Articles | Volume 22, issue 22
https://doi.org/10.5194/bg-22-6787-2025
© 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/bg-22-6787-2025
© Author(s) 2025. This work is distributed under
the Creative Commons Attribution 4.0 License.
the Creative Commons Attribution 4.0 License.
Research article
| 
14 Nov 2025
Research article |
| 14 Nov 2025
| 14 Nov 2025
Relationships between phytoplankton pigments and DNA- or RNA-based abundances support ecological applications
Robert H. Lampe
Integrative Oceanography Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92093, USA
Microbial and Environmental Genomics, J. Craig Venter Institute, La Jolla, CA 92037, USA
Ariel J. Rabines
Integrative Oceanography Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92093, USA
Microbial and Environmental Genomics, J. Craig Venter Institute, La Jolla, CA 92037, USA
Steffaney M. Wood-Rocca
Integrative Oceanography Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92093, USA
Microbial and Environmental Genomics, J. Craig Venter Institute, La Jolla, CA 92037, USA
Center for Marine Biotechnology and Biomedicine, Scripps Institute of Oceanography, University of California San Diego, La Jolla, CA 92093, USA
Anne Schulberg
Integrative Oceanography Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92093, USA
Microbial and Environmental Genomics, J. Craig Venter Institute, La Jolla, CA 92037, USA
Ralf Goericke
Integrative Oceanography Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92093, USA
Pratap Venepally
Microbial and Environmental Genomics, J. Craig Venter Institute, La Jolla, CA 92037, USA
Hong Zheng
Microbial and Environmental Genomics, J. Craig Venter Institute, La Jolla, CA 92037, USA
Michael R. Stukel
Earth, Ocean, and Atmospheric Science Department, Florida State University, Tallahassee, FL 32304, USA
Michael R. Landry
Integrative Oceanography Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92093, USA
Andrew D. Barton
Integrative Oceanography Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92093, USA
Department of Ecology, Behavior and Evolution, University of California San Diego, La Jolla, CA 92093, USA
Andrew E. Allen
CORRESPONDING AUTHOR
Integrative Oceanography Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92093, USA
Microbial and Environmental Genomics, J. Craig Venter Institute, La Jolla, CA 92037, USA
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Salem Ibrahim Salem, Andre Valente, Shubha Sathyendranath, Andrei Chuprin, Théo Renard, Jaime Pitarch, Ruth Airs, Moreno Ana, Maria-Manuel Angelico, David Antoine, Robert Arnone, Florinda Artuso, Paulo O. Oliveira, William Balch, Kathryn Barker, Ray Barlow, Simon Bélanger, Marco Bellacicco, Jean-François Berthon, Şükrü Beşiktepe, Francesco Bignami, Yngve Borsheim, Astrid Bracher, Federica Braga, Vittorio Brando, Robert J. W. Brewin, Vanda Brotas, Elisabetta Canuti, Francisco P. Chavez, Andrés Cianca, Hervé Claustre, Lesley Clementson, Simone Colella, Raul Costa, Cristina Nunes, Richard Crout, Emmanuel Devred, Annalisa Di Cicco, Federico Falcini, Ivan Farace, Afonso Ferreira, Scott Freeman, Robert Frouin, Carlos García-Soto, Isabella Giardina, Stuart W. Gibb, Arthur Gleason, Ralf Goericke, Richard Gould, Michael Grant, Nathalie Guillocheau, Hiroto Higa, Stanford B. Hooker, Chuamin Hu, Joji Ishizaka, Thomas Jackson, Mati Kahru, Milton Kampel, Bokyung Kim, Holger Klein, Piotr Kowalczuk, Susanne Kratzer, Raphael Kudela, Antonia Lai, Rosario Lavezza, Jesus Ledesma, Huiwon Lee, Steven Lohrenz, Hubert Loisel, Vivian Lutz, Antonio Mannino, Francesca Margiotta, Victor Martinez-Vicente, Salvatore Marullo, Luca Massi, Patricia Matrai, Atsushi Matsuoka, David McKee, Chiara Melillo, Carlos B. Mendes, Brian G. Mitchell, Tiffany Moisan, Enrique Montes, Frank Muller-Karger, Aimee Neeley, Michael Novak, Leonie O'Dowd, Michael Ondrusek, Emanuele Organelli, Heeyoon Park, Trevor Platt, Francesca Polonelli, Alex Poulton, Mariella Ragni, Michel Repecaud, Maurizio Ribera d’Alcalà, Tamara Rodriguez-Ramos, Rüdiger Röttgers, Manuel Ruiz-Villarreal, Michela Sammartino, Rosalia Santoleri, Gian Marco Scarpa, Thomas Schroeder, Valeria Segura, Timothy Smyth, Denise Smythe-Wright, Heidi M. Sosik, Joanna Stoń-Egiert, Malcolm Taberner, Jing Tan, Rob Thomas, Crystal Thomas, Gavin Tilstone, Andreia Tracana, Michael Twardowski, Vincenzo Vellucci, Gianluca Volpe, Kenneth Voss, Jeremy Werdell, Marcel Wernand, Bozena Wojtasiewicz, Simon Wright, Sunmi Yang, Giuseppe Zibordi, Maria Laura Zoffoli, and Steve Groom
Earth Syst. Sci. Data Discuss., https://doi.org/10.5194/essd-2026-539, https://doi.org/10.5194/essd-2026-539, 2026
Preprint under review for ESSD
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This paper presents the fourth version of the ESA Ocean Colour Climate Change Initiative global in situ bio-optical database. The updated compilation combines observations from many international data sources collected between 1996 and 2025 and includes major expansions in coverage and variables. The dataset provides a consistent reference for validating satellite ocean-colour products and supports algorithm development and long-term climate studies.
Riss M. Kell, Adam V. Subhas, Nicole L. Schanke, Lauren E. Lees, Rebecca J. Chmiel, Deepa Rao, Margaret M. Brisbin, Dawn M. Moran, Matthew R. McIlvin, Francesco Bolinesi, Olga Mangoni, Raffaella Casotti, Cecilia Balestra, Tristan J. Horner, Robert B. Dunbar, Andrew E. Allen, Giacomo R. DiTullio, and Mak A. Saito
Biogeosciences, 22, 5877–5896, https://doi.org/10.5194/bg-22-5877-2025, https://doi.org/10.5194/bg-22-5877-2025, 2025
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Photosynthetic productivity is strongly influenced by water column nutrient availability. Despite the importance of zinc, definitive evidence for oceanic zinc limitation of photosynthesis has been scarce. We applied multiple biogeochemical measurements to a field site in Terra Nova Bay, Antarctica, to demonstrate that the phytoplankton community was experiencing zinc limitation. This field evidence paves the way for future experimental studies to consider Zn as a limiting oceanic micronutrient.
Gabriela Negrete-García, Jessica Y. Luo, Colleen M. Petrik, Manfredi Manizza, and Andrew D. Barton
Biogeosciences, 21, 4951–4973, https://doi.org/10.5194/bg-21-4951-2024, https://doi.org/10.5194/bg-21-4951-2024, 2024
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The Arctic Ocean experiences significant seasonal and year-to-year changes, impacting marine plankton populations. Using a plankton community model, we studied these effects on plankton communities and their influence on fish production. Our findings revealed earlier plankton blooms, shifts towards more carnivorous zooplankton, and increased fishery potential during summertime, especially in warmer years with less ice, highlighting the delicate balance of Arctic ecosystems.
Benjamin Post, Esteban Acevedo-Trejos, Andrew D. Barton, and Agostino Merico
Geosci. Model Dev., 17, 1175–1195, https://doi.org/10.5194/gmd-17-1175-2024, https://doi.org/10.5194/gmd-17-1175-2024, 2024
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Creating computational models of how phytoplankton grows in the ocean is a technical challenge. We developed a new tool set (Xarray-simlab-ODE) for building such models using the programming language Python. We demonstrate the tool set in a library of plankton models (Phydra). Our goal was to allow scientists to develop models quickly, while also allowing the model structures to be changed easily. This allows us to test many different structures of our models to find the most appropriate one.
André Valente, Shubha Sathyendranath, Vanda Brotas, Steve Groom, Michael Grant, Thomas Jackson, Andrei Chuprin, Malcolm Taberner, Ruth Airs, David Antoine, Robert Arnone, William M. Balch, Kathryn Barker, Ray Barlow, Simon Bélanger, Jean-François Berthon, Şükrü Beşiktepe, Yngve Borsheim, Astrid Bracher, Vittorio Brando, Robert J. W. Brewin, Elisabetta Canuti, Francisco P. Chavez, Andrés Cianca, Hervé Claustre, Lesley Clementson, Richard Crout, Afonso Ferreira, Scott Freeman, Robert Frouin, Carlos García-Soto, Stuart W. Gibb, Ralf Goericke, Richard Gould, Nathalie Guillocheau, Stanford B. Hooker, Chuamin Hu, Mati Kahru, Milton Kampel, Holger Klein, Susanne Kratzer, Raphael Kudela, Jesus Ledesma, Steven Lohrenz, Hubert Loisel, Antonio Mannino, Victor Martinez-Vicente, Patricia Matrai, David McKee, Brian G. Mitchell, Tiffany Moisan, Enrique Montes, Frank Muller-Karger, Aimee Neeley, Michael Novak, Leonie O'Dowd, Michael Ondrusek, Trevor Platt, Alex J. Poulton, Michel Repecaud, Rüdiger Röttgers, Thomas Schroeder, Timothy Smyth, Denise Smythe-Wright, Heidi M. Sosik, Crystal Thomas, Rob Thomas, Gavin Tilstone, Andreia Tracana, Michael Twardowski, Vincenzo Vellucci, Kenneth Voss, Jeremy Werdell, Marcel Wernand, Bozena Wojtasiewicz, Simon Wright, and Giuseppe Zibordi
Earth Syst. Sci. Data, 14, 5737–5770, https://doi.org/10.5194/essd-14-5737-2022, https://doi.org/10.5194/essd-14-5737-2022, 2022
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A compiled set of in situ data is vital to evaluate the quality of ocean-colour satellite data records. Here we describe the global compilation of bio-optical in situ data (spanning from 1997 to 2021) used for the validation of the ocean-colour products from the ESA Ocean Colour Climate Change Initiative (OC-CCI). The compilation merges and harmonizes several in situ data sources into a simple format that could be used directly for the evaluation of satellite-derived ocean-colour data.
Michael R. Stukel, Moira Décima, and Michael R. Landry
Biogeosciences, 19, 3595–3624, https://doi.org/10.5194/bg-19-3595-2022, https://doi.org/10.5194/bg-19-3595-2022, 2022
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The biological carbon pump (BCP) transports carbon into the deep ocean, leading to long-term marine carbon sequestration. It is driven by many physical, chemical, and ecological processes. We developed a model of the BCP constrained using data from 11 cruises in 4 different ocean regions. Our results show that sinking particles and vertical mixing are more important than transport mediated by vertically migrating zooplankton. They also highlight the uncertainty in current estimates of the BCP.
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Short summary
With the likely emergence of satellite-based phytoplankton pigment data, it is increasingly important to examine relationships between phytoplankton pigments and other metrics of phytoplankton community composition. By using quantitative approaches, we show that phytoplankton pigments correlate with nucleic acid-based abundances, and examine how integration of these data addresses ecological questions relating to diversity patterns, harmful algal blooms, and inferring cellular activity.
With the likely emergence of satellite-based phytoplankton pigment data, it is increasingly...
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