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Vale F, Sousa CA, Sousa H, Simões LC, McBain AJ, Simões M. Bacteria and microalgae associations in periphyton-mechanisms and biotechnological opportunities. FEMS Microbiol Rev 2023; 47:fuad047. [PMID: 37586879 DOI: 10.1093/femsre/fuad047] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 08/02/2023] [Accepted: 08/14/2023] [Indexed: 08/18/2023] Open
Abstract
Phototrophic and heterotrophic microorganisms coexist in complex and dynamic structures called periphyton. These structures shape the biogeochemistry and biodiversity of aquatic ecosystems. In particular, microalgae-bacteria interactions are a prominent focus of study by microbial ecologists and can provide biotechnological opportunities for numerous applications (i.e. microalgal bloom control, aquaculture, biorefinery, and wastewater bioremediation). In this review, we analyze the species dynamics (i.e. periphyton formation and factors determining the prevalence of one species over another), coexisting communities, exchange of resources, and communication mechanisms of periphytic microalgae and bacteria. We extend periphyton mathematical modelling as a tool to comprehend complex interactions. This review is expected to boost the applicability of microalgae-bacteria consortia, by drawing out knowledge from natural periphyton.
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Affiliation(s)
- Francisca Vale
- ALiCE - Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
- LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
| | - Cátia A Sousa
- ALiCE - Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
- LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
| | - Henrique Sousa
- ALiCE - Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
- LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
| | - Lúcia C Simões
- CEB - Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
- LABBELS - Associate Laboratory in Biotechnology, Bioengineering and Microelectromechanical Systems, Braga/Guimarães, Portugal
| | - Andrew J McBain
- School of Health Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester M13 9PT, United Kingdom
| | - Manuel Simões
- ALiCE - Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
- LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
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Lenton TM, Kohler TA, Marquet PA, Boyle RA, Crucifix M, Wilkinson DM, Scheffer M. Survival of the Systems. Trends Ecol Evol 2021; 36:333-344. [PMID: 33414020 DOI: 10.1016/j.tree.2020.12.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 11/26/2020] [Accepted: 12/04/2020] [Indexed: 02/07/2023]
Abstract
Since Darwin, individuals and more recently genes, have been the focus of evolutionary thinking. The idea that selection operates on nonreproducing, higher-level systems including ecosystems or societies, has met with scepticism. But research emphasising that natural selection can be based solely on differential persistence invites reconsideration of their evolution. Self-perpetuating feedback cycles involving biotic as well as abiotic components are critical to determining persistence. Evolution of autocatalytic networks of molecules is well studied, but the principles hold for any 'self-perpetuating' system. Ecosystem examples include coral reefs, rainforests, and savannahs. Societal examples include agricultural systems, dominant belief systems, and economies. Persistence-based selection of feedbacks can help us understand how ecological and societal systems survive or fail in a changing world.
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Affiliation(s)
- Timothy M Lenton
- Global Systems Institute, University of Exeter, Exeter, EX4 4QE, UK.
| | - Timothy A Kohler
- Department of Anthropology, Washington State University, Pullman, WA 99164-4910, USA; Santa Fe Institute, Santa Fe, NM 87501, USA; Crow Canyon Archaeological Center, Cortez, CO 81321, USA
| | - Pablo A Marquet
- Santa Fe Institute, Santa Fe, NM 87501, USA; Departamento de Ecología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Alameda 340, Santiago, Chile; Instituto de Ecología y Biodiversidad (IEB), Centro de Cambio Global UC, Laboratorio Internacional de Cambio Global (LINCGlobal), Santiago, Chile
| | - Richard A Boyle
- Global Systems Institute, University of Exeter, Exeter, EX4 4QE, UK
| | - Michel Crucifix
- Université Catholique de Louvain, Earth and Life Institute, Louvain-la-Neuve, Belgium
| | - David M Wilkinson
- School of Life Sciences, University of Lincoln, Lincoln, LN6 7DL, UK; Classics and Archaeology, University of Nottingham, Nottingham, NG7 2RD, UK
| | - Marten Scheffer
- Aquatic Ecology and Water Quality Management, Wageningen University, 6700AA Wageningen, The Netherlands
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Stump SM, Johnson EC, Klausmeier CA. Local interactions and self-organized spatial patterns stabilize microbial cross-feeding against cheaters. J R Soc Interface 2019; 15:rsif.2017.0822. [PMID: 29563243 DOI: 10.1098/rsif.2017.0822] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Accepted: 02/27/2018] [Indexed: 12/13/2022] Open
Abstract
Mutualisms are ubiquitous, but models predict they should be susceptible to cheating. Resolving this paradox has become relevant to synthetic ecology: cooperative cross-feeding, a nutrient-exchange mutualism, has been proposed to stabilize microbial consortia. Previous attempts to understand how cross-feeders remain robust to non-producing cheaters have relied on complex behaviour (e.g. cheater punishment) or group selection. Using a stochastic spatial model, we demonstrate two novel mechanisms that can allow cross-feeders to outcompete cheaters, rather than just escape from them. Both mechanisms work through the spatial segregation of the resources, which prevents individual cheaters from acquiring the resources they need to reproduce. First, if microbe dispersal is low but resources are shared widely, then the cross-feeders self-organize into stable spatial patterns. Here the cross-feeders can build up where the resource they need is abundant, and send their resource to where their partner is, separating resources at regular intervals in space. Second, if dispersal is high but resource sharing is local, then random variation in population density creates small-scale variation in resource density, separating the resources from each other by chance. These results suggest that cross-feeding may be more robust than previously expected and offer strategies to engineer stable consortia.
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Affiliation(s)
- Simon Maccracken Stump
- W. K. Kellogg Biological StationBehavior, Michigan State University, 3700 East Gull Lake Drive, Hickory Corners, MI 49060, USA .,School of Forestry and Environmental Studies, Yale University, 195 Prospect Street, New Haven, CT 06511, USA
| | - Evan Curtis Johnson
- W. K. Kellogg Biological StationBehavior, Michigan State University, 3700 East Gull Lake Drive, Hickory Corners, MI 49060, USA.,Population Biology Graduate Group, University of California, Davis 2320 Storer Hall, One Shields Avenue, Davis, CA 95616, USA
| | - Christopher A Klausmeier
- W. K. Kellogg Biological StationBehavior, Michigan State University, 3700 East Gull Lake Drive, Hickory Corners, MI 49060, USA.,Department of Plant BiologyBehavior, Michigan State University, 3700 East Gull Lake Drive, Hickory Corners, MI 49060, USA.,Program in Ecology, Evolutionary Biology, and Behavior, Michigan State University, 3700 East Gull Lake Drive, Hickory Corners, MI 49060, USA
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Stump SM, Johnson EC, Klausmeier CA. How leaking and overproducing resources affect the evolutionary robustness of cooperative cross-feeding. J Theor Biol 2018; 454:278-291. [DOI: 10.1016/j.jtbi.2018.06.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Revised: 05/11/2018] [Accepted: 06/12/2018] [Indexed: 11/30/2022]
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Selection for Gaia across Multiple Scales. Trends Ecol Evol 2018; 33:633-645. [DOI: 10.1016/j.tree.2018.05.006] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Revised: 05/17/2018] [Accepted: 05/18/2018] [Indexed: 11/18/2022]
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Garcia J, Kao-Kniffin J. Microbial Group Dynamics in Plant Rhizospheres and Their Implications on Nutrient Cycling. Front Microbiol 2018; 9:1516. [PMID: 30050510 PMCID: PMC6050453 DOI: 10.3389/fmicb.2018.01516] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Accepted: 06/18/2018] [Indexed: 12/20/2022] Open
Abstract
Plant rhizospheres encompass a dynamic zone of interactions between microorganisms and their respective plant hosts. For decades, researchers have worked to understand how these complex interactions influence different aspects of plant growth, development, and evolution. Studies of plant-microbial interactions in the root zone have typically focused on the effect of single microbial species or strains on a plant host. These studies, however, provide only a snapshot of the complex interactions that occur in the rhizosphere, leaving researchers with a limited understanding of how the complex microbiome influences the biology of the plant host. To better understand how rhizosphere interactions influence plant growth and development, novel frameworks and research methodologies could be implemented. In this perspective, we propose applying concepts in evolutionary biology to microbiome experiments for improved understanding of group-to-group and community-level microbial interactions influencing soil nutrient cycling. We also put forth simple experimental designs utilizing -omics techniques that can reveal important changes in the rhizosphere impacting the plant host. A greater focus on the components of complexity of the microbiome and how these impact plant host biology could yield more insight into previously unexplored aspects of host-microbe biology relevant to crop production and protection.
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Affiliation(s)
| | - Jenny Kao-Kniffin
- School of Integrative Plant Science, Cornell University, Ithaca, NY, United States
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Stump SM, Johnson EC, Sun Z, Klausmeier CA. How spatial structure and neighbor uncertainty promote mutualists and weaken black queen effects. J Theor Biol 2018; 446:33-60. [PMID: 29499252 DOI: 10.1016/j.jtbi.2018.02.031] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Revised: 02/17/2018] [Accepted: 02/26/2018] [Indexed: 10/17/2022]
Abstract
The ubiquity of cooperative cross-feeding (a resource-exchange mutualism) raises two related questions: Why is cross-feeding favored over self-sufficiency, and how are cross-feeders protected from non-producing cheaters? The Black Queen Hypothesis suggests that if leaky resources are costly, then there should be selection for either gene loss or self-sufficiency, but selection against mutualistic inter-dependency. Localized interactions have been shown to protect mutualists against cheaters, though their effects in the presence of self-sufficient organisms are not well understood. Here we develop a stochastic spatial model to examine how spatial effects alter the predictions of the Black Queen Hypothesis. Microbes need two essential resources to reproduce, which they can produce themselves (at a cost) or take up from neighbors. Additionally, microbes need empty sites to give birth into. Under well mixed mean-field conditions, the cross-feeders will always be displaced by a non-producer and a self-sufficient microbe. However, localized interactions have two effects that favor production. First, a microbe that interacts with a small number of neighbors will not always receive the essential resources it needs; this effect slightly harms cross-feeders but greatly harms non-producers. Second, microbes tend to displace other microbes that produce resources they need; this effect also slightly harms cross-feeders but greatly harms non-producers. Our work therefore suggests localized interactions produce an accelerating cost of non-production. Thus, the right trade-off between the cost of producing resources and the cost of sometimes being resource-limited can favor mutualistic inter-dependence over both self-sufficiency and non-production.
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Affiliation(s)
- Simon Maccracken Stump
- W. K. Kellogg Biological Station, Michigan State University, 3700 East Gull Lake Drive, Hickory Corners, MI 49060, USA.
| | - Evan Curtis Johnson
- W. K. Kellogg Biological Station, Michigan State University, 3700 East Gull Lake Drive, Hickory Corners, MI 49060, USA; Population Biology Graduate Group, University of California, Davis, 2320 Storer Hall, One Shields Avenue, Davis, CA 95616, USA
| | - Zepeng Sun
- W. K. Kellogg Biological Station, Michigan State University, 3700 East Gull Lake Drive, Hickory Corners, MI 49060, USA
| | - Christopher A Klausmeier
- W. K. Kellogg Biological Station, Michigan State University, 3700 East Gull Lake Drive, Hickory Corners, MI 49060, USA; Department of Plant Biology, Michigan State University, 612 Wilson Road, East Lansing, MI 48824-1312, USA; Program in Ecology, Evolutionary Biology, and Behavior, Michigan State University, 293 Farm Lane, East Lansing, MI 48824-1312, USA
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Rocabert C, Knibbe C, Consuegra J, Schneider D, Beslon G. Beware batch culture: Seasonality and niche construction predicted to favor bacterial adaptive diversification. PLoS Comput Biol 2017; 13:e1005459. [PMID: 28358919 PMCID: PMC5391122 DOI: 10.1371/journal.pcbi.1005459] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Revised: 04/13/2017] [Accepted: 03/16/2017] [Indexed: 12/26/2022] Open
Abstract
Metabolic cross-feeding interactions between microbial strains are common in nature, and emerge during evolution experiments in the laboratory, even in homogeneous environments providing a single carbon source. In sympatry, when the environment is well-mixed, the reasons why emerging cross-feeding interactions may sometimes become stable and lead to monophyletic genotypic clusters occupying specific niches, named ecotypes, remain unclear. As an alternative to evolution experiments in the laboratory, we developed Evo2Sim, a multi-scale model of in silico experimental evolution, equipped with the whole tool case of experimental setups, competition assays, phylogenetic analysis, and, most importantly, allowing for evolvable ecological interactions. Digital organisms with an evolvable genome structure encoding an evolvable metabolic network evolved for tens of thousands of generations in environments mimicking the dynamics of real controlled environments, including chemostat or batch culture providing a single limiting resource. We show here that the evolution of stable cross-feeding interactions requires seasonal batch conditions. In this case, adaptive diversification events result in two stably co-existing ecotypes, with one feeding on the primary resource and the other on by-products. We show that the regularity of serial transfers is essential for the maintenance of the polymorphism, as it allows for at least two stable seasons and thus two temporal niches. A first season is externally generated by the transfer into fresh medium, while a second one is internally generated by niche construction as the provided nutrient is replaced by secreted by-products derived from bacterial growth. In chemostat conditions, even if cross-feeding interactions emerge, they are not stable on the long-term because fitter mutants eventually invade the whole population. We also show that the long-term evolution of the two stable ecotypes leads to character displacement, at the level of the metabolic network but also of the genome structure. This difference of genome structure between both ecotypes impacts the stability of the cross-feeding interaction, when the population is propagated in chemostat conditions. This study shows the crucial role played by seasonality in temporal niche partitioning and in promoting cross-feeding subgroups into stable ecotypes, a premise to sympatric speciation. Stable bacterial cross-feeding interactions, where one strain feeds on the waste of the other, are important to understand, as they can be a first step toward bacterial speciation. Their emergence is commonly observed in laboratory experiments using Escherichia coli as a model organism. Yet it is not clear how cross-feeding interactions can resist the invasion of a fitter mutant when the environment contains a single resource since there seems to be a single ecological niche. Here, we used another kind of “model organism”, a digital one, allowing for detailed and fast investigations, and providing a way to disentangle generic evolutionary mechanisms from specificities associated with E. coli. Digital organisms with evolvable genomes and metabolic networks compete for resources in conditions mimicking laboratory evolution experiments. In chemostat simulations, although cross-feeding interactions regularly emerged, selective sweeps regularly purged the population of its diversity. By contrast, batch culture allowed for much more stable cross-feeding interactions, because it includes seasons and thus distinct temporal niches, thereby favoring the adaptive diversification of proto-species.
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Affiliation(s)
- Charles Rocabert
- Univ. de Lyon, CNRS, INRIA, INSA-Lyon, UCB Lyon 1, LIRIS UMR5205, Lyon, France
| | - Carole Knibbe
- Univ. de Lyon, CNRS, INRIA, INSA-Lyon, UCB Lyon 1, LIRIS UMR5205, Lyon, France
| | - Jessika Consuegra
- Univ. Grenoble Alpes, Laboratoire Techniques de l’Ingénierie Médicale et de la Complexité - Informatique, Mathématiques et Applications, Grenoble (TIMC-IMAG), Grenoble, France
- Centre National de la Recherche Scientifique (CNRS), TIMC-IMAG, Grenoble, France
| | - Dominique Schneider
- Univ. Grenoble Alpes, Laboratoire Techniques de l’Ingénierie Médicale et de la Complexité - Informatique, Mathématiques et Applications, Grenoble (TIMC-IMAG), Grenoble, France
- Centre National de la Recherche Scientifique (CNRS), TIMC-IMAG, Grenoble, France
| | - Guillaume Beslon
- Univ. de Lyon, CNRS, INRIA, INSA-Lyon, UCB Lyon 1, LIRIS UMR5205, Lyon, France
- * E-mail:
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Barraclough TG. How Do Species Interactions Affect Evolutionary Dynamics Across Whole Communities? ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2015. [DOI: 10.1146/annurev-ecolsys-112414-054030] [Citation(s) in RCA: 102] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Theories of how species evolve in changing environments mostly consider single species in isolation or pairs of interacting species. Yet all organisms live in diverse communities containing many hundreds of species. This review discusses how species interactions influence the evolution of constituent species across whole communities. When species interactions are weak or inconsistent, evolutionary dynamics should be predictable by factors identified by single-species theory. Stronger species interactions, however, can alter evolutionary outcomes and either dampen or promote evolution of constituent species depending on the number of species and the distribution of interaction strengths across the interaction network. Genetic interactions, such as horizontal gene transfer, might also affect evolutionary outcomes. These evolutionary mechanisms in turn affect whole-community properties, such as the level of ecosystem functioning. Successful management of both ecosystems and focal species requires new understanding of evolutionary interactions across whole communities.
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Affiliation(s)
- Timothy G. Barraclough
- Department of Life Sciences, Imperial College London, Silwood Park Campus, Ascot, Berkshire SL5 7PY, United Kingdom
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Modeling microbial growth and dynamics. Appl Microbiol Biotechnol 2015; 99:8831-46. [DOI: 10.1007/s00253-015-6877-6] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Revised: 07/13/2015] [Accepted: 07/16/2015] [Indexed: 12/11/2022]
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Werner GDA, Strassmann JE, Ivens ABF, Engelmoer DJP, Verbruggen E, Queller DC, Noë R, Johnson NC, Hammerstein P, Kiers ET. Evolution of microbial markets. Proc Natl Acad Sci U S A 2014; 111:1237-44. [PMID: 24474743 PMCID: PMC3910570 DOI: 10.1073/pnas.1315980111] [Citation(s) in RCA: 121] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Biological market theory has been used successfully to explain cooperative behavior in many animal species. Microbes also engage in cooperative behaviors, both with hosts and other microbes, that can be described in economic terms. However, a market approach is not traditionally used to analyze these interactions. Here, we extend the biological market framework to ask whether this theory is of use to evolutionary biologists studying microbes. We consider six economic strategies used by microbes to optimize their success in markets. We argue that an economic market framework is a useful tool to generate specific and interesting predictions about microbial interactions, including the evolution of partner discrimination, hoarding strategies, specialized versus diversified mutualistic services, and the role of spatial structures, such as flocks and consortia. There is untapped potential for studying the evolutionary dynamics of microbial systems. Market theory can help structure this potential by characterizing strategic investment of microbes across a diversity of conditions.
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Affiliation(s)
- Gijsbert D. A. Werner
- Department of Ecological Science, Vrije Universiteit Amsterdam, 1081 HV, Amsterdam, The Netherlands
| | - Joan E. Strassmann
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130
| | - Aniek B. F. Ivens
- Theoretical Biology Group, Centre for Ecological and Evolutionary Studies, University of Groningen, 9700 CC, Groningen, The Netherlands
- Laboratory of Insect Social Evolution, The Rockefeller University, New York, NY 10065
| | - Daniel J. P. Engelmoer
- Department of Ecological Science, Vrije Universiteit Amsterdam, 1081 HV, Amsterdam, The Netherlands
| | - Erik Verbruggen
- Institut für Biologie, Plant Ecology, Freie Universität Berlin, 14195 Berlin, Germany
| | - David C. Queller
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130
| | - Ronald Noë
- Faculté de Psychologie, Université de Strasbourg et Ethologie Evolutive, Département Ecologie, Physiologie et Ethologie, Centre National de la Recherche Scientifique, 67087 Strasbourg Cedex, France
- Netherlands Institute of Advanced Studies, 2242 PR, Wassenaar, The Netherlands
| | - Nancy Collins Johnson
- School of Earth Sciences and Environmental Sustainability and Biological Sciences, Northern Arizona University, Flagstaff, AZ 86011-5694; and
| | - Peter Hammerstein
- Institute for Theoretical Biology, Humboldt University, 10115 Berlin, Germany
| | - E. Toby Kiers
- Department of Ecological Science, Vrije Universiteit Amsterdam, 1081 HV, Amsterdam, The Netherlands
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