51
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McNally L, Brown SP. Visualizing evolution as it happens. Science 2016; 353:1096-7. [DOI: 10.1126/science.aah5641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
A meter-scale growth plate allows the evolution of antibiotic resistance to be tracked
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Affiliation(s)
- Luke McNally
- Centre for Immunity, Infection and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, UK
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Sam P. Brown
- School of Biology, Georgia Institute of Technology, Atlanta, GA 30332, USA
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52
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Abstract
Rising atmospheric CO2 concentrations are likely to affect many ecosystems worldwide. However, to what extent elevated CO2 will induce evolutionary changes in photosynthetic organisms is still a major open question. Here, we show rapid microevolutionary adaptation of a harmful cyanobacterium to changes in inorganic carbon (Ci) availability. We studied the cyanobacterium Microcystis, a notorious genus that can develop toxic cyanobacterial blooms in many eutrophic lakes and reservoirs worldwide. Microcystis displays genetic variation in the Ci uptake systems BicA and SbtA, where BicA has a low affinity for bicarbonate but high flux rate, and SbtA has a high affinity but low flux rate. Our laboratory competition experiments show that bicA + sbtA genotypes were favored by natural selection at low CO2 levels, but were partially replaced by the bicA genotype at elevated CO2 Similarly, in a eutrophic lake, bicA + sbtA strains were dominant when Ci concentrations were depleted during a dense cyanobacterial bloom, but were replaced by strains with only the high-flux bicA gene when Ci concentrations increased later in the season. Hence, our results provide both laboratory and field evidence that increasing carbon concentrations induce rapid adaptive changes in the genotype composition of harmful cyanobacterial blooms.
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53
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Abstract
There are not only many links between microbiological and philosophical topics, but good educational reasons for microbiologists to explore the philosophical issues in their fields. I examine three broad issues of classification, causality and model systems, showing how these philosophical dimensions have practical implications. I conclude with a discussion of the educational benefits for recognising the philosophy in microbiology.
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Affiliation(s)
- Maureen A O'Malley
- UMR5164, University of Bordeaux, 146 Rue Leo Saignat, Bordeaux 33076, France
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54
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Ketola T, Mikonranta L, Mappes J. Evolution of bacterial life-history traits is sensitive to community structure. Evolution 2016; 70:1334-41. [DOI: 10.1111/evo.12947] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Revised: 04/20/2016] [Accepted: 04/30/2016] [Indexed: 11/30/2022]
Affiliation(s)
- Tarmo Ketola
- Department of Biological and Environmental Science, Centre of Excellence in Biological Interactions; University of Jyvaskyla; P. O. Box 35 Jyväskylä 40014 Finland
| | - Lauri Mikonranta
- Department of Biological and Environmental Science, Centre of Excellence in Biological Interactions; University of Jyvaskyla; P. O. Box 35 Jyväskylä 40014 Finland
| | - Johanna Mappes
- Department of Biological and Environmental Science, Centre of Excellence in Biological Interactions; University of Jyvaskyla; P. O. Box 35 Jyväskylä 40014 Finland
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55
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Pieczynska MD, Wloch-Salamon D, Korona R, de Visser JAGM. Rapid multiple-level coevolution in experimental populations of yeast killer and nonkiller strains. Evolution 2016; 70:1342-53. [PMID: 27168531 DOI: 10.1111/evo.12945] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2015] [Revised: 04/26/2016] [Accepted: 04/28/2016] [Indexed: 01/09/2023]
Abstract
Coevolution between different biological entities is considered an important evolutionary mechanism at all levels of biological organization. Here, we provide evidence for coevolution of a yeast killer strain (K) carrying cytoplasmic dsRNA viruses coding for anti-competitor toxins and an isogenic toxin-sensitive strain (S) during 500 generations of laboratory propagation. Signatures of coevolution developed at two levels. One of them was coadaptation of K and S. Killing ability of K first increased quickly and was followed by the rapid invasion of toxin-resistant mutants derived from S, after which killing ability declined. High killing ability was shown to be advantageous when sensitive cells were present but costly when they were absent. Toxin resistance evolved via a two-step process, presumably involving the fitness-enhancing loss of one chromosome followed by selection of a recessive resistant mutation on the haploid chromosome. The other level of coevolution occurred between cell and killer virus. By swapping the killer viruses between ancestral and evolved strains, we could demonstrate that changes observed in both host and virus were beneficial only when combined, suggesting that they involved reciprocal changes. Together, our results show that the yeast killer system shows a remarkable potential for rapid multiple-level coevolution.
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Affiliation(s)
- Magdalena D Pieczynska
- Laboratory of Genetics, Wageningen University, 6708 PB Wageningen, The Netherlands.,Institute of Environmental Sciences, Jagiellonian University, Gronostajowa 7, Krakow, Poland.,Current address: Kavli Institute of NanoScience, Delft University of Technology, 2600 GD Delft, The Netherlands
| | - Dominika Wloch-Salamon
- Institute of Environmental Sciences, Jagiellonian University, Gronostajowa 7, Krakow, Poland
| | - Ryszard Korona
- Institute of Environmental Sciences, Jagiellonian University, Gronostajowa 7, Krakow, Poland
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56
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Abstract
Plasmids play a key role in bacterial evolution by providing bacteria with new and important functions, such as antibiotic resistance. New research shows how bacterial regulatory evolution can stabilize bacteria-plasmid associations and catalyze evolutionary innovation.
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Affiliation(s)
- R Craig MacLean
- Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK.
| | - Alvaro San Millan
- Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK
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57
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Churton NWV, Misra RV, Howlin RP, Allan RN, Jefferies J, Faust SN, Gharbia SE, Edwards RJ, Clarke SC, Webb JS. Parallel Evolution in Streptococcus pneumoniae Biofilms. Genome Biol Evol 2016; 8:1316-26. [PMID: 27190203 PMCID: PMC4898793 DOI: 10.1093/gbe/evw072] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Streptococcus pneumoniae is a commensal human pathogen and the causative agent of various invasive and noninvasive diseases. Carriage of the pneumococcus in the nasopharynx is thought to be mediated by biofilm formation, an environment where isogenic populations frequently give rise to morphological colony variants, including small colony variant (SCV) phenotypes. We employed metabolic characterization and whole-genome sequencing of biofilm-derived S. pneumoniae serotype 22F pneumococcal SCVs to investigate diversification during biofilm formation. Phenotypic profiling revealed that SCVs exhibit reduced growth rates, reduced capsule expression, altered metabolic profiles, and increased biofilm formation compared to the ancestral strain. Whole-genome sequencing of 12 SCVs from independent biofilm experiments revealed that all SCVs studied had mutations within the DNA-directed RNA polymerase delta subunit (RpoE). Mutations included four large-scale deletions ranging from 51 to 264 bp, one insertion resulting in a coding frameshift, and seven nonsense single-nucleotide substitutions that result in a truncated gene product. This work links mutations in the rpoE gene to SCV formation and enhanced biofilm development in S. pneumoniae and therefore may have important implications for colonization, carriage, and persistence of the organism. Furthermore, recurrent mutation of the pneumococcal rpoE gene presents an unprecedented level of parallel evolution in pneumococcal biofilm development.
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Affiliation(s)
- Nicholas W V Churton
- Centre for Biological Sciences, Faculty of Natural and Environmental Sciences, University of Southampton, United Kingdom Academic Unit of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, United Kingdom Institute for Life Sciences, Faculty of Natural and Environmental Sciences, University of Southampton, United Kingdom
| | - Raju V Misra
- Genomics Research Unit, Microbiology Services, Public Health England, Colindale, United Kingdom
| | - Robert P Howlin
- Centre for Biological Sciences, Faculty of Natural and Environmental Sciences, University of Southampton, United Kingdom Institute for Life Sciences, Faculty of Natural and Environmental Sciences, University of Southampton, United Kingdom NIHR Southampton Respiratory Biomedical Research Unit, Southampton, United Kingdom
| | - Raymond N Allan
- Academic Unit of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, United Kingdom Institute for Life Sciences, Faculty of Natural and Environmental Sciences, University of Southampton, United Kingdom NIHR Southampton Respiratory Biomedical Research Unit, Southampton, United Kingdom Southampton NIHR Wellcome Trust Clinical Research Facility, University Hospital Southampton NHS Foundation Trust, United Kingdom
| | - Johanna Jefferies
- Academic Unit of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, United Kingdom Institute for Life Sciences, Faculty of Natural and Environmental Sciences, University of Southampton, United Kingdom NIHR Southampton Respiratory Biomedical Research Unit, Southampton, United Kingdom
| | - Saul N Faust
- Academic Unit of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, United Kingdom NIHR Southampton Respiratory Biomedical Research Unit, Southampton, United Kingdom Southampton NIHR Wellcome Trust Clinical Research Facility, University Hospital Southampton NHS Foundation Trust, United Kingdom
| | - Saheer E Gharbia
- Genomics Research Unit, Microbiology Services, Public Health England, Colindale, United Kingdom
| | - Richard J Edwards
- Centre for Biological Sciences, Faculty of Natural and Environmental Sciences, University of Southampton, United Kingdom Institute for Life Sciences, Faculty of Natural and Environmental Sciences, University of Southampton, United Kingdom School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia
| | - Stuart C Clarke
- Academic Unit of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, United Kingdom Institute for Life Sciences, Faculty of Natural and Environmental Sciences, University of Southampton, United Kingdom NIHR Southampton Respiratory Biomedical Research Unit, Southampton, United Kingdom Public Health England, Southampton, United Kingdom
| | - Jeremy S Webb
- Centre for Biological Sciences, Faculty of Natural and Environmental Sciences, University of Southampton, United Kingdom Institute for Life Sciences, Faculty of Natural and Environmental Sciences, University of Southampton, United Kingdom NIHR Southampton Respiratory Biomedical Research Unit, Southampton, United Kingdom
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58
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Toll-Riera M, San Millan A, Wagner A, MacLean RC. The Genomic Basis of Evolutionary Innovation in Pseudomonas aeruginosa. PLoS Genet 2016; 12:e1006005. [PMID: 27149698 PMCID: PMC4858143 DOI: 10.1371/journal.pgen.1006005] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Accepted: 04/04/2016] [Indexed: 11/29/2022] Open
Abstract
Novel traits play a key role in evolution, but their origins remain poorly understood. Here we address this problem by using experimental evolution to study bacterial innovation in real time. We allowed 380 populations of Pseudomonas aeruginosa to adapt to 95 different carbon sources that challenged bacteria with either evolving novel metabolic traits or optimizing existing traits. Whole genome sequencing of more than 80 clones revealed profound differences in the genetic basis of innovation and optimization. Innovation was associated with the rapid acquisition of mutations in genes involved in transcription and metabolism. Mutations in pre-existing duplicate genes in the P. aeruginosa genome were common during innovation, but not optimization. These duplicate genes may have been acquired by P. aeruginosa due to either spontaneous gene amplification or horizontal gene transfer. High throughput phenotype assays revealed that novelty was associated with increased pleiotropic costs that are likely to constrain innovation. However, mutations in duplicate genes with close homologs in the P. aeruginosa genome were associated with low pleiotropic costs compared to mutations in duplicate genes with distant homologs in the P. aeruginosa genome, suggesting that functional redundancy between duplicates facilitates innovation by buffering pleiotropic costs.
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Affiliation(s)
- Macarena Toll-Riera
- Department of Zoology, University of Oxford, Oxford, United Kingdom
- Institute of Evolutionary Biology and Environmental Studies, University of Zurich, Zürich, Switzerland
- The Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | | | - Andreas Wagner
- Institute of Evolutionary Biology and Environmental Studies, University of Zurich, Zürich, Switzerland
- The Swiss Institute of Bioinformatics, Lausanne, Switzerland
- The Santa Fe Institute, Santa Fe, New Mexico, United States of America
| | - R. Craig MacLean
- Department of Zoology, University of Oxford, Oxford, United Kingdom
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59
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Betts A, Gifford DR, MacLean RC, King KC. Parasite diversity drives rapid host dynamics and evolution of resistance in a bacteria-phage system. Evolution 2016; 70:969-78. [PMID: 27005577 PMCID: PMC4982092 DOI: 10.1111/evo.12909] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Revised: 03/02/2016] [Accepted: 03/11/2016] [Indexed: 12/01/2022]
Abstract
Host–parasite evolutionary interactions are typically considered in a pairwise species framework. However, natural infections frequently involve multiple parasites. Altering parasite diversity alters ecological and evolutionary dynamics as parasites compete and hosts resist multiple infection. We investigated the effects of parasite diversity on host–parasite population dynamics and evolution using the pathogen Pseudomonas aeruginosa and five lytic bacteriophage parasites. To manipulate parasite diversity, bacterial populations were exposed for 24 hours to either phage monocultures or diverse communities containing up to five phages. Phage communities suppressed host populations more rapidly but also showed reduced phage density, likely due to interphage competition. The evolution of resistance allowed rapid bacterial recovery that was greater in magnitude with increases in phage diversity. We observed no difference in the extent of resistance with increased parasite diversity, but there was a profound impact on the specificity of resistance; specialized resistance evolved to monocultures through mutations in a diverse set of genes. In summary, we demonstrate that parasite diversity has rapid effects on host–parasite population dynamics and evolution by selecting for different resistance mutations and affecting the magnitude of bacterial suppression and recovery. Finally, we discuss the implications of phage diversity for their use as biological control agents.
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Affiliation(s)
- Alex Betts
- Department of Zoology, University of Oxford, Oxford, OX1 3PS, United Kingdom.
| | - Danna R Gifford
- Department of Zoology, University of Oxford, Oxford, OX1 3PS, United Kingdom
| | - R Craig MacLean
- Department of Zoology, University of Oxford, Oxford, OX1 3PS, United Kingdom
| | - Kayla C King
- Department of Zoology, University of Oxford, Oxford, OX1 3PS, United Kingdom
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60
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Padfield D, Yvon-Durocher G, Buckling A, Jennings S, Yvon-Durocher G. Rapid evolution of metabolic traits explains thermal adaptation in phytoplankton. Ecol Lett 2016; 19:133-142. [PMID: 26610058 PMCID: PMC4991271 DOI: 10.1111/ele.12545] [Citation(s) in RCA: 158] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Revised: 10/06/2015] [Accepted: 10/19/2015] [Indexed: 11/28/2022]
Abstract
Understanding the mechanisms that determine how phytoplankton adapt to warming will substantially improve the realism of models describing ecological and biogeochemical effects of climate change. Here, we quantify the evolution of elevated thermal tolerance in the phytoplankton, Chlorella vulgaris. Initially, population growth was limited at higher temperatures because respiration was more sensitive to temperature than photosynthesis meaning less carbon was available for growth. Tolerance to high temperature evolved after ≈ 100 generations via greater down-regulation of respiration relative to photosynthesis. By down-regulating respiration, phytoplankton overcame the metabolic constraint imposed by the greater temperature sensitivity of respiration and more efficiently allocated fixed carbon to growth. Rapid evolution of carbon-use efficiency provides a potentially general mechanism for thermal adaptation in phytoplankton and implies that evolutionary responses in phytoplankton will modify biogeochemical cycles and hence food web structure and function under warming. Models of climate futures that ignore adaptation would usefully be revisited.
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Affiliation(s)
- Daniel Padfield
- Environment and Sustainability Institute, University of Exeter, Penryn, Cornwall, TR10 9FE, UK
| | - Genevieve Yvon-Durocher
- School of Biological and Chemical Sciences, Queen Mary University of London, London, E1 4NS, UK
| | - Angus Buckling
- Environment and Sustainability Institute, University of Exeter, Penryn, Cornwall, TR10 9FE, UK
| | - Simon Jennings
- Centre for Environment, Fisheries and Aquaculture Science, Lowestoft, NR33 0HT, UK
- School of Environmental Sciences, University of East Anglia, Norwich, NR4 7TJ, UK
| | - Gabriel Yvon-Durocher
- Environment and Sustainability Institute, University of Exeter, Penryn, Cornwall, TR10 9FE, UK
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61
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Bromham L. Testing hypotheses in macroevolution. STUDIES IN HISTORY AND PHILOSOPHY OF SCIENCE 2016; 55:47-59. [PMID: 26774069 DOI: 10.1016/j.shpsa.2015.08.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Revised: 07/02/2015] [Accepted: 08/17/2015] [Indexed: 06/05/2023]
Abstract
Experimental manipulation of microevolution (changes in frequency of heritable traits in populations) has shed much light on evolutionary processes. But many evolutionary processes occur on scales that are not amenable to experimental manipulation. Indeed, one of the reasons that macroevolution (changes in biodiversity over time, space and lineages) has sometimes been a controversial topic is that processes underlying the generation of biological diversity generally operate at scales that are not open to direct observation or manipulation. Macroevolutionary hypotheses can be tested by using them to generate predictions then asking whether observations from the biological world match those predictions. Each study that identifies significant correlations between evolutionary events, processes or outcomes can generate new predictions that can be further tested with different datasets, allowing a cumulative process that may narrow down on plausible explanations, or lead to rejection of other explanations as inconsistent or unsupported. A similar approach can be taken even for unique events, for example by comparing patterns in different regions, lineages, or time periods. I will illustrate the promise and pitfalls of these approaches using a range of examples, and discuss the problems of inferring causality from significant evolutionary associations.
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Affiliation(s)
- Lindell Bromham
- Centre for Macroevolution and Macroecology, Research School of Biology, Australian National University, Canberra, ACT 0200, Australia.
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62
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Bailey SF, Bataillon T. Can the experimental evolution programme help us elucidate the genetic basis of adaptation in nature? Mol Ecol 2016; 25:203-18. [PMID: 26346808 PMCID: PMC5019151 DOI: 10.1111/mec.13378] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2015] [Revised: 08/26/2015] [Accepted: 09/04/2015] [Indexed: 02/04/2023]
Abstract
There have been a variety of approaches taken to try to characterize and identify the genetic basis of adaptation in nature, spanning theoretical models, experimental evolution studies and direct tests of natural populations. Theoretical models can provide formalized and detailed hypotheses regarding evolutionary processes and patterns, from which experimental evolution studies can then provide important proofs of concepts and characterize what is biologically reasonable. Genetic and genomic data from natural populations then allow for the identification of the particular factors that have and continue to play an important role in shaping adaptive evolution in the natural world. Further to this, experimental evolution studies allow for tests of theories that may be difficult or impossible to test in natural populations for logistical and methodological reasons and can even generate new insights, suggesting further refinement of existing theories. However, as experimental evolution studies often take place in a very particular set of controlled conditions--that is simple environments, a small range of usually asexual species, relatively short timescales--the question remains as to how applicable these experimental results are to natural populations. In this review, we discuss important insights coming from experimental evolution, focusing on four key topics tied to the evolutionary genetics of adaptation, and within those topics, we discuss the extent to which the experimental work compliments and informs natural population studies. We finish by making suggestions for future work in particular a need for natural population genomic time series data, as well as the necessity for studies that combine both experimental evolution and natural population approaches.
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Affiliation(s)
- Susan F. Bailey
- Bioinformatics Research CentreAarhus UniversityC.F. Møllers Allé 8DK‐8000Aarhus CDenmark
| | - Thomas Bataillon
- Bioinformatics Research CentreAarhus UniversityC.F. Møllers Allé 8DK‐8000Aarhus CDenmark
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63
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Koskella B, Vos M. Adaptation in Natural Microbial Populations. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2015. [DOI: 10.1146/annurev-ecolsys-112414-054458] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Britt Koskella
- Department of Integrative Biology, University of California, Berkeley, California 94720;
- Department of Biosciences, University of Exeter, Penryn Campus, Cornwall TR10 9FE, United Kingdom
| | - Michiel Vos
- European Centre for Environment and Human Health, University of Exeter Medical School, Penryn Campus, Cornwall TR10 9FE, United Kingdom;
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64
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Knight SJ, Goddard MR. Sporulation in soil as an overwinter survival strategy in Saccharomyces cerevisiae. FEMS Yeast Res 2015; 16:fov102. [PMID: 26568201 PMCID: PMC5815064 DOI: 10.1093/femsyr/fov102] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/09/2015] [Indexed: 01/12/2023] Open
Abstract
Due to its commercial value and status as a research model there is an extensive body of knowledge concerning Saccharomyces cerevisiae's cell biology and genetics. Investigations into S. cerevisiae's ecology are comparatively lacking, and are mostly focused on the behaviour of this species in high sugar, fruit-based environments; however, fruit is ephemeral, and presumably, S. cerevisiae has evolved a strategy to survive when this niche is not available. Among other places, S. cerevisiae has been isolated from soil which, in contrast to fruit, is a permanent habitat. We hypothesize that S. cerevisiae employs a life history strategy targeted at self-preservation rather than growth outside of the fruit niche, and resides in forest niches, such as soil, in a dormant and resistant sporulated state, returning to fruit via vectors such as insects. One crucial aspect of this hypothesis is that S. cerevisiae must be able to sporulate in the ‘forest’ environment. Here, we provide the first evidence for a natural environment (soil) where S. cerevisiae sporulates. While there are further aspects of this hypothesis that require experimental verification, this is the first step towards an inclusive understanding of the more cryptic aspects of S. cerevisiae's ecology. The ability of Saccharomyces cerevisiae to sporulate in soil supports a ‘fruit forest-reservoir’ life-cycle.
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Affiliation(s)
- Sarah J Knight
- School of Biological Sciences, The University of Auckland, Auckland 1142, New Zealand;
| | - Matthew R Goddard
- School of Biological Sciences, The University of Auckland, Auckland 1142, New Zealand; School of Life Sciences, University of Lincoln, Lincoln, LN6 7DL, UK
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65
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Abstract
Viruses that infect bacteria (bacteriophages; also known as phages) were discovered 100 years ago. Since then, phage research has transformed fundamental and translational biosciences. For example, phages were crucial in establishing the central dogma of molecular biology - information is sequentially passed from DNA to RNA to proteins - and they have been shown to have major roles in ecosystems, and help drive bacterial evolution and virulence. Furthermore, phage research has provided many techniques and reagents that underpin modern biology - from sequencing and genome engineering to the recent discovery and exploitation of CRISPR-Cas phage resistance systems. In this Timeline, we discuss a century of phage research and its impact on basic and applied biology.
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66
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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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67
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Single gene locus changes perturb complex microbial communities as much as apex predator loss. Nat Commun 2015; 6:8235. [PMID: 26354365 PMCID: PMC4579780 DOI: 10.1038/ncomms9235] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2014] [Accepted: 07/30/2015] [Indexed: 02/08/2023] Open
Abstract
Many bacterial species are highly social, adaptively shaping their local environment through the production of secreted molecules. This can, in turn, alter interaction strengths among species and modify community composition. However, the relative importance of such behaviours in determining the structure of complex communities is unknown. Here we show that single-locus changes affecting biofilm formation phenotypes in Bacillus subtilis modify community structure to the same extent as loss of an apex predator and even to a greater extent than loss of B. subtilis itself. These results, from experimentally manipulated multitrophic microcosm assemblages, demonstrate that bacterial social traits are key modulators of the structure of their communities. Moreover, they show that intraspecific genetic variability can be as important as strong trophic interactions in determining community dynamics. Microevolution may therefore be as important as species extinctions in shaping the response of microbial communities to environmental change. Some species of social bacteria can chemically modify their nutrient environments, which may influence community interactions. Here, McClean et al. show that changes at a single gene locus in a biofilm-forming bacteria can perturb community structure to the same extent as the loss of an apex predator.
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68
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Hernández-Alonso P, Garijo R, Cuevas JM, Sanjuán R. Experimental evolution of an RNA virus in cells with innate immunity defects. Virus Evol 2015; 1:vev008. [PMID: 27774280 PMCID: PMC5014476 DOI: 10.1093/ve/vev008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Experimental evolution studies have shown that RNA viruses respond rapidly to directional selection and thus can adapt efficiently to changes in host cell tropism, antiviral drugs, or other imposed selective pressures. However, the evolution of RNA viruses under relaxed selection has been less extensively explored. Here, we evolved vesicular stomatitis virus in mouse embryonic fibroblasts knocked-out for PKR, a protein with a central role in antiviral innate immunity. Vesicular stomatitis virus adapted to PKR-negative mouse embryonic fibroblasts in a gene-specific manner, since the evolved viruses exhibited little or no fitness improvement in PKR-positive cells. Full-length sequencing revealed the presence of multiple parallel nucleotide substitutions arising in independent evolution lines. However, site-directed mutagenesis showed that the effects of these substitutions were not PKR dependent. In contrast, we found evidence for sign epistasis, such that a given substitution which was positively selected was strongly deleterious when tested as a single mutation. Our results suggest that virus evolution in cells with specific innate immunity defects may drive viral specialization. However, this process is not deterministic at the molecular level, probably because the fixation of mutations which are tolerated under a relaxed selection regime is governed mainly by random genetic drift.
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Affiliation(s)
- Pablo Hernández-Alonso
- Instituto Cavanilles de Biodiversidad y Biología Evolutiva and Departament de Genètica, Universitat de València, Paterna 46980, Spain
| | - Raquel Garijo
- Instituto Cavanilles de Biodiversidad y Biología Evolutiva and Departament de Genètica, Universitat de València, Paterna 46980, Spain
| | - José M Cuevas
- Instituto Cavanilles de Biodiversidad y Biología Evolutiva and Departament de Genètica, Universitat de València, Paterna 46980, Spain
| | - Rafael Sanjuán
- Instituto Cavanilles de Biodiversidad y Biología Evolutiva and Departament de Genètica, Universitat de València, Paterna 46980, Spain
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69
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Acevedo-Rocha CG, Schulze-Makuch D. How Many Biochemistries Are Available To Build a Cell? Chembiochem 2015; 16:2137-9. [DOI: 10.1002/cbic.201500379] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Indexed: 11/12/2022]
Affiliation(s)
- Carlos G. Acevedo-Rocha
- Max-Planck-Institut für Terrestrische Mikrobiologie; Small Prokaryotic RNA Biology Group; Karl-von-Frisch-Strasse 10 35043 Marburg Germany
- Landes-Offensive zur Entwicklung Wissenschafltich-Ökonomischer Exzellenz (LOEWE); Zentrum für Synthetische Mikrobiologie (SYNMIKRO); Philipps-Universität Marburg; Hans-Meerwein-Strasse 6 35042 Marburg Germany
| | - Dirk Schulze-Makuch
- School of the Environment; Washington State University; Webster Hall 1148 Pullman WA 99163 USA
- Beyond Center; Arizona State University; P. O. Box 871504 Tempe AZ 85827 USA
- Center for Astronomy and Astrophysics; Technical University Berlin; Hardenbergstrasse 36 10623 Berlin Germany
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70
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O'Malley MA, Travisano M, Velicer GJ, Bolker JA. How Do Microbial Populations and Communities Function as Model Systems? QUARTERLY REVIEW OF BIOLOGY 2015; 90:269-93. [DOI: 10.1086/682588] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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71
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Voordeckers K, Verstrepen KJ. Experimental evolution of the model eukaryote Saccharomyces cerevisiae yields insight into the molecular mechanisms underlying adaptation. Curr Opin Microbiol 2015. [PMID: 26202939 DOI: 10.1016/j.mib.2015.06.018] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Understanding how changes in DNA drive the emergence of new phenotypes and fuel evolution remains a major challenge. One major hurdle is the lack of a fossil record of DNA that allows linking mutations to phenotypic changes. However, the emergence of high-throughput sequencing technologies now allows sequencing genomes of natural and experimentally evolved microbial populations to study how mutations arise and spread through a population, how new phenotypes arise and how this ultimately leads to adaptation. Here, we highlight key studies that have increased our mechanistic understanding of evolution. We specifically focus on the model eukaryote Saccharomyces cerevisiae because its relatively short replication time, much-studied biology and available molecular toolbox have made it a prime model for molecular evolution studies.
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Affiliation(s)
- Karin Voordeckers
- CMPG Laboratory for Genetics and Genomics, KU Leuven, Gaston Geenslaan 1, B-3001 Leuven, Belgium; VIB Laboratory for Systems Biology, Gaston Geenslaan 1, B-3001 Leuven, Belgium
| | - Kevin J Verstrepen
- CMPG Laboratory for Genetics and Genomics, KU Leuven, Gaston Geenslaan 1, B-3001 Leuven, Belgium; VIB Laboratory for Systems Biology, Gaston Geenslaan 1, B-3001 Leuven, Belgium.
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72
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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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73
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Brockhurst MA. Experimental evolution can unravel the complex causes of natural selection in clinical infections. MICROBIOLOGY-SGM 2015; 161:1175-9. [PMID: 25957311 DOI: 10.1099/mic.0.000107] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
It is increasingly clear that rapid evolutionary dynamics are an important process in microbial ecology. Experimental evolution, wherein microbial evolution is observed in real-time, has revealed many instances of appreciable evolutionary change occurring on very short timescales of a few days or weeks in response to a variety of biotic and abiotic selection pressures. From clinical infections, including the chronic bacterial lung infections associated with cystic fibrosis that form a focus of my research, there is now abundant evidence suggesting that rapid evolution by infecting microbes contributes to host adaptation, treatment failure and worsening patient prognosis. However, disentangling the drivers of natural selection in complex infection environments is extremely challenging and limits our understanding of the selective pressures acting upon microbes in infections. Controlled evolution experiments can make a vital contribution to this by determining the causal links between predicted drivers of natural selection and the evolutionary responses of microbes. Integration of experimental evolution into studies of clinical infections is a key next step towards a better understanding of the causes and consequences of rapid microbial evolution in infections, and discovering how these evolutionary processes might be influenced to improve patient health.A video of this Prize Lecture, presented at the Society for General Microbiology Annual Conference 2015, can be viewed via this link: Michael A. Brockhurst https://www.youtube.com/watch?v=N1bodVSl27E.
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74
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Morange M. Synthetic Biology: A Bridge Between Functional and Evolutionary Biology. ACTA ACUST UNITED AC 2015. [DOI: 10.1162/biot_a_00003] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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75
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Couce A, Tenaillon OA. The rule of declining adaptability in microbial evolution experiments. Front Genet 2015; 6:99. [PMID: 25815007 PMCID: PMC4356158 DOI: 10.3389/fgene.2015.00099] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Accepted: 02/24/2015] [Indexed: 11/25/2022] Open
Abstract
One of the most recurrent observations after two decades of microbial evolution experiments regards the dynamics of fitness change. In a given environment, low-fitness genotypes are recurrently observed to adapt faster than their more fit counterparts. Since adaptation is the main macroscopic outcome of Darwinian evolution, studying its patterns of change could potentially provide insight into key issues of evolutionary theory, from fixation dynamics to the genetic architecture of organisms. Here, we re-analyze several published datasets from experimental evolution with microbes and show that, despite large differences in the origin of the data, a pattern of inverse dependence of adaptability with fitness clearly emerges. In quantitative terms, it is remarkable to observe little if any degree of idiosyncrasy across systems as diverse as virus, bacteria and yeast. The universality of this phenomenon suggests that its emergence might be understood from general principles, giving rise to the exciting prospect that evolution might be statistically predictable at the macroscopic level. We discuss these possibilities in the light of the various theories of adaptation that have been proposed and delineate future directions of research.
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76
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Getting Wrinkly Spreaders to demonstrate evolution in schools. Trends Microbiol 2015; 22:301-3. [PMID: 24881493 DOI: 10.1016/j.tim.2014.03.007] [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: 02/24/2014] [Revised: 03/10/2014] [Accepted: 03/19/2014] [Indexed: 11/22/2022]
Abstract
Understanding evolution is crucial to modern biology, but most teachers would assume that practical demonstrations of evolution in school laboratories are unfeasible. However, perhaps they have not heard of 'evolution in a test tube' and how Wrinkly Spreaders can form the basis for both practical demonstrations of bacterial evolution and further work.
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77
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Soto W, Nishiguchi MK. Microbial experimental evolution as a novel research approach in the Vibrionaceae and squid-Vibrio symbiosis. Front Microbiol 2014; 5:593. [PMID: 25538686 PMCID: PMC4260504 DOI: 10.3389/fmicb.2014.00593] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2014] [Accepted: 10/20/2014] [Indexed: 12/21/2022] Open
Abstract
The Vibrionaceae are a genetically and metabolically diverse family living in aquatic habitats with a great propensity toward developing interactions with eukaryotic microbial and multicellular hosts (as either commensals, pathogens, and mutualists). The Vibrionaceae frequently possess a life history cycle where bacteria are attached to a host in one phase and then another where they are free from their host as either part of the bacterioplankton or adhered to solid substrates such as marine sediment, riverbeds, lakebeds, or floating particulate debris. These two stages in their life history exert quite distinct and separate selection pressures. When bound to solid substrates or to host cells, the Vibrionaceae can also exist as complex biofilms. The association between bioluminescent Vibrio spp. and sepiolid squids (Cephalopoda: Sepiolidae) is an experimentally tractable model to study bacteria and animal host interactions, since the symbionts and squid hosts can be maintained in the laboratory independently of one another. The bacteria can be grown in pure culture and the squid hosts raised gnotobiotically with sterile light organs. The partnership between free-living Vibrio symbionts and axenic squid hatchlings emerging from eggs must be renewed every generation of the cephalopod host. Thus, symbiotic bacteria and animal host can each be studied alone and together in union. Despite virtues provided by the Vibrionaceae and sepiolid squid-Vibrio symbiosis, these assets to evolutionary biology have yet to be fully utilized for microbial experimental evolution. Experimental evolution studies already completed are reviewed, along with exploratory topics for future study.
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Affiliation(s)
- William Soto
- BEACON Center for the Study of Evolution in Action, Michigan State UniversityEast Lansing, MI, USA
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78
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Abstract
Two of the central problems in biology are determining the molecular basis of adaptive evolution and understanding how cells regulate their growth. The chemostat is a device for culturing cells that provides great utility in tackling both of these problems: it enables precise control of the selective pressure under which organisms evolve and it facilitates experimental control of cell growth rate. The aim of this review is to synthesize results from studies of the functional basis of adaptive evolution in long-term chemostat selections using Escherichia coli and Saccharomyces cerevisiae. We describe the principle of the chemostat, provide a summary of studies of experimental evolution in chemostats, and use these studies to assess our current understanding of selection in the chemostat. Functional studies of adaptive evolution in chemostats provide a unique means of interrogating the genetic networks that control cell growth, which complements functional genomic approaches and quantitative trait loci (QTL) mapping in natural populations. An integrated approach to the study of adaptive evolution that accounts for both molecular function and evolutionary processes is critical to advancing our understanding of evolution. By renewing efforts to integrate these two research programs, experimental evolution in chemostats is ideally suited to extending the functional synthesis to the study of genetic networks.
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Affiliation(s)
- David Gresham
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY, USA
| | - Jungeui Hong
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY, USA
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79
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Steensels J, Snoek T, Meersman E, Nicolino MP, Voordeckers K, Verstrepen KJ. Improving industrial yeast strains: exploiting natural and artificial diversity. FEMS Microbiol Rev 2014; 38:947-95. [PMID: 24724938 PMCID: PMC4293462 DOI: 10.1111/1574-6976.12073] [Citation(s) in RCA: 257] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2013] [Revised: 01/31/2014] [Accepted: 04/02/2014] [Indexed: 12/23/2022] Open
Abstract
Yeasts have been used for thousands of years to make fermented foods and beverages, such as beer, wine, sake, and bread. However, the choice for a particular yeast strain or species for a specific industrial application is often based on historical, rather than scientific grounds. Moreover, new biotechnological yeast applications, such as the production of second-generation biofuels, confront yeast with environments and challenges that differ from those encountered in traditional food fermentations. Together, this implies that there are interesting opportunities to isolate or generate yeast variants that perform better than the currently used strains. Here, we discuss the different strategies of strain selection and improvement available for both conventional and nonconventional yeasts. Exploiting the existing natural diversity and using techniques such as mutagenesis, protoplast fusion, breeding, genome shuffling and directed evolution to generate artificial diversity, or the use of genetic modification strategies to alter traits in a more targeted way, have led to the selection of superior industrial yeasts. Furthermore, recent technological advances allowed the development of high-throughput techniques, such as 'global transcription machinery engineering' (gTME), to induce genetic variation, providing a new source of yeast genetic diversity.
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Affiliation(s)
- Jan Steensels
- Laboratory for Genetics and Genomics, Centre of Microbial and Plant Genetics (CMPG), KU LeuvenLeuven, Belgium
- Laboratory for Systems Biology, VIBLeuven, Belgium
| | - Tim Snoek
- Laboratory for Genetics and Genomics, Centre of Microbial and Plant Genetics (CMPG), KU LeuvenLeuven, Belgium
- Laboratory for Systems Biology, VIBLeuven, Belgium
| | - Esther Meersman
- Laboratory for Genetics and Genomics, Centre of Microbial and Plant Genetics (CMPG), KU LeuvenLeuven, Belgium
- Laboratory for Systems Biology, VIBLeuven, Belgium
| | - Martina Picca Nicolino
- Laboratory for Genetics and Genomics, Centre of Microbial and Plant Genetics (CMPG), KU LeuvenLeuven, Belgium
- Laboratory for Systems Biology, VIBLeuven, Belgium
| | - Karin Voordeckers
- Laboratory for Genetics and Genomics, Centre of Microbial and Plant Genetics (CMPG), KU LeuvenLeuven, Belgium
- Laboratory for Systems Biology, VIBLeuven, Belgium
| | - Kevin J Verstrepen
- Laboratory for Genetics and Genomics, Centre of Microbial and Plant Genetics (CMPG), KU LeuvenLeuven, Belgium
- Laboratory for Systems Biology, VIBLeuven, Belgium
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80
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Marchetti M, Jauneau A, Capela D, Remigi P, Gris C, Batut J, Masson-Boivin C. Shaping bacterial symbiosis with legumes by experimental evolution. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2014; 27:956-964. [PMID: 25105803 DOI: 10.1094/mpmi-03-14-0083-r] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Nitrogen-fixing symbionts of legumes have appeared after the emergence of legumes on earth, approximately 70 to 130 million years ago. Since then, symbiotic proficiency has spread to distant genera of α- and β-proteobacteria, via horizontal transfer of essential symbiotic genes and subsequent recipient genome remodeling under plant selection pressure. To tentatively replay rhizobium evolution in laboratory conditions, we previously transferred the symbiotic plasmid of the Mimosa symbiont Cupriavidus taiwanensis in the plant pathogen Ralstonia solanacearum, and selected spontaneous nodulating variants of the chimeric Ralstonia sp. using Mimosa pudica as a trap. Here, we pursued the evolution experiment by submitting two of the rhizobial drafts to serial ex planta-in planta (M. pudica) passages that may mimic alternating of saprophytic and symbiotic lives of rhizobia. Phenotyping 16 cycle-evolved clones showed strong and parallel evolution of several symbiotic traits (i.e., nodulation competitiveness, intracellular infection, and bacteroid persistence). Simultaneously, plant defense reactions decreased within nodules, suggesting that the expression of symbiotic competence requires the capacity to limit plant immunity. Nitrogen fixation was not acquired in the frame of this evolutionarily short experiment, likely due to the still poor persistence of final clones within nodules compared with the reference rhizobium C. taiwanensis. Our results highlight the potential of experimental evolution in improving symbiotic proficiency and for the elucidation of relationship between symbiotic capacities and elicitation of immune responses.
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81
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The underlying structure of adaptation under strong selection in 12 experimental yeast populations. EUKARYOTIC CELL 2014; 13:1200-6. [PMID: 25016004 DOI: 10.1128/ec.00122-14] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The aims of this study were to determine (i) whether adaptation under strong selection occurred through mutations in a narrow target of one or a few nucleotide sites or a broad target of numerous sites and (ii) whether the programs of adaptation previously observed from three experimental populations were unique or shared among populations that underwent parallel evolution. We used archived population samples from a previous study, representing 500 generations of experimental evolution in 12 populations under strong selection, 6 populations in a high-salt environment and 6 populations in a low-glucose environment. Each set of six populations included four with sexual reproduction and two with exclusively asexual reproduction. Populations were sampled as resequenced genomes of 115 individuals and as bulk samples from which frequencies of mutant alleles were estimated. In a high-salt environment, a broad target of 11 mutations within the proton exporter, PMA1, was observed among the six populations, in addition to expansions of the ENA gene cluster. This pattern was shared among populations that underwent parallel evolution. In a low-glucose environment, two programs of adaptation were observed. The originally observed pattern of mutation in MDS3/MKT1 in population M8 was a narrow target of a single nucleotide, unique to this population. Among the other five populations, the three mutations were shared in a broad target, sensing/signaling genes RAS1 and RAS2. RAS1/RAS2 mutations were not observed in the high-salt populations; PMA1 mutations were observed only in a high-salt environment.
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82
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Garijo R, Hernández-Alonso P, Rivas C, Diallo JS, Sanjuán R. Experimental evolution of an oncolytic vesicular stomatitis virus with increased selectivity for p53-deficient cells. PLoS One 2014; 9:e102365. [PMID: 25010337 PMCID: PMC4092128 DOI: 10.1371/journal.pone.0102365] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2014] [Accepted: 06/18/2014] [Indexed: 12/17/2022] Open
Abstract
Experimental evolution has been used for various biotechnological applications including protein and microbial cell engineering, but less commonly in the field of oncolytic virotherapy. Here, we sought to adapt a rapidly evolving RNA virus to cells deficient for the tumor suppressor gene p53, a hallmark of cancer cells. To achieve this goal, we established four independent evolution lines of the vesicular stomatitis virus (VSV) in p53-knockout mouse embryonic fibroblasts (p53-/- MEFs) under conditions favoring the action of natural selection. We found that some evolved viruses showed increased fitness and cytotoxicity in p53-/- cells but not in isogenic p53+/+ cells, indicating gene-specific adaptation. However, full-length sequencing revealed no obvious or previously described genetic changes associated with oncolytic activity. Half-maximal effective dose (EC50) assays in mouse p53-positive colon cancer (CT26) and p53-deficient breast cancer (4T1) cells indicated that the evolved viruses were more effective against 4T1 cells than the parental virus or a reference oncolytic VSV (MΔ51), but showed no increased efficacy against CT26 cells. In vivo assays using 4T1 syngeneic tumor models showed that one of the evolved lines significantly delayed tumor growth compared to mice treated with the parental virus or untreated controls, and was able to induce transient tumor suppression. Our results show that RNA viruses can be specifically adapted typical cancer features such as p53 inactivation, and illustrate the usefulness of experimental evolution for oncolytic virotherapy.
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Affiliation(s)
- Raquel Garijo
- Instituto Cavanilles de Biodiversidad y Biologia Evolutiva, Universidad de Valencia, Valencia, Spain
- Center for Innovative Cancer Research, Ottawa Hospital Research Institute, Ottawa, ON, Canada
| | - Pablo Hernández-Alonso
- Instituto Cavanilles de Biodiversidad y Biologia Evolutiva, Universidad de Valencia, Valencia, Spain
| | - Carmen Rivas
- Departamento de Biología Molecular y Celular, Centro Nacional de Biotecnología, Madrid, Spain
- Centro de Investigación en Medicina Molecular (CIMUS) and Instituto de Investigaciones Sanitarias (IDIS), Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Jean-Simon Diallo
- Center for Innovative Cancer Research, Ottawa Hospital Research Institute, Ottawa, ON, Canada
| | - Rafael Sanjuán
- Instituto Cavanilles de Biodiversidad y Biologia Evolutiva, Universidad de Valencia, Valencia, Spain
- Department of Genetics, Universidad de Valencia, Valencia, Spain
- * E-mail:
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83
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A single evolutionary innovation drives the deep evolution of symbiotic N2-fixation in angiosperms. Nat Commun 2014; 5:4087. [PMID: 24912610 PMCID: PMC4059933 DOI: 10.1038/ncomms5087] [Citation(s) in RCA: 151] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2014] [Accepted: 05/09/2014] [Indexed: 01/16/2023] Open
Abstract
Symbiotic associations occur in every habitat on earth, but we know very little about their evolutionary histories. Current models of trait evolution cannot adequately reconstruct the deep history of symbiotic innovation, because they assume homogenous evolutionary processes across millions of years. Here we use a recently developed, heterogeneous and quantitative phylogenetic framework to study the origin of the symbiosis between angiosperms and nitrogen-fixing (N2) bacterial symbionts housed in nodules. We compile the largest database of global nodulating plant species and reconstruct the symbiosis’ evolution. We identify a single, cryptic evolutionary innovation driving symbiotic N2-fixation evolution, followed by multiple gains and losses of the symbiosis, and the subsequent emergence of ‘stable fixers’ (clades extremely unlikely to lose the symbiosis). Originating over 100 MYA, this innovation suggests deep homology in symbiotic N2-fixation. Identifying cryptic innovations on the tree of life is key to understanding the evolution of complex traits, including symbiotic partnerships. Symbiotic associations are widespread, yet their evolutionary histories remain poorly understood. Here, Werner et. al. show a single evolutionary innovation driving symbiotic nitrogen fixation, followed by multiple gains and losses of the symbiosis and the emergence of groups with stable nitrogen fixers.
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84
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Harpak A, Sella G. Neutral null models for diversity in serial transfer evolution experiments. Evolution 2014; 68:2727-36. [PMID: 24889376 DOI: 10.1111/evo.12454] [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: 12/10/2013] [Accepted: 05/14/2014] [Indexed: 01/14/2023]
Abstract
Evolution experiments with microorganisms coupled with genome-wide sequencing now allow for the systematic study of population genetic processes under a wide range of conditions. In learning about these processes in natural, sexual populations, neutral models that describe the behavior of diversity and divergence summaries have played a pivotal role. It is therefore natural to ask whether neutral models, suitably modified, could be useful in the context of evolution experiments. Here, we introduce coalescent models for polymorphism and divergence under the most common experimental evolution assay, a serial transfer experiment. This relatively simple setting allows us to address several issues that could affect diversity patterns in evolution experiments, whether selection is operating or not: the transient behavior of neutral polymorphism in an experiment beginning from a single clone, the effects of randomness in the timing of cell division and noisiness in population size in the dilution stage. In our analyses and discussion, we emphasize the implications for experiments aimed at measuring diversity patterns and making inferences about population genetic processes based on these measurements.
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Affiliation(s)
- Arbel Harpak
- Department of Ecology, Evolution and Behavior, Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel.
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85
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Zarin T, Moses AM. Insights into molecular evolution from yeast genomics. Yeast 2014; 31:233-41. [PMID: 24760744 DOI: 10.1002/yea.3018] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2014] [Revised: 04/09/2014] [Accepted: 04/10/2014] [Indexed: 12/13/2022] Open
Abstract
Enabled by comparative genomics, yeasts have increasingly developed into a powerful model system for molecular evolution. Here we survey several areas in which yeast studies have made important contributions, including regulatory evolution, gene duplication and divergence, evolution of gene order and evolution of complexity. In each area we highlight key studies and findings based on techniques ranging from statistical analysis of large datasets to direct laboratory measurements of fitness. Future work will combine traditional evolutionary genetics analysis and experimental evolution with tools from systems biology to yield mechanistic insight into complex phenotypes.
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Affiliation(s)
- Taraneh Zarin
- Department of Cell and Systems Biology, University of Toronto, ON, Canada
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86
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Cornish-Bowden A, Peretó J, Cárdenas ML. Biochemistry and evolutionary biology: Two disciplines that need each other. J Biosci 2014; 39:13-27. [DOI: 10.1007/s12038-014-9414-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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87
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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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88
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Gray JC, Cutter AD. Mainstreaming Caenorhabditis elegans in experimental evolution. Proc Biol Sci 2014; 281:20133055. [PMID: 24430852 DOI: 10.1098/rspb.2013.3055] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Experimental evolution provides a powerful manipulative tool for probing evolutionary process and mechanism. As this approach to hypothesis testing has taken purchase in biology, so too has the number of experimental systems that use it, each with its own unique strengths and weaknesses. The depth of biological knowledge about Caenorhabditis nematodes, combined with their laboratory tractability, positions them well for exploiting experimental evolution in animal systems to understand deep questions in evolution and ecology, as well as in molecular genetics and systems biology. To date, Caenorhabditis elegans and related species have proved themselves in experimental evolution studies of the process of mutation, host-pathogen coevolution, mating system evolution and life-history theory. Yet these organisms are not broadly recognized for their utility for evolution experiments and remain underexploited. Here, we outline this experimental evolution work undertaken so far in Caenorhabditis, detail simple methodological tricks that can be exploited and identify research areas that are ripe for future discovery.
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Affiliation(s)
- Jeremy C Gray
- Department of Ecology and Evolutionary Biology, University of Toronto, , 25 Willcocks Street, Toronto, Ontario, Canada , M5S 3B2
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89
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Guyot S, Pottier L, Hartmann A, Ragon M, Hauck Tiburski J, Molin P, Ferret E, Gervais P. Extremely rapid acclimation of Escherichia coli to high temperature over a few generations of a fed-batch culture during slow warming. Microbiologyopen 2013; 3:52-63. [PMID: 24357618 PMCID: PMC3937729 DOI: 10.1002/mbo3.146] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2013] [Revised: 10/27/2013] [Accepted: 11/07/2013] [Indexed: 11/08/2022] Open
Abstract
This study aimed to demonstrate that adequate slow heating rate allows two strains of Escherichia coli rapid acclimation to higher temperature than upper growth and survival limits known to be strain-dependent. A laboratory (K12-TG1) and an environmental (DPD3084) strain of E. coli were subjected to rapid (few seconds) or slow warming (1°C 12 h(-1)) in order to (re)evaluate upper survival and growth limits. The slow warming was applied from the ancestral temperature 37°C to total cell death 46-54°C: about 30 generations were propagated. Upper survival and growth limits for rapid warming (46°C) were lower than for slow warming (46-54°C). The thermal limit of survival for slow warming was higher for DPD3084 (50-54°C). Further experiments conducted on DPD3084, showed that mechanisms involved in this type of thermotolerance were abolished by a following cooling step to 37°C, which allowed to imply reversible mechanisms as acclimation ones. Acquisition of acclimation mechanisms was related to physical properties of the plasma membrane but was not inhibited by unavoidable appearance of aggregated proteins. In conclusion, E.coli could be rapidly acclimated within few generations over thermal limits described in the literature. Such a study led us to propose that rapid acclimation may give supplementary time to the species to acquire a stable adaptation through a random mutation.
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Affiliation(s)
- Stéphane Guyot
- UMR A 02.102 Procédés Alimentaires et Microbiologiques, Equipe Procédés Microbiologiques et Biotechnologiques, AgroSup Dijon, Université de Bourgogne, 1 Esplanade Erasme, 21000, Dijon, France
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90
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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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91
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Taylor TB, Rodrigues AMM, Gardner A, Buckling A. The social evolution of dispersal with public goods cooperation. J Evol Biol 2013; 26:2644-53. [DOI: 10.1111/jeb.12259] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2012] [Revised: 08/27/2013] [Accepted: 09/02/2013] [Indexed: 01/18/2023]
Affiliation(s)
- T. B. Taylor
- Department of Zoology; University of Oxford; Oxford UK
- School of Biological Sciences; University of Reading; Reading UK
| | | | - A. Gardner
- Department of Zoology; University of Oxford; Oxford UK
- Balliol College, University of Oxford; Oxford UK
- School of Biology; University of St Andrews; St Andrews UK
| | - A. Buckling
- Department of Zoology; University of Oxford; Oxford UK
- Biosciences; University of Exeter; Penryn UK
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92
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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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93
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Betts A, Vasse M, Kaltz O, Hochberg ME. Back to the future: evolving bacteriophages to increase their effectiveness against the pathogen Pseudomonas aeruginosa PAO1. Evol Appl 2013; 6:1054-63. [PMID: 24187587 PMCID: PMC3804238 DOI: 10.1111/eva.12085] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2012] [Accepted: 05/30/2013] [Indexed: 12/26/2022] Open
Abstract
Antibiotic resistance is becoming increasingly problematic for the treatment of infectious disease in both humans and livestock. The bacterium Pseudomonas aeruginosa is often found to be resistant to multiple antibiotics and causes high patient mortality in hospitals. Bacteriophages represent a potential option to combat pathogenic bacteria through their application in phage therapy. Here, we capitalize on previous studies showing how evolution may increase phage infection capacity relative to ancestral genotypes. We passaged four different phage isolates (podoviridae, myoviridae) through six serial transfers on the ancestral strain of Pseudomonas aeruginosa PAO1. We first demonstrate that repeated serial passage on ancestral bacteria increases infection capacity of bacteriophage on ancestral hosts and on those evolved for one transfer. This result is confirmed when examining the ability of evolved phage to reduce ancestral host population sizes. Second, through interaction with a single bacteriophage for 24 h, P. aeruginosa can evolve resistance to the ancestor of that bacteriophage; this also provides these evolved bacteria with cross-resistance to the other three bacteriophages. We discuss how the evolutionary training of phages could be employed as effective means of combatting bacterial infections or disinfecting surfaces in hospital settings, with reduced risk of bacterial resistance compared with conventional methods.
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Affiliation(s)
- Alex Betts
- Institut des Sciences de l'Evolution, UMR 5554, Université Montpellier 2 Montpellier CEDEX 05, France
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94
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Jezequel N, Lagomarsino MC, Heslot F, Thomen P. Long-term diversity and genome adaptation of Acinetobacter baylyi in a minimal-medium chemostat. Genome Biol Evol 2013; 5:87-97. [PMID: 23254395 PMCID: PMC3595037 DOI: 10.1093/gbe/evs120] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Laboratory-based evolution experiments on microorganisms that do not recombine frequently show two distinct phases: an initial rapid increase in fitness followed by a slower regime. To explore the population structure and the evolutionary tree in the later stages of adaptation, we evolved a very large population (∼3 × 10) of Acinetobacter baylyi bacteria for approximately 2,800 generations from a single clone. The population was maintained in a chemostat at a high dilution rate. Nitrate in limiting amount and as the sole nitrogen source was used as a selection pressure. Analysis via resequencing of genomes extracted from populations at different generations provides evidence that long-term diversity can be established in the chemostat in a very simple medium. To find out which biological parameters were targeted by adaptation, we measured the maximum growth rate, the nitrate uptake, and the resistance to starvation. Overall, we find that maximum growth rate could be a reasonably good proxy for fitness. The late slow adaptation is compatible with selection coefficients spanning a typical range of 10–10 per generation as estimated by resequencing, pointing to a possible subpopulations structuring.
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Affiliation(s)
- Nadia Jezequel
- Université Pierre et Marie Curie, Paris, France
- Laboratoire Pierre Aigrain, Ecole Normale Supérieure, CNRS (UMR 8551), Université P. et M. Curie, Université D. Diderot, Paris, France
| | - Marco Cosentino Lagomarsino
- Université Pierre et Marie Curie, Paris, France
- Génophysique/Genomic Physics Group, CNRS (UMR 7238) “Microorganism Genomics,” Paris, France
- Dipartimento di Fisica, Università degli Studi di Torino, Torino, Italy
| | - Francois Heslot
- Université Pierre et Marie Curie, Paris, France
- Laboratoire Pierre Aigrain, Ecole Normale Supérieure, CNRS (UMR 8551), Université P. et M. Curie, Université D. Diderot, Paris, France
| | - Philippe Thomen
- Université Pierre et Marie Curie, Paris, France
- Laboratoire Pierre Aigrain, Ecole Normale Supérieure, CNRS (UMR 8551), Université P. et M. Curie, Université D. Diderot, Paris, France
- *Corresponding author: E-mail: ;
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95
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Harrison F. Dynamic social behaviour in a bacterium: pseudomonas aeruginosa partially compensates for siderophore loss to cheats. J Evol Biol 2013; 26:1370-8. [PMID: 23662904 DOI: 10.1111/jeb.12126] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2012] [Revised: 12/20/2012] [Accepted: 01/10/2013] [Indexed: 11/28/2022]
Abstract
Cooperation underlies diverse phenomena including the origins of multicellular life, human behaviour in economic markets and the mechanisms by which pathogenic bacteria cause disease. Experiments with microorganisms have advanced our understanding of how, when and why cooperation evolves, but the extent to which microbial cooperation can recapitulate aspects of animal behaviour is debated. For instance, understanding the evolution of behavioural response rules (how should one individual respond to another's decision to cooperate or defect?) is a key part of social evolution theory, but the possible existence of such rules in social microbes has not been explored. In one specific context (biparental care in animals), cooperation is maintained if individuals respond to a partner's defection by increasing their own investment into cooperation, but not so much that this fully compensates for the defector's lack of investment. This is termed 'partial compensation'. Here, I show that partial compensation for the presence of noncooperating 'cheats' is also observed in a microbial social behaviour: the cooperative production of iron-scavenging siderophores by the bacterium Pseudomonas aeruginosa. A period of evolution in the presence of cheats maintains this response, whereas evolution in the absence of cheats leads to a loss of compensatory behaviour. These results demonstrate (i) the remarkable flexibility of bacterial social behaviour, (ii) the potential generality of partial compensation as a social response rule and (iii) the need for mathematical models to explore the evolution of response rules in multi-player social interactions.
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Affiliation(s)
- F Harrison
- Department of Zoology, University of Oxford, Oxford, United Kingdom.
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96
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Lagator M, Vogwill T, Mead A, Colegrave N, Neve P. Herbicide mixtures at high doses slow the evolution of resistance in experimentally evolving populations of Chlamydomonas reinhardtii. THE NEW PHYTOLOGIST 2013; 198:938-945. [PMID: 23432427 DOI: 10.1111/nph.12195] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2012] [Accepted: 01/21/2013] [Indexed: 06/01/2023]
Abstract
The widespread evolution of resistance to herbicides is a pressing issue in global agriculture. Evolutionary principles and practices are key to the management of this threat to global food security. The application of mixtures of herbicides has been advocated as an anti-resistance strategy, without substantial empirical support for its validation. We evolved experimentally populations of the unicellular green chlorophyte, Chlamydomonas reinhardtii, to minimum inhibitory concentrations (MICs) of single-herbicide modes of action and to pair-wise and three-way mixtures between different herbicides at various total combined doses. Herbicide mixtures were most effective when each component was applied at or close to its MIC. When doses were high, increasing the number of mixture components was also effective in reducing the evolution of resistance. Employing mixtures at low combined doses did not retard resistance evolution, even accelerating the evolution of resistance to some components. At low doses, increasing the number of herbicides in the mixture tended to select for more generalist resistance (cross-resistance). Our results reinforce findings from the antibiotic resistance literature and confirm that herbicide mixtures can be very effective for resistance management, but that mixtures should only be employed where the economic and environmental context permits the applications of high combined doses.
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Affiliation(s)
- Mato Lagator
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | - Tom Vogwill
- Department of Zoology, University of Oxford, Oxford, OX1 3PS, UK
| | - Andrew Mead
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | - Nick Colegrave
- School of Biological Sciences, Institute of Evolutionary Biology, University of Edinburgh, West Mains Road, Edinburgh, EH9 3JT, UK
| | - Paul Neve
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
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97
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Poisot T, Péquin B, Gravel D. High-throughput sequencing: a roadmap toward community ecology. Ecol Evol 2013; 3:1125-39. [PMID: 23610649 PMCID: PMC3631419 DOI: 10.1002/ece3.508] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2012] [Revised: 01/22/2013] [Accepted: 01/23/2013] [Indexed: 11/11/2022] Open
Abstract
High-throughput sequencing is becoming increasingly important in microbial ecology, yet it is surprisingly under-used to generate or test biogeographic hypotheses. In this contribution, we highlight how adding these methods to the ecologist toolbox will allow the detection of new patterns, and will help our understanding of the structure and dynamics of diversity. Starting with a review of ecological questions that can be addressed, we move on to the technical and analytical issues that will benefit from an increased collaboration between different disciplines.
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Affiliation(s)
- Timothée Poisot
- Département de biologie, chimie et géographie, Université du Québec à Rimouski300 Allée des Ursulines, Rimouski, QC, G5L 3A1, Canada
- Québec Centre for Biodiversity Sciences, Stewart Biological Sciences Building1205 Dr. Penfield Avenue, Montréal, QC, H3A 1B1, Canada
| | - Bérangère Péquin
- Département de Biologie, Université LavalQuébec, QC, G1V 0A6, Canada
- Québec-OcéanQuébec, QC, G1V 0A6, Canada
- Institut de Biologie Intégrative et des (IBIS) SystèmesQuébec, QC, G1V 0A6, Canada
| | - Dominique Gravel
- Département de biologie, chimie et géographie, Université du Québec à Rimouski300 Allée des Ursulines, Rimouski, QC, G5L 3A1, Canada
- Québec Centre for Biodiversity Sciences, Stewart Biological Sciences Building1205 Dr. Penfield Avenue, Montréal, QC, H3A 1B1, Canada
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98
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O'Brien S, Hodgson DJ, Buckling A. The interplay between microevolution and community structure in microbial populations. Curr Opin Biotechnol 2013; 24:821-5. [PMID: 23545440 DOI: 10.1016/j.copbio.2013.02.022] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2012] [Revised: 02/14/2013] [Accepted: 02/24/2013] [Indexed: 11/18/2022]
Abstract
The structure of microbial communities is key to their functionality. However, this structure is likely to be influenced by adaptive genetic change in members of the community, which can occur over a matter of days. Changes in community structure can in turn influence the evolutionary trajectories of species within the community, further altering community structure. Microbial communities provide evidence for this interplay between rapid evolution and community structure. To date, studies are primarily limited to simple in vitro systems, but we suggest similar processes are inevitably operating in both natural and derived communities, which are important for biotechnology.
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Affiliation(s)
- Siobhán O'Brien
- Biosciences, University of Exeter, Penryn, Cornwall TR10 9EZ, United Kingdom.
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99
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Brockhurst MA, Koskella B. Experimental coevolution of species interactions. Trends Ecol Evol 2013; 28:367-75. [PMID: 23523051 DOI: 10.1016/j.tree.2013.02.009] [Citation(s) in RCA: 141] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2012] [Revised: 02/20/2013] [Accepted: 02/21/2013] [Indexed: 11/29/2022]
Abstract
Coevolution, the process of reciprocal adaptation and counter-adaptation between ecologically interacting species, affects most organisms and is considered a key force structuring biological diversity. Our understanding of the pattern and process of coevolution, particularly of antagonistic species interactions, has been hugely advanced in recent years by an upsurge in experimental studies that directly observe coevolution in the laboratory. These experiments pose new questions by revealing novel facets of the coevolutionary process not captured by current theory, while also providing the first empirical tests of longstanding coevolutionary ideas, including the influential Red Queen hypothesis. In this article, we highlight emerging directions for this field, including experimental coevolution of mutualistic interactions and understanding how pairwise coevolutionary processes scale up within species-rich communities.
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100
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Guan SH, Gris C, Cruveiller S, Pouzet C, Tasse L, Leru A, Maillard A, Médigue C, Batut J, Masson-Boivin C, Capela D. Experimental evolution of nodule intracellular infection in legume symbionts. ISME JOURNAL 2013; 7:1367-77. [PMID: 23426010 DOI: 10.1038/ismej.2013.24] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Soil bacteria known as rhizobia are able to establish an endosymbiosis with legumes that takes place in neoformed nodules in which intracellularly hosted bacteria fix nitrogen. Intracellular accommodation that facilitates nutrient exchange between the two partners and protects bacteria from plant defense reactions has been a major evolutionary step towards mutualism. Yet the forces that drove the selection of the late event of intracellular infection during rhizobium evolution are unknown. To address this question, we took advantage of the previous conversion of the plant pathogen Ralstonia solanacearum into a legume-nodulating bacterium that infected nodules only extracellularly. We experimentally evolved this draft rhizobium into intracellular endosymbionts using serial cycles of legume-bacterium cocultures. The three derived lineages rapidly gained intracellular infection capacity, revealing that the legume is a highly selective environment for the evolution of this trait. From genome resequencing, we identified in each lineage a mutation responsible for the extracellular-intracellular transition. All three mutations target virulence regulators, strongly suggesting that several virulence-associated functions interfere with intracellular infection. We provide evidence that the adaptive mutations were selected for their positive effect on nodulation. Moreover, we showed that inactivation of the type three secretion system of R. solanacearum that initially allowed the ancestral draft rhizobium to nodulate, was also required to permit intracellular infection, suggesting a similar checkpoint for bacterial invasion at the early nodulation/root infection and late nodule cell entry levels. We discuss our findings with respect to the spread and maintenance of intracellular infection in rhizobial lineages during evolutionary times.
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Affiliation(s)
- Su Hua Guan
- INRA, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR441, Castanet-Tolosan, France
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