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Parallel genome reduction in symbionts descended from closely related free-living bacteria

A Publisher Correction to this article was published on 27 February 2018

This article has been updated

Abstract

Endosymbiosis plays an important role in ecology and evolution, but fundamental aspects of the origin of intracellular symbionts remain unclear. The extreme age of many symbiotic relationships, lack of data on free-living ancestors and uniqueness of each event hinder investigations. Here, we describe multiple strains of the bacterium Polynucleobacter that evolved independently and under similar conditions from closely related, free-living ancestors to become obligate endosymbionts of closely related ciliate hosts. As these genomes reduced in parallel from similar starting states, they provide unique glimpses into the mechanisms underlying genome reduction in symbionts. We found that gene loss is contingently lineage-specific, with no evidence for ordered streamlining. However, some genes in otherwise disrupted pathways are retained, possibly reflecting cryptic genetic network complexity. We also measured substitution rates between many endosymbiotic and free-living pairs for hundreds of genes, which showed that genetic drift, and not mutation pressure, is the main non-selective factor driving molecular evolution in endosymbionts.

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Figure 1: Genomic reduction in symbiotic Polynucleobacter strains.
Figure 2: Phylogenomic tree of symbiotic and free-living Polynucleobacter.
Figure 3: Protein-coding genes shared by symbiotic Polynucleobacter strains.
Figure 4: Examples of within-module gene losses in symbiotic Polynucleobacter.
Figure 5: Pairwise comparisons of dS and dN/dS values.

Change history

  • 27 February 2018

    The Supplementary Information file originally published with this Article was missing Supplementary Figs 1–7. This has now been corrected.

References

  1. 1.

    Jezberová, J. et al. Ubiquity of Polynucleobacter necessarius ssp. asymbioticus in lentic freshwater habitats of a heterogeneous 2000 km2 area. Environ. Microbiol. 12, 658–669 (2010).

    Article  PubMed  Google Scholar 

  2. 2.

    Hahn, M. W. et al. The passive yet successful way of planktonic life: genomic and experimental analysis of the ecology of a free-living Polynucleobacter population. PLoS ONE 7, e32772 (2012).

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  3. 3.

    Hahn, M. W., Jezberová, J., Koll, U., Saueressig-Beck, T. & Schmidt, J. Complete ecological isolation and cryptic diversity in Polynucleobacter bacteria not resolved by 16S rRNA gene sequences. ISME J. 10, 1642–1655 (2016).

    Article  PubMed  PubMed Central  Google Scholar 

  4. 4.

    Heckmann, K. & Schmidt, H. J. Polynucleobacter necessarius gen. nov., sp. nov., an obligately endosymbiotic bacterium living in the cytoplasm of Euplotes aediculatus. Int. J. Syst. Bacteriol. 37, 456–457 (1987).

    Article  Google Scholar 

  5. 5.

    Heckmann, K., Ten Hagen, R. & Görtz, H.-D. Freshwater Euplotes species with a 9 type 1 cirrus pattern depend upon endosymbionts. J. Protozool. 30, 284–289 (1983).

    Article  Google Scholar 

  6. 6.

    Vannini, C., Petroni, G., Verni, F. & Rosati, G. Polynucleobacter bacteria in the brackish-water species Euplotes harpa (Ciliata Hypotrichia). J. Eukaryot. Microbiol. 52, 116–122 (2005).

    CAS  Article  PubMed  Google Scholar 

  7. 7.

    Vannini, C. et al. Endosymbiosis in statu nascendi: close phylogenetic relationship between obligately endosymbiotic and obligately free-living Polynucleobacter strains (Betaproteobacteria). Environ. Microbiol. 9, 347–359 (2007).

    CAS  Article  PubMed  Google Scholar 

  8. 8.

    Hahn, M. W., Schmidt, J., Pitt, A., Taipale, S. J. & Lang, E. Reclassification of four Polynucleobacter necessarius strains as Polynucleobacter asymbioticus comb. nov., Polynucleobacter duraquae sp. nov., Polynucleobacter yangtzensis sp. nov., and Polynucleobacter sinensis sp. nov., and emended description of the species Polynucleobacter necessarius. Int. J. Syst. Evol. Microbiol. 66, 2883–2892 (2016).

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  9. 9.

    Vannini, C., Ferrantini, F., Ristori, A., Verni, F. & Petroni, G. Betaproteobacterial symbionts of the ciliate Euplotes: origin and tangled evolutionary path of an obligate microbial association. Environ. Microbiol. 14, 2553–2563 (2012).

    Article  PubMed  Google Scholar 

  10. 10.

    Gil, R. et al. The genome sequence of Blochmannia floridanus: comparative analysis of reduced genomes. Proc. Natl Acad. Sci. USA 100, 9388–9393 (2003).

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  11. 11.

    Rio, R. V. M., Lefevre, C., Heddi, A. & Aksoy, S. Comparative genomics of insect-symbiotic bacteria: influence of host environment on microbial genome composition. Appl. Environ. Microbiol. 69, 6825–6832 (2003).

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  12. 12.

    Moran, N. A. Accelerated evolution and Muller’s rachet in endosymbiotic bacteria. Proc. Natl Acad. Sci. USA 93, 2873–2878 (1996).

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  13. 13.

    Lamelas, A. et al. Serratia symbiotica from the aphid Cinara cedri: a missing link from facultative to obligate insect endosymbiont. PLoS Genet. 7, e1002357 (2011).

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  14. 14.

    Oakeson, K. F. et al. Genome degeneration and adaptation in a nascent stage of symbiosis. Genome Biol. Evol. 6, 76–93 (2014).

    Article  PubMed  PubMed Central  Google Scholar 

  15. 15.

    Gould, S. J. Wonderful Life (W. W. Norton & Co., New York, 1989).

  16. 16.

    Wernegreen, J. J., Richardson, A. O. & Moran, N. A. Parallel acceleration of evolutionary rates in symbiont genes underlying host nutrition. Mol. Phylogenet. Evol. 19, 479–485 (2001).

    CAS  Article  PubMed  Google Scholar 

  17. 17.

    O’Fallon, B. Population structure, levels of selection, and the evolution of intracellular symbionts. Evolution 62, 361–373 (2008).

    Article  PubMed  Google Scholar 

  18. 18.

    Pettersson, M. E. & Berg, O. G. Muller’s ratchet in symbiont populations. Genetica 130, 199–211 (2007).

    Article  PubMed  Google Scholar 

  19. 19.

    Moran, N. A., McLaughlin, H. J. & Sorek, R. The dynamics and time scale of ongoing genomic erosion in symbiotic bacteria. Science 323, 379–382 (2009).

    CAS  Article  PubMed  Google Scholar 

  20. 20.

    McCutcheon, J. P. & Moran, N. A. Extreme genome reduction in symbiotic bacteria. Nat. Rev. Microbiol. 10, 13–26 (2012).

    CAS  Article  Google Scholar 

  21. 21.

    Burke, G. R. & Moran, N. A. Massive genomic decay in Serratia symbiotica, a recently evolved symbiont of aphids. Genome Biol. Evol. 3, 195–208 (2011).

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  22. 22.

    Clayton, A. L., Jackson, D. G., Weiss, R. B. & Dale, C. Adaptation by deletogenic replication slippage in a nascent symbiont. Mol. Biol. Evol. 33, 1957–1966 (2016).

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  23. 23.

    Husnik, F. & McCutcheon, J. P. Repeated replacement of an intrabacterial symbiont in the tripartite nested mealybug symbiosis. Proc. Natl Acad. Sci. USA 113, E5416–E5424 (2016).

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  24. 24.

    Wernegreen, J. J. & Moran, N. A. Evidence for genetic drift in endosymbionts (Buchnera): analyses of protein-coding genes. Mol. Biol. Evol. 16, 83–87 (1999).

    CAS  Article  PubMed  Google Scholar 

  25. 25.

    Itoh, T., Martin, W. & Nei, M. Acceleration of genomic evolution caused by enhanced mutation rate in endocellular symbionts. Proc. Natl Acad. Sci. USA 99, 12944–12948 (2002).

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  26. 26.

    Nei, M. Selectionism and neutralism in molecular evolution. Mol. Biol. Evol. 22, 2318–2342 (2005).

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  27. 27.

    Boscaro, V. et al. Polynucleobacter necessarius, a model for genome reduction in both free-living and symbiotic bacteria. Proc. Natl Acad. Sci. USA 110, 18590–18595 (2013).

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  28. 28.

    Hao, Z. et al. Genome sequence of a freshwater low-nucleic-acid-content bacterium, betaproteobacterium strain CB. Genome Announc. 1, e0013513 (2013).

    Article  PubMed  Google Scholar 

  29. 29.

    Syberg-Olsen, M. J. et al. Biogeography and character evolution of the ciliate genus Euplotes (Spirotrichea, Euplotia), with description of Euplotes curdsi sp. nov. PLoS ONE 11, e0165442 (2016).

    Article  PubMed  PubMed Central  Google Scholar 

  30. 30.

    Manzano-Marín, A. & Latorre, A. Settling down: the genome of Serratia symbiotica from the aphid Cinara tujafina zooms in on the process of accommodation to a cooperative intracellular life. Genome Biol. Evol. 6, 1683–1698 (2014).

    Article  PubMed  PubMed Central  Google Scholar 

  31. 31.

    Hoetzinger, M., Schmidt, J., Jezberová, J., Koll, U. & Hahn, M. W. Microdiversification of a pelagic Polynucleobacter species is mainly driven by acquisition of genomic islands from a partially interspecific gene pool. Appl. Environ. Microbiol. 83, e02266-16 (2017).

  32. 32.

    Moran, N. A., McCutcheon, J. P. & Nakabachi, A. Genomics and evolution of heritable bacterial symbionts. Annu. Rev. Genet. 42, 165–190 (2008).

    CAS  Article  PubMed  Google Scholar 

  33. 33.

    Clayton, A. L. et al. A novel human-infection-derived bacterium provides insights into the evolutionary origins of mutualistic insect-bacterial symbioses. PLoS Genet. 8, e1002990 (2012).

  34. 34.

    Bennett, G. M., McCutcheon, J. P., McDonald, B. R. & Moran, N. A. Lineage-specific patterns of genome deterioration in obligate symbionts of sharpshooter leafhoppers. Genome Biol. Evol. 8, 296–301 (2016).

    CAS  Article  Google Scholar 

  35. 35.

    Andersson, J. O. & Andersson, S. G. E. Insights into the evolutionary process of genome degradation. Curr. Opin. Genet. Dev. 9, 664–671 (1999).

    CAS  Article  PubMed  Google Scholar 

  36. 36.

    Nilsson, A. I. et al. Bacterial genome size reduction by experimental evolution. Proc. Natl Acad. Sci. USA 102, 12112–12116 (2005).

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  37. 37.

    Hershberg, R., Tang, H. & Petrov, D. A. Reduced selection leads to accelerated gene loss in Shigella. Genome Biol. 8, R164 (2007).

  38. 38.

    McCutcheon, J. P. & von Dohlen, C. D. An interdependent metabolic patchwork in the nested symbiosis of mealybugs. Curr. Biol. 21, 1366–1372 (2011).

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  39. 39.

    Ghignone, S. et al. The genome of the obligate endobacterium of the AM fungus reveals an interphylum network of nutritional interactions. ISME J. 6, 136–145 (2012).

    CAS  Article  PubMed  Google Scholar 

  40. 40.

    Nakabachi, A. et al. The 160-kilobase genome of the bacterial endosymbiont Carsonella. Science 314, 267 (2006).

    CAS  Article  PubMed  Google Scholar 

  41. 41.

    Smith, W. A. et al. Phylogenetic analysis of symbionts in feather-feeding lice of the genus Columbicola: evidence for repeated symbiont replacements. BMC Evol. Biol. 13, 109 (2013).

    Article  PubMed  PubMed Central  Google Scholar 

  42. 42.

    Rosati, G., Modeo, L., Melai, M., Petroni, G. & Verni, F. A multidisciplinary approach to describe protists: a morphological, ultrastructural, and molecular study on Peritromus kahli Villeneuve-Brachon, 1940 (Ciliophora, Heterotrichea). J. Eukaryot. Microbiol. 51, 49–59 (2004).

    Article  PubMed  Google Scholar 

  43. 43.

    Katoh, K. & Standley, D. M. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol. Biol. Evol. 30, 772–780 (2013).

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  44. 44.

    Capella-Gutiérrez, S., Silla-Martínez, J. M. & Gabaldón, T. trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics 25, 1972–1973 (2009).

    Article  PubMed  PubMed Central  Google Scholar 

  45. 45.

    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 (2015).

    CAS  Article  PubMed  Google Scholar 

  46. 46.

    Ronquist, F. et al. MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space. Syst. Biol. 61, 539–542 (2012).

    Article  PubMed  PubMed Central  Google Scholar 

  47. 47.

    Prescott, D. M. Evolution of DNA organization in hypotrichous ciliates. Ann. NY Acad. Sci. 870, 301–313 (1999).

    CAS  Article  PubMed  Google Scholar 

  48. 48.

    Tritt, A., Eisen, J. A., Facciotti, M. T. & Darling, A. E. An integrated pipeline for de novo assembly of microbial genomes. PLoS ONE 7, e42304 (2012).

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  49. 49.

    Aziz, R. K. et al. The RAST server: rapid annotations using subsystems technology. BMC Genomics 9, 75 (2008).

    Article  PubMed  PubMed Central  Google Scholar 

  50. 50.

    Emms, D. M. & Kelly, S. OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthogroup inference accuracy. Genome Biol. 16, 157 (2015).

    Article  PubMed  PubMed Central  Google Scholar 

  51. 51.

    Garcia, S. L. et al. Metabolic potential of a single cell belonging to one of the most abundant lineages in freshwater bacterioplankton. ISME J. 7, 137–147 (2013).

    CAS  Article  PubMed  Google Scholar 

  52. 52.

    Tatusova, T., Ciufo, S., Fedorov, B., O’Neill, K. & Tolstoy, I. RefSeq microbial genomes database: new representation and annotation strategy. Nucleic Acids Res. 42, D553–D559 (2014).

    CAS  Article  PubMed  Google Scholar 

  53. 53.

    Criscuolo, A. & Gribaldo, S. BMGE (block mapping and gathering with entropy): a new software for selection of phylogenetic informative regions from multiple sequence alignments. BMC Evol. Biol. 10, 210 (2010).

    Article  PubMed  PubMed Central  Google Scholar 

  54. 54.

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

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  55. 55.

    Le, S. Q., Dang, C. C. & Gascuel, O. Modeling protein evolution with several amino acid replacement matrices depending on site rates. Mol. Biol. Evol. 29, 2921–2936 (2012).

    CAS  Article  PubMed  Google Scholar 

  56. 56.

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

    CAS  Article  PubMed  Google Scholar 

  57. 57.

    Le, S. Q., Gascuel, O. & Lartillot, N. Empirical profile mixture models for phylogenetic reconstruction. Bioinformatics 24, 2317–2323 (2008).

    Article  Google Scholar 

  58. 58.

    Lartillot, N. & Philippe, H. A Bayesian mixture model for across-site heterogeneities in the amino-acid replacement process. Mol. Biol. Evol. 21, 1095–1109 (2004).

    CAS  Article  PubMed  Google Scholar 

  59. 59.

    Yang, Z. PAML4: phylogenetic analysis by maximum likelihood. Mol. Biol. Evol. 24, 1586–1591 (2007).

    CAS  Article  PubMed  Google Scholar 

  60. 60.

    R Core Team R: A Language and Environment for Statistical Computing. (R Foundation for Statistical Computing, Vienna, 2013).

    Google Scholar 

  61. 61.

    Kanehisa, M., Furumichi, M., Tanabe, M., Sato, Y. & Morishima, K. KEGG: new perspectives on genomes, pathways, diseases and drugs. Nucleic Acids Res. 45, D353–D361 (2017).

    CAS  Article  PubMed  Google Scholar 

  62. 62.

    Caspi, R. et al. The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome databases. Nucleic Acids Res. 42, D459–D471 (2014).

    CAS  Article  PubMed  Google Scholar 

  63. 63.

    Finn, R. D. et al. InterPro in 2017—beyond protein family and domain annotations. Nucleic Acids Res. 45, D190–D199 (2017).

    CAS  Article  PubMed  Google Scholar 

  64. 64.

    Placzek, S. et al. BRENDA in 2017: new perspectives and new tools in BRENDA. Nucleic Acids Res. 45, D380–D388 (2017).

    CAS  Article  PubMed  Google Scholar 

  65. 65.

    Hahn, M. W., Stadler, P., Wu, Q. L. & Pöckl, M. The filtration-acclimatization method for isolation of an important fraction of the not readily cultivable bacteria. J. Microbiol. Methods 57, 379–390 (2004).

    CAS  Article  PubMed  Google Scholar 

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Acknowledgements

We thank S. Gabrielli for helping with the artwork. This work was supported by grants from the Natural Sciences and Engineering Research Council of Canada (227301 and 6544-2013 awarded to P.J.K. and D.H.L, respectively). V.B. and M.K. were supported by fellowships from the Tula Foundation to the Centre for Microbial Diversity and Evolution.

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V.B., D.H.L. and P.J.K. designed the study. V.B. sampled and isolated the ciliates. V.B. and C.V. cultured, screened and identified the Euplotes strains and Polynucleobacter symbionts. C.V. performed the isolation experiments on the symbionts. V.B. and C.V. optimized and performed the genomic DNA extractions. D.H.L. prepared the libraries. V.B. assembled and annotated the genomes. V.B. and M.F. conducted the functional analysis. M.K. performed the phylogenomic inference, clustering analysis and dN/dS calculations. V.B., M.K. and P.J.K. wrote the paper. All authors participated in the drafting process.

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Correspondence to Patrick J. Keeling.

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A correction to this article is available online at https://doi.org/10.1038/s41559-018-0484-8.

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Supplementary Information

Supplementary Figures 1–7 and Supplementary Discussion

Supplementary Data 1

Functional modules

Supplementary Data 2

dS and dN/dS comparisons

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Boscaro, V., Kolisko, M., Felletti, M. et al. Parallel genome reduction in symbionts descended from closely related free-living bacteria. Nat Ecol Evol 1, 1160–1167 (2017). https://doi.org/10.1038/s41559-017-0237-0

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