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Ancient balancing selection on heterocyst function in a cosmopolitan cyanobacterium

Abstract

The conventional view of bacterial adaptation emphasizes the importance of rapidly evolved changes that are highly repeatable in response to similar environments and subject to loss in the absence of selection. Consequently, genetic variation is not expected to persist over long time scales for these organisms. Here, we show that a geographically widespread gene content polymorphism has surprisingly been maintained for tens of millions of years of diversification of the multicellular cyanobacterium Fischerella thermalis. The polymorphism affects gas permeability of the heterocyst—the oxygen-sensitive, nitrogen-fixing cell produced by these bacteria—and spatial variation in temperature favours alternative alleles due to thermodynamic effects on both heterocyst function and organism fitness at physiological temperature extremes. Whether or not ancient balancing selection plays a generally important role in the maintenance of microbial diversity remains to be investigated.

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Fig. 1: Genomic diversity and genetic differentiation of White Creek F. thermalis.
Fig. 2: Genes differentiated between upstream and downstream White Creek F. thermalis are distributed throughout the genome.
Fig. 3: Nitrogen-fixation activities of wild-type Anabaena PCC 7120 and HEP deletion mutant strains.
Fig. 4: Temperature dependence of F. thermalis physiological rates.
Fig. 5: The HEP deletion was a unique event that occurred early during F. thermalis diversification.
Fig. 6: Long-term balancing selection on the HEP indel polymorphism.

References

  1. Hedrick, P. W. Genetic polymorphism in heterogeneous environments: the age of genomics. Ann. Rev. Ecol. Evol. Syst. 37, 67–93 (2006).

    Article  Google Scholar 

  2. Castric, V. & Vekemans, X. Plant self-incompatibility in natural populations: a critical assessment of recent theoretical and empirical advances. Mol. Ecol. 13, 2873–2889 (2004).

    Article  CAS  PubMed  Google Scholar 

  3. Delph, L. & Kelly, J. On the importance of balancing selection in plants. New Phytol. 201, 45–56 (2014).

    Article  PubMed  Google Scholar 

  4. Wu, J., Saupe, S. J. & Glass, N. L. Evidence for balancing selection operating at the het-c heterokaryon incompatibility locus in a group of filamentous fungi. Proc. Natl. Acad. Sci. USA 95, 12398–12403 (1998).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  5. Klein, J., Satta, Y., O’hUigin, C. & Takahata, N. The molecular descent of the major histocompatibility complex. Annu. Rev. Immunol. 11, 269–295 (1993).

    Article  CAS  PubMed  Google Scholar 

  6. Ségurel, L. et al. The ABO blood group is a trans-species polymorphism in primates. Proc. Natl Acad. Sci. USA 109, 18493–18498 (2012).

    Article  PubMed  PubMed Central  Google Scholar 

  7. Leffler, E. et al. Multiple instances of ancient balancing selection shared between humans and chimpanzees. Science 339, 1578–1582 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Stahl, E., Dwyer, G., Mauricio, R. & Kreitman, M. Dynamics of disease resistance polymorphism at the Rpm1 locus of Arabidopsis. Nature 400, 667–671 (1999).

    Article  CAS  PubMed  Google Scholar 

  9. Elena, S. F. & Lenski, R. E. Evolution experiments with microorganisms: the dynamics and genetic bases of adaptation. Nat. Rev. Genet. 4, 457–469 (2003).

    Article  CAS  PubMed  Google Scholar 

  10. Koskella, B. & Vos, M. Adaptation in natural microbial populations. Ann. Rev. Ecol. Evol. Syst. 46, 503–522 (2015).

    Article  Google Scholar 

  11. Andersson, D. I. & Hughes, D. Gene amplification and adaptive evolution in bacteria. Annu. Rev. Genet. 43, 167–195 (2009).

    Article  CAS  PubMed  Google Scholar 

  12. Lee, M.-C. & Marx, C. J. Repeated, selection-driven genome reduction of accessory genes in experimental populations. PLoS Genet. 8, e1002651 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  13. Laehnemann, D. et al. Genomics of rapid adaptation to antibiotics: convergent evolution and scalable sequence amplification. Genome Biol. Evol. 6, 1287–1301 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  14. Tenaillon, O. et al. The molecular diversity of adaptive convergence. Science 335, 457–461 (2012).

    Article  CAS  PubMed  Google Scholar 

  15. Lieberman, T. D. et al. Parallel bacterial evolution within multiple patients identifies candidate pathogenicity genes. Nat. Genet. 43, 1275–1280 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  16. Roumagnac, P., Weill, F., Dolecek, C., Baker, S. & Brisse, S. Evolutionary history of Salmonella typhi. Science 314, 1301–1304 (2006).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Croucher, N., Harris, S., Fraser, C. & Quail, M. Rapid pneumococcal evolution in response to clinical interventions. Science 331, 430–434 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. Kos, N. V. et al. Comparative genomics of vancomycin-resistant Staphylococcus aureus strains and their positions within the clade most commonly associated with methicillin-resistant S. aureus hospital-acquired infection in the United States. mBio 3, e00112-12 (2012).

    Article  PubMed  PubMed Central  Google Scholar 

  19. Thomas, J. C., Godfrey, P. A., Feldgarden, M. & Robinson, D. A. Candidate targets of balancing selection in the genome of Staphylococcus aureus. Mol. Biol. Evol. 29, 1175–1186 (2012).

    Article  CAS  PubMed  Google Scholar 

  20. Seifert, S. N., Khatchikian, C. E., Zhou, W. & Brisson, D. Evolution and population genomics of the Lyme borreliosis pathogen, Borrelia burgdorferi. Trends Genet. 31, 201–207 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  21. Jacquot, M. et al. Comparative population genomics of the Borrelia burgdorferi species complex reveals high degree of genetic isolation among species and underscores benefits and constraints to studying intra-specific epidemiological processes. PLoS ONE 9, e94384 (2014).

    Article  PubMed  PubMed Central  Google Scholar 

  22. Haven, J. et al. Pervasive recombination and sympatric genome diversification driven by frequency-dependent selection in Borrelia burgdorferi, the Lyme disease bacterium. Genetics 189, 951–966 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  23. Kashtan, N. et al. Single-cell genomics reveals hundreds of coexisting subpopulations in wild Prochlorococcus. Science 344, 416–420 (2014).

    Article  CAS  PubMed  Google Scholar 

  24. Shapiro, B. J. et al. Population genomics of early events in the ecological differentiation of bacteria. Science 336, 48–51 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  25. Cordero, O. X. & Polz, M. F. Explaining microbial genomic diversity in light of evolutionary ecology. Nat. Rev. Microbiol. 12, 263–273 (2014).

    Article  CAS  PubMed  Google Scholar 

  26. Rodriguez-Valera, F. et al. Explaining microbial population genomics through phage predation. Nat. Rev. Microbiol. 7, 828–836 (2009).

    Article  CAS  PubMed  Google Scholar 

  27. Miller, S. R., Williams, C., Strong, A. L. & Carvey, D. Ecological specialization in a spatially structured population of the thermophilic cyanobacterium Mastigocladus laminosus. Appl. Environ. Microbiol. 75, 729–734 (2009).

    Article  CAS  PubMed  Google Scholar 

  28. Wall, C. A., Koniges, G. J. & Miller, S. R. Divergence with gene flow in a population of thermophilic bacteria: a potential role for spatially varying selection. Mol. Ecol. 23, 3371–3383 (2014).

    Article  PubMed  Google Scholar 

  29. Hudson, R. R. & Kaplan, N. L. Statistical properties of the number of recombination events in the history of a sample of DNA sequences. Genetics 111, 147–164 (1985).

    CAS  PubMed  PubMed Central  Google Scholar 

  30. Barton, N. Clines in polygenic traits. Genet. Res. 74, 223–236 (1999).

    Article  CAS  PubMed  Google Scholar 

  31. Miller, S. R., Purugganan, M. D. & Curtis, S. E. Molecular population genetics and phenotypic diversification of two populations of the thermophilic cyanobacterium Mastigocladus laminosus. Appl. Environ. Microbiol. 72, 2793–2800 (2006).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  32. Kumar, K., Mella-Herrera, R. A. & Golden, J. W. Cyanobacterial heterocysts. Cold Spring Harb. Perspect. Biol. 2, a000315 (2010).

    Article  PubMed  PubMed Central  Google Scholar 

  33. Staal, M., Metsman, F. J. R. & Stal, L. J. Temperature excludes N2-fixing heterocystous cyanobacteria in the tropical oceans. Nature 425, 504–507 (2003).

    Article  CAS  PubMed  Google Scholar 

  34. Walsby, A. The permeability of heterocysts to the gases nitrogen and oxygen. Proc. R. Soc. Lond. B 226, 345–366 (1985).

    Article  CAS  Google Scholar 

  35. Stal, L. J. Is the distribution of nitrogen‐fixing cyanobacteria in the oceans related to temperature? Environ. Microbiol. 11, 1632–1645 (2009).

    Article  CAS  PubMed  Google Scholar 

  36. Flaherty, B. L., van Nieuwerburgh, F. V., Head, S. R. & Golden, J. W. Directional RNA deep sequencing sheds new light on the transcriptional response of Anabaena sp. strain PCC 7120 to combined-nitrogen deprivation. BMC Genom. 12, 332 (2011).

    Article  CAS  Google Scholar 

  37. Huang, G. et al. Clustered genes required for the synthesis of heterocyst envelope polysaccharide in Anabaena sp. strain PCC 7120. J. Bacteriol. 187, 1114–1123 (2005).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  38. Miller, S. R., Castenholz, R. W. & Pedersen, D. Phylogeography of the thermophilic cyanobacterium Mastigocladus laminosus. Appl. Environ. Microbiol. 73, 4751–4759 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  39. Stewart, W. D. P. Nitrogen fixation by blue-green algae in Yellowstone thermal areas. Phycologia 9, 261–268 (1970).

    Article  CAS  Google Scholar 

  40. Kishino, H., Thorne, J. L. & Bruno, W. J. Performance of a divergence time estimation method under a probabilistic model of rate evolution. Mol. Biol. Evol. 18, 352–361 (2001).

    Article  CAS  PubMed  Google Scholar 

  41. Yang, Z. & Rannala, B. Bayesian estimation of species divergence times under a molecular clock using multiple fossil calibrations with soft bounds. Mol. Biol. Evol. 23, 212–226 (2005).

    Article  PubMed  Google Scholar 

  42. Schierup, M. H. & Hein, J. Consequences of recombination on traditional phylogenetic analysis. Genetics 156, 879–891 (2000).

    CAS  PubMed  PubMed Central  Google Scholar 

  43. Schirrmeister, B. E., Gugger, M. & Donoghue, P. C. J. Cyanobacteria and the Great Oxidation Event: evidence from genes and fossils. Palaeontology 58, 769–785 (2015).

    Article  PubMed  PubMed Central  Google Scholar 

  44. Tajima, F. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123, 585–595 (1989).

    CAS  PubMed  PubMed Central  Google Scholar 

  45. Hudson, R. R. & Kaplan, N. L. The coalescent process in models with selection and recombination. Genetics 120, 831–840 (1988).

    CAS  PubMed  PubMed Central  Google Scholar 

  46. Charlesworth, D. Balancing selection and its effects on sequences in nearby genome regions. PLoS Genet. 2, e64 (2006).

    Article  PubMed  PubMed Central  Google Scholar 

  47. Barroso-Batista, J. et al. The first steps of adaptation of Escherichia coli to the gut are dominated by soft sweeps. PLoS Genet. 10, e1004182 (2014).

    Article  PubMed  PubMed Central  Google Scholar 

  48. Inskeep, W. P. et al. The YNP metagenome project: environmental parameters responsible for microbial distribution in the Yellowstone geothermal ecosystem. Front. Microbiol. 4, 67 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  49. Bolger, A. M., Lohse, M. & Usadel, B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30, 2114–2120 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  50. Zerbino, D. R. & Birney, E. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res. 18, 821–829 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  51. Nei, M. Evolution of human races at the gene level. Prog. Clin. Biol. Res. 103, 167–181 (1982).

    PubMed  Google Scholar 

  52. Jukes, T. H. & Cantor, C. R. in Mammalian Protein Metabolism (ed. Munro, H. N.) 21–132 (Academic Press, New York, 1969).

  53. Dagan, T. et al. Genomes of stigonematalean cyanobacteria (subsection V) and the evolution of oxygenic photosynthesis from prokaryotes to plastids. Genome Biol. Evol. 5, 31–44 (2013).

    Article  PubMed  Google Scholar 

  54. Whitlock, M. C. & Lotterhos, K. E. Reliable detection of loci responsible for local adaptation: inference of a null model through trimming the distribution of F ST. Am. Nat. 186, S24–S36 (2015).

    Article  PubMed  Google Scholar 

  55. Grissa, I., Vergnaud, G. & Pourcel, C. CRISPRFinder: a web tool to identify clustered regularly interspaced short palindromic repeats. Nucleic Acids Res. 35, W52–W57 (2007).

    Article  PubMed  PubMed Central  Google Scholar 

  56. Black, T. A., Cai, Y. & Wolk, C. P. Spatial expression and autoregulation of hetR, a gene involved in the control of heterocyst development in Anabaena. Mol. Microbiol. 9, 77–84 (1993).

    Article  CAS  PubMed  Google Scholar 

  57. Cai, Y. P. & Wolk, C. P. Use of a conditionally lethal gene in Anabaena sp. strain PCC 7120 to select for double recombinants and to entrap insertion sequences. J. Bacteriol. 172, 3138–3145 (1990).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  58. Elhai, J. & Wolk, C. P. Conjugal transfer of DNA to cyanobacteria. Methods Enzymol. 167, 747–754 (1988).

    Article  CAS  PubMed  Google Scholar 

  59. Liang, J., Scappino, L. & Haselkorn, R. The patB gene product, required for growth of the cyanobacterium Anabaena sp. strain PCC 7120 under nitrogen-limiting conditions, contains ferredoxin and helix-turn-helix domains. J. Bacteriol. 175, 1697–1704 (1993).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  60. Meeks, J. C., Wycoff, K. L., Chapman, J. S. & Enderlin, C. S. Regulation of expression of nitrate and dinitrogen assimilation by Anabaena species. Appl. Environ. Microbiol. 45, 1351–1359 (1983).

    CAS  PubMed  PubMed Central  Google Scholar 

  61. Stewart, W. D. P., Fitzgerald, G. P. & Burris, R. H. In situ studies on N2 fixation using the acetylene reduction technique. Proc. Natl Acad. Sci. USA 58, 2071–2078 (1967).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  62. Miller, S. R., Wingard, C. E. & Castenholz, R. W. Effects of visible light and UV radiation on photosynthesis in a population of a hot spring cyanobacterium, a Synechococcus sp., subjected to high-temperature stress. Appl. Environ. Microbiol. 64, 3893–3899 (1998).

    CAS  PubMed  PubMed Central  Google Scholar 

  63. Nguyen, L.-T., Schmidt, H. A., von Haeseler, A. & Minh, B. Q. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol. Biol. Evol. 32, 268–274 (2014).

    Article  PubMed  PubMed Central  Google Scholar 

  64. Salichos, L., Stamatakis, A. & Rokas, A. Novel information theory-based measures for quantifying incongruence among phylogenetic trees. Mol. Biol. Evol. 31, 1261–1271 (2014).

    Article  CAS  PubMed  Google Scholar 

  65. Salichos, L. & Rokas, A. Inferring ancient divergences requires genes with strong phylogenetic signals. Nature 497, 327–331 (2013).

    Article  CAS  PubMed  Google Scholar 

  66. Stamatakis, A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30, 1312–1313 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  67. Kobert, K., Salichos, L., Rokas, A. & Stamatakis, A. Computing the internode certainty and related measures from partial gene trees. Mol. Biol. Evol. 33, 1606–1617 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  68. Le, S. Q. & Gascuel, O. An improved general amino acid replacement matrix. Mol. Biol. Evol. 25, 1307–1320 (2008).

    Article  CAS  PubMed  Google Scholar 

  69. Wang, H.-C., Minh, B. Q., Susko, E. & Roger, A. J. Modeling site heterogeneity with posterior mean site frequency profiles accelerates accurate phylogenomic estimation. Syst. Biol. https://doi.org/10.1093/sysbio/syx068 (2017).

    Google Scholar 

  70. Lartillot, N., Lepage, T. & Blanquart, S. PhyloBayes 3: a Bayesian software package for phylogenetic reconstruction and molecular dating. Bioinformatics 25, 2286–2288 (2009).

    Article  CAS  PubMed  Google Scholar 

  71. Drummond, A. J., Ho, S. Y. W., Phillips, M. J. & Rambaut, A. Relaxed phylogenetics and dating with confidence. PLoS Biol. 4, e88 (2006).

    Article  PubMed  PubMed Central  Google Scholar 

  72. Lepage, T., Bryant, D., Philippe, H. & Lartillot, N. A general comparison of relaxed molecular clock models. Mol. Biol. Evol. 24, 2669–2680 (2007).

    Article  CAS  PubMed  Google Scholar 

  73. Thorne, J. L., Kishino, H. & Painter, I. S. Estimating the rate of evolution of the rate of molecular evolution. Mol. Biol. Evol. 15, 1647–1657 (1998).

    Article  CAS  PubMed  Google Scholar 

  74. Sánchez-Baracaldo, P., Ridgwell, A. & Raven, J. A. A neoproterozoic transition in the marine nitrogen cycle. Curr. Biol. 24, 652–657 (2014).

    Article  PubMed  Google Scholar 

  75. Tomitani, A., Knoll, A. H., Cavanaugh, C. M. & Ohno, T. The evolutionary diversification of cyanobacteria: molecular-phylogenetic and paleontological perspectives. Proc. Natl Acad. Sci. USA 103, 5442–5447 (2006).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  76. Croft, W. N. & George, E. A. Blue-green algae from the Middle Devonian of Rhynie, Aberdeenshire. Bull. Br. Mus. Nat. Hist. Geol. 3, 339–353 (1959).

    Google Scholar 

  77. Sims, P. A., Mann, D. G. & Medlin, L. K. Evolution of the diatoms: insights from fossil, biological and molecular data. Phycologia 45, 361–402 (2006).

    Article  Google Scholar 

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Acknowledgements

We thank the Cory Cleveland laboratory group for use of their gas chromatograph, J. Meeks and his laboratory group for strains and technical advice, and J. Driver at the University of Montana EMtrix electron microscopy facility. We also thank D. Vanderpool for advice and sharing custom Python scripts used in the phylogenomics analyses. We are grateful to L. Fishman, J. McCutcheon, M. Polz, F. Rosenzweig and A. Woods for reading and commenting on earlier versions of the manuscript. Field work was conducted under National Park Service research permit YELL-5482. This work was supported by US National Science Foundation award IOS-1110819 and by NASA Astrobiology Institute award NNA15BB04A to S.R.M.

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S.R.M. conceived the study. C.A.W., E.B.S. and S.R.M. performed the genome sequencing, assembly and annotation. P.R.H. assayed nitrogen fixation by F. thermalis in the laboratory and field. E.B.S. constructed the Anabaena mutant strains and conducted physiological assays of Anabaena strains. E.B.S. measured the oxygen concentration at White Creek. S.R.M. performed the population genomic, phylogenomic and molecular clock dating analyses. S.R.M. and E.B.S. wrote the manuscript. All authors read and commented on the manuscript.

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Correspondence to Scott R. Miller.

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Sano, E.B., Wall, C.A., Hutchins, P.R. et al. Ancient balancing selection on heterocyst function in a cosmopolitan cyanobacterium. Nat Ecol Evol 2, 510–519 (2018). https://doi.org/10.1038/s41559-017-0435-9

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