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Kaare-Rasmussen JO, Moeller HV, Pfab F. Modeling food dependent symbiosis in Exaiptasia pallida. Ecol Modell 2023. [DOI: 10.1016/j.ecolmodel.2023.110325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/19/2023]
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2
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Häfker NS, Andreatta G, Manzotti A, Falciatore A, Raible F, Tessmar-Raible K. Rhythms and Clocks in Marine Organisms. ANNUAL REVIEW OF MARINE SCIENCE 2023; 15:509-538. [PMID: 36028229 DOI: 10.1146/annurev-marine-030422-113038] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
The regular movements of waves and tides are obvious representations of the oceans' rhythmicity. But the rhythms of marine life span across ecological niches and timescales, including short (in the range of hours) and long (in the range of days and months) periods. These rhythms regulate the physiology and behavior of individuals, as well as their interactions with each other and with the environment. This review highlights examples of rhythmicity in marine animals and algae that represent important groups of marine life across different habitats. The examples cover ecologically highly relevant species and a growing number of laboratory model systems that are used to disentangle key mechanistic principles. The review introduces fundamental concepts of chronobiology, such as the distinction between rhythmic and endogenous oscillator-driven processes. It also addresses the relevance of studying diverse rhythms and oscillators, as well as their interconnection, for making better predictions of how species will respond to environmental perturbations, including climate change. As the review aims to address scientists from the diverse fields of marine biology, ecology, and molecular chronobiology, all of which have their own scientific terms, we provide definitions of key terms throughout the article.
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Affiliation(s)
- N Sören Häfker
- Max Perutz Labs, University of Vienna, Vienna BioCenter, Vienna, Austria; ,
- Research Platform "Rhythms of Life," University of Vienna, Vienna BioCenter, Vienna, Austria
| | - Gabriele Andreatta
- Max Perutz Labs, University of Vienna, Vienna BioCenter, Vienna, Austria; ,
- Research Platform "Rhythms of Life," University of Vienna, Vienna BioCenter, Vienna, Austria
| | - Alessandro Manzotti
- Laboratoire de Biologie du Chloroplaste et Perception de la Lumière chez les Microalgues, UMR 7141, CNRS, Sorbonne Université, Institut de Biologie Physico-Chimique, Paris, France;
| | - Angela Falciatore
- Laboratoire de Biologie du Chloroplaste et Perception de la Lumière chez les Microalgues, UMR 7141, CNRS, Sorbonne Université, Institut de Biologie Physico-Chimique, Paris, France;
| | - Florian Raible
- Max Perutz Labs, University of Vienna, Vienna BioCenter, Vienna, Austria; ,
- Research Platform "Rhythms of Life," University of Vienna, Vienna BioCenter, Vienna, Austria
| | - Kristin Tessmar-Raible
- Max Perutz Labs, University of Vienna, Vienna BioCenter, Vienna, Austria; ,
- Research Platform "Rhythms of Life," University of Vienna, Vienna BioCenter, Vienna, Austria
- Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
- Institute for Chemistry and Biology of the Marine Environment, Carl von Ossietzky University of Oldenburg, Oldenburg, Germany
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3
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Brown AL, Pfab F, Baxter EC, Detmer AR, Moeller HV, Nisbet RM, Cunning R. Analysis of a mechanistic model of corals in association with multiple symbionts: within-host competition and recovery from bleaching. CONSERVATION PHYSIOLOGY 2022; 10:coac066. [PMID: 36247693 PMCID: PMC9558299 DOI: 10.1093/conphys/coac066] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 07/25/2022] [Accepted: 09/09/2022] [Indexed: 06/14/2023]
Abstract
Coral reefs are increasingly experiencing stressful conditions, such as high temperatures, that cause corals to undergo bleaching, a process where they lose their photosynthetic algal symbionts. Bleaching threatens both corals' survival and the health of the reef ecosystems they create. One possible mechanism for corals to resist bleaching is through association with stress-tolerant symbionts, which are resistant to bleaching but may be worse partners in mild conditions. Some corals have been found to associate with multiple symbiont species simultaneously, which potentially gives them access to the benefits of both stress-sensitive and -tolerant symbionts. However, within-host competition between symbionts may lead to competitive exclusion of one partner, and the consequences of associating with multiple partners simultaneously are not well understood. We modify a mechanistic model of coral-algal symbiosis to investigate the effect of environmental conditions on within-host competitive dynamics between stress-sensitive and -tolerant symbionts and the effect of access to a tolerant symbiont on the dynamics of recovery from bleaching. We found that the addition of a tolerant symbiont can increase host survival and recovery from bleaching in high-light conditions. Competitive exclusion of the tolerant symbiont occurred slowly at intermediate light levels. Interestingly, there were some cases of post-bleaching competitive exclusion after the tolerant symbiont had helped the host recover.
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Affiliation(s)
- Alexandra Lynne Brown
- Corresponding author: Department of Ecology, Evolution, and Marine Biology, University of California, Santa Barbara, Santa Barbara, CA 93106, USA. E-mail:
| | - Ferdinand Pfab
- Department of Ecology, Evolution, and Marine Biology, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
| | - Ethan C Baxter
- Department of Ecology, Evolution, and Marine Biology, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
| | - A Raine Detmer
- Department of Ecology, Evolution, and Marine Biology, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
| | - Holly V Moeller
- Department of Ecology, Evolution, and Marine Biology, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
| | - Roger M Nisbet
- Department of Ecology, Evolution, and Marine Biology, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
| | - Ross Cunning
- Daniel P. Haerther Center for Conservation and Research, John G. Shedd Aquarium, Chicago, IL 60605, USA
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Pacherres CO, Ahmerkamp S, Koren K, Richter C, Holtappels M. Ciliary flows in corals ventilate target areas of high photosynthetic oxygen production. Curr Biol 2022; 32:4150-4158.e3. [PMID: 36002003 DOI: 10.1016/j.cub.2022.07.071] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 07/01/2022] [Accepted: 07/26/2022] [Indexed: 12/14/2022]
Abstract
Most tropical corals live in symbiosis with Symbiodiniaceae algae whose photosynthetic production of oxygen (O2) may lead to excess O2 in the diffusive boundary layer (DBL) above the coral surface. When flow is low, cilia-induced mixing of the coral DBL is vital to remove excess O2 and prevent oxidative stress that may lead to coral bleaching and mortality. Here, we combined particle image velocimetry using O2-sensitive nanoparticles (sensPIV) with chlorophyll (Chla)-sensitive hyperspectral imaging to visualize the microscale distribution and dynamics of ciliary flows and O2 in the coral DBL in relation to the distribution of Symbiodiniaceae Chla in the tissue of the reef building coral, Porites lutea. Curiously, we found an inverse relation between O2 in the DBL and Chla in the underlying tissue, with patches of high O2 in the DBL above low Chla in the underlying tissue surrounding the polyp mouth areas and pockets of low O2 concentrations in the DBL above high Chla in the coenosarc tissue connecting neighboring polyps. The spatial segregation of Chla and O2 is related to ciliary-induced flows, causing a lateral redistribution of O2 in the DBL. In a 2D transport-reaction model of the coral DBL, we show that the enhanced O2 transport allocates parts of the O2 surplus to areas containing less chla, which minimizes oxidative stress. Cilary flows thus confer a spatially complex mass transfer in the coral DBL, which may play an important role in mitigating oxidative stress and bleaching in corals.
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Affiliation(s)
- Cesar O Pacherres
- Alfred Wegener Institute, Helmholtz Center for Polar and Marine Research, 27568 Bremerhaven, Germany; Department of Biology and Chemistry, University of Bremen, 28359 Bremen, Germany; Marine Biological Section, Department of Biology, University of Copenhagen, 3000 Helsingør, Denmark.
| | - Soeren Ahmerkamp
- Max Planck Institute for Marine Microbiology, 28359 Bremen, Germany; MARUM - Center for Marine Environmental Sciences, University of Bremen, 28359 Bremen, Germany.
| | - Klaus Koren
- Center for Water Technology, Section for Microbiology, Department of Biology, Aarhus University, 8000 Aarhus, Denmark
| | - Claudio Richter
- Alfred Wegener Institute, Helmholtz Center for Polar and Marine Research, 27568 Bremerhaven, Germany; Department of Biology and Chemistry, University of Bremen, 28359 Bremen, Germany
| | - Moritz Holtappels
- Alfred Wegener Institute, Helmholtz Center for Polar and Marine Research, 27568 Bremerhaven, Germany; MARUM - Center for Marine Environmental Sciences, University of Bremen, 28359 Bremen, Germany
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Russo SE, Ledder G, Muller EB, Nisbet RM. Dynamic Energy Budget models: fertile ground for understanding resource allocation in plants in a changing world. CONSERVATION PHYSIOLOGY 2022; 10:coac061. [PMID: 36128259 PMCID: PMC9477497 DOI: 10.1093/conphys/coac061] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 06/08/2022] [Accepted: 08/17/2022] [Indexed: 06/15/2023]
Abstract
Climate change is having dramatic effects on the diversity and distribution of species. Many of these effects are mediated by how an organism's physiological patterns of resource allocation translate into fitness through effects on growth, survival and reproduction. Empirically, resource allocation is challenging to measure directly and so has often been approached using mathematical models, such as Dynamic Energy Budget (DEB) models. The fact that all plants require a very similar set of exogenous resources, namely light, water and nutrients, integrates well with the DEB framework in which a small number of variables and processes linked through pathways represent an organism's state as it changes through time. Most DEB theory has been developed in reference to animals and microorganisms. However, terrestrial vascular plants differ from these organisms in fundamental ways that make resource allocation, and the trade-offs and feedbacks arising from it, particularly fundamental to their life histories, but also challenging to represent using existing DEB theory. Here, we describe key features of the anatomy, morphology, physiology, biochemistry, and ecology of terrestrial vascular plants that should be considered in the development of a generic DEB model for plants. We then describe possible approaches to doing so using existing DEB theory and point out features that may require significant development for DEB theory to accommodate them. We end by presenting a generic DEB model for plants that accounts for many of these key features and describing gaps that would need to be addressed for DEB theory to predict the responses of plants to climate change. DEB models offer a powerful and generalizable framework for modelling resource allocation in terrestrial vascular plants, and our review contributes a framework for expansion and development of DEB theory to address how plants respond to anthropogenic change.
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Affiliation(s)
- Sabrina E Russo
- School of Biological Sciences, University of Nebraska, 1104 T Street Lincoln, Nebraska 68588-0118, USA
- Center for Plant Science Innovation, University of Nebraska, 1901 Vine Street, N300 Beadle Center, Lincoln, Nebraska 68588-0660, USA
| | - Glenn Ledder
- Department of Mathematics, University of Nebraska, 203 Avery Hall, Lincoln, Nebraska 68588-0130, USA
| | - Erik B Muller
- Marine Science Institute, University of California, Santa Barbara, California 93106, USA
- Institut für Biologische Analytik und Consulting IBACON GmbH, Arheilger Weg 17 Roß dorf, Hesse D-64380, Germany
| | - Roger M Nisbet
- Marine Science Institute, University of California, Santa Barbara, California 93106, USA
- Department of Ecology, Evolution and Marine Biology, University of California, Santa Barbara, California 93106, USA
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Raharinirina NA, Acevedo-Trejos E, Merico A. Modelling the acclimation capacity of coral reefs to a warming ocean. PLoS Comput Biol 2022; 18:e1010099. [PMID: 35533201 PMCID: PMC9119535 DOI: 10.1371/journal.pcbi.1010099] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 05/19/2022] [Accepted: 04/12/2022] [Indexed: 12/04/2022] Open
Abstract
The symbiotic relationship between corals and photosynthetic algae is the foundation of coral reef ecosystems. This relationship breaks down, leading to coral death, when sea temperature exceeds the thermal tolerance of the coral-algae complex. While acclimation via phenotypic plasticity at the organismal level is an important mechanism for corals to cope with global warming, community-based shifts in response to acclimating capacities may give valuable indications about the future of corals at a regional scale. Reliable regional-scale predictions, however, are hampered by uncertainties on the speed with which coral communities will be able to acclimate. Here we present a trait-based, acclimation dynamics model, which we use in combination with observational data, to provide a first, crude estimate of the speed of coral acclimation at the community level and to investigate the effects of different global warming scenarios on three iconic reef ecosystems of the tropics: Great Barrier Reef, South East Asia, and Caribbean. The model predicts that coral acclimation may confer some level of protection by delaying the decline of some reefs such as the Great Barrier Reef. However, the current rates of acclimation will not be sufficient to rescue corals from global warming. Based on our estimates of coral acclimation capacities, the model results suggest substantial declines in coral abundances in all three regions, ranging from 12% to 55%, depending on the region and on the climate change scenario considered. Our results highlight the importance and urgency of precise assessments and quantitative estimates, for example through laboratory experiments, of the natural acclimation capacity of corals and of the speed with which corals may be able to acclimate to global warming. Tropical coral reefs are among the most productive and diverse ecosystems on Earth. The success of these ecosystems depends on a symbiotic relationship between corals and unicellular algae. This relationship breaks down when water temperature increases above certain levels causing massive coral deaths. Therefore, the future of coral reef ecosystems depends on the capacity of corals to acclimate to current warming rates. Despite many studies have tried to predict the future of coral reefs, these predictions are impaired by uncertainties related to the speed with which corals can acclimate. We developed a model in which corals can acclimate to changing temperature. By comparing model results with observations of coral cover, we estimated the speed of coral acclimation at the community level in different regions of the tropics. Using this information, we quantified the future changes in coral abundances under different warming scenarios. We found that corals of the Great Barrier Reef have higher acclimation capacities than those of other regions. Our results showed substantial coral declines in South East Asia and Caribbean, especially under the highest warming scenarios. Thus, we provide evidence that natural acclimation alone may not be sufficient to offset the decline of corals caused by the expected warming trends.
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Affiliation(s)
- Nomenjanahary Alexia Raharinirina
- Department of Integrated Modelling, Leibniz Centre for Tropical Marine Research, Bremen, Germany
- Department of Physics & Earth Sciences, Jacobs University Bremen, Bremen, Germany
| | - Esteban Acevedo-Trejos
- Department of Integrated Modelling, Leibniz Centre for Tropical Marine Research, Bremen, Germany
| | - Agostino Merico
- Department of Integrated Modelling, Leibniz Centre for Tropical Marine Research, Bremen, Germany
- Department of Physics & Earth Sciences, Jacobs University Bremen, Bremen, Germany
- * E-mail:
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7
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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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8
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Detmer AR, Cunning R, Pfab F, Brown AL, Stier AC, Nisbet RM, Moeller HV. Fertilization by coral-dwelling fish promotes coral growth but can exacerbate bleaching response. J Theor Biol 2022; 541:111087. [PMID: 35276225 DOI: 10.1016/j.jtbi.2022.111087] [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: 11/23/2021] [Revised: 02/28/2022] [Accepted: 03/02/2022] [Indexed: 10/18/2022]
Abstract
Many corals form close associations with a diverse assortment of coral-dwelling fishes and other fauna. As coral reefs around the world are increasingly threatened by mass bleaching events, it is important to understand how these biotic interactions influence corals' susceptibility to bleaching. We used dynamic energy budget modeling to explore how nitrogen excreted by coral-dwelling fish affects the physiological performance of host corals. In our model, fish presence influenced the functioning of the coral-Symbiodiniaceae symbiosis by altering nitrogen availability, and the magnitude and sign of these effects depended on environmental conditions. Although our model predicted that fish-derived nitrogen can promote coral growth, the relationship between fish presence and coral tolerance of photo-oxidative stress was non-linear. Fish excretions supported denser symbiont populations that provided protection from incident light through self-shading. However, these symbionts also used more of their photosynthetic products for their own growth, rather than sharing with the coral host, putting the coral holobiont at a higher risk of becoming carbon-limited and bleaching. The balance between the benefits of increased symbiont shading and costs of reduced carbon sharing depended on environmental conditions. Thus, while there were some scenarios under which fish presence increased corals' tolerance of light stress, fish could also exacerbate bleaching and slow or prevent subsequent recovery. We discuss how the contrast between the potentially harmful effects of fish predicted by our model and results of empirical studies may relate to key model assumptions that warrant further investigation. Overall, this study provides a foundation for future work on how coral-associated fauna influence the bioenergetics of their host corals, which in turn has implications for how these corals respond to bleaching-inducing stressors.
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Affiliation(s)
- A Raine Detmer
- Department of Ecology, Evolution, and Marine Biology, University of California, Santa Barbara, Santa Barbara, CA 93106, USA.
| | - Ross Cunning
- Daniel P. Haerther Center for Conservation and Research, John G. Shedd Aquarium Chicago, IL 60605, USA
| | - Ferdinand Pfab
- Department of Ecology, Evolution, and Marine Biology, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
| | - Alexandra L Brown
- Department of Ecology, Evolution, and Marine Biology, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
| | - Adrian C Stier
- Department of Ecology, Evolution, and Marine Biology, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
| | - Roger M Nisbet
- Department of Ecology, Evolution, and Marine Biology, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
| | - Holly V Moeller
- Department of Ecology, Evolution, and Marine Biology, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
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Peace A, Frost PC, Wagner ND, Danger M, Accolla C, Antczak P, Brooks BW, Costello DM, Everett RA, Flores KB, Heggerud CM, Karimi R, Kang Y, Kuang Y, Larson JH, Mathews T, Mayer GD, Murdock JN, Murphy CA, Nisbet RM, Pecquerie L, Pollesch N, Rutter EM, Schulz KL, Scott JT, Stevenson L, Wang H. Stoichiometric Ecotoxicology for a Multisubstance World. Bioscience 2021. [DOI: 10.1093/biosci/biaa160] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Abstract
Nutritional and contaminant stressors influence organismal physiology, trophic interactions, community structure, and ecosystem-level processes; however, the interactions between toxicity and elemental imbalance in food resources have been examined in only a few ecotoxicity studies. Integrating well-developed ecological theories that cross all levels of biological organization can enhance our understanding of ecotoxicology. In the present article, we underline the opportunity to couple concepts and approaches used in the theory of ecological stoichiometry (ES) to ask ecotoxicological questions and introduce stoichiometric ecotoxicology, a subfield in ecology that examines how contaminant stress, nutrient supply, and elemental constraints interact throughout all levels of biological organization. This conceptual framework unifying ecotoxicology with ES offers potential for both empirical and theoretical studies to deepen our mechanistic understanding of the adverse outcomes of chemicals across ecological scales and improve the predictive powers of ecotoxicology.
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Affiliation(s)
- Angela Peace
- Department of Mathematics and Statistics, Texas Tech University, Lubbock, Texas, United States
| | - Paul C Frost
- Department of Biology, Trent University, Peterborough, Ontario, Canada
| | - Nicole D Wagner
- Center for Reservoir and Aquatic Systems Research, Baylor University, Waco, Texas, United States
| | | | - Chiara Accolla
- Department of Ecology, Evolution, and Behavior, University of Minnesota, Twin Cities, Minneapolis, Minnesota, United States
| | | | - Bryan W Brooks
- Department of Environmental Science, Baylor University, Waco, Texas, United States
| | - David M Costello
- Department of Biological Sciences, Kent State University, Kent, Ohio, United States
| | - Rebecca A Everett
- Department of Mathematics and Statistics, Haverford College, Haverford, Pennsylvania, United States
| | - Kevin B Flores
- Department of Mathematics and the Center for Research in Scientific Computation, North Carolina State University, Raleigh, North Carolina, United States
| | - Christopher M Heggerud
- Department of Mathematical and Statistical Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Roxanne Karimi
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, New York, United States
| | - Yun Kang
- Arizona State University, Mesa, Arizona, United States
| | - Yang Kuang
- Arizona State University, Tempe, Arizona, United States
| | - James H Larson
- US Geological Survey's Upper Midwest Environmental Sciences Center, La Crosse, Wisconsin, United States
| | - Teresa Mathews
- Environmental Sciences Division of Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States
| | - Gregory D Mayer
- Department of Environmental Toxicology, Texas Tech University, Lubbock, Texas, United States
| | - Justin N Murdock
- Department of Biology, Tennessee Tech University, Cookeville, Tennessee, United States
| | - Cheryl A Murphy
- Department of Fisheries and Wildlife, Michigan State University, East Lansing, Michigan, United States
| | - Roger M Nisbet
- Department of Ecology, Evolution, and Marine Biology, University of California, Santa Barbara, Santa Barbara, California, United States
| | - Laure Pecquerie
- Université de Brest, CNRS, IRD, Ifremer, LEMAR, Plouzane, France
| | - Nathan Pollesch
- University of Wisconsin's Aquatic Sciences Center and with the US Environmental Protection Agency's Great Lakes Toxicology and Ecology Division, Duluth, Minnesota, United States
| | - Erica M Rutter
- Department of Applied Mathematics, University of California, Merced, Merced, California, United States
| | - Kimberly L Schulz
- Department of Environmental and Forest Biology, State University of New York's College of Environmental Science and Forestry, Syracuse, New York, United States
| | - J Thad Scott
- Department of Biology, Baylor University, Waco, Texas, United States
| | - Louise Stevenson
- Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee; with the Department of Ecology, Evolution, and Marine Biology, University of California, Santa Barbara, Santa Barbara, California; and with the Department of Biological Sciences at Bowling Green State University, in Bowling Green, Ohio, United States
| | - Hao Wang
- Department of Mathematical and Statistical Sciences, University of Alberta, Edmonton, Alberta, Canada
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10
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Mason RAB, Wall CB, Cunning R, Dove S, Gates RD. High light alongside elevated P CO2 alleviates thermal depression of photosynthesis in a hard coral ( Pocillopora acuta). ACTA ACUST UNITED AC 2020; 223:223/20/jeb223198. [PMID: 33087470 DOI: 10.1242/jeb.223198] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Accepted: 08/12/2020] [Indexed: 11/20/2022]
Abstract
The absorbtion of human-emitted CO2 by the oceans (elevated P CO2 ) is projected to alter the physiological performance of coral reef organisms by perturbing seawater chemistry (i.e. ocean acidification). Simultaneously, greenhouse gas emissions are driving ocean warming and changes in irradiance (through turbidity and cloud cover), which have the potential to influence the effects of ocean acidification on coral reefs. Here, we explored whether physiological impacts of elevated P CO2 on a coral-algal symbiosis (Pocillopora acuta-Symbiodiniaceae) are mediated by light and/or temperature levels. In a 39 day experiment, elevated P CO2 (962 versus 431 µatm P CO2 ) had an interactive effect with midday light availability (400 versus 800 µmol photons m-2 s-1) and temperature (25 versus 29°C) on areal gross and net photosynthesis, for which a decline at 29°C was ameliorated under simultaneous high-P CO2 and high-light conditions. Light-enhanced dark respiration increased under elevated P CO2 and/or elevated temperature. Symbiont to host cell ratio and chlorophyll a per symbiont increased at elevated temperature, whilst symbiont areal density decreased. The ability of moderately strong light in the presence of elevated P CO2 to alleviate the temperature-induced decrease in photosynthesis suggests that higher substrate availability facilitates a greater ability for photochemical quenching, partially offsetting the impacts of high temperature on the photosynthetic apparatus. Future environmental changes that result in moderate increases in light levels could therefore assist the P. acuta holobiont to cope with the 'one-two punch' of rising temperatures in the presence of an acidifying ocean.
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Affiliation(s)
- Robert A B Mason
- Hawai'i Institute of Marine Biology, School of Ocean and Earth Science and Technology, University of Hawai'i at Mānoa, PO Box 1346, Kāne'ohe, HI 96744, USA .,ARC Centre of Excellence for Coral Reef Studies, and Centre for Marine Science, School of Biological Sciences, University of Queensland, St Lucia, QLD 4072, Australia
| | - Christopher B Wall
- Hawai'i Institute of Marine Biology, School of Ocean and Earth Science and Technology, University of Hawai'i at Mānoa, PO Box 1346, Kāne'ohe, HI 96744, USA.,Pacific Biosciences Research Center, University of Hawai'i at Mānoa, Honolulu, HI 96822, USA
| | - Ross Cunning
- Hawai'i Institute of Marine Biology, School of Ocean and Earth Science and Technology, University of Hawai'i at Mānoa, PO Box 1346, Kāne'ohe, HI 96744, USA.,Daniel P. Haerther Center for Conservation and Research, John G. Shedd Aquarium, Chicago, IL 60605, USA
| | - Sophie Dove
- ARC Centre of Excellence for Coral Reef Studies, and Centre for Marine Science, School of Biological Sciences, University of Queensland, St Lucia, QLD 4072, Australia
| | - Ruth D Gates
- Hawai'i Institute of Marine Biology, School of Ocean and Earth Science and Technology, University of Hawai'i at Mānoa, PO Box 1346, Kāne'ohe, HI 96744, USA
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11
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Ledder G, Russo SE, Muller EB, Peace A, Nisbet RM. Local control of resource allocation is sufficient to model optimal dynamics in syntrophic systems. THEOR ECOL-NETH 2020. [DOI: 10.1007/s12080-020-00464-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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12
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Calosi P, Putnam HM, Twitchett RJ, Vermandele F. Marine Metazoan Modern Mass Extinction: Improving Predictions by Integrating Fossil, Modern, and Physiological Data. ANNUAL REVIEW OF MARINE SCIENCE 2019; 11:369-390. [PMID: 30216738 DOI: 10.1146/annurev-marine-010318-095106] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Evolution, extinction, and dispersion are fundamental processes affecting marine biodiversity. Until recently, studies of extant marine systems focused mainly on evolution and dispersion, with extinction receiving less attention. Past extinction events have, however, helped shape the evolutionary history of marine ecosystems, with ecological and evolutionary legacies still evident in modern seas. Current anthropogenic global changes increase extinction risk and pose a significant threat to marine ecosystems, which are critical for human use and sustenance. The evaluation of these threats and the likely responses of marine ecosystems requires a better understanding of evolutionary processes that affect marine ecosystems under global change. Here, we discuss how knowledge of ( a) changes in biodiversity of ancient marine ecosystems to past extinctions events, ( b) the patterns of sensitivity and biodiversity loss in modern marine taxa, and ( c) the physiological mechanisms underpinning species' sensitivity to global change can be exploited and integrated to advance our critical thinking in this area.
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Affiliation(s)
- Piero Calosi
- Département de Biologie, Chimie et Géographie, Université du Québec à Rimouski, Rimouski, Quebec G5L 3A1, Canada; ,
| | - Hollie M Putnam
- Department of Biological Sciences, University of Rhode Island, Kingston, Rhode Island 02881, USA;
| | - Richard J Twitchett
- Department of Earth Sciences, Natural History Museum, London SW7 5BD, United Kingdom;
| | - Fanny Vermandele
- Département de Biologie, Chimie et Géographie, Université du Québec à Rimouski, Rimouski, Quebec G5L 3A1, Canada; ,
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13
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A mechanistic model of coral bleaching due to temperature-mediated light-driven reactive oxygen build-up in zooxanthellae. Ecol Modell 2018. [DOI: 10.1016/j.ecolmodel.2018.07.013] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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14
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Metaorganisms in extreme environments: do microbes play a role in organismal adaptation? ZOOLOGY 2018; 127:1-19. [DOI: 10.1016/j.zool.2018.02.004] [Citation(s) in RCA: 110] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Revised: 02/08/2018] [Accepted: 02/12/2018] [Indexed: 02/06/2023]
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15
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Cunning R, Muller EB, Gates RD, Nisbet RM. A dynamic bioenergetic model for coral- Symbiodinium symbioses and coral bleaching as an alternate stable state. J Theor Biol 2017; 431:49-62. [DOI: 10.1016/j.jtbi.2017.08.003] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Revised: 07/14/2017] [Accepted: 08/02/2017] [Indexed: 11/26/2022]
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16
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Nisbet RM. Challenges for dynamic energy budget theory: Comment on "Physics of metabolic organization" by Marko Jusup et al. Phys Life Rev 2017; 20:72-74. [PMID: 28117237 DOI: 10.1016/j.plrev.2017.01.018] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Accepted: 01/12/2017] [Indexed: 12/22/2022]
Affiliation(s)
- Roger M Nisbet
- Department of Ecology, Evolution and Marine Biology, University of California, Santa Barbara, CA 93106, USA.
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17
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Rohr JR, Salice CJ, Nisbet RM. The pros and cons of ecological risk assessment based on data from different levels of biological organization. Crit Rev Toxicol 2016; 46:756-84. [PMID: 27340745 PMCID: PMC5141515 DOI: 10.1080/10408444.2016.1190685] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2016] [Revised: 05/12/2016] [Accepted: 05/13/2016] [Indexed: 01/15/2023]
Abstract
Ecological risk assessment (ERA) is the process used to evaluate the safety of manufactured chemicals to the environment. Here we review the pros and cons of ERA across levels of biological organization, including suborganismal (e.g., biomarkers), individual, population, community, ecosystem and landscapes levels. Our review revealed that level of biological organization is often related negatively with ease at assessing cause-effect relationships, ease of high-throughput screening of large numbers of chemicals (it is especially easier for suborganismal endpoints), and uncertainty of the ERA because low levels of biological organization tend to have a large distance between their measurement (what is quantified) and assessment endpoints (what is to be protected). In contrast, level of biological organization is often related positively with sensitivity to important negative and positive feedbacks and context dependencies within biological systems, and ease at capturing recovery from adverse contaminant effects. Some endpoints did not show obvious trends across levels of biological organization, such as the use of vertebrate animals in chemical testing and ease at screening large numbers of species, and other factors lacked sufficient data across levels of biological organization, such as repeatability, variability, cost per study and cost per species of effects assessment, the latter of which might be a more defensible way to compare costs of ERAs than cost per study. To compensate for weaknesses of ERA at any particular level of biological organization, we also review mathematical modeling approaches commonly used to extrapolate effects across levels of organization. Finally, we provide recommendations for next generation ERA, submitting that if there is an ideal level of biological organization to conduct ERA, it will only emerge if ERA is approached simultaneously from the bottom of biological organization up as well as from the top down, all while employing mathematical modeling approaches where possible to enhance ERA. Because top-down ERA is unconventional, we also offer some suggestions for how it might be implemented efficaciously. We hope this review helps researchers in the field of ERA fill key information gaps and helps risk assessors identify the best levels of biological organization to conduct ERAs with differing goals.
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Affiliation(s)
| | | | - Roger M. Nisbet
- University of California at Santa Barbara, Santa Barbara, CA 93106-9620
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18
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Madin JS, Hoogenboom MO, Connolly SR, Darling ES, Falster DS, Huang D, Keith SA, Mizerek T, Pandolfi JM, Putnam HM, Baird AH. A Trait-Based Approach to Advance Coral Reef Science. Trends Ecol Evol 2016; 31:419-428. [DOI: 10.1016/j.tree.2016.02.012] [Citation(s) in RCA: 125] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2015] [Revised: 02/09/2016] [Accepted: 02/11/2016] [Indexed: 11/29/2022]
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19
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Edmunds PJ, Comeau S, Lantz C, Andersson A, Briggs C, Cohen A, Gattuso JP, Grady JM, Gross K, Johnson M, Muller EB, Ries JB, Tambutté S, Tambutté E, Venn A, Carpenter RC. Integrating the Effects of Ocean Acidification across Functional Scales on Tropical Coral Reefs. Bioscience 2016. [DOI: 10.1093/biosci/biw023] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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20
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Jacobson LM, Edmunds PJ, Muller EB, Nisbet RM. The implications of reduced metabolic rate in a resource-limited coral. J Exp Biol 2016; 219:870-7. [DOI: 10.1242/jeb.136044] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Accepted: 01/14/2016] [Indexed: 02/04/2023]
Abstract
Many organisms exhibit depressed metabolism when resources are limited, a change that makes it possible to balance an energy budget. For symbiotic reef corals, daily cycles of light and periods of intense cloud cover can be chronic causes of food limitation through reduced photosynthesis. Furthermore, coral bleaching is common in present day reefs, creating a context in which metabolic depression could have beneficial value to corals. In the present study, corals (massive Porites) were exposed to an extreme case of resource limitation by starving them of food and light for 20 d. When resources were limited, the corals depressed area-normalized respiration to 37% of initial rates, coral biomass declined to 64% of initial amounts, yet the corals continued to produce skeletal mass. However, the declines in biomass cannot account for the declines in area-normalized respiration, as mass-specific respiration declined to 30% of initial rates. Thus, these corals appear to be capable of metabolic depression. It is possible that some coral species are better able to depress metabolic rates, such variation could explain differential survival during conditions that limit resources (e.g., shading). Furthermore, we found that maintenance of existing biomass, in part, supports the production of skeletal mass. This association could be explained if maintenance supplies needed energy (e.g., ATP) or inorganic carbon (i.e., CO2) that otherwise limits the production of skeletal mass. Finally, the observed metabolic depression can be explained as change in pool sizes, and does not require a change in metabolic rules.
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Affiliation(s)
- Lianne M. Jacobson
- Department of Biology, California State University, Northridge, CA 91330, USA
- Department of Biology, University of Florida, Gainesville, FL 32611, USA
| | - Peter J. Edmunds
- Department of Biology, California State University, Northridge, CA 91330, USA
| | - Erik B. Muller
- Marine Science Institute, University of California, Santa Barbara, CA 93106, USA
| | - Roger M. Nisbet
- Department of Ecology, Evolution and Marine Biology, University of California, Santa Barbara, CA 93106, USA
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Cunning R, Vaughan N, Gillette P, Capo TR, Matté JL, Baker AC. Dynamic regulation of partner abundance mediates response of reef coral symbioses to environmental change. Ecology 2015; 96:1411-20. [PMID: 26236853 DOI: 10.1890/14-0449.1] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Regulating partner abunclance may allow symmotic organisms to mediate interaction outcomes, facilitating adaptive responses to environmental change. To explore the capacity for-adaptive regulation in an ecologically important endosymbiosis, we studied the population dynamics of symbiotic algae in reef-building corals under different abiotic contexts. We found high natural variability in symbiont abundance in corals across reefs, but this variability converged to different symbiont-specific abundances when colonies were maintained under constant conditions. When conditions changed seasonally, symbiont abundance readjusted to new equilibria. We explain these patterns using an a priori model of symbiotic costs and benefits to the coral host, which shows that the observed changes in symbiont abundance are consistent with the maximization of interaction benefit under different environmental conditions. These results indicate that, while regulating symbiont abundance helps hosts sustain maximum benefit in a dynamic environment, spatiotemporal variation in abiotic factors creates a broad range of symbiont abundances (and interaction outcomes) among corals that may account for observed natural variability in performance (e.g., growth rate) and stress tolerance (e.g., bleaching susceptibility). This cost or benefit framework provides a new perspective on the dynamic regulation of reef coral symbioses and illustrates that the dependence of interaction outcomes on biotic and abiotic contexts may be important in understanding how diverse mutualisms respond to environmental change.
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22
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Mumby PJ, van Woesik R. Consequences of ecological, evolutionary and biogeochemical uncertainty for coral reef responses to climatic stress. Curr Biol 2015; 24:R413-23. [PMID: 24845674 DOI: 10.1016/j.cub.2014.04.029] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Coral reefs are highly sensitive to the stress associated with greenhouse gas emissions, in particular ocean warming and acidification. While experiments show negative responses of most reef organisms to ocean warming, some autotrophs benefit from ocean acidification. Yet, we are uncertain of the response of coral reefs as systems. We begin by reviewing sources of uncertainty and complexity including the translation of physiological effects into demographic processes, indirect ecological interactions among species, the ability of coral reefs to modify their own chemistry, adaptation and trans-generational plasticity. We then incorporate these uncertainties into two simple qualitative models of a coral reef system under climate change. Some sources of uncertainty are far more problematic than others. Climate change is predicted to have an unambiguous negative effect on corals that is robust to several sources of uncertainty but sensitive to the degree of biogeochemical coupling between benthos and seawater. Macroalgal, zoanthid, and herbivorous fish populations are generally predicted to increase, but the ambiguity (confidence) of such predictions are sensitive to the source of uncertainty. For example, reversing the effect of climate-related stress on macroalgae from being positive to negative had no influence on system behaviour. By contrast, the system was highly sensitive to a change in the stress upon herbivorous fishes. Minor changes in competitive interactions had profound impacts on system behaviour, implying that the outcomes of mesocosm studies could be highly sensitive to the choice of taxa. We use our analysis to identify new hypotheses and suggest that the effects of climatic stress on coral reefs provide an exceptional opportunity to test emerging theories of ecological inheritance.
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Affiliation(s)
- Peter J Mumby
- Marine Spatial Ecology Lab & ARC Centre of Excellence for Coral Reef Studies, School of Biological Sciences, University of Queensland, St Lucia, Qld 4072, Australia.
| | - Robert van Woesik
- Department of Biological Sciences, Florida Institute of Technology, 150 West University Blvd, Melbourne, Florida, 32901, USA
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23
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Hill MS. Production possibility frontiers in phototroph:heterotroph symbioses: trade-offs in allocating fixed carbon pools and the challenges these alternatives present for understanding the acquisition of intracellular habitats. Front Microbiol 2014; 5:357. [PMID: 25101064 PMCID: PMC4101577 DOI: 10.3389/fmicb.2014.00357] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2014] [Accepted: 06/25/2014] [Indexed: 11/13/2022] Open
Abstract
Intracellular habitats have been invaded by a remarkable diversity of organisms, and strategies employed to successfully reside in another species' cellular space are varied. Common selective pressures may be experienced in symbioses involving phototrophic symbionts and heterotrophic hosts. Here I refine and elaborate the Arrested Phagosome Hypothesis that proposes a mechanism that phototrophs use to gain access to their host's intracellular habitat. I employ the economic concept of production possibility frontiers (PPF) as a useful heuristic to clearly define the trade-offs that an intracellular phototroph is likely to face as it allocates photosynthetically-derived pools of energy. Fixed carbon can fuel basic metabolism/respiration, it can support mitotic division, or it can be translocated to the host. Excess photosynthate can be stored for future use. Thus, gross photosynthetic productivity can be divided among these four general categories, and natural selection will favor phenotypes that best match the demands presented to the symbiont by the host cellular habitat. The PPF highlights trade-offs that exist between investment in growth (i.e., mitosis) or residency (i.e., translocating material to the host). Insights gained from this perspective might help explain phenomena such as coral bleaching because deficits in photosynthetic production are likely to diminish a symbiont's ability to "afford" the costs of intracellular residency. I highlight deficits in our current understanding of host:symbiont interactions at the molecular, genetic, and cellular level, and I also discuss how semantic differences among scientists working with different symbiont systems may diminish the rate of increase in our understanding of phototrophic-based associations. I argue that adopting interdisciplinary (in this case, inter-symbiont-system) perspectives will lead to advances in our general understanding of the phototrophic symbiont's intracellular niche.
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Affiliation(s)
- Malcolm S Hill
- Department of Biology, Gottwald Science Center, University of Richmond Richmond, VA, USA
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24
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Adamson MW, Morozov AY. Defining and detecting structural sensitivity in biological models: developing a new framework. J Math Biol 2014; 69:1815-48. [PMID: 24448657 DOI: 10.1007/s00285-014-0753-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2013] [Revised: 12/21/2013] [Indexed: 11/25/2022]
Abstract
When we construct mathematical models to represent biological systems, there is always uncertainty with regards to the model specification--whether with respect to the parameters or to the formulation of model functions. Sometimes choosing two different functions with close shapes in a model can result in substantially different model predictions: a phenomenon known in the literature as structural sensitivity, which is a significant obstacle to improving the predictive power of biological models. In this paper, we revisit the general definition of structural sensitivity, compare several more specific definitions and discuss their usefulness for the construction and analysis of biological models. Then we propose a general approach to reveal structural sensitivity with regards to certain system properties, which considers infinite-dimensional neighbourhoods of the model functions: a far more powerful technique than the conventional approach of varying parameters for a fixed functional form. In particular, we suggest a rigorous method to unearth sensitivity with respect to the local stability of systems' equilibrium points. We present a method for specifying the neighbourhood of a general unknown function with [Formula: see text] inflection points in terms of a finite number of local function properties, and provide a rigorous proof of its completeness. Using this powerful result, we implement our method to explore sensitivity in several well-known multicomponent ecological models and demonstrate the existence of structural sensitivity in these models. Finally, we argue that structural sensitivity is an important intrinsic property of biological models, and a direct consequence of the complexity of the underlying real systems.
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Affiliation(s)
- M W Adamson
- Department of Mathematics, University of Leicester, University Road, Leicester , LE1 7RH, UK,
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25
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Eynaud Y, Nerini D, Baklouti M, Poggiale JC. Towards a simplification of models using regression trees. J R Soc Interface 2013; 10:20120613. [PMID: 23173194 DOI: 10.1098/rsif.2012.0613] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Over-parametrization in modelling is a well-known issue that makes it hard to identify which part of a model is responsible for a given behaviour. In line with that ascertainment, this work presents the outline of an empirical method to simplify models by decreasing the number of parameters. By using regression trees to classify outputs according to related input parameters, the method provides the modeller with an objective tool to reduce the range of the used parameters and, under certain conditions, to establish relations between them. Thereby, the complexity of the model is reduced on the basis of mathematical arguments. As an example, a dynamic energy budget-based model of a mesopelagic bacterial ecosystem is simplified using the presented method. The main benefits of such a method are thus highlighted: (i) more robust parameter estimations; (ii) less complex formulations; and (iii) fewer modelling assumptions. To conclude, the difficulties encountered are discussed, and several solutions are proposed to deal with them.
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Affiliation(s)
- Y Eynaud
- Aix-Marseille Université, Université du Sud Toulon-Var, Mediterranean Institute of Oceanography (MIO), Marseille Cedex 09, France.
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26
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The interchangeability of autotrophic and heterotrophic nitrogen sources in Scleractinian coral symbiotic relationships: A numerical study. Ecol Modell 2013. [DOI: 10.1016/j.ecolmodel.2012.11.003] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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27
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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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Malcolm H, April H. The magnesium inhibition and arrested phagosome hypotheses: new perspectives on the evolution and ecology ofSymbiodiniumsymbioses. Biol Rev Camb Philos Soc 2012; 87:804-21. [DOI: 10.1111/j.1469-185x.2012.00223.x] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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29
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Fablet R, Pecquerie L, de Pontual H, Høie H, Millner R, Mosegaard H, Kooijman SALM. Shedding light on fish otolith biomineralization using a bioenergetic approach. PLoS One 2011; 6:e27055. [PMID: 22110601 PMCID: PMC3215717 DOI: 10.1371/journal.pone.0027055] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2011] [Accepted: 10/10/2011] [Indexed: 11/19/2022] Open
Abstract
Otoliths are biocalcified bodies connected to the sensory system in the inner ears of fish. Their layered, biorhythm-following formation provides individual records of the age, the individual history and the natural environment of extinct and living fish species. Such data are critical for ecosystem and fisheries monitoring. They however often lack validation and the poor understanding of biomineralization mechanisms has led to striking examples of misinterpretations and subsequent erroneous conclusions in fish ecology and fisheries management. Here we develop and validate a numerical model of otolith biomineralization. Based on a general bioenergetic theory, it disentangles the complex interplay between metabolic and temperature effects on biomineralization. This model resolves controversial issues and explains poorly understood observations of otolith formation. It represents a unique simulation tool to improve otolith interpretation and applications, and, beyond, to address the effects of both climate change and ocean acidification on other biomineralizing organisms such as corals and bivalves.
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Affiliation(s)
- Ronan Fablet
- Institut TELECOM, TELECOM Bretagne, Lab-STICC, Brest, France.
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30
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Benchmarks in organism performance and their use in comparative analyses. Oecologia 2011; 167:379-90. [DOI: 10.1007/s00442-011-2004-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2010] [Accepted: 04/11/2011] [Indexed: 10/18/2022]
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31
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32
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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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33
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Nisbet RM, McCauley E, Johnson LR. Dynamic energy budget theory and population ecology: lessons from Daphnia. Philos Trans R Soc Lond B Biol Sci 2010; 365:3541-52. [PMID: 20921052 PMCID: PMC2981978 DOI: 10.1098/rstb.2010.0167] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Dynamic energy budget (DEB) theory offers a perspective on population ecology whose starting point is energy utilization by, and homeostasis within, individual organisms. It is natural to ask what it adds to the existing large body of individual-based ecological theory. We approach this question pragmatically--through detailed study of the individual physiology and population dynamics of the zooplankter Daphnia and its algal food. Standard DEB theory uses several state variables to characterize the state of an individual organism, thereby making the transition to population dynamics technically challenging, while ecologists demand maximally simple models that can be used in multi-scale modelling. We demonstrate that simpler representations of individual bioenergetics with a single state variable (size), and two life stages (juveniles and adults), contain sufficient detail on mass and energy budgets to yield good fits to data on growth, maturation and reproduction of individual Daphnia in response to food availability. The same simple representations of bioenergetics describe some features of Daphnia mortality, including enhanced mortality at low food that is not explicitly incorporated in the standard DEB model. Size-structured, population models incorporating this additional mortality component resolve some long-standing questions on stability and population cycles in Daphnia. We conclude that a bioenergetic model serving solely as a 'regression' connecting organismal performance to the history of its environment can rest on simpler representations than those of standard DEB. But there are associated costs with such pragmatism, notably loss of connection to theory describing interspecific variation in physiological rates. The latter is an important issue, as the type of detailed study reported here can only be performed for a handful of species.
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Affiliation(s)
- Roger M Nisbet
- Department of Ecology, Evolution and Marine Biology, University of California, Santa Barbara, CA 93106, USA.
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34
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Integrate-and-fire models of insolation-driven entrainment of broadcast spawning in corals. THEOR ECOL-NETH 2010. [DOI: 10.1007/s12080-010-0075-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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