Articles | Volume 22, issue 18
https://doi.org/10.5194/bg-22-4743-2025
© 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-22-4743-2025
© Author(s) 2025. This work is distributed under
the Creative Commons Attribution 4.0 License.
the Creative Commons Attribution 4.0 License.
Research article
| 
17 Sep 2025
Research article |
| 17 Sep 2025
| 17 Sep 2025
Phytoplankton community succession and biogeochemistry in a bloom simulation experiment at an estuary–ocean interface
Department of Geosciences, Princeton University, Princeton, NJ 08544, USA
Joseph H. Vineis
Department of Geosciences, Princeton University, Princeton, NJ 08544, USA
current address: Marine Biological Laboratory, University of Chicago, Woods Hole, MA 02543, USA
Mathieu A. Poupon
Department of Geosciences, Princeton University, Princeton, NJ 08544, USA
Atmospheric and Oceanic Sciences Program, Princeton University, Princeton, NJ 08544, USA
Laure Resplandy
Department of Geosciences, Princeton University, Princeton, NJ 08544, USA
High Meadows Environmental Institute, Princeton University, Princeton, NJ 08544, USA
Bess B. Ward
Department of Geosciences, Princeton University, Princeton, NJ 08544, USA
High Meadows Environmental Institute, Princeton University, Princeton, NJ 08544, USA
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Abigale M. Wyatt, Laure Resplandy, and Adrian Marchetti
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Pierre Friedlingstein, Michael O'Sullivan, Matthew W. Jones, Robbie M. Andrew, Luke Gregor, Judith Hauck, Corinne Le Quéré, Ingrid T. Luijkx, Are Olsen, Glen P. Peters, Wouter Peters, Julia Pongratz, Clemens Schwingshackl, Stephen Sitch, Josep G. Canadell, Philippe Ciais, Robert B. Jackson, Simone R. Alin, Ramdane Alkama, Almut Arneth, Vivek K. Arora, Nicholas R. Bates, Meike Becker, Nicolas Bellouin, Henry C. Bittig, Laurent Bopp, Frédéric Chevallier, Louise P. Chini, Margot Cronin, Wiley Evans, Stefanie Falk, Richard A. Feely, Thomas Gasser, Marion Gehlen, Thanos Gkritzalis, Lucas Gloege, Giacomo Grassi, Nicolas Gruber, Özgür Gürses, Ian Harris, Matthew Hefner, Richard A. Houghton, George C. Hurtt, Yosuke Iida, Tatiana Ilyina, Atul K. Jain, Annika Jersild, Koji Kadono, Etsushi Kato, Daniel Kennedy, Kees Klein Goldewijk, Jürgen Knauer, Jan Ivar Korsbakken, Peter Landschützer, Nathalie Lefèvre, Keith Lindsay, Junjie Liu, Zhu Liu, Gregg Marland, Nicolas Mayot, Matthew J. McGrath, Nicolas Metzl, Natalie M. Monacci, David R. Munro, Shin-Ichiro Nakaoka, Yosuke Niwa, Kevin O'Brien, Tsuneo Ono, Paul I. Palmer, Naiqing Pan, Denis Pierrot, Katie Pocock, Benjamin Poulter, Laure Resplandy, Eddy Robertson, Christian Rödenbeck, Carmen Rodriguez, Thais M. Rosan, Jörg Schwinger, Roland Séférian, Jamie D. Shutler, Ingunn Skjelvan, Tobias Steinhoff, Qing Sun, Adrienne J. Sutton, Colm Sweeney, Shintaro Takao, Toste Tanhua, Pieter P. Tans, Xiangjun Tian, Hanqin Tian, Bronte Tilbrook, Hiroyuki Tsujino, Francesco Tubiello, Guido R. van der Werf, Anthony P. Walker, Rik Wanninkhof, Chris Whitehead, Anna Willstrand Wranne, Rebecca Wright, Wenping Yuan, Chao Yue, Xu Yue, Sönke Zaehle, Jiye Zeng, and Bo Zheng
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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
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Pierre Friedlingstein, Matthew W. Jones, Michael O'Sullivan, Robbie M. Andrew, Dorothee C. E. Bakker, Judith Hauck, Corinne Le Quéré, Glen P. Peters, Wouter Peters, Julia Pongratz, Stephen Sitch, Josep G. Canadell, Philippe Ciais, Rob B. Jackson, Simone R. Alin, Peter Anthoni, Nicholas R. Bates, Meike Becker, Nicolas Bellouin, Laurent Bopp, Thi Tuyet Trang Chau, Frédéric Chevallier, Louise P. Chini, Margot Cronin, Kim I. Currie, Bertrand Decharme, Laique M. Djeutchouang, Xinyu Dou, Wiley Evans, Richard A. Feely, Liang Feng, Thomas Gasser, Dennis Gilfillan, Thanos Gkritzalis, Giacomo Grassi, Luke Gregor, Nicolas Gruber, Özgür Gürses, Ian Harris, Richard A. Houghton, George C. Hurtt, Yosuke Iida, Tatiana Ilyina, Ingrid T. Luijkx, Atul Jain, Steve D. Jones, Etsushi Kato, Daniel Kennedy, Kees Klein Goldewijk, Jürgen Knauer, Jan Ivar Korsbakken, Arne Körtzinger, Peter Landschützer, Siv K. Lauvset, Nathalie Lefèvre, Sebastian Lienert, Junjie Liu, Gregg Marland, Patrick C. McGuire, Joe R. Melton, David R. Munro, Julia E. M. S. Nabel, Shin-Ichiro Nakaoka, Yosuke Niwa, Tsuneo Ono, Denis Pierrot, Benjamin Poulter, Gregor Rehder, Laure Resplandy, Eddy Robertson, Christian Rödenbeck, Thais M. Rosan, Jörg Schwinger, Clemens Schwingshackl, Roland Séférian, Adrienne J. Sutton, Colm Sweeney, Toste Tanhua, Pieter P. Tans, Hanqin Tian, Bronte Tilbrook, Francesco Tubiello, Guido R. van der Werf, Nicolas Vuichard, Chisato Wada, Rik Wanninkhof, Andrew J. Watson, David Willis, Andrew J. Wiltshire, Wenping Yuan, Chao Yue, Xu Yue, Sönke Zaehle, and Jiye Zeng
Earth Syst. Sci. Data, 14, 1917–2005, https://doi.org/10.5194/essd-14-1917-2022, https://doi.org/10.5194/essd-14-1917-2022, 2022
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Alizée Roobaert, Laure Resplandy, Goulven G. Laruelle, Enhui Liao, and Pierre Regnier
Ocean Sci., 18, 67–88, https://doi.org/10.5194/os-18-67-2022, https://doi.org/10.5194/os-18-67-2022, 2022
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This study uses a global oceanic model to investigate the seasonal dynamics of the sea surface partial pressure of CO2 (pCO2) in the global coastal ocean. Our method quantifies the respective effects of thermal changes, biological activity, ocean circulation and freshwater fluxes on the temporal pCO2 variations. The performance of our model is also evaluated against a data product derived from observations to identify coastal regions where our approach is most robust.
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
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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.
Pierre Friedlingstein, Michael O'Sullivan, Matthew W. Jones, Robbie M. Andrew, Judith Hauck, Are Olsen, Glen P. Peters, Wouter Peters, Julia Pongratz, Stephen Sitch, Corinne Le Quéré, Josep G. Canadell, Philippe Ciais, Robert B. Jackson, Simone Alin, Luiz E. O. C. Aragão, Almut Arneth, Vivek Arora, Nicholas R. Bates, Meike Becker, Alice Benoit-Cattin, Henry C. Bittig, Laurent Bopp, Selma Bultan, Naveen Chandra, Frédéric Chevallier, Louise P. Chini, Wiley Evans, Liesbeth Florentie, Piers M. Forster, Thomas Gasser, Marion Gehlen, Dennis Gilfillan, Thanos Gkritzalis, Luke Gregor, Nicolas Gruber, Ian Harris, Kerstin Hartung, Vanessa Haverd, Richard A. Houghton, Tatiana Ilyina, Atul K. Jain, Emilie Joetzjer, Koji Kadono, Etsushi Kato, Vassilis Kitidis, Jan Ivar Korsbakken, Peter Landschützer, Nathalie Lefèvre, Andrew Lenton, Sebastian Lienert, Zhu Liu, Danica Lombardozzi, Gregg Marland, Nicolas Metzl, David R. Munro, Julia E. M. S. Nabel, Shin-Ichiro Nakaoka, Yosuke Niwa, Kevin O'Brien, Tsuneo Ono, Paul I. Palmer, Denis Pierrot, Benjamin Poulter, Laure Resplandy, Eddy Robertson, Christian Rödenbeck, Jörg Schwinger, Roland Séférian, Ingunn Skjelvan, Adam J. P. Smith, Adrienne J. Sutton, Toste Tanhua, Pieter P. Tans, Hanqin Tian, Bronte Tilbrook, Guido van der Werf, Nicolas Vuichard, Anthony P. Walker, Rik Wanninkhof, Andrew J. Watson, David Willis, Andrew J. Wiltshire, Wenping Yuan, Xu Yue, and Sönke Zaehle
Earth Syst. Sci. Data, 12, 3269–3340, https://doi.org/10.5194/essd-12-3269-2020, https://doi.org/10.5194/essd-12-3269-2020, 2020
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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
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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.
Cited articles
Adolf, J. E., Yeager, C. L., Miller, W. D., Mallonee, M. E., and Harding, L. W.: Environmental forcing of phytoplankton floral composition, biomass, and primary productivity in Chesapeake Bay, USA, Estuar. Coast. Shelf Sci., 67, 108–122, https://doi.org/10.1016/j.ecss.2005.11.030, 2006.
Arteaga, L., Pahlow, M., and Oschlies, A.: Modeled Chl:C ratio and derived estimates of phytoplankton carbon biomass and its contribution to total particulate organic carbon in the global surface ocean, Global Biogeochem. Cy., 30, 1791–1810, https://doi.org/10.1002/2016GB005458, 2016.
Banse, K.: Determining the carbon-to-chlorophyll ratio of natural phytoplankton, Mar. Biol., 41, 199–212, https://doi.org/10.1007/BF00394907, 1977.
Barnett, D., Arts, I., and Penders, J.: microViz: an R package for microbiome data visualization and statistics, J. Open Source Softw., 6, 3201, https://doi.org/10.21105/joss.03201, 2021.
Bauer, J. E., Cai, W.-J., Raymond, P. A., Bianchi, T. S., Hopkinson, C. S., and Regnier, P. A. G.: The changing carbon cycle of the coastal ocean, Nature, 504, 61–70, https://doi.org/10.1038/nature12857, 2013.
Behrenfeld, M. J., Boss, E., Siegel, D. A., and Shea, D. M.: Carbon-based ocean productivity and phytoplankton physiology from space, Global Biogeochem. Cy., 19, 2004GB002299, https://doi.org/10.1029/2004GB002299, 2005.
Bilkovic, D. M., Mitchell, M. M., Havens, K. J., and Hershner, C. H.: Chesapeake Bay, in: World Seas: an Environmental Evaluation, Elsevier, 379–404, https://doi.org/10.1016/B978-0-12-805068-2.00019-X, 2019.
Bradley, P. B., Lomas, M. W., and Bronk, D. A.: Inorganic and Organic Nitrogen Use by Phytoplankton Along Chesapeake Bay, Measured Using a Flow Cytometric Sorting Approach, Estuar. Coast., 33, 971–984, https://doi.org/10.1007/s12237-009-9252-y, 2010.
Braman, R. S. and Hendrix, S. A.: Nanogram nitrite and nitrate determination in environmental and biological materials by vanadium(III) reduction with chemiluminescence detection, Anal. Chem., 61, 2715–2718, https://doi.org/10.1021/ac00199a007, 1989.
Bronk, D. A.: Dynamics of DON, in: Biogeochemistry of marine dissolved organic matter, edited by: Hansell, D. A. and Carlson, C. A., Elsevier, Science & Technology, 153–247, https://doi.org/10.1016/B978-012323841-2/50007-5, 2002.
Brzezinski, M. A.: The Si:C ratio of marine diatoms: Interspecific variability and the effect of some environmental variables, J. Phycol., 21, 347–357, 1985.
Caporaso, J. G., Lauber, C. L., Walters, W. A., Berg-Lyons, D., Lozupone, C. A., Turnbaugh, P. J., Fierer, N., and Knight, R.: Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample, P. Natl. Acad. Sci., 108, 4516–4522, https://doi.org/10.1073/pnas.1000080107, 2011.
Cerco, C. F.: Phytoplankton Kinetics in the Chesapeake Bay Eutrophication Model, Tech. Rep. January 2000 Chesap. Bay Program Off. Annap. MD, Water Quality and Ecosystems Modeling, Springer, 1, 5–49, https://doi.org/10.1023/A:1013964231397, 2000.
Collos, Y.: Nitrate uptake, nitrite release and uptake, and new production estimates, Mar. Ecol. Prog. Ser., 171, 293–301, https://doi.org/10.3354/meps171293, 1998.
Costa, P. and Garrido, S.: Domoic acid accumulation in the sardine Sardina pilchardus and its relationship to Pseudo-nitzschia diatom ingestion, Mar. Ecol. Prog. Ser., 284, 261–268, https://doi.org/10.3354/meps284261, 2004.
Cram, J. A., Hollins, A., McCarty, A. J., Martinez, G., Cui, M., Gomes, M. L., and Fuchsman, C. A.: Microbial diversity and abundance vary along salinity, oxygen, and particle size gradients in the Chesapeake Bay, Environ. Microbiol., 26, e16557, https://doi.org/10.1111/1462-2920.16557, 2024.
Dugdale, R. C. and Goering, J. J.: Uptake of new and regenerated forms of nitrogen in primary productivity1, Limnol. Oceanogr., 12, 196–206, https://doi.org/10.4319/lo.1967.12.2.0196, 1967.
Dursun, F., Tas, S., and Ediger, D.: Assessment of phytoplankton group composition in the Golden Horn Estuary (Sea of Marmara, Turkey) determined with pigments measured by HPLC-CHEMTAX analyses and microscopy, J. Mar. Biol. Assoc. UK, 101, 649–665, https://doi.org/10.1017/S0025315421000631, 2021.
Edgar, R. C., Haas, B. J., Clemente, J. C., Quince, C., and Knight, R.: UCHIME improves sensitivity and speed of chimera detection, Bioinformatics, 27, 2194–2200, https://doi.org/10.1093/bioinformatics/btr381, 2011.
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.
Fawcett, S. and Ward, B.: Phytoplankton succession and nitrogen utilization during the development of an upwelling bloom, Mar. Ecol. Prog. Ser., 428, 13–31, https://doi.org/10.3354/meps09070, 2011.
Field, C. B., Behrenfeld, M. J., Randerson, J. T., and Falkowski, P.: Primary Production of the Biosphere: Integrating Terrestrial and Oceanic Components, Science, 281, 237–240, https://doi.org/10.1126/science.281.5374.237, 1998.
Fisher, T., Peele, E., Ammerman, J., and Harding, L.: Nutrient limitation of phytoplankton in Chesapeake Bay, Mar. Ecol. Prog. Ser., 82, 51–63, https://doi.org/10.3354/meps082051, 1992.
Fox, J. and Weisberg, S.: An R Companion to Applied Regression, Third., Sage, Sage Publications, Thousand Oaks CA, ISBN 978-1-5443-3645-9, 2019.
Glibert, P. M., Conley, D. J., Fisher, T. R., Jr, L. W. H., and Malone, T. C.: Dynamics of the 1990 winter/spring bloom in Chesapeake Bay, Mar. Ecol. Prog. Ser., 122, 27–43, 1995.
Glibert, P. M., Icarus Allen, J., Artioli, Y., Beusen, A., Bouwman, L., Harle, J., Holmes, R., and Holt, J.: Vulnerability of coastal ecosystems to changes in harmful algal bloom distribution in response to climate change: projections based on model analysis, Glob. Change Biol., 20, 3845–3858, https://doi.org/10.1111/gcb.12662, 2014.
Graham, J. H. and Duda, J. J.: The Humpbacked Species Richness-Curve: A Contingent Rule for Community Ecology, Int. J. Ecol., 2011, 1–15, https://doi.org/10.1155/2011/868426, 2011.
Grønning, J. and Kiørboe, T.: Diatom defence: Grazer induction and cost of shell-thickening, Funct. Ecol., 34, 1790–1801, https://doi.org/10.1111/1365-2435.13635, 2020.
Guillou, L., Bachar, D., Audic, S., Bass, D., Berney, C., Bittner, L., Boutte, C., Burgaud, G., De Vargas, C., Decelle, J., Del Campo, J., Dolan, J. R., Dunthorn, M., Edvardsen, B., Holzmann, M., Kooistra, W. H. C. F., Lara, E., Le Bescot, N., Logares, R., Mahé, F., Massana, R., Montresor, M., Morard, R., Not, F., Pawlowski, J., Probert, I., Sauvadet, A. L., Siano, R., Stoeck, T., Vaulot, D., Zimmermann, P., and Christen, R.: The Protist Ribosomal Reference database (PR2): a catalog of unicellular eukaryote Small Sub-Unit rRNA sequences with curated taxonomy, Nucl. Acids Res., 41, D597–D604, https://doi.org/10.1093/nar/gks1160, 2012.
Guo, L., Santschi, P. H., Cifuentes, L. A., Trumbore, S. E., and Southon, J.: Cycling of high-molecular-weight dissolved organic matter in the Middle Atlantic Bight as revealed by carbon isotopic (13C and 14C) signatures, Limnol. Oceanogr., 41, 1242–1252, https://doi.org/10.4319/lo.1996.41.6.1242, 1996.
Guo, L., Sui, Z., and Liu, Y.: Quantitative analysis of dinoflagellates and diatoms community via Miseq sequencing of actin gene and v9 region of 18S rDNA, Sci. Rep., 6, 34709, https://doi.org/10.1038/srep34709, 2016.
Hansen, G., Daugbjerg, N., and Henriksen, P.: Comparative study of Gymnodinium mikimotoi and Gymnodinium aureolum, comb. nov. (= Gyrodinium aureolum) based on morphology, pigment composition, and molecular data, J. Phycol., 36, 394–410, https://doi.org/10.1046/j.1529-8817.2000.99172.x, 2000.
Harding, L. W., Adolf, J. E., Mallonee, M. E., Miller, W. D., Gallegos, C. L., Perry, E. S., Johnson, J. M., Sellner, K. G., and Paerl, H. W.: Climate effects on phytoplankton floral composition in Chesapeake Bay, Estuar. Coast. Shelf Sci., 162, 53–68, https://doi.org/10.1016/j.ecss.2014.12.030, 2015.
Harding, L. W., Mallonee, M. E., Perry, E. S., Miller, W. D., Adolf, J. E., Gallegos, C. L., and Paerl, H. W.: Long-term trends, current status, and transitions of water quality in Chesapeake Bay, Sci. Rep., 9, 6709, https://doi.org/10.1038/s41598-019-43036-6, 2019.
Hooker, S. B., Thomas, C. S., Heukelem, L. V., Schlüter, L., Russ, M. E., Ras, J., Claustre, H., Clementson, L., Canuti, E., Berthon, J.-F., Perl, J., Normandeau, C., Cullen, J., Kienast, M., and Pinckney, J. L.: The Fourth SeaWiFS HPLC Analysis Round-Robin Experiment (SeaHARRE-4), No. NASATM-2010-215857, https://ntrs.nasa.gov/api/citations/20110008482/downloads/20110008482.pdf (last access: 8 September 2025), 2010.
Irigoien, X., Huisman, J., and Harris, R. P.: Global biodiversity patterns of marine phytoplankton and zooplankton, Nature, 429, 863–867, https://doi.org/10.1038/nature02593, 2004.
Jackson, T., Bouman, H. A., Sathyendranath, S., and Devred, E.: Regional-scale changes in diatom distribution in the Humboldt upwelling system as revealed by remote sensing: implications for fisheries, ICES J. Mar. Sci., 68, 729–736, https://doi.org/10.1093/icesjms/fsq181, 2011.
Jakobsen, H. H. and Markager, S.: Carbon-to-chlorophyll ratio for phytoplankton in temperate coastal waters: Seasonal patterns and relationship to nutrients: C:Chl for phytoplankton in temperate coastal waters, Limnol. Oceanogr., 61, 1853–1868, https://doi.org/10.1002/lno.10338, 2016.
Jin, X., Gruber, N., Dunne, J. P., Sarmiento, J. L., and Armstrong, R. A.: Diagnosing the contribution of phytoplankton functional groups to the production and export of particulate organic carbon, CaCO3, and opal from global nutrient and alkalinity distributions, Global Biogeochem. Cy., 20, 2005GB002532, https://doi.org/10.1029/2005GB002532, 2006.
Kudela, R. M. and Dugdale, R. C.: Nutrient regulation of phytoplankton productivity in Monterey Bay, California, Deep-Sea Res. Pt. II, 47, 1023–1053, https://doi.org/10.1016/S0967-0645(99)00135-6, 2000.
Lampe, R. H., Cohen, N. R., Ellis, K. A., Bruland, K. W., Maldonado, M. T., Peterson, T. D., Till, C. P., Brzezinski, M. A., Bargu, S., Thamatrakoln, K., Kuzminov, F. I., Twining, B. S., and Marchetti, A.: Divergent gene expression among phytoplankton taxa in response to upwelling, Environ. Microbiol., 20, 3069–3082, https://doi.org/10.1111/1462-2920.14361, 2018.
Laws, E. A. and Bannister, T. T.: Nutrient- and light-limited growth of Thalassiosira fluviatilis in continuous culture, with implications for phytoplankton growth in the ocean1, Limnol. Oceanogr., 25, 457–473, https://doi.org/10.4319/lo.1980.25.3.0457, 1980.
Lee, D. Y., Owens, M. S., Doherty, M., Eggleston, E. M., Hewson, I., Crump, B. C., and Cornwell, J. C.: The Effects of Oxygen Transition on Community Respiration and Potential Chemoautotrophic Production in a Seasonally Stratified Anoxic Estuary, Estuar. Coast., 38, 104–117, https://doi.org/10.1007/s12237-014-9803-8, 2015.
Legendre, L. and Le Fèvre, J.: Microbial food webs and the export of biogenic carbon in oceans, Aquat. Microb. Ecol., 9, 69–77, https://doi.org/10.3354/ame009069, 1995.
Lepère, C., Domaizon, I., Hugoni, M., Vellet, A., and Debroas, D.: Diversity and Dynamics of Active Small Microbial Eukaryotes in the Anoxic Zone of a Freshwater Meromictic Lake (Pavin, France), Front. Microbiol., 7, 130, https://doi.org/10.3389/fmicb.2016.00130, 2016.
Li, J., Glibert, P. M., and Gao, Y.: Temporal and spatial changes in Chesapeake Bay water quality and relationships to Prorocentrum minimum, Karlodinium veneficum, and CyanoHAB events, 1991–2008, Harmful Algae, 42, 1–14, https://doi.org/10.1016/j.hal.2014.11.003, 2015.
Li, X., Yan, T., Yu, R., and Zhou, M.: A review of karenia mikimotoi: Bloom events, physiology, toxicity and toxic mechanism, Harmful Algae, 90, 101702, https://doi.org/10.1016/j.hal.2019.101702, 2019.
Li, Z. and Cassar, N.: Satellite estimates of net community production based on O2
Liang, Y., Zhang, G., Wan, A., Zhao, Z., Wang, S., and Liu, Q.: Nutrient-limitation induced diatom-dinoflagellate shift of spring phytoplankton community in an offshore shellfish farming area, Mar. Pollut. Bull., 141, 1–8, https://doi.org/10.1016/j.marpolbul.2019.02.009, 2019.
Lima-Mendez, G., Faust, K., Henry, N., Decelle, J., Colin, S., Carcillo, F., Chaffron, S., Ignacio-Espinosa, J. C., Roux, S., Vincent, F., Bittner, L., Darzi, Y., Wang, J., Audic, S., Berline, L., Bontempi, G., Cabello, A. M., Coppola, L., Cornejo-Castillo, F. M., d'Ovidio, F., De Meester, L., Ferrera, I., Garet-Delmas, M.-J., Guidi, L., Lara, E., Pesant, S., Royo-Llonch, M., Salazar, G., Sánchez, P., Sebastian, M., Souffreau, C., Dimier, C., Picheral, M., Searson, S., Kandels-Lewis, S., Tara Oceans coordinators, Gorsky, G., Not, F., Ogata, H., Speich, S., Stemmann, L., Weissenbach, J., Wincker, P., Acinas, S. G., Sunagawa, S., Bork, P., Sullivan, M. B., Karsenti, E., Bowler, C., De Vargas, C., and Raes, J.: Determinants of community structure in the global plankton interactome, Science, 348, 1262073, https://doi.org/10.1126/science.1262073, 2015.
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.
Lomas, M. W., Baer, S. E., Acton, S., and Krause, J. W.: Pumped Up by the Cold: Elemental Quotas and Stoichiometry of Cold-Water Diatoms, Front. Mar. Sci., 6, 286, https://doi.org/10.3389/fmars.2019.00286, 2019.
López-García, P., Rodríguez-Valera, F., Pedrós-Alió, C., and Moreira, D.: Unexpected diversity of small eukaryotes in deep-sea Antarctic plankton, Nature, 409, 603–607, https://doi.org/10.1038/35054537, 2001.
Mahé, F., Czech, L., Stamatakis, A., Quince, C., De Vargas, C., Dunthorn, M., and Rognes, T.: Swarm v3: towards tera-scale amplicon clustering, Bioinformatics, 38, 267–269, https://doi.org/10.1093/bioinformatics/btab493, 2021.
Malone, T. C., Conley, D. J., Fisher, T. R., Glibert, P. M., Harding, L. W., and Sellner, K. G.: Scales of Nutrient-Limited Phytoplankton Productivity in Chesapeake Bay, Estuaries, 19, 371, https://doi.org/10.2307/1352457, 1996.
Mangot, J., Domaizon, I., Taib, N., Marouni, N., Duffaud, E., Bronner, G., and Debroas, D.: Short-term dynamics of diversity patterns: evidence of continual reassembly within lacustrine small eukaryotes, Environ. Microbiol., 15, 1745–1758, https://doi.org/10.1111/1462-2920.12065, 2013.
Marshall, H. G. and Nesius, K. K.: Phytoplankton composition in relation to primary production in Chesapeake Bay, Mar. Biol., 125, 611–617, https://doi.org/10.1007/BF00353272, 1996.
Marshall, H. G., Burchardt, L., and Lacouture, R.: A review of phytoplankton composition within Chesapeake Bay and its tidal estuaries, J. Plankton Res., 27, 1083–1102, https://doi.org/10.1093/plankt/fbi079, 2005.
Martin, J. L., Santi, I., Pitta, P., John, U., and Gypens, N.: Towards quantitative metabarcoding of eukaryotic plankton: an approach to improve 18S rRNA gene copy number bias, Metabarcoding Metagenomics, 6, e85794, https://doi.org/10.3897/mbmg.6.85794, 2022.
Massana, R. and Pedrós-Alió, C.: Unveiling new microbial eukaryotes in the surface ocean, Curr. Opin. Microbiol., 11, 213–218, https://doi.org/10.1016/j.mib.2008.04.004, 2008.
MathWorks Inc.: MATLAB version: 24.1.0.2689473 (R2024a) Update 6, Natick, Massachusetts, https://www.mathworks.com, 2024.
McMurdie, P. J. and Holmes, S.: phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data, PLoS ONE, 8, e61217, https://doi.org/10.1371/journal.pone.0061217, 2013.
Minoche, A. E., Dohm, J. C., and Himmelbauer, H.: Evaluation of genomic high-throughput sequencing data generated on Illumina HiSeq and Genome Analyzer systems, Genome Biol., 12, R112, https://doi.org/10.1186/gb-2011-12-11-r112, 2011.
National Library of Medicine (US): Marine Phytoplankton Relationships in an Estuarine Bloom, National Center for Biotechnology Information [data set], BioProject ID PRJNA1222857, Bethesda, USA, https://www.ncbi.nlm.nih.gov/bioproject/1222857 (last access: 11 September 2025), 2025.
Oksanen, J., Simpson, G. L., Blanchet, F. G., Kindt, R., Legendre, P., Minchin, P. R., O'Hara, R. B., Solymos, P., Stevens, M. H. H., Szoecs, E., Wagner, H., Barbour, M., Bedward, M., Bolker, B., Borcard, D., Carvalho, G., Chirico, M., Caceres, M. D., Durand, S., Evangelista, H. B. A., FitzJohn, R., Friendly, M., Furneaux, B., Hannigan, G., Hill, M. O., Lahti, L., McGlinn, D., Ouellette, M.-H., Cunha, E. R., Smith, T., Stier, A., Braak, C. J. F. T., and Weedon, J.: vegan: Community Ecology Package, https://doi.org/10.32614/CRAN.package.vegan, 2024.
Park, M. G., Yih, W., and Coats, D. W.: Parasites and Phytoplankton, with Special Emphasis on Dinoflagellate Infections, J. Eukaryot. Microbiol., 51, 145–155, https://doi.org/10.1111/j.1550-7408.2004.tb00539.x, 2004.
Pinckney, J. L., Millie, D. F., Howe, K. E., Paerl, H. W., and Hurley, J. P.: Flow scintillation counting of 14C-labeled microalgal photosynthetic pigments, J. Plankton Res., 18, 1867–1880, https://doi.org/10.1093/plankt/18.10.1867, 1996.
Pinckney, J. L., Richardson, T. L., Millie, D. F., and Paerl, H. W.: Application of photopigment biomarkers for quantifying microalgal community composition and in situ growth rates, Org. Geochem., 32, 585–595, https://doi.org/10.1016/S0146-6380(00)00196-0, 2001.
R Core Team: R: A Language and Environment for Statistical Computing, R Foundation for Statistical Computing, Vienna, Austria, https://www.R-project.org/ (last access: 8 September 2025), 2023.
Redfield, A. C.: On the proportions of organic derivatives in sea water and their relation to the composition of plankton, James Johnstone Meml. Vol. Univ. Press Liverp., 176–192, 1934.
Richardson, T. L. and Pinckney, J. L.: Monitoring of the toxic dinoflagellate Karenia brevis using gyroxanthin-based detection methods, J. Appl. Phycol., 16, 315–328, https://doi.org/10.1023/B:JAPH.0000047788.31312.4f, 2004.
Rognes, T., Flouri, T., Nichols, B., Quince, C., and Mahé, F.: VSEARCH: a versatile open source tool for metagenomics, PeerJ, 4, e2584, https://doi.org/10.7717/peerj.2584, 2016.
Rosenzweig, M. L.: Species Diversity Gradients: We Know More and Less Than We Thought, J. Mammal., 73, 715–730, https://doi.org/10.2307/1382191, 1992.
Ryther, J. H.: Photosynthesis and Fish Production in the Sea: The production of organic matter and its conversion to higher forms of life vary throughout the world ocean, Science, 166, 72–76, https://doi.org/10.1126/science.166.3901.72, 1969.
Sal, S., López-Urrutia, Á., Irigoien, X., Harbour, D. S., and Harris, R. P.: Marine microplankton diversity database: Ecological Archives E094-149, Ecology, 94, 1658–1658, https://doi.org/10.1890/13-0236.1, 2013.
Sathyendranath, S., Stuart, V., Nair, A., Oka, K., Nakane, T., Bouman, H., Forget, M., Maass, H., and Platt, T.: Carbon-to-chlorophyll ratio and growth rate of phytoplankton in the sea, Mar. Ecol. Prog. Ser., 383, 73–84, https://doi.org/10.3354/meps07998, 2009.
Schmieder, R. and Edwards, R.: Quality control and preprocessing of metagenomic datasets, Bioinformatics, 27, 863–864, https://doi.org/10.1093/bioinformatics/btr026, 2011.
Schoemann, V., Becquevort, S., Stefels, J., Rousseau, V., and Lancelot, C.: Phaeocystis blooms in the global ocean and their controlling mechanisms: a review, J. Sea Res., 53, 43–66, https://doi.org/10.1016/j.seares.2004.01.008, 2005.
Sellner, K. G.: Plankton productivity and biomass in a tributary of the upper Chesapeake Bay, I. Importance of size-fractionated phytoplankton productivity, biomass and species composition in carbon export, Estuar. Coast. Shelf Sci., 17, 197–206, https://doi.org/10.1016/0272-7714(83)90064-1, 1983.
Skácelová, O. and Lepš, J.: The relationship of diversity and biomass in phytoplankton communities weakens when accounting for species proportions, Hydrobiologia, 724, 67–77, https://doi.org/10.1007/s10750-013-1723-2, 2014.
Smith, V. H.: Microbial diversity-productivity relationships in aquatic ecosystems: Diversity-productivity relationships, FEMS Microbiol. Ecol., 62, 181–186, https://doi.org/10.1111/j.1574-6941.2007.00381.x, 2007.
Sommer, U., Stibor, H., Katechakis, A., Sommer, F., and Hansen, T.: Pelagic food web configurations at different levels of nutrient richness and their implications for the ratio fish production:primary production, in: Sustainable Increase of Marine Harvesting: Fundamental Mechanisms and New Concepts, edited by: Vadstein, O. and Olsen, Y., Springer Netherlands, Dordrecht, 11–20, https://doi.org/10.1007/978-94-017-3190-4_2, 2002.
Spiker, E. C.: The Behavior of 14 C and 13 C in Estuarine Water: Effects of In Situ CO 2 Production and Atmospheric Exchange, Radiocarbon, 22, 647–654, https://doi.org/10.1017/S0033822200010018, 1980.
Stock, C. A., Dunne, J. P., Fan, S., Ginoux, P., John, J., Krasting, J. P., Laufkötter, C., Paulot, F., and Zadeh, N.: Ocean Biogeochemistry in GFDL's Earth System Model 4.1 and Its Response to Increasing Atmospheric CO2, J. Adv. Model. Earth Syst., 12, e2019MS002043, https://doi.org/10.1029/2019MS002043, 2020.
Strickland, J. D. H. and Parsons, T. R.: A Practical Handbook of Seawater Analysis, 2nd Edn., Fisheries Research Board of Canada, Ottawa, Canada, 310 pp., ISBN 0-660-11596-4, 1972.
Tada, K., Pithakpol, S., Ichimi, K., and Montani, S.: Carbon, nitrogen, phosphorus, and chlorophyll a content of the large diatom, Coscinodiscus wailesii and its abundance in the Seto Inland Sea, Japan, Fish. Sci., 66, 509–514, https://doi.org/10.1046/j.1444-2906.2000.00080.x, 2000.
Vallina, S. M., Follows, M. J., Dutkiewicz, S., Montoya, J. M., Cermeno, P., and Loreau, M.: Global relationship between phytoplankton diversity and productivity in the ocean, Nat. Commun., 5, 4299, https://doi.org/10.1038/ncomms5299, 2014.
Van Der Lingen, C. D.: Diet of sardine Sardinops sagax in the southern Benguela upwelling ecosystem, South Afr. J. Mar. Sci., 24, 301–316, https://doi.org/10.2989/025776102784528691, 2002.
Van Oostende, N., Fawcett, S. E., Marconi, D., Lueders-Dumont, J., Sabadel, A. J. M., Woodward, E. M. S., Jönsson, B. F., Sigman, D. M., and Ward, B. B.: Variation of summer phytoplankton community composition and its relationship to nitrate and regenerated nitrogen assimilation across the North Atlantic Ocean, Deep-Sea Res. Pt. I, 121, 79–94, https://doi.org/10.1016/j.dsr.2016.12.012, 2017.
Wang, H., Liu, F., Wang, M., Bettarel, Y., Eissler, Y., Chen, F., and Kan, J.: Planktonic eukaryotes in the Chesapeake Bay: contrasting responses of abundant and rare taxa to estuarine gradients, Microbiol. Spectr., 12, e04048, https://doi.org/10.1128/spectrum.04048-23, 2024.
Wang, S., Tang, W., Delage, E., Gifford, S., Whitby, H., González, A. G., Eveillard, D., Planquette, H., and Cassar, N.: Investigating the microbial ecology of coastal hotspots of marine nitrogen fixation in the western North Atlantic, Sci. Rep., 11, 5508, https://doi.org/10.1038/s41598-021-84969-1, 2021.
Ward, Bess B.: Project: Marine Diatom-Parasite Relationships in Upwelling Systems, Biological and Chemical Oceanography Data Management Office (BCO-DMO) [data set], (Version 1) Version Date 16 May 2025, https://demo.bco-dmo.org/project/869541 (last access: 16 May 2025), 2025.
Xu, S., Li, G., He, C., Huang, Y., Yu, D., Deng, H., Tong, Z., Wang, Y., Dupuy, C., Huang, B., Shen, Z., Xu, J., and Gong, J.: Diversity, community structure, and quantity of eukaryotic phytoplankton revealed using 18S rRNA and plastid 16S rRNA genes and pigment markers: a case study of the Pearl River Estuary, Mar. Life Sci. Technol., 5, 415–430, https://doi.org/10.1007/s42995-023-00186-x, 2023.
Short summary
Concurrent sampling of environmental parameters, productivity rates, photopigments, and DNA was used to analyze 24 L estuarine diatom bloom microcosms. Biogeochemical data and an ecological model indicated that the bloom was terminated by grazing. Comparisons to previous studies revealed (1) additional community and diversity complexity using 18S amplicon vs. traditional pigment–based analyses and (2) a potential global productivity–diversity relationship using 18S and carbon transport rates.
Concurrent sampling of environmental parameters, productivity rates, photopigments, and DNA was...
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