Most viruses can infect multiple hosts, yet the selective mechanisms that maintain multi-host generalists over single-host specialists remain an open question. Here we propagate populations of the newly identified bacteriophage øJB01 in coculture with many host genotypes and find that while phage can adapt to infect any of the new hosts, increasing the number of hosts slows the rate of adaptation. We quantify trade-offs in the capacity for individual phage to infect different hosts and find that phage from evolved populations with more hosts are more likely to be generalists. Sequencing of evolved phage reveals strong selection and the genetic basis of adaptation, supporting a model that shows how the addition of more potential hosts to a community can select for low-fitness generalists over high-fitness specialists. Our results show how evolution with multiple hosts alters the rate of viral adaptation and provides empirical support for an evolutionary mechanism that promotes generalists over specialists.
Subscribe to Journal
Get full journal access for 1 year
only $8.25 per issue
All prices are NET prices.
VAT will be added later in the checkout.
Rent or Buy article
Get time limited or full article access on ReadCube.
All prices are NET prices.
Koskella, B. & Brockhurst, M. A. Bacteria–phage coevolution as a driver of ecological and evolutionary processes in microbial communities. FEMS Microbiol. Rev. 38, 916–931 (2014).
Fernandez, L., Rodriguez, A. & Garcia, P. Phage or foe: an insight into the impact of viral predation on microbial communities. ISME J. 12, 1171–1179 (2018).
Zimmerman, A. E. et al. Metabolic and biogeochemical consequences of viral infection in aquatic ecosystems. Nat. Rev. Microbiol. 18, 21–34 (2020).
Gordillo Altamirano, F. L. & Barr, J. J. Phage therapy in the postantibiotic era. Clin. Microbiol. Rev. 32, e00066-18 (2019).
Flores, C. O., Valverde, S. & Weitz, J. S. Multi-scale structure and geographic drivers of cross-infection within marine bacteria and phages. ISME J. 7, 520–532 (2013).
Koskella, B. & Meaden, S. Understanding bacteriophage specificity in natural microbial communities. Viruses 5, 806–823 (2013).
Olival, K. J. et al. Host and viral traits predict zoonotic spillover from mammals. Nature 546, 646–650 (2017).
Law, R. Optimal life histories under age-specific predation. Am. Nat. 114, 399–417 (1979).
Williams, G. C. Natural selection, the costs of reproduction, and a refinement of Lack’s principle. Am. Nat. 100, 687–690 (1966).
Woolhouse, M. E., Taylor, L. H. & Haydon, D. T. Population biology of multihost pathogens. Science 292, 1109–1112 (2001).
MacLean, R. C., Bell, G. & Rainey, P. B. The evolution of a pleiotropic fitness tradeoff in Pseudomonas fluorescens. Proc. Natl Acad. Sci. USA 101, 8072–8077 (2004).
Zhong, S., Khodursky, A., Dykhuizen, D. E. & Dean, A. M. Evolutionary genomics of ecological specialization. Proc. Natl Acad. Sci. USA 101, 11719–11724 (2004).
Bennett, A. F. & Lenski, R. E. An experimental test of evolutionary trade-offs during temperature adaptation. Proc. Natl Acad. Sci. USA 104, 8649–8654 (2007).
Lee, M. C., Chou, H. H. & Marx, C. J. Asymmetric, bimodal trade-offs during adaptation of Methylobacterium to distinct growth substrates. Evolution 63, 2816–2830 (2009).
Bono, L. M., Smith, L. B. Jr., Pfennig, D. W. & Burch, C. L. The emergence of performance trade-offs during local adaptation: insights from experimental evolution. Mol. Ecol. 26, 1720–1733 (2017).
Duffy, S., Turner, P. E. & Burch, C. L. Pleiotropic costs of niche expansion in the RNA bacteriophage phi 6. Genetics 172, 751–757 (2006).
Duffy, S., Burch, C. L. & Turner, P. E. Evolution of host specificity drives reproductive isolation among RNA viruses. Evolution 61, 2614–2622 (2007).
Buckling, A. & Rainey, P. B. Antagonistic coevolution between a bacterium and a bacteriophage. Proc. Biol. Sci. 269, 931–936 (2002).
Burch, C. L. & Chao, L. Evolvability of an RNA virus is determined by its mutational neighbourhood. Nature 406, 625–628 (2000).
Crill, W. D., Wichman, H. A. & Bull, J. J. Evolutionary reversals during viral adaptation to alternating hosts. Genetics 154, 27–37 (2000).
Brockhurst, M. A., Buckling, A. & Rainey, P. B. The effect of a bacteriophage on diversification of the opportunistic bacterial pathogen, Pseudomonas aeruginosa. Proc. Biol. Sci. 272, 1385–1391 (2005).
Gomez, P. & Buckling, A. Bacteria–phage antagonistic coevolution in soil. Science 332, 106–109 (2011).
Paterson, S. et al. Antagonistic coevolution accelerates molecular evolution. Nature 464, 275–278 (2010).
Pal, C., Macia, M. D., Oliver, A., Schachar, I. & Buckling, A. Coevolution with viruses drives the evolution of bacterial mutation rates. Nature 450, 1079–1081 (2007).
Bono, L. M., Gensel, C. L., Pfennig, D. W. & Burch, C. L. Competition and the origins of novelty: experimental evolution of niche-width expansion in a virus. Biol. Lett. 9, 20120616 (2013).
Bono, L. M., Gensel, C. L., Pfennig, D. W. & Burch, C. L. Evolutionary rescue and the coexistence of generalist and specialist competitors: an experimental test. Proc. Biol. Sci. 282, 20151932 (2015).
Petrie, K. L. et al. Destabilizing mutations encode nongenetic variation that drives evolutionary innovation. Science 359, 1542–1545 (2018).
Dennehy, J. J., Friedenberg, N. A., Holt, R. D. & Turner, P. E. Viral ecology and the maintenance of novel host use. Am. Nat. 167, 429–439 (2006).
Heineman, R. H., Springman, R. & Bull, J. J. Optimal foraging by bacteriophages through host avoidance. Am. Nat. 171, E149–E157 (2008).
Jerison, E. R., Nguyen, Ba,A. N., Desai, M. M. & Kryazhimskiy, S. Chance and necessity in the pleiotropic consequences of adaptation for budding yeast. Nat. Ecol. Evol. 4, 601–611 (2020).
Remold, S. Understanding specialism when the jack of all trades can be the master of all. Proc. Biol. Sci. 279, 4861–4869 (2012).
Betts, A., Gray, C., Zelek, M., MacLean, R. C. & King, K. C. High parasite diversity accelerates host adaptation and diversification. Science 360, 907–911 (2018).
Betts, A., Rafaluk, C. & King, K. C. Host and parasite evolution in a tangled bank. Trends Parasitol. 32, 863–873 (2016).
Iguchi, A. et al. Complete genome sequence and comparative genome analysis of enteropathogenic Escherichia coli O127:H6 strain E2348/69. J. Bacteriol. 191, 347–354 (2009).
Scheuerl, T. et al. Bacterial adaptation is constrained in complex communities. Nat. Commun. 11, 754 (2020).
Lanfear, R., Kokko, H. & Eyre-Walker, A. Population size and the rate of evolution. Trends Ecol. Evol. 29, 33–41 (2014).
Li, Y., Petrov, D. A. & Sherlock, G. Single nucleotide mapping of trait space reveals Pareto fronts that constrain adaptation. Nat. Ecol. Evol. 3, 1539–155 (2019).
Bachmann, H. et al. Availability of public goods shapes the evolution of competing metabolic strategies. Proc. Natl Acad. Sci. USA 110, 14302–14307 (2013).
Keen, E. C. Tradeoffs in bacteriophage life histories. Bacteriophage 4, e28365 (2014).
Gonzalez-Garcia, V. A. et al. Conformational changes leading to T7 DNA delivery upon interaction with the bacterial receptor. J. Biol. Chem. 290, 10038–10044 (2015).
Holtzman, T. et al. A continuous evolution system for contracting the host range of bacteriophage T7. Sci. Rep. 10, 307 (2020).
McDonald, M. J. Microbial experimental evolution—a proving ground for evolutionary theory and a tool for discovery. EMBO Rep. 20, e46992 (2019).
Whitlock, M. C. The red queen beats the jack-of-all-trades: the limitations on the evolution of phenotypic plasticity and niche breadth. Am. Nat. 148, S65–S77 (1996).
Zhao, J. et al. Characterizing the biology of lytic bacteriophage vB_EaeM_phiEap-3 infecting multidrug-resistant Enterobacter aerogenes. Front. Microbiol. 10, 420 (2019).
Buttimer, C. et al. Pectobacterium atrosepticum phage vB_PatP_CB5: a member of the proposed genus ‘Phimunavirus’. Viruses 10, 394 (2018).
Van Twest, R. & Kropinski, A. M. Bacteriophage enrichment from water and soil. Methods Mol. Biol. 501, 15–21 (2009).
Bonilla, N. et al. Phage on tap—a quick and efficient protocol for the preparation of bacteriophage laboratory stocks. PeerJ 4, e2261 (2016).
Jakociune, D. & Moodley, A. A rapid bacteriophage DNA extraction method. Methods Protoc. 1, 27 (2018).
Wick, R. R., Judd, L. M., Gorrie, C. L. & Holt, K. E. Unicycler: resolving bacterial genome assemblies from short and long sequencing reads. PLoS Comput. Biol. 13, e1005595 (2017).
Deatherage, D. E. & Barrick, J. E. Identification of mutations in laboratory-evolved microbes from next-generation sequencing data using breseq. Methods Mol. Biol. 1151, 165–188 (2014).
Kumar, S., Stecher, G., Li, M., Knyaz, C. & Tamura, K. MEGA X: molecular evolutionary genetics analysis across computing platforms. Mol. Biol. Evol. 35, 1547–1549 (2018).
Stecher, G., Tamura, K. & Kumar, S. Molecular evolutionary genetics analysis (MEGA) for macOS. Mol. Biol. Evol. 37, 1237–1239 (2020).
Dereeper, A. et al. Phylogeny.fr: robust phylogenetic analysis for the non-specialist. Nucleic Acids Res. 36, W465–W469 (2008).
Guindon, S. et al. New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst. Biol. 59, 307–321 (2010).
Whelan, S. & Goldman, N. A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach. Mol. Biol. Evol. 18, 691–699 (2001).
M.J.M. was supported by ARC Discovery Grant (grant no. DP180102161) and ARC Future Fellowship (grant no. FT170100441).
The authors declare no competing interests.
Peer review information Nature Ecology & Evolution thanks Britt Koskella and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.
Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
The number of øJB01 plaque-forming units were monitored over a period of 90 min in coculture with exponential phase E. coli EPEC at MOI 0.1(A). The growth of E. coli EPEC was assayed using a plate reader. E. coli EPEC was propagated either in monoculture, or in coculture with phage øJB01 added at two different MOIs (1 and 0.1) (B). Error bars represent standard error of the mean (SEM) (n = 3).
Panels a-c correspond to three-host treatment (EPEC, MG1655, BL21). Panels d-f correspond to the three-host treatment (EPEC, MG1655, REPEC). Measurements of infectivity (PFU) for phage clones isolated from MG1655 (blue circles), EPEC (orange triangles), BL21(red squares) and REPEC (green diamonds). Filled markers show the measurements for phage clones obtained at the end point of the experiment (Day 10). Open markers show phage clones sampled at early timepoints (day 4 - day 9). Error bars are SEM, n = 3.
The amino acid sequence of Escherichia øJB01 phage, gp17 was aligned with homologous sequences from Escherichia phage N30 and T7 phage. Identical amino acids are marked with asterisks and non-identical are marked by dots. The gp17 conserved region is from position 1- 250 and the hypervariable region from 300–554.
Extended Data Fig. 4 Phylogenetic tree based on the gp17 sequences of 26 phage clones from the three-host treatment (EPEC, MG1655, REPEC).
Sequences were aligned with MUSCLE (v3.8.31) in MEGA X51,52. The phylogenetic tree was reconstructed using the maximum likelihood method as implemented in PhyML (v3.1/3.0)53,54. The WAG substitution model55 was selected assuming an estimated proportion of invariant sites (of 0.951) and 4 gamma-distributed rate categories to account for rate heterogeneity across sites. The gamma shape parameter was estimated directly from the data (gamma=91.073). Reliability of internal branches was assessed using the aLRT test (SH-Like). Final Log-Liklihood: −1839.18. Phage clones labelled by phenotype and day of generation. ‘S’ or ‘G’ refers to specialist or generalist according to phenotypic measurements (Figs. 3–4) and the number refers to the day of isolation. C8, D8, C9, D9, E8, F8 refer to the specific three-host experimental population from which the phage clone was isolated. Each phage clone was obtained by plating the whole population lysate onto an individual host (Figs. 3–4). The strain name refers to that host of isolation. For example, ‘G10 C8 MG1655’ refers to a phage clone with a generalist phenotype isolated from a day 10 population C8, isolated from a plaque on MG1655. Numbers on branches show bootstrapping support for that branch (percent, 100 bootstraps). Strains are clustered based on those clades with greater than 80% support. Dashed lines are for labels and are not part of the tree.
Supplementary Tables 1–7.
The genetic variants discovered in gp17 in all sequenced clones. For example, Day 4, Generalist, C8 REPEC is a clone that originated from Day 4 of the evolution experiment in the ‘C8’ replicate population within the three-host treatment with EPEC, MG1655 and REPEC. The clone itself was isolated as a plaque from a lawn of E. coli REPEC on an agar plate.
About this article
Cite this article
Sant, D.G., Woods, L.C., Barr, J.J. et al. Host diversity slows bacteriophage adaptation by selecting generalists over specialists. Nat Ecol Evol 5, 350–359 (2021). https://doi.org/10.1038/s41559-020-01364-1