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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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Hesse E, O’Brien S. Ecological dependencies and the illusion of cooperation in microbial communities. MICROBIOLOGY (READING, ENGLAND) 2024; 170:001442. [PMID: 38385784 PMCID: PMC10924460 DOI: 10.1099/mic.0.001442] [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: 11/24/2023] [Accepted: 02/09/2024] [Indexed: 02/23/2024]
Abstract
Ecological dependencies - where organisms rely on other organisms for survival - are a ubiquitous feature of life on earth. Multicellular hosts rely on symbionts to provide essential vitamins and amino acids. Legume plants similarly rely on nitrogen-fixing rhizobia to convert atmospheric nitrogen to ammonia. In some cases, dependencies can arise via loss-of-function mutations that allow one partner to benefit from the actions of another. It is common in microbiology to label ecological dependencies between species as cooperation - making it necessary to invoke cooperation-specific frameworks to explain the phenomenon. However, in many cases, such traits are not (at least initially) cooperative, because they are not selected for because of the benefits they confer on a partner species. In contrast, dependencies in microbial communities may originate from fitness benefits gained from genomic-streamlining (i.e. Black Queen Dynamics). Here, we outline how the Black Queen Hypothesis predicts the formation of metabolic dependencies via loss-of-function mutations in microbial communities, without needing to invoke any cooperation-specific explanations. Furthermore we outline how the Black Queen Hypothesis can act as a blueprint for true cooperation as well as discuss key outstanding questions in the field. The nature of interactions in microbial communities can predict the ability of natural communities to withstand and recover from disturbances. Hence, it is vital to gain a deeper understanding of the factors driving these dynamic interactions over evolutionary time.
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Affiliation(s)
- Elze Hesse
- College of Life and Environmental Science, University of Exeter, Penryn, Cornwall, TR10 9FE, UK
| | - Siobhán O’Brien
- Moyne Institute of Preventive Medicine, Department of Microbiology, School of Genetics and Microbiology, Trinity College Dublin, Dublin 2, Ireland
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3
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Lässig M, Mustonen V, Nourmohammad A. Steering and controlling evolution - from bioengineering to fighting pathogens. Nat Rev Genet 2023; 24:851-867. [PMID: 37400577 PMCID: PMC11137064 DOI: 10.1038/s41576-023-00623-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/30/2023] [Indexed: 07/05/2023]
Abstract
Control interventions steer the evolution of molecules, viruses, microorganisms or other cells towards a desired outcome. Applications range from engineering biomolecules and synthetic organisms to drug, therapy and vaccine design against pathogens and cancer. In all these instances, a control system alters the eco-evolutionary trajectory of a target system, inducing new functions or suppressing escape evolution. Here, we synthesize the objectives, mechanisms and dynamics of eco-evolutionary control in different biological systems. We discuss how the control system learns and processes information about the target system by sensing or measuring, through adaptive evolution or computational prediction of future trajectories. This information flow distinguishes pre-emptive control strategies by humans from feedback control in biotic systems. We establish a cost-benefit calculus to gauge and optimize control protocols, highlighting the fundamental link between predictability of evolution and efficacy of pre-emptive control.
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Affiliation(s)
- Michael Lässig
- Institute for Biological Physics, University of Cologne, Cologne, Germany.
| | - Ville Mustonen
- Organismal and Evolutionary Biology Research Programme, Department of Computer Science, Institute of Biotechnology, University of Helsinki, Helsinki, Finland.
| | - Armita Nourmohammad
- Department of Physics, University of Washington, Seattle, WA, USA.
- Department of Applied Mathematics, University of Washington, Seattle, WA, USA.
- Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, WA, USA.
- Herbold Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, WA, USA.
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4
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Barbour KM, Weihe C, Walters KE, Martiny JBH. Testing the contribution of dispersal to microbial succession following a wildfire. mSystems 2023; 8:e0057923. [PMID: 37747204 PMCID: PMC10654055 DOI: 10.1128/msystems.00579-23] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 07/28/2023] [Indexed: 09/26/2023] Open
Abstract
IMPORTANCE Identifying the mechanisms underlying microbial community succession is necessary for predicting how microbial communities, and their functioning, will respond to future environmental change. Dispersal is one mechanism expected to affect microbial succession, yet the difficult nature of manipulating microorganisms in the environment has limited our understanding of its contribution. Using a dispersal exclusion experiment, this study isolates the specific effect of environmental dispersal on bacterial and fungal community assembly over time following a wildfire. The work demonstrates the potential to quantify dispersal impacts on soil microbial communities over time and test how dispersal might further interact with other assembly processes in response to environmental change.
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Affiliation(s)
- Kristin M. Barbour
- Department of Ecology and Evolutionary Biology, University of California-Irvine, Irvine, California, USA
| | - Claudia Weihe
- Department of Ecology and Evolutionary Biology, University of California-Irvine, Irvine, California, USA
| | | | - Jennifer B. H. Martiny
- Department of Ecology and Evolutionary Biology, University of California-Irvine, Irvine, California, USA
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5
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Leale A, Auxier B, Smid EJ, Schoustra S. Influence of metabolic guilds on a temporal scale in an experimental fermented food derived microbial community. FEMS Microbiol Ecol 2023; 99:fiad112. [PMID: 37771082 PMCID: PMC10550249 DOI: 10.1093/femsec/fiad112] [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: 06/07/2023] [Revised: 09/06/2023] [Accepted: 09/27/2023] [Indexed: 09/30/2023] Open
Abstract
The influence of community diversity, which can be measured at the level of metabolic guilds, on community function is a central question in ecology. Particularly, the long-term temporal dynamic between a community's function and its diversity remains unclear. We investigated the influence of metabolic guild diversity on associated community function by propagating natural microbial communities from a traditionally fermented milk beverage diluted to various levels. Specifically, we assessed the influence of less abundant microbial types, such as yeast, on community functionality and bacterial community compositions over repeated propagation cycles amounting to ∼100 generations. The starting richness of metabolic guilds had a repeatable effect on bacterial community compositions, metabolic profiles, and acidity. The influence of a single metabolic guild, yeast in our study, played a dramatic role on function, but interestingly not on long-term species sorting trajectories of the remaining bacterial community. Our results together suggest an unexpected niche division between yeast and bacterial communities and evidence ecological selection on the microbial communities in our system.
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Affiliation(s)
- Alanna Leale
- Laboratory of Genetics, Wageningen University and Research, 6700 HB Wageningen, The Netherlands
| | - Ben Auxier
- Laboratory of Genetics, Wageningen University and Research, 6700 HB Wageningen, The Netherlands
| | - Eddy J Smid
- Food Microbiology, Wageningen University and Research, 6700 HB Wageningen, The Netherlands
| | - Sijmen Schoustra
- Laboratory of Genetics, Wageningen University and Research, 6700 HB Wageningen, The Netherlands
- Department of Food Science and Nutrition, School of Agricultural Sciences, University of Zambia, Lusaka 10101, Zambia
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6
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Li S, Chen J, Zhao J, Qi W, Liu H. The response of microbial compositions and functions to chronic single and multiple antibiotic exposure by batch experiment. ENVIRONMENT INTERNATIONAL 2023; 179:108181. [PMID: 37683505 DOI: 10.1016/j.envint.2023.108181] [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: 06/01/2023] [Revised: 07/23/2023] [Accepted: 08/31/2023] [Indexed: 09/10/2023]
Abstract
Understanding the response of the microbial community to external disturbances such as micropollutants is vital for ecological risk evaluation. In this study, the effect of chronic antibiotic exposure on community compositions and functions was investigated by two batch experiments. The first experiment investigated the effect of chronic sulfamethoxazole (SMX) exposure, while the second investigated the combined effect of dissolved organic matter (DOM) sources and multi-antibiotic exposure. The results showed that the community responses to chronic antibiotic exposure depended on the dynamic balance among community resistance, adaptation, recovery, and selection, leading to nonlinear composition diversity variations. The disturbance strength of chronic SMX exposure increased with concentration (0.5-50 μg/L). However, complex sources and structures of coexisting organic matter might delay the disturbance by elevating metabolic activity and generating functional redundancy. Especially, when nutrient was a limiting factor, the disturbance strength by DOM source was greater than that by chronic antibiotic exposure. The resistance of abundant taxa to external distributions resulted in a low explanation of community diversity, while rare taxa played key roles in response to community variation and thereby affected community assembly. Long-term SMX exposure reduced the number of key species and favored the deterministic assembly process by 21%. However, elevated community adaptability might weaken the influence of antibiotic selection. Chronic SMX exposure elevated the relative abundance of sulfonamide resistance genes (sul1, sul2) by a factor of 1.2-4.3, while that of nitrogen-fixing genes (nifH, nifK) and the metabolic pathways related to the toluene, ethylbenzene, and dioxin degradation decreased. However, the combined influence of DOM sources and multi-antibiotic exposure barely caused the difference in the genes linking to element metabolism and drug resistance of microbial communities between blank and exposed groups. This study suggested that more concern should be given to the chronic environmental effect of organic micropollutants.
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Affiliation(s)
- Siling Li
- Center for Water and Ecology, State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Junwen Chen
- Center for Water and Ecology, State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Jian Zhao
- Center for Water and Ecology, State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Weixiao Qi
- Center for Water and Ecology, State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China.
| | - Huijuan Liu
- Center for Water and Ecology, State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
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7
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Münch PC, Eberl C, Woelfel S, Ring D, Fritz A, Herp S, Lade I, Geffers R, Franzosa EA, Huttenhower C, McHardy AC, Stecher B. Pulsed antibiotic treatments of gnotobiotic mice manifest in complex bacterial community dynamics and resistance effects. Cell Host Microbe 2023; 31:1007-1020.e4. [PMID: 37279755 DOI: 10.1016/j.chom.2023.05.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 03/11/2023] [Accepted: 05/11/2023] [Indexed: 06/08/2023]
Abstract
Bacteria can evolve to withstand a wide range of antibiotics (ABs) by using various resistance mechanisms. How ABs affect the ecology of the gut microbiome is still poorly understood. We investigated strain-specific responses and evolution during repeated AB perturbations by three clinically relevant ABs, using gnotobiotic mice colonized with a synthetic bacterial community (oligo-mouse-microbiota). Over 80 days, we observed resilience effects at the strain and community levels, and we found that they were correlated with modulations of the estimated growth rate and levels of prophage induction as determined from metagenomics data. Moreover, we tracked mutational changes in the bacterial populations, and this uncovered clonal expansion and contraction of haplotypes and selection of putative AB resistance-conferring SNPs. We functionally verified these mutations via reisolation of clones with increased minimum inhibitory concentration (MIC) of ciprofloxacin and tetracycline from evolved communities. This demonstrates that host-associated microbial communities employ various mechanisms to respond to selective pressures that maintain community stability.
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Affiliation(s)
- Philipp C Münch
- Computational Biology of Infection Research, Helmholtz Centre for Infection Research, Braunschweig 38124, Germany; Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Braunschweig 38124, Germany; Max von Pettenkofer-Institute for Hygiene and Clinical Microbiology, Ludwig-Maximilian University of Munich, 80336 Munich, Germany; Department of Biostatistics, Harvard School of Public Health, Boston, MA, USA; Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, Hannover, Germany
| | - Claudia Eberl
- Max von Pettenkofer-Institute for Hygiene and Clinical Microbiology, Ludwig-Maximilian University of Munich, 80336 Munich, Germany
| | - Simon Woelfel
- Max von Pettenkofer-Institute for Hygiene and Clinical Microbiology, Ludwig-Maximilian University of Munich, 80336 Munich, Germany
| | - Diana Ring
- Max von Pettenkofer-Institute for Hygiene and Clinical Microbiology, Ludwig-Maximilian University of Munich, 80336 Munich, Germany
| | - Adrian Fritz
- Computational Biology of Infection Research, Helmholtz Centre for Infection Research, Braunschweig 38124, Germany; Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Braunschweig 38124, Germany
| | - Simone Herp
- Max von Pettenkofer-Institute for Hygiene and Clinical Microbiology, Ludwig-Maximilian University of Munich, 80336 Munich, Germany
| | - Iris Lade
- Max von Pettenkofer-Institute for Hygiene and Clinical Microbiology, Ludwig-Maximilian University of Munich, 80336 Munich, Germany
| | - Robert Geffers
- Genome Analytics, Helmholtz Center for Infection Research, 38124 Braunschweig, Germany
| | - Eric A Franzosa
- Department of Biostatistics, Harvard School of Public Health, Boston, MA, USA
| | - Curtis Huttenhower
- Department of Biostatistics, Harvard School of Public Health, Boston, MA, USA; Harvard Chan Microbiome in Public Health Center, Harvard T.H. Chan School of Public Health, Boston, MA, USA; Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Alice C McHardy
- Computational Biology of Infection Research, Helmholtz Centre for Infection Research, Braunschweig 38124, Germany; Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Braunschweig 38124, Germany; Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, Hannover, Germany.
| | - Bärbel Stecher
- Max von Pettenkofer-Institute for Hygiene and Clinical Microbiology, Ludwig-Maximilian University of Munich, 80336 Munich, Germany; German Center for Infection Research, Partner site LMU Munich, Munich, Germany.
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8
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Venkataram S, Kryazhimskiy S. Evolutionary repeatability of emergent properties of ecological communities. Philos Trans R Soc Lond B Biol Sci 2023; 378:20220047. [PMID: 37004728 PMCID: PMC10067272 DOI: 10.1098/rstb.2022.0047] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 12/07/2022] [Indexed: 04/04/2023] Open
Abstract
Most species belong to ecological communities where their interactions give rise to emergent community-level properties, such as diversity and productivity. Understanding and predicting how these properties change over time has been a major goal in ecology, with important practical implications for sustainability and human health. Less attention has been paid to the fact that community-level properties can also change because member species evolve. Yet, our ability to predict long-term eco-evolutionary dynamics hinges on how repeatably community-level properties change as a result of species evolution. Here, we review studies of evolution of both natural and experimental communities and make the case that community-level properties at least sometimes evolve repeatably. We discuss challenges faced in investigations of evolutionary repeatability. In particular, only a handful of studies enable us to quantify repeatability. We argue that quantifying repeatability at the community level is critical for approaching what we see as three major open questions in the field: (i) Is the observed degree of repeatability surprising? (ii) How is evolutionary repeatability at the community level related to repeatability at the level of traits of member species? (iii) What factors affect repeatability? We outline some theoretical and empirical approaches to addressing these questions. Advances in these directions will not only enrich our basic understanding of evolution and ecology but will also help us predict eco-evolutionary dynamics. This article is part of the theme issue 'Interdisciplinary approaches to predicting evolutionary biology'.
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Affiliation(s)
- Sandeep Venkataram
- Department of Ecology, Behavior and Evolution, UC San Diego, La Jolla, CA 92093, USA
| | - Sergey Kryazhimskiy
- Department of Ecology, Behavior and Evolution, UC San Diego, La Jolla, CA 92093, USA
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9
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Nair RR, Andersson DI. Interspecies interaction reduces selection for antibiotic resistance in Escherichia coli. Commun Biol 2023; 6:331. [PMID: 36973402 PMCID: PMC10043022 DOI: 10.1038/s42003-023-04716-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 03/15/2023] [Indexed: 03/29/2023] Open
Abstract
Evolution of microbial traits depends on the interaction of a species with its environment as well as with other coinhabiting species. However, our understanding of the evolution of specific microbial traits, such as antibiotic resistance in complex environments is limited. Here, we determine the role of interspecies interactions on the dynamics of nitrofurantoin (NIT) resistance selection among Escherichia coli. We created a synthetic two-species community comprised of two variants of E. coli (NIT susceptible and resistant) and Bacillus subtilis in minimal media with glucose as the sole carbon source. We show that the presence of B. subtilis significantly slows down the selection for the resistant E. coli mutant when NIT is present and that this slowdown is not due to competition for resources. Instead, the dampening of NIT resistance enrichment is largely mediated by extracellular compounds produced by B. subtilis with the peptide YydF playing a significant role. Our results not only demonstrate the impact of interspecies interactions on the evolution of microbial traits but also show the importance of using synthetic microbial systems in unravelling relevant interactions and mechanisms affecting the evolution of antibiotic resistance. This finding implies that interspecies interactions should be considered to better understand and predict resistance evolution in the clinic as well as in nature.
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Affiliation(s)
- Ramith R Nair
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, SE-75123, Sweden.
| | - Dan I Andersson
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, SE-75123, Sweden
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10
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Coenye T, Bové M, Bjarnsholt T. Biofilm antimicrobial susceptibility through an experimental evolutionary lens. NPJ Biofilms Microbiomes 2022; 8:82. [PMID: 36257971 PMCID: PMC9579162 DOI: 10.1038/s41522-022-00346-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 10/04/2022] [Indexed: 11/19/2022] Open
Abstract
Experimental evolution experiments in which bacterial populations are repeatedly exposed to an antimicrobial treatment, and examination of the genotype and phenotype of the resulting evolved bacteria, can help shed light on mechanisms behind reduced susceptibility. In this review we present an overview of why it is important to include biofilms in experimental evolution, which approaches are available to study experimental evolution in biofilms and what experimental evolution has taught us about tolerance and resistance in biofilms. Finally, we present an emerging consensus view on biofilm antimicrobial susceptibility supported by data obtained during experimental evolution studies.
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Affiliation(s)
- Tom Coenye
- Laboratory of Pharmaceutical Microbiology, Ghent University, Ghent, Belgium.
- Costerton Biofilm Center, University of Copenhagen, Copenhagen, Denmark.
| | - Mona Bové
- Laboratory of Pharmaceutical Microbiology, Ghent University, Ghent, Belgium
| | - Thomas Bjarnsholt
- Costerton Biofilm Center, University of Copenhagen, Copenhagen, Denmark
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11
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Chen J, Qi W, Wang D, Wang Q, Lin H, Mao G, Liang J, Ning X, Bai Y, Liu H, Qu J. Disruption and recovery of river planktonic community during and after the COVID-19 outbreak in Wuhan, China. ISME COMMUNICATIONS 2022; 2:84. [PMID: 37938733 PMCID: PMC9483884 DOI: 10.1038/s43705-022-00168-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/13/2022] [Revised: 08/24/2022] [Accepted: 09/06/2022] [Indexed: 11/09/2022]
Abstract
During the COVID-19 outbreak in Wuhan, large amounts of anti-coronavirus chemicals, such as antiviral drugs and disinfectants were discharged into the surrounding aquatic ecosystem, causing potential ecological damage. Here, we investigated plankton in the Wuhan reaches of the Yangtze River, before, during, and after COVID-19, with the river reaches of three adjacent cities sampled for comparison. During the COVID-19, planktonic microbial density declined significantly. Correspondingly, the eukaryotic and prokaryotic community compositions and functions shifted markedly, with increasing abundance of chlorine-resistant organisms. Abundance of antibiotic resistance genes, virulence factor genes, and bacteria containing both genes increased by 2.3-, 2.7-, and 7.9-fold, respectively, compared to other periods. After COVID-19, all measured plankton community compositional and functional traits recovered in the Yangtze River.
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Affiliation(s)
- Junwen Chen
- Center for Water and Ecology, Tsinghua University, Beijing, 100084, China
| | - Weixiao Qi
- Center for Water and Ecology, Tsinghua University, Beijing, 100084, China
| | - Donglin Wang
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Qiaojuan Wang
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Hui Lin
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Guannan Mao
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Jinsong Liang
- School of Civil and Environmental Engineering, Harbin Institute of Technology, Shenzhen, 518055, China
| | - Xue Ning
- MaREI Centre, Environmental Research Institute, School of Engineering, University College Cork, Cork, T23XE10, Ireland
| | - Yaohui Bai
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China.
| | - Huijuan Liu
- Center for Water and Ecology, Tsinghua University, Beijing, 100084, China
| | - Jiuhui Qu
- Center for Water and Ecology, Tsinghua University, Beijing, 100084, China.
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China.
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12
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Wang Y, Yu Z, Ding P, Lu J, Klümper U, Murray AK, Gaze WH, Guo J. Non-antibiotic pharmaceuticals promote conjugative plasmid transfer at a community-wide level. MICROBIOME 2022; 10:124. [PMID: 35953866 PMCID: PMC9373378 DOI: 10.1186/s40168-022-01314-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 06/13/2022] [Indexed: 05/04/2023]
Abstract
BACKGROUND Horizontal gene transfer (HGT) plays a critical role in the spread of antibiotic resistance and the evolutionary shaping of bacterial communities. Conjugation is the most well characterized pathway for the spread of antibiotic resistance, compared to transformation and transduction. While antibiotics have been found to induce HGT, it remains unknown whether non-antibiotic pharmaceuticals can facilitate conjugation at a microbial community-wide level. RESULTS In this study, we demonstrate that several commonly consumed non-antibiotic pharmaceuticals (including carbamazepine, ibuprofen, naproxen and propranolol), at environmentally relevant concentrations (0.5 mg/L), can promote the conjugative transfer of IncP1-α plasmid-borne antibiotic resistance across entire microbial communities. The over-generation of reactive oxygen species in response to these non-antibiotic pharmaceuticals may contribute to the enhanced conjugation ratios. Cell sorting and 16S rRNA gene amplicon sequencing analyses indicated that non-antibiotic pharmaceuticals modulate transconjugant microbial communities at both phylum and genus levels. Moreover, microbial uptake ability of the IncP1-α plasmid was also upregulated under non-antibiotic pharmaceutical exposure. Several opportunistic pathogens, such as Acinetobacter and Legionella, were more likely to acquire the plasmid conferring multidrug resistance. CONCLUSIONS Considering the high possibility of co-occurrence of pathogenic bacteria, conjugative IncP1-α plasmids and non-antibiotic pharmaceuticals in various environments (e.g., activated sludge systems), our findings illustrate the potential risk associated with increased dissemination of antibiotic resistance promoted by non-antibiotic pharmaceuticals in complex environmental settings. Video abstract.
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Affiliation(s)
- Yue Wang
- Australian Centre for Water and Environmental Biotechnology (ACWEB, Formerly AWMC), The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Zhigang Yu
- Australian Centre for Water and Environmental Biotechnology (ACWEB, Formerly AWMC), The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Pengbo Ding
- Australian Centre for Water and Environmental Biotechnology (ACWEB, Formerly AWMC), The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Ji Lu
- Australian Centre for Water and Environmental Biotechnology (ACWEB, Formerly AWMC), The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Uli Klümper
- Institute for Hydrobiology, Technische Universität Dresden, 01217, Dresden, Germany
| | - Aimee K Murray
- European Centre for Environment and Human Health, University of Exeter Medical School, Environment & Sustainability Institute, Penryn Campus, Penryn, TR10 9FE, UK
| | - William H Gaze
- European Centre for Environment and Human Health, University of Exeter Medical School, Environment & Sustainability Institute, Penryn Campus, Penryn, TR10 9FE, UK
| | - Jianhua Guo
- Australian Centre for Water and Environmental Biotechnology (ACWEB, Formerly AWMC), The University of Queensland, Brisbane, QLD, 4072, Australia.
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13
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Khalighi M, Sommeria-Klein G, Gonze D, Faust K, Lahti L. Quantifying the impact of ecological memory on the dynamics of interacting communities. PLoS Comput Biol 2022; 18:e1009396. [PMID: 35658019 PMCID: PMC9200327 DOI: 10.1371/journal.pcbi.1009396] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 06/15/2022] [Accepted: 05/12/2022] [Indexed: 12/21/2022] Open
Abstract
Ecological memory refers to the influence of past events on the response of an ecosystem to exogenous or endogenous changes. Memory has been widely recognized as a key contributor to the dynamics of ecosystems and other complex systems, yet quantitative community models often ignore memory and its implications. Recent modeling studies have shown how interactions between community members can lead to the emergence of resilience and multistability under environmental perturbations. We demonstrate how memory can be introduced in such models using the framework of fractional calculus. We study how the dynamics of a well-characterized interaction model is affected by gradual increases in ecological memory under varying initial conditions, perturbations, and stochasticity. Our results highlight the implications of memory on several key aspects of community dynamics. In general, memory introduces inertia into the dynamics. This favors species coexistence under perturbation, enhances system resistance to state shifts, mitigates hysteresis, and can affect system resilience both ways depending on the time scale considered. Memory also promotes long transient dynamics, such as long-standing oscillations and delayed regime shifts, and contributes to the emergence and persistence of alternative stable states. Our study highlights the fundamental role of memory in communities, and provides quantitative tools to introduce it in ecological models and analyse its impact under varying conditions. An ecosystem is said to exhibit ecological memory when its future states do not only depend on its current state but also on its initial state and trajectory. Memory may arise through various mechanisms as organisms adapt to their environment, modify it, and accumulate biotic and abiotic material. It may also emerge from phenotypic heterogeneity at the population level. Despite its commonness in nature, ecological memory and its potential influence on ecosystem dynamics have been so far overlooked in many applied contexts. Here, we use modeling to investigate how memory can influence the dynamics, composition, and stability landscape of communities. We incorporate long-term memory effects into a multi-species model recently introduced to investigate alternative stable states in microbial communities. We assess the impact of memory on key aspects of model behavior and further examine our findings using a model parameterized by empirical data from the human gut microbiota. Our approach for modeling long-term memory and studying its implications has the potential to improve our understanding of microbial community dynamics and ultimately our ability to predict, manipulate, and experimentally design microbial ecosystems. It could also be applied more broadly in the study of systems composed of interacting components.
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Affiliation(s)
- Moein Khalighi
- Department of Computing, Faculty of Technology, University of Turku, Turku, Finland
- * E-mail: (MK); (LL)
| | | | - Didier Gonze
- Unité de Chronobiologie Théorique, Faculté des Sciences CP 231, Université Libre de Bruxelles, Brussels, Belgium
| | - Karoline Faust
- Laboratory of Molecular Bacteriology (Rega Institute), Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven, Belgium
| | - Leo Lahti
- Department of Computing, Faculty of Technology, University of Turku, Turku, Finland
- * E-mail: (MK); (LL)
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14
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Fast growth can counteract antibiotic susceptibility in shaping microbial community resilience to antibiotics. Proc Natl Acad Sci U S A 2022; 119:e2116954119. [PMID: 35394868 PMCID: PMC9169654 DOI: 10.1073/pnas.2116954119] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
SignificanceAntibiotic exposure stands among the most used interventions to drive microbial communities away from undesired states. How the ecology of microbial communities shapes their recovery-e.g., posttreatment shifts toward Clostridioides difficile infections in the gut-after antibiotic exposure is poorly understood. We study community response to antibiotics using a model community that can reach two alternative states. Guided by theory, our experiments show that microbial growth following antibiotic exposure can counteract antibiotic susceptibility in driving transitions between alternative community states. This makes it possible to reverse the outcome of antibiotic exposure through modifying growth dynamics, including cooperative growth, of community members. Our research highlights the relevance of simple ecological models to better understand the long-term effects of antibiotic treatment.
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15
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Zhang P, Spaepen S, Bai Y, Hacquard S, Garrido-Oter R. Rbec: a tool for analysis of amplicon sequencing data from synthetic microbial communities. ISME COMMUNICATIONS 2021; 1:73. [PMID: 37938657 PMCID: PMC9723543 DOI: 10.1038/s43705-021-00077-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 11/03/2021] [Accepted: 11/18/2021] [Indexed: 09/30/2023]
Abstract
Synthetic microbial communities (SynComs) constitute an emerging and powerful tool in biological, biomedical, and biotechnological research. Despite recent advances in algorithms for the analysis of culture-independent amplicon sequencing data from microbial communities, there is a lack of tools specifically designed for analyzing SynCom data, where reference sequences for each strain are available. Here we present Rbec, a tool designed for the analysis of SynCom data that accurately corrects PCR and sequencing errors in amplicon sequences and identifies intra-strain polymorphic variation. Extensive evaluation using mock bacterial and fungal communities show that our tool outperforms current methods for samples of varying complexity, diversity, and sequencing depth. Furthermore, Rbec also allows accurate detection of contaminants in SynCom experiments.
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Affiliation(s)
- Pengfan Zhang
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829, Cologne, Germany
| | - Stjin Spaepen
- CMPG Laboratory of Genetics and Genomics, Department M2S, KU Leuven, Gaston Geenslaan 1, 3001, Leuven, Belgium
| | - Yang Bai
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, 100101, Beijing, China
| | - Stephane Hacquard
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829, Cologne, Germany
- Cluster of Excellence on Plant Sciences (CEPLAS), Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Ruben Garrido-Oter
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829, Cologne, Germany.
- Cluster of Excellence on Plant Sciences (CEPLAS), Max Planck Institute for Plant Breeding Research, Cologne, Germany.
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16
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Wang B, Allison SD. Drought legacies mediated by trait trade‐offs in soil microbiomes. Ecosphere 2021. [DOI: 10.1002/ecs2.3562] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Affiliation(s)
- Bin Wang
- Department of Ecology and Evolutionary Biology University of California Irvine California92697USA
| | - Steven D. Allison
- Department of Ecology and Evolutionary Biology University of California Irvine California92697USA
- Department of Earth System Science University of California Irvine California92697USA
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17
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Aguirre de Cárcer D. Experimental and computational approaches to unravel microbial community assembly. Comput Struct Biotechnol J 2020; 18:4071-4081. [PMID: 33363703 PMCID: PMC7736701 DOI: 10.1016/j.csbj.2020.11.031] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 11/16/2020] [Accepted: 11/19/2020] [Indexed: 12/12/2022] Open
Abstract
Microbial communities have a preponderant role in the life support processes of our common home planet Earth. These extremely diverse communities drive global biogeochemical cycles, and develop intimate relationships with most multicellular organisms, with a significant impact on their fitness. Our understanding of their composition and function has enjoyed a significant thrust during the last decade thanks to the rise of high-throughput sequencing technologies. Intriguingly, the diversity patterns observed in nature point to the possible existence of fundamental community assembly rules. Unfortunately, these rules are still poorly understood, despite the fact that their knowledge could spur a scientific, technological, and economic revolution, impacting, for instance, agricultural, environmental, and health-related practices. In this minireview, I recapitulate the most important wet lab techniques and computational approaches currently employed in the study of microbial community assembly, and briefly discuss various experimental designs. Most of these approaches and considerations are also relevant to the study of microbial microevolution, as it has been shown that it can occur in ecological relevant timescales. Moreover, I provide a succinct review of various recent studies, chosen based on the diversity of ecological concepts addressed, experimental designs, and choice of wet lab and computational techniques. This piece aims to serve as a primer to those new to the field, as well as a source of new ideas to the more experienced researchers.
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18
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Santiago-Alarcon D, Tapia-McClung H, Lerma-Hernández S, Venegas-Andraca SE. Quantum aspects of evolution: a contribution towards evolutionary explorations of genotype networks via quantum walks. J R Soc Interface 2020; 17:20200567. [PMID: 33171071 PMCID: PMC7729038 DOI: 10.1098/rsif.2020.0567] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 10/20/2020] [Indexed: 12/14/2022] Open
Abstract
Quantum biology seeks to explain biological phenomena via quantum mechanisms, such as enzyme reaction rates via tunnelling and photosynthesis energy efficiency via coherent superposition of states. However, less effort has been devoted to study the role of quantum mechanisms in biological evolution. In this paper, we used transcription factor networks with two and four different phenotypes, and used classical random walks (CRW) and quantum walks (QW) to compare network search behaviour and efficiency at finding novel phenotypes between CRW and QW. In the network with two phenotypes, at temporal scales comparable to decoherence time TD, QW are as efficient as CRW at finding new phenotypes. In the case of the network with four phenotypes, the QW had a higher probability of mutating to a novel phenotype than the CRW, regardless of the number of mutational steps (i.e. 1, 2 or 3) away from the new phenotype. Before quantum decoherence, the QW probabilities become higher turning the QW effectively more efficient than CRW at finding novel phenotypes under different starting conditions. Thus, our results warrant further exploration of the QW under more realistic network scenarios (i.e. larger genotype networks) in both closed and open systems (e.g. by considering Lindblad terms).
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Affiliation(s)
- Diego Santiago-Alarcon
- Red de Biología y Conservación de Vertebrados, Instituto de Ecología, A.C. Carr. Antigua a Coatepec 351, Col. El Haya, C.P. 91070, Xalapa, Veracruz, Mexico
| | - Horacio Tapia-McClung
- Centro de Investigación en Inteligencia Artificial, Universidad Veracruzana, Sebastián Camacho 5, Centro, Xalapa-Enríquez, Veracruz, Mexico
| | - Sergio Lerma-Hernández
- Facultad de Física, Universidad Veracruzana, Circuito Aguirre Beltrán s/n, Xalapa, Veracruz 91000, Mexico
| | - Salvador E. Venegas-Andraca
- Tecnologico de Monterrey, Escuela de Ingenieria y Ciencias, Avenue Eugenio Garza Sada 2501, Monterrey 64849, Nuevo Leon, Mexico
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