Skip to main content
SpringerLink
Log in

Analysis of intergenic spacer region length polymorphisms to investigate the halophilic archaeal diversity of stromatolites and microbial mats

  • Method Paper
  • Published:
Extremophiles Aims and scope Submit manuscript

Abstract

Hamelin Pool in Western Australia is one of the two major sites in the world with active marine stromatolite formation. Surrounded by living smooth and pustular mats, these ancient laminated structures are associated with cyanobacterial communities. Recent studies have identified a wide diversity of bacteria and archaea in this habitat. By understanding and evaluating the microbial diversity of this environment we can obtain insights into the formation of early life on Earth, as stromatolites have been dated in the geological record as far back as 3.5 billion years. Automated ribosomal intergenic spacer analysis (ARISA) patterns were shown to be a useful method to genetically discriminate halophilic archaea within this environment. Patterns of known halophilic archaea are consistent, by replicate analysis, and the halophilic strains isolated from stromatolites have novel intergenic spacer profiles. ARISA–PCR, performed directly on extracted DNA from different sample sites, provided significant insights into the extent of previous unknown diversity of halophilic archaea within this environment. Cloning and sequence analysis of the spacer regions obtained from stromatolites confirmed the novel and broad diversity of halophilic archaea in this environment.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

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

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2

Similar content being viewed by others

References

  • Acinas SG, Antón J, Rodríguez-Valera F (1999) Diversity of free-living and attached bacteria in offshore western Mediterranean waters as depicted by analysis of genes encoding 16S rRNA. Appl Environ Microbiol 65:514–522

    PubMed  CAS  Google Scholar 

  • 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 4:373–376

    Article  PubMed  CAS  Google Scholar 

  • Arp G, Reimer A, Reitner J (2001) Photosynthesis-induced biofilm calcification and calcium concentrations in phanerozoic oceans. Science 292:1701–1704

    Article  PubMed  CAS  Google Scholar 

  • Benlloch S, Acinas SG, Antón J, López-López A, Luz SP, Rodríguez-Valera F (2001) Archaeal biodiversity in crystallizer ponds from a solar saltern: culture versus PCR. Microb Ecol 41:12–19

    PubMed  CAS  Google Scholar 

  • Boucher Y, Douady CJ, Sharma AK, Kamekura M, Doolittle WF (2004) Intragenomic heterogeneity and intergenomic recombination among haloarchaeal rRNA genes. J Bacteriol 186:3980–3990

    Article  PubMed  CAS  Google Scholar 

  • Briones C, Amils R (2000) Nucleotide sequence of the 23s rRNA from Haloferax mediterranei and phylogenetic analysis of halophilic archaea based on LSU rRNA. Syst Appl Microbiol 23:124–131

    PubMed  CAS  Google Scholar 

  • Burns BP, Goh F, Allen MA, Neilan BA (2004) Microbial diversity of extant stromatolites in the hypersaline marine environment of Shark Bay, Australia. Environ Microbiol 6:1096–1101

    Article  PubMed  CAS  Google Scholar 

  • Cardinale M, Brusetti L, Quatrini P, Borin S, Puglia AM, Rizzi A, Zanardini E, Sorlini C, Corselli C, Daffonchio D (2004) Comparison of different primer sets for use in automated ribosomal intergenic spacer analysis of complex bacterial communities. Appl Environ Microbiol 70:6147–6156

    Article  PubMed  CAS  Google Scholar 

  • DasSarma S, Fleischmann EM, Rodríguez-Valera F (1995) Halophiles. In: Robb FT (ed) Archaea: a laboratory manual. CSHL Press, Cold Spring Harbor, pp 225–230

    Google Scholar 

  • DeLong EF (1992) Archaea in coastal marine environments. Proc Natl Acad Sci USA 89:5685–5689

    Article  PubMed  CAS  Google Scholar 

  • Dennis PP, Ziesche S, Mylvaganam S (1998) Transcription analysis of two disparate rRNA operons in the halophilic Archaeon Haloarcula marismortui. J Bacteriol 180:4804–4813

    PubMed  CAS  Google Scholar 

  • Elshahed MS, Najar FZ, Roe BA, Oren A, Dewers TA, Krumholz LR (2004) Survey of archaeal diversity reveals an abundance of halophilic archaea in a low-salt, sulfide- and sulfur-rich spring. Appl Environ Microbiol 70:2230–2239

    Article  PubMed  CAS  Google Scholar 

  • Fisher MM, Triplett EW (1999) Automated approach for ribosomal intergenic spacer analysis of microbial diversity and its application to freshwater bacterial communities. Appl Environ Microbiol 65:4630–4636

    PubMed  CAS  Google Scholar 

  • García-Martínez J, Rodríguez-Valera F (2000) Microdiversity of uncultured marine prokaryotes: the SAR11 cluster and the marine Archaea of group I. Mol Ecol 9:935–948

    Article  PubMed  Google Scholar 

  • García-Martínez J, Bescós I, Rodríguez-Sala J, Rodríguez-Valera (2001) RISSC: a novel database for ribosomal 16S-23S RNA genes spacer regions. Nucleic Acid Res 29:178–180

    Article  PubMed  Google Scholar 

  • Goh F, Leuko S, Allen MA, Bowman JP, Kamekura M, Neilan BA, Burns BP (2006) Halococcus hamelinensis sp. nov., a novel halophilic archaeon isolated from stromatolites in Shark Bay, Australia. Int J Syst 56:1323–1329

    CAS  Google Scholar 

  • González N, Romero J, Espejo RT (2003) Comprehensive detection of bacterial populations by PCR amplification of the 16S–23S rRNA spacer region. J Microbiol Meth 55:91–97

    Article  CAS  Google Scholar 

  • Grant WD, Gemmell RT, McGenity TJ (1998) Halobacteria: the evidence for longevity. Extremophiles 2:279–287

    Article  PubMed  CAS  Google Scholar 

  • Kushner DJ, Kamekura M (1988) Physiology of halophilic eubacteria. In: Rodríguez-Valera F (ed) Halophilic bacteria, vol I. CRC Press, Boca Raton, pp 109–140

    Google Scholar 

  • Leuko S, Weidler G, Radax C, Legat A, Koemle NI, Kargl G, Stan-Lotter H (2002) Examining the physico-chemical resistance of halobacteria with the LIFE-DEAD kit, following exposure to simulated Martian atmospheric conditions and heat. ESA Special Publication (ESA-SP-518)

  • Martin-Laurent F, Philippot L, Hallet S, Chaussod R, Germon JC, Soulas G, Catroux G (2001) DNA extraction from soils: old bias for new microbial diversity analysis methods. Appl Environ Microbiol 67:2354–2359

    Article  PubMed  CAS  Google Scholar 

  • McGenity TJ, Gemmell RT, Grant WD, Stan-Lotter H (2000) Origins of halophilic microorganisms in ancient salt deposits. Environ Microbiol 2:243–250

    Article  PubMed  CAS  Google Scholar 

  • Monty C (1977) Evolving concepts on the nature and the ecological significance of stromatolites. In: Flügel E (ed) Fossil algae, recent results and developments. Springer, Berlin Heidelberg New York, pp 15–35

    Google Scholar 

  • Mormile MR, Biesen MA, Gutierrez MC, Ventosa A, Pavlovich JB, Onstott TC, Fredrickson JK (2003) Isolation of Halobacterium salinarum retrieved directly from halite brine inclusion. Environ Microbiol 5(11):1094–1102

    Article  PubMed  Google Scholar 

  • Ng WV, Kennedy SP, Mahairas GG, Berquist B, Pan M, Shukla HD, Lasky SR, Baliga NS, Thorsson V, Sbrogna J, Swartzell S, Weir D, Hall J, Dahl TA, Welti R, Goo YA, Leithauser B, Keller K, Cruz R, Danson MJ, Hough DW, Maddocks DG, Jablonksi PE, Krebs MP, Angevine CM, Dale H, Isenbarger TA, Peck RF, Pohlschroder M, Spudich JL, Jung KH, Alam M, Freitas T, Hou S, Daniels CJ, Dennis PP, Omer AD, Ebhardt H, Lowe TM, Liang P, Riley M, Hood L, DasSarma S (2000) Genome sequence of Halobacterium species NRC-1. PNAS 97:12176–12181

    Article  PubMed  CAS  Google Scholar 

  • Oren A (2001) The order Halobacteriales. In: Dworkin M, Falkow S, Rosenberg E, Schleifer K-H, Stackebrand E (eds) The prokaryotes: an evolving electronic resource for the microbiological community, 3rd ed., release 3.2, 25 July 2001. Springer, Berlin Heidelberg New York

    Google Scholar 

  • Oren A, Gurevich P, Gemmell RT, Teske A (1995) Halobaculum gomorrense gen. nov., sp. nov., a novel extremely halophilic archaeon from the Dead Sea. Int J Syst Bacteriol 45:747–754

    Article  PubMed  CAS  Google Scholar 

  • Øvreås L, Daae FL, Torsvik V, Rodríguez-Valera F (2003) Characterization of microbial diversity in hypersaline environments by melting profiles and reassociation kinetics in combination with terminal restriction fragment length polymorphism (T-RFLP). Microb Ecol 46:291–301

    Article  PubMed  CAS  Google Scholar 

  • Palmisano AC, Summons RE, Cronin SE, Des Marias DJ (1989) Lipophilic pigments from cyanobacterial (blue-green algal) and diatom mats in Hamelin pool, Shark Bay, Western Australia. J Phycol 25:655–661

    Article  PubMed  CAS  Google Scholar 

  • Papineau D, Walker JJ, Mojzsis SJ, Pace NR (2005) Composition and structure of microbial communities from stromatolites of Hamelin Pool in Shark Bay, Western Australia. Appl Environ Microbiol 71:4822–4832

    Article  PubMed  CAS  Google Scholar 

  • Petrisor AI, Decho AW (2004) Using geographical information techniques to quantify the spatial structure of endolithic boring processes within sediment grains of marine stromatolites. J Micro Meth 56:173–180

    Article  Google Scholar 

  • Polz MF, Cavanaugh CM (1998) Bias in template to product ratios in multitemplate PCR. Appl Environ Microbiol 64:3724–3730

    PubMed  CAS  Google Scholar 

  • Purdy KJ, Cresswell-Maynard TD, Nedwell DB, McGenity TJ, Grant WD, Timmis KN Embley TM (2004) Isolation of haloarchaea that grow at low salinities. Environ Microbiol 6:591–595

    Article  PubMed  CAS  Google Scholar 

  • Radax C, Gruber C, Stan-Lotter H (2001) Novel haloarchaeal 16S rRNA gene sequences from alpine Permo–Triassic rock salt. Extremophiles 5:221–228

    Article  PubMed  CAS  Google Scholar 

  • Ranjard L, Brothier E, Nazaret S (2000) Sequencing bands of ribosomal intergenic spacer analysis fingerprints for characterization and microscale distribution of soil bacterium populations responding to mercury spiking. Appl Environ Microbiol 66:5334–5339

    Article  PubMed  CAS  Google Scholar 

  • Reid RP, James NP, Macintyre IG, Dupraz CP, Burne RV (2003) Shark Bay stromatolites: microfabrics and reinterpretation of origins. Facies 49:299–324

    Google Scholar 

  • Rodríguez-Valera F, Ruiz-Berraquero F, Ramos-Cormenzana A (1979) Isolation of extreme halophiles from Seawater. Appl Environ Microbiol 38:164–165

    PubMed  Google Scholar 

  • Stan-Lotter H, Pfaffenhuemer M, Legat A, Busse HJ, Gruber C (2002) Halococcus dombrowskii sp. nov., an archaeal isolate from a Permian alpine salt deposit. Int J Syst Evol Microbiol 52:1807–1814

    Article  PubMed  CAS  Google Scholar 

  • Tillett D, Neilan BA (2000) Xanthogenate nucleic acid isolation from cultured and environmental cyanobacteria. J Phycol 36:251–258

    Article  CAS  Google Scholar 

  • Wilson K (1990) Preparation of genomic DNA from bacteria. In: Ausubel FM, Brent R, Kingston RE, Moore DD, Seidman JG, Smith JA, Struhl K (eds) Current protocols in molecular biology. Wiley, New York, pp 2.4.1–2.4.2

    Google Scholar 

  • von Wintzingerode F, Goebel UB, Stackebrandt E (1997) Determination of microbial diversity in environmental samples: pitfalls of PCR-based rRNA analysis. FEMS Microbiol Rev 21:213–229

    Article  Google Scholar 

  • Yannarell AC, Triplett EW (2005) Geographic and environmental sources of variation in lake bacterial community composition. Appl Environ Microbiol 71:227–239

    Article  PubMed  CAS  Google Scholar 

Download references

Acknowledgments

This research was funded by the Australian Research Council and an International Postgraduate Research Scholarship from Macquarie University, Australia. We thank Professor Francisco Rodríguez-Valera for kindly providing us with the updated URL of the RISSC database.

Author information

Authors and Affiliations

  1. Australian Centre for Astrobiology, Biotechnology Research Institute, Macquarie University, NSW 2109, Sydney, Australia

    S. Leuko, B. P. Burns, M. R. Walter & B. A. Neilan

  2. School of Biotechnology and Biomolecular Science, University of New South Wales, NSW 2052, Sydney, Australia

    F. Goh, M. A. Allen, B. P. Burns & B. A. Neilan

Authors
  1. S. Leuko
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. F. Goh
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. M. A. Allen
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. B. P. Burns
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. M. R. Walter
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. B. A. Neilan
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to B. A. Neilan.

Additional information

Communicated by K. Horikoshi.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Leuko, S., Goh, F., Allen, M.A. et al. Analysis of intergenic spacer region length polymorphisms to investigate the halophilic archaeal diversity of stromatolites and microbial mats. Extremophiles 11, 203–210 (2007). https://doi.org/10.1007/s00792-006-0028-z

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00792-006-0028-z

Keywords

Search

Navigation