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Extremophiles

, Volume 14, Issue 4, pp 339–348 | Cite as

Isolation and characterisation of bacteria from the haloalkaline Lake Elmenteita, Kenya

  • Romano MwirichiaEmail author
  • A. W. Muigai
  • B. Tindall
  • H. I. Boga
  • E. Stackebrandt
Original Paper

Abstract

Culture-independent studies show that soda lake environments harbour diverse groups of bacteria and archaea. In this study different enrichment and isolation media were used in an attempt to isolate novel groups of bacteria from Lake Elmenteita. Different media were prepared using filter-sterilised water from the lake. The isolates recovered were purified on tryptic soy agar supplemented with 1% sodium carbonate and 4% sodium chloride. Phylogenetic analysis of 181 partial 16S rRNA gene sequences with excellent quality showed that the majority of the isolates were affiliated to the class Gammaproteobacteria and to the genus Bacillus. Isolates from the genus Halomonas and Bacillus constituted 37 and 31% of the total sequenced isolates, respectively. Other groups recovered were related to Marinospirillum, Idiomarina, Vibrio, Enterococcus, Alkalimonas, Alkalibacterium, Amphibacillus, Marinilactibacillus and the actinobacteria Nocardiopsis and Streptomyces. Fifty-one different genera were represented with 31 and 15 cultures scoring with their nearest neighbour similarities below 98 and 97%, respectively. Some novel taxa were identified which had not been isolated previously from the soda environment. The results show that the use of different media with varying compositions can help retrieve novel bacterial diversity from the soda lake environment.

Keywords

Soda lakes Diversity Alkaliphiles 

Notes

Acknowledgments

This work was supported by DAAD within the frame work of a Sandwich Ph.D. scholarship to Romano Mwirichia.

References

  1. Adams MWW, Kelly RM (1995) Enzymes isolated from microorganisms that grow in extreme environments. Chem Eng News 73:32–42Google Scholar
  2. Altschul S, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215:403–410Google Scholar
  3. Ballot A, Krienitz L, Kotut K, Wiegand C, Metcalf JS, Codd GA, Pflugmacher S (2004) Cyanobacteria and cyanobacterial toxins in three alkaline Rift Valley lakes of Kenya––Lakes Bogoria, Nakuru and Elmenteita. J Plankton Res 26:925–935CrossRefGoogle Scholar
  4. Duckworth AW, Grant WD, Jones BE, van Steenbergen R (1996) Phylogenetic diversity of soda Lake Alkaliphiles. FEMS Microbiol Ecol 19:181–191CrossRefGoogle Scholar
  5. Duckworth AW, Grant WD, Jones BE, Meyer D (1998) Dietzia natronolimnaios sp. nov., a new species of the genus Dietzia isolated from an East African soda lake. Extremophiles 2:359–366CrossRefGoogle Scholar
  6. Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783–791CrossRefGoogle Scholar
  7. Fritze D, Flossdorf J, Claus D (1990) Taxonomy of alkaliphilic Bacillus strains. Int J Syst Bacteriol 40:92–97CrossRefGoogle Scholar
  8. Garcia MT, Mellado E, Ostos JC, Ventosa A (2004) Halomonas organivorans sp. nov., a moderate halophile able to degrade aromatic compounds. Int J Syst Evol Microbiol 54:1723–1738CrossRefGoogle Scholar
  9. Gatesoupe FJ (1999) The use of probiotics in aquaculture. Aquaculture 180:147–165CrossRefGoogle Scholar
  10. Groth I, Schumann P, Rainey FA, Martin K, Schütze B, Augsten K (1997) Bogoriella caseilytica gen. nov., sp. nov., a new alkaliphilic actinomycete from a soda lake in Africa. Int J Syst Bacteriol 47:788–794CrossRefGoogle Scholar
  11. Guffanti AA, Blanco R, Benenson RA, Krulwich TA (1980) Bioenergetic properties of alkaline-tolerant and alkalophilic strains of Bacillus firmus. J Gen Microbiol 119:79–86Google Scholar
  12. Guffanti AA, Finkelthal O, Hicks DB, Falk L, Sidhu A, Garro A, Krulwich TA (1986) Isolation and characterization of new facultatively alkalophilic strains of Bacillus. J Bacteriol 167:766–773Google Scholar
  13. Horikoshi K (1991) General view of alkaliphiles and thermophiles. In: Horikoshi K, Grant WD (eds) Superbugs: micro-organisms in extreme environments. Springer, Berlin, pp 3–13Google Scholar
  14. Horikoshi K, Akiba T (1982) Alkalophilic microorganisms: a new microbial world. Springer, New YorkGoogle Scholar
  15. Ishikawa M, Nakajima K, Yanagi M, Yamamoto Y, Yamasato K (2003) Marinilactibacillus psychrotolerans gen. nov., sp. nov., a halophilic and alkaliphilic marine lactic acid bacterium isolated from marine organisms in temperate and subtropical areas of Japan. Int J Syst Evol Microbiol 53:711–720CrossRefGoogle Scholar
  16. Ivanova EP, Romanenko LA, Chun J, Matte MH, Matte GR, Mikhailov VV, Svetashev VI, Huq A, Maugel T, Colwell RR (2000) Idiomarina gen. nov., comprising novel indigenous deep-sea bacteria from the Pacific Ocean, including descriptions of two species, Idiomarina abyssalis sp. nov. and Idiomarina zobellii sp. nov. Int J Syst Evol Microbiol 50:901–907Google Scholar
  17. Jean WD, Leu TY, Lee CY, Chu TJ, Lin SY, Shieh WY (2009) Pseudidiomarina marina sp. nov. and Pseudidiomarina tainanensis sp. nov. and reclassification of Idiomarina homiensis and Idiomarina salinarum as Pseudidiomarina homiensis comb. nov. and Pseudidiomarina salinarum comb. nov., respectively. Int J Syst Evol Microbiol 59:53–59CrossRefGoogle Scholar
  18. Jones BE, Grant WD, Collins NC, Mwatha WE (1994) Alkaliphiles: diversity and identification. In: Priest FG (ed) Bacterial diversity and systematics. Plenum Press, New York, pp 195–230Google Scholar
  19. Jones BE, Grant WD, Duckworth AW, Owenson GG (1998) Microbial diversity of soda lakes. Extremophiles 2:191–200CrossRefGoogle Scholar
  20. Jones BE, Grant WD, Duckworth AW, Schumann P, Weiss N, Stackebrandt E (2005) Cellulomonas bogoriensis sp. nov., an alkaliphilic Cellulomonad. Int J Syst Bacteriol 55:1711–1714Google Scholar
  21. Krulwich TA, Guffanti AA (1983) Physiology of acidophilic and alkalophilic bacteria. Adv Microb Physiol 24:173–214CrossRefGoogle Scholar
  22. Llamas I, del Moral A, Martinez-Checa F, Arco Y, Arias S, Quesada E (2006) Halomonas maura is a physiologically versatile bacterium of both ecological and biotechnological interest. Antonie Van Leeuwenhoek 89:395–403CrossRefGoogle Scholar
  23. Ma Y, Xue Y, Grant WD, Collins NC, Duckworth AW, Van Steenbergen RP, Jones BE (2004) Alkalimonas amylolytica gen. nov., sp. nov., and Alkalimonas delamerensis gen. nov., sp. nov., novel alkaliphilic bacteria from soda lakes in China and East Africa. Extremophiles 8:193–200CrossRefGoogle Scholar
  24. Melack JM (1988) Primary producer dynamics associated with evaporative concentration in a shallow, equatorial soda lake (Lake Elmenteita, Kenya). Hydrobiologia 158:1–14CrossRefGoogle Scholar
  25. Mwaura F (1999) A spatio-chemical survey of hydrogeothermal springs in Lake Elmenteita, Kenya. Int J Salt Lake Res 8:127–138Google Scholar
  26. Mwirichia R, Cousin S, Muigai AW, Boga HI, Stackebrandt E (2009) Archaeal diversity in the haloalkaline lake Elmenteita in Kenya. Curr Microbiol 60:47–52CrossRefGoogle Scholar
  27. Nakayama H, Yoshida K, Ono H, Murooka Y, Shinmyo A (2000) Ectoine, the compatible solute of Halomonas elongata, confers hyperosmotic tolerance in cultured tobacco cells. Plant Physiol 122:1239–1247CrossRefGoogle Scholar
  28. Nielsen P, Rainey FA, Outtrup H, Priest FG, Fritze D (1994) Comparative 16S rDNA sequence analysis of some alkaliphilic bacilli and establishment of a sixth rRNA group within the genus Bacillus. FEMS Microbiol Lett 117:61–66CrossRefGoogle Scholar
  29. Nielsen P, Fritze D, Priest FG (1995) Phenetic diversity of alkaliphilic Bacillus strains: proposal for nine new species. Microbiology 141:1745–1761CrossRefGoogle Scholar
  30. Niimura Y, Koh E, Yanagida F, Suzuki K, Komagata K, Kozaki M (1990) Amphibacillus xylanus gen. nov., sp. nov., a facultatively anaerobic sporeforming xylan-digesting bacterium which lacks cytochrome, quinone, and catalase. Int J Sys Bacteriol 40:297–301CrossRefGoogle Scholar
  31. Olsen GJ, Woese CR (1993) Ribosomal RNA: a key to phylogeny. FASEB J 7:113–123Google Scholar
  32. Palleroni NJ (1997) Prokaryotic diversity and the importance of culturing. Antonie van Leeuwenhoek 72:3–19CrossRefGoogle Scholar
  33. Peltola JSP, Andersson MA, Kämpfer P, Auling G, Kroppenstedt RM, Busse HJ, Salkinoja-Salonen MS, Rainey FA (2001) Isolation of toxigenic Nocardiopsis strains from indoor environments and description of two new Nocardiopsis species, N. exhalans sp. nov. and N. umidischolae sp. nov. App Environ Microbiol 67:4293–4304CrossRefGoogle Scholar
  34. Plummer TH, Tarentino AL (1991) Purification of oligosaccharide-cleaving enzymes of Flavobacterium meningosepticum. Glycobiology 1:257–263CrossRefGoogle Scholar
  35. Rees HC, Grant WD, Jones BE, Heaphy S (2004) Diversity of Kenyan soda Lake Alkaliphiles assessed by molecular methods. Extremophiles 8:63–71CrossRefGoogle Scholar
  36. Ringø E, Gatesoupe FJ (1998) Lactic acid bacteria in fish: a review. Aquaculture 160:177–203CrossRefGoogle Scholar
  37. Shimkets LJ, Dworkin M, Reichenbach H (2006) The myxobacteria. In: Balows A, Trüper HG, Dworkin M, Harder W, Schleifer KH (eds) The prokaryotes II, chap 7. Springer, Berlin, pp 31–115CrossRefGoogle Scholar
  38. Simidu U, Tsukamoto K (1985) Habitat segregation and biochemical activities of marine members of the family Vibrionaceae. Appl Microbiol 50:781–790Google Scholar
  39. Sun-Young A, Ishikawa S, Kasai H, Goto K, Yokota A (2007) Amphibacillus sediminis sp. nov., an endosporeforming bacterium isolated from lake sediment in Japan. Int J Syst Evol Microbiol 57:2489–2492CrossRefGoogle Scholar
  40. Taborda M, Antunes A, Tiago I, Veríssimo A, Nobre MF, Da Costa MS (2009) Description of Idiomarina insulisalsae sp. nov., isolated from the soil of a sea salt evaporation pond, proposal to transfer the species of the genus Pseudidiomarina to the genus Idiomarina and emended description of the genus Idiomarina. Syst Appl Microbiol 32:371–378CrossRefGoogle Scholar
  41. Takami H, Kobata K, Nagahama T, Kobayashi H, Inoue A, Horikoshi K (1999) Biodiversity in deep sea sites located near the south part of Japan. Extremophiles 3:97–102CrossRefGoogle Scholar
  42. Tamura K, Nei M, Kumar S (2004) Prospects for inferring very large phylogenies by using the neighbour-joining method. Proc Natl Acad Sci (USA) 101:11030–11035CrossRefGoogle Scholar
  43. Tamura K, Dudley J, Nei M, Kumar S (2007) MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol Biol Evol 24:1596–1599CrossRefGoogle Scholar
  44. Vareschi E (1978) The ecology of Lake Nakuru (Kenya) I. Abundance and feeding of the Lesser Flamingo. Oecologia 32:11–35CrossRefGoogle Scholar
  45. Véron MM (1965) La position taxonomique des Vibrio et de certaines bacteries comparables. C R Acad Sci Paris 261:5243–5246Google Scholar
  46. Wu G, Wu XQ, Wang YN, Chi CQ, Tang YQ, Kida K, Wu XL, Luan ZK (2008) Halomonas daqingensis sp. nov., a moderately halophilic bacterium isolated from an oilfield soil. Int J Syst Evol Microbiol 58:2859–2865CrossRefGoogle Scholar
  47. Zhilina TN, Garnova ES, Tourova TP, Kostrikina NA, Zavarzin GA (2001) Amphibacillus fermentum sp. nov. and Amphibacillus tropicus sp. nov., new alkaliphilic, facultatively anaerobic, saccharolytic bacilli from Lake Magadi. Microbiology 70:711–722 (English translation of Mikrobiologiia)CrossRefGoogle Scholar
  48. Zinder SH, Salyers AA (2001) Microbial ecology—new directions, new importance. In: Boone DR, Castenholz RW (eds) Bergey’s manual of systematic bacteriology, vol. 1: the Archaea and the deeply branching and phototrophic Bacteria. Springer, New York, pp 101–109Google Scholar

Copyright information

© Springer 2010

Authors and Affiliations

  • Romano Mwirichia
    • 1
    Email author
  • A. W. Muigai
    • 1
  • B. Tindall
    • 2
  • H. I. Boga
    • 1
  • E. Stackebrandt
    • 2
  1. 1.Institute for Biotechnology ResearchJomo Kenyatta University of Agriculture and TechnologyNairobiKenya
  2. 2.Deutsche Sammlung von Mikroorganismen und ZellkulturenBraunschweigGermany

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