Articles | Volume 20, issue 7
https://doi.org/10.5194/bg-20-1277-2023
© Author(s) 2023. This work is distributed under
the Creative Commons Attribution 4.0 License.
the Creative Commons Attribution 4.0 License.
https://doi.org/10.5194/bg-20-1277-2023
© Author(s) 2023. This work is distributed under
the Creative Commons Attribution 4.0 License.
the Creative Commons Attribution 4.0 License.
Research article
| 
05 Apr 2023
Research article |
| 05 Apr 2023
| 05 Apr 2023
Ecological divergence of a mesocosm in an eastern boundary upwelling system assessed with multi-marker environmental DNA metabarcoding
Markus A. Min
Monterey Bay Aquarium Research Institute, Moss Landing, CA, USA
School of Aquatic and Fishery Sciences, University of Washington, Seattle, WA, USA
David M. Needham
Monterey Bay Aquarium Research Institute, Moss Landing, CA, USA
GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
Sebastian Sudek
Monterey Bay Aquarium Research Institute, Moss Landing, CA, USA
Nathan Kobun Truelove
Monterey Bay Aquarium Research Institute, Moss Landing, CA, USA
Kathleen J. Pitz
Monterey Bay Aquarium Research Institute, Moss Landing, CA, USA
Gabriela M. Chavez
Monterey Bay Aquarium Research Institute, Moss Landing, CA, USA
GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
Camille Poirier
Monterey Bay Aquarium Research Institute, Moss Landing, CA, USA
GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
Bente Gardeler
Monterey Bay Aquarium Research Institute, Moss Landing, CA, USA
GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
Elisabeth von der Esch
Institute of Hydrochemistry, Technical University of Munich, Munich, Germany
Andrea Ludwig
GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
Ulf Riebesell
GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
Alexandra Z. Worden
Monterey Bay Aquarium Research Institute, Moss Landing, CA, USA
GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
Francisco P. Chavez
CORRESPONDING AUTHOR
Monterey Bay Aquarium Research Institute, Moss Landing, CA, USA
Related authors
No articles found.
Allanah Joy Paul, Mathias Haunost, Silvan Urs Goldenberg, Jens Hartmann, Nicolás Sánchez, Julieta Schneider, Niels Suitner, and Ulf Riebesell
Biogeosciences, 22, 2749–2766, https://doi.org/10.5194/bg-22-2749-2025, https://doi.org/10.5194/bg-22-2749-2025, 2025
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Ocean alkalinity enhancement (OAE) is being assessed for its potential to absorb atmospheric CO2 and store it for a long time. OAE still needs comprehensive assessment of its safety and effectiveness. We studied an idealised OAE application in a natural low-nutrient ecosystem over 1 month. Our results showed that biogeochemical functioning remained mostly stable but that the long-term capability for storing carbon may be limited at high alkalinity concentration.
Ulf Riebesell
Biogeosciences, 22, 2381–2381, https://doi.org/10.5194/bg-22-2381-2025, https://doi.org/10.5194/bg-22-2381-2025, 2025
Librada Ramírez, Leonardo J. Pozzo-Pirotta, Aja Trebec, Víctor Manzanares-Vázquez, José L. Díez, Javier Arístegui, Ulf Riebesell, Stephen D. Archer, and María Segovia
Biogeosciences, 22, 1865–1886, https://doi.org/10.5194/bg-22-1865-2025, https://doi.org/10.5194/bg-22-1865-2025, 2025
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We studied the potential effects of increasing ocean alkalinity on a natural plankton community in subtropical waters of the Atlantic near Gran Canaria, Spain. Alkalinity is the capacity of water to resist acidification, and plankton are usually microscopic plants (phytoplankton) and animals (zooplankton), often less than 2.5 cm in length. This study suggests that increasing ocean alkalinity did not have a significant negative impact on the plankton community studied.
Julieta Schneider, Ulf Riebesell, Charly André Moras, Laura Marín-Samper, Leila Kittu, Joaquín Ortíz-Cortes, and Kai George Schulz
EGUsphere, https://doi.org/10.5194/egusphere-2025-524, https://doi.org/10.5194/egusphere-2025-524, 2025
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Ocean Alkalinity Enhancement (OAE) is an approach to sequester additional atmospheric CO2 in the ocean and may alleviate ocean acidification. A large-scale mesocosm experiment in Norway tested Ca- and Si-based OAE, increasing total alkalinity (TA) by 0–600 µmol kg-1 and measuring CO2 gas exchange. While TA remained stable, we found mineral-type and/or pCO2/pH effects on coccolithophorid calcification, net community production and zooplankton respiration, providing insights for future OAE trials.
Giulia Faucher, Mathias Haunost, Allanah Joy Paul, Anne Ulrike Christiane Tietz, and Ulf Riebesell
Biogeosciences, 22, 405–415, https://doi.org/10.5194/bg-22-405-2025, https://doi.org/10.5194/bg-22-405-2025, 2025
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Ocean alkalinity enhancement (OAE) is being evaluated for its capacity to absorb atmospheric CO2 in the ocean and store it long term to mitigate climate change. As researchers plan for field tests to gain insights into OAE, sharing knowledge on its environmental impact on marine ecosystems is urgent. Our study examined NaOH-induced OAE in Emiliania huxleyi, a key coccolithophore species, and found that the added total alkalinity (ΔTA) should stay below 600 µmol kg⁻¹ to avoid negative impacts.
Philipp Suessle, Jan Taucher, Silvan Urs Goldenberg, Moritz Baumann, Kristian Spilling, Andrea Noche-Ferreira, Mari Vanharanta, and Ulf Riebesell
Biogeosciences, 22, 71–86, https://doi.org/10.5194/bg-22-71-2025, https://doi.org/10.5194/bg-22-71-2025, 2025
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Ocean alkalinity enhancement (OAE) is a negative emission technology which may alter marine communities and the particle export they drive. Here, impacts of carbonate-based OAE on the flux and attenuation of sinking particles in an oligotrophic plankton community are presented. Whilst biological parameters remained unaffected, abiotic carbonate precipitation occurred. Among counteracting OAE’s efficiency, it influenced mineral ballasting and particle sinking velocities, requiring monitoring.
Laura Marín-Samper, Javier Arístegui, Nauzet Hernández-Hernández, and Ulf Riebesell
Biogeosciences, 21, 5707–5724, https://doi.org/10.5194/bg-21-5707-2024, https://doi.org/10.5194/bg-21-5707-2024, 2024
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This study exposed a natural community to two non-CO2-equilibrated ocean alkalinity enhancement (OAE) deployments using different minerals. Adding alkalinity in this manner decreases dissolved CO2, essential for photosynthesis. While photosynthesis was not suppressed, bloom formation was mildly delayed, potentially impacting marine food webs. The study emphasizes the need for further research on OAE without prior equilibration and on its ecological implications.
Niels Suitner, Giulia Faucher, Carl Lim, Julieta Schneider, Charly A. Moras, Ulf Riebesell, and Jens Hartmann
Biogeosciences, 21, 4587–4604, https://doi.org/10.5194/bg-21-4587-2024, https://doi.org/10.5194/bg-21-4587-2024, 2024
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Recent studies described the precipitation of carbonates as a result of alkalinity enhancement in seawater, which could adversely affect the carbon sequestration potential of ocean alkalinity enhancement (OAE) approaches. By conducting experiments in natural seawater, this study observed uniform patterns during the triggered runaway carbonate precipitation, which allow the prediction of safe and efficient local application levels of OAE scenarios.
Silvan Urs Goldenberg, Ulf Riebesell, Daniel Brüggemann, Gregor Börner, Michael Sswat, Arild Folkvord, Maria Couret, Synne Spjelkavik, Nicolás Sánchez, Cornelia Jaspers, and Marta Moyano
Biogeosciences, 21, 4521–4532, https://doi.org/10.5194/bg-21-4521-2024, https://doi.org/10.5194/bg-21-4521-2024, 2024
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Ocean alkalinity enhancement (OAE) is being evaluated as a carbon dioxide removal technology for climate change mitigation. With an experiment on species communities, we show that larval and juvenile fish can be resilient to the resulting perturbation of seawater. Fish may hence recruit successfully and continue to support fisheries' production in regions of OAE. Our findings help to establish an environmentally safe operating space for this ocean-based solution.
Sebastian I. Cantarero, Edgart Flores, Harry Allbrook, Paulina Aguayo, Cristian A. Vargas, John E. Tamanaha, J. Bentley C. Scholz, Lennart T. Bach, Carolin R. Löscher, Ulf Riebesell, Balaji Rajagopalan, Nadia Dildar, and Julio Sepúlveda
Biogeosciences, 21, 3927–3958, https://doi.org/10.5194/bg-21-3927-2024, https://doi.org/10.5194/bg-21-3927-2024, 2024
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Our study explores lipid remodeling in response to environmental stress, specifically how cell membrane chemistry changes. We focus on intact polar lipids in a phytoplankton community exposed to diverse stressors in a mesocosm experiment. The observed remodeling indicates acyl chain recycling for energy storage in intact polar lipids during stress, reallocating resources based on varying growth conditions. This understanding is essential to grasp the system's impact on cellular pools.
Laura Marín-Samper, Javier Arístegui, Nauzet Hernández-Hernández, Joaquín Ortiz, Stephen D. Archer, Andrea Ludwig, and Ulf Riebesell
Biogeosciences, 21, 2859–2876, https://doi.org/10.5194/bg-21-2859-2024, https://doi.org/10.5194/bg-21-2859-2024, 2024
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Our planet is facing a climate crisis. Scientists are working on innovative solutions that will aid in capturing the hard to abate emissions before it is too late. Exciting research reveals that ocean alkalinity enhancement, a key climate change mitigation strategy, does not harm phytoplankton, the cornerstone of marine ecosystems. Through meticulous study, we may have uncovered a positive relationship: up to a specific limit, enhancing ocean alkalinity boosts photosynthesis by certain species.
Aaron Ferderer, Kai G. Schulz, Ulf Riebesell, Kirralee G. Baker, Zanna Chase, and Lennart T. Bach
Biogeosciences, 21, 2777–2794, https://doi.org/10.5194/bg-21-2777-2024, https://doi.org/10.5194/bg-21-2777-2024, 2024
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Ocean alkalinity enhancement (OAE) is a promising method of atmospheric carbon removal; however, its ecological impacts remain largely unknown. We assessed the effects of simulated silicate- and calcium-based mineral OAE on diatom silicification. We found that increased silicate concentrations from silicate-based OAE increased diatom silicification. In contrast, the enhancement of alkalinity had no effect on community silicification and minimal effects on the silicification of different genera.
David González-Santana, María Segovia, Melchor González-Dávila, Librada Ramírez, Aridane G. González, Leonardo J. Pozzo-Pirotta, Veronica Arnone, Victor Vázquez, Ulf Riebesell, and J. Magdalena Santana-Casiano
Biogeosciences, 21, 2705–2715, https://doi.org/10.5194/bg-21-2705-2024, https://doi.org/10.5194/bg-21-2705-2024, 2024
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In a recent experiment off the coast of Gran Canaria (Spain), scientists explored a method called ocean alkalinization enhancement (OAE), where carbonate minerals were added to seawater. This process changed the levels of certain ions in the water, affecting its pH and buffering capacity. The researchers were particularly interested in how this could impact the levels of essential trace metals in the water.
Xiaoke Xin, Giulia Faucher, and Ulf Riebesell
Biogeosciences, 21, 761–772, https://doi.org/10.5194/bg-21-761-2024, https://doi.org/10.5194/bg-21-761-2024, 2024
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Ocean alkalinity enhancement (OAE) is a promising approach to remove CO2 by accelerating natural rock weathering. However, some of the alkaline substances contain trace metals which could be toxic to marine life. By exposing three representative phytoplankton species to Ni released from alkaline materials, we observed varying responses of phytoplankton to nickel concentrations, suggesting caution should be taken and toxic thresholds should be avoided in OAE with Ni-rich materials.
Ulf Riebesell, Daniela Basso, Sonja Geilert, Andrew W. Dale, and Matthias Kreuzburg
State Planet, 2-oae2023, 6, https://doi.org/10.5194/sp-2-oae2023-6-2023, https://doi.org/10.5194/sp-2-oae2023-6-2023, 2023
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Mesocosm experiments represent a highly valuable tool in determining the safe operating space of ocean alkalinity enhancement (OAE) applications. By combining realism and biological complexity with controllability and replication, they provide an ideal OAE test bed and a critical stepping stone towards field applications. Mesocosm approaches can also be helpful in testing the efficacy, efficiency and permanence of OAE applications.
Moritz Baumann, Allanah Joy Paul, Jan Taucher, Lennart Thomas Bach, Silvan Goldenberg, Paul Stange, Fabrizio Minutolo, and Ulf Riebesell
Biogeosciences, 20, 2595–2612, https://doi.org/10.5194/bg-20-2595-2023, https://doi.org/10.5194/bg-20-2595-2023, 2023
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The sinking velocity of marine particles affects how much atmospheric CO2 is stored inside our oceans. We measured particle sinking velocities in the Peruvian upwelling system and assessed their physical and biochemical drivers. We found that sinking velocity was mainly influenced by particle size and porosity, while ballasting minerals played only a minor role. Our findings help us to better understand the particle sinking dynamics in this highly productive marine system.
Kristian Spilling, Jonna Piiparinen, Eric P. Achterberg, Javier Arístegui, Lennart T. Bach, Maria T. Camarena-Gómez, Elisabeth von der Esch, Martin A. Fischer, Markel Gómez-Letona, Nauzet Hernández-Hernández, Judith Meyer, Ruth A. Schmitz, and Ulf Riebesell
Biogeosciences, 20, 1605–1619, https://doi.org/10.5194/bg-20-1605-2023, https://doi.org/10.5194/bg-20-1605-2023, 2023
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We carried out an enclosure experiment using surface water off Peru with different additions of oxygen minimum zone water. In this paper, we report on enzyme activity and provide data on the decomposition of organic matter. We found very high activity with respect to an enzyme breaking down protein, suggesting that this is important for nutrient recycling both at present and in the future ocean.
Jens Hartmann, Niels Suitner, Carl Lim, Julieta Schneider, Laura Marín-Samper, Javier Arístegui, Phil Renforth, Jan Taucher, and Ulf Riebesell
Biogeosciences, 20, 781–802, https://doi.org/10.5194/bg-20-781-2023, https://doi.org/10.5194/bg-20-781-2023, 2023
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CO2 can be stored in the ocean via increasing alkalinity of ocean water. Alkalinity can be created via dissolution of alkaline materials, like limestone or soda. Presented research studies boundaries for increasing alkalinity in seawater. The best way to increase alkalinity was found using an equilibrated solution, for example as produced from reactors. Adding particles for dissolution into seawater on the other hand produces the risk of losing alkalinity and degassing of CO2 to the atmosphere.
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.
Allanah Joy Paul, Lennart Thomas Bach, Javier Arístegui, Elisabeth von der Esch, Nauzet Hernández-Hernández, Jonna Piiparinen, Laura Ramajo, Kristian Spilling, and Ulf Riebesell
Biogeosciences, 19, 5911–5926, https://doi.org/10.5194/bg-19-5911-2022, https://doi.org/10.5194/bg-19-5911-2022, 2022
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We investigated how different deep water chemistry and biology modulate the response of surface phytoplankton communities to upwelling in the Peruvian coastal zone. Our results show that the most influential drivers were the ratio of inorganic nutrients (N : P) and the microbial community present in upwelling source water. These led to unexpected and variable development in the phytoplankton assemblage that could not be predicted by the amount of inorganic nutrients alone.
Shao-Min Chen, Ulf Riebesell, Kai G. Schulz, Elisabeth von der Esch, Eric P. Achterberg, and Lennart T. Bach
Biogeosciences, 19, 295–312, https://doi.org/10.5194/bg-19-295-2022, https://doi.org/10.5194/bg-19-295-2022, 2022
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Oxygen minimum zones in the ocean are characterized by enhanced carbon dioxide (CO2) levels and are being further acidified by increasing anthropogenic atmospheric CO2. Here we report CO2 system measurements in a mesocosm study offshore Peru during a rare coastal El Niño event to investigate how CO2 dynamics may respond to ongoing ocean deoxygenation. Our observations show that nitrogen limitation, productivity, and plankton community shift play an important role in driving the CO2 dynamics.
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.
Lennart Thomas Bach, Allanah Joy Paul, Tim Boxhammer, Elisabeth von der Esch, Michelle Graco, Kai Georg Schulz, Eric Achterberg, Paulina Aguayo, Javier Arístegui, Patrizia Ayón, Isabel Baños, Avy Bernales, Anne Sophie Boegeholz, Francisco Chavez, Gabriela Chavez, Shao-Min Chen, Kristin Doering, Alba Filella, Martin Fischer, Patricia Grasse, Mathias Haunost, Jan Hennke, Nauzet Hernández-Hernández, Mark Hopwood, Maricarmen Igarza, Verena Kalter, Leila Kittu, Peter Kohnert, Jesus Ledesma, Christian Lieberum, Silke Lischka, Carolin Löscher, Andrea Ludwig, Ursula Mendoza, Jana Meyer, Judith Meyer, Fabrizio Minutolo, Joaquin Ortiz Cortes, Jonna Piiparinen, Claudia Sforna, Kristian Spilling, Sonia Sanchez, Carsten Spisla, Michael Sswat, Mabel Zavala Moreira, and Ulf Riebesell
Biogeosciences, 17, 4831–4852, https://doi.org/10.5194/bg-17-4831-2020, https://doi.org/10.5194/bg-17-4831-2020, 2020
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The eastern boundary upwelling system off Peru is among Earth's most productive ocean ecosystems, but the factors that control its functioning are poorly constrained. Here we used mesocosms, moored ~ 6 km offshore Peru, to investigate how processes in plankton communities drive key biogeochemical processes. We show that nutrient and light co-limitation keep productivity and export at a remarkably constant level while stoichiometry changes strongly with shifts in plankton community structure.
Cited articles
Agarwala, R., Barrett, T., Beck, J., Benson, D. A., Bollin, C., Bolton, E.,
Bourexis, D., Brister, J. R., Bryant, S. H., Canese, K., Cavanaugh, M.,
Charowhas, C., Clark, K., Dondoshansky, I., Feolo, M., Fitzpatrick, L.,
Funk, K., Geer, L. Y., Gorelenkov, V., Graeff, A., Hlavina, W., Holmes, B.,
Johnson, M., Kattman, B., Khotomlianski, V., Kimchi, A., Kimelman, M.,
Kimura, M., Kitts, P., Klimke, W., Kotliarov, A., Krasnov, S., Kuznetsov,
A., Landrum, M. J., Landsman, D., Lathrop, S., Lee, J. M., Leubsdorf, C.,
Lu, Z., Madden, T. L., Marchler-Bauer, A., Malheiro, A., Meric, P.,
Karsch-Mizrachi, I., Mnev, A., Murphy, T., Orris, R., Ostell, J.,
O'Sullivan, C., Palanigobu, V., Panchenko, A. R., Phan, L., Pierov, B.,
Pruitt, K. D., Rodarmer, K., Sayers, E. W., Schneider, V., Schoch, C. L.,
Schuler, G. D., Sherry, S. T., Siyan, K., Soboleva, A., Soussov, V.,
Starchenko, G., Tatusova, T. A., Thibaud-Nissen, F., Todorov, K., Trawick,
B. W., Vakatov, D., Ward, M., Yaschenko, E., Zasypkin, A., and Zbicz, K.:
Database resources of the National Center for Biotechnology Information,
Nucl. Acids Res., 46, D8–D13, https://doi.org/10.1093/nar/gkx1095, 2018.
Amaral-Zettler, L. A., McCliment, E. A., Ducklow, H. W., and Huse, S. M.: A
method for studying protistan diversity using massively parallel sequencing
of V9 hypervariable regions of small-subunit ribosomal RNA Genes, PLoS One,
4, 1–9, https://doi.org/10.1371/journal.pone.0006372, 2009.
Amaral-Zettler, L. A., Bauer, M., Berg-Lyons, D., Betley, J., Caporaso, J.
G., Ducklow, H. W., Fierer, N., Fraser, L., Gilbert, J. A., Gormley, N.,
Huntley, J., Huse, S. M., Jansson, J. K., Jarman, S. N., Knight, R., Lau, C.
L., and Walters, W. A.: EMP 18S Illumina Amplicon Protocol, protocols.io,
https://doi.org/10.17504/protocols.io.nuvdew6, 2018.
Ayón, P., Swartzman, G., Bertrand, A., Gutiérrez, M., and Bertrand,
S.: Zooplankton and forage fish species off Peru: Large-scale bottom-up
forcing and local-scale depletion, Prog. Oceanogr., 79, 208–214,
https://doi.org/10.1016/j.pocean.2008.10.023, 2008.
Bach, L. T., Paul, A. J., Boxhammer, T., von der Esch, E., Graco, M.,
Schulz, K. G., Achterberg, E., Aguayo, P., Arístegui, J., Ayón, P.,
Baños, I., Bernales, A., Boegeholz, A. S., Chavez, F., Chavez, G., Chen,
S. M., Doering, K., Filella, A., Fischer, M., Grasse, P., Haunost, M.,
Hennke, J., Hernández-Hernández, N., Hopwood, M., Igarza, M.,
Kalter, V., Kittu, L., Kohnert, P., Ledesma, J., Lieberum, C., Lischka, S.,
Löscher, C., Ludwig, A., Mendoza, U., Meyer, J., Meyer, J., Minutolo,
F., Cortes, J. O., Piiparinen, J., Sforna, C., Spilling, K., Sanchez, S.,
Spisla, C., Sswat, M., Moreira, M. Z., and Riebesell, U.: Factors
controlling plankton community production, export flux, and particulate
matter stoichiometry in the coastal upwelling system off Peru,
Biogeosciences, 17, 4831–4852, https://doi.org/10.5194/bg-17-4831-2020,
2020.
Bachy, C., Wittmers, F., Muschiol, J., Hamilton, M., Henrissat, B., and
Worden, A. Z.: The Land-Sea Connection: Insights Into the Plant Lineage from
a Green Algal Perspective, Annu. Rev. Plant Biol., 73, 585–616,
https://doi.org/10.1146/annurev-arplant-071921-100530, 2022.
Baker, P., Minzlaff, U., Schoenle, A., Schwabe, E., Hohlfeld, M., Jeuck, A.,
Brenke, N., Prausse, D., Rothenbeck, M., Brix, S., Frutos, I., Jörger,
K. M., Neusser, T. P., Koppelmann, R., Devey, C., Brandt, A., and Arndt, H.:
Potential contribution of surface-dwelling Sargassum algae to deep-sea
ecosystems in the southern North Atlantic, Deep-Sea Res. Pt. II, 148, 21–34, https://doi.org/10.1016/j.dsr2.2017.10.002, 2018.
Berry, O., Bulman, C., Bunce, M., Coghlan, M., Murray, D. C., and Ward, R.
D.: Comparison of morphological and DNA metabarcoding analyses of diets in
exploited marine fishes, Mar. Ecol. Prog. Ser., 540, 167–181,
https://doi.org/10.3354/meps11524, 2015.
Boenigk, J. and Arndt, H.: Particle handling during interception feeding by
four species of heterotrophic nanoflagellates, J. Eukaryot. Microbiol., 47,
350–358, https://doi.org/10.1111/j.1550-7408.2000.tb00060.x, 2000.
Boussarie, G., Bakker, J., Wangensteen, O. S., Mariani, S., Bonnin, L.,
Juhel, J. B., Kiszka, J. J., Kulbicki, M., Manel, S., Robbins, W. D.,
Vigliola, L., and Mouillot, D.: Environmental DNA illuminates the dark
diversity of sharks, Sci. Adv., 4, 5, https://doi.org/10.1126/sciadv.aap9661,
2018.
Buchan, A., LeCleir, G. R., Gulvik, C. A., and González, J. M.: Master
recyclers: features and functions of bacteria associated with phytoplankton
blooms, Nat. Rev. Microbiol., 12, 686–698, https://doi.org/10.1038/nrmicro3326, 2014.
Callahan, B. J., McMurdie, P. J., Rosen, M. J., Han, A. W., Johnson, A. J.
A., 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.
Camacho, C., Coulouris, G., Avagyan, V., Ma, N., Papadopoulos, J., Bealer,
K., and Madden, T. L.: BLAST+: Architecture and applications, BMC
Bioinformatics, 10, 1–9, https://doi.org/10.1186/1471-2105-10-421, 2009.
Carr, M. E.: Estimation of potential productivity in Eastern Boundary
Currents using remote sensing, Deep-Sea Res. Pt. II, 49,
59–80, https://doi.org/10.1016/S0967-0645(01)00094-7, 2001.
Carr, M. E. and Kearns, E. J.: Production regimes in four Eastern Boundary
Current systems, Deep-Sea Res. Pt. II, 50, 3199–3221,
https://doi.org/10.1016/j.dsr2.2003.07.015, 2003.
Chavez, F. P. and Messié, M.: A comparison of Eastern Boundary Upwelling
Ecosystems, Prog. Oceanogr., 83, 80–96,
https://doi.org/10.1016/j.pocean.2009.07.032, 2009.
Chavez, F. P., Pennington, J. T., Michisaki, R. P., Blum, M., Chavez, G. M.,
Friederich, J., Jones, B., Herlien, R., Kieft, B., and Hobson, B.: Climate
variability and change: response of a coastal ocean ecosystem, Oceanography,
30, 128–145, 2017.
Choi, C. J., Jimenez, V., Needham, D. M., Poirier, C., Bachy, C., Alexander, H., Wilken, S., Chavez, F. P., Sudek, S., Giovannoni, S. J., and Worden, A. Z.: Seasonal and geographical transitions in eukaryotic phytoplankton
community structure in the Atlantic and Pacific Oceans, Front. Microbiol., 11, 542372, https://doi.org/10.3389/fmicb.2020.542372, 2020.
Closek, C., Djurhuus, A., Pitz, K., Kelly, R., Michisaki, R., Walz, K., Starks, H., Chavez, F., Boehm, A., and Breitbart, M.: Environmental DNA (eDNA) 18S metabarcoding Illumina MiSeq NGS PCR Protocol, protocols.io,
https://doi.org/10.17504/protocols.io.n2vdge6, 2018a.
Closek, C., Djurhuus, A., Pitz, K., Kelly, R., Michisaki, R., Walz, K., Starks, H., Chavez, F., Boehm, A., and Breitbart, M.: Environmental DNA (eDNA) COI metabarcoding Illumina MiSeq NGS PCR Protocol, protocols.io,
https://doi.org/10.17504/protocols.io.mwnc7de, 2018b.
Coats, D. W.: Duboscquella cachoni N. Sp., a Parasitic Dinoflagellate Lethal
to Its Tintinnine Host Eutintinnus pectinis 1, J. Protozool., 35, 607–617,
1988.
Crouch, E. M., Heilmann-Clausen, C., Brinkhuis, H., Morgans, H. E. G.,
Rogers, K. M., Egger, H., and Schmitz, B.: Global dinoflagellate event
associated with the late Paleocene thermal maximum, Geology, 29, 315–318,
https://doi.org/10.1130/0091-7613(2001)029<0315:GDEAWT>2.0.CO;2, 2001.
Daims, H., Brühl, A., Amann, R., Schleifer, K. H., and Wagner, M.: The
domain-specific probe EUB338 is insufficient for the detection of all
bacteria: Development and evaluation of a more comprehensive probe set,
Syst. Appl. Microbiol., 22, 434–444,
https://doi.org/10.1016/S0723-2020(99)80053-8, 1999.
Decelle, J., Romac, S., Stern, R. F., Bendif, E. M., Zingone, A., Audic, S.,
Guiry, M. D., Guillou, L., Tessier, D., Le Gall, F., Gourvil, P., Dos
Santos, A. L., Probert, I., Vaulot, D., de Vargas, C., and Christen, R.:
PhytoREF: A reference database of the plastidial 16S rRNA gene of
photosynthetic eukaryotes with curated taxonomy, Mol. Ecol. Resour., 15,
1435–1445, https://doi.org/10.1111/1755-0998.12401, 2015.
De La Iglesia, R., Echenique-Subiabre, I., Rodríguez-Marconi, S.,
Espinoza, J. P., Von Dassow, P., Ulloa, O., and Trefault, N.: Distinct
oxygen environments shape picoeukaryote assemblages thriving oxygen minimum
zone waters off central Chile, J. Plankton Res., 42, 514–529,
https://doi.org/10.1093/plankt/fbaa036, 2020.
Didion, J. P., Martin, M., and Collins, F. S.: Atropos: Specific, sensitive,
and speedy trimming of sequencing reads, PeerJ, 2017, 1–19,
https://doi.org/10.7717/peerj.3720, 2017.
Djurhuus, A., Pitz, K., Sawaya, N. A., Rojas-Márquez, J., Michaud, B.,
Montes, E., Muller-Karger, F., and Breitbart, M.: Evaluation of marine
zooplankton community structure through environmental DNA metabarcoding,
Limnol. Oceanogr. Method., 16, 209–221, https://doi.org/10.1002/lom3.10237,
2018.
Du, X., Peterson, W., McCulloch, A., and Liu, G.: An unusual bloom of the
dinoflagellate Akashiwo sanguinea off the central Oregon, USA, coast in
autumn 2009, Harmful Algae, 10, 784–793,
https://doi.org/10.1016/j.hal.2011.06.011, 2011.
Duffy, D. C.: The foraging ecology of Peruvian seabirds, Auk, 100, 800–810,
1983.
Dugdale, R. C., Goering, J. J., Barber, R. T., Smith, R. L., and Packard, T.
T.: Denitrification and hydrogen sulfide in the Peru upwelling region during
1976, Deep-Sea Res., 24, 601–608, 1977.
Dupont, C. L., Rusch, D. B., Yooseph, S., Lombardo, M. J., Alexander
Richter, R., Valas, R., Novotny, M., Yee-Greenbaum, J., Selengut, J. D.,
Haft, D. H., Halpern, A. L., Lasken, R. S., Nealson, K., Friedman, R., and
Craig Venter, J.: Genomic insights to SAR86, an abundant and uncultivated
marine bacterial lineage, ISME J., 6, 1186–1199,
https://doi.org/10.1038/ismej.2011.189, 2012.
Echevin, V., Puillat, I., Grados, C., and Dewitte, B.: Seasonal and
mesoscale variability in the Peru Upwelling System from in situ data during
the years 2000 to 2004, Gayana (Concepción), 68, 167–173,
https://doi.org/10.4067/s0717-65382004000200031, 2004.
Edvarsen, B. and Paasche, E.: Bloom dynamics and physiology of Prymnesium
and Chrysochromulina, Physiol. Ecol. Harmful Algal Bloom., 41, 193–208,
1998.
Espinoza, P. and Bertrand, A.: Revisiting Peruvian anchovy (Engraulis
ringens) trophodynamics provides a new vision of the Humboldt Current
system, Prog. Oceanogr., 79, 215–227,
https://doi.org/10.1016/j.pocean.2008.10.022, 2008.
Evans, N. T., Olds, B. P., Renshaw, M. A., Turner, C. R., Li, Y., Jerde, C.
L., Mahon, A. R., Pfrender, M. E., Lamberti, G. A., and Lodge, D. M.:
Quantification of mesocosm fish and amphibian species diversity via
environmental DNA metabarcoding, Mol. Ecol. Resour., 16, 29–41,
https://doi.org/10.1111/1755-0998.12433, 2016.
Ferrari, B. C., Binnerup, S. J., and Gillings, M.: Microcolony cultivation
on a soil substrate membrane system selects for previously uncultured soil
bacteria, Appl. Environ. Microbiol., 71, 8714–8720,
https://doi.org/10.1128/AEM.71.12.8714-8720.2005, 2005.
Folmer, O., Hoeh, W. R., Black, M. B., and Vrijenhoek, R. C.: Conserved
primers for PCR amplification of mitochondrial DNA from different
invertebrate phyla, Mol. Mar. Biol. Biotechnol., 3, 294–299, 1994.
Garreaud, R. D.: A plausible atmospheric trigger for the 2017 coastal El
Niño, Int. J. Climatol., 38, e1296–e1302,
https://doi.org/10.1002/joc.5426, 2018.
Giovannoni, S. J., Britschgi, T. B., Moyer, C. L., and Field, K. G.: Genetic
diversity in Sargasso Sea bacterioplankton, Nature, 345, 60–63,
https://doi.org/10.1038/345060a0, 1990.
Gold, Z., Curd, E., Goodwin, K., Choi, E., Frable, B., Thompson, A., Burton,
R., Kacev, D., and Barber, P.: Improving metabarcoding taxonomic assignment: A case study of fishes in a large marine ecosystem, Mol. Ecol. Resour., 21, 2546–2564,
https://doi.org/10.22541/au.161407483.33882798/v1, 2021.
Gómez, F.: On the consortium of the tintinnid Eutintinnus and the diatom
Chaetoceros in the Pacific Ocean, Mar. Biol., 151, 1899–1906,
https://doi.org/10.1007/s00227-007-0625-0, 2007.
Gómez, F.: Symbiotic interactions between ciliates (Ciliophora) and
diatoms (Bacillariophyceae), Rev. Biol. Trop., 68, 2020.
Graco, M. I., Purca, S., Dewitte, B., Castro, C. G., Morón, O., Ledesma,
J., Flores, G., and Gutiérrez, D.: The OMZ and nutrient features as a
signature of interannual and low-frequency variability in the Peruvian
upwelling system, Biogeosciences, 14, 4601–4617,
https://doi.org/10.5194/bg-14-4601-2017, 2017.
Gruber, N.: Warming up, turning sour, losing breath: Ocean biogeochemistry
under global change, Philos. T. R. Soc. A, 369,
1980–1996, https://doi.org/10.1098/rsta.2011.0003, 2011.
Guillou, L., Viprey, M., Chambouvet, A., Welsh, R. M., Kirkham, A. R.,
Massana, R., Scanlan, D. J., and Worden, A. Z.: Widespread occurrence and
genetic diversity of marine parasitoids belonging to Syndiniales
(Alveolata), Environ. Microbiol., 10, 3349–3365,
https://doi.org/10.1111/j.1462-2920.2008.01731.x, 2008.
Hare, J. A., Walsh, H. J., and Wuenschel, M. J.: Sinking rates of late-stage
fish larvae: Implications for larval ingress into estuarine nursery
habitats, J. Exp. Mar. Bio. Ecol., 330, 493–504,
https://doi.org/10.1016/j.jembe.2005.09.011, 2006.
Harvey, J. B. J., Johnson, S. B., Fisher, J. L., Peterson, W. T., and
Vrijenhoek, R. C.: Comparison of morphological and next generation DNA
sequencing methods for assessing zooplankton assemblages, J. Exp. Mar. Biol.
Ecol., 487, 113–126, https://doi.org/10.1016/j.jembe.2016.12.002, 2017.
Hattenrath-Lehmann, T. K. and Gobler, C. J.: Identification of unique
microbiomes associated with harmful algal blooms caused by Alexandrium
fundyense and Dinophysis acuminata, Harmful Algae, 68, 17–30,
https://doi.org/10.1016/j.hal.2017.07.003, 2017.
He, X., McLean, J. S., Edlund, A., Yooseph, S., Hall, A. P., Liu, S. Y.,
Dorrestein, P. C., Esquenazi, E., Hunter, R. C., Cheng, G., Nelson, K. E.,
Lux, R., and Shi, W.: Cultivation of a human-associated TM7 phylotype
reveals a reduced genome and epibiotic parasitic lifestyle, P. Natl.
Acad. Sci. USA, 112, 244–249, https://doi.org/10.1073/pnas.1419038112,
2015.
Herring, S. C., Christidis, N., Hoell, A., Hoerling, M. P., and Stott, P.
A.: Explaining Extreme Events of 2017 from a Climate Perspective, Bull. Am.
Meteorol. Soc., 100, S1–S117,
https://doi.org/10.1175/bams-explainingextremeevents2017.1, 2019.
Hird, S. M., Sánchez, C., Carstens, B. C., and Brumfield, R. T.:
Comparative gut microbiota of 59 neotropical bird species, Front.
Microbiol., 6, 1403, https://doi.org/10.3389/fmicb.2015.01403, 2015.
Hitchcock, J. N., Mitrovic, S. M., Hadwen, W. L., Roelke, D. L., Growns, I.
O., and Rohlfs, A. M.: Terrestrial dissolved organic carbon subsidizes
estuarine zooplankton: An in situ mesocosm study, Limnol. Oceanogr., 61,
254–267, https://doi.org/10.1002/lno.10207, 2016.
Hugenholtz, P., Tyson, G. W., Webb, R. I., Wagner, A. M., and Blackall, L.
L.: Investigation of candidate division TM7, a recently recognized major
lineage of the domain Bacteria, with no known pure-culture representatives,
Appl. Environ. Microbiol., 67, 411–419,
https://doi.org/10.1128/AEM.67.1.411-419.2001, 2001.
Huson, D. H., Beier, S., Flade, I., Górska, A., El-Hadidi, M., Mitra,
S., Ruscheweyh, H. J., and Tappu, R.: MEGAN Community Edition – Interactive
Exploration and Analysis of Large-Scale Microbiome Sequencing Data, PLoS
Comput. Biol., 12, 1–12, https://doi.org/10.1371/journal.pcbi.1004957,
2016.
Huyer, A., Knoll, M., Paluszkiewicz, T., and Smith, R. L.: The Peru
Undercurrent: a study in variability, Deep-Sea Res. Pt. A, 38, S247–S271, https://doi.org/10.1016/s0198-0149(12)80012-4, 1991.
Ianora, A.: Copepod life history traits in subtemperate regions, J. Mar.
Syst., 15, 337–349, https://doi.org/10.1016/S0924-7963(97)00085-7, 1998.
Pachauri, R. K., Allen, M. R., Barros, V. R., Broome, J., Cramer, W., Christ, R., Church, J. A., Clarke, L., Dahe, Q., Dasgupta, P., and Dubash, N. K.: Climate change 2014: synthesis report. Contribution of Working Groups I, II and III to the fifth assessment report of the Intergovernmental Panel on Climate Change, p. 151, IPCC, 2014.
Jaffe, A. L., Thomas, A. D., He, C., Keren, R., Valentin-Alvarado, L. E.,
Munk, P., Bouma-Gregson, K., Farag, I. F., Amano, Y., Sachdeva, R., West, P.
T., and Banfield, J. F.: Patterns of gene content and co-occurrence constrain the evolutionary path toward animal association in Candidate Phyla Radiation Bacteria, MBio, 12, e00521-21, https://doi.org/10.1128/mBio.00521-21, 2021.
Kahru, M., Michell, B. G., Diaz, A., and Miura, M.: MODIS detects a
devastating algal bloom in Paracas Bay, Peru, Eos, Trans. Am. Geophys.
Union, 85, 465–472, 2004.
Kelly, R. P., Port, J. A., Yamahara, K. M., and Crowder, L. B.: Using
environmental DNA to census marine fishes in a large mesocosm, PLoS One, 9, e86175,
https://doi.org/10.1371/journal.pone.0086175, 2014.
Kim, S. and Park, M. G.: Paulinella longichromatophora sp. nov., a New
Marine Photosynthetic Testate Amoeba Containing a Chromatophore, Protist,
167, 1–12, https://doi.org/10.1016/j.protis.2015.11.003, 2016.
Kolody, B. C., McCrow, J. P., Allen, L. Z., Aylward, F. O., Fontanez, K. M.,
Moustafa, A., Moniruzzaman, M., Chavez, F. P., Scholin, C. A., Allen, E. E.,
Worden, A. Z., Delong, E. F., and Allen, A. E.: Diel transcriptional
response of a California Current plankton microbiome to light, low iron, and
enduring viral infection, ISME J., 13, 2817–2833,
https://doi.org/10.1038/s41396-019-0472-2, 2019.
Koumandou, V. L., Nisbet, R. E. R., Barbrook, A. C., and Howe, C. J.:
Dinoflagellate chloroplasts – Where have all the genes gone?, Trends Genet.,
20, 261–267, https://doi.org/10.1016/j.tig.2004.03.008, 2004.
Kudela, R. M., Lane, J. Q., and Cochlan, W. P.: The potential role of
anthropogenically derived nitrogen in the growth of harmful algae in
California, USA, Harmful Algae, 8, 103–110,
https://doi.org/10.1016/j.hal.2008.08.019, 2008.
Kudela, R. M., Seeyave, S., and Cochlan, W. P.: The role of nutrients in
regulation and promotion of harmful algal blooms in upwelling systems, Prog.
Oceanogr., 85, 122–135, https://doi.org/10.1016/j.pocean.2010.02.008, 2010.
Kuehbacher, T., Rehman, A., Lepage, P., Hellmig, S., Fölsch, U. R.,
Schreiber, S., and Ott, S. J.: Intestinal TM7 bacterial phylogenies in
active inflammatory bowel disease, J. Med. Microbiol., 57, 1569–1576,
https://doi.org/10.1099/jmm.0.47719-0, 2008.
Lamb, J. S., Satgé, Y. G., and Jodice, P. G. R.: Diet composition and
provisioning rates of nestlings determine reproductive success in a
subtropical seabird, Mar. Ecol. Prog. Ser., 581, 149–164,
https://doi.org/10.3354/meps12301, 2017.
Lemos, L. N., Medeiros, J. D., Dini-Andreote, F., Fernandes, G. R., Varani,
A. M., Oliveira, G., and Pylro, V. S.: Genomic signatures and co-occurrence
patterns of the ultra-small Saccharimonadia (phylum CPR/Patescibacteria)
suggest a symbiotic lifestyle, Mol. Ecol., 28, 4259–4271,
https://doi.org/10.1111/mec.15208, 2019.
Leray, M., Yang, J. Y., Meyer, C. P., Mills, S. C., Agudelo, N., Ranwez, V.,
Boehm, J. T., and Machida, R. J.: A new versatile primer set targeting a
short fragment of the mitochondrial COI region for metabarcoding metazoan
diversity: Application for characterizing coral reef fish gut contents,
Front. Zool., 10, 1–14, https://doi.org/10.1186/1742-9994-10-34, 2013.
Limardo, A. J., Sudek, S., Choi, C. J., Poirier, C., Rii, Y. M., Blum, M.,
Roth, R., Goodenough, U., Church, M. J., and Worden, A. Z.: Quantitative
biogeography of picoprasinophytes establishes ecotype distributions and
significant contributions to marine phytoplankton, Environ. Microbiol., 19,
3219–3234, https://doi.org/10.1111/1462-2920.13812, 2017.
Lin, S., Zhang, H., Hou, Y., Zhuang, Y., and Miranda, L.: High-level
diversity of dinoflagellates in the natural environment, revealed by
assessment of mitochondrial cox1 and cob genes for dinoflagellate DNA
barcoding, Appl. Environ. Microbiol., 75, 1279–1290,
https://doi.org/10.1128/AEM.01578-08, 2009.
Marcy, Y., Ouverney, C., Bik, E. M., Lösekann, T., Ivanova, N., Martin,
H. G., Szeto, E., Platt, D., Hugenholtz, P., Relman, D. A., and Quake, S.
R.: Dissecting biological “dark matter” with single-cell genetic analysis
of rare and uncultivated TM7 microbes from the human mouth, P. Natl.
Acad. Sci. USA, 104, 11889–11894,
https://doi.org/10.1073/pnas.0704662104, 2007.
Margalef, R.: Life-forms of phytoplankton as survival alternatives in an
unstable environment, Ocean. Acta, 1, 493–509, 1978.
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, Metabarcod. Metagenom., 6, 245–259,
https://doi.org/10.3897/mbmg.6.85794, 2022.
Martin, M.: Cutadapt removes adapter sequences from high-throughput
sequencing reads, EMBnet J., 17, 10–12,
https://doi.org/10.14806/ej.17.1.200, 2011.
Martino, C., Morton, J. T., Marotz, C. A., Thompson, L. R., Tripathi, A.,
Knight, R., and Zengler, K.: A Novel Sparse Compositional Technique Reveals
Microbial Perturbations, MSystems, 4, e00016-19,
https://doi.org/10.1128/msystems.00016-19, 2019.
Matsuyama, Y., Miyamoto, M., and Kotani, Y.: Grazing impacts of the
heterotrophic dinoflagellate Polykrikos kofoidii on a bloom of Gymnodinium
catenatum, Aquat. Microb. Ecol., 17, 91–98,
https://doi.org/10.3354/ame017091, 1999.
Messié, M. and Chavez, F. P.: Seasonal regulation of primary production
in eastern boundary upwelling systems, Prog. Oceanogr., 134, 1–18,
https://doi.org/10.1016/j.pocean.2014.10.011, 2015.
Min, M. and Pitz, K.: MBARI-BOG/KOSMOS_eDNA_paper: Initial submission to Biogeosciences (v1.0), Zenodo [code and data set],
https://doi.org/10.5281/zenodo.7255826, 2022.
Miya, M., Sato, Y., Fukunaga, T., Sado, T., Poulsen, J.Y., Sato, K., Minamoto, T., Yamamoto, S., Yamanaka, H., Araki, H., and Kondoh, M.: MiFish, a set of universal PCR primers for metabarcoding environmental DNA from fishes: detection of more than 230 subtropical marine species, Roy. Soc. Open Sci., 2, 150088, https://doi.org/10.1098/rsos.150088, 2015.
Monuki, K., Barber, P. H., and Gold, Z.: eDNA captures depth partitioning in
a kelp forest ecosystem, PLoS One, 16, 1–17,
https://doi.org/10.1371/journal.pone.0253104, 2021.
Morris, A. W. and Riley, J. P.: The determination of nitrate in sea water,
Anal. Chim. Acta, 29, 272–279,
https://doi.org/10.1016/S0003-2670(00)88614-6, 1963.
Morris, R. M., Rappé, M. S., Connon, S. A., Vergin, K. L., Siebold, W.
A., Carlson, C. A., and Giovannoni, S. J.: SAR11 clade dominates ocean
surface bacterioplankton communities, Nature, 420, 806–810,
https://doi.org/10.1038/nature01240, 2002.
Mullin, J. B. and Riley, J. P.: The colorimetric determination of silicate
with special reference to sea and natural waters, Anal. Chim. Acta, 12,
162–176, https://doi.org/10.1016/S0003-2670(00)87825-3, 1955.
Needham, D. M. and Fuhrman, J. A.: Pronounced daily succession of
phytoplankton, archaea and bacteria following a spring bloom, Nat.
Microbiol., 1, 16005, https://doi.org/10.1038/nmicrobiol.2016.5, 2016.
Neufeld, J. D., Schäfer, H., Cox, M. J., Boden, R., McDonald, I. R., and
Murrell, J. C.: Stable-isotope probing implicates Methylophaga spp and novel
Gammaproteobacteria in marine methanol and methylamine metabolism, ISME J.,
1, 480–491, https://doi.org/10.1038/ismej.2007.65, 2007.
O'donnell, J. L., Kelly, R. P., Lowell, N. C., and Port, J. A.: Indexed PCR
primers induce template- Specific bias in Large-Scale DNA sequencing
studies, PLoS One, 11, 1–11, https://doi.org/10.1371/journal.pone.0148698,
2016.
Ohki, K., Yamada, K., Kamiya, M., and Yoshikawa, S.: Morphological,
phylogenetic and physiological studies of pico-cyanobacteria isolated from
the halocline of a saline Meromictic Lake, Lake Suigetsu, Japan, Microbes
Environ., 27, 171–178, https://doi.org/10.1264/jsme2.ME11329, 2012.
Page, F. C.: Marine gymnamoebae, Institute of Terrestrial Ecology, 60 pp., 1983.
Parada, A. E., Needham, D. M., and Fuhrman, J. A.: Every base matters:
Assessing small subunit rRNA primers for marine microbiomes with mock
communities, time series and global field samples, Environ. Microbiol., 18,
1403–1414, https://doi.org/10.1111/1462-2920.13023, 2016.
Park, M. G. and Kim, M.: Prey specificity and feeding of the thecate
mixotrophic dinoflagellate fragilidium duplocampanaeforme, J. Phycol., 46,
424–432, https://doi.org/10.1111/j.1529-8817.2010.00824.x, 2010.
Park, S., Jung, Y. T., Park, J. M., and Yoon, J. H.: Pseudohongiella acticola sp. nov., a novel gammaproteobacterium isolated from seawater, and
emended description of the genus Pseudohongiella, Antonie van Leeuwenhoek,
Int. J. Gen. Mol. Microbiol., 106, 809–815,
https://doi.org/10.1007/s10482-014-0250-0, 2014.
Parks, D. H., Chuvochina, M., Waite, D. W., Rinke, C., Skarshewski, A.,
Chaumeil, P. A., and Hugenholtz, P.: A standardized bacterial taxonomy based
on genome phylogeny substantially revises the tree of life, Nat.
Biotechnol., 36, 996–1004, https://doi.org/10.1038/nbt.4229, 2018.
Partensky, F., Blanchot, J., and Vaulot, D.: Differential distribution and
ecology of Prochlorococcus and Synechococcus in oceanic waters: A review,
Bull. Inst. Ocean., 19, 457–475, 1999.
Patterson, D., Nygaard, K., Steinberg, G., and Turley, C.: Heterotrophic
flagellates and other protists associated with oceanic detritus throughout
the water column in the mid north atlantic, J. Mar. Biol. Assoc. United
Kingdom, 73, 67–95, https://doi.org/10.1017/S0025315400032653, 1993.
Patti, B., Guisande, C., Vergara, A. R., Riveiro, I., Maneiro, I., Barreiro,
A., Bonanno, A., Buscaino, G., Cuttitta, A., Basilone, G., and Mazzola, S.:
Factors responsible for the differences in satellite-based chlorophyll a
concentration between the major global upwelling areas, Estuar. Coast. Shelf
Sci., 76, 775–786, https://doi.org/10.1016/j.ecss.2007.08.005, 2008.
Pennington, J. T., Mahoney, K. L., Kuwahara, V. S., Kolber, D. D., Calienes,
R., and Chavez, F. P.: Primary production in the eastern tropical Pacific: A
review, Prog. Oceanogr., 69, 285–317,
https://doi.org/10.1016/j.pocean.2006.03.012, 2006.
Penven, P., Echevin, V., Pasapera, J., Colas, F., and Tam, J.: Average
circulation, seasonal cycle, and mesoscale dynamics of the Peru Current
System: A modeling approach, J. Geophys. Res. C, 110, 1–21,
https://doi.org/10.1029/2005JC002945, 2005.
Pitz, K., Truelove, N., Nye, C., Michisaki, R. P., and Chavez, F.: Environmental DNA (eDNA) 12S Metabarcoding Illumina MiSeq NGS PCR Protocol (Touchdown), protocols.io,
https://doi.org/10.17504/protocols.io.bcppivmn, 2020.
Quast, C., Pruesse, E., Yilmaz, P., Gerken, J., Schweer, T., Yarza, P.,
Peplies, J., and Glöckner, F. O.: The SILVA ribosomal RNA gene database
project: Improved data processing and web-based tools, Nucl. Acids Res.,
41, 590–596, https://doi.org/10.1093/nar/gks1219, 2013.
R Core Team: R: A Language and Environment for Statistical Computing,
Vienna, Austria, http://www.R-project.org (last access: 21 February 2023), 2019.
Riebesell, U., Bellerby, R. G. J., Grossart, H. P., and Thingstad, F.:
Mesocosm CO2 perturbation studies: From organism to community level,
Biogeosciences, 5, 1157–1164, https://doi.org/10.5194/bg-5-1157-2008, 2008.
Riebesell, U., Czerny, J., Von Bröckel, K., Boxhammer, T.,
Büdenbender, J., Deckelnick, M., Fischer, M., Hoffmann, D., Krug, S. A.,
Lentz, U., Ludwig, A., Muche, R., and Schulz, K. G.: Technical Note: A
mobile sea-going mesocosm system – New opportunities for ocean change
research, Biogeosciences, 10, 1835–1847,
https://doi.org/10.5194/bg-10-1835-2013, 2013.
Riemann, L., Steward, G. F., and Azam, F.: Erratum: Dynamics of bacterial
community composition and activity during a mesocosm diatom bloom, Appl. Environ.
Microbiol., 66, 2282, https://doi.org/10.1128/AEM.66.5.2282-2282.2000, 2000.
Rimet, F., Chaumeil, P., Keck, F., Kermarrec, L., Vasselon, V., Kahlert, M.,
Franc, A., and Bouchez, A.: R-Syst::diatom: An open-access and curated
barcode database for diatoms and freshwater monitoring, Database,
1–21, https://doi.org/10.1093/database/baw016, 2016.
Robertson, D. A.: Possible functions of surface structure and size in some
planktonic eggs of marine fishes, New Zeal. J. Mar. Freshw. Res., 15,
147–153, 1981.
Sandaa, R. A., Gómez-Consarnau, L., Pinhassi, J., Riemann, L., Malits,
A., Weinbauer, M. G., Gasol, J. M., and Thingstad, T. F.: Viral control of
bacterial biodiversity – Evidence from a nutrient-enriched marine mesocosm
experiment, Environ. Microbiol., 11, 2585–2597,
https://doi.org/10.1111/j.1462-2920.2009.01983.x, 2009.
Sassoubre, L. M., Yamahara, K. M., Gardner, L. D., Block, B. A., and Boehm,
A. B.: Quantification of Environmental DNA (eDNA) Shedding and Decay Rates
for Three Marine Fish, Environ. Sci. Technol., 50, 10456–10464,
https://doi.org/10.1021/acs.est.6b03114, 2016.
Schnell, I. B., Bohmann, K., and Gilbert, M. T. P.: Tag jumps illuminated –
reducing sequence-to-sample misidentifications in metabarcoding studies,
Mol. Ecol. Resour., 15, 1289–1303, https://doi.org/10.1111/1755-0998.12402,
2015.
Schoenle, A., Hohlfeld, M., Rosse, M., Filz, P., Wylezich, C., Nitsche, F.,
and Arndt, H.: Global comparison of bicosoecid Cafeteria-like flagellates
from the deep ocean and surface waters, with reorganization of the family
Cafeteriaceae, Eur. J. Protistol., 73, 125665,
https://doi.org/10.1016/j.ejop.2019.125665, 2020.
Silva, A. and Oliva, M.: Revisión sobre aspectos biológicos y de
cultivo del lenguado chileno (Paralichthys adspersus), Lat. Am. J. Aquat.
Res., 38, 377–386, 2010.
Simmons, M. P., Sudek, S., Monier, A., Limardo, A. J., Jimenez, V., Perle,
C. R., Elrod, V. A., Pennington, J. T., and Worden, A. Z.: Abundance and
biogeography of picoprasinophyte ecotypes and other phytoplankton in the
eastern North Pacific Ocean, Appl. Environ. Microbiol., 82, 1693–1705,
https://doi.org/10.1128/AEM.02730-15, 2016.
Skjoldal, H. R., Wiebe, P. H., Postel, L., Knutsen, T., Kaartvedt, S., and
Sameoto, D. D.: Intercomparison of zooplankton (net) sampling systems:
Results from the ICES/GLOBEC sea-going workshop, Prog. Oceanogr., 108,
1–42, https://doi.org/10.1016/j.pocean.2012.10.006, 2013.
Smayda, T. J.: Adaptations and selection of harmful and other dinoflagellate
species in upwelling systems. 2. Motility and migratory behaviour, Prog.
Oceanogr., 85, 71–91, https://doi.org/10.1016/j.pocean.2010.02.005, 2010.
Smayda, T. J. and Trainer, V. L.: Dinoflagellate blooms in upwelling
systems: Seeding, variability, and contrasts with diatom bloom behaviour,
Prog. Oceanogr., 85, 92–107, https://doi.org/10.1016/j.pocean.2010.02.006,
2010.
Spear-bernstein, L. and Miller, K. R.: Unique Location of the
Phycobiliprotein Light-Harvesting Pigment in the Cryptophyceae, J. Phycol.,
25, 412–419, https://doi.org/10.1111/j.1529-8817.1989.tb00245.x, 1989.
Spilling, K., Olli, K., Lehtoranta, J., Kremp, A., Tedesco, L., Tamelander,
T., Klais, R., Peltonen, H., and Tamminen, T.: Shifting
diatom – dinoflagellate dominance during spring bloom in the Baltic Sea and
its potential effects on biogeochemical cycling, Front. Mar. Sci., 5, 327,
2018.
Stewart, R. I. A., Dossena, M., Bohan, D. A., Jeppesen, E., Kordas, R. L.,
Ledger, M. E., Meerhoff, M., Moss, B., Mulder, C., Shurin, J. B., Suttle,
B., Thompson, R., Trimmer, M., and Woodward, G.: Mesocosm Experiments as a
Tool for Ecological Climate-Change Research, 1st Edn., Elsevier Ltd., 71–181, https://doi.org/10.1016/B978-0-12-417199-2.00002-1, 2013.
Stoeck, T., Bass, D., Nebel, M., Christen, R., Jones, M. D. M., Breiner, H.
W., and Richards, T. A.: Multiple marker parallel tag environmental DNA
sequencing reveals a highly complex eukaryotic community in marine anoxic
water, Mol. Ecol., 19, 21–31,
https://doi.org/10.1111/j.1365-294X.2009.04480.x, 2010.
Sudek, S., Everroad, R. C., Gehman, A. L. M., Smith, J. M., Poirier, C. L.,
Chavez, F. P., and Worden, A. Z.: Cyanobacterial distributions along a
physico-chemical gradient in the Northeastern Pacific Ocean, Environ.
Microbiol., 17, 3692–3707, https://doi.org/10.1111/1462-2920.12742, 2015.
Suffrian, K., Simonelli, P., Nejstgaard, J. C., Putzeys, S., Carotenuto, Y.,
and Antia, A. N.: Microzooplankton grazing and phytoplankton growth in
marine mesocosms with increased CO2 levels, Biogeosciences, 5, 1145–1156,
https://doi.org/10.5194/bg-5-1145-2008, 2008.
Taberlet, P., Coissac, E., Hajibabaei, M., and Rieseberg, L.: Environmental
DNA, Mol. Ecol., 21, 1789–1793, 2012.
Taucher, J., Bach, L. T., Boxhammer, T., Nauendorf, A., Achterberg, E. P.,
Algueró-Muñiz, M., Arístegui, J., Czerny, J., Esposito, M.,
Guan, W., Haunost, M., Horn, H. G., Ludwig, A., Meyer, J., Spisla, C.,
Sswat, M., Stange, P., Riebesell, U., Aberle-Malzahn, N., Archer, S.,
Boersma, M., Broda, N., Büdenbender, J., Clemmesen, C., Deckelnick, M.,
Dittmar, T., Dolores-Gelado, M., Dörner, I., Fernández-Urruzola, I.,
Fiedler, M., Fischer, M., Fritsche, P., Gomez, M., Grossart, H. P., Hattich,
G., Hernández-Brito, J., Hernández-Hernández, N.,
Hernández-León, S., Hornick, T., Kolzenburg, R., Krebs, L.,
Kreuzburg, M., Lange, J. A. F., Lischka, S., Linsenbarth, S., Löscher,
C., Martínez, I., Montoto, T., Nachtigall, K., Osma-Prado, N., Packard,
T., Pansch, C., Posman, K., Ramírez-Bordón, B., Romero-Kutzner, V.,
Rummel, C., Salta, M., Martínez-Sánchez, I., Schröder, H.,
Sett, S., Singh, A., Suffrian, K., Tames-Espinosa, M., Voss, M., Walter, E.,
Wannicke, N., Xu, J., and Zark, M.: Influence of ocean acidification and
deep water upwelling on oligotrophic plankton communities in the subtropical
North Atlantic: Insights from an in situ mesocosm study, Front. Mar. Sci.,
4, 85, https://doi.org/10.3389/fmars.2017.00085, 2017.
Tillmann, U.: Interactions between planktonic microalgae and protozoan
grazers, J. Eukaryot. Microbiol., 51, 156–168,
https://doi.org/10.1111/j.1550-7408.2004.tb00540.x, 2004.
Trainer, V. L., Pitcher, G. C., Reguera, B., and Smayda, T. J.: The
distribution and impacts of harmful algal bloom species in eastern boundary
upwelling systems, Prog. Oceanogr., 85, 33–52,
https://doi.org/10.1016/j.pocean.2010.02.003, 2010.
Tyrrell, T. and Merico, A.: Emiliania huxleyi: bloom observations and the
conditions that induce them, in: Coccolithophores, Springer Berlin,
Heidelberg, 75–97, https://doi.org/10.1007/978-3-662-06278-4_4, 2004.
Ushio, M., Murata, K., Sado, T., Nishiumi, I., Takeshita, M., Iwasaki, W.,
and Miya, M.: Demonstration of the potential of environmental DNA as a tool
for the detection of avian species, Sci. Rep., 8, 1–10,
https://doi.org/10.1038/s41598-018-22817-5, 2018.
Valentini, A., Taberlet, P., Miaud, C., Civade, R., Herder, J., Thomsen, P.
F., Bellemain, E., Besnard, A., Coissac, E., Boyer, F., Gaboriaud, C., Jean,
P., Poulet, N., Roset, N., Copp, G. H., Geniez, P., Pont, D., Argillier, C.,
Baudoin, J. M., Peroux, T., Crivelli, A. J., Olivier, A., Acqueberge, M., Le
Brun, M., Møller, P. R., Willerslev, E., and Dejean, T.: Next-generation
monitoring of aquatic biodiversity using environmental DNA metabarcoding,
Mol. Ecol., 25, 929–942, https://doi.org/10.1111/mec.13428, 2016.
Vincent, F. J., Colin, S., Romac, S., Scalco, E., Bittner, L., Garcia, Y.,
Lopes, R. M., Dolan, J. R., Zingone, A., and De Vargas, C.: The epibiotic
life of the cosmopolitan diatom Fragilariopsis doliolus on heterotrophic
ciliates in the open ocean, ISME J., 12, 1094–1108, 2018.
Walz, K., Yamahara, K., Michisaki, R. P., and Chavez, F. P.: MBARI Environmental DNA (eDNA) extraction using Qiagen DNeasy Blood and Tissue Kit, protocols.io,
https://doi.org/10.17504/protocols.io.xjufknw, 2019.
Wear, E. K., Wilbanks, E. G., Nelson, C. E., and Carlson, C. A.: Primer
selection impacts specific population abundances but not community dynamics
in a monthly time-series 16S rRNA gene amplicon analysis of coastal marine
bacterioplankton, Environ. Microbiol., 20, 2709–2726,
https://doi.org/10.1111/1462-2920.14091, 2018.
Wiebe, P. H. and Holland, W. R.: Plankton Patchiness: Effects on Repeated
Net Tows, Limnol. Oceanogr., 13, 315–321,
https://doi.org/10.4319/lo.1968.13.2.0315, 1968.
Worden, A. Z., Nolan, J. K., and Palenik, B.: Assessing the dynamics and
ecology of marine picophytoplankton: The importance of the eukaryotic
component, Limnol. Oceanogr., 49, 168–179,
https://doi.org/10.4319/lo.2004.49.1.0168, 2004.
Xu, L., Wu, Y. H., Jian, S. L., Wang, C. S., Wu, M., Cheng, L., and Xu, X.
W.: Pseudohongiella nitratireducens sp. Nov., isolated from seawater, and
emended description of the genus Pseudohongiella, Int. J. Syst. Evol.
Microbiol., 66, 5155–5160, https://doi.org/10.1099/ijsem.0.001489, 2016.
Yang, C., Li, Y., Zhou, Y., Zheng, W., Tian, Y., and Zheng, T.: Bacterial
community dynamics during a bloom caused by Akashiwo sanguinea in the Xiamen
sea area, China, Harmful Algae, 20, 132–141,
https://doi.org/10.1016/j.hal.2012.09.002, 2012.
Yang, C., Li, Y., Zhou, B., Zhou, Y., Zheng, W., Tian, Y., Van Nostrand, J.
D., Wu, L., He, Z., Zhou, J., and Zheng, T.: Illumina sequencing-based
analysis of free-living bacterial community dynamics during an Akashiwo
sanguine bloom in Xiamen sea, China, Sci. Rep., 5, 1–11,
https://doi.org/10.1038/srep08476, 2015.
Zubkov, M. V.: Faster growth of the major prokaryotic versus eukaryotic CO2
fixers in the oligotrophic ocean, Nat. Commun., 5, 1–6,
https://doi.org/10.1038/ncomms4776, 2014.
Short summary
Emerging molecular methods provide new ways of understanding how marine communities respond to changes in ocean conditions. Here, environmental DNA was used to track the temporal evolution of biological communities in the Peruvian coastal upwelling system and in an adjacent enclosure where upwelling was simulated. We found that the two communities quickly diverged, with the open ocean being one found during upwelling and the enclosure evolving to one found under stratified conditions.
Emerging molecular methods provide new ways of understanding how marine communities respond to...
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