1
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Derelle R, Verdonck R, Jacob S, Huet M, Akerman I, Philippe H, Legrand D. The macronuclear genomic landscape within Tetrahymena thermophila. Microb Genom 2024; 10:001175. [PMID: 38206129 PMCID: PMC10868616 DOI: 10.1099/mgen.0.001175] [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: 09/04/2023] [Accepted: 12/19/2023] [Indexed: 01/12/2024] Open
Abstract
The extent of intraspecific genomic variation is key to understanding species evolutionary history, including recent adaptive shifts. Intraspecific genomic variation remains poorly explored in eukaryotic micro-organisms, especially in the nuclear dimorphic ciliates, despite their fundamental role as laboratory model systems and their ecological importance in many ecosystems. We sequenced the macronuclear genome of 22 laboratory strains of the oligohymenophoran Tetrahymena thermophila, a model species in both cellular biology and evolutionary ecology. We explored polymorphisms at the junctions of programmed eliminated sequences, and reveal their utility to barcode very closely related cells. As for other species of the genus Tetrahymena, we confirm micronuclear centromeres as gene diversification centres in T. thermophila, but also reveal a two-speed evolution in these regions. In the rest of the genome, we highlight recent diversification of genes coding for extracellular proteins and cell adhesion. We discuss all these findings in relation to this ciliate's ecology and cellular characteristics.
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Affiliation(s)
- Romain Derelle
- Station d’Ecologie Théorique et Expérimentale, UAR2029, CNRS, Moulis, France
- Present address: NIHR Health Protection Research Unit in Respiratory Infections, National Heart and Lung Institute, Imperial College London, London, UK
| | - Rik Verdonck
- Station d’Ecologie Théorique et Expérimentale, UAR2029, CNRS, Moulis, France
- Present address: Centre for Environmental Sciences, Environmental Biology, Hasselt University, Diepenbeek, Belgium
| | - Staffan Jacob
- Station d’Ecologie Théorique et Expérimentale, UAR2029, CNRS, Moulis, France
| | - Michèle Huet
- Station d’Ecologie Théorique et Expérimentale, UAR2029, CNRS, Moulis, France
| | - Ildem Akerman
- Institute of Metabolism and Systems Research, University of Birmingham, Birmingham, UK
| | - Hervé Philippe
- Station d’Ecologie Théorique et Expérimentale, UAR2029, CNRS, Moulis, France
| | - Delphine Legrand
- Station d’Ecologie Théorique et Expérimentale, UAR2029, CNRS, Moulis, France
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2
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Del Arco A, Becks L, de Vicente I. Population dynamics hide phenotypic changes driven by subtle chemical exposures: implications for risk assessments. ECOTOXICOLOGY (LONDON, ENGLAND) 2023; 32:281-289. [PMID: 36871096 PMCID: PMC10102127 DOI: 10.1007/s10646-023-02637-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Accepted: 02/15/2023] [Indexed: 06/18/2023]
Abstract
Ecological risk assessment of chemicals focuses on the response of different taxa in isolation not taking ecological and evolutionary interplay in communities into account. Its consideration would, however, allow for an improved assessment by testing for implications within and across trophic levels and changes in the phenotypic and genotypic diversity within populations. We present a simple experimental system that can be used to evaluate the ecological and evolutionary responses to chemical exposure at microbial community levels. We exposed a microbial model system of the ciliate Tetrahymena thermophila (predator) and the bacterium Pseudomonas fluorescens (prey) to iron released from Magnetic Particles (MP-Fedis), which are Phosphorus (P) adsorbents used in lake restoration. Our results show that while the responses of predator single population size differed across concentrations of MP-Fedis and the responses of prey from communities differed also across concentration of MP-Fedis, the community responses (species ratio) were similar for the different MP-Fedis concentrations. Looking further at an evolutionary change in the bacterial preys' defence, we found that MP-Fedis drove different patterns and dynamics of defence evolution. Overall, our study shows how similar community dynamics mask changes at evolutionary levels that would be overlooked in the design of current risk assessment protocols where evolutionary approaches are not considered.
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Affiliation(s)
- Ana Del Arco
- Community Dynamics Group, Department of Evolutionary Ecology, Max Planck Institute for Evolutionary Biology, 24306, Plön, Germany.
- Limnological Institute, Biology Department, University of Konstanz, 78464, Konstanz/Egg, Germany.
| | - Lutz Becks
- Community Dynamics Group, Department of Evolutionary Ecology, Max Planck Institute for Evolutionary Biology, 24306, Plön, Germany
- Limnological Institute, Biology Department, University of Konstanz, 78464, Konstanz/Egg, Germany
| | - Inmaculada de Vicente
- Departamento de Ecología, Facultad de Ciencias, Universidad de Granada, Granada, 18071, Spain
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3
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Plum K, Tarkington J, Zufall RA. Experimental Evolution in Tetrahymena. Microorganisms 2022; 10:414. [PMID: 35208869 PMCID: PMC8877770 DOI: 10.3390/microorganisms10020414] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 01/21/2022] [Accepted: 02/03/2022] [Indexed: 02/06/2023] Open
Abstract
Experimental evolution has provided novel insight into a wide array of biological processes. Species in the genus Tetrahymena are proving to be a highly useful system for studying a range of questions using experimental evolution. Their unusual genomic architecture, diversity of life history traits, importance as both predator and prey, and amenability to laboratory culture allow them to be studied in a variety of contexts. In this paper, we review what we are learning from experimental evolution with Tetrahymena about mutation, adaptation, and eco-evolutionary dynamics. We predict that future experimental evolution studies using Tetrahyemena will continue to shed new light on these processes.
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Affiliation(s)
- Karissa Plum
- Department of Biology and Biochemistry, University of Houston, Houston, TX 77204, USA;
| | - Jason Tarkington
- Department of Genetics, Stanford University, Stanford, CA 94305, USA;
| | - Rebecca A. Zufall
- Department of Biology and Biochemistry, University of Houston, Houston, TX 77204, USA;
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4
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Nguyen VAT, Vural DC. Theoretical guidelines for editing ecological communities. J Theor Biol 2021; 534:110945. [PMID: 34717935 DOI: 10.1016/j.jtbi.2021.110945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 10/21/2021] [Accepted: 10/22/2021] [Indexed: 11/18/2022]
Abstract
Having control over species abundances and community resilience is of great interest for experimental, agricultural, industrial and conservation purposes. Here, we theoretically explore the possibility of manipulating ecological communities by modifying pairwise interactions. Specifically, we establish which interaction values should be modified, and by how much, in order to alter the composition or resilience of a community towards a favorable direction. While doing so, we also take into account the experimental difficulties in making such modifications by including in our optimization process, a cost parameter, which penalizes large modifications. In addition to prescribing what changes should be made to interspecies interactions given some modification cost, our approach also serves to establish the limits of community control, i.e. how well can one approach an ecological goal at best, even when not constrained by cost.
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Affiliation(s)
- Vu A T Nguyen
- University of Notre Dame, South Bend, IN, United States
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5
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Bonkowski M, Tarkka M, Razavi BS, Schmidt H, Blagodatskaya E, Koller R, Yu P, Knief C, Hochholdinger F, Vetterlein D. Spatiotemporal Dynamics of Maize ( Zea mays L.) Root Growth and Its Potential Consequences for the Assembly of the Rhizosphere Microbiota. Front Microbiol 2021; 12:619499. [PMID: 33815308 PMCID: PMC8010349 DOI: 10.3389/fmicb.2021.619499] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 02/16/2021] [Indexed: 12/20/2022] Open
Abstract
Numerous studies have shown that plants selectively recruit microbes from the soil to establish a complex, yet stable and quite predictable microbial community on their roots – their “microbiome.” Microbiome assembly is considered as a key process in the self-organization of root systems. A fundamental question for understanding plant-microbe relationships is where a predictable microbiome is formed along the root axis and through which microbial dynamics the stable formation of a microbiome is challenged. Using maize as a model species for which numerous data on dynamic root traits are available, this mini-review aims to give an integrative overview on the dynamic nature of root growth and its consequences for microbiome assembly based on theoretical considerations from microbial community ecology.
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Affiliation(s)
- Michael Bonkowski
- Terrestrial Ecology, Institute of Zoology, University of Cologne, Cologne, Germany
| | - Mika Tarkka
- Department of Soil Ecology, Helmholtz Centre for Environmental Research - UFZ, Halle, Germany.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
| | - Bahar S Razavi
- Department of Soil and Plant Microbiome, Christian-Albrecht University of Kiel, Kiel, Germany
| | - Hannes Schmidt
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Evgenia Blagodatskaya
- Department of Soil Ecology, Helmholtz Centre for Environmental Research - UFZ, Halle, Germany
| | - Robert Koller
- Institute of Bio- and Geosciences, IBG-2: Plant Sciences, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Peng Yu
- Emmy Noether Group Root Functional Biology, Institute of Crop Science and Resource Conservation (INRES), University of Bonn, Bonn, Germany
| | - Claudia Knief
- Institute of Crop Science and Resource Conservation - Molecular Biology of the Rhizosphere, University of Bonn, Bonn, Germany
| | - Frank Hochholdinger
- Crop Functional Genomics, Institute of Crop Science and Resource Conservation (INRES), University of Bonn, Bonn, Germany
| | - Doris Vetterlein
- Department of Soil System Science, Helmholtz Centre for Environmental Research - UFZ, Halle, Germany.,Soil Science, Martin-Luther-University Halle-Wittenberg, Halle, Germany
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6
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Paranjape K, Bédard É, Shetty D, Hu M, Choon FCP, Prévost M, Faucher SP. Unravelling the importance of the eukaryotic and bacterial communities and their relationship with Legionella spp. ecology in cooling towers: a complex network. MICROBIOME 2020; 8:157. [PMID: 33183356 PMCID: PMC7664032 DOI: 10.1186/s40168-020-00926-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 09/20/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND Cooling towers are a major source of large community-associated outbreaks of Legionnaires' disease, a severe pneumonia. This disease is contracted when inhaling aerosols that are contaminated with bacteria from the genus Legionella, most importantly Legionella pneumophila. How cooling towers support the growth of this bacterium is still not well understood. As Legionella species are intracellular parasites of protozoa, it is assumed that protozoan community in cooling towers play an important role in Legionella ecology and outbreaks. However, the exact mechanism of how the eukaryotic community contributes to Legionella ecology is still unclear. Therefore, we used 18S rRNA gene amplicon sequencing to characterize the eukaryotic communities of 18 different cooling towers. The data from the eukaryotic community was then analysed with the bacterial community of the same towers in order to understand how each community could affect Legionella spp. ecology in cooling towers. RESULTS We identified several microbial groups in the cooling tower ecosystem associated with Legionella spp. that suggest the presence of a microbial loop in these systems. Dissolved organic carbon was shown to be a major factor in shaping the eukaryotic community and may be an important factor for Legionella ecology. Network analysis, based on co-occurrence, revealed that Legionella was correlated with a number of different organisms. Out of these, the bacterial genus Brevundimonas and the ciliate class Oligohymenophorea were shown, through in vitro experiments, to stimulate the growth of L. pneumophila through direct and indirect mechanisms. CONCLUSION Our results suggest that Legionella ecology depends on the host community, including ciliates and on several groups of organisms that contribute to its survival and growth in the cooling tower ecosystem. These findings further support the idea that some cooling tower microbiomes may promote the survival and growth of Legionella better than others. Video Abstract.
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Affiliation(s)
- Kiran Paranjape
- Department of Natural Resource Sciences, Faculty of Agricultural and Environmental Sciences, McGill University, Sainte-Anne-de-Bellevue, QC, Canada
| | - Émilie Bédard
- Department of Civil Engineering, Polytechnique Montreal, Montréal, QC, Canada
| | - Deeksha Shetty
- Department of Natural Resource Sciences, Faculty of Agricultural and Environmental Sciences, McGill University, Sainte-Anne-de-Bellevue, QC, Canada
| | - Mengqi Hu
- Department of Natural Resource Sciences, Faculty of Agricultural and Environmental Sciences, McGill University, Sainte-Anne-de-Bellevue, QC, Canada
| | - Fiona Chan Pak Choon
- Department of Natural Resource Sciences, Faculty of Agricultural and Environmental Sciences, McGill University, Sainte-Anne-de-Bellevue, QC, Canada
| | - Michèle Prévost
- Department of Civil Engineering, Polytechnique Montreal, Montréal, QC, Canada
| | - Sébastien P Faucher
- Department of Natural Resource Sciences, Faculty of Agricultural and Environmental Sciences, McGill University, Sainte-Anne-de-Bellevue, QC, Canada.
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7
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Koch HR, Wagner S, Becks L. Antagonistic species interaction drives selection for sex in a predator-prey system. J Evol Biol 2020; 33:1180-1191. [PMID: 32500538 DOI: 10.1111/jeb.13658] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Accepted: 05/22/2020] [Indexed: 01/26/2023]
Abstract
The evolutionary maintenance of sexual reproduction has long challenged biologists as the majority of species reproduce sexually despite inherent costs. Providing a general explanation for the evolutionary success of sex has thus proven difficult and resulted in numerous hypotheses. A leading hypothesis suggests that antagonistic species interaction can generate conditions selecting for increased sex due to the production of rare or novel genotypes that are beneficial for rapid adaptation to recurrent environmental change brought on by antagonism. To test this ecology-based hypothesis, we conducted experimental evolution in a predator (rotifer)-prey (algal) system by using continuous cultures to track predator-prey dynamics and in situ rates of sex in the prey over time and within replicated experimental populations. Overall, we found that predator-mediated fluctuating selection for competitive versus defended prey resulted in higher rates of genetic mixing in the prey. More specifically, our results showed that fluctuating population sizes of predator and prey, coupled with a trade-off in the prey, drove the sort of recurrent environmental change that could provide a benefit to sex in the prey, despite inherent costs. We end with a discussion of potential population genetic mechanisms underlying increased selection for sex in this system, based on our application of a general theoretical framework for measuring the effects of sex over time, and interpreting how these effects can lead to inferences about the conditions selecting for or against sexual reproduction in a system with antagonistic species interaction.
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Affiliation(s)
- Hanna R Koch
- Community Dynamics Group, Department of Evolutionary Ecology, Max Planck Institute for Evolutionary Biology, D-Plön, Germany
| | - Sophia Wagner
- Community Dynamics Group, Department of Evolutionary Ecology, Max Planck Institute for Evolutionary Biology, D-Plön, Germany
| | - Lutz Becks
- Community Dynamics Group, Department of Evolutionary Ecology, Max Planck Institute for Evolutionary Biology, D-Plön, Germany
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8
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Cairns J, Moerman F, Fronhofer EA, Altermatt F, Hiltunen T. Evolution in interacting species alters predator life-history traits, behaviour and morphology in experimental microbial communities. Proc Biol Sci 2020; 287:20200652. [PMID: 32486984 DOI: 10.1098/rspb.2020.0652] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Predator-prey interactions heavily influence the dynamics of many ecosystems. An increasing body of evidence suggests that rapid evolution and coevolution can alter these interactions, with important ecological implications, by acting on traits determining fitness, including reproduction, anti-predatory defence and foraging efficiency. However, most studies to date have focused only on evolution in the prey species, and the predator traits in (co)evolving systems remain poorly understood. Here, we investigated changes in predator traits after approximately 600 generations in a predator-prey (ciliate-bacteria) evolutionary experiment. Predators independently evolved on seven different prey species, allowing generalization of the predator's evolutionary response. We used highly resolved automated image analysis to quantify changes in predator life history, morphology and behaviour. Consistent with previous studies, we found that prey evolution impaired growth of the predator, although the effect depended on the prey species. By contrast, predator evolution did not cause a clear increase in predator growth when feeding on ancestral prey. However, predator evolution affected morphology and behaviour, increasing size, speed and directionality of movement, which have all been linked to higher prey search efficiency. These results show that in (co)evolving systems, predator adaptation can occur in traits relevant to foraging efficiency without translating into an increased ability of the predator to grow on the ancestral prey type.
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Affiliation(s)
- Johannes Cairns
- Wellcome Sanger Institute, Cambridge CB10 1SA, UK.,Organismal and Evolutionary Biology Research Programme, Department of Computer Science, University of Helsinki, 00014 Helsinki, Finland.,Department of Microbiology, University of Helsinki, PO Box 56, 00014 Helsinki, Finland
| | - Felix Moerman
- Department of Aquatic Ecology, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Überlandstrasse 133, 8600 Dübendorf, Switzerland.,Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, 8057 Zürich, Switzerland.,ISEM, University of Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | | | - Florian Altermatt
- Department of Aquatic Ecology, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Überlandstrasse 133, 8600 Dübendorf, Switzerland.,Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Teppo Hiltunen
- Department of Microbiology, University of Helsinki, PO Box 56, 00014 Helsinki, Finland.,Department of Biology, University of Turku, 20014 Turku, Finland
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9
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A remark on "Biological control through provision of additional food to predators: A theoretical study" [Theor. Popul. Biol. 72 (2007) 111-120]. Theor Popul Biol 2019; 132:60-68. [PMID: 31836473 DOI: 10.1016/j.tpb.2019.11.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Revised: 11/26/2019] [Accepted: 11/27/2019] [Indexed: 11/23/2022]
Abstract
Biological control, the use of predators and pathogens to control target pests, is a promising alternative to chemical control. It is hypothesized that the introduced predators efficacy can be boosted by providing them with an additional food source. The current literature (Srinivasu, 2007; 2010; 2011) claims that if the additional food is of sufficiently large quantity and quality then pest eradication is possible in finite time. The purpose of the current manuscript is to show that to the contrary, pest eradication is not possible in finite time, for any quantity and quality of additional food. We show that pest eradication will occur only in infinite time, and derive decay rates to the extinction state. We posit a new modeling framework to yield finite time pest extinction. Our results have large scale implications for the effective design of biological control methods involving additional food.
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10
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McClean D, Friman V, Finn A, Salzberg LI, Donohue I. Coping with multiple enemies: pairwise interactions do not predict evolutionary change in complex multitrophic communities. OIKOS 2019. [DOI: 10.1111/oik.06586] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Deirdre McClean
- Centre for Immunity, Infection and Evolution, Univ. of Edinburgh Edinburgh UK
- Centre for Synthetic and Systems Biology, School of Biological Sciences Univ. of Edinburgh Edinburgh UK
| | | | - Alain Finn
- Dept of Zoology, School of Natural Sciences, Trinity College Dublin Ireland
| | - Letal I. Salzberg
- Smurfit Inst. of Genetics, School of Genetics and Microbiology, Trinity College Dublin Ireland
| | - Ian Donohue
- Dept of Zoology, School of Natural Sciences, Trinity College Dublin Ireland
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11
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Kurm V, van der Putten WH, Weidner S, Geisen S, Snoek BL, Bakx T, Hol WHG. Competition and predation as possible causes of bacterial rarity. Environ Microbiol 2019; 21:1356-1368. [PMID: 30803145 PMCID: PMC6850713 DOI: 10.1111/1462-2920.14569] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2018] [Accepted: 02/21/2019] [Indexed: 12/05/2022]
Abstract
We assembled communities of bacteria and exposed them to different nutrient concentrations with or without predation by protists. Taxa that were rare in the field were less abundant at low nutrient concentrations than common taxa, independent of predation. However, some taxa that were rare in the field became highly abundant in the assembled communities, especially under ample nutrient availability. This high abundance points at a possible competitive advantage of some rare bacterial taxa under nutrient-rich conditions. In contrast, the abundance of most rare bacterial taxa decreased at low resource availability. Since low resource availability will be the prevailing situation in most soils, our data suggests that under those conditions poor competitiveness for limiting resources may contribute to bacterial rarity. Interestingly, taxa that were rare in the field and most successful under predator-free conditions in the lab also tended to be more reduced by predation than common taxa. This suggests that predation contributes to rarity of bacterial taxa in the field. We further discuss whether there may be a trade-off between competitiveness and predation resistance. The substantial variability among taxa in their responses to competition and predation suggests that other factors, for example abiotic conditions and dispersal ability, also influence the local abundance of soil bacteria.
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Affiliation(s)
- Viola Kurm
- Department of Terrestrial EcologyNetherlands Institute of Ecology (NIOO‐KNAW)P.O. Box 50, 6700 AB, WageningenThe Netherlands
| | - Wim H. van der Putten
- Department of Terrestrial EcologyNetherlands Institute of Ecology (NIOO‐KNAW)P.O. Box 50, 6700 AB, WageningenThe Netherlands
- Laboratory of NematologyWageningen UniversityP.O. Box 8123, 6700 ES, WageningenThe Netherlands
| | - Simone Weidner
- Institute of Environmental Biology, Ecology and BiodiversityUtrecht UniversityPadualaan 8, 3584 CH, UtrechtThe Netherlands
| | - Stefan Geisen
- Department of Terrestrial EcologyNetherlands Institute of Ecology (NIOO‐KNAW)P.O. Box 50, 6700 AB, WageningenThe Netherlands
| | - Basten L. Snoek
- Department of Terrestrial EcologyNetherlands Institute of Ecology (NIOO‐KNAW)P.O. Box 50, 6700 AB, WageningenThe Netherlands
- Laboratory of NematologyWageningen UniversityP.O. Box 8123, 6700 ES, WageningenThe Netherlands
- Theoretical Biology and BioinformaticsUtrecht UniversityPadualaan 8, 3584 CH, UtrechtThe Netherlands
| | - Tanja Bakx
- Department of Terrestrial EcologyNetherlands Institute of Ecology (NIOO‐KNAW)P.O. Box 50, 6700 AB, WageningenThe Netherlands
| | - Wilhelmina H. Gera Hol
- Department of Terrestrial EcologyNetherlands Institute of Ecology (NIOO‐KNAW)P.O. Box 50, 6700 AB, WageningenThe Netherlands
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12
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Van den Bergh B, Swings T, Fauvart M, Michiels J. Experimental Design, Population Dynamics, and Diversity in Microbial Experimental Evolution. Microbiol Mol Biol Rev 2018; 82:e00008-18. [PMID: 30045954 PMCID: PMC6094045 DOI: 10.1128/mmbr.00008-18] [Citation(s) in RCA: 90] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
In experimental evolution, laboratory-controlled conditions select for the adaptation of species, which can be monitored in real time. Despite the current popularity of such experiments, nature's most pervasive biological force was long believed to be observable only on time scales that transcend a researcher's life-span, and studying evolution by natural selection was therefore carried out solely by comparative means. Eventually, microorganisms' propensity for fast evolutionary changes proved us wrong, displaying strong evolutionary adaptations over a limited time, nowadays massively exploited in laboratory evolution experiments. Here, we formulate a guide to experimental evolution with microorganisms, explaining experimental design and discussing evolutionary dynamics and outcomes and how it is used to assess ecoevolutionary theories, improve industrially important traits, and untangle complex phenotypes. Specifically, we give a comprehensive overview of the setups used in experimental evolution. Additionally, we address population dynamics and genetic or phenotypic diversity during evolution experiments and expand upon contributing factors, such as epistasis and the consequences of (a)sexual reproduction. Dynamics and outcomes of evolution are most profoundly affected by the spatiotemporal nature of the selective environment, where changing environments might lead to generalists and structured environments could foster diversity, aided by, for example, clonal interference and negative frequency-dependent selection. We conclude with future perspectives, with an emphasis on possibilities offered by fast-paced technological progress. This work is meant to serve as an introduction to those new to the field of experimental evolution, as a guide to the budding experimentalist, and as a reference work to the seasoned expert.
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Affiliation(s)
- Bram Van den Bergh
- Laboratory of Symbiotic and Pathogenic Interactions, Centre of Microbial and Plant Genetics, KU Leuven-University of Leuven, Leuven, Belgium
- Michiels Lab, Center for Microbiology, VIB, Leuven, Belgium
- Douglas Lab, Department of Entomology, Cornell University, Ithaca, New York, USA
| | - Toon Swings
- Laboratory of Symbiotic and Pathogenic Interactions, Centre of Microbial and Plant Genetics, KU Leuven-University of Leuven, Leuven, Belgium
- Michiels Lab, Center for Microbiology, VIB, Leuven, Belgium
| | - Maarten Fauvart
- Laboratory of Symbiotic and Pathogenic Interactions, Centre of Microbial and Plant Genetics, KU Leuven-University of Leuven, Leuven, Belgium
- Michiels Lab, Center for Microbiology, VIB, Leuven, Belgium
- imec, Leuven, Belgium
| | - Jan Michiels
- Laboratory of Symbiotic and Pathogenic Interactions, Centre of Microbial and Plant Genetics, KU Leuven-University of Leuven, Leuven, Belgium
- Michiels Lab, Center for Microbiology, VIB, Leuven, Belgium
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13
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Cairns J, Ruokolainen L, Hultman J, Tamminen M, Virta M, Hiltunen T. Ecology determines how low antibiotic concentration impacts community composition and horizontal transfer of resistance genes. Commun Biol 2018; 1:35. [PMID: 30271921 PMCID: PMC6123812 DOI: 10.1038/s42003-018-0041-7] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2017] [Accepted: 03/28/2018] [Indexed: 01/20/2023] Open
Abstract
Low concentrations of antibiotics have numerous effects on bacteria. However, it is unknown whether ecological factors such as trophic interactions and spatial structuring influence the effects of low concentrations of antibiotics on multispecies microbial communities. Here, we address this question by investigating the effects of low antibiotic concentration on community composition and horizontal transfer of an antibiotic resistance plasmid in a 62-strain bacterial community in response to manipulation of the spatial environment and presence of predation. The strong effects of antibiotic treatment on community composition depend on the presence of predation and spatial structuring that have strong community effects on their own. Overall, we find plasmid transfer to diverse recipient taxa. Plasmid transfer is likely to occur to abundant strains, occurs to a higher number of strains in the presence of antibiotic, and also occurs to low-abundance strains in the presence of spatial structures. These results fill knowledge gaps concerning the effects of low antibiotic concentrations in complex ecological settings.
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Affiliation(s)
- Johannes Cairns
- Department of Microbiology, University of Helsinki, P.O. Box 56, 00014, Helsinki, Finland
| | - Lasse Ruokolainen
- Department of Biosciences, University of Helsinki, P.O. Box 65, 00014, Helsinki, Finland
| | - Jenni Hultman
- Department of Microbiology, University of Helsinki, P.O. Box 56, 00014, Helsinki, Finland
| | - Manu Tamminen
- Department of Aquatic Ecology, Eawag, Dubendorf, 8600, Zurich, Switzerland.,Department of Environmental Systems Science, ETH Zurich, 8092, Zurich, Switzerland
| | - Marko Virta
- Department of Microbiology, University of Helsinki, P.O. Box 56, 00014, Helsinki, Finland
| | - Teppo Hiltunen
- Department of Microbiology, University of Helsinki, P.O. Box 56, 00014, Helsinki, Finland.
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Flues S, Bass D, Bonkowski M. Grazing of leaf‐associated Cercomonads (Protists: Rhizaria: Cercozoa) structures bacterial community composition and function. Environ Microbiol 2017; 19:3297-3309. [DOI: 10.1111/1462-2920.13824] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Revised: 06/06/2017] [Accepted: 06/07/2017] [Indexed: 01/06/2023]
Affiliation(s)
- Sebastian Flues
- Department of Terrestrial Ecology, Institute of ZoologyUniversity of CologneZülpicher Straße 47bKöln 50674 Germany
| | - David Bass
- Department of Life SciencesThe Natural History MuseumCromwell RoadLondonSW7 5BD UK
- CefasBarrack Road, The Nothe, Weymouth, Dorset DT4 8UB UK
| | - Michael Bonkowski
- Department of Terrestrial Ecology, Institute of ZoologyUniversity of CologneZülpicher Straße 47bKöln 50674 Germany
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Hiltunen T, Ayan GB, Becks L. Environmental fluctuations restrict eco-evolutionary dynamics in predator-prey system. Proc Biol Sci 2016; 282:20150013. [PMID: 25994670 DOI: 10.1098/rspb.2015.0013] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Environmental fluctuations, species interactions and rapid evolution are all predicted to affect community structure and their temporal dynamics. Although the effects of the abiotic environment and prey evolution on ecological community dynamics have been studied separately, these factors can also have interactive effects. Here we used bacteria-ciliate microcosm experiments to test for eco-evolutionary dynamics in fluctuating environments. Specifically, we followed population dynamics and a prey defence trait over time when populations were exposed to regular changes of bottom-up or top-down stressors, or combinations of these. We found that the rate of evolution of a defence trait was significantly lower in fluctuating compared with stable environments, and that the defence trait evolved to lower levels when two environmental stressors changed recurrently. The latter suggests that top-down and bottom-up changes can have additive effects constraining evolutionary response within populations. The differences in evolutionary trajectories are explained by fluctuations in population sizes of the prey and the predator, which continuously alter the supply of mutations in the prey and strength of selection through predation. Thus, it may be necessary to adopt an eco-evolutionary perspective on studies concerning the evolution of traits mediating species interactions.
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Affiliation(s)
- Teppo Hiltunen
- Division of Microbiology and Biotechnology, Department of Food and Environmental Sciences, University of Helsinki, PO Box 65, Helsinki 00014, Finland
| | - Gökçe B Ayan
- Department of Evolutionary Ecology, Community Dynamics Group, Max Planck Institute for Evolutionary Biology, August Thienemann Street 2, Plön 24306, Germany
| | - Lutz Becks
- Department of Evolutionary Ecology, Community Dynamics Group, Max Planck Institute for Evolutionary Biology, August Thienemann Street 2, Plön 24306, Germany
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Kinnison MT, Hairston NG, Hendry AP. Cryptic eco-evolutionary dynamics. Ann N Y Acad Sci 2016; 1360:120-44. [PMID: 26619300 DOI: 10.1111/nyas.12974] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Revised: 10/22/2015] [Accepted: 10/23/2015] [Indexed: 12/17/2022]
Abstract
Natural systems harbor complex interactions that are fundamental parts of ecology and evolution. These interactions challenge our inclinations and training to seek the simplest explanations of patterns in nature. Not least is the likelihood that some complex processes might be missed when their patterns look similar to predictions for simpler mechanisms. Along these lines, theory and empirical evidence increasingly suggest that environmental, ecological, phenotypic, and genetic processes can be tightly intertwined, resulting in complex and sometimes surprising eco-evolutionary dynamics. The goal of this review is to temper inclinations to unquestioningly seek the simplest explanations in ecology and evolution, by recognizing that some eco-evolutionary outcomes may appear very similar to purely ecological, purely evolutionary, or even null expectations, and thus be cryptic. We provide theoretical and empirical evidence for observational biases and mechanisms that might operate among the various links in eco-evolutionary feedbacks to produce cryptic patterns. Recognition that cryptic dynamics can be associated with outcomes like stability, resilience, recovery, or coexistence in a dynamically changing world provides added impetus for finding ways to study them.
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Affiliation(s)
| | - Nelson G Hairston
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York
| | - Andrew P Hendry
- Redpath Museum and Department of Biology, McGill University, Montreal, Quebec, Canada
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17
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Relative importance of evolutionary dynamics depends on the composition of microbial predator-prey community. ISME JOURNAL 2015; 10:1352-62. [PMID: 26684728 DOI: 10.1038/ismej.2015.217] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Revised: 10/08/2015] [Accepted: 10/16/2015] [Indexed: 11/09/2022]
Abstract
Community dynamics are often studied in subsets of pairwise interactions. Scaling pairwise interactions back to the community level is, however, problematic because one given interaction might not reflect ecological and evolutionary outcomes of other functionally similar species interactions or capture the emergent eco-evolutionary dynamics arising only in more complex communities. Here we studied this experimentally by exposing Pseudomonas fluorescens SBW25 prey bacterium to four different protist predators (Tetrahymena pyriformis, Tetrahymena vorax, Chilomonas paramecium and Acanthamoeba polyphaga) in all possible single-predator, two-predator and four-predator communities for hundreds of prey generations covering both ecological and evolutionary timescales. We found that only T. pyriformis selected for prey defence in single-predator communities. Although T. pyriformis selection was constrained in the presence of the intraguild predator, T. vorax, T. pyriformis selection led to evolution of specialised prey defence strategies in the presence of C. paramecium or A. polyphaga. At the ecological level, adapted prey populations were phenotypically more diverse, less stable and less productive compared with non-adapted prey populations. These results suggest that predator community composition affects the relative importance of ecological and evolutionary processes and can crucially determine when rapid evolution has the potential to change ecological properties of microbial communities.
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Abstract
Understanding biological range expansions and invasions is of great ecological and economical interest. Importantly, spatial dynamics can be deeply affected by rapid evolution depending on the ecological context. Using experimental evolution in replicated microcosm landscapes and numerical analyses we show experimentally that the ecological process of range expansions leads to the evolution of increased dispersal. This evolutionary change counter-intuitively feeds back on (macro-)ecological patterns affecting the spatial distribution of population densities. While existing theory suggests that densities decrease from range cores to range margins due to K-selection, we show the reverse to be true when competition is considered explicitly including resource dynamics. We suggest that a dispersal-foraging trade-off, leading to more ‘prudent' foraging at range margins, is the driving mechanism behind the macroecological pattern reported. In conclusion, rapid multi-trait evolution and eco-evolutionary feedbacks are highly relevant for understanding macroecological patterns and designing appropriate conservation strategies. Biological range expansions and invasions can be affected by rapid evolution. Here the authors show an evolutionary increase of dispersal during range expansions and an increase of population densities from range cores to range margins in microcosm experiments with a freshwater ciliate.
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Affiliation(s)
- Emanuel A Fronhofer
- Eawag: Swiss Federal Institute of Aquatic Science and Technology, Department of Aquatic Ecology, Überlandstrasse 133, CH-8600 Dübendorf, Switzerland
| | - Florian Altermatt
- 1] Eawag: Swiss Federal Institute of Aquatic Science and Technology, Department of Aquatic Ecology, Überlandstrasse 133, CH-8600 Dübendorf, Switzerland [2] Institute of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
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Nuismer SL, Harmon LJ. Predicting rates of interspecific interaction from phylogenetic trees. Ecol Lett 2014; 18:17-27. [DOI: 10.1111/ele.12384] [Citation(s) in RCA: 85] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2014] [Revised: 06/10/2014] [Accepted: 09/17/2014] [Indexed: 11/29/2022]
Affiliation(s)
- Scott L. Nuismer
- Department of Biological Sciences; Institute for Bioinformatics and Evolutionary Studies (IBEST); University of Idaho; Moscow ID USA
| | - Luke J. Harmon
- Department of Biological Sciences; Institute for Bioinformatics and Evolutionary Studies (IBEST); University of Idaho; Moscow ID USA
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20
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Consumer co-evolution as an important component of the eco-evolutionary feedback. Nat Commun 2014; 5:5226. [DOI: 10.1038/ncomms6226] [Citation(s) in RCA: 73] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2014] [Accepted: 09/10/2014] [Indexed: 11/08/2022] Open
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21
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Koch H, Frickel J, Valiadi M, Becks L. Why rapid, adaptive evolution matters for community dynamics. Front Ecol Evol 2014. [DOI: 10.3389/fevo.2014.00017] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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22
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