1
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Gu S, Wu S, Zeng W, Deng Y, Luo G, Li P, Yang Y, Wang Z, Hu Q, Tan L. High-elevation-induced decrease in soil pH weakens ecosystem multifunctionality by influencing soil microbiomes. ENVIRONMENTAL RESEARCH 2024; 257:119330. [PMID: 38830394 DOI: 10.1016/j.envres.2024.119330] [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: 03/26/2024] [Revised: 05/27/2024] [Accepted: 06/01/2024] [Indexed: 06/05/2024]
Abstract
Plant environmental stress response has become a global research hotspot, yet there is a lack of clear understanding regarding the mechanisms that maintain microbial diversity and their ecosystem services under environmental stress. In our research, we examined the effects of moderate elevation on the rhizosphere soil characteristics, microbial community composition, and ecosystem multifunctionality (EMF) within agricultural systems. Our findings revealed a notable negative correlation between EMF and elevation, indicating a decline in multifunctionality at higher elevations. Additionally, our analysis across bacterial and protistan communities showed a general decrease in microbial richness with increasing elevation. Using random forest models, pH was identified as the key environmental stressor influencing microbial communities. Furthermore, we found that microbial community diversity is negatively correlated with stability by mediating complexity. Interestingly, while pH was found to affect the complexity within bacterial networks, it did not significantly impact the ecosystem stability along the elevation gradients. Using a Binary-State Speciation and Extinction (BiSSE) model to explore the evolutionary dynamics, we found that Generalists had higher speciation rates and lower extinction rates compared to specialists, resulting in a skewed distribution towards higher net diversification for generalists under increasing environmental stress. Moreover, structural equation modeling (SEM) analysis highlighted a negative correlation between environmental stress and community diversity, but showed a positive correlation between environmental stress and degree of cooperation & competition. These interactions under environmental stress indirectly increased community stability and decreased multifunctionality. Our comprehensive study offers valuable insights into the intricate relationship among environmental factors, microbial communities, and ecosystem functions, especially in the context of varying elevation gradients. These findings contribute significantly to our understanding of how environmental stressors affect microbial diversity and ecosystem services, providing a foundation for future ecological research and management strategies in similar contexts.
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Affiliation(s)
- Songsong Gu
- Hunan Agricultural University, Changsha, China; CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Shaolong Wu
- Tobacco Company of Hunan Province, Changsha, Hunan, China
| | - Weiai Zeng
- Changsha Tobacco Company of Hunan Province, Changsha, Hunan, China
| | - Ye Deng
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing, China
| | - Gongwen Luo
- Hunan Agricultural University, Changsha, China
| | - Pengfei Li
- Wenshan Tobacco Company of Yunnan Province, Wenshan, Yunnan, China
| | | | | | - Qiulong Hu
- Hunan Agricultural University, Changsha, China.
| | - Lin Tan
- Hunan Agricultural University, Changsha, China.
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2
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Vos M, Padfield D, Quince C, Vos R. Adaptive radiations in natural populations of prokaryotes: innovation is key. FEMS Microbiol Ecol 2023; 99:fiad154. [PMID: 37996397 PMCID: PMC10710302 DOI: 10.1093/femsec/fiad154] [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: 09/13/2023] [Revised: 11/08/2023] [Accepted: 11/22/2023] [Indexed: 11/25/2023] Open
Abstract
Prokaryote diversity makes up most of the tree of life and is crucial to the functioning of the biosphere and human health. However, the patterns and mechanisms of prokaryote diversification have received relatively little attention compared to animals and plants. Adaptive radiation, the rapid diversification of an ancestor species into multiple ecologically divergent species, is a fundamental process by which macrobiological diversity is generated. Here, we discuss whether ecological opportunity could lead to similar bursts of diversification in bacteria. We explore how adaptive radiations in prokaryotes can be kickstarted by horizontally acquired key innovations allowing lineages to invade new niche space that subsequently is partitioned among diversifying specialist descendants. We discuss how novel adaptive zones are colonized and exploited after the evolution of a key innovation and whether certain types of are more prone to adaptive radiation. Radiation into niche specialists does not necessarily lead to speciation in bacteria when barriers to recombination are absent. We propose that in this scenario, niche-specific genes could accumulate within a single lineage, leading to the evolution of an open pangenome.
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Affiliation(s)
- Michiel Vos
- European Centre for Environment and Human Health, University of Exeter Medical School, Environment and Sustainability Institute, Treliever Road, Penryn Campus, Penryn, TR10 9FE, United Kingdom
- Environment and Sustainability Institute, University of Exeter, Treliever Road, Penryn Campus, Penryn, TR10 9FE, United Kingdom
| | - Daniel Padfield
- European Centre for Environment and Human Health, University of Exeter Medical School, Environment and Sustainability Institute, Treliever Road, Penryn Campus, Penryn, TR10 9FE, United Kingdom
- Environment and Sustainability Institute, University of Exeter, Treliever Road, Penryn Campus, Penryn, TR10 9FE, United Kingdom
| | - Christopher Quince
- Organisms and Ecosystems, Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, United Kingdom
- Gut Microbes and Health, Quadram Institute, Norwich Research Park, Norwich NR4 7UQ, United Kingdom
| | - Rutger Vos
- Naturalis Biodiversity Center, Understanding Evolution, Darwinweg 2, Leiden 2333 CR, the Netherlands
- Institute of Biology Leiden, Leiden University, Sylviusweg 72, Leiden 2333 BE, the Netherlands
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3
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Genner MJ. Cichlid fish seized an ecological opportunity to diversify. Nature 2023; 622:243-244. [PMID: 37794147 DOI: 10.1038/d41586-023-03014-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/06/2023]
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4
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Heydari A, Kim ND, Biggs PJ, Horswell J, Gielen GJHP, Siggins A, Taylor MD, Bromhead C, Palmer BR. Co-Selection of Bacterial Metal and Antibiotic Resistance in Soil Laboratory Microcosms. Antibiotics (Basel) 2023; 12:antibiotics12040772. [PMID: 37107134 PMCID: PMC10135173 DOI: 10.3390/antibiotics12040772] [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: 02/28/2023] [Revised: 04/06/2023] [Accepted: 04/15/2023] [Indexed: 04/29/2023] Open
Abstract
Accumulation of heavy metals (HMs) in agricultural soil following the application of superphosphate fertilisers seems to induce resistance of soil bacteria to HMs and appears to co-select for resistance to antibiotics (Ab). This study aimed to investigate the selection of co-resistance of soil bacteria to HMs and Ab in uncontaminated soil incubated for 6 weeks at 25 °C in laboratory microcosms spiked with ranges of concentrations of cadmium (Cd), zinc (Zn) and mercury (Hg). Co-selection of HM and Ab resistance was assessed using plate culture on media with a range of HM and Ab concentrations, and pollution-induced community tolerance (PICT) assays. Bacterial diversity was profiled via terminal restriction fragment length polymorphism (TRFLP) assay and 16S rDNA sequencing of genomic DNA isolated from selected microcosms. Based on sequence data, the microbial communities exposed to HMs were found to differ significantly compared to control microcosms with no added HM across a range of taxonomic levels.
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Affiliation(s)
- Ali Heydari
- School of Health Sciences, Massey University, Wellington 6021, New Zealand
| | - Nick D Kim
- School of Health Sciences, Massey University, Wellington 6021, New Zealand
| | - Patrick J Biggs
- School of Natural Sciences, Massey University, Palmerston North 4410, New Zealand
- School of Veterinary Science, Massey University, Palmerston North 4410, New Zealand
| | - Jacqui Horswell
- School of Health Sciences, Massey University, Wellington 6021, New Zealand
| | | | - Alma Siggins
- School of Biological and Chemical Sciences and Ryan Institute, University of Galway, H91 TK33 Galway, Ireland
| | | | - Collette Bromhead
- School of Health Sciences, Massey University, Wellington 6021, New Zealand
| | - Barry R Palmer
- School of Health Sciences, Massey University, Wellington 6021, New Zealand
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5
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Lücken L, Lennartz ST, Froehlich J, Blasius B. Emergent Diversity and Persistent Turnover in Evolving Microbial Cross-Feeding Networks. FRONTIERS IN NETWORK PHYSIOLOGY 2022; 2:834057. [PMID: 36926111 PMCID: PMC10013070 DOI: 10.3389/fnetp.2022.834057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Accepted: 02/01/2022] [Indexed: 11/13/2022]
Abstract
A distinguishing feature of many ecological networks in the microbial realm is the diversity of substrates that could potentially serve as energy sources for microbial consumers. The microorganisms are themselves the agents of compound diversification via metabolite excretion or overflow metabolism. It has been suggested that the emerging richness of different substrates is an important condition for the immense biological diversity in microbial ecosystems. In this work, we study how complex cross-feeding networks (CFN) of microbial species may develop from a simple initial community given some elemental evolutionary mechanisms of resource-dependent speciation and extinctions using a network flow model. We report results of several numerical experiments and report an in-depth analysis of the evolutionary dynamics. We find that even in stable environments, the system is subject to persisting turnover, indicating an ongoing co-evolution. Further, we compare the impact of different parameters, such as the ratio of mineralization, as well as the metabolic versatility and variability on the evolving community structure. The results imply that high microbial and molecular diversity is an emergent property of evolution in cross-feeding networks, which affects transformation and accumulation of substrates in natural systems, such as soils and oceans, with potential relevance to biotechnological applications.
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Affiliation(s)
- Leonhard Lücken
- Institute for Chemistry and Biology of the Marine Environment, Carl von Ossietzky University of Oldenburg, Oldenburg, Germany
| | - Sinikka T. Lennartz
- Institute for Chemistry and Biology of the Marine Environment, Carl von Ossietzky University of Oldenburg, Oldenburg, Germany
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Jule Froehlich
- Institute for Chemistry and Biology of the Marine Environment, Carl von Ossietzky University of Oldenburg, Oldenburg, Germany
| | - Bernd Blasius
- Institute for Chemistry and Biology of the Marine Environment, Carl von Ossietzky University of Oldenburg, Oldenburg, Germany
- Helmholtz Institute for Functional Marine Biodiversity, Carl von Ossietzky University of Oldenburg, Oldenburg, Germany
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6
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Co-Selection of Heavy Metal and Antibiotic Resistance in Soil Bacteria from Agricultural Soils in New Zealand. SUSTAINABILITY 2022. [DOI: 10.3390/su14031790] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Accumulation of trace elements (including heavy metals) in soil from usage of superphosphate fertilisers induces resistance of soil bacteria to trace elements of environmental concern (TEoEC) and may co-select for resistance to antibiotics (Ab). This study aimed to investigate selection of co-resistance of soil bacteria to Cd, Zn and Hg, and Ab in soils with varied management histories. Genetic diversity of these bacteria and horizontal transfer of Cd resistance genes (cadA and czcA) were also investigated. Soils with either pastoral and arable management histories and either high levels of Cd and Zn, or indigenous bush with background levels of these TEoEC from the Waikato region, New Zealand were sampled. Plate culturing with a range of TEoEC and Ab concentrations, Pollution Induced Community Tolerance (PICT) assay, antibiotic sensitivity, terminal restriction fragment length polymorphism (TRFLP) and horizontal gene transfer (HGT) analyses were employed to investigate co-selection of TEoEC and Ab resistance. Higher levels of bacterial resistance to TEoEC and Ab correlated with higher levels of TEoEC in soil. Bacterial community structures were altered in soils with high TEoEC levels. Cd resistance genes were transferred from donor bacterial isolates, to recipients and the transconjugants also had resistance to Zn and/or Hg and a range of Ab.
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7
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Paccard A, Hanson D, Stuart YE, von Hippel FA, Kalbe M, Klepaker T, Skúlason S, Kristjánsson BK, Bolnick DI, Hendry AP, Barrett RDH. Repeatability of Adaptive Radiation Depends on Spatial Scale: Regional Versus Global Replicates of Stickleback in Lake Versus Stream Habitats. J Hered 2021; 111:43-56. [PMID: 31690947 DOI: 10.1093/jhered/esz056] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 09/30/2019] [Indexed: 11/13/2022] Open
Abstract
The repeatability of adaptive radiation is expected to be scale-dependent, with determinism decreasing as greater spatial separation among "replicates" leads to their increased genetic and ecological independence. Threespine stickleback (Gasterosteus aculeatus) provide an opportunity to test whether this expectation holds for the early stages of adaptive radiation-their diversification in freshwater ecosystems has been replicated many times. To better understand the repeatability of that adaptive radiation, we examined the influence of geographic scale on levels of parallel evolution by quantifying phenotypic and genetic divergence between lake and stream stickleback pairs sampled at regional (Vancouver Island) and global (North America and Europe) scales. We measured phenotypes known to show lake-stream divergence and used reduced representation genome-wide sequencing to estimate genetic divergence. We assessed the scale dependence of parallel evolution by comparing effect sizes from multivariate models and also the direction and magnitude of lake-stream divergence vectors. At the phenotypic level, parallelism was greater at the regional than the global scale. At the genetic level, putative selected loci showed greater lake-stream parallelism at the regional than the global scale. Generally, the level of parallel evolution was low at both scales, except for some key univariate traits. Divergence vectors were often orthogonal, highlighting possible ecological and genetic constraints on parallel evolution at both scales. Overall, our results confirm that the repeatability of adaptive radiation decreases at increasing spatial scales. We suggest that greater environmental heterogeneity at larger scales imposes different selection regimes, thus generating lower repeatability of adaptive radiation at larger spatial scales.
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Affiliation(s)
- Antoine Paccard
- Redpath Museum and Department of Biology, McGill University, Montreal, Canada
| | - Dieta Hanson
- Redpath Museum and Department of Biology, McGill University, Montreal, Canada
| | - Yoel E Stuart
- Department of Integrative Biology, University of Texas at Austin, Austin, TX
| | - Frank A von Hippel
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ
| | - Martin Kalbe
- Department of Evolutionary Ecology, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Tom Klepaker
- University of Bergen, Department of Biology, Bergen, Norway
| | - Skúli Skúlason
- Department of Aquaculture and Fish Biology, Hólar University College, Sauðárkrókur, Iceland
| | - Bjarni K Kristjánsson
- Department of Aquaculture and Fish Biology, Hólar University College, Sauðárkrókur, Iceland
| | - Daniel I Bolnick
- Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT
| | - Andrew P Hendry
- Redpath Museum and Department of Biology, McGill University, Montreal, Canada
| | - Rowan D H Barrett
- Redpath Museum and Department of Biology, McGill University, Montreal, Canada
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8
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Tusso S, Nieuwenhuis BPS, Weissensteiner B, Immler S, Wolf JBW. Experimental evolution of adaptive divergence under varying degrees of gene flow. Nat Ecol Evol 2021; 5:338-349. [PMID: 33432131 DOI: 10.1038/s41559-020-01363-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 11/12/2020] [Indexed: 01/28/2023]
Abstract
Adaptive divergence is the key evolutionary process generating biodiversity by means of natural selection. Yet, the conditions under which it can arise in the presence of gene flow remain contentious. To address this question, we subjected 132 sexually reproducing fission yeast populations, sourced from two independent genetic backgrounds, to disruptive ecological selection and manipulated the level of migration between environments. Contrary to theoretical expectations, adaptive divergence was most pronounced when migration was either absent (allopatry) or maximal (sympatry), but was much reduced at intermediate rates (parapatry and local mating). This effect was apparent across central life-history components (survival, asexual growth and mating) but differed in magnitude between ancestral genetic backgrounds. The evolution of some fitness components was constrained by pervasive negative correlations (trade-off between asexual growth and mating), while others changed direction under the influence of migration (for example, survival and mating). In allopatry, adaptive divergence was mainly conferred by standing genetic variation and resulted in ecological specialization. In sympatry, divergence was mainly mediated by novel mutations enriched in a subset of genes and was characterized by the repeated emergence of two strategies: an ecological generalist and an asexual growth specialist. Multiple loci showed consistent evidence for antagonistic pleiotropy across migration treatments providing a conceptual link between adaptation and divergence. This evolve-and-resequence experiment shows that rapid ecological differentiation can arise even under high rates of gene flow. It further highlights that adaptive trajectories are governed by complex interactions of gene flow, ancestral variation and genetic correlations.
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Affiliation(s)
- Sergio Tusso
- Division of Evolutionary Biology, Faculty of Biology, Ludwig-Maximilians-Universität Munich, Munich, Germany. .,Science for Life Laboratory, Uppsala University, Uppsala, Sweden. .,Department of Evolutionary Biology, Uppsala University, Uppsala, Sweden.
| | - Bart P S Nieuwenhuis
- Division of Evolutionary Biology, Faculty of Biology, Ludwig-Maximilians-Universität Munich, Munich, Germany
| | - Bernadette Weissensteiner
- Division of Evolutionary Biology, Faculty of Biology, Ludwig-Maximilians-Universität Munich, Munich, Germany
| | - Simone Immler
- Science for Life Laboratory, Uppsala University, Uppsala, Sweden.,Department of Evolutionary Biology, Uppsala University, Uppsala, Sweden.,School of Biological Sciences, University of East Anglia, Norwich, UK
| | - Jochen B W Wolf
- Division of Evolutionary Biology, Faculty of Biology, Ludwig-Maximilians-Universität Munich, Munich, Germany. .,Science for Life Laboratory, Uppsala University, Uppsala, Sweden. .,Department of Evolutionary Biology, Uppsala University, Uppsala, Sweden.
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9
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Visher E, Boots M. The problem of mediocre generalists: population genetics and eco-evolutionary perspectives on host breadth evolution in pathogens. Proc Biol Sci 2020; 287:20201230. [PMID: 32811306 PMCID: PMC7482275 DOI: 10.1098/rspb.2020.1230] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 07/22/2020] [Indexed: 01/29/2023] Open
Abstract
Many of our theories for the generation and maintenance of diversity in nature depend on the existence of specialist biotic interactions which, in host-pathogen systems, also shape cross-species disease emergence. As such, niche breadth evolution, especially in host-parasite systems, remains a central focus in ecology and evolution. The predominant explanation for the existence of specialization in the literature is that niche breadth is constrained by trade-offs, such that a generalist is less fit on any particular environment than a given specialist. This trade-off theory has been used to predict niche breadth (co)evolution in both population genetics and eco-evolutionary models, with the different modelling methods providing separate, complementary insights. However, trade-offs may be far from universal, so population genetics theory has also proposed alternate mechanisms for costly generalism, including mutation accumulation. However, these mechanisms have yet to be integrated into eco-evolutionary models in order to understand how the mechanism of costly generalism alters the biological and ecological circumstances predicted to maintain specialism. In this review, we outline how population genetics and eco-evolutionary models based on trade-offs have provided insights for parasite niche breadth evolution and argue that the population genetics-derived mutation accumulation theory needs to be better integrated into eco-evolutionary theory.
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Affiliation(s)
- Elisa Visher
- Department of Integrative Biology, University of California Berkeley, Berkeley, CA, USA
| | - Mike Boots
- Department of Integrative Biology, University of California Berkeley, Berkeley, CA, USA
- College of Life and Environmental Sciences, University of Exeter, Cornwall Campus, Ringgold Standard Institution, Penryn, Cornwall, UK
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10
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Warsi O, Lundin E, Lustig U, Näsvall J, Andersson DI. Selection for novel metabolic capabilities in Salmonella enterica. Evolution 2019; 73:990-1000. [PMID: 30848832 PMCID: PMC6593847 DOI: 10.1111/evo.13713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Revised: 02/20/2019] [Accepted: 02/28/2019] [Indexed: 11/29/2022]
Abstract
Bacteria are known to display extensive metabolic diversity and many studies have shown that they can use an extensive repertoire of small molecules as carbon‐ and energy sources. However, it is less clear to what extent a bacterium can expand its existing metabolic capabilities by acquiring mutations that, for example, rewire its metabolic pathways. To investigate this capability and potential for evolution of novel phenotypes, we sampled large populations of mutagenized Salmonella enterica to select very rare mutants that can grow on minimal media containing 124 low molecular weight compounds as sole carbon sources. We found mutants growing on 18 of these novel carbon sources, and identified the causal mutations that allowed growth for four of them. Mutations that relieve physiological constraints or increase expression of existing pathways were found to be important contributors to the novel phenotypes. For the remaining 14 novel phenotypes, whole genome sequencing of independent mutants and genetic analysis suggested that these novel metabolic phenotypes result from a combination of multiple mutations. This work, by virtue of identifying the genetic and mechanistic basis for new metabolic capabilities, sheds light on the properties of adaptive landscapes underlying the evolution of novel phenotypes.
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Affiliation(s)
- Omar Warsi
- Department of Medical Biochemistry and Microbiology, Biomedical Center, Uppsala University, S-751 23, Uppsala, Sweden
| | - Erik Lundin
- Department of Medical Biochemistry and Microbiology, Biomedical Center, Uppsala University, S-751 23, Uppsala, Sweden
| | - Ulrika Lustig
- Department of Medical Biochemistry and Microbiology, Biomedical Center, Uppsala University, S-751 23, Uppsala, Sweden
| | - Joakim Näsvall
- Department of Medical Biochemistry and Microbiology, Biomedical Center, Uppsala University, S-751 23, Uppsala, Sweden
| | - Dan I Andersson
- Department of Medical Biochemistry and Microbiology, Biomedical Center, Uppsala University, S-751 23, Uppsala, Sweden
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11
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Edwards KF, Kremer CT, Miller ET, Osmond MM, Litchman E, Klausmeier CA. Evolutionarily stable communities: a framework for understanding the role of trait evolution in the maintenance of diversity. Ecol Lett 2018; 21:1853-1868. [PMID: 30272831 DOI: 10.1111/ele.13142] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Revised: 04/16/2018] [Accepted: 07/23/2018] [Indexed: 01/15/2023]
Abstract
Biological diversity depends on the interplay between evolutionary diversification and ecological mechanisms allowing species to coexist. Current research increasingly integrates ecology and evolution over a range of timescales, but our common conceptual framework for understanding species coexistence requires better incorporation of evolutionary processes. Here, we focus on the idea of evolutionarily stable communities (ESCs), which are theoretical endpoints of evolution in a community context. We use ESCs as a unifying framework to highlight some important but under-appreciated theoretical results, and we review empirical research relevant to these theoretical predictions. We explain how, in addition to generating diversity, evolution can also limit diversity by reducing the effectiveness of coexistence mechanisms. The coevolving traits of competing species may either diverge or converge, depending on whether the number of species in the community is low (undersaturated) or high (oversaturated) relative to the ESC. Competition in oversaturated communities can lead to extinction or neutrally coexisting, ecologically equivalent species. It is critical to consider trait evolution when investigating fundamental ecological questions like the strength of different coexistence mechanisms, the feasibility of ecologically equivalent species, and the interpretation of different patterns of trait dispersion.
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Affiliation(s)
- Kyle F Edwards
- Department of Oceanography, University of Hawai'i at Manoa, Honolulu, HI, 96822, USA
| | - Colin T Kremer
- Department of Ecology & Evolutionary Biology, Yale University, New Haven, CT, 06520, USA.,Kellogg Biological Station, Michigan State University, Hickory Corners, MI, 49060, USA.,Program in Ecology, Evolutionary Biology, & Behavior, Michigan State University, East Lansing, MI, 48824, USA
| | - Elizabeth T Miller
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR, 97403, USA
| | - Matthew M Osmond
- Department of Zoology, University of British Columbia, Vancouver, BC, V6T 1Z4, USA
| | - Elena Litchman
- Kellogg Biological Station, Michigan State University, Hickory Corners, MI, 49060, USA.,Program in Ecology, Evolutionary Biology, & Behavior, Michigan State University, East Lansing, MI, 48824, USA.,Department of Integrative Biology, Michigan State University, East Lansing, MI, 48824, USA
| | - Christopher A Klausmeier
- Kellogg Biological Station, Michigan State University, Hickory Corners, MI, 49060, USA.,Program in Ecology, Evolutionary Biology, & Behavior, Michigan State University, East Lansing, MI, 48824, USA.,Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA
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12
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Koza A, Kusmierska A, McLaughlin K, Moshynets O, Spiers AJ. Adaptive radiation of Pseudomonas fluorescens SBW25 in experimental microcosms provides an understanding of the evolutionary ecology and molecular biology of A-L interface biofilm formation. FEMS Microbiol Lett 2018; 364:3850210. [PMID: 28535292 DOI: 10.1093/femsle/fnx109] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Accepted: 05/22/2017] [Indexed: 12/17/2022] Open
Abstract
Combined experimental evolutionary and molecular biology approaches have been used to investigate the adaptive radiation of Pseudomonas fluorescens SBW25 in static microcosms leading to the colonisation of the air-liquid interface by biofilm-forming mutants such as the Wrinkly Spreader (WS). In these microcosms, the ecosystem engineering of the early wild-type colonists establishes the niche space for subsequent WS evolution and colonisation. Random WS mutations occurring in the developing population that deregulate diguanylate cyclases and c-di-GMP homeostasis result in cellulose-based biofilms at the air-liquid interface. These structures allow Wrinkly Spreaders to intercept O2 diffusing into the liquid column and limit the growth of competitors lower down. As the biofilm matures, competition increasingly occurs between WS lineages, and niche divergence within the biofilm may support further diversification before system failure when the structure finally sinks. A combination of pleiotropic and epistasis effects, as well as secondary mutations, may explain variations in WS phenotype and fitness. Understanding how mutations subvert regulatory networks to express intrinsic genome potential and key innovations providing a selective advantage in novel environments is key to understanding the versatility of bacteria, and how selection and ecological opportunity can rapidly lead to substantive changes in phenotype and in community structure and function.
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Affiliation(s)
- Anna Koza
- School of Science, Engineering and Technology, Abertay University, Dundee DD1 1HG, UK
| | - Anna Kusmierska
- School of Science, Engineering and Technology, Abertay University, Dundee DD1 1HG, UK
| | - Kimberley McLaughlin
- School of Science, Engineering and Technology, Abertay University, Dundee DD1 1HG, UK
| | - Olena Moshynets
- Institute of Molecular Biology and Genetics of the National Academy of Sciences of Ukraine, Kiev 03143, Ukraine
| | - Andrew J Spiers
- School of Science, Engineering and Technology, Abertay University, Dundee DD1 1HG, UK
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13
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Sriswasdi S, Yang CC, Iwasaki W. Generalist species drive microbial dispersion and evolution. Nat Commun 2017; 8:1162. [PMID: 29079803 PMCID: PMC5660117 DOI: 10.1038/s41467-017-01265-1] [Citation(s) in RCA: 110] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Accepted: 09/01/2017] [Indexed: 11/19/2022] Open
Abstract
Microbes form fundamental bases of every Earth ecosystem. As their key survival strategies, some microbes adapt to broad ranges of environments, while others specialize to certain habitats. While ecological roles and properties of such “generalists” and “specialists” had been examined in individual ecosystems, general principles that govern their distribution patterns and evolutionary processes have not been characterized. Here, we thoroughly identified microbial generalists and specialists across 61 environments via meta-analysis of community sequencing data sets and reconstructed their evolutionary histories across diverse microbial groups. This revealed that generalist lineages possess 19-fold higher speciation rates and significant persistence advantage over specialists. Yet, we also detected three-fold more frequent generalist-to-specialist transformations than the reverse transformations. These results support a model of microbial evolution in which generalists play key roles in introducing new species and maintaining taxonomic diversity. Microbes adapting to broad and specialized ranges of environments (generalists and specialists) have distinct ecological roles and properties. Via meta-analysis of community sequencing datasets, Sriswasdi et al. show that generalists have higher speciation rates and persistence advantage over specialists.
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Affiliation(s)
- Sira Sriswasdi
- Department of Biological Sciences, Graduate School of Science, the University of Tokyo, Bunkyo-ku, Tokyo, 113-0032, Japan. .,Research Affairs, Faculty of Medicine, Chulalongkorn University, Pathum Wan, Bangkok, 10330, Thailand.
| | - Ching-Chia Yang
- Department of Biological Sciences, Graduate School of Science, the University of Tokyo, Bunkyo-ku, Tokyo, 113-0032, Japan
| | - Wataru Iwasaki
- Department of Biological Sciences, Graduate School of Science, the University of Tokyo, Bunkyo-ku, Tokyo, 113-0032, Japan. .,Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, the University of Tokyo, Kashiwa, Chiba, 277-8568, Japan. .,Atmosphere and Ocean Research Institute, the University of Tokyo, Kashiwa, Chiba, 277-8564, Japan.
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14
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Marin J, Battistuzzi FU, Brown AC, Hedges SB. The Timetree of Prokaryotes: New Insights into Their Evolution and Speciation. Mol Biol Evol 2017; 34:437-446. [PMID: 27965376 DOI: 10.1093/molbev/msw245] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The increasing size of timetrees in recent years has led to a focus on diversification analyses to better understand patterns of macroevolution. Thus far, nearly all studies have been conducted with eukaryotes primarily because phylogenies have been more difficult to reconstruct and calibrate to geologic time in prokaryotes. Here, we have estimated a timetree of 11,784 'species' of prokaryotes and explored their pattern of diversification. We used data from the small subunit ribosomal RNA along with an evolutionary framework from previous multi-gene studies to produce three alternative timetrees. For each timetree we surprisingly found a constant net diversification rate derived from an exponential increase of lineages and showing no evidence of saturation (rate decline), the same pattern found previously in eukaryotes. The implication is that prokaryote diversification as a whole is the result of the random splitting of lineages and is neither limited by existing diversity (filled niches) nor responsive in any major way to environmental changes.
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Affiliation(s)
- Julie Marin
- Center for Biodiversity, Temple University, SERC Suite 502, 1925 N 12th Street, Philadelphia, PA.,Institut de Systématique, Evolution, Biodiversité UMR 7205, Département Systématique et Evolution, Muséum National d'Histoire Naturelle, Sorbonne-Universités, Paris, France
| | | | - Anais C Brown
- Department of Biological Sciences, Oakland University, Rochester, MI
| | - S Blair Hedges
- Center for Biodiversity, Temple University, SERC Suite 502, 1925 N 12th Street, Philadelphia, PA
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15
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Li Y, Jiang L, Wu Q, Wang P, Gooi H, Li K, Liu Y, Lu P, Cao M, Imura J. Wind-thermal power system dispatch using MLSAD model and GSOICLW algorithm. Knowl Based Syst 2017. [DOI: 10.1016/j.knosys.2016.10.028] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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16
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New Insights into the Effects of Several Environmental Parameters on the Relative Fitness of a Numerically Dominant Class of Evolved Niche Specialist. INTERNATIONAL JOURNAL OF EVOLUTIONARY BIOLOGY 2016; 2016:4846565. [PMID: 28101396 PMCID: PMC5214101 DOI: 10.1155/2016/4846565] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Accepted: 11/24/2016] [Indexed: 11/17/2022]
Abstract
Adaptive radiation in bacteria has been investigated using Wrinkly Spreaders (WS), a morphotype which colonises the air-liquid (A-L) interface of static microcosms by biofilm formation with a significant fitness advantage over competitors growing lower down in the O2-limited liquid column. Here, we investigate several environmental parameters which impact the ecological opportunity that the Wrinkly Spreaders exploit in this model system. Manipulation of surface area/volume ratios suggests that the size of the WS niche was not as important as the ability to dominate the A-L interface and restrict competitor growth. The value of this niche to the Wrinkly Spreaders, as determined by competitive fitness assays, was found to increase as O2 flux to the A-L interface was reduced, confirming that competition for O2 was the main driver of WS fitness. The effect of O2 on fitness was also found to be dependent on the availability of nutrients, reflecting the need to take up both for optimal growth. Finally, the meniscus trap, a high-O2 region formed by the interaction of the A-L interface with the vial walls, was also important for fitness during the early stages of biofilm formation. These findings reveal the complexity of this seemingly simple model system and illustrate how changes in environmental physicality alter ecological opportunity and the fitness of the adaptive morphotype.
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17
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Villa Martín P, Hidalgo J, Rubio de Casas R, Muñoz MA. Eco-evolutionary Model of Rapid Phenotypic Diversification in Species-Rich Communities. PLoS Comput Biol 2016; 12:e1005139. [PMID: 27736874 PMCID: PMC5063285 DOI: 10.1371/journal.pcbi.1005139] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Accepted: 09/09/2016] [Indexed: 12/30/2022] Open
Abstract
Evolutionary and ecosystem dynamics are often treated as different processes –operating at separate timescales– even if evidence reveals that rapid evolutionary changes can feed back into ecological interactions. A recent long-term field experiment has explicitly shown that communities of competing plant species can experience very fast phenotypic diversification, and that this gives rise to enhanced complementarity in resource exploitation and to enlarged ecosystem-level productivity. Here, we build on progress made in recent years in the integration of eco-evolutionary dynamics, and present a computational approach aimed at describing these empirical findings in detail. In particular we model a community of organisms of different but similar species evolving in time through mechanisms of birth, competition, sexual reproduction, descent with modification, and death. Based on simple rules, this model provides a rationalization for the emergence of rapid phenotypic diversification in species-rich communities. Furthermore, it also leads to non-trivial predictions about long-term phenotypic change and ecological interactions. Our results illustrate that the presence of highly specialized, non-competing species leads to very stable communities and reveals that phenotypically equivalent species occupying the same niche may emerge and coexist for very long times. Thus, the framework presented here provides a simple approach –complementing existing theories, but specifically devised to account for the specificities of the recent empirical findings for plant communities– to explain the collective emergence of diversification at a community level, and paves the way to further scrutinize the intimate entanglement of ecological and evolutionary processes, especially in species-rich communities. Population ecology and evolutionary biology have been traditionally studied as separate disciplines, even if feedbacks between community and evolutionary processes are known to exist, having been empirically characterized in recent years in different types of communities (from microbes to plants and vertebrates), and theoretically analyzed with novel and powerful mathematical tools. Recent long-term field experiments with plants have proven that rapid co-evolution and diversification of species traits results in an overall enhancement of the ecosystem productivity, with important consequences for agriculture and conservation. Here, we propose a relatively simple computational eco-evolutionary model specifically devised to describe rapid phenotypic diversification in this type of species-rich communities. Our model captures the main phenomenology observed experimentally, and it also makes non-trivial predictions for long term phenotypic change and ecological interactions, such as the stable coexistence of highly specialized species or the possible emergence of phenotypically equivalent species occupying the same niche. Finally, the model is easily generalizable to analyze different eco-evolutionary problems within a relatively simple and unified computational framework.
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Affiliation(s)
- Paula Villa Martín
- Departamento de Electromagnetismo y Física de la Materia and Instituto Carlos I de Física Teórica y Computacional, Universidad de Granada, Granada, Spain
| | - Jorge Hidalgo
- Departamento de Electromagnetismo y Física de la Materia and Instituto Carlos I de Física Teórica y Computacional, Universidad de Granada, Granada, Spain
- Dipartimento di Fisica ’G.Galilei’ and CNISM, INFN, Università di Padova, Padova, Italy
| | - Rafael Rubio de Casas
- Estación Experimental de Zonas Áridas, EEZA-CSIC, Almería, Spain
- UMR 5175 Centre d’Ecologie Fonctionnelle et Evolutive (CNRS), Montpellier, France
- Departamento de Ecología, Universidad de Granada, Granada, Spain
| | - Miguel A. Muñoz
- Departamento de Electromagnetismo y Física de la Materia and Instituto Carlos I de Física Teórica y Computacional, Universidad de Granada, Granada, Spain
- * E-mail:
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18
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Adaptive radiation by waves of gene transfer leads to fine-scale resource partitioning in marine microbes. Nat Commun 2016; 7:12860. [PMID: 27653556 PMCID: PMC5036157 DOI: 10.1038/ncomms12860] [Citation(s) in RCA: 89] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Accepted: 08/09/2016] [Indexed: 11/17/2022] Open
Abstract
Adaptive radiations are important drivers of niche filling, since they rapidly adapt a single clade of organisms to ecological opportunities. Although thought to be common for animals and plants, adaptive radiations have remained difficult to document for microbes in the wild. Here we describe a recent adaptive radiation leading to fine-scale ecophysiological differentiation in the degradation of an algal glycan in a clade of closely related marine bacteria. Horizontal gene transfer is the primary driver in the diversification of the pathway leading to several ecophysiologically differentiated Vibrionaceae populations adapted to different physical forms of alginate. Pathway architecture is predictive of function and ecology, underscoring that horizontal gene transfer without extensive regulatory changes can rapidly assemble fully functional pathways in microbes. Adaptive radiations are well-known for animals and plants, but not for microbes. Here, Hehemann et al. show that there has been a recent adaptive radiation of bacteria in the Vibrionaceae to use different forms of alginate and that this radiation has been mediated by horizontal gene transfer.
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19
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Abstract
The plague bacillus Yersinia pestis is unique among the pathogenic Enterobacteriaceae in utilizing an arthropod-borne transmission route. Transmission by fleabite is a recent evolutionary adaptation that followed the divergence of Y. pestis from the closely related food- and waterborne enteric pathogen Yersinia pseudotuberculosis A combination of population genetics, comparative genomics, and investigations of Yersinia-flea interactions have disclosed the important steps in the evolution and emergence of Y. pestis as a flea-borne pathogen. Only a few genetic changes, representing both gene gain by lateral transfer and gene loss by loss-of-function mutation (pseudogenization), were fundamental to this process. The emergence of Y. pestis fits evolutionary theories that emphasize ecological opportunity in adaptive diversification and rapid emergence of new species.
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20
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Jerison ER, Desai MM. Genomic investigations of evolutionary dynamics and epistasis in microbial evolution experiments. Curr Opin Genet Dev 2015; 35:33-9. [PMID: 26370471 DOI: 10.1016/j.gde.2015.08.008] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Revised: 08/20/2015] [Accepted: 08/25/2015] [Indexed: 12/20/2022]
Abstract
Microbial evolution experiments enable us to watch adaptation in real time, and to quantify the repeatability and predictability of evolution by comparing identical replicate populations. Further, we can resurrect ancestral types to examine changes over evolutionary time. Until recently, experimental evolution has been limited to measuring phenotypic changes, or to tracking a few genetic markers over time. However, recent advances in sequencing technology now make it possible to extensively sequence clones or whole-population samples from microbial evolution experiments. Here, we review recent work exploiting these techniques to understand the genomic basis of evolutionary change in experimental systems. We first focus on studies that analyze the dynamics of genome evolution in microbial systems. We then survey work that uses observations of sequence evolution to infer aspects of the underlying fitness landscape, concentrating on the epistatic interactions between mutations and the constraints these interactions impose on adaptation.
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Affiliation(s)
- Elizabeth R Jerison
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, United States; Department of Physics, Harvard University, Cambridge, MA 02138, United States; FAS Center for Systems Biology, Harvard University, Cambridge, MA 02138, United States
| | - Michael M Desai
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, United States; Department of Physics, Harvard University, Cambridge, MA 02138, United States; FAS Center for Systems Biology, Harvard University, Cambridge, MA 02138, United States.
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21
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Evolution of coexistence in a crowded microplate well. Proc Natl Acad Sci U S A 2015; 112:11148-9. [PMID: 26311847 DOI: 10.1073/pnas.1514399112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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22
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Frenkel EM, McDonald MJ, Van Dyken JD, Kosheleva K, Lang GI, Desai MM. Crowded growth leads to the spontaneous evolution of semistable coexistence in laboratory yeast populations. Proc Natl Acad Sci U S A 2015; 112:11306-11. [PMID: 26240355 PMCID: PMC4568650 DOI: 10.1073/pnas.1506184112] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Identifying the mechanisms that create and maintain biodiversity is a central challenge in biology. Stable diversification of microbial populations often requires the evolution of differences in resource utilization. Alternatively, coexistence can be maintained by specialization to exploit spatial heterogeneity in the environment. Here, we report spontaneous diversification maintained by a related but distinct mechanism: crowding avoidance. During experimental evolution of laboratory Saccharomyces cerevisiae populations, we observed the repeated appearance of "adherent" (A) lineages able to grow as a dispersed film, in contrast to their crowded "bottom-dweller" (B) ancestors. These two types stably coexist because dispersal reduces interference competition for nutrients among kin, at the cost of a slower maximum growth rate. This tradeoff causes the frequencies of the two types to oscillate around equilibrium over the course of repeated cycles of growth, crowding, and dispersal. However, further coevolution of the A and B types can perturb and eventually destroy their coexistence over longer time scales. We introduce a simple mathematical model of this "semistable" coexistence, which explains the interplay between ecological and evolutionary dynamics. Because crowded growth generally limits nutrient access in biofilms, the mechanism we report here may be broadly important in maintaining diversity in these natural environments.
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Affiliation(s)
- Evgeni M Frenkel
- Department of Organismic and Evolutionary Biology, Department of Physics, and Faculty of Arts and Sciences Center for Systems Biology, Harvard University, Cambridge, MA 02138; Program in Biophysics, Harvard University, Boston, MA 02115
| | - Michael J McDonald
- Department of Organismic and Evolutionary Biology, Department of Physics, and Faculty of Arts and Sciences Center for Systems Biology, Harvard University, Cambridge, MA 02138
| | | | - Katya Kosheleva
- Department of Organismic and Evolutionary Biology, Department of Physics, and Faculty of Arts and Sciences Center for Systems Biology, Harvard University, Cambridge, MA 02138
| | - Gregory I Lang
- Department of Biological Sciences, Lehigh University, Bethlehem, PA 18015
| | - Michael M Desai
- Department of Organismic and Evolutionary Biology, Department of Physics, and Faculty of Arts and Sciences Center for Systems Biology, Harvard University, Cambridge, MA 02138;
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23
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Udall YC, Deeni Y, Hapca SM, Raikes D, Spiers AJ. The evolution of biofilm-forming Wrinkly Spreaders in static microcosms and drip-fed columns selects for subtle differences in wrinkleality and fitness. FEMS Microbiol Ecol 2015; 91:fiv057. [DOI: 10.1093/femsec/fiv057] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/20/2015] [Indexed: 12/30/2022] Open
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24
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Seabloom EW, Borer ET, Gross K, Kendig AE, Lacroix C, Mitchell CE, Mordecai EA, Power AG. The community ecology of pathogens: coinfection, coexistence and community composition. Ecol Lett 2015; 18:401-15. [PMID: 25728488 DOI: 10.1111/ele.12418] [Citation(s) in RCA: 117] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2014] [Revised: 09/20/2014] [Accepted: 01/14/2015] [Indexed: 12/11/2022]
Abstract
Disease and community ecology share conceptual and theoretical lineages, and there has been a resurgence of interest in strengthening links between these fields. Building on recent syntheses focused on the effects of host community composition on single pathogen systems, we examine pathogen (microparasite) communities using a stochastic metacommunity model as a starting point to bridge community and disease ecology perspectives. Such models incorporate the effects of core community processes, such as ecological drift, selection and dispersal, but have not been extended to incorporate host-pathogen interactions, such as immunosuppression or synergistic mortality, that are central to disease ecology. We use a two-pathogen susceptible-infected (SI) model to fill these gaps in the metacommunity approach; however, SI models can be intractable for examining species-diverse, spatially structured systems. By placing disease into a framework developed for community ecology, our synthesis highlights areas ripe for progress, including a theoretical framework that incorporates host dynamics, spatial structuring and evolutionary processes, as well as the data needed to test the predictions of such a model. Our synthesis points the way for this framework and demonstrates that a deeper understanding of pathogen community dynamics will emerge from approaches working at the interface of disease and community ecology.
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Affiliation(s)
- Eric W Seabloom
- Department of Ecology, Evolution, and Behavior, University of Minnesota, St. Paul, MN, USA
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25
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Recent radiation in a marine and freshwater dinoflagellate species flock. ISME JOURNAL 2015; 9:1821-34. [PMID: 25603395 DOI: 10.1038/ismej.2014.267] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2014] [Revised: 12/03/2014] [Accepted: 12/12/2014] [Indexed: 11/09/2022]
Abstract
Processes of rapid radiation among unicellular eukaryotes are much less studied than among multicellular organisms. We have investigated a lineage of cold-water microeukaryotes (protists) that appear to have diverged recently. This lineage stands in stark contrast to known examples of phylogenetically closely related protists, in which genetic difference is typically larger than morphological differences. We found that the group not only consists of the marine-brackish dinoflagellate species Scrippsiella hangoei and the freshwater species Peridinium aciculiferum as discovered previously but also of a whole species flock. The additional species include Peridinium euryceps and Peridinium baicalense, which are restricted to a few lakes, in particular to the ancient Lake Baikal, Russia, and freshwater S. hangoei from Lake Baikal. These species are characterized by relatively large conspicuous morphological differences, which have given rise to the different species descriptions. However, our scanning electron microscopic studies indicate that they belong to a single genus according to traditional morphological characterization of dinoflagellates (thecal plate patterns). Moreover, we found that they have identical SSU (small subunit) rDNA fragments and distinct but very small differences in the DNA markers LSU (large subunit) rDNA, ITS2 (internal transcribed spacer 2) and COB (cytochrome b) gene, which are used to delineate dinoflagellates species. As some of the species co-occur, and all four have small but species-specific sequence differences, we suggest that these taxa are not a case of phenotypic plasticity but originated via recent adaptive radiation. We propose that this is the first clear example among free-living microeukaryotes of recent rapid diversification into several species followed by dispersion to environments with different ecological conditions.
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26
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Sun YC, Jarrett CO, Bosio CF, Hinnebusch BJ. Retracing the evolutionary path that led to flea-borne transmission of Yersinia pestis. Cell Host Microbe 2015; 15:578-86. [PMID: 24832452 DOI: 10.1016/j.chom.2014.04.003] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2014] [Revised: 03/07/2014] [Accepted: 03/25/2014] [Indexed: 11/18/2022]
Abstract
Yersinia pestis is an arthropod-borne bacterial pathogen that evolved recently from Yersinia pseudotuberculosis, an enteric pathogen transmitted via the fecal-oral route. This radical ecological transition can be attributed to a few discrete genetic changes from a still-extant recent ancestor, thus providing a tractable case study in pathogen evolution and emergence. Here, we determined the genetic and mechanistic basis of the evolutionary adaptation of Y. pestis to flea-borne transmission. Remarkably, only four minor changes in the bacterial progenitor, representing one gene gain and three gene losses, enabled transmission by flea vectors. All three loss-of-function mutations enhanced cyclic-di-GMP-mediated bacterial biofilm formation in the flea foregut, which greatly increased transmissibility. Our results suggest a step-wise evolutionary model in which Y. pestis emerged as a flea-borne clone, with each genetic change incrementally reinforcing the transmission cycle. The model conforms well to the ecological theory of adaptive radiation.
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Affiliation(s)
- Yi-Cheng Sun
- Laboratory of Zoonotic Pathogens, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 903 South 4(th) Street, Hamilton, MT 59840, USA
| | - Clayton O Jarrett
- Laboratory of Zoonotic Pathogens, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 903 South 4(th) Street, Hamilton, MT 59840, USA
| | - Christopher F Bosio
- Laboratory of Zoonotic Pathogens, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 903 South 4(th) Street, Hamilton, MT 59840, USA
| | - B Joseph Hinnebusch
- Laboratory of Zoonotic Pathogens, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 903 South 4(th) Street, Hamilton, MT 59840, USA.
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28
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Hall AR, Corno G. Tetracycline modifies competitive interactions in experimental microcosms containing bacteria isolated from freshwater. FEMS Microbiol Ecol 2014; 90:168-74. [PMID: 25056916 DOI: 10.1111/1574-6941.12388] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2014] [Revised: 07/03/2014] [Accepted: 07/06/2014] [Indexed: 12/24/2022] Open
Abstract
Interspecific microbial interactions are important for community structure, function and evolution, but it is not fully understood how interactions among bacterial species are influenced by some types of abiotic environmental variation, such as exposure to antibiotics. We tested for the effect of an antibiotic, tetracycline, on interspecific interactions in vitro among four species of aquatic bacteria isolated from European water bodies. Interactions among species in experimental microcosms containing artificial lake water (ALW) supplemented with glucose were largely competitive, as detected by comparing mixed cultures to pure cultures of their constituent species. Sublethal concentrations of tetracycline changed the relative competitive abilities of different species and revealed considerable variation in antibiotic sensitivity, but did not reduce the average strength of competition. Interspecific interactions at a given concentration were largely predictable from growth in pure cultures and indirect interactions with other species. These results suggest that antibiotics such as tetracycline may have important consequences for interactions among bacterial species, but in our experiments this was because species varied in their capacities for growth in the presence of tetracycline, rather than reduced competition at increasing tetracycline concentrations.
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Affiliation(s)
- Alex R Hall
- Institute of Integrative Biology, ETH Zürich, Zürich, Switzerland
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29
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Abstract
The evolutionary success of bacteria depends greatly on their capacity to continually generate phenotypic diversity. Structured environments are particularly favorable for diversification because of attenuated clonal interference, which renders selective sweeps nearly impossible and enhances opportunities for adaptive radiation. We examined at the microscale level the emergence and the spatial and temporal dynamics of phenotypic diversity and their underlying causes in Escherichia coli colonies. An important dynamic heterogeneity in the growth, metabolic activity, morphology, gene expression patterns, stress response induction, and death patterns among cells within colonies was observed. Genetic analysis indicated that the phenotypic variation resulted mostly from mutations and that indole production, oxidative stress, and the RpoS-regulated general stress response played an important role in the generation of diversity. We observed the emergence and persistence of phenotypic variants within single colonies that exhibited variable fitness compared to the parental strain. Some variants showed improved capacity to produce biofilms, whereas others were able to use different nutrients or to tolerate antibiotics or oxidative stress. Taken together, our data show that bacterial colonies provide an ecological opportunity for the generation and maintenance of vast phenotypic diversity, which may increase the probability of population survival in unpredictable environments.
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30
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Soto W, Rivera FM, Nishiguchi MK. Ecological diversification of Vibrio fischeri serially passaged for 500 generations in novel squid host Euprymna tasmanica. MICROBIAL ECOLOGY 2014; 67:700-721. [PMID: 24402368 PMCID: PMC3965629 DOI: 10.1007/s00248-013-0356-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2013] [Accepted: 12/16/2013] [Indexed: 06/03/2023]
Abstract
Vibrio fischeri isolated from Euprymna scolopes (Cephalopoda: Sepiolidae) was used to create 24 lines that were serially passaged through the non-native host Euprymna tasmanica for 500 generations. These derived lines were characterized for biofilm formation, swarming motility, carbon source utilization, and in vitro bioluminescence. Phenotypic assays were compared between "ES" (E. scolopes) and "ET" (E. tasmanica) V. fischeri wild isolates to determine if convergent evolution was apparent between E. tasmanica evolved lines and ET V. fischeri. Ecological diversification was observed in utilization of most carbon sources examined. Convergent evolution was evident in motility, biofilm formation, and select carbon sources displaying hyperpolymorphic usage in V. fischeri. Convergence in bioluminescence (a 2.5-fold increase in brightness) was collectively evident in the derived lines relative to the ancestor. However, dramatic changes in other properties--time points and cell densities of first light emission and maximal light output and emergence of a lag phase in growth curves of derived lines--suggest that increased light intensity per se was not the only important factor. Convergent evolution implies that gnotobiotic squid light organs subject colonizing V. fischeri to similar selection pressures. Adaptation to novel hosts appears to involve flexible microbial metabolism, establishment of biofilm and swarmer V. fischeri ecotypes, and complex changes in bioluminescence. Our data demonstrate that numerous alternate fitness optima or peaks are available to V. fischeri in host adaptive landscapes, where novel host squids serve as habitat islands. Thus, V. fischeri founder flushes occur during the initiation of light organ colonization that ultimately trigger founder effect diversification.
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Affiliation(s)
- William Soto
- University of Minnesota-Twin Cities, Department of Ecology, Evolution, & Behavior, 100 Ecology Building, 1987 Upper Buford Circle, Saint Paul, MN 55108, (612) 626-6200
| | - Ferdinand M. Rivera
- New Mexico State University, Department of Biology, Box 30001, MSC 3AF, Las Cruces, NM 88003, (575) 646-3721 FAX (575) 646-5665
| | - Michele K. Nishiguchi
- New Mexico State University, Department of Biology, Box 30001, MSC 3AF, Las Cruces, NM 88003, (575) 646-3721 FAX (575) 646-5665
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A mechanistic explanation linking adaptive mutation, niche change, and fitness advantage for the wrinkly spreader. INTERNATIONAL JOURNAL OF EVOLUTIONARY BIOLOGY 2014; 2014:675432. [PMID: 24551477 PMCID: PMC3914426 DOI: 10.1155/2014/675432] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/25/2013] [Accepted: 11/08/2013] [Indexed: 11/17/2022]
Abstract
Experimental evolution studies have investigated adaptive radiation in static liquid microcosms using the environmental bacterium Pseudomonas fluorescens SBW25. In evolving populations a novel adaptive mutant known as the Wrinkly Spreader arises within days having significant fitness advantage over the ancestral strain. A molecular investigation of the Wrinkly Spreader has provided a mechanistic explanation linking mutation with fitness improvement through the production of a cellulose-based biofilm at the air-liquid interface. Colonisation of this niche provides greater access to oxygen, allowing faster growth than that possible for non-biofilm-forming competitors located in the lower anoxic region of the microcosm. Cellulose is probably normally used for attachment to plant and soil aggregate surfaces and to provide protection in dehydrating conditions. However, the evolutionary innovation of the Wrinkly Spreader in static microcosms is the use of cellulose as the matrix of a robust biofilm, and is achieved through mutations that deregulate multiple diguanylate cyclases leading to the over-production of cyclic-di-GMP and the stimulation of cellulose expression. The mechanistic explanation of the Wrinkly Spreader success is an exemplar of the modern evolutionary synthesis, linking molecular biology with evolutionary ecology, and provides an insight into the phenomenal ability of bacteria to adapt to novel environments.
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Vos M, Wolf AB, Jennings SJ, Kowalchuk GA. Micro-scale determinants of bacterial diversity in soil. FEMS Microbiol Rev 2013; 37:936-54. [DOI: 10.1111/1574-6976.12023] [Citation(s) in RCA: 338] [Impact Index Per Article: 30.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2012] [Revised: 03/08/2013] [Accepted: 03/15/2013] [Indexed: 11/29/2022] Open
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Pekkonen M, Ketola T, Laakso JT. Resource availability and competition shape the evolution of survival and growth ability in a bacterial community. PLoS One 2013; 8:e76471. [PMID: 24098791 PMCID: PMC3787024 DOI: 10.1371/journal.pone.0076471] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2013] [Accepted: 08/29/2013] [Indexed: 11/19/2022] Open
Abstract
Resource availability is one of the main factors determining the ecological dynamics of populations or species. Fluctuations in resource availability can increase or decrease the intensity of resource competition. Resource availability and competition can also cause evolutionary changes in life-history traits. We studied how community structure and resource fluctuations affect the evolution of fitness related traits using a two-species bacterial model system. Replicated populations of Serratia marcescens (copiotroph) and Novosphingobium capsulatum (oligotroph) were reared alone or together in environments with intergenerational, pulsed resource renewal. The comparison of ancestral and evolved bacterial clones with 1 or 13 weeks history in pulsed resource environment revealed species-specific changes in life-history traits. Co-evolution with S. marcescens caused N. capsulatum clones to grow faster. The evolved S. marcescens clones had higher survival and slower growth rate then their ancestor. The survival increased in all treatments after one week, and thereafter continued to increase only in the S. marcescens monocultures that experienced large resource pulses. Though adaptive radiation is often reported in evolution studies with bacteria, clonal variation increased only in N. capsulatum growth rate. Our results suggest that S. marcescens adapted to the resource renewal cycle whereas N. capsulatum was more affected by the interspecific competition. Our results exemplify species-specific evolutionary response to both competition and environmental variation.
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Affiliation(s)
- Minna Pekkonen
- Integrative Ecology Unit, Centre of Excellence in Biological Interactions, Department of Biosciences, University of Helsinki, Helsinki, Finland
| | - Tarmo Ketola
- Centre of Excellence in Biological Interactions, Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland
| | - Jouni T. Laakso
- Integrative Ecology Unit, Centre of Excellence in Biological Interactions, Department of Biosciences, University of Helsinki, Helsinki, Finland
- Centre of Excellence in Biological Interactions, Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland
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Adaptive divergence in experimental populations of Pseudomonas fluorescens. V. Insight into the niche specialist fuzzy spreader compels revision of the model Pseudomonas radiation. Genetics 2013; 195:1319-35. [PMID: 24077305 DOI: 10.1534/genetics.113.154948] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Pseudomonas fluorescens is a model for the study of adaptive radiation. When propagated in a spatially structured environment, the bacterium rapidly diversifies into a range of niche specialist genotypes. Here we present a genetic dissection and phenotypic characterization of the fuzzy spreader (FS) morphotype-a type that arises repeatedly during the course of the P. fluorescens radiation and appears to colonize the bottom of static broth microcosms. The causal mutation is located within gene fuzY (pflu0478)-the fourth gene of the five-gene fuzVWXYZ operon. fuzY encodes a β-glycosyltransferase that is predicted to modify lipopolysaccharide (LPS) O antigens. The effect of the mutation is to cause cell flocculation. Analysis of 92 independent FS genotypes showed each to have arisen as the result of a loss-of-function mutation in fuzY, although different mutations have subtly different phenotypic and fitness effects. Mutations within fuzY were previously shown to suppress the phenotype of mat-forming wrinkly spreader (WS) types. This prompted a reinvestigation of FS niche preference. Time-lapse photography showed that FS colonizes the meniscus of broth microcosms, forming cellular rafts that, being too flimsy to form a mat, collapse to the vial bottom and then repeatably reform only to collapse. This led to a reassessment of the ecology of the P. fluorescens radiation. Finally, we show that ecological interactions between the three dominant emergent types (smooth, WS, and FS), combined with the interdependence of FS and WS on fuzY, can, at least in part, underpin an evolutionary arms race with bacteriophage SBW25Φ2, to which mutation in fuzY confers resistance.
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Herron MD, Doebeli M. Parallel evolutionary dynamics of adaptive diversification in Escherichia coli. PLoS Biol 2013; 11:e1001490. [PMID: 23431270 PMCID: PMC3576414 DOI: 10.1371/journal.pbio.1001490] [Citation(s) in RCA: 148] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2012] [Accepted: 01/09/2013] [Indexed: 11/19/2022] Open
Abstract
The divergence of Escherichia coli bacteria into metabolically distinct ecotypes has a similar genetic basis and similar evolutionary dynamics across independently evolved populations. The causes and mechanisms of evolutionary diversification are central issues in biology. Geographic isolation is the traditional explanation for diversification, but recent theoretical and empirical studies have shown that frequency-dependent selection can drive diversification without isolation and that adaptive diversification occurring in sympatry may be an important source of biological diversity. However, there are no empirical examples in which sympatric lineage splits have been understood at the genetic level, and it is unknown how predictable this process is—that is, whether similar ecological settings lead to parallel evolutionary dynamics of diversification. We documented the genetic basis and the evolutionary dynamics of adaptive diversification in three replicate evolution experiments, in which competition for two carbon sources caused initially isogenic populations of the bacterium Escherichia coli to diversify into two coexisting ecotypes representing different physiological adaptations in the central carbohydrate metabolism. Whole-genome sequencing of clones of each ecotype from different populations revealed many parallel and some unique genetic changes underlying the derived phenotypes, including changes to the same genes and sometimes to the same nucleotide. Timelines of allele frequencies extracted from the frozen “fossil” record of the three evolving populations suggest parallel evolutionary dynamics driven at least in part by a co-evolutionary process in which mutations causing one type of physiology changed the ecological environment, allowing the invasion of mutations causing an alternate physiology. This process closely corresponds to the evolutionary dynamics seen in mathematical models of adaptive diversification due to frequency-dependent ecological interactions. The parallel genetic changes underlying similar phenotypes in independently evolved lineages provide empirical evidence of adaptive diversification as a predictable evolutionary process. The causes and mechanisms of evolutionary diversification are central issues in biology. There is well-established theory that predicts that adaptive diversification can arise because of ecological interactions between individuals, such as competition or predation, but there are no empirical examples in which this process has been observed at the genetic level. We documented the genetic basis of adaptive diversification resulting from competition for resources in populations of the bacterium Escherichia coli. The populations diversified into two coexisting ecotypes representing different physiological adaptations. We found that similar but independently evolved phenotypes often shared mutations in the same gene and, in four cases, shared identical mutations at the same nucleotide position. Timelines of allele frequencies extracted from the frozen “fossil record” of three evolving populations showed parallel evolutionary dynamics, suggesting that mutations causing one type of physiology changed the ecological environment and allowed invasion of mutations causing an alternate physiology. The results provide empirical evidence of adaptive diversification as a predictable evolutionary process.
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Affiliation(s)
- Matthew D. Herron
- Department of Zoology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Michael Doebeli
- Department of Zoology, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Mathematics, University of British Columbia, Vancouver, British Columbia, Canada
- * E-mail:
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36
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Gray JC, Goddard MR. Gene-flow between niches facilitates local adaptation in sexual populations. Ecol Lett 2012; 15:955-62. [DOI: 10.1111/j.1461-0248.2012.01814.x] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2012] [Revised: 02/28/2012] [Accepted: 05/06/2012] [Indexed: 12/15/2022]
Affiliation(s)
- Jeremy C. Gray
- The School of Biological Sciences; University of Auckland; Private Bag 92019; Auckland; 1142; New Zealand
| | - Matthew R. Goddard
- The School of Biological Sciences; University of Auckland; Private Bag 92019; Auckland; 1142; New Zealand
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Abstract
The current diversity of life on earth is the product of macroevolutionary processes that have shaped the dynamics of diversification. Although the tempo of diversification has been studied extensively in macroorganisms, much less is known about the rates of diversification in the exceedingly diverse and species-rich microbiota. Decreases in diversification rates over time, a signature of explosive radiations, are commonly observed in plant and animal lineages. However, the few existing analyses of microbial lineages suggest that the tempo of diversification in prokaryotes may be fundamentally different. Here, we use multilocus and genomic sequence data to test hypotheses about the rate of diversification in a well-studied pathogenic bacterial lineage, Borrelia burgdorferi sensu lato (sl). Our analyses support the hypothesis that an explosive radiation of lineages occurred near the origin of the clade, followed by a sharp decay in diversification rates. These results suggest that explosive radiations may be a general feature of evolutionary history across the tree of life.
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Affiliation(s)
- Hélène Morlon
- Center for Applied Mathematics, UMR 7641 CNRS, Ecole Polytechnique, 91128 Palaiseau, France.
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38
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Bonsall MB, Wright AE. Altruism and the evolution of resource generalism and specialism. Ecol Evol 2012; 2:515-24. [PMID: 22822431 PMCID: PMC3399141 DOI: 10.1002/ece3.206] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2011] [Accepted: 12/15/2011] [Indexed: 11/10/2022] Open
Abstract
The evolution of resource specialism and generalism has attracted widespread interest. Evolutionary drivers affecting niche differentiation and resource specialization have focused on the role of trade-offs. Here, however, we explore how the role of cooperation, mediated through altruistic behaviors, and classic resource-consumer dynamics can influence the evolution of resource utilization. Using an evolutionary invasion approach, we investigate how critical thresholds in levels of altruism are needed for resource specialization to arise and be maintained. Differences between complementary (essential) and substitutable resources affect the evolution of resource generalists. The strength of resource preferences coupled with the levels of altruism are predicted to influence the evolution of generalism. Coupling appropriate evolutionary game and ecological dynamics lead to novel expectations in the feedbacks between social behaviors and population dynamics for understanding classic ecological problems.
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Affiliation(s)
- Michael B Bonsall
- Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, United Kingdom
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Suntsov VV. Origin of the plague microbe Yersinia pestis: Structure of the process of speciation. BIOL BULL+ 2012. [DOI: 10.1134/s1062359012010104] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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40
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Abstract
The ecological forces shaping adaptive radiations are of great interest to evolutionary ecologists. Here, we experimentally test the hypothesis that the diversification of a lineage should be limited in the presence of competition from another taxon. We do this by studying a model microbial adaptive radiation (the generation of phenotypic diversity in asexual lineages of the bacterium Pseudomonas fluorescens) in the presence or absence of a competitor (Pseudomonas putida). In a spatially heterogeneous environment, the competitor P. putida reduced P. fluorescens population size only slightly and had no effect on diversification. In a spatially homogeneous environment, the competitor reduced P. fuoresecens population size to a much greater extent. Again the final extent of diversification in P. fluorescens was not affected by the competitor, but early diversification was accelerated. In this environment, P. putida suppressed the growth of a common variant of P. fluorescens and directly or indirectly facilitated the growth of a rare morph. Our results suggest that competition experienced by diversifying lineages may have complex effects on adaptive radiations not fully captured by current theory.
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Affiliation(s)
- Quan-Guo Zhang
- NERC Centre for Population Biology, Imperial College London, Silwood Park Campus, Ascot, Berkshire SL5 7PY, United Kingdom.
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41
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Poisot T, Thrall PH, Hochberg ME. Trophic network structure emerges through antagonistic coevolution in temporally varying environments. Proc Biol Sci 2012; 279:299-308. [PMID: 21653583 PMCID: PMC3223677 DOI: 10.1098/rspb.2011.0826] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2011] [Accepted: 05/18/2011] [Indexed: 11/12/2022] Open
Abstract
Understanding the mechanisms underlying ecological specialization is central to our understanding of community ecology and evolution. Although theoretical work has investigated how variable environments may affect specialization in single species, little is known about how such variation impacts bipartite network structure in antagonistically coevolving systems. Here, we develop and analyse a general model of victim-enemy coevolution that explicitly includes resource and population dynamics. We investigate how temporal environmental heterogeneity affects the evolution of specialization and associated community structure. Environmental productivity influences victim investment in resistance, which will shape patterns of specialization through its regulating effect on enemy investment in infectivity. We also investigate the epidemiological consequences of environmental variability and show that enemy population density is maximized for intermediate lengths of productive seasons, which corresponds to situations where enemies can evolve higher infectivity than victims can evolve defence. We discuss our results in the light of empirical studies, and further highlight ways in which our model applies to a range of natural systems.
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Affiliation(s)
- Timothée Poisot
- Institut des Sciences de l'Evolution, UMR 5554, Université Montpellier II, Place Eugène Bataillon, 34095 Montpellier Cedex 05, France.
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42
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De Paepe M, Gaboriau-Routhiau V, Rainteau D, Rakotobe S, Taddei F, Cerf-Bensussan N. Trade-off between bile resistance and nutritional competence drives Escherichia coli diversification in the mouse gut. PLoS Genet 2011; 7:e1002107. [PMID: 21698140 PMCID: PMC3116916 DOI: 10.1371/journal.pgen.1002107] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2011] [Accepted: 04/10/2011] [Indexed: 12/12/2022] Open
Abstract
Bacterial diversification is often observed, but underlying mechanisms are difficult to disentangle and remain generally unknown. Moreover, controlled diversification experiments in ecologically relevant environments are lacking. We studied bacterial diversification in the mammalian gut, one of the most complex bacterial environments, where usually hundreds of species and thousands of bacterial strains stably coexist. Herein we show rapid genetic diversification of an Escherichia coli strain upon colonisation of previously germ-free mice. In addition to the previously described mutations in the EnvZ/OmpR operon, we describe the rapid and systematic selection of mutations in the flagellar flhDC operon and in malT, the transcriptional activator of the maltose regulon. Moreover, within each mouse, the three mutant types coexisted at different levels after one month of colonisation. By combining in vivo studies and determination of the fitness advantages of the selected mutations in controlled in vitro experiments, we provide evidence that the selective forces that drive E. coli diversification in the mouse gut are the presence of bile salts and competition for nutrients. Altogether our results indicate that a trade-off between stress resistance and nutritional competence generates sympatric diversification of the gut microbiota. These results illustrate how experimental evolution in natural environments enables identification of both the selective pressures that organisms face in their natural environment and the diversification mechanisms.
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Weigand MR, Tran VN, Sundin GW. Growth parameter components of adaptive specificity during experimental evolution of the UVR-inducible mutator Pseudomonas cichorii 302959. PLoS One 2011; 6:e15975. [PMID: 21264242 PMCID: PMC3021522 DOI: 10.1371/journal.pone.0015975] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2010] [Accepted: 12/07/2010] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Mutagenic DNA repair (MDR) transiently increases mutation rate through the activation of low-fidelity repair polymerases in response to specific, DNA-damaging environmental stress conditions such as ultraviolet radiation (UVR) exposure. These repair polymerases also confer UVR tolerance, intimately linking mutability and survival in bacteria that colone habitats subject to regular UVR exposure. METHODOLOGY/PRINCIPAL FINDINGS Here, we investigate adaptive specificity in experimental lineages of the highly UVR-mutable epiphytic plant pathogen Pseudomonas cichorii 302959. Relative fitness measurements of isolates and population samples from replicate lineages indicated that adaptive improvements emerged early in all lineages of our evolution experiment and specific increases in relative fitness correlated with distinct improvements in doubling and lag times. Adaptive improvements gained under UVR and non-UVR conditions were acquired preferentially, and differentially contributed to relative fitness under varied growth conditions. CONCLUSIONS These results support our earlier observations that MDR activation may contribute to gains in relative fitness without impeding normal patterns of adaptive specificity in P. cichorii 302959.
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Affiliation(s)
- Michael R. Weigand
- Program in Genetics, Michigan State University, East Lansing, Michigan, United States of America
| | - Vinh N. Tran
- Department of Plant Pathology, Michigan State University, East Lansing, Michigan, United States of America
| | - George W. Sundin
- Program in Genetics, Michigan State University, East Lansing, Michigan, United States of America
- Department of Plant Pathology, Michigan State University, East Lansing, Michigan, United States of America
- Centers for Microbial Ecology and Pathogenesis, Michigan State University, East Lansing, Michigan, United States of America
- * E-mail:
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44
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Gravel D, Bell T, Barbera C, Bouvier T, Pommier T, Venail P, Mouquet N. Experimental niche evolution alters the strength of the diversity–productivity relationship. Nature 2010; 469:89-92. [DOI: 10.1038/nature09592] [Citation(s) in RCA: 155] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2010] [Accepted: 10/20/2010] [Indexed: 11/09/2022]
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45
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Environmental modification and niche construction: developing O2 gradients drive the evolution of the Wrinkly Spreader. ISME JOURNAL 2010; 5:665-73. [PMID: 20962880 DOI: 10.1038/ismej.2010.156] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The evolutionary success of the novel Wrinkly Spreader (WS) genotypes in diversifying Pseudomonas fluorescens SBW25 populations in static liquid microcosms has been attributed to the greater availability of O(2) at the air-liquid (A-L) interface where the WS produces a physically cohesive-class biofilm. However, the importance of O(2) gradients in SBW25 adaptation has never been examined. We have explicitly tested the role of O(2) in evolving populations using microsensor profiling and experiments conducted under high and low O(2) conditions. Initial colonists of static microcosms were found to establish O(2) gradients before significant population growth had occurred, converting a previously homogenous environment into one containing a resource continuum with high and low O(2) regions. These gradients were found to persist for long periods by which time significant numbers of WS had appeared colonising the high O(2) niches. Growth was O(2) limited in static microcosms, but high O(2) conditions like those found near the A-L interface supported greater growth and favoured the emergence of WS-like genotypes. A fitness advantage to biofilm formation was seen under high but not low O(2) conditions, suggesting that the cost of biofilm production could only be offset when O(2) levels above the A-L interface were high. Profiling of mature WS biofilms showed that they also contained high and low O(2) regions. Niches within these may support further diversification and succession of the developing biofilm population. O(2) availability has been found to be a major factor underlying the evolutionary success of the WS genotype in static microcosms and illustrates the importance of this resource continuum in microbial diversification and adaptation.
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Marks ME, Castro-Rojas CM, Teiling C, Du L, Kapatral V, Walunas TL, Crosson S. The genetic basis of laboratory adaptation in Caulobacter crescentus. J Bacteriol 2010; 192:3678-88. [PMID: 20472802 PMCID: PMC2897358 DOI: 10.1128/jb.00255-10] [Citation(s) in RCA: 119] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2010] [Accepted: 05/03/2010] [Indexed: 11/20/2022] Open
Abstract
The dimorphic bacterium Caulobacter crescentus has evolved marked phenotypic changes during its 50-year history of culture in the laboratory environment, providing an excellent system for the study of natural selection and phenotypic microevolution in prokaryotes. Combining whole-genome sequencing with classical molecular genetic tools, we have comprehensively mapped a set of polymorphisms underlying multiple derived phenotypes, several of which arose independently in separate strain lineages. The genetic basis of phenotypic differences in growth rate, mucoidy, adhesion, sedimentation, phage susceptibility, and stationary-phase survival between C. crescentus strain CB15 and its derivative NA1000 is determined by coding, regulatory, and insertion/deletion polymorphisms at five chromosomal loci. This study evidences multiple genetic mechanisms of bacterial evolution as driven by selection for growth and survival in a new selective environment and identifies a common polymorphic locus, zwf, between lab-adapted C. crescentus and clinical isolates of Pseudomonas aeruginosa that have adapted to a human host during chronic infection.
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Affiliation(s)
- Melissa E. Marks
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois, Committee on Microbiology, University of Chicago, Chicago, Illinois, 454 Life Sciences, Branford, Connecticut, Integrated Genomics, Chicago, Illinois
| | - Cyd Marie Castro-Rojas
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois, Committee on Microbiology, University of Chicago, Chicago, Illinois, 454 Life Sciences, Branford, Connecticut, Integrated Genomics, Chicago, Illinois
| | - Clotilde Teiling
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois, Committee on Microbiology, University of Chicago, Chicago, Illinois, 454 Life Sciences, Branford, Connecticut, Integrated Genomics, Chicago, Illinois
| | - Lei Du
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois, Committee on Microbiology, University of Chicago, Chicago, Illinois, 454 Life Sciences, Branford, Connecticut, Integrated Genomics, Chicago, Illinois
| | - Vinayak Kapatral
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois, Committee on Microbiology, University of Chicago, Chicago, Illinois, 454 Life Sciences, Branford, Connecticut, Integrated Genomics, Chicago, Illinois
| | - Theresa L. Walunas
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois, Committee on Microbiology, University of Chicago, Chicago, Illinois, 454 Life Sciences, Branford, Connecticut, Integrated Genomics, Chicago, Illinois
| | - Sean Crosson
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois, Committee on Microbiology, University of Chicago, Chicago, Illinois, 454 Life Sciences, Branford, Connecticut, Integrated Genomics, Chicago, Illinois
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Yoder JB, Clancey E, Des Roches S, Eastman JM, Gentry L, Godsoe W, Hagey TJ, Jochimsen D, Oswald BP, Robertson J, Sarver BAJ, Schenk JJ, Spear SF, Harmon LJ. Ecological opportunity and the origin of adaptive radiations. J Evol Biol 2010; 23:1581-96. [PMID: 20561138 DOI: 10.1111/j.1420-9101.2010.02029.x] [Citation(s) in RCA: 430] [Impact Index Per Article: 30.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Ecological opportunity--through entry into a new environment, the origin of a key innovation or extinction of antagonists--is widely thought to link ecological population dynamics to evolutionary diversification. The population-level processes arising from ecological opportunity are well documented under the concept of ecological release. However, there is little consensus as to how these processes promote phenotypic diversification, rapid speciation and adaptive radiation. We propose that ecological opportunity could promote adaptive radiation by generating specific changes to the selective regimes acting on natural populations, both by relaxing effective stabilizing selection and by creating conditions that ultimately generate diversifying selection. We assess theoretical and empirical evidence for these effects of ecological opportunity and review emerging phylogenetic approaches that attempt to detect the signature of ecological opportunity across geological time. Finally, we evaluate the evidence for the evolutionary effects of ecological opportunity in the diversification of Caribbean Anolis lizards. Some of the processes that could link ecological opportunity to adaptive radiation are well documented, but others remain unsupported. We suggest that more study is required to characterize the form of natural selection acting on natural populations and to better describe the relationship between ecological opportunity and speciation rates.
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Affiliation(s)
- J B Yoder
- Department of Biological Sciences, University of Idaho, Moscow, ID 83844-3051, USA
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Adaptation in a mouse colony monoassociated with Escherichia coli K-12 for more than 1,000 days. Appl Environ Microbiol 2010; 76:4655-63. [PMID: 20472724 DOI: 10.1128/aem.00358-10] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Although mice associated with a single bacterial species have been used to provide a simple model for analysis of host-bacteria relationships, bacteria have been shown to display adaptability when grown in a variety of novel environments. In this study, changes associated with the host-bacterium relationship in mice monoassociated with Escherichia coli K-12 over a period of 1,031 days were evaluated. After 80 days, phenotypic diversification of E. coli was observed, with the colonizing bacteria having a broader distribution of growth rates in the laboratory than the parent E. coli. After 1,031 days, which included three generations of mice and an estimated 20,000 generations of E. coli, the initially homogeneous bacteria colonizing the mice had evolved to have widely different growth rates on agar, a potential decrease in tendency for spontaneous lysis in vivo, and an increased tendency for spontaneous lysis in vitro. Importantly, mice at the end of the experiment were colonized at an average density of bacteria that was more than 3-fold greater than mice colonized on day 80. Evaluation of selected isolates on day 1,031 revealed unique restriction endonuclease patterns and differences between isolates in expression of more than 10% of the proteins identified by two-dimensional electrophoresis, suggesting complex changes underlying the evolution of diversity during the experiment. These results suggest that monoassociated mice might be used as a tool for characterizing niches occupied by the intestinal flora and potentially as a method of targeting the evolution of bacteria for applications in biotechnology.
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49
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GostinÄar C, Grube M, De Hoog S, Zalar P, Gunde-Cimerman N. Extremotolerance in fungi: evolution on the edge. FEMS Microbiol Ecol 2010; 71:2-11. [DOI: 10.1111/j.1574-6941.2009.00794.x] [Citation(s) in RCA: 169] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
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50
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Zhang QG, Buckling A, Ellis RJ, Godfray HCJ. COEVOLUTION BETWEEN COOPERATORS AND CHEATS IN A MICROBIAL SYSTEM. Evolution 2009; 63:2248-56. [DOI: 10.1111/j.1558-5646.2009.00708.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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