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Filatov DA, Kirkpatrick M. How does evolution work in superabundant microbes? Trends Microbiol 2024:S0966-842X(24)00024-6. [PMID: 38360431 DOI: 10.1016/j.tim.2024.01.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 01/24/2024] [Accepted: 01/26/2024] [Indexed: 02/17/2024]
Abstract
Marine phytoplankton play crucial roles in the Earth's ecological, chemical, and geological processes. They are responsible for about half of global primary production and drive the ocean biological carbon pump. Understanding how plankton species may adapt to the Earth's rapidly changing environments is evidently an urgent priority. This problem requires evolutionary genetic approaches as evolution occurs at the level of allele frequency change within populations driven by genetic drift and natural selection (microevolution). Plankters such as the coccolithophore Gephyrocapsa huxleyi and the cyanobacterium Prochlorococcus 'marinus' are among Earth's most abundant organisms. In this opinion paper we discuss how evolution in astronomically large populations of superabundant microbes (SAMs) may act fundamentally differently than it does in the populations of more modest size found in well-studied organisms. This offers exciting opportunities to study evolution in the conditions that have yet to be explored and also leads to unique challenges. Exploring these opportunities and challenges is the goal of this article.
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Affiliation(s)
- Dmitry A Filatov
- Department of Biology, University of Oxford, Oxford, OX1 3RB, UK.
| | - Mark Kirkpatrick
- Department of Integrative Biology, University of Texas, Austin, TX 78712, USA
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2
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Weisberg SJ, Pershing AJ, Grigoratou M, Mills KE, Fenwick IF, Frisk MG, McBride R, Lucey SM, Kemberling A, Beltz B, Nye JA. Merging trait-based ecology and regime shift theory to anticipate community responses to warming. GLOBAL CHANGE BIOLOGY 2024; 30:e17065. [PMID: 38273564 DOI: 10.1111/gcb.17065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 10/10/2023] [Accepted: 10/31/2023] [Indexed: 01/27/2024]
Abstract
Anthropogenic warming is altering species abundance, distribution, physiology, and more. How changes observed at the species level alter emergent community properties is an active and urgent area of research. Trait-based ecology and regime shift theory provide complementary ways to understand climate change impacts on communities, but these two bodies of work are only rarely integrated. Lack of integration handicaps our ability to understand community responses to warming, at a time when such understanding is critical. Therefore, we advocate for merging trait-based ecology with regime shift theory. We propose a general set of principles to guide this merger and apply these principles to research on marine communities in the rapidly warming North Atlantic. In our example, combining trait distribution and regime shift analyses at the community level yields greater insight than either alone. Looking forward, we identify a clear need for expanding quantitative approaches to collecting and merging trait-based and resilience metrics in order to advance our understanding of climate-driven community change.
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Affiliation(s)
- Sarah J Weisberg
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, New York, USA
| | | | - Maria Grigoratou
- Mercator Ocean International, Toulouse, France
- Gulf of Maine Research Institute, Portland, Maine, USA
| | | | - Ileana F Fenwick
- Department of Earth, Marine and Environmental Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Michael G Frisk
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, New York, USA
| | - Richard McBride
- National Oceanic and Atmospheric Administration, Northeast Fisheries Science Center, Woods Hole, Massachusetts, USA
| | - Sean M Lucey
- National Oceanic and Atmospheric Administration, Northeast Fisheries Science Center, Woods Hole, Massachusetts, USA
| | | | - Brandon Beltz
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, New York, USA
| | - Janet A Nye
- Department of Earth, Marine and Environmental Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
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3
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Pohl A, Stockey RG, Dai X, Yohler R, Le Hir G, Hülse D, Brayard A, Finnegan S, Ridgwell A. Why the Early Paleozoic was intrinsically prone to marine extinction. SCIENCE ADVANCES 2023; 9:eadg7679. [PMID: 37647393 PMCID: PMC10468122 DOI: 10.1126/sciadv.adg7679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 05/26/2023] [Accepted: 07/27/2023] [Indexed: 09/01/2023]
Abstract
The geological record of marine animal biodiversity reflects the interplay between changing rates of speciation versus extinction. Compared to mass extinctions, background extinctions have received little attention. To disentangle the different contributions of global climate state, continental configuration, and atmospheric oxygen concentration (pO2) to variations in background extinction rates, we drive an animal physiological model with the environmental outputs from an Earth system model across intervals spanning the past 541 million years. We find that climate and continental configuration combined to make extinction susceptibility an order of magnitude higher during the Early Paleozoic than during the rest of the Phanerozoic, consistent with extinction rates derived from paleontological databases. The high extinction susceptibility arises in the model from the limited geographical range of marine organisms. It stands even when assuming present-day pO2, suggesting that increasing oxygenation through the Paleozoic is not necessary to explain why extinction rates apparently declined with time.
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Affiliation(s)
- Alexandre Pohl
- Biogéosciences, UMR 6282 CNRS, Université de Bourgogne, 6 Boulevard Gabriel, 21000 Dijon, France
| | - Richard G. Stockey
- School of Ocean and Earth Science, National Oceanography Centre Southampton, University of Southampton, Southampton, UK
| | - Xu Dai
- Biogéosciences, UMR 6282 CNRS, Université de Bourgogne, 6 Boulevard Gabriel, 21000 Dijon, France
| | - Ryan Yohler
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Guillaume Le Hir
- Université de Paris, Institut de Physique du Globe de Paris, CNRS, 1 rue Jussieu, 75005 Paris, France
| | - Dominik Hülse
- Max-Planck-Institute for Meteorology, Hamburg, Germany
- Department of Earth and Planetary Sciences, University of California, Riverside, CA, USA
| | - Arnaud Brayard
- Biogéosciences, UMR 6282 CNRS, Université de Bourgogne, 6 Boulevard Gabriel, 21000 Dijon, France
| | - Seth Finnegan
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Andy Ridgwell
- Department of Earth and Planetary Sciences, University of California, Riverside, CA, USA
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4
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Cherabier P, Ferrière R. Eco-evolutionary responses of the microbial loop to surface ocean warming and consequences for primary production. THE ISME JOURNAL 2022; 16:1130-1139. [PMID: 34864820 PMCID: PMC8940968 DOI: 10.1038/s41396-021-01166-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 11/19/2021] [Accepted: 11/26/2021] [Indexed: 11/09/2022]
Abstract
Predicting the response of ocean primary production to climate warming is a major challenge. One key control of primary production is the microbial loop driven by heterotrophic bacteria, yet how warming alters the microbial loop and its function is poorly understood. Here we develop an eco-evolutionary model to predict the physiological response and adaptation through selection of bacterial populations in the microbial loop and how this will impact ecosystem function such as primary production. We find that the ecophysiological response of primary production to warming is driven by a decrease in regenerated production which depends on nutrient availability. In nutrient-poor environments, the loss of regenerated production to warming is due to decreasing microbial loop activity. However, this ecophysiological response can be opposed or even reversed by bacterial adaptation through selection, especially in cold environments: heterotrophic bacteria with lower bacterial growth efficiency are selected, which strengthens the "link" behavior of the microbial loop, increasing both new and regenerated production. In cold and rich environments such as the Arctic Ocean, the effect of bacterial adaptation on primary production exceeds the ecophysiological response. Accounting for bacterial adaptation through selection is thus critically needed to improve models and projections of the ocean primary production in a warming world.
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Affiliation(s)
- Philippe Cherabier
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Université Paris Sciences et Lettres, CNRS, INSERM, Paris, 75005, France.
| | - Régis Ferrière
- grid.462036.5Institut de Biologie de l’Ecole Normale Supérieure (IBENS), Université Paris Sciences et Lettres, CNRS, INSERM, Paris, 75005 France ,grid.134563.60000 0001 2168 186XDepartment of Ecology & Evolutionary Biology, University of Arizona, Tucson, AZ 85721 USA ,grid.134563.60000 0001 2168 186XInternational Research Laboratory for Interdisciplinary Global Environmental Studies (iGLOBES), CNRS, ENS-PSL University, University of Arizona, Tucson, AZ 85721 USA
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5
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Sauterey B, Ward BA. Environmental control of marine phytoplankton stoichiometry in the North Atlantic Ocean. Proc Natl Acad Sci U S A 2022; 119:e2114602118. [PMID: 34949718 PMCID: PMC8740720 DOI: 10.1073/pnas.2114602118] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/17/2021] [Indexed: 01/14/2023] Open
Abstract
The stoichiometric coupling of carbon to limiting nutrients in marine phytoplankton regulates the magnitude of biological carbon sequestration in the ocean. While clear links between plankton C:N ratios and environmental drivers have been identified, the nature and direction of these links, as well as their underlying physiological and ecological controls, remain uncertain. We show, with a well-constrained mechanistic model of plankton ecophysiology, that while nitrogen availability and temperature emerge as the main drivers of phytoplankton C:N stoichiometry in the North Atlantic, the biological mechanisms involved vary depending on the spatiotemporal scale and region considered. We find that phytoplankton C:N stoichiometry is overall controlled by nitrogen availability below 40° N, predominantly driven by ecoevolutionary shifts in the functional composition of the phytoplankton communities, while phytoplankton stoichiometric plasticity in response to dropping temperatures and increased grazing pressure dominates at higher latitudes. Our findings highlight the potential of "organisms-to-ecosystems" modeling approaches based on mechanistic models of plankton biology accounting for physiology, ecology, and trait evolution to explore and explain complex observational data and ultimately improve the predictions of global ocean models.
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Affiliation(s)
- Boris Sauterey
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721;
- Institut de Biologie de l'École Normale Supérieure, CNRS, INSERM, Université Paris Sciences et Lettres, 75005 Paris, France
| | - Ben A Ward
- Ocean and Earth Science, University of Southampton, SO14 3ZH Southampton, United Kingdom
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6
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Cropp R, Norbury J. The eco-evolutionary modelling of populations and their traits using a measure of trait differentiation. J Theor Biol 2021; 531:110893. [PMID: 34481861 DOI: 10.1016/j.jtbi.2021.110893] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 08/27/2021] [Accepted: 08/30/2021] [Indexed: 11/29/2022]
Abstract
We develop new equations for the eco-evolutionary dynamics of populations and their traits. These equations resolve the change in the phenotypic differentiation within a population, which better estimates how the variance of the trait distribution changes. We note that traits may be bounded, assume they may be described by beta distributions with small variances, and develop a coupled ordinary differential equation system to describe the dynamics of the total population, the mean trait value, and a measure of phenotype differentiation. The variance of the trait in the population is calculated from its mean and the population's phenotype differentiation. We consider an example of two competing plant populations to demonstrate the efficacy of the new approach. Each population may trade-off its growth rate against its susceptibility to direct competition from the other population. We create two models of this system: a population model based on our new eco-evolutionary equations; and a phenotype model, in which the growth or demise of each fraction of each population with a defined phenotype is simulated as it interacts with a shared limiting resource and its competing phenotypes and populations. Comparison of four simulation scenarios reveals excellent agreement between the predicted quantities from both models: total populations, the average trait values, the trait variances, and the degree of phenotypic differentiation within each population. In each of the four scenarios simulated, three of which are initially subject to competitive exclusion in the absence of evolution, the populations adapt to coexist. One population maximises growth and dominates, while the other minimises competitive losses. These simulations suggest that our new eco-evolutionary equations may provide an excellent approximation to phenotype changes in populations.
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Affiliation(s)
- Roger Cropp
- School of Environment and Science, Griffith University, Gold Coast, Qld 4215, Australia; Centre for Applications in Natural Resource Mathematics, School of Mathematics and Physics, The University of Queensland, St Lucia, Qld 4072, Australia.
| | - John Norbury
- Mathematical Institute, University of Oxford, Andrew Wiles Building, ROQ, Woodstock Road, Oxford OX2 6GG, UK
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7
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Scucchia F, Malik A, Putnam HM, Mass T. Genetic and physiological traits conferring tolerance to ocean acidification in mesophotic corals. GLOBAL CHANGE BIOLOGY 2021; 27:5276-5294. [PMID: 34310005 DOI: 10.1111/gcb.15812] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Revised: 07/15/2021] [Accepted: 07/20/2021] [Indexed: 06/13/2023]
Abstract
The integrity of coral reefs worldwide is jeopardized by ocean acidification (OA). Most studies conducted so far have focused on the vulnerability to OA of corals inhabiting shallow reefs while nothing is currently known about the response of mesophotic scleractinian corals. In this study, we assessed the susceptibility to OA of corals, together with their algal partners, inhabiting a wide depth range. We exposed fragments of the depth generalist coral Stylophora pistillata collected from either 5 or 45 m to simulated future OA conditions, and assessed key molecular, physiological and photosynthetic processes influenced by the lowered pH. Our comparative analysis reveals that mesophotic and shallow S. pistillata corals are genetically distinct and possess different symbiont types. Under the exposure to acidification conditions, we observed a 50% drop of metabolic rate in shallow corals, whereas mesophotic corals were able to maintain unaltered metabolic rates. Overall, our gene expression and physiological analyses show that mesophotic corals possess a greater capacity to cope with the effects of OA compared to their shallow counterparts. Such capability stems from physiological characteristics (i.e., biomass and lipids energetics), a greater capacity to regulate cellular acid-base parameters, and a higher baseline expression of cell adhesion and extracellular matrix genes. Moreover, our gene expression analysis suggests that the enhanced symbiont photochemical efficiency under high pCO2 levels could prevent acidosis of the host cells and it could support a greater translocation of photosynthates, increasing the energy pool available to the host. With this work, we provide new insights on the response to OA of corals living at mesophotic depths. Our investigation discloses key genetic and physiological traits underlying the potential for corals to cope with future OA conditions.
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Affiliation(s)
- Federica Scucchia
- Department of Marine Biology, Leon H. Charney school of Marine Sciences, University of Haifa, Haifa, Israel
- The Interuniversity Institute of Marine Sciences, Eilat, Israel
| | - Assaf Malik
- Department of Marine Biology, Leon H. Charney school of Marine Sciences, University of Haifa, Haifa, Israel
| | - Hollie M Putnam
- Department of Biological Sciences, University of Rhode Island, Kingston, Rhode Island, USA
| | - Tali Mass
- Department of Marine Biology, Leon H. Charney school of Marine Sciences, University of Haifa, Haifa, Israel
- Morris Kahn Marine Research Station, The Leon H. Charney School of Marine Sciences, University of Haifa, Sdot Yam, Israel
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8
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Walworth NG, Hinners J, Argyle PA, Leles SG, Doblin MA, Collins S, Levine NM. The evolution of trait correlations constrains phenotypic adaptation to high CO 2 in a eukaryotic alga. Proc Biol Sci 2021; 288:20210940. [PMID: 34130504 PMCID: PMC8206706 DOI: 10.1098/rspb.2021.0940] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Microbes form the base of food webs and drive biogeochemical cycling. Predicting the effects of microbial evolution on global elemental cycles remains a significant challenge due to the sheer number of interacting environmental and trait combinations. Here, we present an approach for integrating multivariate trait data into a predictive model of trait evolution. We investigated the outcome of thousands of possible adaptive walks parameterized using empirical evolution data from the alga Chlamydomonas exposed to high CO2. We found that the direction of historical bias (existing trait correlations) influenced both the rate of adaptation and the evolved phenotypes (trait combinations). Critically, we use fitness landscapes derived directly from empirical trait values to capture known evolutionary phenomena. This work demonstrates that ecological models need to represent both changes in traits and changes in the correlation between traits in order to accurately capture phytoplankton evolution and predict future shifts in elemental cycling.
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Affiliation(s)
- Nathan G Walworth
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089-0371, USA
| | - Jana Hinners
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Phoebe A Argyle
- Climate Change Cluster, University of Technology Sydney, Sydney, New South Wales 2007, Australia
| | - Suzana G Leles
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089-0371, USA
| | - Martina A Doblin
- Climate Change Cluster, University of Technology Sydney, Sydney, New South Wales 2007, Australia
| | - Sinéad Collins
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Naomi M Levine
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089-0371, USA
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9
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Scucchia F, Malik A, Zaslansky P, Putnam HM, Mass T. Combined responses of primary coral polyps and their algal endosymbionts to decreasing seawater pH. Proc Biol Sci 2021; 288:20210328. [PMID: 34157872 PMCID: PMC8220278 DOI: 10.1098/rspb.2021.0328] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
With coral reefs declining globally, resilience of these ecosystems hinges on successful coral recruitment. However, knowledge of the acclimatory and/or adaptive potential in response to environmental challenges such as ocean acidification (OA) in earliest life stages is limited. Our combination of physiological measurements, microscopy, computed tomography techniques and gene expression analysis allowed us to thoroughly elucidate the mechanisms underlying the response of early-life stages of corals, together with their algal partners, to the projected decline in oceanic pH. We observed extensive physiological, morphological and transcriptional changes in surviving recruits, and the transition to a less-skeleton/more-tissue phenotype. We found that decreased pH conditions stimulate photosynthesis and endosymbiont growth, and gene expression potentially linked to photosynthates translocation. Our unique holistic study discloses the previously unseen intricate net of interacting mechanisms that regulate the performance of these organisms in response to OA.
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Affiliation(s)
- Federica Scucchia
- Department of Marine Biology, The Leon H. Charney School of Marine Sciences, University of Haifa, Haifa 3498838, Israel.,The Interuniversity Institute of Marine Sciences, Eilat 88103, Israel
| | - Assaf Malik
- Department of Marine Biology, The Leon H. Charney School of Marine Sciences, University of Haifa, Haifa 3498838, Israel
| | - Paul Zaslansky
- Department for Operative and Preventive Dentistry, Charité-Center for Dental and Craniofacial Sciences, Universitätsmedizin Berlin, Berlin 14197, Germany
| | - Hollie M Putnam
- Department of Biological Sciences, University of Rhode Island, Kingston, RI 02881, USA
| | - Tali Mass
- Department of Marine Biology, The Leon H. Charney School of Marine Sciences, University of Haifa, Haifa 3498838, Israel.,Morris Kahn Marine Research Station, The Leon H. Charney School of Marine Sciences, University of Haifa, Sdot Yam, Israel
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10
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Dutkiewicz S, Boyd PW, Riebesell U. Exploring biogeochemical and ecological redundancy in phytoplankton communities in the global ocean. GLOBAL CHANGE BIOLOGY 2021; 27:1196-1213. [PMID: 33342048 PMCID: PMC7986797 DOI: 10.1111/gcb.15493] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 12/07/2020] [Accepted: 12/08/2020] [Indexed: 06/01/2023]
Abstract
Climate-change-induced alterations of oceanic conditions will lead to the ecological niches of some marine phytoplankton species disappearing, at least regionally. How will such losses affect the ecosystem and the coupled biogeochemical cycles? Here, we couch this question in terms of ecological redundancy (will other species be able to fill the ecological roles of the extinct species) and biogeochemical redundancy (can other species replace their biogeochemical roles). Prior laboratory and field studies point to a spectrum in the degree of redundancy. We use a global three-dimensional computer model with diverse planktonic communities to explore these questions further. The model includes 35 phytoplankton types that differ in size, biogeochemical function and trophic strategy. We run two series of experiments in which single phytoplankton types are either partially or fully eliminated. The niches of the targeted types were not completely reoccupied, often with a reduction in the transfer of matter from autotrophs to heterotrophs. Primary production was often decreased, but sometimes increased due to reduction in grazing pressure. Complex trophic interactions (such as a decrease in the stocks of a predator's grazer) led to unexpected reshuffling of the community structure. Alterations in resource utilization may cause impacts beyond the regions where the type went extinct. Our results suggest a lack of redundancy, especially in the 'knock on' effects on higher trophic levels. Redundancy appeared lowest for types on the edges of trait space (e.g. smallest) or with unique competitive strategies. Though highly idealized, our modelling findings suggest that the results from laboratory or field studies often do not adequately capture the ramifications of functional redundancy. The modelled, often counterintuitive, responses-via complex food web interactions and bottom-up versus top-down controls-indicate that changes in planktonic community will be key determinants of future ocean global change ecology and biogeochemistry.
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Affiliation(s)
- Stephanie Dutkiewicz
- Department of Earth, Atmospheric and Planetary SciencesMassachusetts Institute of TechnologyCambridgeMAUSA
- Center for Global Change ScienceMassachusetts Institute of TechnologyCambridgeMAUSA
| | - Philip W. Boyd
- Institute for Marine and Antarctic StudiesUniversity of TasmaniaHobartTas.Australia
| | - Ulf Riebesell
- GEOMAR Helmholtz Centre for Ocean Research KielKielGermany
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11
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Ofaim S, Sulheim S, Almaas E, Sher D, Segrè D. Dynamic Allocation of Carbon Storage and Nutrient-Dependent Exudation in a Revised Genome-Scale Model of Prochlorococcus. Front Genet 2021; 12:586293. [PMID: 33633777 PMCID: PMC7900632 DOI: 10.3389/fgene.2021.586293] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 01/14/2021] [Indexed: 12/02/2022] Open
Abstract
Microbial life in the oceans impacts the entire marine ecosystem, global biogeochemistry and climate. The marine cyanobacterium Prochlorococcus, an abundant component of this ecosystem, releases a significant fraction of the carbon fixed through photosynthesis, but the amount, timing and molecular composition of released carbon are still poorly understood. These depend on several factors, including nutrient availability, light intensity and glycogen storage. Here we combine multiple computational approaches to provide insight into carbon storage and exudation in Prochlorococcus. First, with the aid of a new algorithm for recursive filling of metabolic gaps (ReFill), and through substantial manual curation, we extended an existing genome-scale metabolic model of Prochlorococcus MED4. In this revised model (iSO595), we decoupled glycogen biosynthesis/degradation from growth, thus enabling dynamic allocation of carbon storage. In contrast to standard implementations of flux balance modeling, we made use of forced influx of carbon and light into the cell, to recapitulate overflow metabolism due to the decoupling of photosynthesis and carbon fixation from growth during nutrient limitation. By using random sampling in the ensuing flux space, we found that storage of glycogen or exudation of organic acids are favored when the growth is nitrogen limited, while exudation of amino acids becomes more likely when phosphate is the limiting resource. We next used COMETS to simulate day-night cycles and found that the model displays dynamic glycogen allocation and exudation of organic acids. The switch from photosynthesis and glycogen storage to glycogen depletion is associated with a redistribution of fluxes from the Entner–Doudoroff to the Pentose Phosphate pathway. Finally, we show that specific gene knockouts in iSO595 exhibit dynamic anomalies compatible with experimental observations, further demonstrating the value of this model as a tool to probe the metabolic dynamic of Prochlorococcus.
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Affiliation(s)
- Shany Ofaim
- Bioinformatics Program and Biological Design Center, Boston University, Boston, MA, United States.,Department of Marine Biology, University of Haifa, Haifa, Israel
| | - Snorre Sulheim
- Bioinformatics Program and Biological Design Center, Boston University, Boston, MA, United States.,Department of Biotechnology and Food Science, NTNU - Norwegian University of Science and Technology, Trondheim, Norway.,Department of Biotechnology and Nanomedicine, SINTEF Industry, Trondheim, Norway
| | - Eivind Almaas
- Department of Biotechnology and Food Science, NTNU - Norwegian University of Science and Technology, Trondheim, Norway.,K.G. Jebsen Center for Genetic Epidemiology, NTNU - Norwegian University of Science and Technology, Trondheim, Norway
| | - Daniel Sher
- Department of Marine Biology, University of Haifa, Haifa, Israel
| | - Daniel Segrè
- Bioinformatics Program and Biological Design Center, Boston University, Boston, MA, United States.,Department of Biomedical Engineering, Boston University, Boston, MA, United States.,Department of Physics, Boston University, Boston, MA, United States.,Department of Biology, Boston University, Boston, MA, United States
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12
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Walworth NG, Zakem EJ, Dunne JP, Collins S, Levine NM. Microbial evolutionary strategies in a dynamic ocean. Proc Natl Acad Sci U S A 2020; 117:5943-5948. [PMID: 32123112 PMCID: PMC7084144 DOI: 10.1073/pnas.1919332117] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Marine microbes form the base of ocean food webs and drive ocean biogeochemical cycling. Yet little is known about the ability of microbial populations to adapt as they are advected through changing conditions. Here, we investigated the interplay between physical and biological timescales using a model of adaptation and an eddy-resolving ocean circulation climate model. Two criteria were identified that relate the timing and nature of adaptation to the ratio of physical to biological timescales. Genetic adaptation was impeded in highly variable regimes by nongenetic modifications but was promoted in more stable environments. An evolutionary trade-off emerged where greater short-term nongenetic transgenerational effects (low-γ strategy) enabled rapid responses to environmental fluctuations but delayed genetic adaptation, while fewer short-term transgenerational effects (high-γ strategy) allowed faster genetic adaptation but inhibited short-term responses. Our results demonstrate that the selective pressures for organisms within a single water mass vary based on differences in generation timescales resulting in different evolutionary strategies being favored. Organisms that experience more variable environments should favor a low-γ strategy. Furthermore, faster cell division rates should be a key factor in genetic adaptation in a changing ocean. Understanding and quantifying the relationship between evolutionary and physical timescales is critical for robust predictions of future microbial dynamics.
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Affiliation(s)
- Nathan G Walworth
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 91011
| | - Emily J Zakem
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 91011
| | - John P Dunne
- Geophysical Fluid Dynamics Laboratory, National Oceanic and Atmospheric Administration, Princeton, NJ 08540
| | - Sinéad Collins
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, United Kingdom
| | - Naomi M Levine
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 91011;
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13
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Séférian R, Berthet S, Yool A, Palmiéri J, Bopp L, Tagliabue A, Kwiatkowski L, Aumont O, Christian J, Dunne J, Gehlen M, Ilyina T, John JG, Li H, Long MC, Luo JY, Nakano H, Romanou A, Schwinger J, Stock C, Santana-Falcón Y, Takano Y, Tjiputra J, Tsujino H, Watanabe M, Wu T, Wu F, Yamamoto A. Tracking Improvement in Simulated Marine Biogeochemistry Between CMIP5 and CMIP6. CURRENT CLIMATE CHANGE REPORTS 2020; 6:95-119. [PMID: 32837849 PMCID: PMC7431553 DOI: 10.1007/s40641-020-00160-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
PURPOSE OF REVIEW The changes or updates in ocean biogeochemistry component have been mapped between CMIP5 and CMIP6 model versions, and an assessment made of how far these have led to improvements in the simulated mean state of marine biogeochemical models within the current generation of Earth system models (ESMs). RECENT FINDINGS The representation of marine biogeochemistry has progressed within the current generation of Earth system models. However, it remains difficult to identify which model updates are responsible for a given improvement. In addition, the full potential of marine biogeochemistry in terms of Earth system interactions and climate feedback remains poorly examined in the current generation of Earth system models. SUMMARY Increasing availability of ocean biogeochemical data, as well as an improved understanding of the underlying processes, allows advances in the marine biogeochemical components of the current generation of ESMs. The present study scrutinizes the extent to which marine biogeochemistry components of ESMs have progressed between the 5th and the 6th phases of the Coupled Model Intercomparison Project (CMIP).
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Affiliation(s)
- Roland Séférian
- CNRM, Université de Toulouse, Météo-France, CNRS, Toulouse, France
| | - Sarah Berthet
- CNRM, Université de Toulouse, Météo-France, CNRS, Toulouse, France
| | - Andrew Yool
- National Oceanography Centre, European Way, Southampton, SO14 3ZH UK
| | - Julien Palmiéri
- National Oceanography Centre, European Way, Southampton, SO14 3ZH UK
| | - Laurent Bopp
- LMD-IPSL, Ecole Normale Supérieure / Université PSL, CNRS, Ecole Polytechnique, Sorbonne Université, Paris, PSL University, Paris, France
| | | | | | - Olivier Aumont
- LOCEAN Laboratory, Sorbonne Université-CNRS-IRD-MNHN, Paris, France
| | - James Christian
- Canadian Centre for Climate Modelling and Analysis, Victoria, BC Canada
| | - John Dunne
- NOAA/Geophysical Fluid Dynamics Laboratory, Princeton, NJ USA
| | - Marion Gehlen
- LSCE-IPSL, Université Paris Saclay, Gif-sur-Yvette, France
| | | | - Jasmin G. John
- NOAA/Geophysical Fluid Dynamics Laboratory, Princeton, NJ USA
| | - Hongmei Li
- Max Planck Institute for Meteorology, Hamburg, Germany
| | | | - Jessica Y. Luo
- NOAA/Geophysical Fluid Dynamics Laboratory, Princeton, NJ USA
| | | | | | - Jörg Schwinger
- NORCE Climate, Bjerknes Centre for Climate Research, Bergen, Norway
| | - Charles Stock
- NOAA/Geophysical Fluid Dynamics Laboratory, Princeton, NJ USA
| | | | - Yohei Takano
- Max Planck Institute for Meteorology, Hamburg, Germany
- Present Address: Los Alamos National Laboratory, Los Alamos, NM USA
| | - Jerry Tjiputra
- NORCE Climate, Bjerknes Centre for Climate Research, Bergen, Norway
| | | | - Michio Watanabe
- Research Center for Environmental Modeling and Application, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokohama, Japan
| | - Tongwen Wu
- Beijing Climate Center, China Meteorological Administration, Beijing, China
| | - Fanghua Wu
- Beijing Climate Center, China Meteorological Administration, Beijing, China
| | - Akitomo Yamamoto
- Research Center for Environmental Modeling and Application, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokohama, Japan
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