Skip to main content

Detection and Genetic Characterization of Bacteria of the Genus Pseudomonas from Microbial Communities of Lake Baikal

Russian Journal of Genetics volume 54, pages 514–524 (2018)Cite this article

Abstract

The genus Pseudomonas is one of the most diverse and ecologically important groups of bacteria. Numerous representatives of the genus are found in microbial communities of all natural environments, including those closely associated with plants and animals. This ubiquitous distribution determines a necessity of their physiological and genetic adaptations. Molecular methods revealed that bacteria of the genus Pseudomonas were predominant in ulcerative lesions on the skin of Baikal yellowfin Cottocomephorus grewingkii (Dybowski, 1874). According to ribosomal phylogeny, cultivated Pseudomonas spp. isolated from both ulcerative lesions and the water column of Lake Baikal were grouped into the intrageneric cluster IG P. fluorescens. The topology of the phylogenetic tree based on the gene for outer membrane porin OprF generally coincided with that based on the 16S rRNA genes at the intrageneric level; however, it reflected ecological features of the strains of the genus Pseudomonas at the subgroup level. Screening of pathogenicity determinants detected the oprL, ecfX, fliC, and algD genes in the genomes of Pseudomonas spp. isolated from the ulcerative lesions of fish, whereas oprL and gyrB genes were determined in the strains isolated from the water column.

This is a preview of subscription content, access via your institution.

Access options

Buy single article

Instant access to the full article PDF.

USD 39.95

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

References

  1. Peix, A., Berge, O., Rivas, R., et al., Pseudomonas argentinensis sp. nov., a novel yellow pigment-producing bacterial species, isolated from rhizospheric soil in Cordoba, Argentina, Int. J. Syst. Evol. Microbiol., 2005, vol. 55, no. 3, pp. 1107–1112. doi 10.1099/ijs.0.63445-0

    Article  CAS  Google Scholar 

  2. Pavlova, O.N., Dryukker, V.V., Kostornova, T.Ya., and Nikulina, I.G., Pseudomonas bacteria distribution in Lake Baikal, Sib. Ekol. Zh., 2003, vol. 3, pp. 267–272.

    Google Scholar 

  3. Schwartz, T., Armant, O., Bretschneider, N., et al., Whole genome and transcriptome analyses of environmental antibiotic sensitive and multi-resistant Pseudomonas aeruginosa isolates exposed to waste water and tap water, Microbiol. Biotechnol., 2015, vol. 8, no. 1, pp. 116–130. doi 10.1111/1751-7915.12156

    Article  CAS  Google Scholar 

  4. Mohanram, R., Jagtap, C., and Kumar, P., Isolation, screening, and characterization of surface-active agentproducing, oil-degrading marine bacteria of Mumbai Harbor, Mar. Pollut. Bull., 2016, vol. 105, pp. 131–138. doi 10.1016/j.marpolbul.2016.02.040

    Article  PubMed  CAS  Google Scholar 

  5. Bel’kova, N.L., Denikina, N.N., Sukhanova, E.V., et al., Heterogeneity of populations of organotrophic microorganisms on outer tegumental layers of sick fish, Voda: Khim. Ekol., 2016, no. 4 (94), pp. 32–39.

    Google Scholar 

  6. Nishimori, E., Kita-Tsukamoto, K., and Wakabayashi, H., Pseudomonas plecoglossicida sp. nov., the causative agent of bacterial haemorrhagic ascites of ayu, Plecoglossus altivelis, Int. J. Syst. Evol. Microbiol., 2000, vol. 50, no. 1, pp. 83–89. doi 10.1099/00207713-50-1-83

    Article  PubMed  CAS  Google Scholar 

  7. Saiman, L. and Siegel, J., Infection control in cystic fibrosis, Clin. Microbiol. Rev., 2004, vol. 17, pp. 57–71. doi 10.1128/CMR.17.1.57-71.2004

    Article  PubMed  PubMed Central  Google Scholar 

  8. Reddy, G.S., Matsumoto, G.I., Schumann, P., et al., Psychrophilic pseudomonads from Antarctica: Pseudomonas antarctica sp. nov., Pseudomonas meridiana sp. nov. and Pseudomonas proteolytica sp. nov., Int. J. Syst. Evol. Microbiol., 2004, vol. 54, no. 3, pp. 713–719. doi 10.1099/ijs.0.02827-0

    Article  PubMed  CAS  Google Scholar 

  9. Yumoto, I., Yamazaki, K., Hishinuma, M., et al., Pseudomonas alcaliphila sp. nov., a novel facultatively psychrophilic alkaliphile isolated from seawater, Int. J. Syst. Evol. Microbiol., 2001, vol. 51, pp. 349–355. doi 10.1099/00207713-51-2-349

    Article  PubMed  CAS  Google Scholar 

  10. Zhong, Z.P., Liu, Y., Hou, T.T., et al., Pseudomonas salina sp. nov., isolated from a salt lake, Int. J. Syst. Evol. Microbiol., 2015, vol. 65, no. 9, pp. 2846–2851. doi 10.1099/ijs.0.000341

    Article  PubMed  CAS  Google Scholar 

  11. Moore, E.R.B., Mau, M., Arnscheidt, A., et al., The determination and comparison of the 16S rRNA gene sequences of species of the genus Pseudomonas (sensu stricto) and estimation of the natural intrageneric relationships, Syst. Appl. Microbiol., 1996, vol. 19, pp. 478–492. https://doi.org/10.1016/S0723-2020(96)80021-X.

    Article  CAS  Google Scholar 

  12. Yamamoto, S., Kasai, H., Arnold, D.L., et al., Phylogeny of the genus Pseudomonas: intrageneric structure reconstructed from the nucleotide sequences of gyrB and rpoD genes, Microbiology, 2000, vol. 146, pp. 2385–2394. doi 10.1099/00221287-146-10-2385

    Article  PubMed  CAS  Google Scholar 

  13. Mulet, M., Lalucat, J., and Garcia-Valdes, E., DNA sequence-based analysis of the Pseudomonas species, Environ. Microbiol., 2010, vol. 12, pp. 1513–1530. doi 10.1111/j.1462-2920.2010.02181.x

    PubMed  CAS  Google Scholar 

  14. Bodilis, J., Nsigue Meilo, S., Cornelis, P., et al., A long-branch attraction artifact reveals an adaptive radiation in Pseudomonas, Mol. Biol. Evol., 2011, vol. 28, no. 10, pp. 2723–2726. doi 10.1093/molbev/msr099

    Article  PubMed  CAS  Google Scholar 

  15. Ullstrom, C.A., Siehnel, R., Woodruff, W., et al., Conservation of the gene for outer membrane protein OprF in the family Pseudomonadaceae: sequence of the Pseudomonas synringae oprF gene, J. Bacteriol., 1991, vol. 173, pp. 768–775. doi 10.1128/jb.173.2.768-775.1991

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  16. Bodilis, J. and Barray, S., Molecular evolution of the major outer membrane protein gene (oprF) of Pseudomonas, Microbiology, 2006, vol. 152, pp. 1075–1088. doi 10.1099/mic.0.28656-0

    Article  PubMed  CAS  Google Scholar 

  17. Bodilis, J., Hedde, M., Orange, N., and Barray, S., OprF polymorphism as a marker of ecological niche in Pseudomonas, Environ. Microbiol., 2006, vol. 8, no. 9, pp. 1544–1551. doi 10.1111/j.1462-2920.2006.01045.x

    Article  PubMed  CAS  Google Scholar 

  18. Bodilis, J., Calbrix, R., Guerillon, J., et al., Phylogenetic relationships between environmental and clinical isolates of Pseudomonas fluorescens and related species deduced from 16S rRNA gene and OprF protein sequences, Syst. Appl. Microbiol., 2004, vol. 27, pp. 93–108. doi 10.1078/0723-2020-00253

    Article  PubMed  CAS  Google Scholar 

  19. Lavenir, R., Jocktane, D., Laurent, F., et al., Improved reliability of Pseudomonas aeruginosa PCR detection by the use of the species-specific ecfX gene target, J. Microbiol. Methods, 2007, vol. 70, no. 1, pp. 20–29. doi 10.1016/j.mimet.2007.03.008

    Article  PubMed  CAS  Google Scholar 

  20. Matthijs, S., Coorevits, A., Gebrekidan, T.T., et al., Evaluation of oprI and oprL genes as molecular markers for the genus Pseudomonas and their use in studying the biodiversity of a small Belgian River, Res. Microbiol., 2013, vol. 164, no. 3, pp. 254–261. doi 10.1016/j.resmic. 2012.12.001

    Article  PubMed  CAS  Google Scholar 

  21. Kravtsova, L.S., Izhboldina, L.A., Khanaev, I.V., et al., Disturbances of the vertical zoning of green algae in the coastal part of the Listvennichnyi gulf of Lake Baikal, Dokl. Biol. Sci., 2012, vol. 447, nos. 1-6, pp. 350–352.

    Article  PubMed  CAS  Google Scholar 

  22. Denikina, N.N., Dzyuba, E.V., Bel’kova, N.L., et al., The first case of disease of the sponge Lubomirskia baicalensis: investigation of its microbiome, Biol. Bull. (Moscow), 2016, vol. 43, no. 3, pp. 263–270. https://doi.org/10.1134/S106235901603002X.

    Article  CAS  Google Scholar 

  23. Khanaev, I.V., Dzyuba, E.V., Kravtsova, L.S., and Grachev, M.A., The effect of bloom of filamentous green algae on the reproduction of yellowfin sculpin Cottocomephorus grewingkii (Dybowski, 1874) (Cottoidae) during ecological crisis in Lake Baikal, Dokl. Biol. Sci., 2016, vol. 467, nos. 1-6, pp. 63–64.

    Article  PubMed  CAS  Google Scholar 

  24. Belykh, M.P., Sukhanova, E.V., and Bel’kova, N.L., Specific features of cultured heterotrophic microorganisms from the Lake Baikal littoral zone, Izv. Irkutsk. Gos. Univ.: Ser. Biol. Ekol., 2013, vol. 6, no. 3(1), pp. 20–26.

    Google Scholar 

  25. Bel’kova, N.L., Molecular and genetic methods for the analysis of microbial communities, in Raznoobrazie mikrobnykh soobshchestv vnutrennikh vodoemov Rossii: uchebno-metodicheskoe posobie (Diversity of Microbial Communities in Inland Water Bodies of Russia: Study Guide), 2009, pp. 53–63.

    Google Scholar 

  26. Sambrook, J., Fritsch, E.F., Maniatis, T., Molecular Cloning: A Laboratory Manual, Cold Spring Harbor: Cold Spring Harbor Laboratory, 1989, vols. 1, 2, 3.

    Google Scholar 

  27. Brosius, J., Dull, T.J., Sleeter, D.D., and Noller, H.F., Gene organization and primary structure of a ribosomal RNA operon from Escherichia coli, J. Mol. Biol., 1981, vol. 148, pp. 107–127. https://doi.org/10.1016/ 0022-2836(81)90508-8.

    Article  PubMed  CAS  Google Scholar 

  28. Hall, T.A., BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT, Nucleic Acids. Symp. Ser., 1999, vol. 41, pp. 95–98.

    CAS  Google Scholar 

  29. Garrity, G.M., Brenner, D.J., Krieg, N.R., et al., Bergey’s Manual of Systematic Bacteriology, vol. 2: The Proteobacteria, part B: The Gammaproteobacteria, New York: Springer-Verlag, 2005, 2nd ed. doi 10.1007/0-387-28022-7

    Google Scholar 

  30. Garrity, G.M., Brenner, D.J., Krieg, N.R., et al., Bergey’s Manual of Systematic Bacteriology, vol. 2: The Proteobacteria, part C: The Alpha-, Beta-, Delta-, and Epsilonproteobacteria, New York: Springer-Verlag, 2005. doi 10.1007/0-387-29298-5

    Google Scholar 

  31. López-Cortés, A., Schumann, P., Pukall, R., and Stackebrandt, E., Exiguobacterium mexicanum sp. nov. and Exiguobacterium artemiae sp. nov., isolated from the brine shrimp Artemia franciscana, Syst. Appl. Microbiol., 2006, vol. 29, no. 3, pp. 183–190. doi 10.1016/j.syapm.2005.09.007

    Article  PubMed  CAS  Google Scholar 

  32. Zhang, Y. and Qiu, S., Examining phylogenetic relationships of Erwinia and Pantoea species using whole genome sequence data, Antonie van Leeuwenhoek, 2015, vol. 108, no. 5, pp. 1037–1046. doi 10.1007/s10482-015-0556-6

    Article  PubMed  Google Scholar 

  33. Vos, P., Garrity, G., Jones, D., et al., Bergey’s Manual of Systematic Bacteriology, vol. 3: The Firmicutes, New York: Springer-Verlag, 2009. doi 10.1007/978-0-387-68489-5

    Google Scholar 

  34. Hilario, E., Buckley, T., and Young, J., Improved resolution on the phylogenetic relationships among Pseudomonas by the combined analysis of atpD, carA, recA and 16S rDNA, Antonie van Leeuwenhoek, 2004, vol. 86, pp. 51–64. doi 10.1023/B:ANTO.0000024910.57117.16

    Article  PubMed  CAS  Google Scholar 

  35. Khan, A.A. and Cerniglia, C.E., Detection of Pseudomonas aeruginosa from clinical and environmental samples by amplification of the exotoxin A gene using PCR, Appl. Environ. Microbiol., 1994, vol. 60, no. 10, pp. 3739–3745.

    PubMed  PubMed Central  CAS  Google Scholar 

  36. Watanabe, K., Nelson, J., Harayama, S., and Kasai, H., ICB database: the gyrB database for identification and classification of bacteria, Nucleic Acids Res., 2001, vol. 29, no. 1, pp. 344–345.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  37. Lee, C.S. and Lee, J., Evaluation of new gyrB-based real-time PCR system for the detection of B. fragilis as an indicator of human-specific fecal contamination, J. Microbiol. Methods, 2010, vol. 82, pp. 311–318. doi 10.1016/j.mimet.2010.07.012

    Article  PubMed  CAS  Google Scholar 

  38. Qin, X., Emerson, J., Stapp, J., et al., Use of real time PCR with multiple targets to identify Pseudomonas aeruginosa and other nonfermenting gram-negative bacilli from patients with cystic fibrosis, J. Clin. Microbiol., 2003, vol. 41, no. 9, pp. 4312–4317. doi 10.1128/JCM.41.9.4312-4317.2003

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  39. Spangenberg, C., Heuer, T., Burger, C., and Tummler, B., Genetic diversity of flagellins of Pseudomonas aeruginosa, FEBS Lett., 1996, vol. 396, no. 4, pp. 213–217. doi 10.1016/0014-5793(96)01099-X

    Article  PubMed  CAS  Google Scholar 

  40. De Vos, D., Lim, A., Jr., Pirnay, J.P., et al., Direct detection and identification of Pseudomonas aeruginosa in clinical samples such as skin biopsy specimens and expectorations by multiplex PCR based on two outer membrane lipoprotein genes, oprI and oprL, J. Clin. Microbiol., 1997, vol. 35, no. 6, pp. 1295–1299.

    PubMed  PubMed Central  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Limnological Institute, Siberian Branch, Russian Academy of Sciences, Irkutsk, 664033, Russia

    N. L. Bel’kova, E. V. Dzyuba, I. V. Khanaev & N. N. Denikina

  2. Scientific Centre for Family Health and Human Reproduction Problems, Irkutsk, 664003, Russia

    N. L. Bel’kova

  3. Department of Physical and Chemical Biology, Irkutsk State University, Irkutsk, 664003, Russia

    E. S. Klimenko

Authors
  1. N. L. Bel’kova
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. E. V. Dzyuba
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. E. S. Klimenko
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. I. V. Khanaev
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. N. N. Denikina
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to N. L. Bel’kova.

Additional information

Original Russian Text © N.L. Bel’kova, E.V. Dzyuba, E.S. Klimenko, I.V. Khanaev, N.N. Denikina, 2018, published in Genetika, 2018, Vol. 54, No. 5.

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Bel’kova, N.L., Dzyuba, E.V., Klimenko, E.S. et al. Detection and Genetic Characterization of Bacteria of the Genus Pseudomonas from Microbial Communities of Lake Baikal. Russ J Genet 54, 514–524 (2018). https://doi.org/10.1134/S1022795418040038

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1134/S1022795418040038

Keywords

  • Pseudomonas
  • Cottocomephorus grewingkii
  • Lake Baikal
  • 16S rDNA
  • gene for outer membrane protein porin OprF
  • pathogenicity genes