DNA of ‘minimal’ cells (mycoplasmas) in the metagenomes of Arctic permafrost



Cite item

Full Text

Open Access Open Access
Restricted Access Access granted
Restricted Access Subscription or Fee Access

Abstract

During the long geological time enzymes, nucleic acids, viruses and viable microorganisms can be kept in permafrost. It is difficult to get a holistic view of the microbial community of permafrost using only classical microbiological methods. The analysis of metagenomes of permafrost allowed us to identify the genetic material of ancient mycoplasmas - pathogens of humans, animals and plants Sampling, isolation of total DNA from soil, sequencing (Illumina), metagenomic data processing (MG-RAST, M5nr, UniProt, Krona). Mycoplasma species composition in permafrost soil samples of different origin, but of comparable age (31-32 thousand years), was predicted A comparative analysis of short polypeptides encoded by fragments of ancient DNA with corresponding parts of proteins of modern mycoplasmas was done We discuss the phylogenetic history of Mollicutes, the plasticity of mycoplasma genomes, and the pathogenic potential of the permafrost

Full Text

Restricted Access

About the authors

I. E Vishnyakov

Institute of Cytology, Russian Academy of Sciences Peter the Great Saint-Petersburg Rolytechnic University Saint-Petersburg, Russia

S. N Borchsenius

Institute of Cytology, Russian Academy of Sciences Saint-Petersburg, Russia

A. R Kayumov

Kazan (Volga region) Federal University Kazan, Russia

L. A Shmakova

Institute of Physicochemical and Biological Problems of Soil Science Russian Academy of Sciences Pushchino, Russia

E. M Rivkina

Institute of Physicochemical and Biological Problems of Soil Science Russian Academy of Sciences Pushchino, Russia

References

  1. Vorobyova E., Soina V., Gorlenko M. et al. The deep cold biosphere: facts and hypothesis. FEMS Microbiol. Rev. 1997; 20(3): 277-90.
  2. Gilichinsky D.A., Wagener S., Vishnivetskaya T.A. Permafrost microbiology. Permafrost Periglacial Processes 1995; 6: 281-91.
  3. Gilichinsky D.A., Rivkina E. M. Permafrost Microbiology. In: Reitner J., Thiel V., editors. Encyclopedia of Geobiology. New York: Springer; 2011. p. 726-32.
  4. Legendre M., Bartoli J., Shmakova L. et al. Thirty-thousand-year-old distant relative of giant icosahedral DNA viruses with a pandoravirus morphology. PNAS USA 2014; 111(11): 4274-9.
  5. Legendre M., Lartigue A., Bertaux L. et al. In-depth study of Mollivirus sibericum, a new 30,000-y-old giant virus infecting Acanthamoeba. PNAS USA 2015; 112(38): E5327-35.
  6. Steven B., Briggs G., McKay С. P. et al. Characterization of the microbial diversity in a permafrost sample from the Canadian high Arctic using culture-dependent and culture-independent methods FEMS Microbiol. Ecol. 2007; 59(2): 513-23.
  7. Graham D., Wallenstein M., Vishnivetskaya T. et al. Microbes in thawing permafrost: the unknown variable in the climate change equation. ISME J. 2012; 6(4): 709-12.
  8. Jansson J. K., Taş N. The microbial ecology of permafrost. Nature Rev. Microbiol. 2014; 12(6): 414-25.
  9. Mackelprang R., Waldrop M.P., DeAngelis K.M. et al. Metagenomic analysis of a permafrost microbial community reveals a rapid response to thaw. Nature 2011; 480(7377): 368-71.
  10. Razin S., Yogev D., Naot Y. Molecular biology and pathogenicity of mycoplasmas. Microbiol. Mol. Biol. Rev. 1998; 62(4): 1094-156.
  11. Morowitz H. J., Tourtelotte M. E. The smallest living cells. Scientific American 1962; 206: 117-26
  12. Morowitz H.J. The completeness of molecular biology Isr. J. Med. Sci. 1984; 20(9): 750-3.
  13. Woese С. R. Bacterial evolution. Microbiol. Rev. 1987; 51(2): 221-71.
  14. Вишняков И. Е., Борхсениус С. Н. Белки теплового шока микоплазм и кодирующие их гены. Микробиология 2013; 82(6): 643-59. (перевод: Vishnyakov I. E., Borchsenius S. N. Mycoplasma heat shock proteins and their genes. Microbiology (Mikrobiologija) 2013; 82(6): 653-67
  15. Shi T., Reeves R. H., Gilichinsky D.A. et al. Characterization of viable bacteria from Siberian permafrost by 16S rDNA sequencing Microbiol. Ecol. 1997; 33(3): 169-79.
  16. Краев Г. Н., Шульце Э.Д., Ривкина Е.М. Криогенез как фактор распределения метана в горизонтах мёрзлых пород. ДАН 2013; 451(6): 684-7.
  17. Martin M. Cutadapt removes adapter sequences from high--throughput sequencing reads. EMBnet J. 2011; 17(1): 10-2.
  18. Aronesty E. Comparison of sequencing utility programs. The Open Bioinformatics J. 2013; 7: 1-8.
  19. Meyer F., Paarmann D., D'Souza M. et al. The metagenomics RAST server - a public resource for the automatic phylogenetic and functional analysis of metagenomes BMC Bioinformatics 2008; 9: 386
  20. Wilke A., Harrison T., Wilkening J. et al. The M5nr: a novel non-redundant database containing protein sequences and annotations from multiple sources and associated tools BMC Bioinformatics 2012; 13: 141.
  21. Krivushin K., Kondrashov F., Shmakova L. et al. Two metagenomes from Late Pleistocene Northeast Siberian permafrost Genome Ann. 2015; 3(1): e01380-14.
  22. UniProt Consortium. UniProt: a hub for protein information. Nucl. Acids Res. 2014; 43(Database issue): D204-12.
  23. Ondov B.D., Bergman N.H., Phillippy A.M. Interactive metagenomic visualization in a web browser BMC Bioinformatics 2011; 12: 385.
  24. Medjo B., Atanaskovic-Markovic M., Radic S. et al. Mycoplasma pneumoniae as a causative agent of community-acquired pneumonia in children: clinical features and laboratory diagnosis Ital J. Pediatr. 2014; 40: 104.
  25. March J.B., Harrison J.C., Borich S.M. Humoral immune responses following experimental infection of goats with Mycoplasma capricolum subsp. capripneumoniae. Vet. Microbiol. 2002; 84(1-2): 29-45
  26. Kumar A., Rahal A., Chakraborty S. et al. Mycoplasma agalactiae, an etiological agent of contagious agalactia in small ruminants: a review. Vet. Med. Int. 2014; 2014: 286752.
  27. Koening C.L., Mu H.H., Van Schelt A. et al. Hepcidin is elevated in mice injected with Mycoplasma arthritidis J Inflamm (Lond ) 2009 6: 33
  28. Thiaucourt F., Bolske G. Contagious caprine pleuropneumonia and other pulmonary mycoplasmoses of sheep and goats. Rev. Sci. Tech. 1996; 15(4): 1397-414.
  29. Jacoby R.O., Lindsey J.R. Health care for research animals is essential and affordable. FaSeB J. 1997; 11(8): 609-14.
  30. Kirchhoff H., Rosengarten R. Isolation of a motile mycoplasma from fish. J. Gen. Microbiol. 1984; 130(9): 2439-45.
  31. Wijesurendra D.S., Kanci A., Tivendale K.A. et al. Development of a Mycoplasma gallisepticum infection model in turkeys Avian Pathol 2015; 44(1): 35-42.
  32. Kursa O., Wozniakowski G., Tomczyk G. et al. Rapid detection of Mycoplasma synoviae by loop-mediated isothermal amplification Arch. Microbiol. 2015; 197(2): 319-25.
  33. Murtha A. P., Edwards J. M. The role of Mycoplasma and Ureaplasma in adverse pregnancy outcomes Obstet Gynecol Clin North Am. 2014; 41(4): 615-27.
  34. Whitcomb R., Tully J., Rose D. et al. Wall-less prokaryotes from fall flowers in central United States and Maryland. Curr. Microbiol. 1982; 7: 285-90
  35. Carpane P., Melcher U., Wayadande A. et al. An analysis of the genomic variability of the phytopathogenic mollicute Spiroplasma kunkelii. Phytopathology 2013; 103(2): 129-34.
  36. Duret S., Batailler B., Dubrana M.P. et al. Invasion of insect cells by Spiroplasma citri involves spiralin relocalization and lectin/ glycoconjugate-type interactions. Cell. Microbiol. 2014; 16(7): 1119-32.
  37. Kirkpatrick B.C. Mycoplasma-like organisms: plant and invertebrate pathogens. In: Balows A., Truper H. G., Dworkin M. et al., editors. The Prokaryotes. 2nd ed. New York: Springer-Verlag; 1992. p.4050-67.
  38. Maniloff J. Phylogeny and evolution In: Rasin S., Herrmann R., editors Molecular biology and pathogenisity of mycoplasmas New York: Kluwer Academic/Plenum Publishers; 2002. p. 31-44.
  39. Brown D. R., Bradbury J. M. The contentious taxonomy of Mollicutes In: Browning G F, Citti C, editors Mollicutes: Molecular Biology and Pathogenesis. Norfolk, UK: Horizon Scientific Press; 2014. p. 1-14.
  40. Marenda M. Genomic mosaics In: Browning G.F., Citti C., editors. Mollicutes: Molecular Biology and Pathogenesis. Norfolk, UK: Horizon Scientific Press; 2014. p. 15-54.

Supplementary files

Supplementary Files
Action
1. JATS XML
Download

Copyright (c) 2015 Eco-Vector


СМИ зарегистрировано Федеральной службой по надзору в сфере связи, информационных технологий и массовых коммуникаций (Роскомнадзор).
Регистрационный номер и дата принятия решения о регистрации СМИ: 

This website uses cookies

You consent to our cookies if you continue to use our website.

About Cookies