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de la Cruz Barron M, van Velzen E, Klümper U, Weitere M, Berendonk TU, Kneis D. Shifts from cooperative to individual-based predation defense determine microbial predator-prey dynamics. ISME J 2023. [PMID: 36854789 DOI: 10.1038/s41396-023-01381-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 02/03/2023] [Accepted: 02/07/2023] [Indexed: 03/02/2023]
Abstract
Predation defense is an important feature of predator-prey interactions adding complexity to ecosystem dynamics. Prey organisms have developed various strategies to escape predation which differ in mode (elude vs. attack), reversibility (inducible vs. permanent), and scope (individual vs. cooperative defenses). While the mechanisms and controls of many singular defenses are well understood, important ecological and evolutionary facets impacting long-term predator-prey dynamics remain underexplored. This pertains especially to trade-offs and interactions between alternative defenses occurring in prey populations evolving under predation pressure. Here, we explored the dynamics of a microbial predator-prey system consisting of bacterivorous flagellates (Poteriospumella lacustris) feeding on Pseudomonas putida. Within five weeks of co-cultivation corresponding to about 35 predator generations, we observed a consistent succession of bacterial defenses in all replicates (n = 16). Initially, bacteria expressed a highly effective cooperative defense based on toxic metabolites, which brought predators close to extinction. This initial strategy, however, was consistently superseded by a second mechanism of predation defense emerging via de novo mutations. Combining experiments with mathematical modeling, we demonstrate how this succession of defenses is driven by the maximization of individual rather than population benefits, highlighting the role of rapid evolution in the breakdown of social cooperation.
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2
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Plum K, Tarkington J, Zufall RA. Experimental Evolution in Tetrahymena. Microorganisms 2022; 10:microorganisms10020414. [PMID: 35208869 PMCID: PMC8877770 DOI: 10.3390/microorganisms10020414] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [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;
- Correspondence:
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3
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Hogle SL, Hepolehto I, Ruokolainen L, Cairns J, Hiltunen T. Effects of phenotypic variation on consumer coexistence and prey community structure. Ecol Lett 2021; 25:307-319. [PMID: 34808704 PMCID: PMC9299012 DOI: 10.1111/ele.13924] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 09/06/2021] [Accepted: 10/15/2021] [Indexed: 12/29/2022]
Abstract
A popular idea in ecology is that trait variation among individuals from the same species may promote the coexistence of competing species. However, theoretical and empirical tests of this idea have yielded inconsistent findings. We manipulated intraspecific trait diversity in a ciliate competing with a nematode for bacterial prey in experimental microcosms. We found that intraspecific trait variation inverted the original competitive hierarchy to favour the consumer with variable traits, ultimately resulting in competitive exclusion. This competitive outcome was driven by foraging traits (size, speed and directionality) that increased the ciliate's fitness ratio and niche overlap with the nematode. The interplay between consumer trait variation and competition resulted in non‐additive cascading effects—mediated through prey defence traits—on prey community assembly. Our results suggest that predicting consumer competitive population dynamics and the assembly of prey communities will require understanding the complexities of trait variation within consumer species.
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Affiliation(s)
- Shane L Hogle
- Department of Biology, University of Turku, Turku, Finland
| | - Iina Hepolehto
- Department of Microbiology, University of Helsinki, Helsinki, Finland.,Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Lasse Ruokolainen
- Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Johannes Cairns
- Organismal and Evolutionary Biology Research Programme, University of Helsinki, Finland.,Department of Computer Science, University of Helsinki, Finland
| | - Teppo Hiltunen
- Department of Biology, University of Turku, Turku, Finland
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4
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Scheuerl T, Kaitala V. The effect of dilution on eco-evolutionary dynamics of experimental microbial communities. Ecol Evol 2021; 11:13430-13444. [PMID: 34646480 PMCID: PMC8495831 DOI: 10.1002/ece3.8065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 07/02/2021] [Accepted: 08/10/2021] [Indexed: 11/08/2022] Open
Abstract
Changing environmental conditions can infer structural modifications of predator-prey communities. New conditions often increase mortality which reduces population sizes. Following this, predation pressure may decrease until populations are dense again. Dilution may thus have substantial impact not only on ecological but also on evolutionary dynamics because it amends population densities. Experimental studies, in which microbial populations are maintained by a repeated dilution into fresh conditions after a certain period, are extensively used approaches allowing us to obtain mechanistic insights into fundamental processes. By design, dilution, which depends on transfer volume (modifying mortality) and transfer interval (determining the time of interaction), is an inherent feature of these experiments, but often receives little attention. We further explore previously published data from a live predator-prey (bacteria and ciliates) system which investigated eco-evolutionary principles and apply a mathematical model to predict how various transfer volumes and transfer intervals would affect such an experiment. We find not only the ecological dynamics to be modified by both factors but also the evolutionary rates to be affected. Our work predicts that the evolution of the anti-predator defense in the bacteria, and the evolution of the predation efficiency in the ciliates, both slow down with lower transfer volume, but speed up with longer transfer intervals. Our results provide testable hypotheses for future studies of predator-prey systems, and we hope this work will help improve our understanding of how ecological and evolutionary processes together shape composition of microbial communities.
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Affiliation(s)
- Thomas Scheuerl
- Department of Plant SciencesUniversity of CambridgeCambridgeUK
- Research Department for LimnologyUniversity of InnsbruckMondseeAustria
| | - Veijo Kaitala
- Organismal and Evolutionary Biology Research ProgrammeUniversity of HelsinkiHelsinkiFinland
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5
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Mayrhofer N, Velicer GJ, Schaal KA, Vasse M. Behavioral Interactions between Bacterivorous Nematodes and Predatory Bacteria in a Synthetic Community. Microorganisms 2021; 9:1362. [PMID: 34201688 DOI: 10.3390/microorganisms9071362] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 06/07/2021] [Accepted: 06/12/2021] [Indexed: 11/17/2022] Open
Abstract
Theory and empirical studies in metazoans predict that apex predators should shape the behavior and ecology of mesopredators and prey at lower trophic levels. Despite the ecological importance of microbial communities, few studies of predatory microbes examine such behavioral res-ponses and the multiplicity of trophic interactions. Here, we sought to assemble a three-level microbial food chain and to test for behavioral interactions between the predatory nematode Caenorhabditis elegans and the predatory social bacterium Myxococcus xanthus when cultured together with two basal prey bacteria that both predators can eat—Escherichia coli and Flavobacterium johnsoniae. We found that >90% of C. elegans worms failed to interact with M. xanthus even when it was the only potential prey species available, whereas most worms were attracted to pure patches of E. coli and F. johnsoniae. In addition, M. xanthus altered nematode predatory behavior on basal prey, repelling C. elegans from two-species patches that would be attractive without M. xanthus, an effect similar to that of C. elegans pathogens. The nematode also influenced the behavior of the bacterial predator: M. xanthus increased its predatory swarming rate in response to C. elegans in a manner dependent both on basal-prey identity and on worm density. Our results suggest that M. xanthus is an unattractive prey for some soil nematodes and is actively avoided when other prey are available. Most broadly, we found that nematode and bacterial predators mutually influence one another’s predatory behavior, with likely consequences for coevolution within complex microbial food webs.
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Manriquez B, Muller D, Prigent-Combaret C. Experimental Evolution in Plant-Microbe Systems: A Tool for Deciphering the Functioning and Evolution of Plant-Associated Microbial Communities. Front Microbiol 2021; 12:619122. [PMID: 34025595 PMCID: PMC8137971 DOI: 10.3389/fmicb.2021.619122] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 03/29/2021] [Indexed: 12/22/2022] Open
Abstract
In natural environments, microbial communities must constantly adapt to stressful environmental conditions. The genetic and phenotypic mechanisms underlying the adaptive response of microbial communities to new (and often complex) environments can be tackled with a combination of experimental evolution and next generation sequencing. This combination allows to analyse the real-time evolution of microbial populations in response to imposed environmental factors or during the interaction with a host, by screening for phenotypic and genotypic changes over a multitude of identical experimental cycles. Experimental evolution (EE) coupled with comparative genomics has indeed facilitated the monitoring of bacterial genetic evolution and the understanding of adaptive evolution processes. Basically, EE studies had long been done on single strains, allowing to reveal the dynamics and genetic targets of natural selection and to uncover the correlation between genetic and phenotypic adaptive changes. However, species are always evolving in relation with other species and have to adapt not only to the environment itself but also to the biotic environment dynamically shaped by the other species. Nowadays, there is a growing interest to apply EE on microbial communities evolving under natural environments. In this paper, we provide a non-exhaustive review of microbial EE studies done with systems of increasing complexity (from single species, to synthetic communities and natural communities) and with a particular focus on studies between plants and plant-associated microorganisms. We highlight some of the mechanisms controlling the functioning of microbial species and their adaptive responses to environment changes and emphasize the importance of considering bacterial communities and complex environments in EE studies.
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Affiliation(s)
| | | | - Claire Prigent-Combaret
- UMR 5557 Ecologie Microbienne, VetAgro Sup, CNRS, INRAE, University of Lyon, Université Claude Bernard Lyon 1, Villeurbanne, France
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Abinandan S, Perera IA, Subashchandrabose SR, Venkateswarlu K, Cole N, Megharaj M. Acid-adapted microalgae exhibit phenotypic changes for their survival in acid mine drainage samples. FEMS Microbiol Ecol 2021; 96:5851742. [PMID: 32501474 DOI: 10.1093/femsec/fiaa113] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 06/04/2020] [Indexed: 01/01/2023] Open
Abstract
Phenotypic plasticity or genetic adaptation in an organism provides phenotypic changes when exposed to the extreme environmental conditions. The resultant physiological and metabolic changes greatly enhance the organism's potential for its survival in such harsh environments. In the present novel approach, we tested the hypothesis whether acid-adapted microalgae, initially isolated from non-acidophilic environments, can survive and grow in acid-mine-drainage (AMD) samples. Two acid-adapted microalgal strains, Desmodesmus sp. MAS1 and Heterochlorella sp. MAS3, were tested individually or in combination (co-culture) for phenotypic changes during their growth in samples collected from AMD. The acid-adapted microalgae in AMD exhibited a two-fold increase in growth when compared with those grown at pH 3.5 in BBM up to 48 h and then declined. Furthermore, oxidative stress triggered several alterations such as increased cell size, granularity, and enhanced lipid accumulation in AMD-grown microalgae. Especially, the apparent limitation of phosphate in AMD inhibited the uptake of copper and iron in the cultures. Interestingly, growth of the acid-adapted microalgae in AMD downregulated amino acid metabolic pathways as a survival mechanism. This study demonstrates for the first time that acid-adapted microalgae can survive under extreme environmental conditions as exist in AMD by effecting significant phenotypic changes.
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Affiliation(s)
- Sudharsanam Abinandan
- Global Centre for Environmental Remediation (GCER), Faculty of Science, ATC Building, University of Newcastle, University Drive, Callaghan, NSW 2308, Australia
| | - Isiri Adhiwarie Perera
- Global Centre for Environmental Remediation (GCER), Faculty of Science, ATC Building, University of Newcastle, University Drive, Callaghan, NSW 2308, Australia
| | - Suresh R Subashchandrabose
- Global Centre for Environmental Remediation (GCER), Faculty of Science, ATC Building, University of Newcastle, University Drive, Callaghan, NSW 2308, Australia.,Cooperative Research Centre for Contamination Assessment and Remediation of Environment (CRC CARE), University of Newcastle, ATC Building, University Drive, Callaghan, NSW 2308 Australia
| | - Kadiyala Venkateswarlu
- Formerly Department of Microbiology, Sri Krishnadevaraya University, Anantapuramu 515003, India
| | - Nicole Cole
- Analytical and Biomolecular Research Facility (ABRF), University of Newcastle, University Drive, Callaghan, NSW 2308 Australia
| | - Mallavarapu Megharaj
- Global Centre for Environmental Remediation (GCER), Faculty of Science, ATC Building, University of Newcastle, University Drive, Callaghan, NSW 2308, Australia.,Cooperative Research Centre for Contamination Assessment and Remediation of Environment (CRC CARE), University of Newcastle, ATC Building, University Drive, Callaghan, NSW 2308 Australia
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8
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de Roos AM. Effects of life history and individual development on community dynamics: A review of counterintuitive consequences. Ecol Res 2020; 35:930-946. [PMID: 33380774 PMCID: PMC7756606 DOI: 10.1111/1440-1703.12174] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 05/30/2020] [Accepted: 08/07/2020] [Indexed: 11/27/2022]
Abstract
Even though individual life history is the focus of much ecological research, its importance for the dynamics and structure of ecological communities is unclear, or is it a topic of much ongoing research. In this paper I highlight the key life history traits that may lead to effects of life history or ontogeny on ecological communities. I show that asymmetries in the extent of food limitation between individuals in different life stage can give rise to an increase in efficiency with which resources are used for population growth when conditions change. This change in efficiency may result in a positive relationship between stage-specific density and mortality. The positive relationship between density and mortality in turn leads to predictions about community structure that are not only diametrically opposite to the expectations based on theory that ignores population structure but are also intuitively hard to accept. I provide a few examples that illustrate how taking into account intraspecific differences due to ontogeny radically changes the theoretical expectations regarding the possible outcomes of community dynamics. As the most compelling example I show how a so-called double-handicapped looser, that is, a consumer species that is both competitively inferior in the absence of predators and experiences higher mortality when predators are present, can nonetheless oust its opponent that it competes with for the same resource and is exposed to the same predator.
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Affiliation(s)
- André M. de Roos
- Institute for Biodiversity and Ecosystem DynamicsUniversity of AmsterdamAmsterdamNetherlands
- The Santa Fe InstituteSanta FeNew MexicoUSA
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9
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Moerman F, Fronhofer EA, Wagner A, Altermatt F. Gene swamping alters evolution during range expansions in the protist Tetrahymena thermophila. Biol Lett 2020; 16:20200244. [PMID: 32544380 PMCID: PMC7336843 DOI: 10.1098/rsbl.2020.0244] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2020] [Accepted: 05/15/2020] [Indexed: 12/17/2022] Open
Abstract
At species' range edges, individuals often face novel environmental conditions that may limit range expansion until populations adapt. The potential to adapt depends on genetic variation upon which selection can act. However, populations at species' range edges are often genetically depauperate. One mechanism increasing genetic variation is reshuffling existing variation through sex. Sex, however, can potentially limit adaptation by breaking up existing beneficial allele combinations (recombination load). The gene swamping hypothesis predicts this is specifically the case when populations expand along an abiotic gradient and asymmetric dispersal leads to numerous maladapted dispersers from the range core swamping the range edge. We used the ciliate Tetrahymena thermophila as a model for testing the gene swamping hypothesis. We performed replicated range expansions in landscapes with or without a pH-gradient, while simultaneously manipulating the occurrence of gene flow and sexual versus asexual reproduction. We show that sex accelerated evolution of local adaptation in the absence of gene flow, but hindered it in the presence of gene flow. However, sex affected adaptation independently of the pH-gradient, indicating that both abiotic gradients and the biotic gradient in population density lead to gene swamping. Overall, our results show that gene swamping alters adaptation in life-history strategies.
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Affiliation(s)
- Felix Moerman
- Department of Evolutionary Biology and Environmental Studies, University of Zürich, Winterthurerstrasse 190, Zürich CH-8057, Switzerland
- Department of Aquatic Ecology, Eawag: Swiss Federal Institute of Aquatic Science and Technology, Überlandstrasse 133, Dübendorf CH-8600, Switzerland
- Swiss Institute of Bioinformatics, Quartier Sorge—Bâtiment Génopode, Lausanne 1015, Switzerland
- ISEM, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | | | - Andreas Wagner
- Department of Evolutionary Biology and Environmental Studies, University of Zürich, Winterthurerstrasse 190, Zürich CH-8057, Switzerland
- Swiss Institute of Bioinformatics, Quartier Sorge—Bâtiment Génopode, Lausanne 1015, Switzerland
- The Santa Fe Institute, Santa Fe, New Mexico 87501, USA
| | - Florian Altermatt
- Department of Evolutionary Biology and Environmental Studies, University of Zürich, Winterthurerstrasse 190, Zürich CH-8057, Switzerland
- Department of Aquatic Ecology, Eawag: Swiss Federal Institute of Aquatic Science and Technology, Überlandstrasse 133, Dübendorf CH-8600, Switzerland
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Scheuerl T, Cairns J, Becks L, Hiltunen T. Predator coevolution and prey trait variability determine species coexistence. Proc Biol Sci 2019; 286:20190245. [PMID: 31088272 PMCID: PMC6532513 DOI: 10.1098/rspb.2019.0245] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Accepted: 04/25/2019] [Indexed: 01/08/2023] Open
Abstract
Predation is one of the key ecological mechanisms allowing species coexistence and influencing biological diversity. However, ecological processes are subject to contemporary evolutionary change, and the degree to which predation affects diversity ultimately depends on the interplay between evolution and ecology. Furthermore, ecological interactions that influence species coexistence can be altered by reciprocal coevolution especially in the case of antagonistic interactions such as predation or parasitism. Here we used an experimental evolution approach to test for the role of initial trait variation in the prey population and coevolutionary history of the predator in the ecological dynamics of a two-species bacterial community predated by a ciliate. We found that initial trait variation both at the bacterial and ciliate level enhanced species coexistence, and that subsequent trait evolutionary trajectories depended on the initial genetic diversity present in the population. Our findings provide further support to the notion that the ecology-centric view of diversity maintenance must be reinvestigated in light of recent findings in the field of eco-evolutionary dynamics.
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Affiliation(s)
- Thomas Scheuerl
- Department of Microbiology, University of Helsinki, PO Box 56, Helsinki 00014, Finland
| | - Johannes Cairns
- Department of Microbiology, University of Helsinki, PO Box 56, Helsinki 00014, Finland
- Organismal and Evolutionary Biology Research Programme, University of Helsinki, PO Box 65, Helsinki 00014Finland
| | - Lutz Becks
- Department of Evolutionary Ecology, Community Dynamics Group, Max Planck Institute for Evolutionary Biology, August Thienemann Strasse 2, 24306 Plön, Germany
- Aquatic Ecology and Evolution, Limnological Institute University Konstanz, Konstanz, Germany
| | - Teppo Hiltunen
- Department of Microbiology, University of Helsinki, PO Box 56, Helsinki 00014, Finland
- Department of Biology, University of Turku, Turku 20014, Finland
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