Advertisement

Extremophiles

, Volume 13, Issue 1, pp 31–37 | Cite as

Intraspecific polymorphism of 16S rRNA genes in two halophilic archaeal genera, Haloarcula and Halomicrobium

  • Heng-Lin Cui
  • Pei-Jin Zhou
  • Aharon Oren
  • Shuang-Jiang LiuEmail author
Original Paper

Abstract

All members of the genera Haloarcula and Halomicrobium whose names have been validly published were surveyed for 16S rRNA gene polymorphism, and the transcription of the genes from two species was investigated during growth at different NaCl concentrations. The species of Haloarcula and Halomicrobium harbour at least two different 16S rRNA gene copies, and 18 new sequences of 16S rRNA genes were obtained. The type I and type II 16S rRNA genes of Haloarcula are divergent at 4.8–5.6% of their nucleotide positions. The type III and type IV 16S rRNA genes from Halomicrobium mukohataei JCM 9738T are 9.0% divergent, which represents the highest intraspecific divergent 16S rRNA genes so far seen. Phylogenetic analysis based on 16S rRNA genes indicated that all type I 16S rRNA genes were clustered, and the same was true for the type II 16S rRNA genes of Haloarcula species. The two clusters, respectively generated from type I and type II 16S rRNA genes, were sharply separated and their divergences (4.8–5.6%) are in the range of various divergence usually found between genera in the order Halobacteriales (about 5–10%). Results from reverse transcription-PCR showed that the type I and type II copies of Har. amylolytica BD-3T and type III and type IV copies of Hmc. mukohataei JCM 9738T were all transcribed to 16S rRNA molecules under different salt concentrations (15–28% NaCl).

Keywords

Halophilic archaea Haloarcula Halomicrobium 16S rRNA gene polymorphism 

Notes

Acknowledgments

This study was supported by the National Basic Research Program from the Ministry of Science and Technology (MOST) of China (Grant No. 2004CB719601) and a start-up grant from Jiangsu University (Grant No. 08JDG016).

References

  1. Amann G, Stetter KO, Llobet-Brossa E, Amann R, Antón J (2000) Direct proof for the presence and expression of two 5% different 16S rRNA genes in individual cells of Haloarcula marismortui. Extremophiles 4:373–376PubMedCrossRefGoogle Scholar
  2. Baliga NS, Bonneau R, Facciotti MT, Pan M, Glusman G, Deutsch EW, Shannon P, Chiu Y, Weng RS, Gan RR, Hung P, Date SV, Marcotte E, Hood L, Ng WV (2004) Genome sequence of Haloarcula marismortui: a halophilic archaeon from the Dead Sea. Genome Res 14:2221–2234PubMedCrossRefGoogle Scholar
  3. Boucher Y, Douady CJ, Sharma AK, Kamekura M, Doolittle WF (2004) Intragenomic heterogeneity and intergenomic recombination among haloarchaeal rRNA genes. J Bacteriol 186:3980–3990PubMedCrossRefGoogle Scholar
  4. Burns DG, Janssen PH, Itoh T, Kamekura M, Li Z, Jensen G, Rodríguez-Valera F, Bolhuis H, Dyall-Smith ML (2007) Haloquadratum walsbyi gen. nov., sp. nov., the square haloarchaeon of Walsby, isolated from saltern crystallizers in Australia and Spain. Int J Syst Evol Microbiol 57:387–392PubMedCrossRefGoogle Scholar
  5. Carranza S, Giribet G, Riberat C, Baguna J, Riutort M (1996) Evidence that two types of 18S rDNA coexist in the genome of Dugesia (Schmidtea) mediterranea (Platyhelminthes, Turbellaria, Tricladida). Mol Biol Evol 13:824–832PubMedGoogle Scholar
  6. Case RJ, Boucher Y, Dahllöf I, Holmström C, Doolittle WF, Kjelleberg S (2007) Use of 16S rRNA and rpoB genes as molecular markers for microbial ecology studies. Appl Environ Microbiol 73:278–288PubMedCrossRefGoogle Scholar
  7. Clayton RA, Sutton G, Hinkle PS Jr, Bult C, Fields C (1995) Intraspecific variation in small-subunit rRNA sequences in GenBank: why single sequences may not adequately represent prokaryotic taxa. Int J Syst Bacteriol 45:595–599PubMedGoogle Scholar
  8. Cole JR, Chai B, Marsh TL, Farris RJ, Wang Q, Kulam SA, Chandra S, McGarrell DM, Schmidt TM, Garrity GM, Tiedje JM (2003) The Ribosomal Database Project (RDP-II): previewing a new autoaligner that allows regular updates and the new prokaryotic taxonomy. Nucleic Acids Res 31:442–443PubMedCrossRefGoogle Scholar
  9. Crosby LD, Criddle CS (2003) Understanding bias in microbial community analysis techniques due to rrn operon copy number heterogeneity. Biotechniques 34:790–794PubMedGoogle Scholar
  10. Dennis PP (1999) Expression of ribosomal RNA operons in halophilic archaea. In: Oren A (ed) Microbiology and biogeochemistry of hypersaline environments. CRC Press, Boca Raton, pp 319–329Google Scholar
  11. Dennis PP, Shimmin LC (1997) Evolutionary divergence and salinity-mediated selection in halophilic archaea. Microbiol Mol Biol Rev 61:90–104PubMedGoogle Scholar
  12. Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783–791CrossRefGoogle Scholar
  13. Gemmell RT, McGenity TJ, Grant WD (1998) Use of molecular techniques to investigate possible long-term dormancy of halobacteria in ancient halite deposits. Ancient Biomol 2:125–133Google Scholar
  14. Gunderson JH, Sogin ML, Wollett G, Hollingdale M, de la Cruz VF, Waters AP, McCutchan TF (1987) Structurally distinct, stage-specific ribosomes occur in Plasmodium. Science 238:933–937PubMedCrossRefGoogle Scholar
  15. Harth E, Romero J, Torres R, Espejo RT (2007) Intragenomic heterogeneity and intergenomic recombination among Vibrio parahaemolyticus 16S rRNA genes. Microbiology 153:2640–2647PubMedCrossRefGoogle Scholar
  16. Ihara K, Watanabe S, Tamura T (1997) Haloarcula argentinensis sp. nov. and Haloarcula mukohataei sp. nov., two new extremely halophilic archaea collected in Argentina. Int J Syst Bacteriol 47:73–77PubMedGoogle Scholar
  17. Kimura M (1980) A simple method for estimating evolutionary rate of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16:111–120PubMedCrossRefGoogle Scholar
  18. Kumar S, Tamura K, Nei M (2004) MEGA3: Integrated software for molecular evolutionary genetics analysis and sequence alignment. Brief Bioinform 5:150–163PubMedCrossRefGoogle Scholar
  19. López-López A, Benlloch S, Bonfá M, Rodríguez-Valera F, Mira A (2007) Intragenomic 16S rDNA divergence in Haloarcula marismortui is an adaptation to different temperatures. J Mol Evol 65:687–696PubMedCrossRefGoogle Scholar
  20. Marchandin H, Teyssier C, Simeon De Buochberg M, Jean-Pierre H, Carriere C, Jumas-Bilak E (2003) Intra-chromosomal heterogeneity between the four 16S rRNA gene copies in the genus Veillonella: implications for phylogeny and taxonomy. Microbiology 149:1493–1501PubMedCrossRefGoogle Scholar
  21. Mylvaganam S, Dennis PP (1992) Sequence heterogeneity between the two genes encoding 16S rRNA from the halophilic archaebacterium Haloarcula marismortui. Genetics 130:399–410PubMedGoogle Scholar
  22. Ng WL, Yang CF, Halladay JT, Arora P, DasSarma S (1995) Protocol 25: isolation of genomic and plasmid DNAs from Halobacterium halobium. In: DasSarma S, Fleischmann EM (eds) Archaea: a laboratory manual: halophiles. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, pp 179–180Google Scholar
  23. Nieuwlandt DT, Palmer JR, Armbruster DT, Kuo YP, Oda W, Daniels CJ (1995) Protocol 23: a rapid procedure for the isolation of RNA from Haloferax volcanii. In: DasSarma S, Fleischmann EM (eds) Archaea: a laboratory manual: halophiles. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, pp 161–162Google Scholar
  24. Oren A, Elevi R, Watanabe S, Ihara K, Corcelli A (2002) Halomicrobium mukohataei gen. nov., comb. nov., and emended description of Halomicrobium mukohataei. Int J Syst Evol Microbiol 52:1831–1835PubMedCrossRefGoogle Scholar
  25. Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425PubMedGoogle Scholar
  26. Savage KNL, Krumholz LR, Oren A, Elshahed MS (2007) Haladaptatus paucihalophilus gen. nov., sp. nov., a halophilic archaeon isolated from a low-salt, sulfide-rich spring. Int J Syst Evol Microbiol 57:19–24PubMedCrossRefGoogle Scholar
  27. Sehgal SN, Gibbons NE (1960) Effect of some metal ions on the growth of halobacterium cutirubrum. Can J Microbiol 6:165–169PubMedCrossRefGoogle Scholar
  28. Tu D, Blaha G, Moore PB, Steitz TA (2005) Gene replacement in Haloarcula marismortui: construction of a strain with two of its three chromosomal rRNA operons deleted. Extremophiles 9:427–435PubMedCrossRefGoogle Scholar
  29. Vreeland RH, Straight S, Krammes J, Dougherty K, Rosenzweig WD, Kamekura M (2002) Halosimplex carlsbadense gen. nov., sp. nov., a unique halophilic archaeon, with three 16S rRNA genes, that grows only in defined medium with glycerol and acetate or pyruvate. Extremophiles 6:445–452PubMedCrossRefGoogle Scholar
  30. Wang Y, Zhang ZS, Ramanan N (1997) The actinomycete Thermobispora bispora contains two distinct types of transcriptionally active 16S rRNA genes. J Bacteriol 179:3270–3276PubMedGoogle Scholar
  31. Woese CR, Kandler O, Wheelis ML (1990) Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. Proc Natl Acad Sci USA 87:4576–4579PubMedCrossRefGoogle Scholar
  32. Yang Y, Cui HL, Zhou PJ, Liu SJ (2007) Haloarcula amylolytica sp. nov., an extremely halophilic archaeon isolated from Aibi salt lake in Xin-Jiang, China. Int J Syst Evol Microbiol 57:103–106PubMedCrossRefGoogle Scholar
  33. Yap WH, Zhang Z, Wang Y (1999) Distinct types of rRNA operons exist in the genome of the actinomycete Thermomonospora chromogena and evidence for horizontal transfer of an entire rRNA operon. J Bacteriol 181:5201–5209PubMedGoogle Scholar

Copyright information

© Springer 2008

Authors and Affiliations

  • Heng-Lin Cui
    • 1
    • 2
  • Pei-Jin Zhou
    • 1
  • Aharon Oren
    • 3
  • Shuang-Jiang Liu
    • 1
    • 4
    Email author
  1. 1.State Key Laboratory of Microbial Resources, Institute of MicrobiologyChinese Academy of SciencesBeijingPeople’s Republic of China
  2. 2.School of Food and Biological EngineeringJiangsu UniversityZhenjiangPeople’s Republic of China
  3. 3.The Institute of Life Sciences and the Moshe Shilo Minerva Center for Marine BiogeochemistryThe Hebrew University of JerusalemJerusalemIsrael
  4. 4.Institute of MicrobiologyChinese Academy of SciencesBeijingPeople’s Republic of China

Personalised recommendations