
Tang, W., Li, Z., and Cassar, N.: Machine learning estimates of global marine nitrogen fixation, J. Geophys. Res.-Biogeo., 124, 717–730, https://doi.org/10.1029/2018JG004828, 2019.
Tang, W., Cerdan-Garcia, E., Berthelot, H., Polyviou, D., Wang, S., Baylay, A., Whitby, H., Planquette, H., Mowlem, M., Robidart, J., and Cassar, N.: New insights into the distributions of nitrogen fixation and diazotrophsrevealed by high-resolution sensing and sampling methods, ISME J., 14, 2514–2526, https://doi.org/10.1038/s41396-020-0703-6, 2020.
Taylor, L. J., Abbas, A., and Bushman, F. D.: grabseqs: Simple downloading of reads and metadata from multiple next-generation sequencing data repositories, Bioinformatics, 36, 3607–3609, https://doi.org/10.1093/bioinformatics/btaa167, 2020.
Turk, K., Rees, A. P., Zehr, J. P., Pereira, N., Swift, P., Shelley, R., Lohan, M., Woodward, E. M. S., and Gilbert, J.: Nitrogen fixation and nitrogenase (nifH) expression in tropical waters of the eastern North Atlantic, ISME J., 5, 1201–1212, https://doi.org/10.1038/ismej.2010.205, 2011.
Turk-Kubo, K. A., Karamchandani, M., Capone, D. G., and Zehr, J. P.: The paradox of marine heterotrophic nitrogen fixation: abundances of heterotrophic diazotrophs do not account for nitrogen fixation rates in the Eastern Tropical South Pacific, Environ. Microbiol., 16, 3095–3114, https://doi.org/10.1111/1462-2920.12346, 2014.
Turk-Kubo, K. A., Frank, I. E., Hogan, M. E., Desnues, A., Bonnet, S., and Zehr, J. P.: Diazotroph community succession during the VAHINE mesocosm experiment (New Caledonia lagoon), Biogeosciences, 12, 7435–7452, https://doi.org/10.5194/bg-12-7435-2015, 2015.
Turk-Kubo, K. A., Farnelid, H. M., Shilova, I. N., Henke, B., and Zehr, J. P.: Distinct ecological niches of marine symbiotic N2-fixing cyanobacterium Candidatus Atelocyanobacterium thalassa sublineages, J. Phycol., 53, 451–461, https://doi.org/10.1111/jpy.12505, 2017.
Turk-Kubo, K. A., Mills, M. M., Arrigo, K. R., van Dijken, G., Henke, B. A., Stewart, B., Wilson, S. T., and Zehr, J. P.: UCYN-A/haptophyte symbioses dominate N2 fixation in the Southern California Current System, ISME Communications, 1, 1–13, https://doi.org/10.1038/s43705-021-00039-7, 2021.
Turk-Kubo, K. A., Gradoville, M. R., Cheung, S., Cornejo-Castillo, F., Harding, K. J., Morando, M., Mills, M., and Zehr, J. P.: Non-cyanobacterial diazotrophs: global diversity, distribution, ecophysiology, and activity in marine waters, FEMS Microbiol. Rev., 47, fuac046, https://doi.org/10.1093/femsre/fuac046, 2022.
Villareal, T. A.: Widespread occurrence of the Hemiaulus-cyanobacterial symbiosis in the southwest North-Atlantic Ocean, B. Mar. Sci., 54, 1–7, 1994.
Wu, C., Kan, J., Liu, H., Pujari, L., Guo, C., Wang, X., and Sun, J.: Heterotrophic bacteria dominate the diazotrophic community in the Eastern Indian Ocean (EIO) during pre-southwest monsoon, Microb. Ecol., 78, 804–819, https://doi.org/10.1007/s00248-019-01355-1, 2019.
Wu, C., Sun, J., Liu, H., Xu, W., Zhang, G., Lu, H., and Guo, Y.: Evidence of the significant contribution of heterotrophic diazotrophs to nitrogen fixation in the Eastern Indian Ocean during pre-southwest monsoon period, Ecosystems, 25, 1066–1083, https://doi.org/10.1007/s10021-021-00702-z, 2021.
Zani, S., Mellon, M. T., Collier, J. L., and Zehr, J. P.: Expression of nifH genes in natural microbial assemblages in Lake George, New York, detected by reverse transcriptase PCR, Appl. Environ. Microbiol., 66, 3119–3124, https://doi.org/10.1128/AEM.66.7.3119-3124, 2000.
Zehr, J. and McReynolds, L.: Use of degenerate oligonucleotides for amplification of the nifH gene from the marine cyanobacterium Trichodesmium thiebautii, Appl. Environ. Microb., 55, 2522–2526, https://doi.org/10.1128/aem.55.10.2522-2526.1989, 1989.
Zehr, J., Mellon, M., and Zani, S.: New nitrogen-fixing microorganisms detected in oligotrophic oceans by amplification of nitrogenase (nifH) genes, Appl. Environ. Microb., 64, 3444–3450, https://doi.org/10.1128/AEM.64.9.3444-3450.1998, 1998.
Zehr, J. P. and Capone, D. G.: Changing perspectives in marine nitrogen fixation, Science, 368, eaay9514, https://doi.org/10.1126/science.aay9514, 2020.
Zehr, J. P., Waterbury, J. B., Turner, P. J., Montoya, J. P., Omoregie, E., Steward, G. F., Hansen, A., and Karl, D. M.: Unicellular cyanobacteria fix N2 in the subtropical North Pacific Ocean, Nature, 412, 635–638, https://doi.org/10.1038/35088063, 2001.
Zehr, J. P., Crumbliss, L. L., Church, M. J., Omoregie, E. O., and Jenkins, B. D.: Nitrogenase genes in PCR and RT-PCR reagents: implications for studies of diversity of functional genes, Biotechniques, 35, 996–1002, https://doi.org/10.2144/03355st08, 2003.
Short summary
Nitrogen is crucial in ocean food webs, but only some microbes can fix N2 gas into a bioavailable form. Most are known only by their nifH gene sequence. We created a software workflow for nifH data and ran it on 944 ocean samples, producing a database (DB) that captures the global diversity of N2-fixing marine microbes and the environmental factors that influence them. The workflow and DB can standardize analyses of past and future nifH datasets to enable insights into marine communities.
Nitrogen is crucial in ocean food webs, but only some microbes can fix N2 gas into a...
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