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Cornejo-Castillo FM, Inomura K, Zehr JP, Follows MJ. Metabolic trade-offs constrain the cell size ratio in a nitrogen-fixing symbiosis. Cell 2024; 187:1762-1768.e9. [PMID: 38471501 DOI: 10.1016/j.cell.2024.02.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 10/06/2023] [Accepted: 02/14/2024] [Indexed: 03/14/2024]
Abstract
Biological dinitrogen (N2) fixation is a key metabolic process exclusively performed by prokaryotes, some of which are symbiotic with eukaryotes. Species of the marine haptophyte algae Braarudosphaera bigelowii harbor the N2-fixing endosymbiotic cyanobacteria UCYN-A, which might be evolving organelle-like characteristics. We found that the size ratio between UCYN-A and their hosts is strikingly conserved across sublineages/species, which is consistent with the size relationships of organelles in this symbiosis and other species. Metabolic modeling showed that this size relationship maximizes the coordinated growth rate based on trade-offs between resource acquisition and exchange. Our findings show that the size relationships of N2-fixing endosymbionts and organelles in unicellular eukaryotes are constrained by predictable metabolic underpinnings and that UCYN-A is, in many regards, functioning like a hypothetical N2-fixing organelle (or nitroplast).
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Affiliation(s)
- Francisco M Cornejo-Castillo
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar, ICM-CSIC, Barcelona 08003, Spain; Department of Ocean Sciences, University of California, Santa Cruz, CA 95064, USA.
| | - Keisuke Inomura
- Graduate School of Oceanography, University of Rhode Island, Narragansett, RI 02882, USA.
| | - Jonathan P Zehr
- Department of Ocean Sciences, University of California, Santa Cruz, CA 95064, USA
| | - Michael J Follows
- Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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2
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Rao D, Füssy Z, Brisbin MM, McIlvin MR, Moran DM, Allen AE, Follows MJ, Saito MA. Flexible B 12 ecophysiology of Phaeocystis antarctica due to a fusion B 12-independent methionine synthase with widespread homologues. Proc Natl Acad Sci U S A 2024; 121:e2204075121. [PMID: 38306482 PMCID: PMC10861871 DOI: 10.1073/pnas.2204075121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Accepted: 11/13/2023] [Indexed: 02/04/2024] Open
Abstract
Coastal Antarctic marine ecosystems are significant in carbon cycling because of their intense seasonal phytoplankton blooms. Southern Ocean algae are primarily limited by light and iron (Fe) and can be co-limited by cobalamin (vitamin B12). Micronutrient limitation controls productivity and shapes the composition of blooms which are typically dominated by either diatoms or the haptophyte Phaeocystis antarctica. However, the vitamin requirements and ecophysiology of the keystone species P. antarctica remain poorly characterized. Using cultures, physiological analysis, and comparative omics, we examined the response of P. antarctica to a matrix of Fe-B12 conditions. We show that P. antarctica is not auxotrophic for B12, as previously suggested, and identify mechanisms underlying its B12 response in cultures of predominantly solitary and colonial cells. A combination of proteomics and proteogenomics reveals a B12-independent methionine synthase fusion protein (MetE-fusion) that is expressed under vitamin limitation and interreplaced with the B12-dependent isoform under replete conditions. Database searches return homologues of the MetE-fusion protein in multiple Phaeocystis species and in a wide range of marine microbes, including other photosynthetic eukaryotes with polymorphic life cycles as well as bacterioplankton. Furthermore, we find MetE-fusion homologues expressed in metaproteomic and metatranscriptomic field samples in polar and more geographically widespread regions. As climate change impacts micronutrient availability in the coastal Southern Ocean, our finding that P. antarctica has a flexible B12 metabolism has implications for its relative fitness compared to B12-auxotrophic diatoms and for the detection of B12-stress in a more diverse set of marine microbes.
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Affiliation(s)
- Deepa Rao
- Earth Atmospheric Planetary Sciences Department, Massachusetts Institute of Technology, Cambridge, MA02139
- Marine Chemistry and Geochemistry Department, Woods Hole, MA02543
| | - Zoltán Füssy
- Microbial and Environmental Genomics Department, J.C. Venter Institute, La Jolla, CA92037
| | | | | | - Dawn M. Moran
- Marine Chemistry and Geochemistry Department, Woods Hole, MA02543
| | - Andrew E. Allen
- Microbial and Environmental Genomics Department, J.C. Venter Institute, La Jolla, CA92037
- Integrative Oceanography Division, Scripps Instition of Oceanography, University of California San Diego, La Jolla, CA92037
| | - Michael J. Follows
- Earth Atmospheric Planetary Sciences Department, Massachusetts Institute of Technology, Cambridge, MA02139
| | - Mak A. Saito
- Marine Chemistry and Geochemistry Department, Woods Hole, MA02543
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3
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Ser-Giacomi E, Martinez-Garcia R, Dutkiewicz S, Follows MJ. A Lagrangian model for drifting ecosystems reveals heterogeneity-driven enhancement of marine plankton blooms. Nat Commun 2023; 14:6092. [PMID: 37773229 PMCID: PMC10541867 DOI: 10.1038/s41467-023-41469-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 09/05/2023] [Indexed: 10/01/2023] Open
Abstract
Marine plankton play a crucial role in carbon storage, global climate, and ecosystem function. Planktonic ecosystems are embedded in patches of water that are continuously moving, stretching, and diluting. These processes drive inhomegeneities on a range of scales, with implications for the integrated ecosystem properties, but are hard to characterize. We present a theoretical framework that accounts for all these aspects; tracking the water patch hosting a drifting ecosystem along with its physical, environmental, and biochemical features. The theory resolves patch dilution and internal physical mixing as a function of oceanic strain and diffusion. Ecological dynamics are parameterized by an idealized nutrient and phytoplankton population and we specifically capture the time evolution of the biochemical spatial variances to represent within-patch heterogeneity. We find that, depending only on the physical processes to which the water patch is subjected, the plankton biomass response to a resource perturbation can vary in size up to six times. This work indicates that we must account for these processes when interpreting and modeling marine ecosystems and provides a framework with which to do so.
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Affiliation(s)
- Enrico Ser-Giacomi
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, 54-1514 MIT, Cambridge, MA, 02139, USA.
- IFISC (CSIC-UIB), Institute for Cross-Disciplinary Physics and Complex Systems, Palma de Mallorca, Spain.
| | - Ricardo Martinez-Garcia
- ICTP South American Institute for Fundamental Research & Institute of Theoretical Physics, Universidade Estadual Paulista - UNESP, Rua Dr.Bento Teobaldo Ferraz 271, Bloco 2 - Barra Funda, 01140-070, São Paulo, SP, Brazil
- Center for Advanced Systems Understanding (CASUS); Helmholtz-Zentrum Dresden-Rossendorf (HZDR), Görlitz, Germany
| | - Stephanie Dutkiewicz
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, 54-1514 MIT, Cambridge, MA, 02139, USA
| | - Michael J Follows
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, 54-1514 MIT, Cambridge, MA, 02139, USA
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4
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Krinos AI, Cohen NR, Follows MJ, Alexander H. Correction: Reverse engineering environmental metatranscriptomes clarifies best practices for eukaryotic assembly. BMC Bioinformatics 2023; 24:185. [PMID: 37147597 PMCID: PMC10163689 DOI: 10.1186/s12859-023-05313-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/07/2023] Open
Affiliation(s)
- Arianna I Krinos
- MIT-WHOI Joint Program in Oceanography and Applied Ocean Science and Engineering, Cambridge and Woods Hole, MA, USA.
- Department of Biology, Woods Hole Oceanographic Institution, Woods Hole, MA, USA.
- Department of Earth, Atmospheric, and Planetary Science, Massachusetts Institute of Technology, Cambridge, MA, USA.
| | - Natalie R Cohen
- Skidaway Institute of Oceanography, University of Georgia, Savannah, GA, USA
| | - Michael J Follows
- Department of Earth, Atmospheric, and Planetary Science, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Harriet Alexander
- Department of Biology, Woods Hole Oceanographic Institution, Woods Hole, MA, USA.
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5
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Krinos AI, Cohen NR, Follows MJ, Alexander H. Reverse engineering environmental metatranscriptomes clarifies best practices for eukaryotic assembly. BMC Bioinformatics 2023; 24:74. [PMID: 36869298 PMCID: PMC9983209 DOI: 10.1186/s12859-022-05121-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 12/21/2022] [Indexed: 03/05/2023] Open
Abstract
BACKGROUND Diverse communities of microbial eukaryotes in the global ocean provide a variety of essential ecosystem services, from primary production and carbon flow through trophic transfer to cooperation via symbioses. Increasingly, these communities are being understood through the lens of omics tools, which enable high-throughput processing of diverse communities. Metatranscriptomics offers an understanding of near real-time gene expression in microbial eukaryotic communities, providing a window into community metabolic activity. RESULTS Here we present a workflow for eukaryotic metatranscriptome assembly, and validate the ability of the pipeline to recapitulate real and manufactured eukaryotic community-level expression data. We also include an open-source tool for simulating environmental metatranscriptomes for testing and validation purposes. We reanalyze previously published metatranscriptomic datasets using our metatranscriptome analysis approach. CONCLUSION We determined that a multi-assembler approach improves eukaryotic metatranscriptome assembly based on recapitulated taxonomic and functional annotations from an in-silico mock community. The systematic validation of metatranscriptome assembly and annotation methods provided here is a necessary step to assess the fidelity of our community composition measurements and functional content assignments from eukaryotic metatranscriptomes.
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Affiliation(s)
- Arianna I Krinos
- MIT-WHOI Joint Program in Oceanography and Applied Ocean Science and Engineering, Cambridge and Woods Hole, MA, USA. .,Department of Biology, Woods Hole Oceanographic Institution, Woods Hole, MA, USA. .,Department of Earth, Atmospheric, and Planetary Science, Massachusetts Institute of Technology, Cambridge, MA, USA.
| | - Natalie R Cohen
- Skidaway Institute of Oceanography, University of Georgia, Savannah, GA, USA
| | - Michael J Follows
- Department of Earth, Atmospheric, and Planetary Science, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Harriet Alexander
- Department of Biology, Woods Hole Oceanographic Institution, Woods Hole, MA, USA.
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6
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Inomura K, Deutsch C, Jahn O, Dutkiewicz S, Follows MJ. Global patterns in marine organic matter stoichiometry driven by phytoplankton ecophysiology. Nat Geosci 2022; 15:1034-1040. [PMID: 36530964 PMCID: PMC9749492 DOI: 10.1038/s41561-022-01066-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 09/29/2022] [Indexed: 05/28/2023]
Abstract
The proportion of major elements in marine organic matter links cellular processes to global nutrient, oxygen and carbon cycles. Differences in the C:N:P ratios of organic matter have been observed between ocean biomes, but these patterns have yet to be quantified from the underlying small-scale physiological and ecological processes. Here we use an ecosystem model that includes adaptive resource allocation within and between ecologically distinct plankton size classes to attribute the causes of global patterns in the C:N:P ratios. We find that patterns of N:C variation are largely driven by common physiological adjustment strategies across all phytoplankton, while patterns of N:P are driven by ecological selection for taxonomic groups with different phosphorus storage capacities. Although N:C varies widely due to cellular adjustment to light and nutrients, its latitudinal gradient is modest because of depth-dependent trade-offs between nutrient and light availability. Strong latitudinal variation in N:P reflects an ecological balance favouring small plankton with lower P storage capacity in the subtropics, and larger eukaryotes with a higher cellular P storage capacity in nutrient-rich high latitudes. A weaker N:P difference between southern and northern hemispheres, and between the Atlantic and Pacific oceans, reflects differences in phosphate available for cellular storage. Despite simulating only two phytoplankton size classes, the emergent global variability of elemental ratios resembles that of all measured species, suggesting that the range of growth conditions and ecological selection sustain the observed diversity of stoichiometry among phytoplankton.
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Affiliation(s)
- Keisuke Inomura
- Graduate School of Oceanography, University of Rhode Island, Narragansett, RI USA
- School of Oceanography, University of Washington, Seattle, WA USA
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA USA
| | - Curtis Deutsch
- School of Oceanography, University of Washington, Seattle, WA USA
- Department of Geosciences and High Meadows Environmental Institute, Princeton University, Princeton, NJ USA
| | - Oliver Jahn
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA USA
| | - Stephanie Dutkiewicz
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA USA
| | - Michael J. Follows
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA USA
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7
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Casey JR, Boiteau RM, Engqvist MKM, Finkel ZV, Li G, Liefer J, Müller CL, Muñoz N, Follows MJ. Basin-scale biogeography of marine phytoplankton reflects cellular-scale optimization of metabolism and physiology. Sci Adv 2022; 8:eabl4930. [PMID: 35061539 PMCID: PMC8782455 DOI: 10.1126/sciadv.abl4930] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 11/29/2021] [Indexed: 06/14/2023]
Abstract
Extensive microdiversity within Prochlorococcus, the most abundant marine cyanobacterium, occurs at scales from a single droplet of seawater to ocean basins. To interpret the structuring role of variations in genetic potential, as well as metabolic and physiological acclimation, we developed a mechanistic constraint-based modeling framework that incorporates the full suite of genes, proteins, metabolic reactions, pigments, and biochemical compositions of 69 sequenced isolates spanning the Prochlorococcus pangenome. Optimizing each strain to the local, observed physical and chemical environment along an Atlantic Ocean transect, we predicted variations in strain-specific patterns of growth rate, metabolic configuration, and physiological state, defining subtle niche subspaces directly attributable to differences in their encoded metabolic potential. Predicted growth rates covaried with observed ecotype abundances, affirming their significance as a measure of fitness and inferring a nonlinear density dependence of mortality. Our study demonstrates the potential to interpret global-scale ecosystem organization in terms of cellular-scale processes.
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Affiliation(s)
- John R. Casey
- Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
- School of Ocean and Earth Science and Technology, University of Hawai‘i at Ma¯noa, Honolulu, HI, USA
| | - Rene M. Boiteau
- College of Earth, Ocean, and Atmospheric Sciences, Oregon State University, Corvallis, OR, USA
| | - Martin K. M. Engqvist
- Department of Biology and Biological Engineering, Chalmers University of Technology, Göteborg, Sweden
| | - Zoe V. Finkel
- Department of Oceanography, Dalhousie University, Halifax, NS, Canada
| | - Gang Li
- Department of Biology and Biological Engineering, Chalmers University of Technology, Göteborg, Sweden
| | - Justin Liefer
- Department of Biology, Mount Allison University, Sackville, NB, Canada
| | | | - Nathalie Muñoz
- Environmental Molecular Sciences Division, Pacific Northwest National Laboratories, Richland, WA, USA
| | - Michael J. Follows
- Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
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8
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Follett CL, Dutkiewicz S, Ribalet F, Zakem E, Caron D, Armbrust EV, Follows MJ. Trophic interactions with heterotrophic bacteria limit the range of Prochlorococcus. Proc Natl Acad Sci U S A 2022; 119:e2110993118. [PMID: 34983874 PMCID: PMC8764666 DOI: 10.1073/pnas.2110993118] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/08/2021] [Indexed: 11/26/2022] Open
Abstract
Prochlorococcus is both the smallest and numerically most abundant photosynthesizing organism on the planet. While thriving in the warm oligotrophic gyres, Prochlorococcus concentrations drop rapidly in higher-latitude regions. Transect data from the North Pacific show the collapse occurring at a wide range of temperatures and latitudes (temperature is often hypothesized to cause this shift), suggesting an ecological mechanism may be at play. An often used size-based theory of phytoplankton community structure that has been incorporated into computational models correctly predicts the dominance of Prochlorococcus in the gyres, and the relative dominance of larger cells at high latitudes. However, both theory and computational models fail to explain the poleward collapse. When heterotrophic bacteria and predators that prey nonspecifically on both Prochlorococcus and bacteria are included in the theoretical framework, the collapse of Prochlorococcus occurs with increasing nutrient supplies. The poleward collapse of Prochlorococcus populations then naturally emerges when this mechanism of "shared predation" is implemented in a complex global ecosystem model. Additionally, the theory correctly predicts trends in both the abundance and mean size of the heterotrophic bacteria. These results suggest that ecological controls need to be considered to understand the biogeography of Prochlorococcus and predict its changes under future ocean conditions. Indirect interactions within a microbial network can be essential in setting community structure.
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Affiliation(s)
- Christopher L Follett
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139;
| | - Stephanie Dutkiewicz
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - François Ribalet
- School of Oceanography, University of Washington, Seattle, WA 98195
| | - Emily Zakem
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089
| | - David Caron
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089
| | | | - Michael J Follows
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139
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9
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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: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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10
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Chakraborty S, Andersen KH, Visser AW, Inomura K, Follows MJ, Riemann L. Quantifying nitrogen fixation by heterotrophic bacteria in sinking marine particles. Nat Commun 2021; 12:4085. [PMID: 34215729 PMCID: PMC8253789 DOI: 10.1038/s41467-021-23875-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 05/21/2021] [Indexed: 02/06/2023] Open
Abstract
Nitrogen ([Formula: see text]) fixation by heterotrophic bacteria associated with sinking particles contributes to marine N cycling, but a mechanistic understanding of its regulation and significance are not available. Here we develop a mathematical model for unicellular heterotrophic bacteria growing on sinking marine particles. These bacteria can fix [Formula: see text] under suitable environmental conditions. We find that the interactive effects of polysaccharide and polypeptide concentrations, sinking speed of particles, and surrounding [Formula: see text] and [Formula: see text] concentrations determine the [Formula: see text] fixation rate inside particles. [Formula: see text] fixation inside sinking particles is mainly fueled by [Formula: see text] respiration rather than [Formula: see text] respiration. Our model suggests that anaerobic processes, including heterotrophic [Formula: see text] fixation, can take place in anoxic microenvironments inside sinking particles even in fully oxygenated marine waters. The modelled [Formula: see text] fixation rates are similar to bulk rates measured in the aphotic ocean, and our study consequently suggests that particle-associated heterotrophic [Formula: see text] fixation contributes significantly to oceanic [Formula: see text] fixation.
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Affiliation(s)
- Subhendu Chakraborty
- grid.5254.60000 0001 0674 042XDepartment of Biology, Marine Biological Section, University of Copenhagen, Helsingør, Denmark ,grid.5170.30000 0001 2181 8870Centre for Ocean Life, DTU Aqua, Technical University of Denmark, Kgs.Lyngby, Denmark ,grid.461729.f0000 0001 0215 3324Present Address: Systems Ecology Group, Leibniz Centre for Tropical Marine Research (ZMT), Bremen, Germany
| | - Ken H. Andersen
- grid.5170.30000 0001 2181 8870Centre for Ocean Life, DTU Aqua, Technical University of Denmark, Kgs.Lyngby, Denmark
| | - André W. Visser
- grid.5170.30000 0001 2181 8870Centre for Ocean Life, DTU Aqua, Technical University of Denmark, Kgs.Lyngby, Denmark
| | - Keisuke Inomura
- grid.20431.340000 0004 0416 2242Graduate School of Oceanography, University of Rhode Island, Narragansett, RI USA
| | - Michael J. Follows
- grid.116068.80000 0001 2341 2786Department of Earth, Atmospheric and Planetary Sciences, MIT, Cambridge, MA USA
| | - Lasse Riemann
- grid.5254.60000 0001 0674 042XDepartment of Biology, Marine Biological Section, University of Copenhagen, Helsingør, Denmark
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11
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Follett CL, Dutkiewicz S, Forget G, Cael BB, Follows MJ. Moving ecological and biogeochemical transitions across the North Pacific. Limnol Oceanogr 2021; 66:2442-2454. [PMID: 34248205 PMCID: PMC8252044 DOI: 10.1002/lno.11763] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 12/22/2020] [Accepted: 03/17/2021] [Indexed: 06/13/2023]
Abstract
In the North Pacific Ocean, nutrient rich surface waters flow south from the subpolar gyre through a transitional region and into the subtropics. Along the way, nutrients are used, recycled, and exported, leading to lower biomass and a commensurate change in ecosystem structure moving southward. We focus on the region between the two gyres (the Transition Zone) using a coupled biophysical ocean model, remote sensing, floats, and cruise data to explore the nature of the physical, biogeochemical, and ecological fields in this region. Nonlinear interactions between biological processes and the meridional gradient in nutrient supply lead to sharp shifts across this zone. These transitions between a southern region with more uniform biological and biogeochemical properties and steep meridional gradients to the north are diagnosed from extrema in the first derivative of the properties with latitude. Some transitions like that for chlorophyll a (the transition zone chlorophyll front [TZCF]) experience large seasonal excursions while the location of the transitions in other properties moves very little. The seasonal shifts are not caused by changes in the horizontal flow field, but rather by the interaction of seasonal, depth related, forcing with the mean latitudinal gradients. Focusing on the TZCF as a case study, we express its phase velocity in terms of vertical nutrient flux and internal ecosystem processes, demonstrating their nearly equal influence on its motion. This framework of propagating biogeochemical transitions can be systematically expanded to better understand the processes that structure ecosystems and biogeochemistry in the North Pacific and beyond.
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Affiliation(s)
- Christopher L. Follett
- Department of Earth, Atmospheric and Planetary SciencesMassachusetts Institute of TechnologyCambridgeMassachusettsUSA
| | - Stephanie Dutkiewicz
- Department of Earth, Atmospheric and Planetary SciencesMassachusetts Institute of TechnologyCambridgeMassachusettsUSA
| | - Gael Forget
- Department of Earth, Atmospheric and Planetary SciencesMassachusetts Institute of TechnologyCambridgeMassachusettsUSA
| | - B. B. Cael
- National Oceanography CentreSouthamptonUK
| | - Michael J. Follows
- Department of Earth, Atmospheric and Planetary SciencesMassachusetts Institute of TechnologyCambridgeMassachusettsUSA
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12
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Kempes CP, Follows MJ, Smith H, Graham H, House CH, Levin SA. Generalized Stoichiometry and Biogeochemistry for Astrobiological Applications. Bull Math Biol 2021; 83:73. [PMID: 34008062 PMCID: PMC8131296 DOI: 10.1007/s11538-021-00877-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 02/25/2021] [Indexed: 11/03/2022]
Abstract
A central need in the field of astrobiology is generalized perspectives on life that make it possible to differentiate abiotic and biotic chemical systems McKay (2008). A key component of many past and future astrobiological measurements is the elemental ratio of various samples. Classic work on Earth's oceans has shown that life displays a striking regularity in the ratio of elements as originally characterized by Redfield (Redfield 1958; Geider and La Roche 2002; Eighty years of Redfield 2014). The body of work since the original observations has connected this ratio with basic ecological dynamics and cell physiology, while also documenting the range of elemental ratios found in a variety of environments. Several key questions remain in considering how to best apply this knowledge to astrobiological contexts: How can the observed variation of the elemental ratios be more formally systematized using basic biological physiology and ecological or environmental dynamics? How can these elemental ratios be generalized beyond the life that we have observed on our own planet? Here, we expand recently developed generalized physiological models (Kempes et al. 2012, 2016, 2017, 2019) to create a simple framework for predicting the variation of elemental ratios found in various environments. We then discuss further generalizing the physiology for astrobiological applications. Much of our theoretical treatment is designed for in situ measurements applicable to future planetary missions. We imagine scenarios where three measurements can be made-particle/cell sizes, particle/cell stoichiometry, and fluid or environmental stoichiometry-and develop our theory in connection with these often deployed measurements.
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Affiliation(s)
| | - Michael J Follows
- Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Hillary Smith
- Department of Geosciences, Pennsylvania State University, University Park, PA, USA
| | - Heather Graham
- NASA Goddard Spaceflight Center, Greenbelt, MD, USA
- Catholic University of America, Washington, DC, USA
| | - Christopher H House
- Department of Geosciences, Pennsylvania State University, University Park, PA, USA
| | - Simon A Levin
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA
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13
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Inomura K, Deutsch C, Masuda T, Prášil O, Follows MJ. Quantitative models of nitrogen-fixing organisms. Comput Struct Biotechnol J 2020; 18:3905-3924. [PMID: 33335688 PMCID: PMC7733014 DOI: 10.1016/j.csbj.2020.11.022] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 11/11/2020] [Accepted: 11/13/2020] [Indexed: 10/26/2022] Open
Abstract
Nitrogen-fixing organisms are of importance to the environment, providing bioavailable nitrogen to the biosphere. Quantitative models have been used to complement the laboratory experiments and in situ measurements, where such evaluations are difficult or costly. Here, we review the current state of the quantitative modeling of nitrogen-fixing organisms and ways to enhance the bridge between theoretical and empirical studies.
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Affiliation(s)
- Keisuke Inomura
- School of Oceanography, University of Washington, Seattle, WA, USA
| | - Curtis Deutsch
- School of Oceanography, University of Washington, Seattle, WA, USA
| | - Takako Masuda
- Institute of Microbiology, The Czech Academy of Sciences, Opatovický mlýn, Třeboň, Czech Republic
| | - Ondřej Prášil
- Institute of Microbiology, The Czech Academy of Sciences, Opatovický mlýn, Třeboň, Czech Republic
| | - Michael J. Follows
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
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14
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Abstract
Microbial activity mediates the fluxes of greenhouse gases. However, in the global models of the marine and terrestrial biospheres used for climate change projections, typically only photosynthetic microbial activity is resolved mechanistically. To move forward, we argue that global biogeochemical models need a theoretically grounded framework with which to constrain parameterizations of diverse microbial metabolisms. Here, we explain how the key redox chemistry underlying metabolisms provides a path towards this goal. Using this first-principles approach, the presence or absence of metabolic functional types emerges dynamically from ecological interactions, expanding model applicability to unobserved environments. “Nothing is less real than realism. It is only by selection, by elimination, by emphasis, that we get at the real meaning of things.” –Georgia O’Keefe Marine microbial activities fuel biogeochemical cycles that impact the climate, but global models do not account for the myriad physiological processes that microbes perform. Here the authors argue for a model framework that reinterprets the ocean as physics coupled to biologically-driven redox chemistry.
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Affiliation(s)
- Emily J Zakem
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089, USA.
| | - Martin F Polz
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.,Department of Microbial Ecology, Center for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Michael J Follows
- Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
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15
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Omta AW, Talmy D, Inomura K, Irwin AJ, Finkel ZV, Sher D, Liefer JD, Follows MJ. Quantifying nutrient throughput and DOM production by algae in continuous culture. J Theor Biol 2020; 494:110214. [PMID: 32142805 DOI: 10.1016/j.jtbi.2020.110214] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Revised: 11/07/2019] [Accepted: 02/24/2020] [Indexed: 01/04/2023]
Abstract
Freshwater and marine algae can balance nutrient demand and availability by regulating uptake, accumulation and exudation. To obtain insight into these processes under nitrogen (N) and phosphorus (P) limitation, we reanalyze published data from continuous cultures of the chlorophyte Selenastrum minutum. Based on mass budgets, we argue that much of the non-limiting N and P had passed through the organisms and was present as dissolved organic phosphorus or nitrogen (DOP or DON). We construct a model that describes the production of biomass and dissolved organic matter (DOM) as a function of the growth rate. A fit of this model against the chemostat data suggests a high turnover of the non-limiting N and P: at the highest growth rates, N and P atoms spent on average only about 3 h inside an organism, before they were exuded as DON and DOP, respectively. This DOM exudation can explain the observed trends in the algal stoichiometric ratios as a function of the dilution rate. We discuss independent evidence from isotope experiments for this apparently wasteful behavior and we suggest experiments to quantify and characterize DON and DOP exudation further.
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Affiliation(s)
- A W Omta
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, United States.
| | - D Talmy
- Department of Microbiology, University of Tennessee, 1311 Cumberland Avenue, Knoxville, TN 37916, United States.
| | - K Inomura
- School of Oceanography, University of Washington, 1492 NE Boat Street, Seattle, WA 98105, United States.
| | - A J Irwin
- Department of Mathematics and Statistics, Dalhousie University, 6316 Coburg Road, Halifax, NS B3H 4R2, Canada.
| | - Z V Finkel
- Department of Oceanography, Dalhousie University, 1355 Oxford Street, Halifax, NS B3H 4R2, Canada.
| | - D Sher
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, 199 Aba Khoushy Avenue, Mount Carmel 3498838, Haifa, Israel.
| | - J D Liefer
- Department of Biology, Mount Allison University, 63B York Street, Sackville, NB E4L 1G7, Canada.
| | - M J Follows
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, United States.
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16
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Inomura K, Omta AW, Talmy D, Bragg J, Deutsch C, Follows MJ. A Mechanistic Model of Macromolecular Allocation, Elemental Stoichiometry, and Growth Rate in Phytoplankton. Front Microbiol 2020; 11:86. [PMID: 32256456 PMCID: PMC7093025 DOI: 10.3389/fmicb.2020.00086] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Accepted: 01/15/2020] [Indexed: 01/09/2023] Open
Abstract
We present a model of the growth rate and elemental stoichiometry of phytoplankton as a function of resource allocation between and within broad macromolecular pools under a variety of resource supply conditions. The model is based on four, empirically-supported, cornerstone assumptions: that there is a saturating relationship between light and photosynthesis, a linear relationship between RNA/protein and growth rate, a linear relationship between biosynthetic proteins and growth rate, and a constant macromolecular composition of the light-harvesting machinery. We combine these assumptions with statements of conservation of carbon, nitrogen, phosphorus, and energy. The model can be solved algebraically for steady state conditions and constrained with data on elemental stoichiometry from published laboratory chemostat studies. It interprets the relationships between macromolecular and elemental stoichiometry and also provides quantitative predictions of the maximum growth rate at given light intensity and nutrient supply rates. The model is compatible with data sets from several laboratory studies characterizing both prokaryotic and eukaryotic phytoplankton from marine and freshwater environments. It is conceptually simple, yet mechanistic and quantitative. Here, the model is constrained only by elemental stoichiometry, but makes predictions about allocation to measurable macromolecular pools, which could be tested in the laboratory.
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Affiliation(s)
- Keisuke Inomura
- School of Oceanography, University of Washington, Seattle, WA, United States
| | - Anne Willem Omta
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - David Talmy
- Department of Microbiology, University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Jason Bragg
- National Herbarium of New South Wales, The Royal Botanic Gardens and Domain Trust, Sydney, NSW, Australia
| | - Curtis Deutsch
- School of Oceanography, University of Washington, Seattle, WA, United States
| | - Michael J. Follows
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, United States
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17
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Zakem EJ, Mahadevan A, Lauderdale JM, Follows MJ. Stable aerobic and anaerobic coexistence in anoxic marine zones. ISME J 2020; 14:288-301. [PMID: 31624350 PMCID: PMC6908664 DOI: 10.1038/s41396-019-0523-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 08/23/2019] [Accepted: 09/13/2019] [Indexed: 02/06/2023]
Abstract
Mechanistic description of the transition from aerobic to anaerobic metabolism is necessary for diagnostic and predictive modeling of fixed nitrogen loss in anoxic marine zones (AMZs). In a metabolic model where diverse oxygen- and nitrogen-cycling microbial metabolisms are described by underlying redox chemical reactions, we predict a transition from strictly aerobic to predominantly anaerobic regimes as the outcome of ecological interactions along an oxygen gradient, obviating the need for prescribed critical oxygen concentrations. Competing aerobic and anaerobic metabolisms can coexist in anoxic conditions whether these metabolisms represent obligate or facultative populations. In the coexistence regime, relative rates of aerobic and anaerobic activity are determined by the ratio of oxygen to electron donor supply. The model simulates key characteristics of AMZs, such as the accumulation of nitrite and the sustainability of anammox at higher oxygen concentrations than denitrification, and articulates how microbial biomass concentrations relate to associated water column transformation rates as a function of redox stoichiometry and energetics. Incorporating the metabolic model into an idealized two-dimensional ocean circulation results in a simulated AMZ, in which a secondary chlorophyll maximum emerges from oxygen-limited grazing, and where vertical mixing and dispersal in the oxycline also contribute to metabolic co-occurrence. The modeling approach is mechanistic yet computationally economical and suitable for global change applications.
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Affiliation(s)
- Emily J Zakem
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA.
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA.
| | | | - Jonathan M Lauderdale
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Michael J Follows
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
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18
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Zakem EJ, Al-Haj A, Church MJ, van Dijken GL, Dutkiewicz S, Foster SQ, Fulweiler RW, Mills MM, Follows MJ. Publisher Correction: Ecological control of nitrite in the upper ocean. Nat Commun 2019; 10:4618. [PMID: 31601794 PMCID: PMC6787228 DOI: 10.1038/s41467-019-12252-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Affiliation(s)
- Emily J Zakem
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA. .,Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089, USA.
| | - Alia Al-Haj
- Department of Earth and Environment, Boston University, Boston, MA, 02215, USA
| | - Matthew J Church
- Flathead Lake Biological Station, University of Montana, Polson, MT, 59860, USA
| | - Gert L van Dijken
- Department of Earth System Science, Stanford University, Stanford, CA, 94305, USA
| | - Stephanie Dutkiewicz
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Sarah Q Foster
- Department of Earth and Environment, Boston University, Boston, MA, 02215, USA
| | - Robinson W Fulweiler
- Department of Earth and Environment, Boston University, Boston, MA, 02215, USA.,Department of Biology, Boston University, Boston, MA, 02215, USA
| | - Matthew M Mills
- Department of Earth System Science, Stanford University, Stanford, CA, 94305, USA
| | - Michael J Follows
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
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19
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Wilson ST, Hawco NJ, Armbrust EV, Barone B, Björkman KM, Boysen AK, Burgos M, Burrell TJ, Casey JR, DeLong EF, Dugenne M, Dutkiewicz S, Dyhrman ST, Ferrón S, Follows MJ, Foreman RK, Funkey CP, Harke MJ, Henke BA, Hill CN, Hynes AM, Ingalls AE, Jahn O, Kelly RL, Knapp AN, Letelier RM, Ribalet F, Shimabukuro EM, Tabata RKS, Turk-Kubo KA, White AE, Zehr JP, John S, Karl DM. Kīlauea lava fuels phytoplankton bloom in the North Pacific Ocean. Science 2019; 365:1040-1044. [DOI: 10.1126/science.aax4767] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Accepted: 07/17/2019] [Indexed: 11/02/2022]
Affiliation(s)
- Samuel T. Wilson
- Department of Oceanography, Daniel K. Inouye Center for Microbial Oceanography: Research and Education (C-MORE), University of Hawai‘i at Manoa, Honolulu, HI 96822, USA
| | - Nicholas J. Hawco
- Department of Earth Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | | | - Benedetto Barone
- Department of Oceanography, Daniel K. Inouye Center for Microbial Oceanography: Research and Education (C-MORE), University of Hawai‘i at Manoa, Honolulu, HI 96822, USA
| | - Karin M. Björkman
- Department of Oceanography, Daniel K. Inouye Center for Microbial Oceanography: Research and Education (C-MORE), University of Hawai‘i at Manoa, Honolulu, HI 96822, USA
| | - Angela K. Boysen
- School of Oceanography, University of Washington, Seattle, WA 98195, USA
| | - Macarena Burgos
- Department of Oceanography, Daniel K. Inouye Center for Microbial Oceanography: Research and Education (C-MORE), University of Hawai‘i at Manoa, Honolulu, HI 96822, USA
| | - Timothy J. Burrell
- Department of Oceanography, Daniel K. Inouye Center for Microbial Oceanography: Research and Education (C-MORE), University of Hawai‘i at Manoa, Honolulu, HI 96822, USA
| | - John R. Casey
- Department of Oceanography, Daniel K. Inouye Center for Microbial Oceanography: Research and Education (C-MORE), University of Hawai‘i at Manoa, Honolulu, HI 96822, USA
- Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Edward F. DeLong
- Department of Oceanography, Daniel K. Inouye Center for Microbial Oceanography: Research and Education (C-MORE), University of Hawai‘i at Manoa, Honolulu, HI 96822, USA
| | - Mathilde Dugenne
- Department of Oceanography, Daniel K. Inouye Center for Microbial Oceanography: Research and Education (C-MORE), University of Hawai‘i at Manoa, Honolulu, HI 96822, USA
| | - Stephanie Dutkiewicz
- Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Sonya T. Dyhrman
- Department of Earth and Environmental Sciences, Columbia University, Palisades, NY 10964, USA
- Lamont-Doherty Earth Observatory, Columbia University, Palisades, NY 10964, USA
| | - Sara Ferrón
- Department of Oceanography, Daniel K. Inouye Center for Microbial Oceanography: Research and Education (C-MORE), University of Hawai‘i at Manoa, Honolulu, HI 96822, USA
| | - Michael J. Follows
- Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Rhea K. Foreman
- Department of Oceanography, Daniel K. Inouye Center for Microbial Oceanography: Research and Education (C-MORE), University of Hawai‘i at Manoa, Honolulu, HI 96822, USA
| | - Carolina P. Funkey
- Department of Oceanography, Daniel K. Inouye Center for Microbial Oceanography: Research and Education (C-MORE), University of Hawai‘i at Manoa, Honolulu, HI 96822, USA
| | - Matthew J. Harke
- Lamont-Doherty Earth Observatory, Columbia University, Palisades, NY 10964, USA
| | - Britt A. Henke
- Department of Ocean Sciences, University of California, Santa Cruz, CA 95064, USA
| | - Christopher N. Hill
- Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Annette M. Hynes
- School of Oceanography, University of Washington, Seattle, WA 98195, USA
| | - Anitra E. Ingalls
- School of Oceanography, University of Washington, Seattle, WA 98195, USA
| | - Oliver Jahn
- Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Rachel L. Kelly
- Department of Earth Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Angela N. Knapp
- Department of Earth, Ocean, and Atmospheric Science, Florida State University, Tallahassee, FL 32306, USA
| | - Ricardo M. Letelier
- College of Earth, Ocean, and Atmospheric Sciences, Oregon State University, Corvallis, OR 97331, USA
| | - Francois Ribalet
- School of Oceanography, University of Washington, Seattle, WA 98195, USA
| | - Eric M. Shimabukuro
- Department of Oceanography, Daniel K. Inouye Center for Microbial Oceanography: Research and Education (C-MORE), University of Hawai‘i at Manoa, Honolulu, HI 96822, USA
| | - Ryan K. S. Tabata
- Department of Oceanography, Daniel K. Inouye Center for Microbial Oceanography: Research and Education (C-MORE), University of Hawai‘i at Manoa, Honolulu, HI 96822, USA
| | - Kendra A. Turk-Kubo
- Department of Ocean Sciences, University of California, Santa Cruz, CA 95064, USA
| | - Angelicque E. White
- Department of Oceanography, Daniel K. Inouye Center for Microbial Oceanography: Research and Education (C-MORE), University of Hawai‘i at Manoa, Honolulu, HI 96822, USA
| | - Jonathan P. Zehr
- Department of Ocean Sciences, University of California, Santa Cruz, CA 95064, USA
| | - Seth John
- Department of Earth Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - David M. Karl
- Department of Oceanography, Daniel K. Inouye Center for Microbial Oceanography: Research and Education (C-MORE), University of Hawai‘i at Manoa, Honolulu, HI 96822, USA
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20
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Nissimov JI, Talmy D, Haramaty L, Fredricks HF, Zelzion E, Knowles B, Eren AM, Vandzura R, Laber CP, Schieler BM, Johns CT, More KD, Coolen MJL, Follows MJ, Bhattacharya D, Van Mooy BAS, Bidle KD. Biochemical diversity of glycosphingolipid biosynthesis as a driver of Coccolithovirus competitive ecology. Environ Microbiol 2019; 21:2182-2197. [PMID: 31001863 DOI: 10.1111/1462-2920.14633] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 04/15/2019] [Indexed: 11/29/2022]
Abstract
Coccolithoviruses (EhVs) are large, double-stranded DNA-containing viruses that infect the single-celled, marine coccolithophore Emiliania huxleyi. Given the cosmopolitan nature and global importance of E. huxleyi as a bloom-forming, calcifying, photoautotroph, E. huxleyi-EhV interactions play a key role in oceanic carbon biogeochemistry. Virally-encoded glycosphingolipids (vGSLs) are virulence factors that are produced by the activity of virus-encoded serine palmitoyltransferase (SPT). Here, we characterize the dynamics, diversity and catalytic production of vGSLs in an array of EhV strains in relation to their SPT sequence composition and explore the hypothesis that they are a determinant of infectivity and host demise. vGSL production and diversity was positively correlated with increased virulence, virus replication rate and lytic infection dynamics in laboratory experiments, but they do not explain the success of less-virulent EhVs in natural EhV communities. The majority of EhV-derived SPT amplicon sequences associated with infected cells in the North Atlantic derived from slower infecting, less virulent EhVs. Our lab-, field- and mathematical model-based data and simulations support ecological scenarios whereby slow-infecting, less-virulent EhVs successfully compete in North Atlantic populations of E. huxleyi, through either the preferential removal of fast-infecting, virulent EhVs during active infection or by having access to a broader host range.
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Affiliation(s)
- Jozef I Nissimov
- Department of Marine and Coastal Sciences, Rutgers University, New Brunswick, NJ, 08901, USA.,Scottish Association for Marine Science, Scottish Marine Institute, Oban, Argyll, PA37 1QA, Scotland, UK
| | - David Talmy
- Department of Microbiology, University of Tennessee-Knoxville, Knoxville, TN, 37996, USA
| | - Liti Haramaty
- Department of Marine and Coastal Sciences, Rutgers University, New Brunswick, NJ, 08901, USA
| | - Helen F Fredricks
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA, 02543, USA
| | - Ehud Zelzion
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ, 08901, USA
| | - Ben Knowles
- Department of Marine and Coastal Sciences, Rutgers University, New Brunswick, NJ, 08901, USA
| | - A Murat Eren
- Marine Biological Laboratory, Josephine Bay Paul Center, Woods Hole, Massachusetts, 02543, USA.,Department of Medicine, The University of Chicago, Chicago, IL, 60637, USA
| | - Rebecca Vandzura
- Department of Marine and Coastal Sciences, Rutgers University, New Brunswick, NJ, 08901, USA
| | - Christien P Laber
- Department of Marine and Coastal Sciences, Rutgers University, New Brunswick, NJ, 08901, USA
| | - Brittany M Schieler
- Department of Marine and Coastal Sciences, Rutgers University, New Brunswick, NJ, 08901, USA
| | - Christopher T Johns
- Department of Marine and Coastal Sciences, Rutgers University, New Brunswick, NJ, 08901, USA
| | - Kuldeep D More
- WA-Organic and Isotope Geochemistry Centre, School of Earth and Planetary Sciences, Curtin University, Bentley, WA, 6102, Australia
| | - Marco J L Coolen
- WA-Organic and Isotope Geochemistry Centre, School of Earth and Planetary Sciences, Curtin University, Bentley, WA, 6102, Australia
| | - Michael J Follows
- Department of Earth, Atmosphere and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Debashish Bhattacharya
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ, 08901, USA
| | - Benjamin A S Van Mooy
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA, 02543, USA
| | - Kay D Bidle
- Department of Marine and Coastal Sciences, Rutgers University, New Brunswick, NJ, 08901, USA
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21
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Talmy D, Beckett SJ, Taniguchi DAA, Brussaard CPD, Weitz JS, Follows MJ. An empirical model of carbon flow through marine viruses and microzooplankton grazers. Environ Microbiol 2019; 21:2171-2181. [PMID: 30969467 DOI: 10.1111/1462-2920.14626] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Revised: 04/03/2019] [Accepted: 04/08/2019] [Indexed: 12/13/2022]
Abstract
Viruses and microzooplankton grazers represent major sources of mortality for marine phytoplankton and bacteria, redirecting the flow of organic material throughout the world's oceans. Here, we investigate the use of nonlinear population models of interactions between phytoplankton, viruses and grazers as a means to quantitatively constrain the flow of carbon through marine microbial ecosystems. We augment population models with a synthesis of laboratory-based estimates of prey, predator and viral life history traits that constrain transfer efficiencies. We then apply the model framework to estimate loss rates in the California Current Ecosystem (CCE). With our empirically parameterized model, we estimate that, of the total losses mediated by viruses and microzooplankton grazing at the focal CCE site, 22 ± 3%, 46 ± 27%, 3 ± 2% and 29 ± 20% were directed to grazers, sloppy feeding (as well as excretion and respiration), viruses and viral lysate respectively. We identify opportunities to leverage ecosystem models and conventional mortality assays to further constrain the quantitative rates of critical ecosystem processes.
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Affiliation(s)
- David Talmy
- Department of Microbiology, University of Tennessee-Knoxville, Knoxville, TN, USA
| | - Stephen J Beckett
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Darcy A A Taniguchi
- Biology Department, California State University San Marcos, San Marcos, CA, USA
| | - Corina P D Brussaard
- Department of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute of Sea Research and University of Utrecht, Utrecht, the Netherlands
| | - Joshua S Weitz
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA.,School of Physics, Georgia Institute of Technology, Atlanta, GA, USA
| | - Michael J Follows
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
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22
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Liefer JD, Garg A, Fyfe MH, Irwin AJ, Benner I, Brown CM, Follows MJ, Omta AW, Finkel ZV. The Macromolecular Basis of Phytoplankton C:N:P Under Nitrogen Starvation. Front Microbiol 2019; 10:763. [PMID: 31057501 PMCID: PMC6479212 DOI: 10.3389/fmicb.2019.00763] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Accepted: 03/26/2019] [Indexed: 12/21/2022] Open
Abstract
Biogeochemical cycles in the ocean are strongly affected by the elemental stoichiometry (C:N:P) of phytoplankton, which largely reflects their macromolecular content. A greater understanding of how this macromolecular content varies among phytoplankton taxa and with resource limitation may strengthen physiological and biogeochemical modeling efforts. We determined the macromolecular basis (protein, carbohydrate, lipid, nucleic acids, pigments) of C:N:P in diatoms and prasinophytes, two globally important phytoplankton taxa, in response to N starvation. Despite their differing cell sizes and evolutionary histories, the relative decline in protein during N starvation was similar in all four species studied and largely determined variations in N content. The accumulation of carbohydrate and lipid dominated the increase in C content and C:N in all species during N starvation, but these processes differed greatly between diatoms and prasinophytes. Diatoms displayed far greater accumulation of carbohydrate with N starvation, possibly due to their greater cell size and storage capacity, resulting in larger increases in C content and C:N. In contrast, the prasinophytes had smaller increases in C and C:N that were largely driven by lipid accumulation. Variation in C:P and N:P was species-specific and mainly determined by residual P pools, which likely represent intracellular storage of inorganic P and accounted for the majority of cellular P in all species throughout N starvation. Our findings indicate that carbohydrate and lipid accumulation may play a key role in determining the environmental and taxonomic variability in phytoplankton C:N. This quantitative assessment of macromolecular and elemental content spanning several marine phytoplankton species can be used to develop physiological models for ecological and biogeochemical applications.
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Affiliation(s)
- Justin D. Liefer
- Department of Geography and Environment, Mount Allison University, Sackville, NB, Canada
| | - Aneri Garg
- Department of Geography and Environment, Mount Allison University, Sackville, NB, Canada
| | - Matthew H. Fyfe
- Department of Geography and Environment, Mount Allison University, Sackville, NB, Canada
| | - Andrew J. Irwin
- Department of Mathematics and Computer Science, Mount Allison University, Sackville, NB, Canada
| | - Ina Benner
- Department of Geography and Environment, Mount Allison University, Sackville, NB, Canada
| | - Christopher M. Brown
- Department of Geography and Environment, Mount Allison University, Sackville, NB, Canada
| | - Michael J. Follows
- Department of Earth, Atmospheric and Planetary Science, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Anne Willem Omta
- Department of Earth, Atmospheric and Planetary Science, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Zoe V. Finkel
- Department of Geography and Environment, Mount Allison University, Sackville, NB, Canada
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23
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Thamatrakoln K, Talmy D, Haramaty L, Maniscalco C, Latham JR, Knowles B, Natale F, Coolen MJL, Follows MJ, Bidle KD. Light regulation of coccolithophore host-virus interactions. New Phytol 2019; 221:1289-1302. [PMID: 30368816 DOI: 10.1111/nph.15459] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Accepted: 08/20/2018] [Indexed: 06/08/2023]
Abstract
Viruses that infect photoautotrophs have a fundamental relationship with light, given the need for host resources. We investigated the role of light on Coccolithovirus (EhV) infection of the globally distributed coccolithophore, Emiliania huxleyi. Light was required for EhV adsorption, and viral production was highest when host cultures were maintained in continuous light or at irradiance levels of 150-300 μmol m-2 s-1 . During the early stages of infection, photosynthetic electron transport remained high, while RuBisCO expression decreased concomitant with an induction of the pentose phosphate pathway, the primary source of de novo nucleotides. A mathematical model developed and fitted to the laboratory data supported the hypothesis that EhV replication was controlled by a trade-off between host nucleotide recycling and de novo synthesis, and that photoperiod and photon flux could toggle this switch. Laboratory results supported field observations that light was the most robust driver of EhV replication within E. huxleyi populations collected across a 2000 nautical mile transect in the North Atlantic. Collectively, these findings demonstrate that light can drive host-virus interactions through a mechanistic interplay between host metabolic processes, which serve to structure infection and phytoplankton mortality in the upper ocean.
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Affiliation(s)
- Kimberlee Thamatrakoln
- Department of Marine and Coastal Sciences, Rutgers, The State University of New Jersey, 71 Dudley Road, New Brunswick, NJ, 08901, USA
| | - David Talmy
- Department of Microbiology, The University of Tennessee, Ken and Blaire Mossman Bldg, 1311 Cumberland Ave #307, Knoxville, TN 37996, USA
| | - Liti Haramaty
- Department of Marine and Coastal Sciences, Rutgers, The State University of New Jersey, 71 Dudley Road, New Brunswick, NJ, 08901, USA
| | - Christopher Maniscalco
- Department of Marine and Coastal Sciences, Rutgers, The State University of New Jersey, 71 Dudley Road, New Brunswick, NJ, 08901, USA
| | - Jason R Latham
- Department of Marine and Coastal Sciences, Rutgers, The State University of New Jersey, 71 Dudley Road, New Brunswick, NJ, 08901, USA
| | - Ben Knowles
- Department of Marine and Coastal Sciences, Rutgers, The State University of New Jersey, 71 Dudley Road, New Brunswick, NJ, 08901, USA
| | - Frank Natale
- Department of Marine and Coastal Sciences, Rutgers, The State University of New Jersey, 71 Dudley Road, New Brunswick, NJ, 08901, USA
| | - Marco J L Coolen
- WA Organic and Isotope Geochemistry Centre, School of Earth and Planetary Sciences, Curtin University, Bentley, WA, 6102, Australia
| | - Michael J Follows
- Department of Earth, Atmosphere and Planetary Sciences, MIT, Cambridge, MA, 02139, USA
| | - Kay D Bidle
- Department of Marine and Coastal Sciences, Rutgers, The State University of New Jersey, 71 Dudley Road, New Brunswick, NJ, 08901, USA
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24
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Abstract
Nitrogen fixation provides bioavailable nitrogen, supporting global ecosystems and influencing global cycles of other elements. It provides an additional source of nitrogen to organisms at a cost of lower growth efficiency, largely due to respiratory control of intra-cellular oxygen. Nitrogen-fixing bacteria can, however, utilize both dinitrogen gas and fixed nitrogen, decreasing energetic costs. Here we present an idealized metabolic model of the heterotrophic nitrogen fixer Azotobacter vinelandii which, constrained by laboratory data, provides quantitative predictions for conditions under which the organism uses either ammonium or nitrogen fixation, or both, as a function of the relative supply rates of carbohydrate, fixed nitrogen as well as the ambient oxygen concentration. The model reveals that the organism respires carbohydrate in excess of energetic requirements even when nitrogen fixation is inhibited and respiratory protection is not essential. The use of multiple nitrogen source expands the potential niche and range for nitrogen fixation. The model provides a quantitative framework which can be employed in ecosystem and biogeochemistry models.
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Affiliation(s)
- Keisuke Inomura
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, United States of America
- * E-mail:
| | - Jason Bragg
- National Herbarium of New South Wales, The Royal Botanic Gardens and Domain Trust, Sydney, NSW, Australia
| | - Lasse Riemann
- Marine Biological Section, Department of Biology, University of Copenhagen, Helsingør, Denmark
| | - Michael J. Follows
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, United States of America
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25
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Zakem EJ, Al-Haj A, Church MJ, van Dijken GL, Dutkiewicz S, Foster SQ, Fulweiler RW, Mills MM, Follows MJ. Ecological control of nitrite in the upper ocean. Nat Commun 2018; 9:1206. [PMID: 29572474 PMCID: PMC5865239 DOI: 10.1038/s41467-018-03553-w] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Accepted: 02/22/2018] [Indexed: 11/15/2022] Open
Abstract
Microorganisms oxidize organic nitrogen to nitrate in a series of steps. Nitrite, an intermediate product, accumulates at the base of the sunlit layer in the subtropical ocean, forming a primary nitrite maximum, but can accumulate throughout the sunlit layer at higher latitudes. We model nitrifying chemoautotrophs in a marine ecosystem and demonstrate that microbial community interactions can explain the nitrite distributions. Our theoretical framework proposes that nitrite can accumulate to a higher concentration than ammonium because of differences in underlying redox chemistry and cell size between ammonia- and nitrite-oxidizing chemoautotrophs. Using ocean circulation models, we demonstrate that nitrifying microorganisms are excluded in the sunlit layer when phytoplankton are nitrogen-limited, but thrive at depth when phytoplankton become light-limited, resulting in nitrite accumulation there. However, nitrifying microorganisms may coexist in the sunlit layer when phytoplankton are iron- or light-limited (often in higher latitudes). These results improve understanding of the controls on nitrification, and provide a framework for representing chemoautotrophs and their biogeochemical effects in ocean models. Nitrite tends to peak at the base of the sunlit zone in the ocean, but the ecological drivers of the local and global distributions of nitrite are not known. Here, Zakem et al. use a marine ecosystem model to show how the interactions of nitrifying microbes mediate nitrite accumulation.
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Affiliation(s)
- Emily J Zakem
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA. .,Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089, USA.
| | - Alia Al-Haj
- Department of Earth and Environment, Boston University, Boston, MA, 02215, USA
| | - Matthew J Church
- Flathead Lake Biological Station, University of Montana, Polson, MT, 59860, USA
| | - Gert L van Dijken
- Department of Earth System Science, Stanford University, Stanford, CA, 94305, USA
| | - Stephanie Dutkiewicz
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Sarah Q Foster
- Department of Earth and Environment, Boston University, Boston, MA, 02215, USA
| | - Robinson W Fulweiler
- Department of Earth and Environment, Boston University, Boston, MA, 02215, USA.,Department of Biology, Boston University, Boston, MA, 02215, USA
| | - Matthew M Mills
- Department of Earth System Science, Stanford University, Stanford, CA, 94305, USA
| | - Michael J Follows
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
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26
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Cael BB, Carlson MCG, Follett CL, Follows MJ. Marine Virus-Like Particles and Microbes: A Linear Interpretation. Front Microbiol 2018; 9:358. [PMID: 29545784 PMCID: PMC5838382 DOI: 10.3389/fmicb.2018.00358] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Accepted: 02/15/2018] [Indexed: 11/13/2022] Open
Affiliation(s)
- B B Cael
- Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, United States.,Woods Hole Oceanographic Institution, Woods Hole, MA, United States
| | | | - Christopher L Follett
- Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Michael J Follows
- Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, United States
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27
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Follett CL, Dutkiewicz S, Karl DM, Inomura K, Follows MJ. Seasonal resource conditions favor a summertime increase in North Pacific diatom-diazotroph associations. ISME J 2018; 12:1543-1557. [PMID: 29449611 PMCID: PMC5955908 DOI: 10.1038/s41396-017-0012-x] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Revised: 10/07/2017] [Accepted: 10/24/2017] [Indexed: 12/04/2022]
Abstract
In the North Pacific Subtropical Gyre (NPSG), an annual pulse of sinking organic carbon is observed at 4000 m between July and August, driven by large diatoms found in association with nitrogen fixing, heterocystous, cyanobacteria: Diatom–Diazotroph Associations (DDAs). Here we ask what drives the bloom of DDAs and present a simplified trait-based model of subtropical phototroph populations driven by observed, monthly averaged, environmental characteristics. The ratio of resource supply rates favors nitrogen fixation year round. The relative fitness of DDA traits is most competitive in early summer when the mixed layer is shallow, solar irradiance is high, and phosphorus and iron are relatively abundant. Later in the season, as light intensity drops and phosphorus is depleted, the traits of small unicellular diazotrophs become more competitive. The competitive transition happens in August, at the time when the DDA export event occurs. This seasonal dynamic is maintained when embedded in a more complex, global-scale, ecological model, and provides predictions for the extent of the North Pacific DDA bloom. The model provides a parsimonious and testable hypothesis for the stimulation of DDA blooms.
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Affiliation(s)
- Christopher L Follett
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA.
| | - Stephanie Dutkiewicz
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - David M Karl
- Department of Oceanography, School of Ocean and Earth Science and Technology, University of Hawai'i at Mānoa, Honolulu, HI, USA.,Daniel K. Inouye Center for Microbial Oceanography: Research and Education, University of Hawai'i at Mānoa, Honolulu, HI, USA
| | - Keisuke Inomura
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Michael J Follows
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
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28
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Abstract
Mesozoic and Early Cenozoic marine animals across multiple phyla record secular trends in morphology, environmental distribution, and inferred behaviour that are parsimoniously explained in terms of increased selection pressure from durophagous predators. Another systemic change in Mesozoic marine ecosystems, less widely appreciated than the first, may help to explain the observed animal record. Fossils, biomarker molecules, and molecular clocks indicate a major shift in phytoplankton composition, as mixotrophic dinoflagellates, coccolithophorids and, later, diatoms radiated across shelves. Models originally developed to probe the ecology and biogeography of modern phytoplankton enable us to evaluate the ecosystem consequences of these phytoplankton radiations. In particular, our models suggest that the radiation of mixotrophic dinoflagellates and the subsequent diversification of marine diatoms would have accelerated the transfer of primary production upward into larger size classes and higher trophic levels. Thus, phytoplankton evolution provides a mechanism capable of facilitating the observed evolutionary shift in Mesozoic marine animals.
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Affiliation(s)
- Andrew H Knoll
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Michael J Follows
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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29
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Abstract
Metabolism mediates the flow of matter and energy through the biosphere. We examined how metabolic evolution shapes ecosystems by reconstructing it in the globally abundant oceanic phytoplankter Prochlorococcus To understand what drove observed evolutionary patterns, we interpreted them in the context of its population dynamics, growth rate, and light adaptation, and the size and macromolecular and elemental composition of cells. This multilevel view suggests that, over the course of evolution, there was a steady increase in Prochlorococcus' metabolic rate and excretion of organic carbon. We derived a mathematical framework that suggests these adaptations lower the minimal subsistence nutrient concentration of cells, which results in a drawdown of nutrients in oceanic surface waters. This, in turn, increases total ecosystem biomass and promotes the coevolution of all cells in the ecosystem. Additional reconstructions suggest that Prochlorococcus and the dominant cooccurring heterotrophic bacterium SAR11 form a coevolved mutualism that maximizes their collective metabolic rate by recycling organic carbon through complementary excretion and uptake pathways. Moreover, the metabolic codependencies of Prochlorococcus and SAR11 are highly similar to those of chloroplasts and mitochondria within plant cells. These observations lead us to propose a general theory relating metabolic evolution to the self-amplification and self-organization of the biosphere. We discuss the implications of this framework for the evolution of Earth's biogeochemical cycles and the rise of atmospheric oxygen.
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Affiliation(s)
- Rogier Braakman
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139;
- Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Michael J Follows
- Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Sallie W Chisholm
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139;
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139
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30
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Soccodato A, d'Ovidio F, Lévy M, Jahn O, Follows MJ, De Monte S. Estimating planktonic diversity through spatial dominance patterns in a model ocean. Mar Genomics 2016; 29:9-17. [PMID: 27210279 DOI: 10.1016/j.margen.2016.04.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Revised: 03/07/2016] [Accepted: 04/28/2016] [Indexed: 10/21/2022]
Abstract
In the open ocean, the observation and quantification of biodiversity patterns is challenging. Marine ecosystems are indeed largely composed by microbial planktonic communities whose niches are affected by highly dynamical physico-chemical conditions, and whose observation requires advanced methods for morphological and molecular classification. Optical remote sensing offers an appealing complement to these in-situ techniques. Global-scale coverage at high spatiotemporal resolution is however achieved at the cost of restrained information on the local assemblage. Here, we use a coupled physical and ecological model ocean simulation to explore one possible metrics for comparing measures performed on such different scales. We show that a large part of the local diversity of the virtual plankton ecosystem - corresponding to what accessible by genomic methods - can be inferred from crude, but spatially extended, information - as conveyed by remote sensing. Shannon diversity of the local community is indeed highly correlated to a 'seascape' index, which quantifies the surrounding spatial heterogeneity of the most abundant functional group. The error implied in drastically reducing the resolution of the plankton community is shown to be smaller in frontal regions as well as in regions of intermediate turbulent energy. On the spatial scale of hundreds of kms, patterns of virtual plankton diversity are thus largely sustained by mixing communities that occupy adjacent niches. We provide a proof of principle that in the open ocean information on spatial variability of communities can compensate for limited local knowledge, suggesting the possibility of integrating in-situ and satellite observations to monitor biodiversity distribution at the global scale.
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Affiliation(s)
- Alice Soccodato
- Sorbonne Université (UPMC, Paris 6)/CNRS/UPMC/IRD/MNHN, LOCEAN-IPSL, Paris, France
| | - Francesco d'Ovidio
- Sorbonne Université (UPMC, Paris 6)/CNRS/UPMC/IRD/MNHN, LOCEAN-IPSL, Paris, France
| | - Marina Lévy
- Sorbonne Université (UPMC, Paris 6)/CNRS/UPMC/IRD/MNHN, LOCEAN-IPSL, Paris, France
| | - Oliver Jahn
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, USA
| | - Michael J Follows
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, USA
| | - Silvia De Monte
- Ecole Normale Supérieure, PSL Research University, CNRS, Inserm, Institut de Biologie de l'Ecole Normale Supérieure (IBENS), F-75005 Paris, France
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31
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Lévy M, Jahn O, Dutkiewicz S, Follows MJ, d'Ovidio F. The dynamical landscape of marine phytoplankton diversity. J R Soc Interface 2015; 12:20150481. [PMID: 26400196 PMCID: PMC4614488 DOI: 10.1098/rsif.2015.0481] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Accepted: 08/28/2015] [Indexed: 11/12/2022] Open
Abstract
Observations suggest that the landscape of marine phytoplankton assemblage might be strongly heterogeneous at the dynamical mesoscale and submesoscale (10-100 km, days to months), with potential consequences in terms of global diversity and carbon export. But these variations are not well documented as synoptic taxonomic data are difficult to acquire. Here, we examine how phytoplankton assemblage and diversity vary between mesoscale eddies and submesoscale fronts. We use a multi-phytoplankton numerical model embedded in a mesoscale flow representative of the North Atlantic. Our model results suggest that the mesoscale flow dynamically distorts the niches predefined by environmental contrasts at the basin scale and that the phytoplankton diversity landscape varies over temporal and spatial scales that are one order of magnitude smaller than those of the basin-scale environmental conditions. We find that any assemblage and any level of diversity can occur in eddies and fronts. However, on a statistical level, the results suggest a tendency for larger diversity and more fast-growing types at fronts, where nutrient supplies are larger and where populations of adjacent water masses are constantly brought into contact; and lower diversity in the core of eddies, where water masses are kept isolated long enough to enable competitive exclusion.
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Affiliation(s)
- Marina Lévy
- Sorbonne Université (UPMC, Paris 6)/CNRS/IRD/MNHN, Laboratoire d'Océanographie et du Climat (LOCEAN), Institut Pierre Simon Laplace (IPSL), 75252 Paris Cedex 05, France
| | - Oliver Jahn
- Department of Earth, Atmospheric and Planetary Sciences (DEAPS), Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
| | - Stephanie Dutkiewicz
- Department of Earth, Atmospheric and Planetary Sciences (DEAPS), Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
| | - Michael J Follows
- Department of Earth, Atmospheric and Planetary Sciences (DEAPS), Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
| | - Francesco d'Ovidio
- Sorbonne Université (UPMC, Paris 6)/CNRS/IRD/MNHN, Laboratoire d'Océanographie et du Climat (LOCEAN), Institut Pierre Simon Laplace (IPSL), 75252 Paris Cedex 05, France
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32
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Weitz JS, Stock CA, Wilhelm SW, Bourouiba L, Coleman ML, Buchan A, Follows MJ, Fuhrman JA, Jover LF, Lennon JT, Middelboe M, Sonderegger DL, Suttle CA, Taylor BP, Frede Thingstad T, Wilson WH, Eric Wommack K. A multitrophic model to quantify the effects of marine viruses on microbial food webs and ecosystem processes. ISME J 2015; 9:1352-64. [PMID: 25635642 PMCID: PMC4438322 DOI: 10.1038/ismej.2014.220] [Citation(s) in RCA: 131] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2014] [Revised: 10/15/2014] [Accepted: 10/17/2014] [Indexed: 11/08/2022]
Abstract
Viral lysis of microbial hosts releases organic matter that can then be assimilated by nontargeted microorganisms. Quantitative estimates of virus-mediated recycling of carbon in marine waters, first established in the late 1990s, were originally extrapolated from marine host and virus densities, host carbon content and inferred viral lysis rates. Yet, these estimates did not explicitly incorporate the cascade of complex feedbacks associated with virus-mediated lysis. To evaluate the role of viruses in shaping community structure and ecosystem functioning, we extend dynamic multitrophic ecosystem models to include a virus component, specifically parameterized for processes taking place in the ocean euphotic zone. Crucially, we are able to solve this model analytically, facilitating evaluation of model behavior under many alternative parameterizations. Analyses reveal that the addition of a virus component promotes the emergence of complex communities. In addition, biomass partitioning of the emergent multitrophic community is consistent with well-established empirical norms in the surface oceans. At steady state, ecosystem fluxes can be probed to characterize the effects that viruses have when compared with putative marine surface ecosystems without viruses. The model suggests that ecosystems with viruses will have (1) increased organic matter recycling, (2) reduced transfer to higher trophic levels and (3) increased net primary productivity. These model findings support hypotheses that viruses can have significant stimulatory effects across whole-ecosystem scales. We suggest that existing efforts to predict carbon and nutrient cycling without considering virus effects are likely to miss essential features of marine food webs that regulate global biogeochemical cycles.
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Affiliation(s)
- Joshua S Weitz
- School of Biology, Georgia Institute of Technology, Atlanta, GA, USA
- School of Physics, Georgia Institute of Technology, Atlanta, GA, USA
| | - Charles A Stock
- Geophysical Fluid Dynamics Laboratory, NOAA, Princeton, NJ, USA
| | - Steven W Wilhelm
- Department of Microbiology, University of Tennessee, Knoxville, TN, USA
| | - Lydia Bourouiba
- Department of Applied Mathematics, Massachusetts Institute of Technology, Cambridge, MA, USA
| | | | - Alison Buchan
- Department of Microbiology, University of Tennessee, Knoxville, TN, USA
| | - Michael J Follows
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Jed A Fuhrman
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - Luis F Jover
- School of Physics, Georgia Institute of Technology, Atlanta, GA, USA
| | - Jay T Lennon
- Department of Biology, Indiana University, Bloomington, IN, USA
| | - Mathias Middelboe
- Marine Biological Section, University of Copenhagen, Copenhagen, Denmark
| | | | - Curtis A Suttle
- Department of Earth and Ocean Sciences, Department of Botany, and Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Bradford P Taylor
- School of Physics, Georgia Institute of Technology, Atlanta, GA, USA
| | | | | | - K Eric Wommack
- Delaware Biotechnology Institute, University of Delaware, Newark, DE, USA
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33
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Sauterey B, Ward BA, Follows MJ, Bowler C, Claessen D. When everything is not everywhere but species evolve: an alternative method to model adaptive properties of marine ecosystems. J Plankton Res 2015; 37:28-47. [PMID: 25852217 PMCID: PMC4378374 DOI: 10.1093/plankt/fbu078] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/25/2013] [Accepted: 08/12/2014] [Indexed: 05/11/2023]
Abstract
The functional and taxonomic biogeography of marine microbial systems reflects the current state of an evolving system. Current models of marine microbial systems and biogeochemical cycles do not reflect this fundamental organizing principle. Here, we investigate the evolutionary adaptive potential of marine microbial systems under environmental change and introduce explicit Darwinian adaptation into an ocean modelling framework, simulating evolving phytoplankton communities in space and time. To this end, we adopt tools from adaptive dynamics theory, evaluating the fitness of invading mutants over annual timescales, replacing the resident if a fitter mutant arises. Using the evolutionary framework, we examine how community assembly, specifically the emergence of phytoplankton cell size diversity, reflects the combined effects of bottom-up and top-down controls. When compared with a species-selection approach, based on the paradigm that "Everything is everywhere, but the environment selects", we show that (i) the selected optimal trait values are similar; (ii) the patterns emerging from the adaptive model are more robust, but (iii) the two methods lead to different predictions in terms of emergent diversity. We demonstrate that explicitly evolutionary approaches to modelling marine microbial populations and functionality are feasible and practical in time-varying, space-resolving settings and provide a new tool for exploring evolutionary interactions on a range of timescales in the ocean.
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Affiliation(s)
- Boris Sauterey
- Environmental and Evolutionary Genomics Section, Institut De Biologie De L'Ecole Normale Supérieure (IBENS), CNRS UMR 8197, INSERM U1024, Ecole Normale Supérieure, 46 RUE D'ULM, 75005 Paris, France
- Environmental Research and Teaching Institute (CERES-ERTI), Ecole Normale Supérieure, 24 RUE Lhomond, 75005 Paris, France
| | - Ben A. Ward
- Environmental and Evolutionary Genomics Section, Institut De Biologie De L'Ecole Normale Supérieure (IBENS), CNRS UMR 8197, INSERM U1024, Ecole Normale Supérieure, 46 RUE D'ULM, 75005 Paris, France
- Laboratoire Des Sciences De L'Environnement Marin, Institut Universitaire Européen De La Mer, Place Nicolas Copernic, Plouzané, France
| | - Michael J. Follows
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Chris Bowler
- Environmental and Evolutionary Genomics Section, Institut De Biologie De L'Ecole Normale Supérieure (IBENS), CNRS UMR 8197, INSERM U1024, Ecole Normale Supérieure, 46 RUE D'ULM, 75005 Paris, France
| | - David Claessen
- Environmental and Evolutionary Genomics Section, Institut De Biologie De L'Ecole Normale Supérieure (IBENS), CNRS UMR 8197, INSERM U1024, Ecole Normale Supérieure, 46 RUE D'ULM, 75005 Paris, France
- Environmental Research and Teaching Institute (CERES-ERTI), Ecole Normale Supérieure, 24 RUE Lhomond, 75005 Paris, France
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Lévy M, Jahn O, Dutkiewicz S, Follows MJ. Phytoplankton diversity and community structure affected by oceanic dispersal and mesoscale turbulence. ACTA ACUST UNITED AC 2014. [DOI: 10.1215/21573689-2768549] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Kashtan N, Roggensack SE, Rodrigue S, Thompson JW, Biller SJ, Coe A, Ding H, Marttinen P, Malmstrom RR, Stocker R, Follows MJ, Stepanauskas R, Chisholm SW. Single-cell genomics reveals hundreds of coexisting subpopulations in wild Prochlorococcus. Science 2014; 344:416-20. [PMID: 24763590 DOI: 10.1126/science.1248575] [Citation(s) in RCA: 304] [Impact Index Per Article: 30.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Extensive genomic diversity within coexisting members of a microbial species has been revealed through selected cultured isolates and metagenomic assemblies. Yet, the cell-by-cell genomic composition of wild uncultured populations of co-occurring cells is largely unknown. In this work, we applied large-scale single-cell genomics to study populations of the globally abundant marine cyanobacterium Prochlorococcus. We show that they are composed of hundreds of subpopulations with distinct "genomic backbones," each backbone consisting of a different set of core gene alleles linked to a small distinctive set of flexible genes. These subpopulations are estimated to have diverged at least a few million years ago, suggesting ancient, stable niche partitioning. Such a large set of coexisting subpopulations may be a general feature of free-living bacterial species with huge populations in highly mixed habitats.
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Affiliation(s)
- Nadav Kashtan
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology (MIT), 77 Massachusetts Avenue, Cambridge, MA 02139, USA
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Abstract
A major theme driving research in biology is the relationship between form and function. In particular, a longstanding goal has been to understand how the evolution of multicellularity conferred fitness advantages. Here we show that biofilms of the bacterium Pseudomonas aeruginosa produce structures that maximize cellular reproduction. Specifically, we develop a mathematical model of resource availability and metabolic response within colony features. This analysis accurately predicts the measured distribution of two types of electron acceptors: oxygen, which is available from the atmosphere, and phenazines, redox-active antibiotics produced by the bacterium. Using this model, we demonstrate that the geometry of colony structures is optimal with respect to growth efficiency. Because our model is based on resource dynamics, we also can anticipate shifts in feature geometry based on changes to the availability of electron acceptors, including variations in the external availability of oxygen and genetic manipulation that renders the cells incapable of phenazine production.
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Affiliation(s)
- Christopher P. Kempes
- Exobiology Branch, National Aeronautics and Space Administration Ames Research Center, Moffett Field, CA 94035
- Control and Dynamical Systems, California Institute of Technology, Pasadena, CA 91125
- SETI Institute, Mountain View, CA 94034
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139; and
| | - Chinweike Okegbe
- Department of Biological Sciences, Columbia University, New York, NY 10027
| | | | - Michael J. Follows
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139; and
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Goebel NL, Edwards CA, Follows MJ, Zehr JP. Modeled diversity effects on microbial ecosystem functions of primary production, nutrient uptake, and remineralization. Ecology 2014; 95:153-63. [DOI: 10.1890/13-0421.1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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Abstract
Mixotrophic organisms combine autotrophic and heterotrophic nutrition and are abundant in both freshwater and marine environments. Recent observations indicate that mixotrophs constitute a large fraction of the biomass, bacterivory, and primary production in oligotrophic environments. While mixotrophy allows greater flexibility in terms of resource acquisition, any advantage must be traded off against an associated increase in metabolic costs, which appear to make mixotrophs uncompetitive relative to obligate autotrophs and heterotrophs. Using an idealized model of cell physiology and community competition, we identify one mechanism by which mixotrophs can effectively outcompete specialists for nutrient elements. At low resource concentrations, when the uptake of nutrients is limited by diffusion toward the cell, the investment in cell membrane transporters can be minimized. In this situation, mixotrophs can acquire limiting elements in both organic and inorganic forms, outcompeting their specialist competitors that can utilize only one of these forms. This advantage can be enough to offset as much as a twofold increase in additional metabolic costs incurred by mixotrophs. This mechanism is particularly relevant for the maintenance of mixotrophic populations and productivity in the highly oligotrophic subtropical oceans.
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Affiliation(s)
- Ben A Ward
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.
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Abstract
Biogeochemical cycles in the ocean are mediated by complex and diverse microbial communities. Over the past decade, marine ecosystem and biogeochemistry models have begun to address some of this diversity by resolving several groups of (mostly autotrophic) plankton, differentiated by biogeochemical function. Here, we review recent model approaches that are rooted in the notion that an even richer diversity is fundamental to the organization of marine microbial communities. These models begin to resolve, and address the significance of, diversity within functional groups. Seeded with diverse populations spanning prescribed regions of trait space, these simulations self-select community structure according to relative fitness in the virtual environment. Such models are suited to considering ecological questions, such as the regulation of patterns of biodiversity, and to simulating the response to changing environments. A key issue for all such models is the constraint of viable trait space and trade-offs. Size-structuring and mechanistic descriptions of energy and resource allocation at the individual level can rationalize these constraints.
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Affiliation(s)
- Michael J Follows
- Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.
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Abstract
Huisman argues that environments of intermediate variability promote coexistence of model phytoplankton, apparently contrasting our hypothesis that stability allows for greater diversity of equivalent competitors in the ocean. We argue that our original interpretations of the mechanisms governing model diversity patterns remain valid and that Huisman’s results are complementary to our hypotheses.
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Affiliation(s)
- Andrew D. Barton
- Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Stephanie Dutkiewicz
- Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Glenn Flierl
- Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Jason Bragg
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Michael J. Follows
- Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
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Abstract
Spatial diversity gradients are a pervasive feature of life on Earth. We examined a global ocean circulation, biogeochemistry, and ecosystem model that indicated a decrease in phytoplankton diversity with increasing latitude, consistent with observations of many marine and terrestrial taxa. In the modeled subpolar oceans, seasonal variability of the environment led to competitive exclusion of phytoplankton with slower growth rates and lower diversity. The relatively weak seasonality of the stable subtropical and tropical oceans in the global model enabled long exclusion time scales and prolonged coexistence of multiple phytoplankton with comparable fitness. Superimposed on the decline in diversity seen from equator to pole were "hot spots" of enhanced diversity in some regions of energetic ocean circulation, which reflected lateral dispersal.
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Affiliation(s)
- Andrew D Barton
- Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA.
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Abstract
A marine ecosystem model seeded with many phytoplankton types, whose physiological traits were randomly assigned from ranges defined by field and laboratory data, generated an emergent community structure and biogeography consistent with observed global phytoplankton distributions. The modeled organisms included types analogous to the marine cyanobacterium Prochlorococcus. Their emergent global distributions and physiological properties simultaneously correspond to observations. This flexible representation of community structure can be used to explore relations between ecosystems, biogeochemical cycles, and climate change.
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Affiliation(s)
- Michael J Follows
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, 54-1514 MIT, Cambridge, MA 02139, USA.
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