Advertisement

Horizontal Gene Transfer Elements: Plasmids in Antarctic Microorganisms

  • Matías Giménez
  • Gastón Azziz
  • Paul R. Gill
  • Silvia BatistaEmail author
Chapter
Part of the Springer Polar Sciences book series (SPPS)

Abstract

Plasmids play an important role in the evolution of microbial communities. These mobile genetic elements can improve host survival and may also be involved in horizontal gene transfer (HGT) events between individuals. Diverse culture-dependent and culture-independent approaches have been used to characterize these mobile elements. Culture-dependent methods are usually associated with classical microbiological techniques. In the second approach, development of specific protocols for analysis of metagenomes involves many challenges, including assembly of sequences and availability of a reliable database, which are crucial. In addition, alternative strategies have been developed for the characterization of plasmid DNA in a sample, generically referred to as plasmidome.

The Antarctic continent has environments with diverse characteristics, including some with very low temperatures, humidity levels, and nutrients. The presence of microorganisms and genetic elements capable of being transferred horizontally has been confirmed in these environments, and it is generally accepted that some of these elements, such as plasmids, actively participate in adaptation mechanisms of host microorganisms.

Information related to structure and function of HGT elements in Antarctic bacteria is very limited compared to what is known about HGT in bacteria from temperate/tropical environments. Some studies are done with biotechnological objectives. The search for mobile elements, such as plasmids, may be related to improve the expression of heterologous genes in host organisms growing at very low temperatures. More recently, however, additional studies have been done to detect plasmids in isolates, associated or not with specific phenotypes such as drug resistance. Although various Antarctic metagenomes are available in public databases, corresponding studies of plasmidomes are needed. The difficulties usually associated with the study of metagenomes are increased in these cases by the limited number of sequences in functionally characterized databases.

Keywords

Horizontal gene transfer Plastmidome Global climate change Animal and human influence Antibiotic resistance genes 

References

  1. Akiyama, M., Kanda, H., & Ohyama, Y. (1986). Allelopathic effect of penguin excrements and guanos on the growth of Antarctic soil algae. Memoirs of National Institute of Polar Research. Series E Biology and Medical Science, 37, 11–16.Google Scholar
  2. Alcántara-Hernández, R. J., Centeno, C. M., Ponce-Mendoza, A., et al. (2014). Characterization and comparison of potential denitrifiers in microbial mats from King George Island, Maritime Antarctica. Polar Biology, 37, 403–416.  https://doi.org/10.1007/s00300-013-1440-3.CrossRefGoogle Scholar
  3. Antelo, V., Guerout, A. M., Mazel, D., et al. (2018). Bacteria from Fildes Peninsula carry class 1 integrons and antibiotic resistance genes in conjugative plasmids. Antarctic Science, 30, 22–28.  https://doi.org/10.1017/S0954102017000414.CrossRefGoogle Scholar
  4. Boto, L. (2010). Horizontal gene transfer in evolution: Facts and challenges. Proceedings of the Royal Society B: Biological Sciences, 277, 819–827.  https://doi.org/10.1098/rspb.2009.1679.CrossRefPubMedGoogle Scholar
  5. Callejas, C., Gill, P. R., Catalán, A. I., et al. (2011). Phylotype diversity in a benthic cyanobacterial mat community on King George Island, maritime Antarctica. World Journal of Microbiology and Biotechnology, 27, 1507–1512.  https://doi.org/10.1007/s11274-010-0578-1.CrossRefPubMedGoogle Scholar
  6. Callejas, C., Azziz, G., Souza, E. M., et al. (2018). Prokaryotic diversity in four microbial mats on the Fildes Peninsula, King George Island, maritime Antarctica. Polar Biology.  https://doi.org/10.1007/s00300-018-2256-y.CrossRefGoogle Scholar
  7. Cambray, G., Guerout, A.-M., & Mazel, D. (2010). Integrons. Annual Review of Genetics, 44, 141–166.  https://doi.org/10.1146/annurev-genet-102209-163504.CrossRefPubMedGoogle Scholar
  8. Carattoli, A., Aschbacher, R., March, A., et al. (2010). Complete nucleotide sequence of the IncN plasmid pKOX105 encoding VIM-1, QnrS1 and SHV-12 proteins in Enterobacteriaceae from Bolzano, Italy compared with IncN plasmids encoding KPC enzymes in the USA. The Journal of Antimicrobial Chemotherapy, 65, 2070–2075.  https://doi.org/10.1093/jac/dkq269.CrossRefPubMedGoogle Scholar
  9. Che, S., Song, L., Song, W., Yang, M., Guiming, L., & Lin, X. (2013). Complete genome sequence of Antarctic bacterium Psychrobacter sp. strain G. Genome, 1, 2012–2013.  https://doi.org/10.1093/nar/gkm321.2.CrossRefGoogle Scholar
  10. Cieśliński, H., Werbowy, K., Kur, J., & Turkiewicz, M. (2008). Molecular characterization of a cryptic plasmid from the psychrotrophic antarctic bacterium Pseudoalteromonas sp. 643A. Plasmid, 60, 154–158.  https://doi.org/10.1016/j.plasmid.2008.06.002.CrossRefPubMedGoogle Scholar
  11. Convey, P. (2010). Terrestrial biodiversity in Antarctica – Recent advances and future challenges. Polar Science, 4, 135–147.  https://doi.org/10.1016/j.polar.2010.03.003.CrossRefGoogle Scholar
  12. Cowan, D. A. (2014). Antarctic terrestrial microbiology. Berlin: Springer.CrossRefGoogle Scholar
  13. Darling, C. A., & Siple, P. A. (1941). Bacteria of Antarctica. Journal of Bacteriology, 42, 83–98.PubMedPubMedCentralGoogle Scholar
  14. de los Rios, A., Ascaso, C., Wierzchos, J., et al. (2004). Microstructural characterization of cyanobacterial mats from the McMurdo Ice Shelf, Antarctica. Applied and Environmental Microbiology, 70, 569–580.  https://doi.org/10.1128/AEM.70.1.569.
  15. De Maayer, P., Anderson, D., Cary, C., & Cowan, D. A. (2014). Some like it cold: Understanding the survival strategies of psychrophiles. EMBO Reports, 15, 508–517.  https://doi.org/10.1002/embr.201338170.CrossRefPubMedPubMedCentralGoogle Scholar
  16. DeMaere, M. Z., Williams, T. J., Allen, M. A., et al. (2013). High level of intergenera gene exchange shapes the evolution of haloarchaea in an isolated Antarctic lake. Proceedings of the National Academy of Sciences, 110, 16939–16944.  https://doi.org/10.1073/pnas.1307090110.CrossRefGoogle Scholar
  17. Dziewit, L., & Bartosik, D. (2014). Plasmids of psychrophilic and psychrotolerant bacteria and their role in adaptation to cold environments. Frontiers in Microbiology, 5, 1–14.  https://doi.org/10.3389/fmicb.2014.00596.CrossRefGoogle Scholar
  18. Dziewit, L., Grzesiak, J., Ciok, A., et al. (2013). Sequence determination and analysis of three plasmids of Pseudomonas sp. GLE121, a psychrophile isolated from surface ice of Ecology Glacier (Antarctica). Plasmid, 70, 254–262.  https://doi.org/10.1016/j.plasmid.2013.05.007.CrossRefPubMedGoogle Scholar
  19. Erdmann, S., Tschitschko, B., Zhong, L., et al. (2017). A plasmid from an Antarctic haloarchaeon uses specialized membrane vesicles to disseminate and infect plasmid-free cells. Nature Microbiology, 2, 1446–1455.  https://doi.org/10.1038/s41564-017-0009-2.CrossRefPubMedGoogle Scholar
  20. Guo, S., & Mahillon, J. (2013). pGIAK1, a heavy metal resistant plasmid from an obligate alkaliphilic and halotolerant bacterium isolated from the Antarctic Concordia Station confined environment. PLoS One, 8, 1–8.  https://doi.org/10.1371/journal.pone.0072461.CrossRefGoogle Scholar
  21. Han, S. R., Yu, S. C., Ahn, D. H., et al. (2016). Complete genome sequence of Burkholderia sp. strain PAMC28687, a potential octopine-utilizing bacterium isolated from Antarctica lichen. Journal of Biotechnology, 226, 16–17.  https://doi.org/10.1016/j.jbiotec.2016.03.043.CrossRefPubMedGoogle Scholar
  22. Helmke, E., & Weyland, H. (2004). Psychrophilic versus psychrotolerant bacteria – Occurrence and significance in polar and temperate marine habitats. Cellular and Molecular Biology (Noisy-le-Grand, France), 50, 553–561.  https://doi.org/10.1170/T545.CrossRefGoogle Scholar
  23. Hirsch, P., Gallikowski, C. A., Siebert, J., et al. (2004). Deinococcus frigens sp. nov., Deinococcus saxicola sp. nov., and Deinococcus marmoris sp. nov., low temperature and draught-tolerating, UV-resistant bacteria from continental Antarctica. Systematic and Applied Microbiology, 27, 636–645.  https://doi.org/10.1078/0723202042370008.CrossRefPubMedGoogle Scholar
  24. Imperio, T., Bargagli, R., & Marri, L. (2007). Detection of IncP replicon-specific regions in DNA from Antarctic microbiota. Open Life Sciences, 2, 378–384.  https://doi.org/10.2478/s11535-007-0025-y.CrossRefGoogle Scholar
  25. Jungblut, A. D., & Neilan, B. A. (2010). nifH gene diversity and expression in a microbial mat community on the McMurdo Ice Shelf, Antarctica. Antarctic Science, 22, 117–122.  https://doi.org/10.1017/S0954102009990514.CrossRefGoogle Scholar
  26. Kobori, H., Sullivan, C. W., & Shizuya, H. (1984). Bacterial plasmids in antarctic natural microbial assemblages. Applied and Environmental Microbiology, 48, 515–518.PubMedPubMedCentralGoogle Scholar
  27. Komárek, O., & Komárek, J. (1999). Diversity of freshwater and terrestrial habitats and their oxyphototroph microflora in the Arctowski Station region, South Shetland Islands. Polish Polar Research, 20, 259–282.Google Scholar
  28. Komárek, O., & Komárek, J. (2003). Diversity and ecology of cyanobacterial microflora of Antarctic seepage habitats: Comparison of King George Island, Shetland Islands, and James Ross Island, Nw Weddell Sea, Antarctica. In Microbial mats. Modern and ancient microorganisms in stratified systems (pp. 517–539). Springer: Dordrecht.Google Scholar
  29. Konrad, H., Shepherd, A., Gilbert, L., et al. (2018). Net retreat of Antarctic glacier grounding lines. Nature Geoscience.  https://doi.org/10.1038/s41561-018-0082-z.CrossRefGoogle Scholar
  30. Ma, Y., Wang, L., & Shao, Z. (2006). Pseudomonas, the dominant polycyclic aromatic hydrocarbon-degrading bacteria isolated from Antarctic soils and the role of large plasmids in horizontal gene transfer. Environmental Microbiology, 8, 455–465.  https://doi.org/10.1111/j.1462-2920.2005.00911.x.CrossRefPubMedGoogle Scholar
  31. Mangano, S., Caruso, C., Michaud, L., et al. (2011). Incidence of plasmid and antibiotic resistance in psychrotrophic bacteria isolated from Antarctic sponges. AAPP Atti della Accademia Peloritana dei Pericolanti, Classe di Scienze Fisiche Matematiche e Naturali, 89, 1–9.  https://doi.org/10.1478/C1A8901003.CrossRefGoogle Scholar
  32. Martínez-Rosales, C., Fullana, N., Musto, H., & Castro-Sowinski, S. (2012). Antarctic DNA moving forward: Genomic plasticity and biotechnological potential. FEMS Microbiology Letters, 331, 1–9.  https://doi.org/10.1111/j.1574-6968.2012.02531.x.CrossRefPubMedGoogle Scholar
  33. Martinez-Rosales, C., Marizcurrena, J. J., Iriarte, A., et al. (2015). Characterizing proteases in an Antarctic Janthinobacterium sp. isolate: Evidence of a protease horizontal gene transfer event. Advances in Polar Science, 1, 012.  https://doi.org/10.13679/j.advps.2015.1.00088.CrossRefGoogle Scholar
  34. Médigue, C., Krin, E., Pascal, G., et al. (2005). Coping with cold: The genome of the versatile marine Antarctica bacterium Pseudoalteromonas haloplanktis TAC125. Genome Research, 15, 1325–1335.  https://doi.org/10.1101/gr.4126905.CrossRefPubMedPubMedCentralGoogle Scholar
  35. Michaud, L., Di Cello, F., Brilli, M., et al. (2004). Biodiversity of cultivable psychrotrophic marine bacteria isolated from Terra Nova Bay (Ross Sea, Antarctica). FEMS Microbiology Letters, 230, 63–71.  https://doi.org/10.1016/S0378-1097(03)00857-7.CrossRefPubMedGoogle Scholar
  36. Miller, R. V., Gammon, K., & Day, M. J. (2009). Antibiotic resistance among bacteria isolated from seawater and penguin fecal samples collected near Palmer Station, Antarctica. Canadian Journal of Microbiology, 55, 37–45.  https://doi.org/10.1139/W08-119.CrossRefPubMedGoogle Scholar
  37. Morita, R. Y. (1975). Psychrophilic Bacteria. Bacteriological Reviews, 39, 144–167.PubMedPubMedCentralGoogle Scholar
  38. Peeters, K., Verleyen, E., Hodgson, D. A., et al. (2012). Heterotrophic bacterial diversity in aquatic microbial mat communities from Antarctica. Polar Biology, 35, 543–554.  https://doi.org/10.1007/s00300-011-1100-4.CrossRefGoogle Scholar
  39. Pini, F., Grossi, C., Nereo, S., et al. (2007). Molecular and physiological characterisation of psychrotrophic hydrocarbon-degrading bacteria isolated from Terra Nova Bay (Antarctica). European Journal of Soil Biology, 43, 368–379.  https://doi.org/10.1016/j.ejsobi.2007.03.012.CrossRefGoogle Scholar
  40. Ramsay, A. J. (1983). Bacterial biomass in ornithogenic soils of Antarctica. Polar Biology, 1, 221–225.  https://doi.org/10.1007/BF00443192.CrossRefGoogle Scholar
  41. Romaniuk, K., Krucon, T., Decewicz, P., et al. (2017). Molecular characterization of the pA3J1 plasmid from the psychrotolerant Antarctic bacterium Pseudomonas sp. ANT_J3. Plasmid, 92, 49–56.  https://doi.org/10.1016/j.plasmid.2017.08.001.CrossRefPubMedGoogle Scholar
  42. Sancho, L. G., Pintado, A., Navarro, F., et al. (2017). Recent warming and cooling in the Antarctic Peninsula region has rapid and large effects on lichen vegetation. Scientific Reports, 7, 1–8.  https://doi.org/10.1038/s41598-017-05989-4.CrossRefGoogle Scholar
  43. Shepherd, A., Ivins, E. R., Geruo, A., et al. (2012). A reconciled estimate of ice-sheet mass balance. Science, 338, 1183–1189.  https://doi.org/10.1126/science.1228102.CrossRefPubMedGoogle Scholar
  44. Smith, R. I. L. (1994). Vascular plants as bioindicators of regional warming in Antarctica. Oecologia, 99, 322–328.CrossRefGoogle Scholar
  45. Straka, R. P., & Stokes, J. L. (1960). Psychrophilic bacteria in Antarctica. Journal of Applied Microbiology, 80, 622–625.Google Scholar
  46. Sundin, G. W., Kidambi, S. P., Ullrich, M., & Bender, C. L. (1996). Resistance to ultraviolet light in Pseudomonas syringae: Sequence and functional analysis of the plasmid-encoded rulAB genes. Gene, 177, 77–81.  https://doi.org/10.1016/0378-1119(96)00273-9.CrossRefPubMedGoogle Scholar
  47. Terauds, A., & Lee, J. R. (2016). Antarctic biogeography revisited: Updating the Antarctic Conservation Biogeographic regions. Diversity and Distributions, 22, 836–840.  https://doi.org/10.1111/ddi.12453.CrossRefGoogle Scholar
  48. Tomova, I., Stoilova-Disheva, M., Lazarkevich, I., & Vasileva-Tonkova, E. (2015). Antimicrobial activity and resistance to heavy metals and antibiotics of heterotrophic bacteria isolated from sediment and soil samples collected from two Antarctic islands. Front Life Science, 8, 348–357.  https://doi.org/10.1080/21553769.2015.1044130.CrossRefGoogle Scholar
  49. Tutino, M. L., Duilio, A., Moretti, M. A., et al. (2000). A rolling-circle plasmid from Psychrobacter sp. TA144: Evidence for a novel Rep subfamily. Biochemical and Biophysical Research Communications, 274, 488–495.  https://doi.org/10.1006/bbrc.2000.3148.CrossRefPubMedGoogle Scholar
  50. Tutino, M. L., Duilio, A., Parrilli, E., et al. (2001). A novel replication element from an Antarctic plasmid as a tool for the expression of proteins at low temperature. Extremophiles, 5, 257–264.  https://doi.org/10.1007/s007920100203.CrossRefPubMedGoogle Scholar
  51. Velázquez, D., López-Bueno, A., Aguirre De Cárcer, D., et al. (2016). Ecosystem function decays by fungal outbreaks in Antarctic microbial mats. Scientific Reports, 6, 1–7.  https://doi.org/10.1038/srep22954.CrossRefGoogle Scholar
  52. Vollmers, J., Voget, S., Dietrich, S., et al. (2013). Poles apart: Arctic and Antarctic Octadecabacter strains share high genome plasticity and a new type of Xanthorhodopsin. PLoS One.  https://doi.org/10.1371/journal.pone.0063422.CrossRefGoogle Scholar
  53. Wagner, A., Whitaker, R. J., Krause, D. J., et al. (2017). Mechanisms of gene flow in archaea. Nature Reviews Microbiology, 15, 492–501.  https://doi.org/10.1038/nrmicro.2017.41.CrossRefPubMedGoogle Scholar
  54. Wong, C. M. V. L., Tam, H. K., Ng, W. M., et al. (2013). Characterisation of a cryptic plasmid from an Antarctic bacterium Pedobacter cryoconitis strain BG5. Plasmid, 69, 186–193.  https://doi.org/10.1016/j.plasmid.2012.12.002.CrossRefPubMedGoogle Scholar

Copyright information

© Springer Nature Switzerland AG 2019

Authors and Affiliations

  • Matías Giménez
    • 1
  • Gastón Azziz
    • 1
  • Paul R. Gill
    • 2
  • Silvia Batista
    • 1
    Email author
  1. 1.Unidad Microbiología MolecularInstituto de Investigaciones Biológicas Clemente EstableMontevideoUruguay
  2. 2.Nevada City BiolabsNevada CityUSA

Personalised recommendations