Ocean and Polar Research

Korea Institute of Ocean Science & Technology (한국해양과학기술원)
권호 표지
DOI QR코드

DOI QR Code

Phylogenetic Analysis of Culturable Arctic Bacteria

  • Published : 2004.03.31
Download PDF
⟨ Previous Next ⟩

Abstract

We isolated and identified culturable Arctic bacteria that had inhabited soils around the Korean Arctic Research Station Dasan located at Ny-Alsund, Svalbard, Norway $(79^{\circ}N,\;12^{\circ}E)$. The collected soils were diluted in distilled water; the diluted soil-water was spread on 3M petri-films at Dasan Station. The petri-films were transported to the laboratory at KORDI, and cultured at $4^{\circ}C$. Colonies grown on the petri-films were subsequently cultured on nutrient agar plates at $4^{\circ}C$ every 7 days. The pure colonies were inoculated into nutrient liquid media, genomic DNA was extracted, and phylogenetic analysis was performed on the basis of 165 rDNA sequences. A total of 227 strains of bacteria were isolated. Among them, 16S rDNA sequences of 185 strains were identical with those of known strains isolated in this study, and 42 strains were finally identified. Phylogenetic analysis using 16S rDNA indicated that the 30 strains belonged to Pseudomonas, 7 strains to Arthrobacter, two strains to Flavobacterium, and the remaining to Achromobacter, Pedobacter, and Psychrobacter. Among the 42 strains, 14 bacteria produced protease: they were 6 strains of Pseudomonax, 4 strains of Arthrobater, an Achromobacter strain, 2 strains of Flavobacterium, and a Pedohacter strain. We expect these Arctic bacteria can be used for screening to develop new industrial enzymes that are active at low temperatures.

Keywords

References

  1. Bowman, J.P., J.J. Gosink, S.A. McCammon, T.E. Lewis, D.S. Nichols, P.D. Nichols, J.H. Skerrat, J.T. Staley, and T.A. McMeekin. 1998a. Colwellia demingae sp. nov., Colwellia hornerae sp. nov., Colwellia rossensis sp. nov. and Colwellia psychrotropica sp. nov.: psychrophilic Antarctic species with the ability to synthesize docosahexaenoic acid (22:6 n(omega)-3). Int. J. Syst. Bacteriol., 48, 1171-1180. https://doi.org/10.1099/00207713-48-4-1171
  2. Bowman, J.P., S.A. McCammon, J.L. Brown, and T.A. McMeekin. 1998b. Glaciecola punicea gen. nov., sp. nov., and Glaciecola pallidula gen. nov., sp. nov.: psychrophilic bacteria from Antarctic sea-ice habitats. Int. J. Syst. Bacteriol., 48, 1205-1212. https://doi.org/10.1099/00207713-48-4-1205
  3. Bowman, J.P., S.A. McCammon, J.L. Brown, P.D. Nichols, and T.A. McMeekin. 1997a. Psychroserpens burtonensis gen. nov., sp. nov., and Gelidibacter algens gen. nov., sp. nov., psychrophilic bacteria isolated from Antarctic lacustrine and sea-ice habitats. Int. J. Syst. Bacteriol., 47, 670-677. https://doi.org/10.1099/00207713-47-3-670
  4. Bowman, J.P., S.A. McCammon, M.V. Brown, D.S. Nichols, and T.A. McMeekin. 1997b. Diversity and association of psychrophilic bacteria in Antarctic sea ice. Appl. Environ Microbiol., 63, 3068-3078.
  5. Bowman, J.P., S.A. McCammon, T.E. Lewis, J.L. Brown, P.D. Nichols, and T.A. McMeekin. 1998c. Psychroflexus torquis gen. nov., sp. nov., a psychrophilic bacterium from Antarctic Sea ice with the ability to form polyunsaturated fatty acids and the reclassification of Flavobacterium gondwanense Dobson, Franzmann 1993 as Psychroflexus gondwanense gen. nov., comb. nov. Microbiol., 144, 1601-1609. https://doi.org/10.1099/00221287-144-6-1601
  6. Bowman, J.P., S.A. McCammon, D.S. Nichols, J.H. Skerrat, S.M. Rea, P.D. Nichols, and T.A. McMeekin. 1997c. Shewanella gelidimarina sp. nov. and Shewanella frigidimarina sp. nov. -novel species with the ability to produce eicosapentaenoic acid (20:5w3) and grow anaerobically by dissimilatory Fe(III) reduction. Int. J. Syst. Bacteriol., 47, 1040-1047. https://doi.org/10.1099/00207713-47-4-1040
  7. Bowman, J.P., D.S. Nichols, and T.A. McMeekin. 1997d. Psychrobacter glacincola sp. nov., a halotolerant, psychrophilic bacterium isolated from Antarctic sea ice. Syst. Appl. Microbiol., 20, 209-215. https://doi.org/10.1016/S0723-2020(97)80067-7
  8. Chun, J. 1995. Computer-assisted classification and identification of actinomycetes. Ph.D. Thesis, Univ. Newcastle, Newcastle upon Tyne, UK.
  9. Cowan, D.A. 1997. The marine biosphere: a global resource for biotechnology. TIBTEC 15, 129-131. https://doi.org/10.1016/S0167-7799(97)01027-5
  10. Davail, S., G. Feller, E. Narinx, and C. Gerday. 1994. Cold adaptation of proteins. Purification, characterization, and sequence of the heat-labile subtilisin from the antarctic psychrophile Bacillus TA41. J. Biol. Chem., 269, 17448-17453.
  11. Denner, E.B., B. Mark, H.J. Busse, M. Turkiewicz, and W. Lubitz. 2001. Psychrobacter proteolyticus sp. nov., a psychrotrophic, halotolerant bacterium isolated from the Antarctic krill Euphausia superba Dana, excreting a cold-adapted metalloprotease. Syst. Appl. Microbiol., 24, 44-53. https://doi.org/10.1078/0723-2020-00006
  12. Felsenstein, J. 1993. PHYLIP (Phylogeny inference package), version 3.5c. Department of Genetics, University of Washington, Seattle, WA, USA.
  13. Gosink, J.J., C.R. Woese, and J.T. Staley. 1998. Polaribacter gen. nov., with three new species, P. irgensii sp. nov., P. franzmannii sp. nov., and P. filamentus sp. nov., gas vacuolate polar marine bacteria of the Cytophaga- Flavobacterium-Bacteroides group and reclassification of Flectobacillus glomeratus as Polaribacter glomeratus comb. nov. Int. J. Syst. Bacteriol., 48, 223-235. https://doi.org/10.1099/00207713-48-1-223
  14. Humphry, D.R., A. George, G.W. Black, and S.P. Cummings. 2001. Flavobacterium frigidarium sp. nov., an aerobic, psychrophilic, xylanolytic and laminarinolytic bacterium from Antarctica. Int. J. Syst. Evol. Microbiol., 51, 1235-1243. https://doi.org/10.1099/00207713-51-4-1235
  15. Huston, A.L., B.B. Krieger-Brockett, and J.W. Deming. 2000. Remarkably low temperature optima for extracellular enzyme activity from Arctic bacteria and sea ice. Environ. Microbiol., 2, 383-388. https://doi.org/10.1046/j.1462-2920.2000.00118.x
  16. Irgens, R.L., J.J. Gosink, and J.T. Staley. 1996. Polaromonas vacuolata gen. nov., sp. nov., a psychrophilic, marine, gas vacuolate bacterium from Antarctica. Int. J. Syst. Bacteriol., 46, 822-826. https://doi.org/10.1099/00207713-46-3-822
  17. Irwin, J.A., G.A. Alfredsson, A.J. Lanzetti, H.M. Gudmundsson, and P.C. Engel. 2001. Purification and characterisation of serine peptidase from the marine phychrophile strain PA- 43. FEMS Microbiol. Lett., 201, 285-290. https://doi.org/10.1111/j.1574-6968.2001.tb10770.x
  18. James, J. and B.K. Simpson. 1996. Application of enzymes in food processing. Crit. Rev. Food Sci. Nutr., 36, 437-463. https://doi.org/10.1080/10408399609527735
  19. Junge, K., F. Imhoff, T. Staley, and J.W. Deming. 2002. Phylogenetic diversity of numerically important Arctic sea-ice bacteria cultured at subzero temperature. Microb. Ecol., 43, 315-328. https://doi.org/10.1007/s00248-001-1026-4
  20. Kang, S.-H., Y. Kim, J.-S. Kang, K.-C. Yoo, H.I. Yoon, and W. Lee. 2003. Monitoring on the Marine Environment and Phytoplankton of Kongsfjorden, Svalbard, Arctic. Ocean Polar Res., 25, 213-226. https://doi.org/10.4217/OPR.2003.25.2.213
  21. Knoblauch, C., B.B. Jorgensen, and J. Harder. 1999. Community size and metabolic rates of psychrophilic sulfatereducing bacteria in Arctic marine sediments. Appl. Environ Microbiol., 65, 4230-4233.
  22. Maruyama, A., D. Honda, H. Yamamoto, K. Kitamura, and T. Higashihara. 2000. Phylogenetic analysis of psychrophilic bacteria isolated from the Japan Trench, including a description of the deep-sea species Psychrobacter pacificensis sp. nov. Int. J. Syst. Evol. Microbiol., 50, 835-846. https://doi.org/10.1099/00207713-50-2-835
  23. McCammon, S.A. and J.P. Bowman. 2000. Taxonomy of Antarctic Flavobacterium species: description of Flavobacterium gillisiae sp. nov., Flavobacterium tegetincola sp. nov., and Flavobacterium xanthum sp. nov., nom. rev. and reclassification of Flavobacterium salegens as Salegentibacter salegens gen. nov., comb. nov. Int. J. Syst. Evol. Microbiol., 50, 1055-1063. https://doi.org/10.1099/00207713-50-3-1055
  24. McCammon, S.A., B.H. Innes, J.P. Bowman, P.D. Franzmann, S.J. Dobson, P.E. Holloway, J.H. Skerratt, P.D. Nichols, and L.M. Rankin. 1998. Flavobacterium hibernum sp. nov., a lactose-utilizing bacterium from a freshwater Antarctic lake. Int. J. Syst. Bacteriol., 48, 1405-1412. https://doi.org/10.1099/00207713-48-4-1405
  25. Moore, ERB., M. Mau, A. Arnscheidt, E.C. Bottger, R.A. Hutson, M.D. Collins, Y. van de Peer, R. de Wachter, and K.N. Timmis. 1996. The determination and comparison of the 16S rRNA gene sequence of species of the genus Pseudomonas (sensu stricto) and estimation of the natural intrageneric relationships. Syst. Appl. Microbiol., 19, 478-492. https://doi.org/10.1016/S0723-2020(96)80021-X
  26. Morita, R.Y. 1975. Psychrophilic bacteria. Bacteriol. Rev., 39, 144-167.
  27. Nakagawa, T., Y. Fujimoto, M. Uchino, T. Miyaji, K. Takano, and N. Tomizuka. 2003. Isolation and characterization of psychrophiles producing cold-active beta-galactosidase. Lett. Appl. Microbiol., 37, 154-157. https://doi.org/10.1046/j.1472-765X.2003.01369.x
  28. Nelson, K., I. Paulsen, C. Weinel, R. Dodson, H. Hilbert, D. Fouts, S. Gill, M. Pop, V. Martins Dos Santos, M. Holmes, L. Brinkac, M. Beanan, R. DeBoy, S. Daugherty, J. Kolonay, R. Madupu, W. Nelson, O. White, J. Peterson, H. Khouri, I. Hance, P. Lee, E. Holtzapple, D. Scanlan, K. Tran, A. Moazzez, T. Utterback, M. Rizzo, K. Lee, D. Kosack, D. Moestl, H. Wedler, J. Lauber, J. Hoheisel, M. Straetz, S. Heim, C. Kiewitz, J. Eisen, K. Timmis, A. Duesterhoft, B. Tummler, and C. Fraser. 2002. Complete genome sequence and comparative analysis of the metabolically versatile Pseudomonas putida KT2440. Environ. Microbiol., 4, 799-808. https://doi.org/10.1046/j.1462-2920.2002.00366.x
  29. Osorio, C.R., J.L. Barja, R.A. Hutson, and M.D. Collins. 1999. Arthrobacter rhombi sp. nov., isolated from Greenland halibut (Reinhardtius hippoglossoides). Int. J. Syst. Bacteriol., 49, 1217-1220. https://doi.org/10.1099/00207713-49-3-1217
  30. Phadtare, S., K. Yamanaka, and M. Inouye. 2000. The cold shock response. p. 33-45. In: Bacterial stress responses. eds. by G. Storz, R. Hengge-Aronis. American Society for Microbiology, Washington, D.C.
  31. Ravenschlag, K., K. Sahm, and R. Amann. 2001. Quantitative molecular analysis of the microbial community in marine arctic sediments (Svalbard). Appl. Environ. Microbiol., 67, 387-395. https://doi.org/10.1128/AEM.67.1.387-395.2001
  32. Reddy, G.S., R.K. Aggarwal, G.I. Matsumoto, and S. Shivaji. 2000. Arthrobacter flavus sp. nov., a psychrophilic bacterium isolated from a pond in McMurdo Dry Valley, Antarctica. Int. J. Syst. Evol. Microbiol., 50, 1553-1561. https://doi.org/10.1099/00207713-50-4-1553
  33. Reddy, G.S., J.S. Prakash, G.I. Matsumoto, E. Stackebrandt, and S. Shivaji. 2002. Arthrobacter roseus sp. nov., a psychrophilic bacterium isolated from an antarctic cyanobacterial mat sample. Int. J. Syst. Evol. Microbiol., 52, 1017-1021. https://doi.org/10.1099/ijs.0.02131-0
  34. Romanenko, L.A., P. Schumann, M. Rohde, A.M. Lysenko, V.V. Mikhailov, and E. Stackebrandt. 2002. Psychrobacter submarinus sp. nov. and Psychrobacter marincola sp. nov., psychrophilic halophiles from marine environments. Int. J. Syst. Evol. Microbiol., 52, 1291-1297. https://doi.org/10.1099/ijs.0.02087-0
  35. Sahm, K., C. Knoblauch, and R. Amann. 1999. Phylogenetic affiliation and quantification of psychrophilic sulfatereducing isolates in marine Arctic sediments. Appl. Environ. Microbiol., 65, 3976-3981.
  36. Saitou, N. and M. Nei. 1987. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol., 4, 406-425.
  37. Secades, P., B. Alvarez, and J.A. Guijarro. 2001. Purification and characterization of a psychrophilic, calcium-induced, growth-phase-dependent metalloprotease from the fish pathogen Flavobacterium psychrophilum. Appl. Environ. Microbiol., 67, 2436-2444. https://doi.org/10.1128/AEM.67.6.2436-2444.2001
  38. Spiers, A.J., A. Buckling, and P.B. Rainey. 2000. The causes of Pseudomonas diversity. Microbiol., 146, 2345-2350. https://doi.org/10.1099/00221287-146-10-2345
  39. Steyn, P.L., P. Segers, M. Vancanneyt, P. Sandra, K. Kersters, and J.J. Joubert. 1998. Classification of heparinolytic bacteria into a new genus, Pedobacter, comprising four species: Pedobacter heparinus comb. nov., Pedobacter piscium comb. nov., Pedobacter africanus sp. nov. and Pedobacter saltans sp. nov. Proposal of the family Sphingobacteriaceae. Int. J. Syst. Bacteriol., 48, 165-177. https://doi.org/10.1099/00207713-48-1-165
  40. Storer, A.C. 1991. Engineering of proteases and protease inhibition. Curr. Opin. Biotechnol., 2, 606-613. https://doi.org/10.1016/0958-1669(91)90087-L
  41. Stover, C.K., X.-Q.T. Pham, A.L. Erwin, S.D. Mizoguchi, P. Warrener, M.J. Hickey, F.S.L. Brinkman, W.O. Hufnagle, D.J. Kowalik, M. Lagrou, R.L. Garber, L. Goltry, E. Tolentino, S. Westbrook-Wadman, Y. Yuan, L.L. Brody, S.N. Coulter, K.R. Folger, A. Kas, K. Larbig, R.M. Lim, K.A. Smith, D.H. Spencer, G.K.-S. Wong, Z. Wu, IT. Paulsen, J. Reizer, M.H. Saier, R.E.W. Hancock, S. Lory, and M.V. Olson. 2000. Complete genome sequence of Pseudomonas aeruginosa PA01, an opportunistic pathogen. Nature, 406, 959-964. https://doi.org/10.1038/35023079
  42. Thompson, J.D., D.G. Higgins, and T.J. Gibson. 1994. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res., 22, 4673-4680. https://doi.org/10.1093/nar/22.22.4673
  43. Vermeij, P. and D. Blok. 1996. New peptide and protein drugs. Pharm World Sci., 18, 87-93. https://doi.org/10.1007/BF00417755
  44. Wauters, G., J. Charlier, M. Janssens, and M. Delmee. 2000. Identification of Arthrobacter oxydans, Arthrobacter luteolus sp. nov., and Arthrobacter albus sp. nov., isolated from human clinical specimens. J. Clin. Microbiol., 38, 2412-2415.
  45. Yamamoto, S., H. Kasai, D.L. Arnold, R.W. Jackson, A. Vivian, and S. Harayama. 2000. Phylogeny of the genus Pseudomonas: intrageneric structure reconstructed from the nucleotide sequences of gyrB and rpoD genes. Microbiol., 146, 2385-2394. https://doi.org/10.1099/00221287-146-10-2385
  46. Zeng, R., R. Zhang, J. Zhao, and N. Lin. 2003. Cold-active serine alkaline protease from the psychrophilic bacterium Pseudomonas strain DY-A: enzyme purification and characterization. Extremophiles, 7, 335-337. https://doi.org/10.1007/s00792-003-0323-x
  47. Zhou, J., M.E. Davey, J.B. Figueras, E. Rivkina, D. Gilichinsky, and J.M. Tiedje. 1997. Phylogenetic diversity of a bacterial community determined from Siberian tundra soil DNA. Microbiol., 143, 3913-3919. https://doi.org/10.1099/00221287-143-12-3913

Cited by

  1. Isolation of facultatively anaerobic soil bacteria from Ny-Ålesund, Svalbard vol.36, pp.6, 2013, https://doi.org/10.1007/s00300-013-1302-z
  2. Isolation and identification of protease-producing bacteria from the intertidal zone in Jeju Island, Korea vol.51, pp.4, 2015, https://doi.org/10.7845/kjm.2015.5053
  3. Prospecting for ice association: characterization of freeze–thaw selected enrichment cultures from latitudinally distant soils vol.58, pp.4, 2012, https://doi.org/10.1139/w2012-010
  4. List of Korean Names for the Vascular Plants in Spitsbergen Island, in the Arctic Region vol.34, pp.1, 2012, https://doi.org/10.4217/OPR.2012.34.1.101
  5. Isolation of Protease-Producing Arctic Marine Bacteria vol.27, pp.2, 2005, https://doi.org/10.4217/OPR.2005.27.2.215