1
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Gibson AK, Mundim FM, Ramirez AL, Timper P. Do biological control agents adapt to local pest genotypes? A multiyear test across geographic scales. Evol Appl 2024; 17:e13682. [PMID: 38617827 PMCID: PMC11009426 DOI: 10.1111/eva.13682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 02/05/2024] [Accepted: 03/05/2024] [Indexed: 04/16/2024] Open
Abstract
Parasite local adaptation has been a major focus of (co)evolutionary research on host-parasite interactions. Studies of wild host-parasite systems frequently find that parasites paired with local, sympatric host genotypes perform better than parasites paired with allopatric host genotypes. In contrast, there are few such tests in biological control systems to establish whether biological control parasites commonly perform better on sympatric pest genotypes. This knowledge gap prevents the optimal design of biological control programs: strong local adaptation could argue for the use of sympatric parasites to achieve consistent pest control. To address this gap, we tested for local adaptation of the biological control bacterium Pasteuria penetrans to the root-knot nematode Meloidogyne arenaria, a global threat to a wide range of crops. We measured the probability and intensity of P. penetrans infection on sympatric and allopatric M. arenaria over the course of 4 years. Our design accounted for variation in adaptation across scales by conducting tests within and across fields, and we isolated the signature of parasite adaptation by comparing parasites collected over the course of the growing season. Our results are largely inconsistent with local adaptation of P. penetrans to M. arenaria: in 3 of 4 years, parasites performed similarly well in sympatric and allopatric combinations. In 1 year, however, infection probability was 28% higher for parasites paired with hosts from their sympatric plot, relative to parasites paired with hosts from other plots within the same field. These mixed results argue for population genetic data to characterize the scale of gene flow and genetic divergence in this system. Overall, our findings do not provide strong support for using P. penetrans from local fields to enhance biological control of Meloidogyne.
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Affiliation(s)
| | - Fabiane M. Mundim
- Department of BiologyUniversity of VirginiaCharlottesvilleVirginiaUSA
- Department of BiologyUtah State UniversityLoganUtahUSA
| | - Abbey L. Ramirez
- Department of BiologyUniversity of VirginiaCharlottesvilleVirginiaUSA
| | - Patricia Timper
- United States Department of Agriculture Agricultural Research ServiceTiftonGeorgiaUSA
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2
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Guillemet M, Chabas H, Nicot A, Gatchich F, Ortega-Abboud E, Buus C, Hindhede L, Rousseau GM, Bataillon T, Moineau S, Gandon S. Competition and coevolution drive the evolution and the diversification of CRISPR immunity. Nat Ecol Evol 2022; 6:1480-1488. [PMID: 35970864 DOI: 10.1038/s41559-022-01841-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 06/28/2022] [Indexed: 01/21/2023]
Abstract
The diversity of resistance challenges the ability of pathogens to spread and to exploit host populations. Yet, how this host diversity evolves over time remains unclear because it depends on the interplay between intraspecific competition among host genotypes and coevolution with pathogens. Here we study experimentally the effect of coevolving phage populations on the diversification of bacterial CRISPR immunity across space and time. We demonstrate that the negative-frequency-dependent selection generated by coevolution is a powerful force that maintains host resistance diversity and selects for new resistance mutations in the host. We also find that host evolution is driven by asymmetries in competitive abilities among different host genotypes. Even if the fittest host genotypes are targeted preferentially by the evolving phages, they often escape extinctions through the acquisition of new CRISPR immunity. Together, these fluctuating selective pressures maintain diversity, but not by preserving the pre-existing host composition. Instead, we repeatedly observe the introduction of new resistance genotypes stemming from the fittest hosts in each population. These results highlight the importance of competition on the transient dynamics of host-pathogen coevolution.
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Affiliation(s)
| | - Hélène Chabas
- CEFE, CNRS, Univ Montpellier, EPHE, IRD, Montpellier, France
- Institute of Integrative Biology, Department for Environmental System Science, ETH Zurich, Zurich, Switzerland
| | - Antoine Nicot
- CEFE, CNRS, Univ Montpellier, EPHE, IRD, Montpellier, France
| | | | | | - Cornelia Buus
- Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark
| | - Lotte Hindhede
- Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark
| | - Geneviève M Rousseau
- Département de biochimie, microbiologie, et bio-informatique, Faculté des sciences et de génie, Université Laval, Québec City, Canada
- Groupe de recherche en écologie buccale, Faculté de médecine dentaire, Université Laval, Québec City, Canada
| | - Thomas Bataillon
- Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark
| | - Sylvain Moineau
- Département de biochimie, microbiologie, et bio-informatique, Faculté des sciences et de génie, Université Laval, Québec City, Canada
- Groupe de recherche en écologie buccale, Faculté de médecine dentaire, Université Laval, Québec City, Canada
- Félix d'Hérelle Reference Center for Bacterial Viruses, Faculté de médecine dentaire, Université Laval, Québec City, Canada
| | - Sylvain Gandon
- CEFE, CNRS, Univ Montpellier, EPHE, IRD, Montpellier, France.
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3
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Phage-host coevolution in natural populations. Nat Microbiol 2022; 7:1075-1086. [PMID: 35760840 DOI: 10.1038/s41564-022-01157-1] [Citation(s) in RCA: 51] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 05/23/2022] [Indexed: 01/21/2023]
Abstract
Coevolution between bacteriophages (phages) and their bacterial hosts occurs through changes in resistance and counter-resistance mechanisms. To assess phage-host evolution in wild populations, we isolated 195 Vibrio crassostreae strains and 243 vibriophages during a 5-month time series from an oyster farm and combined these isolates with existing V. crassostreae and phage isolates. Cross-infection studies of 81,926 host-phage pairs delineated a modular network where phages are best at infecting co-occurring hosts, indicating local adaptation. Successful propagation of phage is restricted by the ability to adsorb to closely related bacteria and further constrained by strain-specific defence systems. These defences are highly diverse and predominantly located on mobile genetic elements, and multiple defences are active within a single genome. We further show that epigenetic and genomic modifications enable phage to adapt to bacterial defences and alter host range. Our findings reveal that the evolution of bacterial defences and phage counter-defences is underpinned by frequent genetic exchanges with, and between, mobile genetic elements.
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4
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Affinity maturation for an optimal balance between long-term immune coverage and short-term resource constraints. Proc Natl Acad Sci U S A 2022; 119:2113512119. [PMID: 35177475 PMCID: PMC8872716 DOI: 10.1073/pnas.2113512119] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/07/2022] [Indexed: 12/15/2022] Open
Abstract
Humoral immunity relies on the mutation and selection of B cells to better recognize pathogens. This affinity maturation process produces cells with diverse recognition capabilities. Examining optimal immune strategies that maximize the long-term immune coverage at a minimal metabolic cost, we show when the immune system should mount a de novo response rather than rely on existing memory cells. Our theory recapitulates known modes of the B cell response, predicts the empirical form of the distribution of clone sizes, and rationalizes as a trade-off between metabolic and immune costs the antigenic imprinting effects that limit the efficacy of vaccines (original antigenic sin). Our predictions provide a framework to interpret experimental results that could be used to inform vaccination strategies. In order to target threatening pathogens, the adaptive immune system performs a continuous reorganization of its lymphocyte repertoire. Following an immune challenge, the B cell repertoire can evolve cells of increased specificity for the encountered strain. This process of affinity maturation generates a memory pool whose diversity and size remain difficult to predict. We assume that the immune system follows a strategy that maximizes the long-term immune coverage and minimizes the short-term metabolic costs associated with affinity maturation. This strategy is defined as an optimal decision process on a finite dimensional phenotypic space, where a preexisting population of cells is sequentially challenged with a neutrally evolving strain. We show that the low specificity and high diversity of memory B cells—a key experimental result—can be explained as a strategy to protect against pathogens that evolve fast enough to escape highly potent but narrow memory. This plasticity of the repertoire drives the emergence of distinct regimes for the size and diversity of the memory pool, depending on the density of de novo responding cells and on the mutation rate of the strain. The model predicts power-law distributions of clonotype sizes observed in data and rationalizes antigenic imprinting as a strategy to minimize metabolic costs while keeping good immune protection against future strains.
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5
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Dewald-Wang EA, Parr N, Tiley K, Lee A, Koskella B. Multiyear Time-Shift Study of Bacteria and Phage Dynamics in the Phyllosphere. Am Nat 2022; 199:126-140. [DOI: 10.1086/717181] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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6
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Vahsen ML, Gentile RM, Summers JL, Kleiner HS, Foster B, McCormack RM, James EW, Koch RA, Metts DL, Saunders C, Megonigal JP, Blum MJ, McLachlan JS. Accounting for variability when resurrecting dormant propagules substantiates their use in eco-evolutionary studies. Evol Appl 2021; 14:2831-2847. [PMID: 34950232 PMCID: PMC8674891 DOI: 10.1111/eva.13316] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 09/28/2021] [Accepted: 10/11/2021] [Indexed: 11/29/2022] Open
Abstract
There has been a steady rise in the use of dormant propagules to study biotic responses to environmental change over time. This is particularly important for organisms that strongly mediate ecosystem processes, as changes in their traits over time can provide a unique snapshot into the structure and function of ecosystems from decades to millennia in the past. Understanding sources of bias and variation is a challenge in the field of resurrection ecology, including those that arise because often-used measurements like seed germination success are imperfect indicators of propagule viability. Using a Bayesian statistical framework, we evaluated sources of variability and tested for zero-inflation and overdispersion in data from 13 germination trials of soil-stored seeds of Schoenoplectus americanus, an ecosystem engineer in coastal salt marshes in the Chesapeake Bay. We hypothesized that these two model structures align with an ecological understanding of dormancy and revival: zero-inflation could arise due to failed germinations resulting from inviability or failed attempts to break dormancy, and overdispersion could arise by failing to measure important seed traits. A model that accounted for overdispersion, but not zero-inflation, was the best fit to our data. Tetrazolium viability tests corroborated this result: most seeds that failed to germinate did so because they were inviable, not because experimental methods failed to break their dormancy. Seed viability declined exponentially with seed age and was mediated by seed provenance and experimental conditions. Our results provide a framework for accounting for and explaining variability when estimating propagule viability from soil-stored natural archives which is a key aspect of using dormant propagules in eco-evolutionary studies.
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Affiliation(s)
- Megan L. Vahsen
- Department of Biological SciencesUniversity of Notre DameNotre DameIndianaUSA
| | - Rachel M. Gentile
- Department of Biological SciencesUniversity of Notre DameNotre DameIndianaUSA
| | - Jennifer L. Summers
- Department of Ecology & Evolutionary BiologyUniversity of TennesseeKnoxvilleTennesseeUSA
| | - Helena S. Kleiner
- Department of Biological SciencesUniversity of Notre DameNotre DameIndianaUSA
- Smithsonian Environmental Research CenterEdgewaterMarylandUSA
| | - Benjamin Foster
- Department of Biological SciencesUniversity of Notre DameNotre DameIndianaUSA
| | - Regina M. McCormack
- Department of Biological SciencesUniversity of Notre DameNotre DameIndianaUSA
| | - Evan W. James
- Department of Biological SciencesUniversity of Notre DameNotre DameIndianaUSA
| | - Rachel A. Koch
- Department of Biological SciencesUniversity of Notre DameNotre DameIndianaUSA
| | - Dailee L. Metts
- Department of Ecology & Evolutionary BiologyUniversity of TennesseeKnoxvilleTennesseeUSA
| | - Colin Saunders
- Southeast Environmental Research CenterFlorida International UniversityMiamiFloridaUSA
| | | | - Michael J. Blum
- Department of Ecology & Evolutionary BiologyUniversity of TennesseeKnoxvilleTennesseeUSA
| | - Jason S. McLachlan
- Department of Biological SciencesUniversity of Notre DameNotre DameIndianaUSA
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7
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Salazar KC, Ma L, Green SI, Zulk JJ, Trautner BW, Ramig RF, Clark JR, Terwilliger AL, Maresso AW. Antiviral Resistance and Phage Counter Adaptation to Antibiotic-Resistant Extraintestinal Pathogenic Escherichia coli. mBio 2021; 12:e00211-21. [PMID: 33906920 PMCID: PMC8092219 DOI: 10.1128/mbio.00211-21] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 03/19/2021] [Indexed: 12/14/2022] Open
Abstract
Extraintestinal pathogenic Escherichia coli (ExPEC), often multidrug resistant (MDR), is a leading cause of urinary tract and systemic infections. The crisis of emergent MDR pathogens has led some to propose bacteriophages as a therapeutic. However, bacterial resistance to phage is a concerning issue that threatens to undermine phage therapy. Here, we demonstrate that E. coli sequence type 131, a circulating pandemic strain of ExPEC, rapidly develops resistance to a well-studied and therapeutically active phage (ϕHP3). Whole-genome sequencing of the resisters revealed truncations in genes involved in lipopolysaccharide (LPS) biosynthesis, the outer membrane transporter ompA, or both, implicating them as phage receptors. We found ExPEC resistance to phage is associated with a loss of fitness in host microenvironments and attenuation in a murine model of systemic infection. Furthermore, we constructed a novel phage-bacterium bioreactor to generate an evolved phage isolate with restored infectivity to all LPS-truncated ExPEC resisters. This study suggests that although the resistance of pandemic E. coli to phage is frequent, it is associated with attenuation of virulence and susceptibility to new phage variants that arise by directed evolution.IMPORTANCE In response to the rising crisis of antimicrobial resistance, bacteriophage (phage) therapy has gained traction. In the United States, there have been over 10 cases of largely successful compassionate-use phage therapy to date. The resilience of pathogens allowing their broad antibiotic resistance means we must also consider resistance to therapeutic phages. This work fills gaps in knowledge regarding development of phage resisters in a model of infection and finds critical fitness losses in those resisters. We also found that the phage was able to rapidly readapt to these resisters.
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Affiliation(s)
- Keiko C Salazar
- Department of Integrative Molecular and Biomedical Science, Baylor College of Medicine, Houston, Texas, USA
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
| | - Li Ma
- School of Biological and Physical Sciences, Northwestern State University, Natchitoches, Louisiana, USA
| | - Sabrina I Green
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
| | - Jacob J Zulk
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
| | - Barbara W Trautner
- Michael E. DeBakey Veterans Affairs Medical Center, Houston, Texas, USA
- Department of Medicine, Baylor College of Medicine, Houston, Texas, USA
| | - Robert F Ramig
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
| | - Justin R Clark
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
| | - Austen L Terwilliger
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
| | - Anthony W Maresso
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
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8
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Goehlich H, Sartoris L, Wagner KS, Wendling CC, Roth O. Pipefish Locally Adapted to Low Salinity in the Baltic Sea Retain Phenotypic Plasticity to Cope With Ancestral Salinity Levels. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.626442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Genetic adaptation and phenotypic plasticity facilitate the migration into new habitats and enable organisms to cope with a rapidly changing environment. In contrast to genetic adaptation that spans multiple generations as an evolutionary process, phenotypic plasticity allows acclimation within the life-time of an organism. Genetic adaptation and phenotypic plasticity are usually studied in isolation, however, only by including their interactive impact, we can understand acclimation and adaptation in nature. We aimed to explore the contribution of adaptation and plasticity in coping with an abiotic (salinity) and a biotic (Vibriobacteria) stressor using six different populations of the broad-nosed pipefishSyngnathus typhlethat originated from either high [14–17 Practical Salinity Unit (PSU)] or low (7–11 PSU) saline environments along the German coastline of the Baltic Sea. We exposed wild caught animals, to either high (15 PSU) or low (7 PSU) salinity, representing native and novel salinity conditions and allowed animals to mate. After male pregnancy, offspring was split and each half was exposed to one of the two salinities and infected withVibrio alginolyticusbacteria that were evolved at either of the two salinities in a fully reciprocal design. We investigated life-history traits of fathers and expression of 47 target genes in mothers and offspring. Pregnant males originating from high salinity exposed to low salinity were highly susceptible to opportunistic fungi infections resulting in decreased offspring size and number. In contrast, no signs of fungal infection were identified in fathers originating from low saline conditions suggesting that genetic adaptation has the potential to overcome the challenges encountered at low salinity. Offspring from parents with low saline origin survived better at low salinity suggesting genetic adaptation to low salinity. In addition, gene expression analyses of juveniles indicated patterns of local adaptation,trans-generational plasticity and developmental plasticity. In conclusion, our study suggests that pipefish are locally adapted to the low salinity in their environment, however, they are retaining phenotypic plasticity, which allows them to also cope with ancestral salinity levels and prevailing pathogens.
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9
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Measuring Coevolutionary Dynamics in Species-Rich Communities. Trends Ecol Evol 2020; 35:539-550. [DOI: 10.1016/j.tree.2020.02.002] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 01/24/2020] [Accepted: 02/03/2020] [Indexed: 12/18/2022]
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10
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Week B, Nuismer SL. The measurement of coevolution in the wild. Ecol Lett 2019; 22:717-725. [PMID: 30775838 DOI: 10.1111/ele.13231] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Revised: 10/14/2018] [Accepted: 01/11/2019] [Indexed: 11/27/2022]
Abstract
Coevolution has long been thought to drive the exaggeration of traits, promote major evolutionary transitions such as the evolution of sexual reproduction and influence epidemiological dynamics. Despite coevolution's long suspected importance, we have yet to develop a quantitative understanding of its strength and prevalence because we lack generally applicable statistical methods that yield numerical estimates for coevolution's strength and significance in the wild. Here, we develop a novel method that derives maximum likelihood estimates for the strength of direct pairwise coevolution by coupling a well-established coevolutionary model to spatially structured phenotypic data. Applying our method to two well-studied interactions reveals evidence for coevolution in both systems. Broad application of this approach has the potential to further resolve long-standing evolutionary debates such as the role species interactions play in the evolution of sexual reproduction and the organisation of ecological communities.
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Affiliation(s)
- Bob Week
- Department of Biological Sciences, University of Idaho, Idaho, NW, USA
| | - Scott L Nuismer
- Department of Biological Sciences, University of Idaho, Idaho, NW, USA
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11
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Sun B, Ma L, Li S, Williams CM, Wang Y, Hao X, Du W. Phenology and the physiological niche are co‐adapted in a desert‐dwelling lizard. Funct Ecol 2018. [DOI: 10.1111/1365-2435.13201] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Bao‐Jun Sun
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology Chinese Academy of Sciences Beijing China
- Department of Integrative Biology University of California Berkeley California
| | - Liang Ma
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology Chinese Academy of Sciences Beijing China
- University of Chinese Academy of Sciences Beijing China
| | - Shu‐Ran Li
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology Chinese Academy of Sciences Beijing China
- University of Chinese Academy of Sciences Beijing China
| | | | - Yang Wang
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology Chinese Academy of Sciences Beijing China
- University of Chinese Academy of Sciences Beijing China
| | - Xin Hao
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology Chinese Academy of Sciences Beijing China
- University of Chinese Academy of Sciences Beijing China
| | - Wei‐Guo Du
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology Chinese Academy of Sciences Beijing China
- Center for Excellence in Animal Evolution and Genetics Chinese Academy of SciencesKunming China
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12
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Blanquart F, Valero M, Alves-de-Souza C, Dia A, Lepelletier F, Bigeard E, Jeanthon C, Destombe C, Guillou L. Evidence for parasite-mediated selection during short-lasting toxic algal blooms. Proc Biol Sci 2017; 283:rspb.2016.1870. [PMID: 27798309 PMCID: PMC5095388 DOI: 10.1098/rspb.2016.1870] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Accepted: 09/28/2016] [Indexed: 11/30/2022] Open
Abstract
Parasites play a role in the control of transient algal blooms, but it is not known whether parasite-mediated selection results in coevolution of the host and the parasites over this short time span. We investigated the presence of coevolution between the toxic dinoflagellate Alexandrium minutum and two naturally occurring endoparasites during blooms lasting a month in two river estuaries, using cross-inoculation experiments across time and space. Higher parasite abundance was associated with a large daily reduction in relative A. minutum abundances, demonstrating strong parasite-mediated selection. There was genetic variability in infectivity in both parasite species, and in resistance in the host. We found no evidence for coevolution in one estuary; however, in the other estuary, we found high genetic diversity in the two parasite species, fluctuations in infectivity and suggestion that the two parasites are well adapted to their host, as in ‘Red Queen’ dynamics. Thus, coevolution is possible over the short time span of a bloom, but geographically variable, and may feedback on community dynamics.
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Affiliation(s)
- François Blanquart
- Department of Infectious Disease Epidemiology, Imperial College London, Norfolk Place, London W2 1PG, UK
| | - Myriam Valero
- Station Biologique de Roscoff, Sorbonne Universités, Université Pierre et Marie Curie (Paris VI), Place Georges Teissier, CS90074, 29688 Roscoff, France.,CNRS, UMI 3614, Pontifica Universidad Catolica de Chile, Universidad Austral de Chile, Place Georges Teissier, CS90074, 29688 Roscoff, France
| | - Catharina Alves-de-Souza
- Departamento de Botânica, Museu Nacional, Universidade Federal do Rio de Janeiro, Quinta da Boa Vista, s/n, São Cristovão, Rio de Janeiro, RJ, Brazil
| | - Aliou Dia
- Station Biologique de Roscoff, Sorbonne Universités, Université Pierre et Marie Curie (Paris VI), Place Georges Teissier, CS90074, 29688 Roscoff, France.,Station Biologique de Roscoff, CNRS, UMR 7144, Place Georges Teissier, CS90074, 29688 Roscoff, France
| | - Frédéric Lepelletier
- Station Biologique de Roscoff, Sorbonne Universités, Université Pierre et Marie Curie (Paris VI), Place Georges Teissier, CS90074, 29688 Roscoff, France.,Station Biologique de Roscoff, CNRS, UMR 7144, Place Georges Teissier, CS90074, 29688 Roscoff, France
| | - Estelle Bigeard
- Station Biologique de Roscoff, Sorbonne Universités, Université Pierre et Marie Curie (Paris VI), Place Georges Teissier, CS90074, 29688 Roscoff, France.,Station Biologique de Roscoff, CNRS, UMR 7144, Place Georges Teissier, CS90074, 29688 Roscoff, France
| | - Christian Jeanthon
- Station Biologique de Roscoff, Sorbonne Universités, Université Pierre et Marie Curie (Paris VI), Place Georges Teissier, CS90074, 29688 Roscoff, France.,Station Biologique de Roscoff, CNRS, UMR 7144, Place Georges Teissier, CS90074, 29688 Roscoff, France
| | - Christophe Destombe
- Station Biologique de Roscoff, Sorbonne Universités, Université Pierre et Marie Curie (Paris VI), Place Georges Teissier, CS90074, 29688 Roscoff, France.,CNRS, UMI 3614, Pontifica Universidad Catolica de Chile, Universidad Austral de Chile, Place Georges Teissier, CS90074, 29688 Roscoff, France
| | - Laure Guillou
- Station Biologique de Roscoff, Sorbonne Universités, Université Pierre et Marie Curie (Paris VI), Place Georges Teissier, CS90074, 29688 Roscoff, France .,Station Biologique de Roscoff, CNRS, UMR 7144, Place Georges Teissier, CS90074, 29688 Roscoff, France
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13
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Auld SKJR, Brand J. Environmental variation causes different (co) evolutionary routes to the same adaptive destination across parasite populations. Evol Lett 2017; 1:245-254. [PMID: 30283653 PMCID: PMC6121849 DOI: 10.1002/evl3.27] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Accepted: 09/15/2017] [Indexed: 11/13/2022] Open
Abstract
Epidemics are engines for host-parasite coevolution, where parasite adaptation to hosts drives reciprocal adaptation in host populations. A key challenge is to understand whether parasite adaptation and any underlying evolution and coevolution is repeatable across ecologically realistic populations that experience different environmental conditions, or if each population follows a completely unique evolutionary path. We established twenty replicate pond populations comprising an identical suite of genotypes of crustacean host, Daphnia magna, and inoculum of their parasite, Pasteuria ramosa. Using a time-shift experiment, we compared parasite infection traits before and after epidemics and linked patterns of parasite evolution with shifts in host genotype frequencies. Parasite adaptation to the sympatric suite of host genotypes came at a cost of poorer performance on foreign genotypes across populations and environments. However, this consistent pattern of parasite adaptation was driven by different types of frequency-dependent selection that was contingent on an ecologically relevant environmental treatment (whether or not there was physical mixing of water within ponds). In unmixed ponds, large epidemics drove rapid and strong host-parasite coevolution. In mixed ponds, epidemics were smaller and host evolution was driven mainly by the mixing treatment itself; here, host evolution and parasite evolution were clear, but coevolution was absent. Population mixing breaks an otherwise robust coevolutionary cycle. These findings advance our understanding of the repeatability of (co)evolution across noisy, ecologically realistic populations.
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Affiliation(s)
- Stuart K. J. R. Auld
- Biological and Environmental SciencesUniversity of StirlingStirlingUnited Kingdom
| | - June Brand
- Biological and Environmental SciencesUniversity of StirlingStirlingUnited Kingdom
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14
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Lenormand T, Nougué O, Jabbour-Zahab R, Arnaud F, Dezileau L, Chevin LM, Sánchez MI. Resurrection ecology in Artemia. Evol Appl 2017; 11:76-87. [PMID: 29302273 PMCID: PMC5748519 DOI: 10.1111/eva.12522] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2017] [Accepted: 07/10/2017] [Indexed: 12/25/2022] Open
Abstract
Resurrection ecology (RE) is a very powerful approach to address a wide range of question in ecology and evolution. This approach rests on using appropriate model systems, and only few are known to be available. In this study, we show that Artemia has multiple attractive features (short generation time, cyst bank and collections, well‐documented phylogeography, and ecology) for a good RE model. We show in detail with a case study how cysts can be recovered from sediments to document the history and dynamics of a biological invasion. We finally discuss with precise examples the many RE possibilities with this model system: adaptation to climate change, to pollution, to parasites, to invaders and evolution of reproductive systems.
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Affiliation(s)
- Thomas Lenormand
- CEFE UMR 5175 CNRS, Université de Montpellier, Université Paul-Valéry Montpellier Montpellier Cedex 5 France
| | - Odrade Nougué
- CEFE UMR 5175 CNRS, Université de Montpellier, Université Paul-Valéry Montpellier Montpellier Cedex 5 France
| | - Roula Jabbour-Zahab
- CEFE UMR 5175 CNRS, Université de Montpellier, Université Paul-Valéry Montpellier Montpellier Cedex 5 France
| | - Fabien Arnaud
- Laboratoire EDYTEM UMR 5204 du CNRS, Environnements, Dynamiques et Territoires de la Montagne, Université de SavoieLe Bourget du Lac Cedex France
| | - Laurent Dezileau
- Géosciences Montpellier, UMR 5243 Université de Montpellier Montpellier Cedex 05 France
| | - Luis-Miguel Chevin
- CEFE UMR 5175 CNRS, Université de Montpellier, Université Paul-Valéry Montpellier Montpellier Cedex 5 France
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15
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Persoons A, Hayden KJ, Fabre B, Frey P, De Mita S, Tellier A, Halkett F. The escalatory Red Queen: Population extinction and replacement following arms race dynamics in poplar rust. Mol Ecol 2017; 26:1902-1918. [PMID: 28012228 DOI: 10.1111/mec.13980] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Accepted: 12/15/2016] [Indexed: 01/14/2023]
Abstract
Host-parasite systems provide convincing examples of Red Queen co-evolutionary dynamics. Yet, a key process underscored in Van Valen's theory - that arms race dynamics can result in extinction - has never been documented. One reason for this may be that most sampling designs lack the breadth needed to illuminate the rapid pace of adaptation by pathogen populations. In this study, we used a 25-year temporal sampling to decipher the demographic history of a plant pathogen: the poplar rust fungus, Melampsora larici-populina. A major adaptive event occurred in 1994 with the breakdown of R7 resistance carried by several poplar cultivars widely planted in Western Europe since 1982. The corresponding virulence rapidly spread in M. larici-populina populations and nearly reached fixation in northern France, even on susceptible hosts. Using both temporal records of virulence profiles and temporal population genetic data, our analyses revealed that (i) R7 resistance breakdown resulted in the emergence of a unique and homogeneous genetic group, the so-called cultivated population, which predominated in northern France for about 20 years, (ii) selection for Vir7 individuals brought with it multiple other virulence types via hitchhiking, resulting in an overall increase in the population-wide number of virulence types and (iii) - above all - the emergence of the cultivated population superseded the initial population which predominated at the same place before R7 resistance breakdown. Our temporal analysis illustrates how antagonistic co-evolution can lead to population extinction and replacement, hence providing direct evidence for the escalation process which is at the core of Red Queen dynamics.
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Affiliation(s)
| | | | | | - Pascal Frey
- UMR IAM, INRA, Université de Lorraine, 54000, Nancy, France
| | | | - Aurélien Tellier
- Section of Population Genetics, Center of Life and Food Sciences Weihenstephan, Technische Universität München, 85354, Freising, Germany
| | - Fabien Halkett
- UMR IAM, INRA, Université de Lorraine, 54000, Nancy, France
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16
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Kraemer SA, Kassen R. Temporal patterns of local adaptation in soil pseudomonads. Proc Biol Sci 2016; 283:20161652. [PMID: 27708150 PMCID: PMC5069515 DOI: 10.1098/rspb.2016.1652] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2016] [Accepted: 09/13/2016] [Indexed: 12/25/2022] Open
Abstract
Strong divergent selection leading to local adaptation is often invoked to explain the staggering diversity of bacteria in microbial ecosystems. However, examples of specialization by bacterial clones to alternative niches in nature are rare. Here, we investigate the extent of local adaptation in natural isolates of pseudomonads and their relatives to their soil environments across both space and time. Though most isolates grew well in most environments, patchily distributed low-quality environments were found to drive specialization. In contrast to experimental evolution work on microbial adaptation, temporal adaptation was stronger than spatial adaptation among the isolates and environments we sampled. Time-shift analysis of fitness across two seasons of growth revealed an unexpectedly strong effect of preadaptation. This pattern of apparent future adaptation may be caused by unknown abiotic properties of these environments, phages, bacterial competitors or general mechanisms of ecological niche release, and warrants future study.
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Affiliation(s)
- Susanne A Kraemer
- Institute of Evolutionary Biology, University of Edinburgh, Ashworth Laboratories, Charlotte Auerbach Road, Edinburgh EH9 3FL, UK
| | - Rees Kassen
- University of Ottawa, Ottawa, Ontario, Canada
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17
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Pigeault R, Garnier R, Rivero A, Gandon S. Evolution of transgenerational immunity in invertebrates. Proc Biol Sci 2016; 283:rspb.2016.1136. [PMID: 27683366 DOI: 10.1098/rspb.2016.1136] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Accepted: 09/06/2016] [Indexed: 11/12/2022] Open
Abstract
Over a decade ago, the discovery of transgenerational immunity in invertebrates shifted existing paradigms on the lack of sophistication of their immune system. Nonetheless, the prevalence of this trait and the ecological factors driving its evolution in invertebrates remain poorly understood. Here, we develop a theoretical host-parasite model and predict that long lifespan and low dispersal should promote the evolution of transgenerational immunity. We also predict that in species that produce both philopatric and dispersing individuals, it may pay to have a plastic allocation strategy with a higher transgenerational immunity investment in philopatric offspring because they are more likely to encounter locally adapted pathogens. We review all experimental studies published to date, comprising 21 invertebrate species in nine different orders, and we show that, as expected, longevity and dispersal correlate with the transfer of immunity to offspring. The validity of our prediction regarding the plasticity of investment in transgenerational immunity remains to be tested in invertebrates, but also in vertebrate species. We discuss the implications of our work for the study of the evolution of immunity, and we suggest further avenues of research to expand our knowledge of the impact of transgenerational immune protection in host-parasite interactions.
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Affiliation(s)
- R Pigeault
- MIVEGEC (UMR CNRS 5290), Montpellier, France
| | - R Garnier
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA
| | - A Rivero
- MIVEGEC (UMR CNRS 5290), Montpellier, France
| | - S Gandon
- CEFE (UMR CNRS 5175), Montpellier, France
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18
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Host-Pathogen Coevolution and the Emergence of Broadly Neutralizing Antibodies in Chronic Infections. PLoS Genet 2016; 12:e1006171. [PMID: 27442127 PMCID: PMC4956326 DOI: 10.1371/journal.pgen.1006171] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Accepted: 06/14/2016] [Indexed: 01/21/2023] Open
Abstract
The vertebrate adaptive immune system provides a flexible and diverse set of molecules to neutralize pathogens. Yet, viruses such as HIV can cause chronic infections by evolving as quickly as the adaptive immune system, forming an evolutionary arms race. Here we introduce a mathematical framework to study the coevolutionary dynamics between antibodies and antigens within a host. We focus on changes in the binding interactions between the antibody and antigen populations, which result from the underlying stochastic evolution of genotype frequencies driven by mutation, selection, and drift. We identify the critical viral and immune parameters that determine the distribution of antibody-antigen binding affinities. We also identify definitive signatures of coevolution that measure the reciprocal response between antibodies and viruses, and we introduce experimentally measurable quantities that quantify the extent of adaptation during continual coevolution of the two opposing populations. Using this analytical framework, we infer rates of viral and immune adaptation based on time-shifted neutralization assays in two HIV-infected patients. Finally, we analyze competition between clonal lineages of antibodies and characterize the fate of a given lineage in terms of the state of the antibody and viral populations. In particular, we derive the conditions that favor the emergence of broadly neutralizing antibodies, which may have relevance to vaccine design against HIV.
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19
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Predicting the evolutionary dynamics of seasonal adaptation to novel climates in Arabidopsis thaliana. Proc Natl Acad Sci U S A 2016; 113:E2812-21. [PMID: 27140640 DOI: 10.1073/pnas.1517456113] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Predicting whether and how populations will adapt to rapid climate change is a critical goal for evolutionary biology. To examine the genetic basis of fitness and predict adaptive evolution in novel climates with seasonal variation, we grew a diverse panel of the annual plant Arabidopsis thaliana (multiparent advanced generation intercross lines) in controlled conditions simulating four climates: a present-day reference climate, an increased-temperature climate, a winter-warming only climate, and a poleward-migration climate with increased photoperiod amplitude. In each climate, four successive seasonal cohorts experienced dynamic daily temperature and photoperiod variation over a year. We measured 12 traits and developed a genomic prediction model for fitness evolution in each seasonal environment. This model was used to simulate evolutionary trajectories of the base population over 50 y in each climate, as well as 100-y scenarios of gradual climate change following adaptation to a reference climate. Patterns of plastic and evolutionary fitness response varied across seasons and climates. The increased-temperature climate promoted genetic divergence of subpopulations across seasons, whereas in the winter-warming and poleward-migration climates, seasonal genetic differentiation was reduced. In silico "resurrection experiments" showed limited evolutionary rescue compared with the plastic response of fitness to seasonal climate change. The genetic basis of adaptation and, consequently, the dynamics of evolutionary change differed qualitatively among scenarios. Populations with fewer founding genotypes and populations with genetic diversity reduced by prior selection adapted less well to novel conditions, demonstrating that adaptation to rapid climate change requires the maintenance of sufficient standing variation.
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20
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Koskella B, Parr N. The evolution of bacterial resistance against bacteriophages in the horse chestnut phyllosphere is general across both space and time. Philos Trans R Soc Lond B Biol Sci 2016; 370:rstb.2014.0297. [PMID: 26150663 PMCID: PMC4528495 DOI: 10.1098/rstb.2014.0297] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Insight to the spatial and temporal scales of coevolution is key to predicting the outcome of host-parasite interactions and spread of disease. For bacteria infecting long-lived hosts, selection to overcome host defences is just one factor shaping the course of evolution; populations will also be competing with other microbial species and will themselves be facing infection by bacteriophage viruses. Here, we examine the temporal and spatial patterns of bacterial adaptation against natural phage populations from within leaves of horse chestnut trees. Using a time-shift experiment with both sympatric and allopatric phages from either contemporary or earlier points in the season, we demonstrate that bacterial resistance is higher against phages from the past, regardless of spatial sympatry or how much earlier in the season phages were collected. Similarly, we show that future bacterial hosts are more resistant to both sympatric and allopatric phages than contemporary bacterial hosts. Together, our results suggest the evolution of relatively general bacterial resistance against phages in nature and are contrasting to previously observed patterns of phage adaptation to bacteria from the same tree hosts over the same time frame, indicating a potential asymmetry in coevolutionary dynamics.
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Affiliation(s)
- Britt Koskella
- Department of Biosciences, University of Exeter, Penryn Campus, Cornwall, UK
| | - Nicole Parr
- Department of Biosciences, University of Exeter, Penryn Campus, Cornwall, UK
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21
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Penczykowski RM, Laine A, Koskella B. Understanding the ecology and evolution of host-parasite interactions across scales. Evol Appl 2016; 9:37-52. [PMID: 27087838 PMCID: PMC4780374 DOI: 10.1111/eva.12294] [Citation(s) in RCA: 110] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Accepted: 06/18/2015] [Indexed: 12/19/2022] Open
Abstract
Predicting the emergence, spread and evolution of parasites within and among host populations requires insight to both the spatial and temporal scales of adaptation, including an understanding of within-host up through community-level dynamics. Although there are very few pathosystems for which such extensive data exist, there has been a recent push to integrate studies performed over multiple scales or to simultaneously test for dynamics occurring across scales. Drawing on examples from the literature, with primary emphasis on three diverse host-parasite case studies, we first examine current understanding of the spatial structure of host and parasite populations, including patterns of local adaptation and spatial variation in host resistance and parasite infectivity. We then explore the ways to measure temporal variation and dynamics in host-parasite interactions and discuss the need to examine change over both ecological and evolutionary timescales. Finally, we highlight new approaches and syntheses that allow for simultaneous analysis of dynamics across scales. We argue that there is great value in examining interplay among scales in studies of host-parasite interactions.
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Affiliation(s)
- Rachel M. Penczykowski
- Department of BiosciencesMetapopulation Research CentreUniversity of HelsinkiHelsinkiFinland
| | - Anna‐Liisa Laine
- Department of BiosciencesMetapopulation Research CentreUniversity of HelsinkiHelsinkiFinland
| | - Britt Koskella
- BiosciencesUniversity of ExeterTremoughUK
- Integrative BiologyUniversity of CaliforniaBerkeleyUSA
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22
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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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23
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Hardoim PR, van Overbeek LS, Berg G, Pirttilä AM, Compant S, Campisano A, Döring M, Sessitsch A. The Hidden World within Plants: Ecological and Evolutionary Considerations for Defining Functioning of Microbial Endophytes. Microbiol Mol Biol Rev 2015; 79:293-320. [PMID: 26136581 PMCID: PMC4488371 DOI: 10.1128/mmbr.00050-14] [Citation(s) in RCA: 1077] [Impact Index Per Article: 119.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
All plants are inhabited internally by diverse microbial communities comprising bacterial, archaeal, fungal, and protistic taxa. These microorganisms showing endophytic lifestyles play crucial roles in plant development, growth, fitness, and diversification. The increasing awareness of and information on endophytes provide insight into the complexity of the plant microbiome. The nature of plant-endophyte interactions ranges from mutualism to pathogenicity. This depends on a set of abiotic and biotic factors, including the genotypes of plants and microbes, environmental conditions, and the dynamic network of interactions within the plant biome. In this review, we address the concept of endophytism, considering the latest insights into evolution, plant ecosystem functioning, and multipartite interactions.
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Affiliation(s)
- Pablo R. Hardoim
- Centre of Marine Sciences, University of Algarve, Faro, Portugal
| | | | - Gabriele Berg
- Institute for Environmental Biotechnology, Graz University of Technology, Graz, Austria
| | | | - Stéphane Compant
- Department of Health and Environment, Bioresources Unit, Austrian Institute of Technology GmbH, Tulln, Austria
| | - Andrea Campisano
- Sustainable Agro-Ecosystems and Bioresources Department, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, TN, Italy
| | | | - Angela Sessitsch
- Department of Health and Environment, Bioresources Unit, Austrian Institute of Technology GmbH, Tulln, Austria
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24
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Abstract
The consequences of host–parasite coevolution are highly contingent on the qualitative coevolutionary dynamics: whether selection fluctuates (fluctuating selection dynamic; FSD), or is directional towards increasing infectivity/resistance (arms race dynamic; ARD). Both genetics and ecology can play an important role in determining whether coevolution follows FSD or ARD, but the ecological conditions under which FSD shifts to ARD, and vice versa, are not well understood. The degree of population mixing is thought to increase host exposure to parasites, hence selecting for greater resistance and infectivity ranges, and we hypothesize this promotes ARD. We tested this by coevolving bacteria and viruses in soil microcosms and found that population mixing shifted bacteria–virus coevolution from FSD to ARD. A simple theoretical model produced qualitatively similar results, showing that mechanisms that increase host exposure to parasites tend to push dynamics towards ARD. The shift from FSD to ARD with increased population mixing may help to explain variation in coevolutionary dynamics between different host–parasite systems, and more specifically the observed discrepancies between laboratory and field bacteria–virus coevolutionary studies.
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Affiliation(s)
- Pedro Gómez
- Department of Biosciences, University of Exeter, Penryn Campus, Cornwall TR10 9FE, UK
| | - Ben Ashby
- Department of Biosciences, University of Exeter, Penryn Campus, Cornwall TR10 9FE, UK Department of Zoology, University of Oxford, Oxford OX1 3PS, UK
| | - Angus Buckling
- Department of Biosciences, University of Exeter, Penryn Campus, Cornwall TR10 9FE, UK
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25
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The Hidden World within Plants: Ecological and Evolutionary Considerations for Defining Functioning of Microbial Endophytes. Microbiol Mol Biol Rev 2015. [PMID: 26136581 DOI: 10.1128/mmbr.00050-14.] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
All plants are inhabited internally by diverse microbial communities comprising bacterial, archaeal, fungal, and protistic taxa. These microorganisms showing endophytic lifestyles play crucial roles in plant development, growth, fitness, and diversification. The increasing awareness of and information on endophytes provide insight into the complexity of the plant microbiome. The nature of plant-endophyte interactions ranges from mutualism to pathogenicity. This depends on a set of abiotic and biotic factors, including the genotypes of plants and microbes, environmental conditions, and the dynamic network of interactions within the plant biome. In this review, we address the concept of endophytism, considering the latest insights into evolution, plant ecosystem functioning, and multipartite interactions.
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26
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Hartfield M, Alizon S. Within-host stochastic emergence dynamics of immune-escape mutants. PLoS Comput Biol 2015; 11:e1004149. [PMID: 25785434 PMCID: PMC4365036 DOI: 10.1371/journal.pcbi.1004149] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2014] [Accepted: 01/22/2015] [Indexed: 12/28/2022] Open
Abstract
Predicting the emergence of new pathogenic strains is a key goal of evolutionary epidemiology. However, the majority of existing studies have focussed on emergence at the population level, and not within a host. In particular, the coexistence of pre-existing and mutated strains triggers a heightened immune response due to the larger total pathogen population; this feedback can smother mutated strains before they reach an ample size and establish. Here, we extend previous work for measuring emergence probabilities in non-equilibrium populations, to within-host models of acute infections. We create a mathematical model to investigate the emergence probability of a fitter strain if it mutates from a self-limiting strain that is guaranteed to go extinct in the long-term. We show that ongoing immune cell proliferation during the initial stages of infection causes a drastic reduction in the probability of emergence of mutated strains; we further outline how this effect can be accurately measured. Further analysis of the model shows that, in the short-term, mutant strains that enlarge their replication rate due to evolving an increased growth rate are more favoured than strains that suffer a lower immune-mediated death rate (‘immune tolerance’), as the latter does not completely evade ongoing immune proliferation due to inter-parasitic competition. We end by discussing the model in relation to within-host evolution of human pathogens (including HIV, hepatitis C virus, and cancer), and how ongoing immune growth can affect their evolutionary dynamics. The ongoing evolution of infectious diseases provides a constant health threat. This evolution can either result in the production of new pathogens, or new strains of existing pathogens that escape prevailing drug treatments or immune responses. The latter process, also known as immune escape, is a predominant reason for the persistence of several viruses, including HIV and hepatitis C virus (HCV), in their human host. As a consequence, the within-host emergence of new strains has been the intense focus of modelling studies. However, existing models have neglected important feedbacks that affects this emergence probability. Specifically, once a mutated pathogen arises that spreads more quickly than the initial (resident) strain, it potentially triggers a heightened immune response that can eliminate the mutated strain before it spreads. Our study outlines novel mathematical modelling techniques that accurately quantify how ongoing immune growth reduces the emergence probability of mutated pathogenic strains over the course of an infection. Analysis of this model suggests that, in order to enlarge its emergence probability, it is evolutionary beneficial for a mutated strain to increase its growth rate rather than tolerate immunity by having a lower immune-mediated death-rate. Our model can be readily applied to existing within-host data, as demonstrated with application to HIV, HCV, and cancer dynamics.
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Affiliation(s)
- Matthew Hartfield
- Laboratoire MIVEGEC (UMR CNRS 5290, IRD 224, UM1, UM2), 911 avenue Agropolis, Montpellier, France
- * E-mail:
| | - Samuel Alizon
- Laboratoire MIVEGEC (UMR CNRS 5290, IRD 224, UM1, UM2), 911 avenue Agropolis, Montpellier, France
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27
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Kraemer SA, Kassen R. Patterns of Local Adaptation in Space and Time among Soil Bacteria. Am Nat 2015; 185:317-31. [DOI: 10.1086/679585] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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28
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Fox JW, Harder LD. Using a "time machine" to test for local adaptation of aquatic microbes to temporal and spatial environmental variation. Evolution 2014; 69:136-45. [PMID: 25308325 DOI: 10.1111/evo.12543] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2012] [Accepted: 09/10/2014] [Indexed: 11/30/2022]
Abstract
Local adaptation occurs when different environments are dominated by different specialist genotypes, each of which is relatively fit in its local conditions and relatively unfit under other conditions. Analogously, ecological species sorting occurs when different environments are dominated by different competing species, each of which is relatively fit in its local conditions. The simplest theory predicts that spatial, but not temporal, environmental variation selects for local adaptation (or generates species sorting), but this prediction is difficult to test. Although organisms can be reciprocally transplanted among sites, doing so among times seems implausible. Here, we describe a reciprocal transplant experiment testing for local adaptation or species sorting of lake bacteria in response to both temporal and spatial variation in water chemistry. The experiment used a -80°C freezer as a "time machine." Bacterial isolates and water samples were frozen for later use, allowing transplantation of older isolates "forward in time" and newer isolates "backward in time." Surprisingly, local maladaptation predominated over local adaptation in both space and time. Such local maladaptation may indicate that adaptation, or the analogous species sorting process, fails to keep pace with temporal fluctuations in water chemistry. This hypothesis could be tested with more finely resolved temporal data.
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Affiliation(s)
- Jeremy W Fox
- Department of Biological Sciences, University of Calgary, Calgary, AB T2N 1N4, Canada.
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29
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Lopez Pascua L, Hall AR, Best A, Morgan AD, Boots M, Buckling A. Higher resources decrease fluctuating selection during host-parasite coevolution. Ecol Lett 2014; 17:1380-8. [PMID: 25167763 PMCID: PMC4257576 DOI: 10.1111/ele.12337] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2014] [Revised: 05/29/2014] [Accepted: 07/15/2014] [Indexed: 01/20/2023]
Abstract
We still know very little about how the environment influences coevolutionary dynamics. Here, we investigated both theoretically and empirically how nutrient availability affects the relative extent of escalation of resistance and infectivity (arms race dynamic; ARD) and fluctuating selection (fluctuating selection dynamic; FSD) in experimentally coevolving populations of bacteria and viruses. By comparing interactions between clones of bacteria and viruses both within- and between-time points, we show that increasing nutrient availability resulted in coevolution shifting from FSD, with fluctuations in average infectivity and resistance ranges over time, to ARD. Our model shows that range fluctuations with lower nutrient availability can be explained both by elevated costs of resistance (a direct effect of nutrient availability), and reduced benefits of resistance when population sizes of hosts and parasites are lower (an indirect effect). Nutrient availability can therefore predictably and generally affect qualitative coevolutionary dynamics by both direct and indirect (mediated through ecological feedbacks) effects on costs of resistance.
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Affiliation(s)
- Laura Lopez Pascua
- Oxford Regional Molecular Genetics Laboratory, Oxford University Hospitals NHS Trust, Oxford, UK
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30
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Koskella B. Bacteria-phage interactions across time and space: merging local adaptation and time-shift experiments to understand phage evolution. Am Nat 2014; 184 Suppl 1:S9-21. [PMID: 25061680 DOI: 10.1086/676888] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The study of parasite local adaptation to host populations offers important insight into the spatial scale of host-parasite interactions. For parasites adapting to local hosts, the process is continually driven by change in the host population, in response to either the parasite or alternative selection pressures. In the case of reciprocal coevolutionary change, this adaptation should generate a pattern whereby parasites are most fit against hosts from the recent past (which have not yet responded to parasite-mediated selection) and least fit against future host populations (with increased resistance). I argue that combining data on local adaptation across space with data on evolutionary responses over time can offer novel insight into the process of adaptation. Using bacteriophages from horse chestnut trees, I compare infectivity on bacterial hosts isolated from either the same tree or different trees over multiple months of the growing season and find that phage adaptation to local hosts is most pronounced on bacterial hosts from the recent past. These results confirm that phages are well adapted to bacterial populations living within eukaryotes and more broadly suggest that local adaptation studies may underestimate the magnitude of parasite evolution, as host and parasite adaptation are confounded within contemporary time points.
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Affiliation(s)
- Britt Koskella
- BioSciences, University of Exeter, Penryn Campus, Tremough, Cornwall TR10 9EZ, United Kingdom
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31
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Betts A, Kaltz O, Hochberg ME. Contrasted coevolutionary dynamics between a bacterial pathogen and its bacteriophages. Proc Natl Acad Sci U S A 2014; 111:11109-14. [PMID: 25024215 PMCID: PMC4121802 DOI: 10.1073/pnas.1406763111] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Many antagonistic interactions between hosts and their parasites result in coevolution. Although coevolution can drive diversity and specificity within species, it is not known whether coevolutionary dynamics differ among functionally similar species. We present evidence of coevolution within simple communities of Pseudomonas aeruginosa PAO1 and a panel of bacteriophages. Pathogen identity affected coevolutionary dynamics. For five of six phages tested, time-shift assays revealed temporal peaks in bacterial resistance and phage infectivity, consistent with frequency-dependent selection (Red Queen dynamics). Two of the six phages also imposed additional directional selection, resulting in strongly increased resistance ranges over the entire length of the experiment (ca. 60 generations). Cross-resistance to these two phages was very high, independent of the coevolutionary history of the bacteria. We suggest that coevolutionary dynamics are associated with the nature of the receptor used by the phage for infection. Our results shed light on the coevolutionary process in simple communities and have practical application in the control of bacterial pathogens through the evolutionary training of phages, increasing their virulence and efficacy as therapeutics or disinfectants.
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Affiliation(s)
- Alex Betts
- Institut des Sciences de l'Evolution, Université Montpellier II, Unité Mixte de Recherche 5554, 34095 Montpellier Cedex 05, France;Department of Zoology, University of Oxford, Oxford OX1 3PS, United Kingdom
| | - Oliver Kaltz
- Institut des Sciences de l'Evolution, Université Montpellier II, Unité Mixte de Recherche 5554, 34095 Montpellier Cedex 05, France
| | - Michael E Hochberg
- Institut des Sciences de l'Evolution, Université Montpellier II, Unité Mixte de Recherche 5554, 34095 Montpellier Cedex 05, France;Santa Fe Institute, Santa Fe, NM 87501; andWissenschaftskolleg zu Berlin, 14193 Berlin, Germany
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Heath KD, Nuismer SL. Connecting functional and statistical definitions of genotype by genotype interactions in coevolutionary studies. Front Genet 2014; 5:77. [PMID: 24782890 PMCID: PMC3990044 DOI: 10.3389/fgene.2014.00077] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2014] [Accepted: 03/24/2014] [Indexed: 12/22/2022] Open
Abstract
Predicting how species interactions evolve requires that we understand the mechanistic basis of coevolution, and thus the functional genotype-by-genotype interactions (G × G) that drive reciprocal natural selection. Theory on host-parasite coevolution provides testable hypotheses for empiricists, but depends upon models of functional G × G that remain loosely tethered to the molecular details of any particular system. In practice, reciprocal cross-infection studies are often used to partition the variation in infection or fitness in a population that is attributable to G × G (statistical G × G). Here we use simulations to demonstrate that within-population statistical G × G likely tells us little about the existence of coevolution, its strength, or the genetic basis of functional G × G. Combined with studies of multiple populations or points in time, mapping and molecular techniques can bridge the gap between natural variation and mechanistic models of coevolution, while model-based statistics can formally confront coevolutionary models with cross-infection data. Together these approaches provide a robust framework for inferring the infection genetics underlying statistical G × G, helping unravel the genetic basis of coevolution.
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Affiliation(s)
- Katy D Heath
- Department of Plant Biology, University of Illinois Urbana, IL, USA
| | - Scott L Nuismer
- Department of Biological Sciences, University of Idaho Moscow, ID, USA
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Bustos-Segura C, Fornoni J, Núñez-Farfán J. Evolutionary changes in plant tolerance against herbivory through a resurrection experiment. J Evol Biol 2014; 27:488-96. [PMID: 24417372 DOI: 10.1111/jeb.12307] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2012] [Revised: 11/14/2013] [Accepted: 11/21/2013] [Indexed: 12/01/2022]
Abstract
Both theoretical and empirical works have highlighted the difference in the evolutionary implications of host resistance and tolerance against their enemies. However, it has been difficult to show evolutionary changes in host defences in natural populations; thus, evaluating theoretical predictions of simultaneous evolution of defences remains a challenge. We studied the evolutionary changes in traits related to resistance and tolerance against herbivory in a natural plant population using seeds from two collections made in a period of 20 years. In a common garden experiment, we compared defensive traits of ancestral (1987) and descendant (2007) subpopulations of the annual plant Datura stramonium that shows genetic variation for tolerance and to which the specialist herbivore Lema daturaphila is locally adapted. We also examined the effects of different plant genotypes on the herbivore for testing the plant genetic variation in resistance. Based on the response to the contemporary herbivore populations, results revealed a nonsignificant response in plant resistance traits (herbivore consumption, foliar trichomes and tropane alkaloids), but a significant one in tolerance. The survival of herbivores in laboratory experiments depended on the plant genotype, which suggests genetic variation in plant resistance. Although we cannot identify the selective agent for the change nor exclude genetic drift, the results are consistent with the expectation that when resistance fails to control herbivory, tolerance should play a more important role in the evolution of the interaction.
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Affiliation(s)
- C Bustos-Segura
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Distrito Federal, México
| | - J Fornoni
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Distrito Federal, México
| | - J Núñez-Farfán
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Distrito Federal, México
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34
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How does ecological disturbance influence genetic diversity? Trends Ecol Evol 2013; 28:670-9. [DOI: 10.1016/j.tree.2013.08.005] [Citation(s) in RCA: 161] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2013] [Revised: 08/14/2013] [Accepted: 08/28/2013] [Indexed: 11/21/2022]
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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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Koskella B. Phage-mediated selection on microbiota of a long-lived host. Curr Biol 2013; 23:1256-60. [PMID: 23810533 DOI: 10.1016/j.cub.2013.05.038] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2013] [Revised: 04/27/2013] [Accepted: 05/22/2013] [Indexed: 01/08/2023]
Abstract
It is increasingly apparent that the dynamic microbial communities of long-lived hosts affect their phenotype, including resistance to disease. The host microbiota will change over time due to immigration of new species, interaction with the host immune system, and selection by bacteriophage viruses (phages), but the relative roles of each process are unclear. Previous metagenomic approaches confirm the presence of phages infecting host microbiota, and experimental coevolution of bacteria and phage populations in the laboratory has demonstrated rapid reciprocal change over time. The key challenge is to determine whether phages influence host-associated bacterial communities in nature, in the face of other selection pressures. I use a tree-bacteria-phage system to measure reciprocal changes in phage infectivity and bacterial resistance within microbial communities of tree hosts over one season. An experimental time shift shows that bacterial isolates are most resistant to lytic phages from the prior month and least resistant to those from the future month, providing clear evidence for both phage-mediated selection on bacterial communities and bacterial-mediated selection on phage communities in nature. These reciprocal changes suggest that phages indeed play a key role in shaping the microbiota of their eukaryotic hosts.
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Affiliation(s)
- Britt Koskella
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Cornwall Campus, Penryn, Cornwall, TR10 9EZ, UK.
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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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