Skip to main content
SpringerLink
Log in

Phylogenetic Characterization of Archaea in Saltpan Sediments

  • Original Article
  • Published:
Indian Journal of Microbiology Aims and scope Submit manuscript

Abstract

A study was undertaken to investigate the presence of archaeal diversity in saltpan sediments of Goa, India by 16S rDNA-dependent molecular phylogeny. Small subunit rRNA (16S rDNA) from saltpan sediment metagenome were amplified by polymerase chain reaction (PCR) using primers specific to the domain archaea. 10 unique phylotypes were obtained by PCR based RFLP of 16S rRNA genes using endonuclease Msp 1, which was most suitable to score the genetic diversity. These phylotypes spanned a wide range within the domain archaea including both crenarchaeota and euryarcheaota. None of the retrieved crenarchaeota sequences could be grouped with previously cultured crenarchaeota however; two sequences were related with haloarchaea. Most of the sequences determined were closely related to the sequences that had been previously obtained from metagenome of a variety of marine environments. The phylogenetic study of a site investigated for the first time revealed the presence of low archaeal population but showed yet unclassified species, may specially adapted to the salt pan sediment of Goa.

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

  1. Oren A (1999) Bioenergetic aspects of halophilism. Microbial Mol Biol Rev 63:334–348

    CAS  Google Scholar 

  2. Raghavan TM, Furtado I (2004) Occurrence of extremely halophilic Archaea in sediments from the continental shelf of west coast of India. Curr Sci 86:1065–1067

    Google Scholar 

  3. Auchtung TA, Tackacs-Vesbach CD, Cavanaugh CM (2006) 16S rRNA phylogenetic investigation of the candidate division Korarchaeota. Appl Environ Microbiol 72:5077–50824

    Article  PubMed  CAS  Google Scholar 

  4. Barns SM, Delwiche CF, Palmer JD, Pace NR (1996) Perspectives on archaeal diversity, thermophily and monophyly from environmental rRNA sequences. Proc Natl Acad Sci 93:9188–9193

    Article  PubMed  CAS  Google Scholar 

  5. Brochier C, Gribaldo S, Zivanovic Y, Confalonieri F, Forterr P (2005) Nanoarchaea: representatives of a novel archaeal phylum or a fast-evolving euryarchaeal lineage related to Thermococcales. Genome Biol 6:R42

    Article  PubMed  Google Scholar 

  6. Huber H, Hohn MJ, Rachel R, Fuchs T, Wimmer VC, Stetter KO (2002) A new phylum of archaea represented by a nanosized hyperthermophilic symbiont. Nature 417:63–67

    Article  PubMed  CAS  Google Scholar 

  7. Oline DK, Schmidt, Grant M (2006) Biogeography and landscape-scale diversity of the dominant crenarchaeota of soil. Microbial Ecol 52:480–490

    Article  Google Scholar 

  8. Ahmad N, Johri S, Abdin MZ, Qazi GN (2009) Molecular characterization of bacterial population in the forest soil of Kashmir, India. World J Microbiol Biotechnol 25:107–113

    Article  CAS  Google Scholar 

  9. Amann RI, Ludwig W, Schleifer KH (1995) Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol J Rev 59:143–169

    CAS  Google Scholar 

  10. Weisburg WG, Barns SM, Pelletier DA, Lane DJ (1991) 16S ribosomal DNA amplification for phylogenetic study. J Bacteriol 173:697–703

    PubMed  CAS  Google Scholar 

  11. Ahmad N, Sharma S, Khan FG, Kumar R, Johri S, Abdin MZ, Qazi GN (2008) Phylogenetic analyses of archaeal ribosomal DNA Sequences from Salt Pan Sediment of Mumbai, India. Curr Microbiol 57:145–152

    Article  PubMed  CAS  Google Scholar 

  12. Olsen GJ, Lane DJ, Giovannoni SJ, Pace NR, Stahl DA (1986) Microbial ecology and evolution: a ribosomal RNA approach. Annu Rev Microbiol 40:337–365

    Article  PubMed  CAS  Google Scholar 

  13. Deshmukh SK (2004) Isolation of dermatophytes and other keratinophilic fungi from the vicinity of salt pan soils of Mumbai, India. Mycopathologia 157:265–267

    Article  PubMed  CAS  Google Scholar 

  14. Kerkar S, Lokabharathi PA (2007) Stimulation of sulfate-reducing activity at salt-saturation in the salterns of Ribandar, Goa, India. Geomicrobiol J 24:101–110

    Article  CAS  Google Scholar 

  15. Qian-fu W, Wei L, Hai Y, Yan-li L, Hai-hua C, Dornmayr-Pfaffenhuemer M, Stan-Lotter H, Guang-qin G (2007) Halococcus qingdaonensis sp. nov., a halophilic archaeon isolated from a crude sea-salt sample. Int J Syst Evol Microbiol 57:600–604

    Article  Google Scholar 

  16. Pasic L, Bartual SG, Ulrih NP, Grabnar M, Velikonja BH (2005) Diversity of halophilic archaea in the crystallizers of an Adriatic solar saltern. FEMS Microbiol Ecol 54:491–498

    Article  PubMed  CAS  Google Scholar 

  17. Fourcans A, Bleijswijk JV, Grimalt JO, Kuhl M, Esteve I, Gerard Muyzer, Caumette P, Duran R (2004) Characterization of functional groups in a hypersaline microbial mat community (Salins-de-Giraud, Camargue, France). FEMS Microbiol Ecol 51:55–70

    Article  PubMed  CAS  Google Scholar 

  18. Ochsenreiter T, Pelicitas, Schleper C (2002) Diversity of Archaea in hypersaline environments characterized by molecular phylogenetic and cultivation studies. Extremophiles 6:267–274

    Article  PubMed  CAS  Google Scholar 

  19. 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 

  20. Cytryn E, Minz D, Oremland RS, Cohen Y (2000) Distribution and diversity of archaea corresponding to the limnological cycle of a hypersaline stratified lake (Solar Lake, Sinai, Egypt). Appl Environ Microbiol 66:3269–3276

    Article  PubMed  CAS  Google Scholar 

  21. Eder W, Ludwig W, Huber R (1999) Novel 16S rRNA gene sequences retrieved from highly saline brine sediments of Kebrit Deep, Red Sea. Arch Microbiol 172:213–218

    Article  PubMed  CAS  Google Scholar 

  22. Munson MA, Nedwell BD, Embley TM (1997) Phylogenetic diversity of archaea in sediment samples from a coastal salt marsh. Appl Environ Microbiol 63:4729–4733

    PubMed  CAS  Google Scholar 

  23. Benlloch S, Acinas SG, Anton J, Lopez L, Luz SP, Rodriguez-Valera F (2001) Archaeal biodiversity in crystallizer ponds from a solar saltern: culture versus PCR. Microbiol Ecol 41:12–19

    CAS  Google Scholar 

  24. Vetriani C, Reysenbach AL, Dore J (1998) Recovery and phylogenetic analysis of archaeal rRNA sequences from continental shelf sediments. FEMS Microbiol Lett 161:83–88

    Article  PubMed  CAS  Google Scholar 

  25. Hugenholtz P, Huber T (2003) Chimeric 16S rDNA sequences of diverse origin are accumulating in the public databases. Int J Syst Evol Microbiol 53:289–293

    Article  CAS  Google Scholar 

  26. Komatsoulis GA, Waterman MS (1997) A new computational method for detection of chimeric 16S rRNA artifacts generated by PCR amplification from mixed bacterial populations. Appl Environ Microbiol 63:2338–2346

    PubMed  CAS  Google Scholar 

  27. Kopczynski ED, Batson MM, Ward DM (1994) Recognition of chimeric small-subunit ribosomal DNAs composed of genes from uncultivated microorganisms. Appl Environ Microbiol 60:746–748

    PubMed  CAS  Google Scholar 

  28. Shuldiner AR, Nirula A, Roth J (1989) Hybrid DNA artifact from PCR of closely related target sequences. Nucleic Acids Res 17:4409

    Article  PubMed  CAS  Google Scholar 

  29. Tsiamis G, Katsaveli K, Ntougias S, Kyrpides N, Andersen G, Piceno Y, Bourtzis K (2008) Prokaryotic community profiles at different operational stages of a Greek solar saltern. Res in microbiol 159:609–627

    Article  Google Scholar 

  30. Park SJ, Park BJ, Rhee SK (2008)  Comparative analysis of archaeal 16S rRNA and amoA genes to estimate the abundance and diversity of ammonia-oxidizing archaea in marine sediments. Extremphiles 12:605–615

    Article  CAS  Google Scholar 

  31. Asami H, Aida M, Watanabe K (2005) Accelerated sulphur cycle in coastal marine sediment beneath areas of intensive shellfish aquaculture. Appl Environ Microbiol 6:2925–2933

    Article  Google Scholar 

  32. Kim BS, Oh HM, Chun J (2005) Archaeal Diversity in tidal flat as revealed by 16S rRNA analysis. J. Microbiol 43:144–151

    PubMed  CAS  Google Scholar 

  33. Valenzuela-Encinas C, Neria-Gonzalez I, Alcantara-Hernandez RJ, Enriquez-Aragon JA, Estrada-Alvarado I, Hernandez-Rodriguez C, Dendooven L, Marsch (2008) Phylogenetic analysis of the archaeal community in an alkaline-saline soil of the former lake Texcoco. Extremphiles 12:247–254

    Article  CAS  Google Scholar 

  34. Mesbah NM, Abou-Ela SH, Wiegel J (2007) Novel and unexpected prokaryotic diversity in water and sediments of the alkaline, Hypersaline lakes of the Wadi An Natrun, Egypt. Microbial Ecol 54:598–617

    Article  CAS  Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

  36. Khandavilli S, Sequiera F, Furtado I (1999) Metal tolerance of extremely halophilic bacteria isolated from estuaries of Goa, India. Ecol Env Cons 5:149–152

    CAS  Google Scholar 

  37. Quesada E, Ventosa A, Rodriguez-Valera F, Ramos-Cormenzana A (1982) Types and properties of some bacteria from hypersaline soils. J Appl Bacteriol 53:155–161

    Google Scholar 

  38. Whitman WB, Coleman DC, Wiebe WJ (1998) Prokaryotes: the unseen majority. Proc Natl Acad Sci USA 95:6578–6583

    Article  PubMed  CAS  Google Scholar 

Download references

Acknowledgments

Nasier Ahmad wishes to express his gratitude to Council of Scientific and Industrial Research (CSIR), Govt. of India for the awarding of a Senior Research fellowship. The authors are grateful to Rajinder Kumar for excellent technical assistance in sequencing work. This work was financially supported by CSIR, New Delhi, Project Number NWP006.

Author information

Authors and Affiliations

  1. Biotechnology Division, Indian Institute of Integrative Medicine (Council of Scientific and Industrial Research), Canal Road, Jammu-Tawi, 180001, India

    Nasier Ahmad, Sarojini Johri & Ghulam N. Qazi

  2. Microbiology and Mycology Division, Indian Institute of Integrative Medicine (CSIR) Br, Srinagar, 190005, India

    Phalisteen Sultan

  3. Biotechnology Department, Faculty of Science, Jamia Hamdard University, Hamdard Nagar, New Delhi, 110062, India

    Malik Z. Abdin

Authors
  1. Nasier Ahmad
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Sarojini Johri
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Phalisteen Sultan
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Malik Z. Abdin
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Ghulam N. Qazi
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Nasier Ahmad.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Ahmad, N., Johri, S., Sultan, P. et al. Phylogenetic Characterization of Archaea in Saltpan Sediments. Indian J Microbiol 51, 132–137 (2011). https://doi.org/10.1007/s12088-011-0125-2

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s12088-011-0125-2

Keywords

Search

Navigation