Current Microbiology

, Volume 57, Issue 2, pp 145–152 | Cite as

Phylogenetic Analyses of Archaeal Ribosomal DNA Sequences from Salt Pan Sediment of Mumbai, India

  • Nasier Ahmad
  • Sarika Sharma
  • Farrah G. Khan
  • Rajinder Kumar
  • Sarojini Johri
  • Malik Z. Abdin
  • Ghulam N. Qazi


The archaeal diversity in salt pan sediment from Mumbai, India, was investigated by 16S rDNA-dependent molecular phylogeny. Small-subunit rRNA (16S rDNA) from salt pan sediment metagenome were amplified by polymerase chain reaction (PCR) using primers specific to the domain archaea. Thirty-two unique phylotypes were obtained by PCR-based RFLP of 16S rRNA genes using endonucleases Hae111 and Msp1, which were most suitable to score the genetic diversity. These phylotypes spanned a wide range within the domain Archaea including both Crenarchaeota and Euryarcheaota. However, none of the retrieved Crenarchaeota sequences could be grouped with previously cultured Crenarchaeota. Of all the Euryarcheaota sequences, three sequences were related to Haloarchaea, two were related to cultured Methanosarcina sp., and the remaining sequences were affiliated with uncultured Methanosarcina sp., Methanogenium sp., and Methanolobus sp. 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 a highly diverse archaeal population and may represent novel sequences and organisms specially adapted to the salt pan sediment of Mumbai. These findings are of fundamental value for understanding the complexity of salt pan ecosystems.



This work was supported by the Council of Scientific and Industrial Research (CSIR) Government of India, Project No. SMM0002.


  1. Amann RI, Ludwig W, Schleifer KH (1995) Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol J Rev 59:143–169Google Scholar
  2. Andreae MO, Raemdonck H (1983) Dimethyl sulphide in the surface ocean and the marine atmosphere: a global view. Science 221:744–747PubMedCrossRefGoogle Scholar
  3. Asami H, Aida M, Watanabe K (2005) Accelerated sulphur cycle in coastal marine sediment beneath areas of intensive shellfish aquaculture. Appl Environ Microbiol 6:2925–2933CrossRefGoogle Scholar
  4. Auchtung TA, Tackacs-Vesbach CD, Cavanaugh CM (2006) 16S rRNA phylogenetic investigation of the candidate division “Korarchaeota”. Appl Environ Microbiol 72:5077–5082PubMedCrossRefGoogle Scholar
  5. Barns SM, Delwiche CF, Palmer JD, Pace NR (1996) Perspectives on archaeal diversity, thermophily and monophyly from environmental rRNA sequences. Proc Natl Acad Sci USA 93:9188–9193PubMedCrossRefGoogle Scholar
  6. Benlloch S, Martinez-Murcia AJ, Rodriguez-Valera F (1995) Sequencing of bacterial and archaeal 16S rRNA genes directly amplified from a hypersaline environment. Syst Appl Microbiol 18:574–581Google Scholar
  7. 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 41:12–19Google Scholar
  8. Bissett A, Bowman J, Burke C (2006) Bacterial diversity in organically enriched fish farm sediments. FEMS Microbiol Ecol 55:48–56PubMedCrossRefGoogle Scholar
  9. Boone DR, Whitman WB, Koga Y (2001) Order III: methanosarcinales. In: Boone DR, Castenholz RW, Garrity GM (eds) Bergey’s manual of systematic bacteriology, Vol 1, 2nd edn. Springer, New York, pp 268–293Google Scholar
  10. 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:R42PubMedCrossRefGoogle Scholar
  11. 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 66:3269–3276PubMedCrossRefGoogle Scholar
  12. Deshmukh SK (2004) Isolation of dermatophytes and other keratinophilic fungi from the vicinity of salt pan soils of Mumbai, India. Mycopathologia 157:265–267PubMedCrossRefGoogle Scholar
  13. 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 172:213–218PubMedCrossRefGoogle Scholar
  14. Fourcans A, Bleijswijk JV, Grimalt JO, Kuhl M, Esteve I, Muyzer Gerard, Caumette P, Duran R (2004) Characterization of functional groups in a hypersaline microbial mat community (Salins-de-Giraud, Camargue, France). FEMS Microbiol Ecol 51:55–70PubMedCrossRefGoogle Scholar
  15. Grant WD, Larsen H (1989) Extremely halophilic archaeobacteria. In: Staley, Bryant, Pfennig, Holt (eds) Bergey’s manual of systematic bacteriology, Vol 3, 1st edn. Williams and Wilkins, Baltimore, pp 2216–2219Google Scholar
  16. 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 417:63–67PubMedCrossRefGoogle Scholar
  17. Hugenholtz P, Huber T (2003) Chimeric 16S rDNA sequences of diverse origin are accumulating in the public databases. Int J Syst Evol Microbiol 53:289–293CrossRefGoogle Scholar
  18. Kanokratana P, Chanapan S, Pootanakit K, Eurwilaichitr L (2004) Diversity and abundance of Bacteria and Archaea in the Bor Khlueng Hot Spring in Thailand. J Basic Microbiol 6:430–444CrossRefGoogle Scholar
  19. Kendall MM, Wardlaw GD, Tang CF, Bonin AS, Liu Y, Valentine DL (2007) Diversity of Archaea in marine sediments from Skan Bay, Alaska, including cultivated methanogens, and description of Methanogenium boonei sp. nov Appl Environ Microbiol 73:407–414CrossRefGoogle Scholar
  20. Kerkar S, Lokabharathi PA (2007) Stimulation of sulfate-reducing activity at salt-saturation in the salterns of Ribandar, Goa, India. Geomicrobiol J 24:101–110CrossRefGoogle Scholar
  21. Khandavilli S, Sequiera F, Furtado I (1999) Metal tolerance of extremely halophilic bacteria isolated from estuaries of Goa, India. Ecol Environ Conserv 5:149–152Google Scholar
  22. 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 63:2338–2346PubMedGoogle Scholar
  23. Kopczynski ED, Batson MM, Ward DM (1994) Recognition of chimeric small-subunit ribosomal DNAs composed of genes from uncultivated microorganisms. Appl Environ Microbiol 60:746–748PubMedGoogle Scholar
  24. Lyimo TJ, Pol A, Camp HJMO, Harhangi HR, Vogels GD (2000) Methanosarcina semesiae sp. nov., a dimethylsulfide-utilizing methanogen from mangrove sediment. Int J Syst Evol Micriob 50:171–178Google Scholar
  25. Munson MA, Nedwell BD, Embley TM (1997) Phylogenetic diversity of archaea in sediment samples from a coastal salt marsh. Appl Environ Microbiol 63:4729–4733PubMedGoogle Scholar
  26. Neha S, Melissa MK, Yitai Liu, David RB (2005) Isolation and characterization of methylotrophic methanogens from anoxic marine sediments in Skan Bay, Alaska: description of Methanococcoides alaskense sp. nov., and emended description of Methanosarcina baltica. Int J Syst Evol Microbiol 55:2531–2538CrossRefGoogle Scholar
  27. Ochsenreiter T, Pelicitas, Schleper C (2002) Diversity of Archaea in hypersaline environments characterized by molecular phylogenetic and cultivation studies. Extremophiles 6:267–274PubMedCrossRefGoogle Scholar
  28. Oline D, Schmidt, Grant M (2006) Biogeography and landscape-scale diversity of the dominant Crenarchaeota of soil. Microbial Ecol 52:480–490CrossRefGoogle Scholar
  29. Olsen GJ, Lane DJ, Giovannoni SJ, Pace NR, Stahl DA (1986) Microbial ecology and evolution: a ribosomal RNA approach. Annu Rev Microbiol 40:337–365PubMedCrossRefGoogle Scholar
  30. Oren A (1999) Bioenergetic aspects of halophilism. Microbial Mol Biol Review 63:334–348Google Scholar
  31. 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 54:491–498PubMedCrossRefGoogle Scholar
  32. Purdy KJ, Cresswell-Maynard TD, Nedwell DB, McGenity TJ, Timmis KN, Embley TM (2004) Isolation of haloarchaea that grow at low salinities. Environ Microbiol 6:591–595PubMedCrossRefGoogle Scholar
  33. 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 57:600–604CrossRefGoogle Scholar
  34. Quesada E, Ventosa A, Rodriguez-Valera F, Ramos-Cormenzana A (1982) Types and properties of some bacteria from hypersaline soils. J Appl Bacteriol 53:155–161Google Scholar
  35. Radax C, Gruber C, Stan-Lotter H (2001) Novel haloarchaeal 16S rRNA gene sequences from Alpine Permo-Triassic rock salt. Extremophiles 5:221–228PubMedCrossRefGoogle Scholar
  36. Raghavan TM, Furtado I (2004) Occurrence of extremely halophilic Archaea in sediments from the continental shelf of west coast of India. Curr Sci 86:1065–1067Google Scholar
  37. Savage KN, 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
  38. Shuldiner AR, Nirula A, Roth J (1989) Hybrid DNA artifact from PCR of closely related target sequences. Nucleic Acids Res 17:4409PubMedCrossRefGoogle Scholar
  39. Vetriani C, Reysenbach AL, Dor J (1998) Recovery and Phylogenetic analysis of archaeal rRNA sequences from continental shelf sediments. FEMS Microbiol Lett 161:83–88PubMedCrossRefGoogle Scholar
  40. Ward DM, Weller R, Bateson MM (1990) 16SrRNA sequences reveal numerous uncultured microorganisms in a natural community. Nature 345:63–65PubMedCrossRefGoogle Scholar
  41. Weisburg WG, Barns SM, Pelletier DA, Lane DJ (1991) 16S ribosomal DNA amplification for phylogenetic study. J Bacteriol 173:697–703PubMedGoogle Scholar
  42. 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

Copyright information

© Springer Science+Business Media, LLC 2008

Authors and Affiliations

  • Nasier Ahmad
    • 1
  • Sarika Sharma
    • 1
  • Farrah G. Khan
    • 1
  • Rajinder Kumar
    • 1
  • Sarojini Johri
    • 1
  • Malik Z. Abdin
    • 2
  • Ghulam N. Qazi
    • 1
  1. 1.Biotechnology DivisionIndian Institute of Integrative Medicine (CSIR)Jammu-TawiIndia
  2. 2.Department of BiotechnologyHamdard UniversityNew DelhiIndia

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