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Freilich MA, Poirier C, Dever M, Alou-Font E, Allen J, Cabornero A, Sudek L, Choi CJ, Ruiz S, Pascual A, Farrar JT, Johnston TMS, D’Asaro EA, Worden AZ, Mahadevan A. 3D intrusions transport active surface microbial assemblages to the dark ocean. Proc Natl Acad Sci U S A 2024; 121:e2319937121. [PMID: 38696469 PMCID: PMC11087786 DOI: 10.1073/pnas.2319937121] [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: 11/14/2023] [Accepted: 03/18/2024] [Indexed: 05/04/2024] Open
Abstract
Subtropical oceans contribute significantly to global primary production, but the fate of the picophytoplankton that dominate in these low-nutrient regions is poorly understood. Working in the subtropical Mediterranean, we demonstrate that subduction of water at ocean fronts generates 3D intrusions with uncharacteristically high carbon, chlorophyll, and oxygen that extend below the sunlit photic zone into the dark ocean. These contain fresh picophytoplankton assemblages that resemble the photic-zone regions where the water originated. Intrusions propagate depth-dependent seasonal variations in microbial assemblages into the ocean interior. Strikingly, the intrusions included dominant biomass contributions from nonphotosynthetic bacteria and enrichment of enigmatic heterotrophic bacterial lineages. Thus, the intrusions not only deliver material that differs in composition and nutritional character from sinking detrital particles, but also drive shifts in bacterial community composition, organic matter processing, and interactions between surface and deep communities. Modeling efforts paired with global observations demonstrate that subduction can flux similar magnitudes of particulate organic carbon as sinking export, but is not accounted for in current export estimates and carbon cycle models. Intrusions formed by subduction are a particularly important mechanism for enhancing connectivity between surface and upper mesopelagic ecosystems in stratified subtropical ocean environments that are expanding due to the warming climate.
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Affiliation(s)
- Mara A. Freilich
- Massachusetts Institute of Technology-Wood Hole Oceanographic Institution Joint Program in Oceanography, Woods Hole, MA02543
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA92093
- Department of Earth, Environmental, and Planetary Sciences, Brown University, Providence, RI02912
- Division of Applied Mathematics, Brown University, Providence, RI02912
| | - Camille Poirier
- GEOMAR—Helmholtz Centre for Ocean Research, Kiel24105, Germany
| | - Mathieu Dever
- Department of Physical Oceanography, Woods Hole Oceanographic Institution, Woods Hole, MA02543
| | - Eva Alou-Font
- Sistema de Observación y Predicción Costero de las Illes Balears (SOCIB), Palma de Mallorca 07121, Spain
| | - John Allen
- Sistema de Observación y Predicción Costero de las Illes Balears (SOCIB), Palma de Mallorca 07121, Spain
| | - Andrea Cabornero
- Sistema de Observación y Predicción Costero de las Illes Balears (SOCIB), Palma de Mallorca 07121, Spain
| | - Lisa Sudek
- Physical & Biological Sciences Division, University of California, Santa Cruz, CA95064
| | - Chang Jae Choi
- GEOMAR—Helmholtz Centre for Ocean Research, Kiel24105, Germany
| | - Simón Ruiz
- Instituto Mediterraneo de Estudios Avanzados (IMEDEA), Esporles07190, Spain
| | - Ananda Pascual
- Instituto Mediterraneo de Estudios Avanzados (IMEDEA), Esporles07190, Spain
| | - J. Thomas Farrar
- Department of Physical Oceanography, Woods Hole Oceanographic Institution, Woods Hole, MA02543
| | - T. M. Shaun Johnston
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA92093
| | - Eric A. D’Asaro
- Applied Physics Lab, University of Washington, Seattle, WA98105
| | - Alexandra Z. Worden
- GEOMAR—Helmholtz Centre for Ocean Research, Kiel24105, Germany
- Physical & Biological Sciences Division, University of California, Santa Cruz, CA95064
- Marine Biological Laboratory, Woods Hole, MA02543
| | - Amala Mahadevan
- Department of Physical Oceanography, Woods Hole Oceanographic Institution, Woods Hole, MA02543
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Muñoz-Marín MDC, López-Lozano A, Moreno-Cabezuelo JÁ, Díez J, García-Fernández JM. Mixotrophy in cyanobacteria. Curr Opin Microbiol 2024; 78:102432. [PMID: 38325247 DOI: 10.1016/j.mib.2024.102432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2023] [Revised: 12/22/2023] [Accepted: 01/10/2024] [Indexed: 02/09/2024]
Abstract
Cyanobacteria evolved the oxygenic photosynthesis to generate organic matter from CO2 and sunlight, and they were responsible for the production of oxygen in the Earth's atmosphere. This made them a model for photosynthetic organisms, since they are easier to study than higher plants. Early studies suggested that only a minority among cyanobacteria might assimilate organic compounds, being considered mostly autotrophic for decades. However, compelling evidence from marine and freshwater cyanobacteria, including toxic strains, in the laboratory and in the field, has been obtained in the last decades: by using physiological and omics approaches, mixotrophy has been found to be a more widespread feature than initially believed. Furthermore, dominant clades of marine cyanobacteria can take up organic compounds, and mixotrophy is critical for their survival in deep waters with very low light. Hence, mixotrophy seems to be an essential trait in the metabolism of most cyanobacteria, which can be exploited for biotechnological purposes.
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Affiliation(s)
- María Del Carmen Muñoz-Marín
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Universitario ceiA3, Universidad de Córdoba, Edificio Severo Ochoa, planta 1, ala Este, Campus de Rabanales, 14071 Córdoba, Spain
| | - Antonio López-Lozano
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Universitario ceiA3, Universidad de Córdoba, Edificio Severo Ochoa, planta 1, ala Este, Campus de Rabanales, 14071 Córdoba, Spain
| | - José Ángel Moreno-Cabezuelo
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Universitario ceiA3, Universidad de Córdoba, Edificio Severo Ochoa, planta 1, ala Este, Campus de Rabanales, 14071 Córdoba, Spain
| | - Jesús Díez
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Universitario ceiA3, Universidad de Córdoba, Edificio Severo Ochoa, planta 1, ala Este, Campus de Rabanales, 14071 Córdoba, Spain.
| | - José Manuel García-Fernández
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Universitario ceiA3, Universidad de Córdoba, Edificio Severo Ochoa, planta 1, ala Este, Campus de Rabanales, 14071 Córdoba, Spain.
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3
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Kujawinski EB, Braakman R, Longnecker K, Becker JW, Chisholm SW, Dooley K, Kido Soule MC, Swarr GJ, Halloran K. Metabolite diversity among representatives of divergent Prochlorococcus ecotypes. mSystems 2023; 8:e0126122. [PMID: 37815355 PMCID: PMC10654061 DOI: 10.1128/msystems.01261-22] [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: 12/15/2022] [Accepted: 08/31/2023] [Indexed: 10/11/2023] Open
Abstract
IMPORTANCE Approximately half of the annual carbon fixation on Earth occurs in the surface ocean through the photosynthetic activities of phytoplankton such as the ubiquitous picocyanobacterium Prochlorococcus. Ecologically distinct subpopulations (or ecotypes) of Prochlorococcus are central conduits of organic substrates into the ocean microbiome, thus playing important roles in surface ocean production. We measured the chemical profile of three cultured ecotype strains, observing striking differences among them that have implications for the likely chemical impact of Prochlorococcus subpopulations on their surroundings in the wild. Subpopulations differ in abundance along gradients of temperature, light, and nutrient concentrations, suggesting that these chemical differences could affect carbon cycling in different ocean strata and should be considered in models of Prochlorococcus physiology and marine carbon dynamics.
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Affiliation(s)
- Elizabeth B. Kujawinski
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, USA
| | - Rogier Braakman
- Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Krista Longnecker
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, USA
| | - Jamie W. Becker
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Science Department, Alvernia University, Reading, Pennsylvania, USA
| | - Sallie W. Chisholm
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Keven Dooley
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Department of Ecology and Evolution, University of Chicago, Chicago, Illinois, USA
| | - Melissa C. Kido Soule
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, USA
| | - Gretchen J. Swarr
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, USA
| | - Kathryn Halloran
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, USA
- MIT/WHOI Joint Program in Oceanography/Applied Ocean Sciences and Engineering, Department of Marine Chemistry & Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, USA
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4
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Moreno-Cabezuelo JÁ, Gómez-Baena G, Díez J, García-Fernández JM. Integrated Proteomic and Metabolomic Analyses Show Differential Effects of Glucose Availability in Marine Synechococcus and Prochlorococcus. Microbiol Spectr 2023; 11:e0327522. [PMID: 36722960 PMCID: PMC10100731 DOI: 10.1128/spectrum.03275-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 12/29/2022] [Indexed: 02/02/2023] Open
Abstract
We compared changes induced by the addition of 100 nM and 5 mM glucose on the proteome and metabolome complements in Synechococcus sp. strains WH8102, WH7803, and BL107 and Prochlorococcus sp. strains MED4, SS120, and MIT9313, grown either under standard light conditions or in darkness. Our results suggested that glucose is metabolized by these cyanobacteria, using primarily the oxidative pentoses and Calvin pathways, while no proof was found for the involvement of the Entner-Doudoroff pathway in this process. We observed differences in the effects of glucose availability, both between genera and between Prochlorococcus MED4 and SS120 strains, which might be related to their specific adaptations to the environment. We found evidence for fermentation in Prochlorococcus sp. strain SS120 and Synechococcus sp. strain WH8102 after 5 mM glucose addition. Our results additionally suggested that marine cyanobacteria can detect nanomolar glucose concentrations in the environment and that glucose might be used to sustain metabolism under darkness. Furthermore, the KaiB and KaiC proteins were also affected in Synechococcus sp. WH8102, pointing to a direct link between glucose assimilation and circadian rhythms in marine cyanobacteria. In conclusion, our study provides a wide overview on the metabolic effects induced by glucose availability in representative strains of the diverse marine picocyanobacteria, providing further evidence for the importance of mixotrophy in marine picocyanobacteria. IMPORTANCE Glucose uptake by marine picocyanobacteria has been previously described and strongly suggests they are mixotrophic organisms (capable of using energy from the sun to make organic matter, but also to directly use organic matter from the environment when available). However, a detailed analysis of the effects of glucose addition on the proteome and metabolome of these microorganisms had not been carried out. Here, we analyzed three Prochlorococcus sp. and three Synechococcus sp. strains which were representative of several marine picocyanobacterial clades. We observed differential features in the effects of glucose availability, depending on both the genus and strain; our study illuminated the strategies utilized by these organisms to metabolize glucose and showed unexpected links to other pathways, such as circadian regulation. Furthermore, we found glucose addition had profound effects in the microbiome, favoring the growth of coexisting heterotrophic bacteria.
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Affiliation(s)
- José Ángel Moreno-Cabezuelo
- Departamento de Bioquímica y Biología Molecular-Campus de Excelencia Agroalimentaria CEIA3, Universidad de Córdoba, Cordoba, Spain
| | - Guadalupe Gómez-Baena
- Departamento de Bioquímica y Biología Molecular-Campus de Excelencia Agroalimentaria CEIA3, Universidad de Córdoba, Cordoba, Spain
| | - Jesús Díez
- Departamento de Bioquímica y Biología Molecular-Campus de Excelencia Agroalimentaria CEIA3, Universidad de Córdoba, Cordoba, Spain
| | - José Manuel García-Fernández
- Departamento de Bioquímica y Biología Molecular-Campus de Excelencia Agroalimentaria CEIA3, Universidad de Córdoba, Cordoba, Spain
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5
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Bourgade B, Stensjö K. Synthetic biology in marine cyanobacteria: Advances and challenges. Front Microbiol 2022; 13:994365. [PMID: 36188008 PMCID: PMC9522894 DOI: 10.3389/fmicb.2022.994365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 08/24/2022] [Indexed: 11/19/2022] Open
Abstract
The current economic and environmental context requests an accelerating development of sustainable alternatives for the production of various target compounds. Biological processes offer viable solutions and have gained renewed interest in the recent years. For example, photosynthetic chassis organisms are particularly promising for bioprocesses, as they do not require biomass-derived carbon sources and contribute to atmospheric CO2 fixation, therefore supporting climate change mitigation. Marine cyanobacteria are of particular interest for biotechnology applications, thanks to their rich diversity, their robustness to environmental changes, and their metabolic capabilities with potential for therapeutics and chemicals production without requiring freshwater. The additional cyanobacterial properties, such as efficient photosynthesis, are also highly beneficial for biotechnological processes. Due to their capabilities, research efforts have developed several genetic tools for direct metabolic engineering applications. While progress toward a robust genetic toolkit is continuously achieved, further work is still needed to routinely modify these species and unlock their full potential for industrial applications. In contrast to the understudied marine cyanobacteria, genetic engineering and synthetic biology in freshwater cyanobacteria are currently more advanced with a variety of tools already optimized. This mini-review will explore the opportunities provided by marine cyanobacteria for a greener future. A short discussion will cover the advances and challenges regarding genetic engineering and synthetic biology in marine cyanobacteria, followed by a parallel with freshwater cyanobacteria and their current genetic availability to guide the prospect for marine species.
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Affiliation(s)
- Barbara Bourgade
- Microbial Chemistry, Department of Chemistry-Ångström Laboratory, Uppsala University, Uppsala, Sweden
| | - Karin Stensjö
- Microbial Chemistry, Department of Chemistry-Ångström Laboratory, Uppsala University, Uppsala, Sweden
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Wu Z, Aharonovich D, Roth-Rosenberg D, Weissberg O, Luzzatto-Knaan T, Vogts A, Zoccarato L, Eigemann F, Grossart HP, Voss M, Follows MJ, Sher D. Single-cell measurements and modelling reveal substantial organic carbon acquisition by Prochlorococcus. Nat Microbiol 2022; 7:2068-2077. [PMID: 36329198 PMCID: PMC9712107 DOI: 10.1038/s41564-022-01250-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 09/13/2022] [Indexed: 11/06/2022]
Abstract
Marine phytoplankton are responsible for about half of the photosynthesis on Earth. Many are mixotrophs, combining photosynthesis with heterotrophic assimilation of organic carbon, but the relative contribution of these two lifestyles is unclear. Here single-cell measurements reveal that Prochlorococcus at the base of the photic zone in the Eastern Mediterranean Sea obtain only ~20% of carbon required for growth by photosynthesis. This is supported by laboratory-calibrated calculations based on photo-physiology parameters and compared with in situ growth rates. Agent-based simulations show that mixotrophic cells could grow tens of metres deeper than obligate photo-autotrophs, deepening the nutricline by ~20 m. Time series from the North Atlantic and North Pacific indicate that, during thermal stratification, on average 8-10% of the Prochlorococcus cells live without enough light to sustain obligate photo-autotrophic populations. Together, these results suggest that mixotrophy underpins the ecological success of a large fraction of the global Prochlorococcus population and its collective genetic diversity.
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Affiliation(s)
- Zhen Wu
- grid.116068.80000 0001 2341 2786Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA USA
| | - Dikla Aharonovich
- grid.18098.380000 0004 1937 0562Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel
| | - Dalit Roth-Rosenberg
- grid.18098.380000 0004 1937 0562Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel
| | - Osnat Weissberg
- grid.18098.380000 0004 1937 0562Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel
| | - Tal Luzzatto-Knaan
- grid.18098.380000 0004 1937 0562Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel
| | - Angela Vogts
- grid.423940.80000 0001 2188 0463Leibniz-Institute for Baltic Sea Research, Warnemuende, Germany
| | - Luca Zoccarato
- grid.419247.d0000 0001 2108 8097Department of Experimental Limnology, Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Stechlin, Germany
| | - Falk Eigemann
- grid.423940.80000 0001 2188 0463Leibniz-Institute for Baltic Sea Research, Warnemuende, Germany
| | - Hans-Peter Grossart
- grid.419247.d0000 0001 2108 8097Department of Experimental Limnology, Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Stechlin, Germany ,grid.11348.3f0000 0001 0942 1117Institute of Biochemistry and Biology, Potsdam University, Potsdam, Germany
| | - Maren Voss
- grid.423940.80000 0001 2188 0463Leibniz-Institute for Baltic Sea Research, Warnemuende, Germany
| | - Michael J. Follows
- grid.116068.80000 0001 2341 2786Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA USA
| | - Daniel Sher
- grid.18098.380000 0004 1937 0562Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel
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