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Pfab F, Brown AL, Detmer AR, Baxter EC, Moeller HV, Cunning R, Nisbet RM. Timescale separation and models of symbiosis: state space reduction, multiple attractors and initialization. CONSERVATION PHYSIOLOGY 2022; 10:coac026. [PMID: 35539007 PMCID: PMC9073712 DOI: 10.1093/conphys/coac026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 02/18/2022] [Accepted: 03/28/2022] [Indexed: 06/14/2023]
Abstract
Dynamic Energy Budget models relate whole organism processes such as growth, reproduction and mortality to suborganismal metabolic processes. Much of their potential derives from extensions of the formalism to describe the exchange of metabolic products between organisms or organs within a single organism, for example the mutualism between corals and their symbionts. Without model simplification, such models are at risk of becoming parameter-rich and hence impractical. One natural simplification is to assume that some metabolic processes act on 'fast' timescales relative to others. A common strategy for formulating such models is to assume that 'fast' processes equilibrate immediately, while 'slow' processes are described by ordinary differential equations. This strategy can bring a subtlety with it. What if there are multiple, interdependent fast processes that have multiple equilibria, so that additional information is needed to unambiguously specify the model dynamics? This situation can easily arise in contexts where an organism or community can persist in a 'healthy' or an 'unhealthy' state with abrupt transitions between states possible. To approach this issue, we offer the following: (a) a method to unambiguously complete implicitly defined models by adding hypothetical 'fast' state variables; (b) an approach for minimizing the number of additional state variables in such models, which can simplify the numerical analysis and give insights into the model dynamics; and (c) some implications of the new approach that are of practical importance for model dynamics, e.g. on the bistability of flux dynamics and the effect of different initialization choices on model outcomes. To demonstrate those principles, we use a simplified model for root-shoot dynamics of plants and a related model for the interactions between corals and endosymbiotic algae that describes coral bleaching and recovery.
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Affiliation(s)
- Ferdinand Pfab
- Department of Ecology, Evolution and Marine Biology, University of California, Santa Barbara, CA 93106, USA
| | - Alexandra Lynne Brown
- Department of Ecology, Evolution and Marine Biology, University of California, Santa Barbara, CA 93106, USA
| | - A Raine Detmer
- Department of Ecology, Evolution and Marine Biology, University of California, Santa Barbara, CA 93106, USA
| | - Ethan C Baxter
- Department of Ecology, Evolution and Marine Biology, University of California, Santa Barbara, CA 93106, USA
| | - Holly V Moeller
- Department of Ecology, Evolution and Marine Biology, University of California, Santa Barbara, CA 93106, USA
| | - Ross Cunning
- Daniel P. Haerther Center for Conservation and Research, G. Shedd Aquarium, 1200 S. DuSable Lake Shore Drive, Chicago, IL 60605, USA
| | - Roger M Nisbet
- Department of Ecology, Evolution and Marine Biology, University of California, Santa Barbara, CA 93106, USA
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Mestre A, Poulin R, Hortal J. A niche perspective on the range expansion of symbionts. Biol Rev Camb Philos Soc 2019; 95:491-516. [DOI: 10.1111/brv.12574] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Revised: 11/12/2019] [Accepted: 11/18/2019] [Indexed: 12/14/2022]
Affiliation(s)
- Alexandre Mestre
- Cavanilles Institute of Biodiversity and Evolutionary BiologyUniversity of Valencia Av. Dr. Moliner 50, 46100 Burjassot Spain
- Department of BiologyUniversity of Concordia Richard J. Renaud Science Complex, 7141 Sherbrooke W., H4B 1R6 Montreal Canada
| | - Robert Poulin
- Department of ZoologyUniversity of Otago 340 Great King Street, 9054 Dunedin New Zealand
| | - Joaquín Hortal
- Department of Biogeography and Global ChangeMuseo Nacional de Ciencias Naturales (MNCN‐CSIC) C/José Gutiérrez Abascal 2, 28006 Madrid Spain
- Departamento de EcologiaICB, Universidade Federal de Goiás (UFG), Rodovia Goiânia‐Nerópolis Km 5, Campus II, Setor Itatiaia, Goiânia GO 74001‐970 Brazil
- cE3c–Centre for EcologyEvolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, Edifício C2 Piso 5, 1749‐016 Lisboa Portugal
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Tan DX. Aging: An evolutionary competition between host cells and mitochondria. Med Hypotheses 2019; 127:120-128. [PMID: 31088635 DOI: 10.1016/j.mehy.2019.04.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Revised: 03/20/2019] [Accepted: 04/11/2019] [Indexed: 12/19/2022]
Abstract
Here, a new theory of aging is proposed. This new theory is referred as the Host-Mitochondria Intracellular Innate Immune Theory of Aging (HMIIITA). The main point of this theory is that the aging is rooted from an evolutionary competition, that is, a never ending coevolutionary race between host cells and mitochondria. Mitochondria are the descendants of bacteria. The host cells will inevitably sense their bacterial origin, particularly their circular mtDNA. The host intracellular innate immune pressure (HIIIP) aims to eliminate mtDNA as more as possible while mitochondria have to adapt the HIIIP for survival. Co-evolution is required for both of them. From biological point of view, the larger, the mtDNA, the higher, the chance, it becomes the target of HIIIP. As a result, mitochondria have to reduce their mtDNA size via deletion. This process has last for 1.5-2 billion yeas and the result is that mitochondria have lost excessive 95% of their DNA. This mtDNA deletion is not associated with free radical attack but a unique trait acquired during evolution. In the postmitotic cells, the deletion is passively selected by the mitochondrial fission-fusion cycles. Eventually, the accumulation of deletion will significantly jeopardize the mitochondrial function. The dysfunctional mitochondria no longer provide sufficient ATP to support host cells' continuous demanding for growth. At this stage, the cell or the organism aging is inevitable.
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Affiliation(s)
- Dun-Xian Tan
- The Department of Cell System and Anatomy, The University of Texas, Health, San Antonio, TX 78229, USA.
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Kooijman SALM. Waste to hurry: dynamic energy budgets explain the need of wasting to fully exploit blooming resources. OIKOS 2013. [DOI: 10.1111/j.1600-0706.2012.00098.x] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Lorena A, Marques GM, Kooijman SALM, Sousa T. Stylized facts in microalgal growth: interpretation in a dynamic energy budget context. Philos Trans R Soc Lond B Biol Sci 2011; 365:3509-21. [PMID: 20921049 DOI: 10.1098/rstb.2010.0101] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
A dynamic energy budget (DEB) model for microalgae is proposed. This model deviates from the standard DEB model as it needs more reserves to cope with the variation of assimilation pathways, requiring a different approach to growth based on the synthesizing unit (SU) theory for multiple substrates. It is shown that the model is able to accurately predict experimental data in constant and light-varying conditions with most of the parameter values taken directly from the literature. Also, model simulations are shown to be consistent with stylized facts (SFs) concerning NC ratio. These SFs are reinterpreted and the general conclusion is that all forcing variables (dilution rate, temperature and irradiance) impose changes in the nitrogen or carbon limitation status of the population, and consequently on reserve densities. Model predictions are also evaluated in comparison with SFs on chlorophyll concentration. It is proposed that an extra structure, more dependent on the nitrogen reserve, is required to accurately model chlorophyll dynamics. Finally, SFs concerning extracellular polymeric substances (EPSs) production by benthic diatoms are collected and interpreted and a formulation based on product synthesis and rejection flux is proposed for the EPSs production rate.
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Affiliation(s)
- António Lorena
- Environment and Energy Section, DEM, and IN+ Center for Innovation Technology and Policy Research, Instituto Superior Técnico, Lisbon, Portugal.
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Muller EB. Synthesizing units as modeling tool for photosynthesizing organisms with photoinhibition and nutrient limitation. Ecol Modell 2011. [DOI: 10.1016/j.ecolmodel.2010.10.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Sousa T, Domingos T, Poggiale JC, Kooijman SALM. Dynamic energy budget theory restores coherence in biology. Philos Trans R Soc Lond B Biol Sci 2010; 365:3413-28. [PMID: 20921042 PMCID: PMC2981977 DOI: 10.1098/rstb.2010.0166] [Citation(s) in RCA: 135] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
We present the state of the art of the development of dynamic energy budget theory, and its expected developments in the near future within the molecular, physiological and ecological domains. The degree of formalization in the set-up of the theory, with its roots in chemistry, physics, thermodynamics, evolution and the consistent application of Occam's razor, is discussed. We place the various contributions in the theme issue within this theoretical setting, and sketch the scope of actual and potential applications.
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Affiliation(s)
- Tânia Sousa
- Environment and Energy Section, DEM, Instituto Superior Técnico. Av. Rovisco Pais, 1, 1049-001 Lisboa, Portugal.
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Crane KW, Grover JP. Coexistence of mixotrophs, autotrophs, and heterotrophs in planktonic microbial communities. J Theor Biol 2009; 262:517-27. [PMID: 19878684 DOI: 10.1016/j.jtbi.2009.10.027] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2009] [Revised: 10/14/2009] [Accepted: 10/20/2009] [Indexed: 11/17/2022]
Abstract
We examine what circumstances allow the coexistence of microorganisms following different nutritional strategies, using a mathematical model. This model incorporates four nutritional types commonly found in planktonic ecosystems: (1) heterotrophic bacteria that consume dissolved organic matter and are prey to some of the other organisms; (2) heterotrophic zooflagellates that depend entirely on bacterial prey; (3) phototrophic algae that depend only on light and inorganic nutrients, and (4) mixotrophs that photosynthesize, take up inorganic nutrients, and consume bacterial prey. Mixotrophs are characterized by a parameter representing proportional mixing of phototrophic and heterotrophic nutritional strategies. Varying this parameter, a range of mixotrophic strategies was examined in hypothetical habitats differing in supplies of light, dissolved organic carbon, and dissolved inorganic phosphorous. Mixotrophs expressing a wide range of mixotrophic strategies persisted in model habitats with low phosphorus supply, but only those with a strategy that is mostly autotrophic persisted with high nutrient supply, and then only when light supply was also high. Organisms representing all four nutritional strategies were predicted to coexist in habitats with high phosphorus and light supplies. Coexistence involves predation by zooflagellates and mixotrophs balancing the high competitive ability of bacteria for phosphorus, the partitioning of partially overlapping resources between all populations, and possibly nonequlibrium dynamics. In most habitats, the strategy predicted to maximize the abundance of mixotrophs is to be mostly photosynthetic and supplement nutritional needs by consuming bacteria.
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Affiliation(s)
- Kenneth W Crane
- University of Texas at Arlington, Biology Department Box 19498, Arlington, TX 76019-0498, USA.
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Muller EB, Kooijman SALM, Edmunds PJ, Doyle FJ, Nisbet RM. Dynamic energy budgets in syntrophic symbiotic relationships between heterotrophic hosts and photoautotrophic symbionts. J Theor Biol 2009; 259:44-57. [PMID: 19285512 DOI: 10.1016/j.jtbi.2009.03.004] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2008] [Revised: 02/13/2009] [Accepted: 03/03/2009] [Indexed: 11/30/2022]
Abstract
In this paper we develop and investigate a dynamic energy budget (DEB) model describing the syntrophic symbiotic relationship between a heterotrophic host and an internal photoautotrophic symbiont. The model specifies the flows of matter and energy among host, symbiont and environment with minimal complexity and uses the concept of synthesizing units to describe smoothly the assimilation of multiple limiting factors, in particular inorganic carbon and nitrogen, and irradiance. The model has two passive regulation mechanisms: the symbiont shares only photosynthate that it cannot use itself, and the host delivers only excess nutrients to the symbiont. With parameter values plausible for scleractinian corals, we show that these two regulation mechanisms suffice to obtain a stable symbiotic relationship under constant ambient conditions, provided those conditions support sustenance of host and symbiont. Furthermore, the symbiont density in the host varies relatively little as a function of ambient food density, inorganic nitrogen and irradiance. This symbiont density tends to increase with light deprivation or nitrogen enrichment, either directly or via food. We also investigate the relative benefit each partner derives from the relationship and conclude that this relationship may shift from mutualism to parasitism as environmental conditions change.
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Affiliation(s)
- Erik B Muller
- Department of Ecology, Evolution and Marine Biology, University of California, Santa Barbara, CA 93106, USA.
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Kooijman SALM, Sousa T, Pecquerie L, Van Der Meer J, Jager T. From food-dependent statistics to metabolic parameters, a practical guide to the use of dynamic energy budget theory. Biol Rev Camb Philos Soc 2008; 83:533-52. [DOI: 10.1111/j.1469-185x.2008.00053.x] [Citation(s) in RCA: 115] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Acanthamoeba castellanii promotes the survival of Vibrio parahaemolyticus. Appl Environ Microbiol 2008; 74:7183-8. [PMID: 18849458 DOI: 10.1128/aem.01332-08] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Vibrio parahaemolyticus is a food-borne pathogen that naturally inhabits both marine and estuarine environments. Free-living protozoa exist in similar aquatic environments and function to control bacterial numbers by grazing on free-living bacteria. Protozoa also play an important role in the survival and spread of some pathogenic species of bacteria. We investigated the interaction between the protozoan Acanthamoeba castellanii and the bacterium Vibrio parahaemolyticus. We found that Acanthamoeba castellanii does not prey on Vibrio parahaemolyticus but instead secretes a factor that promotes the survival of Vibrio parahaemolyticus in coculture. These studies suggest that protozoa may provide a survival advantage to an extracellular pathogen in the environment.
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Kooijman SALM, Troost TA. Quantitative steps in the evolution of metabolic organisation as specified by the Dynamic Energy Budget theory. Biol Rev Camb Philos Soc 2007; 82:113-42. [PMID: 17313526 DOI: 10.1111/j.1469-185x.2006.00006.x] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
The Dynamic Energy Budget (DEB) theory quantifies the metabolic organisation of organisms on the basis of mechanistically inspired assumptions. We here sketch a scenario for how its various modules, such as maintenance, storage dynamics, development, differentiation and life stages could have evolved since the beginning of life. We argue that the combination of homeostasis and maintenance induced the development of reserves and that subsequent increases in the maintenance costs came with increases of the reserve capacity. Life evolved from a multiple reserves - single structure system (prokaryotes, many protoctists) to systems with multiple reserves and two structures (plants) or single reserve and single structure (animals). This had profound consequences for the possible effects of temperature on rates. We present an alternative explanation for what became known as the down-regulation of maintenance at high growth rates in microorganisms; the density of the limiting reserve increases with the growth rate, and reserves do not require maintenance while structure-specific maintenance costs are independent of the growth rate. This is also the mechanism behind the variation of the respiration rate with body size among species. The DEB theory specifies reserve dynamics on the basis of the requirements of weak homeostasis and partitionability. We here present a new and simple mechanism for this dynamics which accounts for the rejection of mobilised reserve by busy maintenance/growth machinery. This module, like quite a few other modules of DEB theory, uses the theory of Synthesising Units; we review recent progress in this field. The plasticity of membranes that evolved in early eukaryotes is a major step forward in metabolic evolution; we discuss quantitative aspects of the efficiency of phagocytosis relative to the excretion of digestive enzymes to illustrate its importance. Some processes of adaptation and gene expression can be understood in terms of allocation linked to the relative workload of metabolic modules in (unicellular) prokaryotes and organs in (multicellular) eukaryotes. We argue that the evolution of demand systems can only be understood in the light of that of supply systems. We illustrate some important points with data from the literature.
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Affiliation(s)
- S A L M Kooijman
- Department of Theoretical Biology Vrije Universiteit, de Boelelaan 1087, 1081 HV Amsterdam, The Netherlands.
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Kooijman SALM, Andersen T, Kooi BW. DYNAMIC ENERGY BUDGET REPRESENTATIONS OF STOICHIOMETRIC CONSTRAINTS ON POPULATION DYNAMICS. Ecology 2004. [DOI: 10.1890/02-0250] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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