, Volume 8, Issue 1, pp 45–51 | Cite as

Bacterial diversity of the Inner Mongolian Baer Soda Lake as revealed by 16S rRNA gene sequence analyses

  • Yanhe MaEmail author
  • Weizhou Zhang
  • Yanfen Xue
  • Peijin Zhou
  • Antonio Ventosa
  • William D. Grant
Original Paper


Bacterial diversity associated with Baer Soda Lake in Inner Mongolia of China was investigated using a culture-independent method. Bacterial 16S rRNA gene libraries were generated using bacterial oligonucleotide primers, and 16S rRNA gene sequences of 58 clones were analyzed phylogenetically. The library was dominated by 16S rDNAs of Gram-negative bacteria (24% α-Proteobacteria, 31% β-Proteobacteria, 33% γ-Proteobacteria, and 2% δ-Proteobacteria), with a lower percentage of clones corresponding to Gram-positive bacteria. Forty cloned sequences were similar to that of known bacterial isolates (>97% sequence similarity), represented by the species of the genera Brevundimonas, Comamonas, Alcaligenes, Stenotrophomonas, and Klebsiella. Eighteen cloned sequences showed less affiliation with known taxa (<97% sequence similarity) and may represent novel taxa.


16S rRNA gene Alkaliphilic bacteria Biodiversity Phylogenetic analysis Soda lake 



This work was supported by a grant from the Ministry of Science and Technology of China and a grant from Chinese Academy of Sciences.


  1. Abraham WR, Strompl C, Meyer H, Lindholst S, Moore ER, Christ R, Vancanneyt M, Tindall BJ, Bennasar A, Smit J, Tesar M (1999) Phylogeny and polyphasic taxonomy of aulobacter species. Proposal of Maricaulis gen. nov. with Maricaulis maris (Poindexter) comb. nov. as the type species, and emended description of the genera Brevundimonas and Caulobacter. Int J Syst Bacteriol 49:1053–1073PubMedGoogle Scholar
  2. Amann RI, Ludwig W, Schleifer KH (1995) Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol Rev 59:143–169PubMedGoogle Scholar
  3. Anzai Y, Kim H, Park JY, Wakabayashi H, Oyaizu H (2000) Phylogenetic affiliation of the pseudomonads based on 16S rRNA sequence. Int J Syst Evol Microbiol 50:1563–1589PubMedGoogle Scholar
  4. Bond PL, Hugenholtz P, Keller J, Blackall LL (1995) Bacterial community structures of phosphate-removing and non-phosphate-removing activated sludges from sequencing batch reactors. Appl Environ Microbiol 61:1910–1916PubMedGoogle Scholar
  5. Borneman J, Triplett EW (1997) Molecular microbial diversity in soils from eastern Amazonia: evidence for unusual microorganisms and microbial population shifts associated with deforestation. Appl Environ Microbiol 63:2647–2653PubMedGoogle Scholar
  6. Brosius J, Palmer JL, Kennedy JP, Noller HF (1978) Complete nucleotide sequence of a 16S ribosomal RNA gene from Escherichia coli. Proc Natl Acad Sci USA 75:4801–4805PubMedGoogle Scholar
  7. Burton NP, Norris PR (2000) Microbiology of acidic, geothermal springs of Montserrat: environmental rDNA analysis. Extremophiles 4:315–320PubMedGoogle Scholar
  8. Dojka MA, Harris JK, Pace NR (2000) Expanding the known diversity and environmental distribution of an uncultured phylogenetic division of bacteria. Appl Environ Microbiol 66:1617–1621CrossRefPubMedGoogle Scholar
  9. Drancourt M, Bollet C, Carta A, Rousselier P (2001) Phylogenetic analyses of Klebsiella species delineate Klebsiella and Raoultella gen. nov., with description of Raoultella ornithinolytica comb. nov., Raoultella terrigena comb. nov. and Raoultella planticola comb. nov. Int J Syst Evol Microbiol 51:925–932PubMedGoogle Scholar
  10. Duckworth AW, Grant WD, Jones BE, Steenbergen RV (1996) Phylogenetic diversity of soda lake alkaliphiles. FEMS Microbiol Ecol 19:181–191Google Scholar
  11. Felske A, Rheims H, Wolterink A, Stackebrandt E, Akkermans AD (1997) Ribosome analysis reveals prominent activity of an uncultured member of the class Actinobacteria in grassland soils. Microbiology 143 (Pt 9):2983–2989PubMedGoogle Scholar
  12. Friedrich MW (2002) Phylogenetic analysis reveals multiple lateral transfers of adenosine-5′-phosphosulfate reductase genes among sulfate-reducing microorganisms. J Bacteriol 184(1):278–289PubMedGoogle Scholar
  13. Goto K, Omura T, Hara Y, Sadaie Y (2000) Application of the partial 16S rDNA sequence as an index for rapid identification of species in the genus Bacillus. J Gen Appl Microbiol 46:1–8Google Scholar
  14. Grant WD, Mwatha WE, Jones BE (1990) Alkaliphiles: ecology, diversity and application. FEMS Microbiol Rev 43:260–296Google Scholar
  15. Grant S, Grant WD, Jones BE, Kato C, Li L (1998) Novel archaeal phylotypes from an East African alkaline saltern. Extremophiles 3:139–145Google Scholar
  16. Gray JP, Herwig RP (1996) Phylogenetic analysis of the bacterial communities in marine sediments. Appl Environ Microbiol 62:4049–4059PubMedGoogle Scholar
  17. Hugenholtz P, Goebel BM, Pace NR (1998) Impact of culture-independent studies on the emerging phylogenetic view of bacterial diversity. J Bacteriol 180:4765–4774PubMedGoogle Scholar
  18. Jones BE, Grant WD, Duckworth AW, Owenson GG (1998) Microbial diversity of soda lakes. Extremophiles 2:191–200CrossRefPubMedGoogle Scholar
  19. Jukes TH, Cantor CR (1969) Evolution of protein molecules. In: Munro HN (ed) Mammalian protein metabolism, vol III, Academic, New York, pp 21–132Google Scholar
  20. Liesack W, Weyland H, Stackebrandt E (1991) Potential risks of gene amplification by PCR as determined by 16S rDNA analysis of a mixed-culture of strict barophilic bacteria. Microb Ecol 21:191–198Google Scholar
  21. Maidak BL, Cole JR, Parker CT, Garrity GM, Larsen N, Li B, Lilburn TG, McCaughey MJ, Olsen GJ, Overbeek R, Pramanik S, Schmidt TM, Tiedje JM, Woese CR (1999) A new version of the RDP (Ribosomal Database Project). Nucleic Acids Res 27(1):171–173PubMedGoogle Scholar
  22. Minkwitz A, Berg G (2001) Comparison of antifungal activities and 16S ribosomal DNA sequences of clinical and environmental isolates of Stenotrophomonas maltophilia. J Clin Microbiol 39:139–145CrossRefPubMedGoogle Scholar
  23. Mormile MR, Romine MF, Garcia MT, Ventosa A, Bailey TJ, Peyton BM (1999) Halomonas campisalis sp. nov., a denitrifying, moderately haloalkaliphilic bacterium. Syst Appl Microbiol 22:551–558PubMedGoogle Scholar
  24. Olsen GJ, Lane DJ, Giovannonl SJ, Pace NR, Stahl DA (1986) Microbial ecology and evolution: a ribosomal RNA approach. Annu Rev Microbiol 40:337–365CrossRefPubMedGoogle Scholar
  25. Palleroni NJ, Bradbury JF (1993) Stenotrophomonas, a new bacterial genus for Xanthomonas maltophilia (Hugh 1980) Swings et al. 1983. Int J Syst Bacteriol 43:606–609PubMedGoogle Scholar
  26. Rijkenberg MJ, Kort R, Hellingwerf KJ (2001) Alkalispirillum mobile gen. nov., spec. nov., an alkaliphilic non-phototrophic member of the Ectothiorhodospiraceae. Arch Microbiol 175:369–375CrossRefPubMedGoogle Scholar
  27. Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425PubMedGoogle Scholar
  28. Sambrook J, Fritsch EF, Maniatis T (1989) Molecular cloning: a laboratory manual, 2nd edn. Cold Spring Harbor, NYGoogle Scholar
  29. Schmidt TM, DeLong EF, Pace NR (1991) Analysis of a marine picoplankton community by 16S rRNA gene cloning and sequencing. J Bacteriol 173:4371–4378PubMedGoogle Scholar
  30. Schroll G, Busse HJ, Parrer G, Rolleke S, Lubitz W, Denner EB (2001) Alcaligenes faecalis subsp. parafaecalis subsp. nov., a bacterium accumulating poly-beta-hydroxybutyrate from acetone-butanol bioprocess residues. Syst Appl Microbiol 24:37–43PubMedGoogle Scholar
  31. Sorokin DY, Lysenko AM, Mityushina LL, Tourova TP, Jones BE, Rainey FA, Robertson LA, Kuenen GJ (2001) Thioalkalimicrobium aerophilum gen. nov., sp. nov. and Thioalkalimicrobium sibericum sp. nov., and Thioalkalivibrio versutus gen. nov., sp. nov., Thioalkalivibrio nitratis sp.nov., novel and Thioalkalivibrio denitrificancs sp. nov., novel obligately alkaliphilic and obligately chemolithoautotrophic sulfur-oxidizing bacteria from soda lakes. Int J Syst Evol Microbiol 51:565–580PubMedGoogle Scholar
  32. Stackebrandt E, Rainey FA (1995) Partial and complete 16S rDNA sequences, their use in generation of 16S rDNA phylogenetic trees and their implications in molecular ecological studies. In: Akkermans ADL, van Elsas JD, de Bruijn FJ (eds) Molecular microbial ecology manual. Kluwer, Dordrecht, , pp 1–17Google Scholar
  33. Suzuki MT, Giovannoni SJ (1996) Bias caused by template annealing in the amplification of mixtures of 16S rRNA genes by PCR. Appl Environ Microbiol 62:625–630PubMedGoogle Scholar
  34. Tanner MA, Goebel BM, Dojka MA, Pace NR (1998) Specific ribosomal DNA sequences from diverse environmental settings correlate with environmental contaminants. Appl Environ Microbiol 64:3110–3113PubMedGoogle Scholar
  35. Thompson JD, Higgins DG, Gibson TJ (1994) CLUSTAL W: improving sensitivity of progressive multiple sequence alignments through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22:4673–7680PubMedGoogle Scholar
  36. Torsvik V, Goksoyr J, Daae FL (1990) High diversity in DNA of soil bacteria. Appl Environ Microbiol 56:782–787PubMedGoogle Scholar
  37. Tourova TP, Garnova ES, Zhilina TN (1999) Phylogenetic diversity of alkaliphilic saccharolytic bacteria isolated from soda lakes. Microbiology 68:701–709Google Scholar
  38. Tsai YL, Olson BH (1991) Rapid method for direct extraction of DNA from soil and sediments. Appl Environ Microbiol 57:1070–1074PubMedGoogle Scholar
  39. Van de Peer Y, De Wachter R (1994). TREECON for Windows: a software package for the construction and drawing of evolutionary trees for the Microsoft Windows environment. Comput Appl Biosci 10:569–570PubMedGoogle Scholar
  40. Von Wintzingerode F, Gobel UB, Stackebrandt E (1997) Determination of microbial diversity in environmental samples: pitfalls of PCR-based rRNA analysis. FEMS Microbiol Rev 21:213–229PubMedGoogle Scholar
  41. Ward DM, Weller R, Bateson MM (1990) 16SrRNA sequences reveal numerous uncultured microorganisms in a natural community. Nature 345:63–65Google Scholar
  42. Willems A, Pot B, Falsen E, Vandamme P, Gillis M, Kersters K, De Ley J (1991) Polyphasic taxonomic study of the emended genus Comamonas: relationship to Aquaspirillum aquaticum, E. Falsen group 10, and other clinical isolates. Int J Syst Bacteriol 41:427–444Google Scholar
  43. Zavarzin GA, Zhilina TN, Kevbrin VV (1999) The alkaliphilic microbial community and its functional diversity. Mikrobiologiya 68:579–599Google Scholar
  44. Zhang W, Mao W, Xue Y, Ma Y, Zhou P (2001) Diversity of alkaliphilic bacteria in Hailaer soda lakes, Inner Mongolia Autonomous Region of China (in Chinese). Biodivers Sci 9:44–50Google Scholar
  45. Zhilina TN, Zavarzin GA (1994) Alkaliphilic anaerobic community at pH10. Curr Microbiol 29:109–112Google Scholar

Copyright information

© Springer-Verlag 2004

Authors and Affiliations

  • Yanhe Ma
    • 1
    Email author
  • Weizhou Zhang
    • 1
  • Yanfen Xue
    • 1
  • Peijin Zhou
    • 1
  • Antonio Ventosa
    • 2
  • William D. Grant
    • 3
  1. 1.Department of Microbial Physiology and Ecology, Institute of MicrobiologyChinese Academy of SciencesBeijing China
  2. 2.Department of Microbiology and Parasitology, Faculty of PharmacyUniversity of SevillaSevillaSpain
  3. 3.Department of Microbiology and ImmunologyUniversity of LeceisterLeceister UK

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