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Hesse E, Luján AM, O'Brien S, Newbury A, McAvoy T, Soria Pascual J, Bayer F, Hodgson DJ, Buckling A. Parallel ecological and evolutionary responses to selection in a natural bacterial community. Proc Natl Acad Sci U S A 2024; 121:e2403577121. [PMID: 39190353 PMCID: PMC11388356 DOI: 10.1073/pnas.2403577121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Accepted: 07/09/2024] [Indexed: 08/28/2024] Open
Abstract
Evolution can occur over ecological timescales, suggesting a potentially important role for rapid evolution in shaping community trait distributions. However, evidence of concordant eco-evolutionary dynamics often comes from in vitro studies of highly simplified communities, and measures of ecological and evolutionary dynamics are rarely directly comparable. Here, we quantified how ecological species sorting and rapid evolution simultaneously shape community trait distributions by tracking within- and between-species changes in a key trait in a complex bacterial community. We focused on the production of siderophores; bacteria use these costly secreted metabolites to scavenge poorly soluble iron and to detoxify environments polluted with toxic nonferrous metals. We found that responses to copper-imposed selection within and between species were ultimately the same-intermediate siderophore levels were favored-and occurred over similar timescales. Despite being a social trait, this level of siderophore production was selected regardless of whether species evolved in isolation or in a community context. Our study suggests that evolutionary selection can play a pivotal role in shaping community trait distributions within natural, highly complex, bacterial communities. Furthermore, trait evolution may not always be qualitatively affected by interactions with other community members.
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Affiliation(s)
- Elze Hesse
- Centre for Ecology and Conservation & Environment and Sustainability Institute, Faculty of Environment, Science and Economy, University of Exeter, Cornwall TR10 9FE, United Kingdom
| | - Adela M Luján
- Centre for Ecology and Conservation & Environment and Sustainability Institute, Faculty of Environment, Science and Economy, University of Exeter, Cornwall TR10 9FE, United Kingdom
- Centro de Investigación y Desarrollo en Inmunología y Enfermedades Infecciosas, Consejo Nacional de Investigaciones Científicas y Técnicas/Universidad Católica de Córdoba, Córdoba X5016DHK, Argentina
- Facultad de Ciencias de la Salud, Universidad Católica de Córdoba (UCC), Córdoba X5004ASK, Argentina
| | - Siobhan O'Brien
- Centre for Ecology and Conservation & Environment and Sustainability Institute, Faculty of Environment, Science and Economy, University of Exeter, Cornwall TR10 9FE, United Kingdom
| | - Arthur Newbury
- Centre for Ecology and Conservation & Environment and Sustainability Institute, Faculty of Environment, Science and Economy, University of Exeter, Cornwall TR10 9FE, United Kingdom
| | - Terence McAvoy
- Centre for Ecology and Conservation & Environment and Sustainability Institute, Faculty of Environment, Science and Economy, University of Exeter, Cornwall TR10 9FE, United Kingdom
| | - Jesica Soria Pascual
- Centre for Ecology and Conservation & Environment and Sustainability Institute, Faculty of Environment, Science and Economy, University of Exeter, Cornwall TR10 9FE, United Kingdom
| | - Florian Bayer
- Centre for Ecology and Conservation & Environment and Sustainability Institute, Faculty of Environment, Science and Economy, University of Exeter, Cornwall TR10 9FE, United Kingdom
| | - David J Hodgson
- Centre for Ecology and Conservation, Faculty of Environment, Science and Economy, University of Exeter, Cornwall TR10 9FE, United Kingdom
| | - Angus Buckling
- Centre for Ecology and Conservation & Environment and Sustainability Institute, Faculty of Environment, Science and Economy, University of Exeter, Cornwall TR10 9FE, United Kingdom
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2
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Rzodkiewicz LD, Turcotte MM. Two duckweed species exhibit variable tolerance to microcystin-LR exposure across genotypic lineages. HARMFUL ALGAE 2024; 131:102548. [PMID: 38212081 DOI: 10.1016/j.hal.2023.102548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 11/17/2023] [Accepted: 11/21/2023] [Indexed: 01/13/2024]
Abstract
Cyanotoxins produced by harmful cyanobacteria blooms can damage freshwater ecosystems and threaten human health. Floating macrophytes may be used as a means of biocontrol by limiting light and resources available to cyanobacteria. However, genetic variation in macrophyte sensitivity to cyanotoxins could influence their suitability as biocontrol agents. We investigated the influence of such intraspecific variation on the response of two rapidly growing duckweed species, Lemna minor and Spirodela polyrhiza, often used in nutrient and metal bioremediation. We assessed two biomarkers related to productivity (biomass and chlorophyll A production) and two related to fitness measures (population size and growth rate). Fifteen genetic lineages of each species were grown in media containing common cyanotoxin microcystin-LR at ecologically relevant concentrations or control media for a period of twelve days. Genotype identity had a strong impact on all biomarker responses. Microcystin concentration slightly increased the final population sizes of both macrophyte species with a marginal effect on growth rate of L. minor and the chlorophyll A production of S. polyrhiza, but overall these species were very tolerant of microcystin. The strong tolerance supports the potential use of these plants as bioremediators of cyanobacterial blooms. However, differential impact of microcystin exposure discovered in single lineage models among genotypes indicates a potential for cyanotoxins to act as selective forces, necessitating attention to genotype selection for bioremediation.
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Affiliation(s)
- Lacey D Rzodkiewicz
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, 15260, Pennsylvania, United States of America.
| | - Martin M Turcotte
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, 15260, Pennsylvania, United States of America
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3
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van Dijk B, Buffard P, Farr AD, Giersdorf F, Meijer J, Dutilh BE, Rainey PB. Identifying and tracking mobile elements in evolving compost communities yields insights into the nanobiome. ISME COMMUNICATIONS 2023; 3:90. [PMID: 37640834 PMCID: PMC10462680 DOI: 10.1038/s43705-023-00294-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 08/02/2023] [Accepted: 08/08/2023] [Indexed: 08/31/2023]
Abstract
Microbial evolution is driven by rapid changes in gene content mediated by horizontal gene transfer (HGT). While mobile genetic elements (MGEs) are important drivers of gene flux, the nanobiome-the zoo of Darwinian replicators that depend on microbial hosts-remains poorly characterised. New approaches are necessary to increase our understanding beyond MGEs shaping individual populations, towards their impacts on complex microbial communities. A bioinformatic pipeline (xenoseq) was developed to cross-compare metagenomic samples from microbial consortia evolving in parallel, aimed at identifying MGE dissemination, which was applied to compost communities which underwent periodic mixing of MGEs. We show that xenoseq can distinguish movement of MGEs from demographic changes in community composition that otherwise confounds identification, and furthermore demonstrate the discovery of various unexpected entities. Of particular interest was a nanobacterium of the candidate phylum radiation (CPR) which is closely related to a species identified in groundwater ecosystems (Candidatus Saccharibacterium), and appears to have a parasitic lifestyle. We also highlight another prolific mobile element, a 313 kb plasmid hosted by a Cellvibrio lineage. The host was predicted to be capable of nitrogen fixation, and acquisition of the plasmid coincides with increased ammonia production. Taken together, our data show that new experimental strategies combined with bioinformatic analyses of metagenomic data stand to provide insight into the nanobiome as a driver of microbial community evolution.
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Affiliation(s)
- Bram van Dijk
- Department of Microbial Population Biology, Max Planck Institute for Evolutionary Biology, Plön, Germany.
- Theoretical Biology and Bioinformatics, Department of Biology, Science for Life, Utrecht University, Utrecht, the Netherlands.
| | - Pauline Buffard
- Department of Microbial Population Biology, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Andrew D Farr
- Department of Microbial Population Biology, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Franz Giersdorf
- Department of Microbial Population Biology, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Jeroen Meijer
- Theoretical Biology and Bioinformatics, Department of Biology, Science for Life, Utrecht University, Utrecht, the Netherlands
| | - Bas E Dutilh
- Theoretical Biology and Bioinformatics, Department of Biology, Science for Life, Utrecht University, Utrecht, the Netherlands
- Institute of Biodiversity, Faculty of Biological Sciences, Cluster of Excellence Balance of the Microverse, Friedrich Schiller University, Jena, Germany
| | - Paul B Rainey
- Department of Microbial Population Biology, Max Planck Institute for Evolutionary Biology, Plön, Germany.
- Laboratory of Biophysics and Evolution, CBI, ESPCI Paris, Université PSL CNRS, Paris, France.
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4
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Letten AD, Ludington WB. Pulsed, continuous or somewhere in between? Resource dynamics matter in the optimisation of microbial communities. THE ISME JOURNAL 2023; 17:641-644. [PMID: 36694008 PMCID: PMC10030971 DOI: 10.1038/s41396-023-01369-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Revised: 01/12/2023] [Accepted: 01/13/2023] [Indexed: 01/26/2023]
Abstract
The optimisation of synthetic and natural microbial communities has vast potential for emerging applications in medicine, agriculture and industry. Realising this goal is contingent on a close correlation between theory, experiments, and the real world. Although the temporal pattern of resource supply can play a major role in microbial community assembly, resource dynamics are commonly treated inconsistently in theoretical and experimental research. Here we explore how the composition of communities varies under continuous resource supply, typical of theoretical approaches, versus pulsed resource supply, typical of experiments. Using simulations of classical resource competition models, we show that community composition diverges rapidly between the two regimes, with almost zero overlap in composition once the pulsing interval stretches beyond just four hours. The implication for the rapidly growing field of microbial community optimisation is that the resource supply regime must be tailored to the community being optimised. As such, we argue that resource supply dynamics should be considered both a constraint in the design of novel microbial communities and as a tuning mechanism for the optimisation of pre-existing communities like those found in the human gut.
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Affiliation(s)
- Andrew D Letten
- School of Biological Sciences, University of Queensland, Brisbane, QLD, 4072, Australia.
| | - William B Ludington
- Department of Embryology, Carnegie Institution of Washington, Baltimore, MD, USA
- Department of Biology, Johns Hopkins University, Baltimore, MD, USA
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5
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George AB, Korolev KS. Ecological landscapes guide the assembly of optimal microbial communities. PLoS Comput Biol 2023; 19:e1010570. [PMID: 36626403 PMCID: PMC9831326 DOI: 10.1371/journal.pcbi.1010570] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 09/13/2022] [Indexed: 01/11/2023] Open
Abstract
Assembling optimal microbial communities is key for various applications in biofuel production, agriculture, and human health. Finding the optimal community is challenging because the number of possible communities grows exponentially with the number of species, and so an exhaustive search cannot be performed even for a dozen species. A heuristic search that improves community function by adding or removing one species at a time is more practical, but it is unknown whether this strategy can discover an optimal or nearly optimal community. Using consumer-resource models with and without cross-feeding, we investigate how the efficacy of search depends on the distribution of resources, niche overlap, cross-feeding, and other aspects of community ecology. We show that search efficacy is determined by the ruggedness of the appropriately-defined ecological landscape. We identify specific ruggedness measures that are both predictive of search performance and robust to noise and low sampling density. The feasibility of our approach is demonstrated using experimental data from a soil microbial community. Overall, our results establish the conditions necessary for the success of the heuristic search and provide concrete design principles for building high-performing microbial consortia.
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Affiliation(s)
- Ashish B. George
- Department of Physics and Biological Design Center, Boston University, Boston, Massachusetts, United States of America
- Carl R. Woese Institute for Genomic Biology and Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Kirill S. Korolev
- Department of Physics and Biological Design Center, Boston University, Boston, Massachusetts, United States of America
- Graduate Program in Bioinformatics, Boston University, Boston, Massachusetts, United States of America
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Reyes-González D, De Luna-Valenciano H, Utrilla J, Sieber M, Peña-Miller R, Fuentes-Hernández A. Dynamic proteome allocation regulates the profile of interaction of auxotrophic bacterial consortia. ROYAL SOCIETY OPEN SCIENCE 2022; 9:212008. [PMID: 35592760 PMCID: PMC9066302 DOI: 10.1098/rsos.212008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 03/25/2022] [Indexed: 05/03/2023]
Abstract
Microbial ecosystems are composed of multiple species in constant metabolic exchange. A pervasive interaction in microbial communities is metabolic cross-feeding and occurs when the metabolic burden of producing costly metabolites is distributed between community members, in some cases for the benefit of all interacting partners. In particular, amino acid auxotrophies generate obligate metabolic inter-dependencies in mixed populations and have been shown to produce a dynamic profile of interaction that depends upon nutrient availability. However, identifying the key components that determine the pair-wise interaction profile remains a challenging problem, partly because metabolic exchange has consequences on multiple levels, from allocating proteomic resources at a cellular level to modulating the structure, function and stability of microbial communities. To evaluate how ppGpp-mediated resource allocation drives the population-level profile of interaction, here we postulate a multi-scale mathematical model that incorporates dynamics of proteome partition into a population dynamics model. We compare our computational results with experimental data obtained from co-cultures of auxotrophic Escherichia coli K12 strains under a range of amino acid concentrations and population structures. We conclude by arguing that the stringent response promotes cooperation by inhibiting the growth of fast-growing strains and promoting the synthesis of metabolites essential for other community members.
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Affiliation(s)
- D. Reyes-González
- Synthetic Biology Program, Center for Genomic Sciences, Universidad Autónoma de México, 62220 Cuernavaca, Mexico
| | - H. De Luna-Valenciano
- Synthetic Biology Program, Center for Genomic Sciences, Universidad Autónoma de México, 62220 Cuernavaca, Mexico
- Systems Biology Program, Center for Genomic Sciences, Universidad Nacional Autónoma de México, 62210 Cuernavaca, Mexico
| | - J. Utrilla
- Synthetic Biology Program, Center for Genomic Sciences, Universidad Autónoma de México, 62220 Cuernavaca, Mexico
| | - M. Sieber
- Max Planck Institute for Evolutionary Biology, 24306 Plön, Germany
| | - R. Peña-Miller
- Systems Biology Program, Center for Genomic Sciences, Universidad Nacional Autónoma de México, 62210 Cuernavaca, Mexico
| | - A. Fuentes-Hernández
- Synthetic Biology Program, Center for Genomic Sciences, Universidad Autónoma de México, 62220 Cuernavaca, Mexico
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Azimzade Y, Saberi AA. Geometrically regulating evolutionary dynamics in biofilms. Phys Rev E 2021; 103:L050401. [PMID: 34134254 DOI: 10.1103/physreve.103.l050401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Accepted: 04/21/2021] [Indexed: 11/07/2022]
Abstract
The theoretical understanding of evolutionary dynamics in spatially structured populations often relies on nonspatial models. Biofilms are among such populations where a more accurate understanding is of theoretical interest and can reveal new solutions to existing challenges. Here, we studied how the geometry of the environment affects the evolutionary dynamics of expanding populations, using the Eden model. Our results show that fluctuations of subpopulations during range expansion in two- and three-dimensional environments are not Brownian. Furthermore, we found that the substrate's geometry interferes with the evolutionary dynamics of populations that grow upon it. Inspired by these findings, we propose a periodically wedged pattern on surfaces prone to develop biofilms. On such patterned surfaces, natural selection becomes less effective and beneficial mutants would have a harder time establishing. Additionally, this modification accelerates genetic drift and leads to less diverse biofilms. Both interventions are highly desired for biofilms.
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Affiliation(s)
- Youness Azimzade
- Department of Physics, University of Tehran, Tehran 14395-547, Iran
| | - Abbas Ali Saberi
- Department of Physics, University of Tehran, Tehran 14395-547, Iran.,Institut für Theoretische Physik, Universitat zu Köln, Zülpicher Strasse 77, 50937 Köln, Germany
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Meroz N, Tovi N, Sorokin Y, Friedman J. Community composition of microbial microcosms follows simple assembly rules at evolutionary timescales. Nat Commun 2021; 12:2891. [PMID: 33976223 PMCID: PMC8113234 DOI: 10.1038/s41467-021-23247-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 04/20/2021] [Indexed: 12/14/2022] Open
Abstract
Managing and engineering microbial communities relies on the ability to predict their composition. While progress has been made on predicting compositions on short, ecological timescales, there is still little work aimed at predicting compositions on evolutionary timescales. Therefore, it is still unknown for how long communities typically remain stable after reaching ecological equilibrium, and how repeatable and predictable are changes when they occur. Here, we address this knowledge gap by tracking the composition of 87 two- and three-species bacterial communities, with 3-18 replicates each, for ~400 generations. We find that community composition typically changed during evolution, but that the composition of replicate communities remained similar. Furthermore, these changes were predictable in a bottom-up approach-changes in the composition of trios were consistent with those that occurred in pairs during coevolution. Our results demonstrate that simple assembly rules can hold even on evolutionary timescales, suggesting it may be possible to forecast the evolution of microbial communities.
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Affiliation(s)
- Nittay Meroz
- Department of Plant Pathology and Microbiology, The Hebrew University of Jerusalem, Rehovot, Israel.
| | - Nesli Tovi
- Department of Plant Pathology and Microbiology, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Yael Sorokin
- Department of Plant Pathology and Microbiology, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Jonathan Friedman
- Department of Plant Pathology and Microbiology, The Hebrew University of Jerusalem, Rehovot, Israel.
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Sánchez Á, Vila JCC, Chang CY, Diaz-Colunga J, Estrela S, Rebolleda-Gomez M. Directed Evolution of Microbial Communities. Annu Rev Biophys 2021; 50:323-341. [PMID: 33646814 PMCID: PMC8105285 DOI: 10.1146/annurev-biophys-101220-072829] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Directed evolution is a form of artificial selection that has been used for decades to find biomolecules and organisms with new or enhanced functional traits. Directed evolution can be conceptualized as a guided exploration of the genotype-phenotype map, where genetic variants with desirable phenotypes are first selected and then mutagenized to search the genotype space for an even better mutant. In recent years, the idea of applying artificial selection to microbial communities has gained momentum. In this article, we review the main limitations of artificial selection when applied to large and diverse collectives of asexually dividing microbes and discuss how the tools of directed evolution may be deployed to engineer communities from the top down. We conceptualize directed evolution of microbial communities as a guided exploration of an ecological structure-function landscape and propose practical guidelines for navigating these ecological landscapes.
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Affiliation(s)
- Álvaro Sánchez
- Department of Ecology & Evolutionary Biology and Microbial Sciences Institute, Yale University, New Haven, Connecticut 06520, USA; , , , , ,
| | - Jean C C Vila
- Department of Ecology & Evolutionary Biology and Microbial Sciences Institute, Yale University, New Haven, Connecticut 06520, USA; , , , , ,
| | - Chang-Yu Chang
- Department of Ecology & Evolutionary Biology and Microbial Sciences Institute, Yale University, New Haven, Connecticut 06520, USA; , , , , ,
| | - Juan Diaz-Colunga
- Department of Ecology & Evolutionary Biology and Microbial Sciences Institute, Yale University, New Haven, Connecticut 06520, USA; , , , , ,
| | - Sylvie Estrela
- Department of Ecology & Evolutionary Biology and Microbial Sciences Institute, Yale University, New Haven, Connecticut 06520, USA; , , , , ,
| | - María Rebolleda-Gomez
- Department of Ecology & Evolutionary Biology and Microbial Sciences Institute, Yale University, New Haven, Connecticut 06520, USA; , , , , ,
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