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Delaney O, Letten AD, Engelstädter J. Frequent, infinitesimal bottlenecks maximize the rate of microbial adaptation. Genetics 2023; 225:iyad185. [PMID: 37804525 PMCID: PMC10697810 DOI: 10.1093/genetics/iyad185] [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: 08/09/2023] [Revised: 08/09/2023] [Accepted: 10/02/2023] [Indexed: 10/09/2023] Open
Abstract
Serial passaging is a fundamental technique in experimental evolution. The choice of bottleneck severity and frequency poses a dilemma: longer growth periods allow beneficial mutants to arise and grow over more generations, but simultaneously necessitate more severe bottlenecks with a higher risk of those same mutations being lost. Short growth periods require less severe bottlenecks, but come at the cost of less time between transfers for beneficial mutations to establish. The standard laboratory protocol of 24-h growth cycles with severe bottlenecking has logistical advantages for the experimenter but limited theoretical justification. Here we demonstrate that contrary to standard practice, the rate of adaptive evolution is maximized when bottlenecks are frequent and small, indeed infinitesimally so in the limit of continuous culture. This result derives from revising key assumptions underpinning previous theoretical work, notably changing the metric of optimization from adaptation per serial transfer to per experiment runtime. We also show that adding resource constraints and clonal interference to the model leaves the qualitative results unchanged. Implementing these findings will require liquid-handling robots to perform frequent bottlenecks, or chemostats for continuous culture. Further innovation in and adoption of these technologies has the potential to accelerate the rate of discovery in experimental evolution.
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Affiliation(s)
- Oscar Delaney
- School of the Environment, The University of Queensland, Queensland 4072, Australia
| | - Andrew D Letten
- School of the Environment, The University of Queensland, Queensland 4072, Australia
| | - Jan Engelstädter
- School of the Environment, The University of Queensland, Queensland 4072, Australia
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2
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Chavhan Y, Dey S, Lind PA. Bacteria evolve macroscopic multicellularity by the genetic assimilation of phenotypically plastic cell clustering. Nat Commun 2023; 14:3555. [PMID: 37322016 PMCID: PMC10272148 DOI: 10.1038/s41467-023-39320-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 06/05/2023] [Indexed: 06/17/2023] Open
Abstract
The evolutionary transition from unicellularity to multicellularity was a key innovation in the history of life. Experimental evolution is an important tool to study the formation of undifferentiated cellular clusters, the likely first step of this transition. Although multicellularity first evolved in bacteria, previous experimental evolution research has primarily used eukaryotes. Moreover, it focuses on mutationally driven (and not environmentally induced) phenotypes. Here we show that both Gram-negative and Gram-positive bacteria exhibit phenotypically plastic (i.e., environmentally induced) cell clustering. Under high salinity, they form elongated clusters of ~ 2 cm. However, under habitual salinity, the clusters disintegrate and grow planktonically. We used experimental evolution with Escherichia coli to show that such clustering can be assimilated genetically: the evolved bacteria inherently grow as macroscopic multicellular clusters, even without environmental induction. Highly parallel mutations in genes linked to cell wall assembly formed the genomic basis of assimilated multicellularity. While the wildtype also showed cell shape plasticity across high versus low salinity, it was either assimilated or reversed after evolution. Interestingly, a single mutation could genetically assimilate multicellularity by modulating plasticity at multiple levels of organization. Taken together, we show that phenotypic plasticity can prime bacteria for evolving undifferentiated macroscopic multicellularity.
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Affiliation(s)
- Yashraj Chavhan
- Department of Molecular Biology, Umeå University, Umeå, Sweden.
| | - Sutirth Dey
- Indian Institute of Science Education and Research (IISER) Pune, Pune, India
| | - Peter A Lind
- Department of Molecular Biology, Umeå University, Umeå, Sweden.
- Umeå Centre for Microbial Research, Umeå University, Umeå, Sweden.
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3
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Selveshwari S, Khaire KC, Kadam A, Dey S. The effect of migration and variation on populations of Escherichia coli adapting to complex fluctuating environments. J Evol Biol 2022; 35:1500-1507. [PMID: 36177784 DOI: 10.1111/jeb.14101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Revised: 07/17/2022] [Accepted: 08/23/2022] [Indexed: 11/27/2022]
Abstract
Migration, a critical evolutionary force, can have contrasting effects on adaptation. It can aid as well as impede adaptation. The effects of migration on microbial adaptation have been studied primarily in simple constant environments. Very little is known about the effects of migration on adaptation to complex, fluctuating environments. In our study, we subjected replicate populations of Escherichia coli, adapting to complex and unpredictably fluctuating environments to different proportions of clonal ancestral immigrants. Contrary to the results from simple/constant environments, the presence of clonal immigrants reduced all measured proxies of fitness. However, migration from a source population with a greater variance in fitness resulted in no change in fitness with respect to the no-migration control, except at the highest level of migration. Thus, the presence of variation in the immigrants could counter the adverse effects of migration in complex and unpredictably fluctuating environments. Our study demonstrates that the effects of migration are strongly dependent on the nature of the destination environment and the genetic makeup of immigrants. These results enhance our understanding of the influences of migrating populations, which could help better predict the consequences of migration.
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Affiliation(s)
- S Selveshwari
- Population Biology Laboratory, Biology Division, Indian Institute of Science Education and Research, Pune, Maharashtra, India
| | - Kaustubh Chandrakant Khaire
- Population Biology Laboratory, Biology Division, Indian Institute of Science Education and Research, Pune, Maharashtra, India
| | - Aditee Kadam
- Population Biology Laboratory, Biology Division, Indian Institute of Science Education and Research, Pune, Maharashtra, India
| | - Sutirth Dey
- Population Biology Laboratory, Biology Division, Indian Institute of Science Education and Research, Pune, Maharashtra, India
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Ahlawat N, Geeta Arun M, Maggu K, Prasad NG. Enemies make you stronger: Coevolution between fruit fly host and bacterial pathogen increases postinfection survivorship in the host. Ecol Evol 2021; 11:9563-9574. [PMID: 34306643 PMCID: PMC8293768 DOI: 10.1002/ece3.7774] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 05/01/2021] [Accepted: 05/11/2021] [Indexed: 11/16/2022] Open
Abstract
Multiple laboratory studies have evolved hosts against a nonevolving pathogen to address questions about evolution of immune responses. However, an ecologically more relevant scenario is one where hosts and pathogens can coevolve. Such coevolution between the antagonists, depending on the mutual selection pressure and additive variance in the respective populations, can potentially lead to a different pattern of evolution in the hosts compared to a situation where the host evolves against a nonevolving pathogen. In the present study, we used Drosophila melanogaster as the host and Pseudomonas entomophila as the pathogen. We let the host populations either evolve against a nonevolving pathogen or coevolve with the same pathogen. We found that the coevolving hosts on average evolved higher survivorship against the coevolving pathogen and ancestral (nonevolving) pathogen relative to the hosts evolving against a nonevolving pathogen. The coevolving pathogens evolved greater ability to induce host mortality even in nonlocal (novel) hosts compared to infection by an ancestral (nonevolving) pathogen. Thus, our results clearly show that the evolved traits in the host and the pathogen under coevolution can be different from one-sided adaptation. In addition, our results also show that the coevolving host-pathogen interactions can involve certain general mechanisms in the pathogen, leading to increased mortality induction in nonlocal or novel hosts.
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Affiliation(s)
- Neetika Ahlawat
- Department of Biological SciencesIndian Institute of Science Education and Research MohaliMohaliIndia
| | - Manas Geeta Arun
- Department of Biological SciencesIndian Institute of Science Education and Research MohaliMohaliIndia
| | - Komal Maggu
- Department of Biological SciencesIndian Institute of Science Education and Research MohaliMohaliIndia
| | - Nagaraj Guru Prasad
- Department of Biological SciencesIndian Institute of Science Education and Research MohaliMohaliIndia
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5
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Chavhan Y, Malusare S, Dey S. Interplay of population size and environmental fluctuations: A new explanation for fitness cost rarity in asexuals. Ecol Lett 2021; 24:1943-1954. [PMID: 34145720 DOI: 10.1111/ele.13831] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 05/19/2021] [Accepted: 05/22/2021] [Indexed: 11/29/2022]
Abstract
Theoretical models of ecological specialisation commonly assume that adaptation to one environment leads to fitness reductions (costs) in others. However, experiments often fail to detect such costs. We addressed this conundrum using experimental evolution with Escherichia coli in several constant and fluctuating environments at multiple population sizes. We found that in fluctuating environments, smaller populations paid significant costs, but larger ones avoided them altogether. Contrastingly, in constant environments, larger populations paid more costs than the smaller ones. Overall, large population sizes and fluctuating environments led to cost avoidance only when present together. Mutational frequency distributions obtained from whole-genome whole-population sequencing revealed that the primary mechanism of cost avoidance was the enrichment of multiple beneficial mutations within the same lineage. Since the conditions revealed by our study for avoiding costs are widespread, it provides a novel explanation of the conundrum of why the costs expected in theory are rarely detected in experiments.
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Affiliation(s)
- Yashraj Chavhan
- Indian Institute of Science Education and Research (IISER) Pune, Pune, Maharashtra, India
| | - Sarthak Malusare
- Indian Institute of Science Education and Research (IISER) Pune, Pune, Maharashtra, India
| | - Sutirth Dey
- Indian Institute of Science Education and Research (IISER) Pune, Pune, Maharashtra, India
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Selveshwari S, Lele K, Dey S. Genomic signatures of UV resistance evolution in
Escherichia coli
depend on the growth phase during exposure. J Evol Biol 2021; 34:953-967. [DOI: 10.1111/jeb.13764] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Revised: 12/27/2020] [Accepted: 01/13/2021] [Indexed: 11/28/2022]
Affiliation(s)
- S Selveshwari
- Population Biology Laboratory, Biology Division Indian Institute of Science Education and Research Pune Maharashtra India
| | - Kasturi Lele
- Population Biology Laboratory, Biology Division Indian Institute of Science Education and Research Pune Maharashtra India
| | - Sutirth Dey
- Population Biology Laboratory, Biology Division Indian Institute of Science Education and Research Pune Maharashtra India
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Chavhan Y, Malusare S, Dey S. Larger bacterial populations evolve heavier fitness trade-offs and undergo greater ecological specialization. Heredity (Edinb) 2020; 124:726-736. [PMID: 32203249 DOI: 10.1038/s41437-020-0308-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 03/05/2020] [Accepted: 03/06/2020] [Indexed: 11/09/2022] Open
Abstract
Evolutionary studies over the last several decades have invoked fitness trade-offs to explain why species prefer some environments to others. However, the effects of population size on trade-offs and ecological specialization remain largely unknown. To complicate matters, trade-offs themselves have been visualized in multiple ways in the literature. Thus, it is not clear how population size can affect the various aspects of trade-offs. To address these issues, we conducted experimental evolution with Escherichia coli populations of two different sizes in two nutritionally limited environments, and studied fitness trade-offs from three different perspectives. We found that larger populations evolved greater fitness trade-offs, regardless of how trade-offs are conceptualized. Moreover, although larger populations adapted more to their selection conditions, they also became more maladapted to other environments, ultimately paying heavier costs of adaptation. To enhance the generalizability of our results, we further investigated the evolution of ecological specialization across six different environmental pairs, and found that larger populations specialized more frequently and evolved consistently steeper reaction norms of fitness. This is the first study to demonstrate a relationship between population size and fitness trade-offs, and the results are important in understanding the population genetics of ecological specialization and vulnerability to environmental changes.
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Affiliation(s)
- Yashraj Chavhan
- Indian Institute of Science Education and Research (IISER) Pune, Dr Homi Bhabha Road, Pashan, Pune, Maharashtra, 411008, India
| | - Sarthak Malusare
- Indian Institute of Science Education and Research (IISER) Pune, Dr Homi Bhabha Road, Pashan, Pune, Maharashtra, 411008, India.,Gaia Doctoral School, Institut des Sciences de l'Evolution (ISEM), 1093-1317 Route de Mende, 34090, Montpellier, France
| | - Sutirth Dey
- Indian Institute of Science Education and Research (IISER) Pune, Dr Homi Bhabha Road, Pashan, Pune, Maharashtra, 411008, India.
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Chavhan Y, Karve S, Dey S. Adapting in larger numbers can increase the vulnerability of Escherichia coli populations to environmental changes. Evolution 2019; 73:836-846. [PMID: 30793291 DOI: 10.1111/evo.13700] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Accepted: 02/14/2019] [Indexed: 12/28/2022]
Abstract
Larger populations generally adapt faster to their existing environment. However, it is unknown if the population size experienced during evolution influences the ability to face sudden environmental changes. To investigate this issue, we subjected replicate Escherichia coli populations of different sizes to experimental evolution in an environment containing a cocktail of three antibiotics. In this environment, the ability to actively efflux molecules outside the cell is expected to be a major fitness-affecting trait. We found that all the populations eventually reached similar fitness in the antibiotic cocktail despite adapting at different speeds, with the larger populations adapting faster. Surprisingly, although efflux activity (EA) enhanced in the smaller populations, it decayed in the larger ones. The evolution of EA was largely shaped by pleiotropic responses to selection and not by drift. This demonstrates that quantitative differences in population size can lead to qualitative differences (decay/enhancement) in the fate of a character during adaptation to identical environments. Furthermore, the larger populations showed inferior fitness upon sudden exposure to several alternative stressful environments. These observations provide a novel link between population size and vulnerability to environmental changes. Counterintuitively, adapting in larger numbers can render bacterial populations more vulnerable to abrupt environmental changes.
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Affiliation(s)
- Yashraj Chavhan
- Indian Institute of Science Education and Research (IISER) Pune, Pune, Maharashtra, 411008, India
| | - Shraddha Karve
- Indian Institute of Science Education and Research (IISER) Pune, Pune, Maharashtra, 411008, India.,Current Address: Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, 8057, Switzerland
| | - Sutirth Dey
- Indian Institute of Science Education and Research (IISER) Pune, Pune, Maharashtra, 411008, India
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