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Beckett SJ, Demory D, Coenen AR, Casey JR, Dugenne M, Follett CL, Connell P, Carlson MCG, Hu SK, Wilson ST, Muratore D, Rodriguez-Gonzalez RA, Peng S, Becker KW, Mende DR, Armbrust EV, Caron DA, Lindell D, White AE, Ribalet F, Weitz JS. Disentangling top-down drivers of mortality underlying diel population dynamics of Prochlorococcus in the North Pacific Subtropical Gyre. Nat Commun 2024; 15:2105. [PMID: 38453897 PMCID: PMC10920773 DOI: 10.1038/s41467-024-46165-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 02/16/2024] [Indexed: 03/09/2024] Open
Abstract
Photosynthesis fuels primary production at the base of marine food webs. Yet, in many surface ocean ecosystems, diel-driven primary production is tightly coupled to daily loss. This tight coupling raises the question: which top-down drivers predominate in maintaining persistently stable picocyanobacterial populations over longer time scales? Motivated by high-frequency surface water measurements taken in the North Pacific Subtropical Gyre (NPSG), we developed multitrophic models to investigate bottom-up and top-down mechanisms underlying the balanced control of Prochlorococcus populations. We find that incorporating photosynthetic growth with viral- and predator-induced mortality is sufficient to recapitulate daily oscillations of Prochlorococcus abundances with baseline community abundances. In doing so, we infer that grazers in this environment function as the predominant top-down factor despite high standing viral particle densities. The model-data fits also reveal the ecological relevance of light-dependent viral traits and non-canonical factors to cellular loss. Finally, we leverage sensitivity analyses to demonstrate how variation in life history traits across distinct oceanic contexts, including variation in viral adsorption and grazer clearance rates, can transform the quantitative and even qualitative importance of top-down controls in shaping Prochlorococcus population dynamics.
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Affiliation(s)
- Stephen J Beckett
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA.
- Department of Biology, University of Maryland, College Park, MD, USA.
| | - David Demory
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA.
- Sorbonne Université, CNRS, USR 3579, Laboratoire de Biodiversité et Biotechnologies Microbiennes (LBBM), Observatoire Océanologique, Banyuls-sur-Mer, France.
| | - Ashley R Coenen
- School of Physics, Georgia Institute of Technology, Atlanta, GA, USA
| | - John R Casey
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education, University of Hawai'i at Mānoa, Honolulu, HI, USA
- Department of Oceanography, University of Hawai'i at Mānoa, Honolulu, HI, USA
- Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Mathilde Dugenne
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education, University of Hawai'i at Mānoa, Honolulu, HI, USA
- Department of Oceanography, University of Hawai'i at Mānoa, Honolulu, HI, USA
- Sorbonne Université, CNRS, UMR 7093, Laboratoire d'Océanographie de Villefranche-sur-Mer (LOV), Villefranche-sur-Mer, France
| | - Christopher L Follett
- Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Earth, Ocean and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Paige Connell
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
- Biology Department, San Diego Mesa College, San Diego, CA, USA
| | - Michael C G Carlson
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa, Israel
- Department of Biological Sciences, California State University, Long Beach, CA, USA
| | - Sarah K Hu
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
- Department of Oceanography, Texas A&M University, College Station, TX, USA
| | - Samuel T Wilson
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education, University of Hawai'i at Mānoa, Honolulu, HI, USA
- Department of Oceanography, University of Hawai'i at Mānoa, Honolulu, HI, USA
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Daniel Muratore
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
- Santa Fe Institute, Santa Fe, NM, USA
| | | | - Shengyun Peng
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
- Adobe, San Jose, CA, USA
| | - Kevin W Becker
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
- GEOMAR Helmholtz Centre for Ocean Research, Kiel, Germany
| | - Daniel R Mende
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education, University of Hawai'i at Mānoa, Honolulu, HI, USA
- Department of Oceanography, University of Hawai'i at Mānoa, Honolulu, HI, USA
- Laboratory of Applied Evolutionary Biology, Department of Medical Microbiology, Academic Medical Centre, University of Amsterdam, Amsterdam, The Netherlands
| | | | - David A Caron
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - Debbie Lindell
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa, Israel
| | - Angelicque E White
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education, University of Hawai'i at Mānoa, Honolulu, HI, USA
- Department of Oceanography, University of Hawai'i at Mānoa, Honolulu, HI, USA
| | - François Ribalet
- School of Oceanography, University of Washington, Seattle, WA, USA
| | - Joshua S Weitz
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA.
- Department of Biology, University of Maryland, College Park, MD, USA.
- School of Physics, Georgia Institute of Technology, Atlanta, GA, USA.
- Institut de Biologie, École Normale Supérieure, Paris, France.
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Groussman RD, Coesel SN, Durham BP, Armbrust EV. Diel-Regulated Transcriptional Cascades of Microbial Eukaryotes in the North Pacific Subtropical Gyre. Front Microbiol 2021; 12:682651. [PMID: 34659137 PMCID: PMC8511712 DOI: 10.3389/fmicb.2021.682651] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 08/11/2021] [Indexed: 11/13/2022] Open
Abstract
Open-ocean surface waters host a diverse community of single-celled eukaryotic plankton (protists) consisting of phototrophs, heterotrophs, and mixotrophs. The productivity and biomass of these organisms oscillate over diel cycles, and yet the underlying transcriptional processes are known for few members of the community. Here, we examined a 4-day diel time series of transcriptional abundance profiles for the protist community (0.2-100 μm in cell size) in the North Pacific Subtropical Gyre near Station ALOHA. De novo assembly of poly-A+ selected metatranscriptomes yielded over 30 million contigs with taxonomic and functional annotations assigned to 54 and 25% of translated contigs, respectively. The completeness of the resulting environmental eukaryotic taxonomic bins was assessed, and 48 genera were further evaluated for diel patterns in transcript abundances. These environmental transcriptome bins maintained reproducible temporal partitioning of total gene family abundances, with haptophyte and ochrophyte genera generally showing the greatest diel partitioning of their transcriptomes. The haptophyte Phaeocystis demonstrated the highest proportion of transcript diel periodicity, while most other protists had intermediate levels of periodicity regardless of their trophic status. Dinoflagellates, except for the parasitoid genus Amoebophrya, exhibit the fewest diel oscillations of transcript abundances. Diel-regulated gene families were enriched in key metabolic pathways; photosynthesis, carbon fixation, and fatty acid biosynthesis gene families had peak times concentrated around dawn, while gene families involved in protein turnover (proteasome and protein processing) are most active during the high intensity daylight hours. TCA cycle, oxidative phosphorylation and fatty acid degradation predominantly peaked near dusk. We identified temporal pathway enrichments unique to certain taxa, including assimilatory sulfate reduction at dawn in dictyophytes and signaling pathways at early evening in haptophytes, pointing to possible taxon-specific channels of carbon and nutrients through the microbial community. These results illustrate the synchrony of transcriptional regulation to the diel cycle and how the protist community of the North Pacific Subtropical Gyre structures their transcriptomes to guide the daily flux of matter and energy through the gyre ecosystem.
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Affiliation(s)
- Ryan D. Groussman
- School of Oceanography, University of Washington, Seattle, WA, United States
| | - Sacha N. Coesel
- School of Oceanography, University of Washington, Seattle, WA, United States
| | - Bryndan P. Durham
- School of Oceanography, University of Washington, Seattle, WA, United States
- Department of Biology, Genetics Institute, University of Florida, Gainesville, FL, United States
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