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Labonté JM, Field EK, Lau M, et al. Single cell genomics indicates horizontal gene transfer and viral infections in a deep subsurface Firmicutes population. Front Microbiol. 2015;6:349doi: 10.3389/fmicb.2015.00349.
Labonté, J. M., Field, E. K., Lau, M., Chivian, D., Van Heerden, E., Wommack, K. E., Kieft, T. L., Onstott, T. C., & Stepanauskas, R. (2015). Single cell genomics indicates horizontal gene transfer and viral infections in a deep subsurface Firmicutes population. Frontiers in microbiology, 6349. https://doi.org/10.3389/fmicb.2015.00349
Labonté, Jessica M, et al. "Single cell genomics indicates horizontal gene transfer and viral infections in a deep subsurface Firmicutes population." Frontiers in microbiology vol. 6 (2015): 349. doi: https://doi.org/10.3389/fmicb.2015.00349
Labonté JM, Field EK, Lau M, Chivian D, Van Heerden E, Wommack KE, Kieft TL, Onstott TC, Stepanauskas R. Single cell genomics indicates horizontal gene transfer and viral infections in a deep subsurface Firmicutes population. Front Microbiol. 2015 Apr 22;6:349. doi: 10.3389/fmicb.2015.00349. eCollection 2015. PMID: 25954269; PMCID: PMC4406082.
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Front Microbiol. 2015 Apr 22;6:349. doi: 10.3389/fmicb.2015.00349. eCollection 2015.

Single cell genomics indicates horizontal gene transfer and viral infections in a deep subsurface Firmicutes population.

Frontiers in microbiology

Jessica M Labonté, Erin K Field, Maggie Lau, Dylan Chivian, Esta Van Heerden, K Eric Wommack, Thomas L Kieft, Tullis C Onstott, Ramunas Stepanauskas

Affiliations

  1. Bigelow Laboratory for Ocean Sciences East Boothbay, ME, USA.
  2. Department of Geosciences, Princeton University Princeton, NJ, USA.
  3. Lawrence Berkeley National Laboratory Berkeley, CA, USA.
  4. Department of Microbial, Biochemical and Food Biotechnology, University of the Free State Bloemfontein, South Africa.
  5. Department of Plant and Soil Sciences, University of Delaware Newark, DE, USA.
  6. Department of Biology, New Mexico Institute of Mining and Technology Socorro, NM, USA.

PMID: 25954269 PMCID: PMC4406082 DOI: 10.3389/fmicb.2015.00349

Abstract

A major fraction of Earth's prokaryotic biomass dwells in the deep subsurface, where cellular abundances per volume of sample are lower, metabolism is slower, and generation times are longer than those in surface terrestrial and marine environments. How these conditions impact biotic interactions and evolutionary processes is largely unknown. Here we employed single cell genomics to analyze cell-to-cell genome content variability and signatures of horizontal gene transfer (HGT) and viral infections in five cells of Candidatus Desulforudis audaxviator, which were collected from a 3 km-deep fracture water in the 2.9 Ga-old Witwatersrand Basin of South Africa. Between 0 and 32% of genes recovered from single cells were not present in the original, metagenomic assembly of Desulforudis, which was obtained from a neighboring subsurface fracture. We found a transposable prophage, a retron, multiple clustered regularly interspaced short palindromic repeats (CRISPRs) and restriction-modification systems, and an unusually high frequency of transposases in the analyzed single cell genomes. This indicates that recombination, HGT and viral infections are prevalent evolutionary events in the studied population of microorganisms inhabiting a highly stable deep subsurface environment.

Keywords: Desulforudis; evolution; horizontal gene transfer (HGT); population genomics; single cell genomics; terrestrial deep subsurface; transposable phages; transposases

References

  1. Bioinformatics. 2012 Jul 15;28(14):1823-9 - PubMed
  2. Nature. 2000 May 18;405(6784):299-304 - PubMed
  3. Geobiology. 2014 Jan;12(1):1-19 - PubMed
  4. Nat Rev Microbiol. 2013 Feb;11(2):83-94 - PubMed
  5. Nature. 2014 Dec 18;516(7531):379-82 - PubMed
  6. Genome Res. 2011 Sep;21(9):1552-60 - PubMed
  7. Curr Opin Biotechnol. 2003 Jun;14(3):255-61 - PubMed
  8. ISME J. 2008 Nov;2(11):1112-21 - PubMed
  9. Nucleic Acids Res. 2002 Jun 1;30(11):2478-83 - PubMed
  10. Microbiol Mol Biol Rev. 2003 Jun;67(2):238-76, table of contents - PubMed
  11. Front Microbiol. 2014 Dec 17;5:679 - PubMed
  12. J Appl Microbiol. 2002;92(2):362-75 - PubMed
  13. Int J Syst Evol Microbiol. 2001 Jul;51(Pt 4):1245-56 - PubMed
  14. Bioinformatics. 2012 Jun 15;28(12):1647-9 - PubMed
  15. Cell Mol Life Sci. 2002 Dec;59(12):2044-54 - PubMed
  16. Proc Natl Acad Sci U S A. 1998 Jun 9;95(12):6578-83 - PubMed
  17. Genome Res. 2009 Sep;19(9):1639-45 - PubMed
  18. Annu Rev Microbiol. 1995;49:29-54 - PubMed
  19. ISME J. 2012 Jun;6(6):1186-99 - PubMed
  20. Nat Rev Microbiol. 2011 Feb;9(2):119-30 - PubMed
  21. ISME J. 2013 Jan;7(1):161-72 - PubMed
  22. FEMS Microbiol Ecol. 2011 Aug;77(2):295-309 - PubMed
  23. Appl Environ Microbiol. 2005 Dec;71(12):8773-83 - PubMed
  24. Science. 2011 Sep 2;333(6047):1296-300 - PubMed
  25. J Bacteriol. 2004 Jan;186(2):400-10 - PubMed
  26. Proc Natl Acad Sci U S A. 2012 Oct 2;109(40):16213-6 - PubMed
  27. Proc Natl Acad Sci U S A. 2013 Jul 9;110(28):11463-8 - PubMed
  28. ISME J. 2012 Jan;6(1):113-23 - PubMed
  29. Appl Environ Microbiol. 1999 May;65(5):2253-5 - PubMed
  30. Science. 2008 Oct 10;322(5899):275-8 - PubMed
  31. Nature. 2011 Jun 2;474(7349):79-82 - PubMed
  32. Science. 2006 Oct 20;314(5798):479-82 - PubMed
  33. Microb Ecol. 1994 Jan;28(3):335-49 - PubMed
  34. ISME J. 2013 Jan;7(1):199-209 - PubMed
  35. Nucleic Acids Res. 2004 Mar 19;32(5):1792-7 - PubMed
  36. Appl Environ Microbiol. 2001 Dec;67(12):5750-60 - PubMed
  37. Appl Environ Microbiol. 2007 Aug;73(16):5261-7 - PubMed
  38. Extremophiles. 2013 Mar;17(2):311-27 - PubMed
  39. Science. 2012 Feb 3;335(6068):587-90 - PubMed
  40. Proc Natl Acad Sci U S A. 2007 May 22;104(21):9052-7 - PubMed
  41. Cell Mol Life Sci. 2002 Dec;59(12):2071-82 - PubMed
  42. Nature. 1999 Jun 10;399(6736):541-8 - PubMed
  43. Front Microbiol. 2014 Oct 31;5:531 - PubMed
  44. Nucleic Acids Res. 2014 Jan;42(Database issue):D633-42 - PubMed
  45. J Mol Biol. 1990 Oct 5;215(3):403-10 - PubMed
  46. Curr Opin Microbiol. 2012 Oct;15(5):613-20 - PubMed
  47. Nucleic Acids Res. 2008 Dec;36(22):7219-29 - PubMed
  48. Res Microbiol. 2013 May;164(4):281-7 - PubMed
  49. Mol Biol Evol. 2002 Dec;19(12):2226-38 - PubMed
  50. ISME J. 2012 Jan;6(1):81-93 - PubMed
  51. Nucleic Acids Res. 2010 Jul;38(13):4207-17 - PubMed
  52. ISME J. 2008 May;2(5):571-4 - PubMed
  53. Nucleic Acids Res. 2004 Jan 1;32(Database issue):D45-9 - PubMed
  54. Methods Mol Biol. 2009;532:413-33 - PubMed
  55. Science. 2006 Nov 10;314(5801):932-4 - PubMed
  56. Nature. 2012 Mar 18;484(7392):101-4 - PubMed
  57. Nucleic Acids Res. 2012 Jan;40(Database issue):D115-22 - PubMed
  58. Proc Natl Acad Sci U S A. 2009 Nov 10;106(45):19126-31 - PubMed
  59. Microbiol Mol Biol Rev. 2004 Sep;68(3):560-602, table of contents - PubMed
  60. ISME J. 2009 Dec;3(12):1420-4 - PubMed
  61. BMC Bioinformatics. 2009 Dec 15;10:421 - PubMed
  62. Nat Rev Genet. 2010 Mar;11(3):181-90 - PubMed
  63. ISME J. 2015 Mar 17;9(4):857-70 - PubMed
  64. Annu Rev Microbiol. 2001;55:709-42 - PubMed
  65. Mob DNA. 2010 Jan 25;1(1):4 - PubMed
  66. Bioinformatics. 2009 Sep 1;25(17):2271-8 - PubMed
  67. Syst Biol. 2010 May;59(3):307-21 - PubMed
  68. Nat Methods. 2012 Jul 30;9(8):772 - PubMed
  69. Nucleic Acids Res. 2000 Jan 1;28(1):33-6 - PubMed
  70. Cytogenet Genome Res. 2005;110(1-4):491-9 - PubMed

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