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Cherif M, Brose U, Hirt MR, Ryser R, Silve V, Albert G, Arnott R, Berti E, Cirtwill A, Dyer A, Gauzens B, Gupta A, Ho HC, Portalier SMJ, Wain D, Wootton K. The environment to the rescue: can physics help predict predator-prey interactions? Biol Rev Camb Philos Soc 2024. [PMID: 38855988 DOI: 10.1111/brv.13105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 05/17/2024] [Accepted: 05/24/2024] [Indexed: 06/11/2024]
Abstract
Understanding the factors that determine the occurrence and strength of ecological interactions under specific abiotic and biotic conditions is fundamental since many aspects of ecological community stability and ecosystem functioning depend on patterns of interactions among species. Current approaches to mapping food webs are mostly based on traits, expert knowledge, experiments, and/or statistical inference. However, they do not offer clear mechanisms explaining how trophic interactions are affected by the interplay between organism characteristics and aspects of the physical environment, such as temperature, light intensity or viscosity. Hence, they cannot yet predict accurately how local food webs will respond to anthropogenic pressures, notably to climate change and species invasions. Herein, we propose a framework that synthesises recent developments in food-web theory, integrating body size and metabolism with the physical properties of ecosystems. We advocate for combination of the movement paradigm with a modular definition of the predation sequence, because movement is central to predator-prey interactions, and a generic, modular model is needed to describe all the possible variation in predator-prey interactions. Pending sufficient empirical and theoretical knowledge, our framework will help predict the food-web impacts of well-studied physical factors, such as temperature and oxygen availability, as well as less commonly considered variables such as wind, turbidity or electrical conductivity. An improved predictive capability will facilitate a better understanding of ecosystem responses to a changing world.
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Affiliation(s)
- Mehdi Cherif
- Aquatic Ecosystems and Global Change Research Unit, National Research Institute for Agriculture Food and the Environment, 50 avenue de Verdun, Cestas Cedex, 33612, France
| | - Ulrich Brose
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstrasse 4, Leipzig, 04103, Germany
- Institute of Biodiversity, Friedrich Schiller University Jena, Dornburger Straße 159, Jena, 07743, Germany
| | - Myriam R Hirt
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstrasse 4, Leipzig, 04103, Germany
- Institute of Biodiversity, Friedrich Schiller University Jena, Dornburger Straße 159, Jena, 07743, Germany
| | - Remo Ryser
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstrasse 4, Leipzig, 04103, Germany
- Institute of Biodiversity, Friedrich Schiller University Jena, Dornburger Straße 159, Jena, 07743, Germany
| | - Violette Silve
- Aquatic Ecosystems and Global Change Research Unit, National Research Institute for Agriculture Food and the Environment, 50 avenue de Verdun, Cestas Cedex, 33612, France
| | - Georg Albert
- Department of Forest Nature Conservation, Georg-August-Universität, Büsgenweg 3, Göttingen, 37077, Germany
| | - Russell Arnott
- Sainsbury Laboratory, University of Cambridge, 47 Bateman Street, Cambridge, Cambridgeshire, CB2 1LR, UK
| | - Emilio Berti
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstrasse 4, Leipzig, 04103, Germany
- Institute of Biodiversity, Friedrich Schiller University Jena, Dornburger Straße 159, Jena, 07743, Germany
| | - Alyssa Cirtwill
- Spatial Foodweb Ecology Group, Research Centre for Ecological Change (REC), Faculty of Biological and Environmental Sciences, University of Helsinki, P.O. Box 4 (Yliopistonkatu 3), Helsinki, 00014, Finland
| | - Alexander Dyer
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstrasse 4, Leipzig, 04103, Germany
- Institute of Biodiversity, Friedrich Schiller University Jena, Dornburger Straße 159, Jena, 07743, Germany
| | - Benoit Gauzens
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstrasse 4, Leipzig, 04103, Germany
- Institute of Biodiversity, Friedrich Schiller University Jena, Dornburger Straße 159, Jena, 07743, Germany
| | - Anhubav Gupta
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, Zürich, 8057, Switzerland
| | - Hsi-Cheng Ho
- Institute of Ecology and Evolutionary Biology, National Taiwan University, No. 1, Sec. 4, Roosevelt Rd, Taipei, 106, Taiwan
| | - Sébastien M J Portalier
- Department of Mathematics and Statistics, University of Ottawa, STEM Complex, room 342, 150 Louis-Pasteur Pvt, Ottawa, Ontario, K1N 6N5, Canada
| | - Danielle Wain
- 7 Lakes Alliance, Belgrade Lakes, 137 Main St, Belgrade Lakes, ME, 04918, USA
| | - Kate Wootton
- School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch, 8140, New Zealand
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Widder S, Carmody LA, Opron K, Kalikin LM, Caverly LJ, LiPuma JJ. Microbial community organization designates distinct pulmonary exacerbation types and predicts treatment outcome in cystic fibrosis. Nat Commun 2024; 15:4889. [PMID: 38849369 PMCID: PMC11161516 DOI: 10.1038/s41467-024-49150-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Accepted: 05/23/2024] [Indexed: 06/09/2024] Open
Abstract
Polymicrobial infection of the airways is a hallmark of obstructive lung diseases such as cystic fibrosis (CF), non-CF bronchiectasis, and chronic obstructive pulmonary disease. Pulmonary exacerbations (PEx) in these conditions are associated with accelerated lung function decline and higher mortality rates. Understanding PEx ecology is challenged by high inter-patient variability in airway microbial community profiles. We analyze bacterial communities in 880 CF sputum samples collected during an observational prospective cohort study and develop microbiome descriptors to model community reorganization prior to and during 18 PEx. We identify two microbial dysbiosis regimes with opposing ecology and dynamics. Pathogen-governed PEx show hierarchical community reorganization and reduced diversity, whereas anaerobic bloom PEx display stochasticity and increased diversity. A simulation of antimicrobial treatment predicts better efficacy for hierarchically organized communities. This link between PEx, microbiome organization, and treatment success advances the development of personalized clinical management in CF and, potentially, other obstructive lung diseases.
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Affiliation(s)
- Stefanie Widder
- Department of Medicine 1, Research Division Infection Biology, Medical University of Vienna, 1090, Vienna, Austria.
| | - Lisa A Carmody
- Department of Pediatrics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Kristopher Opron
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Linda M Kalikin
- Department of Pediatrics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Lindsay J Caverly
- Department of Pediatrics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - John J LiPuma
- Department of Pediatrics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
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3
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Arroyo-Esquivel J, Klausmeier CA, Litchman E. Using neural ordinary differential equations to predict complex ecological dynamics from population density data. J R Soc Interface 2024; 21:20230604. [PMID: 38745459 DOI: 10.1098/rsif.2023.0604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 03/25/2024] [Indexed: 05/16/2024] Open
Abstract
Simple models have been used to describe ecological processes for over a century. However, the complexity of ecological systems makes simple models subject to modelling bias due to simplifying assumptions or unaccounted factors, limiting their predictive power. Neural ordinary differential equations (NODEs) have surged as a machine-learning algorithm that preserves the dynamic nature of the data (Chen et al. 2018 Adv. Neural Inf. Process. Syst.). Although preserving the dynamics in the data is an advantage, the question of how NODEs perform as a forecasting tool of ecological communities is unanswered. Here, we explore this question using simulated time series of competing species in a time-varying environment. We find that NODEs provide more precise forecasts than autoregressive integrated moving average (ARIMA) models. We also find that untuned NODEs have a similar forecasting accuracy to untuned long-short term memory neural networks and both are outperformed in accuracy and precision by empirical dynamical modelling . However, we also find NODEs generally outperform all other methods when evaluating with the interval score, which evaluates precision and accuracy in terms of prediction intervals rather than pointwise accuracy. We also discuss ways to improve the forecasting performance of NODEs. The power of a forecasting tool such as NODEs is that it can provide insights into population dynamics and should thus broaden the approaches to studying time series of ecological communities.
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Affiliation(s)
| | - Christopher A Klausmeier
- Department of Global Ecology, Carnegie Institution for Science , Stanford, CA, USA
- W. K. Kellogg Biological Station, Michigan State University , Hickory Corners, MI, USA
- Program in Ecology and Evolutionary Biology, Michigan State University , East Lansing, MI, USA
- Department of Integrative Biology, Michigan State University , East Lansing, MI, USA
- Department of Plant Biology, Michigan State University , East Lansing, MI, USA
| | - Elena Litchman
- Department of Global Ecology, Carnegie Institution for Science , Stanford, CA, USA
- W. K. Kellogg Biological Station, Michigan State University , Hickory Corners, MI, USA
- Program in Ecology and Evolutionary Biology, Michigan State University , East Lansing, MI, USA
- Department of Integrative Biology, Michigan State University , East Lansing, MI, USA
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Widder S, Carmody L, Opron K, Kalikin L, Caverly L, LiPuma J. Microbial community organization designates distinct pulmonary exacerbation types and predicts treatment outcome in cystic fibrosis. RESEARCH SQUARE 2024:rs.3.rs-4128740. [PMID: 38562856 PMCID: PMC10984025 DOI: 10.21203/rs.3.rs-4128740/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Polymicrobial infection of the airways is a hallmark of obstructive lung diseases such as cystic fibrosis (CF), non-CF bronchiectasis, and chronic obstructive pulmonary disease. Pulmonary exacerbations (PEx) in these conditions are associated with accelerated lung function decline and higher mortality rates. An understanding of the microbial underpinnings of PEx is challenged by high inter-patient variability in airway microbial community profiles. We analyzed bacterial communities in 880 CF sputum samples and developed microbiome descriptors to model community reorganization prior to and during 18 PEx. We identified two microbial dysbiosis regimes with opposing ecology and dynamics. Pathogen-governed PEx showed hierarchical community reorganization and reduced diversity, whereas anaerobic bloom PEx displayed stochasticity and increased diversity. A simulation of antimicrobial treatment predicted better efficacy for hierarchically organized communities. This link between PEx type, microbiome organization, and treatment success advances the development of personalized clinical management in CF and, potentially, other obstructive lung diseases.
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5
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Zelnik YR, Galiana N, Barbier M, Loreau M, Galbraith E, Arnoldi JF. How collectively integrated are ecological communities? Ecol Lett 2024; 27:e14358. [PMID: 38288867 DOI: 10.1111/ele.14358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 11/22/2023] [Accepted: 11/26/2023] [Indexed: 02/01/2024]
Abstract
Beyond abiotic conditions, do population dynamics mostly depend on a species' direct predators, preys and conspecifics? Or can indirect feedback that ripples across the whole community be equally important? Determining where ecological communities sit on the spectrum between these two characterizations requires a metric able to capture the difference between them. Here we show that the spectral radius of a community's interaction matrix provides such a metric, thus a measure of ecological collectivity, which is accessible from imperfect knowledge of biotic interactions and related to observable signatures. This measure of collectivity integrates existing approaches to complexity, interaction structure and indirect interactions. Our work thus provides an original perspective on the question of to what degree communities are more than loose collections of species or simple interaction motifs and explains when pragmatic reductionist approaches ought to suffice or fail when applied to ecological communities.
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Affiliation(s)
- Yuval R Zelnik
- Department of Crop Production Ecology, Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden
- Department of Ecology, Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden
| | - Nuria Galiana
- Department of Biogeography and Global Change, National Museum of Natural Sciences (CSIC), Madrid, Spain
| | - Matthieu Barbier
- CIRAD, UMR PHIM, Montpellier, France
- PHIM Plant Health Institute, University of Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
| | - Michel Loreau
- Theoretical and Experimental Ecology Station, CNRS Moulis, Moulis, France
- Institute of Ecology, College of Urban and Environmental Sciences, Peking University, Beijing, China
| | - Eric Galbraith
- Department of Earth and Planetary Science, McGill University, Montreal, Quebec, Canada
- Institut de Ciència i Tecnologia Ambientals (ICTA-UAB), Universitat Autònoma de Barcelona, Barcelona, Spain
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Allen-Perkins A, García-Callejas D, Bartomeus I, Godoy O. Structural asymmetry in biotic interactions as a tool to understand and predict ecological persistence. Ecol Lett 2023; 26:1647-1662. [PMID: 37515408 DOI: 10.1111/ele.14291] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 06/29/2023] [Accepted: 07/05/2023] [Indexed: 07/30/2023]
Abstract
A universal feature of ecological systems is that species do not interact with others with the same sign and strength. Yet, the consequences of this asymmetry in biotic interactions for the short- and long-term persistence of individual species and entire communities remains unclear. Here, we develop a set of metrics to evaluate how asymmetric interactions among species translate to asymmetries in their individual vulnerability to extinction under changing environmental conditions. These metrics, which solve previous limitations of how to independently quantify the size from the shape of the so-called feasibility domain, provide rigorous advances to understand simultaneously why some species and communities present more opportunities to persist than others. We further demonstrate that our shape-related metrics are useful to predict short-term changes in species' relative abundances during 7 years in a Mediterranean grassland. Our approach is designed to be applied to any ecological system regardless of the number of species and type of interactions. With it, we show that is possible to obtain both mechanistic and predictive information on ecological persistence for individual species and entire communities, paving the way for a stronger integration of theoretical and empirical research.
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Affiliation(s)
- Alfonso Allen-Perkins
- Departamento de Ingeniería Eléctrica, Electrónica, Automática y Física Aplicada, ETSIDI, Technical University of Madrid, Madrid, Spain
| | - David García-Callejas
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
- Landcare Research, Lincoln, New Zealand
| | | | - Oscar Godoy
- Departamento de Biología, Instituto Universitario de Ciencias del Mar (INMAR), Universidad de Cádiz, Puerto Real, Spain
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Widder S, Opron K, Carmody LA, Kalikin LM, Caverly LJ, LiPuma JJ. Microbial community organization designates distinct pulmonary exacerbation types and predicts treatment outcome in cystic fibrosis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.21.550012. [PMID: 37546739 PMCID: PMC10401930 DOI: 10.1101/2023.07.21.550012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
Polymicrobial infection of the airways is a hallmark of obstructive lung diseases such as cystic fibrosis (CF), non-CF bronchiectasis, and chronic obstructive pulmonary disease (COPD). Intermittent pulmonary exacerbations (PEx) in these conditions are associated with lung function decline and higher mortality rates. An understanding of the microbial underpinnings of PEx is challenged by high inter-patient variability in airway microbial community profiles. We analyzed 880 near-daily CF sputum samples and developed non-standard microbiome descriptors to model community reorganization prior and during 18 PEx. We identified two communal microbial regimes with opposing ecology and dynamics. Whereas pathogen-governed dysbiosis showed hierarchical community organization and reduced diversity, anaerobic bloom dysbiosis displayed stochasticity and increased diversity. Microbiome organization modulated the relevance of pathogens and a simulation of antimicrobial treatment predicted better efficacy for hierarchically organized microbiota. This causal link between PEx, microbiome organization, and treatment success advances the development of personalized dysbiosis management in CF and, potentially, other obstructive lung diseases.
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Merz E, Saberski E, Gilarranz LJ, Isles PDF, Sugihara G, Berger C, Pomati F. Disruption of ecological networks in lakes by climate change and nutrient fluctuations. NATURE CLIMATE CHANGE 2023; 13:389-396. [PMID: 37038592 PMCID: PMC10079529 DOI: 10.1038/s41558-023-01615-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 01/24/2023] [Indexed: 06/19/2023]
Abstract
Climate change interacts with local processes to threaten biodiversity by disrupting the complex network of ecological interactions. While changes in network interactions drastically affect ecosystems, how ecological networks respond to climate change, in particular warming and nutrient supply fluctuations, is largely unknown. Here, using an equation-free modelling approach on monthly plankton community data in ten Swiss lakes, we show that the number and strength of plankton community interactions fluctuate and respond nonlinearly to water temperature and phosphorus. While lakes show system-specific responses, warming generally reduces network interactions, particularly under high phosphate levels. This network reorganization shifts trophic control of food webs, leading to consumers being controlled by resources. Small grazers and cyanobacteria emerge as sensitive indicators of changes in plankton networks. By exposing the outcomes of a complex interplay between environmental drivers, our results provide tools for studying and advancing our understanding of how climate change impacts entire ecological communities.
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Affiliation(s)
- Ewa Merz
- Department of Aquatic Ecology, Eawag: Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
| | - Erik Saberski
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA USA
| | - Luis J. Gilarranz
- Department of Aquatic Ecology, Eawag: Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
| | - Peter D. F. Isles
- Vermont Department of Environmental Conservation, Montpelier, VT USA
| | - George Sugihara
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA USA
| | - Christine Berger
- Stadt Zuerich, Wasserversorgung, Qualitaetsueberwachung, Zuerich, Switzerland
| | - Francesco Pomati
- Department of Aquatic Ecology, Eawag: Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
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