SpringerLink
Log in

Bacterial biodiversity from Roopkund Glacier, Himalayan mountain ranges, India

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

Abstract

The bacterial diversity of two soil samples collected from the periphery of the Roopkund glacial lake and one soil sample from the surface of the Roopkund Glacier in the Himalayan ranges was determined by constructing three 16S rRNA gene clone libraries. The three clone libraries yielded a total of 798 clones belonging to 25 classes. Actinobacteria was the most predominant class (>10% of the clones) in the three libraries. In the library from the glacial soil, class Betaproteobacteria (24.2%) was the most predominant. The rarefaction analysis indicated coverage of 43.4 and 41.2% in the samples collected from the periphery of the lake thus indicating a limited bacterial diversity covered; at the same time, the coverage of 98.4% in the glacier sample indicated most of the diversity was covered. Further, the bacterial diversity in the Roopkund glacier soil was low, but was comparable with the bacterial diversity of a few other glaciers. The results of principal component analysis based on the 16S rRNA gene clone library data, percentages of OTUs and biogeochemical data revealed that the lake soil samples were different from the glacier soil sample and the biogeochemical properties affected the diversity of microbial communities in the soil samples.

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

Access this article

Log in via an institution

Subscribe and save

Springer+ Basic
EUR 32.99 /Month
  • Get 10 units per month
  • Download Article/Chapter or Ebook
  • 1 Unit = 1 Article or 1 Chapter
  • Cancel anytime
Subscribe now

Buy Now

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

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5
Fig. 6
Fig. 7

Similar content being viewed by others

References

  • Abyzov SS, Mitskevich IN, Poglazova MN (1998) Microflora of the deep glacier horizons of central Antarctica. Microbiology 67:66–73

    Google Scholar 

  • Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215:403–410

    CAS  Google Scholar 

  • Amato P, Hennebelle R, Magand O, Sancelme M, Delort AM, Barbante C, Boutron C, Ferrari C (2007) Bacterial characterization of the snow cover at Spitzberg, Svalbard. FEMS Microbiol Ecol 59:255–264

    Article  CAS  Google Scholar 

  • APHA (1995) Standard methods for the examination of water and wastewater, 19th edn. American Public Health Association, Washington, DC

    Google Scholar 

  • Bill A (1994) The Nanda Devi affair, Penguin Books India, New Delhi. ISBN 0-14-024045-4

  • Blakemore LC, Searle PL, Daly BK (1987) Methods for chemical analysis of soils. NZ Soil Bureau Scientific Report 80

  • Bottos EM, Vincent CW, Greer WF, Whyte LG (2008) Prokaryotic diversity of arctic ice shelf microbial mats. Environ Microbiol 10:950–966

    Article  CAS  Google Scholar 

  • Bowman JP, McCuaig RD (2003) Biodiversity, community structural shifts, and biogeography of prokaryotes within Antarctic continental shelf sediment. Appl Environ Microbiol 69:2463–2483

    Article  CAS  Google Scholar 

  • Bowman JP, Rea SM, McCammon SA, McMeekin TA (2000) Diversity and community structure within anoxic sediment from marine salinity meromictic lakes and a coastal meromictic marine basin, Vestfold Hills, Eastern Antarctica. Environ Microbiol 2:227–237

    Article  CAS  Google Scholar 

  • Brambilla E, Hippe H, Hagelstein A, Tindall BJ, Stackebrandt E (2001) 16S rDNA diversity of cultured and uncultured prokaryotes of a mat sample from Lake Fryxell, McMurdo Dry Valleys, Antarctica. Extremophiles 5:23–33

    Article  CAS  Google Scholar 

  • Bray RH, Kurtz LT (1945) Determination of total organic and available forms of phosphorus in soils. Soil Sci 59:39–45

    Article  CAS  Google Scholar 

  • Burkert U, Warnecke F, Babenzien D, Zwirnmann E, Pernthaler J (2003) Members of a readily enriched beta-proteobacterial clade are common in surface waters of a humic lake. Appl Environ Microbiol 69:6550–6559

    Article  CAS  Google Scholar 

  • Carpenter EJ, Lin S, Capone DG (2000) Bacterial activity in South Pole snow. Appl Environ Microbiol 66:4514–4517

    Article  CAS  Google Scholar 

  • Certini G, Campbell CD, Edwards AC (2004) Rock fragments in soil support a different microbial community from the fine earth. Soil Biol Biochem 36:1119–1128

    Article  CAS  Google Scholar 

  • Cheng SM, Foght JM (2007) Cultivation-independent and -dependent characterization of bacteria resident beneath John Evans Glacier. FEMS Microbiol Ecol 59:318–330

    Article  CAS  Google Scholar 

  • Christner BC, Mosley-Thompson E, Thompson LG, Reeve JN (2001) Isolation of bacteria and 16S rDNAs from Lake Vostok accretion ice. Environ Microbiol 3:570–577

    Article  CAS  Google Scholar 

  • Christner BC, Mosley-Thompson E, Thompson LG, Reeve JN (2003) Bacterial recovery from ancient glacial ice. Environ Microbiol 5:433–436

    Article  CAS  Google Scholar 

  • Chun J, Lee J-H, Jung Y, Kim M, Kim S, Kim BK, Lim YW (2007) EzTaxon: a web-based tool for the identification of prokaryotes based on 16S ribosomal RNA gene sequences. Int J Syst Evol Microbiol 57:2259–2261

    Article  CAS  Google Scholar 

  • Costello EK, Schmidt SK (2006) Microbial diversity in alpine tundra wet meadow soil: novel Chloroflexi from a cold, water-saturated environment. Environ Microbiol 8:1471–1486

    Article  CAS  Google Scholar 

  • Dancer SJ, Shears P, Platt DJ (1997) Isolation and characterization of coliforms from glacial ice and water in Canada’s High Arctic. J Appl Microbiol 82:597–609

    CAS  Google Scholar 

  • Eichorst SA, Breznak JA, Schmidt TM (2007) Isolation and characterization of soil bacteria that define Terriglobus gen. nov. in the phylum Acidobacteria. Appl Environ Microbiol 73:2708–2717

    Article  CAS  Google Scholar 

  • Fierer N, Schimel JP, Holden PA (2003) Controls on microbial CO2 production: a comparison of surface and subsurface soil horizons. Glob Chang Biol 9:1322–1332

    Article  Google Scholar 

  • Fierer N, Bradford MA, Jackson RB (2007) Toward an ecological classification of soil bacteria. Ecology 88:1354–1364

    Article  Google Scholar 

  • Foght J, Aislabie J, Turner S, Brown CE, Ryburn J, Saul DJ, Lawson W (2004) Culturable bacteria in subglacial sediments and ice from two southern hemisphere. Glaciers Microbiol Ecol 47:329–340

    CAS  Google Scholar 

  • Gangwar P, Alam SI, Bansod S, Singh L (2009) Bacterial diversity of soil samples from the western Himalayas, India. Can J Microbiol 55:564–577

    Article  CAS  Google Scholar 

  • Glöckner FO, Zaichikov E, Belkova N, Denissova L, Pernthaler J, Pernthaler A, Amann R (2000) Comparative 16S rRNA analysis of lake bacterioplankton reveals globally distributed phylogenetic clusters including an abundant group of actinobacteria. Appl Environ Microbiol 66:5053–5065

    Article  Google Scholar 

  • Good IJ (1954) The population frequencies of species and the estimation of population parameters. Biometrica 40:237–264

    Google Scholar 

  • Hur I, Chun J (2004) A method for comparing multiple bacterial community structures from 16S rDNA clone library sequences. J Microbiol 42:9–13

    CAS  Google Scholar 

  • Jackson ML (1967) Soil chemical analysis. Prentice-Hall of India, New Delhi

  • Karr EA, Sattley WM, Jung DO, Madigan MT, Achenbach LA (2003) Remarkable diversity of phototrophic purple bacteria in a permanently frozen Antarctic lake. Appl Environ Microbiol 69:4910–4914

    Article  CAS  Google Scholar 

  • Karr EA, Ng JM, Belchik SM, Sattley WM, Madigan MT, Achenbach LA (2006) Biodiversity of methanogenic and other archaea in the permanently frozen Lake Fryxell, Antarctica. Appl Environ Microbiol 72:1663–1666

    Article  CAS  Google Scholar 

  • Kastovská K, Elster J, Stibal M, Santrůcková H (2005) Microbial assemblages in soil microbial succession after glacial retreat in Svalbard (High Arctic). Microbiol Ecol 50:396–407

    Article  Google Scholar 

  • Kimura M (1980) A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16:111–120

    Article  CAS  Google Scholar 

  • Kirchman DL, Yu L, Cottrell MT (2003) Diversity and abundance of uncultured cytophaga-like bacteria in the Delaware estuary. Appl Environ Microbiol 69:6587–6596

    Article  CAS  Google Scholar 

  • LaMontagne MG, Schimel JP, Holden PA (2003) Comparison of subsurface and surface soil bacterial communities in California grassland as assessed by terminal restriction fragment length polymorphisms of PCRamplified 16S rRNA genes. Microbiol Ecol 46:216–227

    Article  CAS  Google Scholar 

  • Lane DJ (1991) 16S/23S rRNA sequencing. In: Stackebrandt E, Goodfellow M (eds) Nucleic acid techniques in bacterial systematics. Wiley, New York, pp 115–147

    Google Scholar 

  • Lefauconnier B, Hagen JO, Rudant JP (1994) Flow speed and calving rate of Kongsbreen glacier, Svalbard, using SPOT images. Polar Res 10:56–65

    Google Scholar 

  • Li S, **ao X, Yin X, Wang F (2006) Bacterial community along a historic lake sediment core of Ardley Island, west Antarctica. Extremophiles 10:461–467

    Article  CAS  Google Scholar 

  • Li Y, Li F, Zhang X, Qin S, Zeng Z, Dang H, Qin Y (2008) Vertical distribution of bacterial and archaeal communities along discrete layers of a deep-sea cold sediment sample at the East Pacific Rise (approximately 13 degrees N). Extremophiles 12:573–585

    Article  CAS  Google Scholar 

  • Liu Y, Yao T, Jiao N, Kang S, Zeng Y, Huang S (2006) Microbial community structure in moraine lakes and glacial meltwaters, Mount Everest. FEMS Microbiol Lett 265:98–105

    Article  CAS  Google Scholar 

  • Liu Y, Yao T, Jiao N, Kang S, Xu B, Zeng Y, Huang S, Liu X (2009) Bacterial diversity in the snow over Tibetan Plateau Glaciers. Extremophiles 13:411–423

    Article  CAS  Google Scholar 

  • López-García P, López-López A, Moreira D, Rodríguez-Valera F (2001) Diversity of free-living prokaryotes from a deep-sea site at the Antarctic Polar Front. FEMS Microbiol Ecol 36:193–202

    Google Scholar 

  • Lysnes K, Thorseth IH, Steinsbu BO, Øvreås L, Torsvik T, Pedersen RB (2004) Microbial community diversity in seafloor basalt from the Arctic spreading ridges. FEMS Microbiol Ecol 50:213–230

    Article  CAS  Google Scholar 

  • Magurran AE (1996) Ecological diversity and its measurement. Chapman & Hall, London, pp 274–286

  • Marcy Y, Ouverney C, Bik EM, Losekann T, Ivanova N, Martin HG, Szeto E, Platt D, Hugenholtz P, Relman DA, Quake SR (2007) Dissecting biological ‘dark matter’ with single-cell genetic analysis of rare and uncultivated TM7 microbes from the human mouth. Proc Natl Acad Sci USA 104:11889–11894

    Article  CAS  Google Scholar 

  • Mikucki JA, Priscu JC (2007) Bacterial diversity associated with Blood Falls, a subglacial outflow from the Taylor Glacier, Antarctica. Appl Environ Microbiol 73:4029–4039

    Article  CAS  Google Scholar 

  • Mindl B, Anesio AM, Meirer K, Hodson AJ, Laybourn-Parry J, Sommaruga R, Sattler B (2007) Factors influencing bacterial dynamics along a transect from supraglacial runoff to proglacial lakes of a high Arctic glacier. FEMS Microbiol Ecol 59:307–317

    Article  CAS  Google Scholar 

  • Mosier AC, Murray AE, Fritsen CH (2007) Microbiota within the perennial ice cover of Lake Vida, Antarctica. FEMS Microbiol Ecol 59:274–288

    Article  CAS  Google Scholar 

  • Nealson KH (1999) Post-Viking microbiology: new approaches, new data, new insights. Orig Life Evol Biosph 29:73–93

    Article  CAS  Google Scholar 

  • Neufeld JD, Yu Z, Lam W, Mohn WW (2004) Serial analysis of ribosomal sequence tags (SARST): a high-throughput method for profiling complex microbial communities. Environ Microbiol 6:131–144

    Article  CAS  Google Scholar 

  • Niederberger TD, McDonald IR, Hacker AL, Soo RM, Barrett JE, Wall DH, Cary SC (2008) Microbial community composition in soils of Northern Victoria Land, Antarctica. Environ Microbiol 10:1713–1724

    Article  CAS  Google Scholar 

  • Perreault NN, Andersen DT, Pollard WH, Greer CW, Whyte LG (2007) Characterization of the prokaryotic diversity in cold saline perennial springs of the Canadian high Arctic. Appl Environ Microbiol 73:1532–1543

    Article  CAS  Google Scholar 

  • Prabagaran SR, Manorama R, Delille D, Shivaji S (2007) Predominance of Roseobacter, Sulfitobacter, Glaciecola and Psychrobacter in seawater collected off Ushuaia, Argentina, Sub-Antarctica. FEMS Microbiol Ecol 59:342–355

    CAS  Google Scholar 

  • Priscu JC, Christner BC (2003) Microbial diversity and bioprocessing. In: Bull AT (ed) Earth’s icy biosphere. ASM press, Washington DC, pp 130–145

  • Reddy GSN, Aggarwal RK, Matsumotto GI, Shivaji S (2000) Arthrobacter flavus sp. nov., a psychrophilic bacterium isolate from a pond in McMurdo Dry Valley, Antarctica. Int J Syst Evol Microbiol 50:1553–1561

    CAS  Google Scholar 

  • Reddy GSN, Uttam A, Shivaji S (2008) Bacillus cecembensis sp. nov., isolated from the Pindari glacier of the Indian Himalayas. Int J Syst Evol Microbiol 58:2330–2335

    Article  CAS  Google Scholar 

  • Reddy GSN, Pradhan S, Manorama R, Shivaji S (2009) Cryobacterium roopkundense sp. nov., a psychrophilic bacterium from a Himalayan glacier. Int J Syst Evol Microbiol 60:866–870

    Google Scholar 

  • Reed AJ, Lutz RA, Vetriani C (2006) Vertical distribution and diversity of bacteria and archaea in sulfide and methane-rich cold seep sediments located at the base of the Florida Escarpment. Extremophiles 10:199–211

    Article  CAS  Google Scholar 

  • Rhoades JD (1982) Soluble salts. In: Page AL (ed) Methods of soil analysis. Chemical and microbiological properties, 2nd edn. Soil Science Society of America, Madison, pp 167–179

  • Segawa T, Miyamoto K, Ushida K, Agata K, Okada N, Kohshima S (2005) Seasonal change in bacterial flora and biomass in mountain snow from the Tateyama Mountains, Japan, analyzed by 16S rRNA gene sequencing and real-time PCR. Appl Environ Microbiol 71:123–130

    Article  CAS  Google Scholar 

  • Shivaji S, Reddy GSN, Aduri RP, Kutty R, Ravenschlag K (2004) Bacterial diversity of a soil sample from Schirmacher Oasis, Antarctica. Cell Mol Biol 50:525–536

    CAS  Google Scholar 

  • Sjöling S, Cowan DA (2003) High 16S rDNA bacterial diversity in glacial meltwater lake sediment, Bratina Island, Antarctica. Extremophiles 7:275–282

    Article  Google Scholar 

  • Skidmore M, Anderson SP, Sharp M, Foght J, Lanoil BD (2005) Comparison of microbial community composition in two subglacial environments reveals a possible role for microbes in chemical weathering processes. Appl Environ Microbiol 71:6986–6997

    Article  CAS  Google Scholar 

  • Smith JJ, Tow LA, Stafford W, Cary C, Cowan DA (2006) Bacterial diversity in three different Antarctic Cold Desert mineral soils. Microbiol Ecol 51:413–421

    Article  Google Scholar 

  • Stackebrandt E, Brambilla E, Cousin S, Dirks W, Pukall R (2004) Culture-independent analysis of bacterial species from an anaerobic mat from Lake Fryxell, Antarctica: prokaryotic diversity revisited. Cell Mol Biol 50:517–524

    CAS  Google Scholar 

  • Steven B, Briggs G, McKay CP, Pollard WH, Greer CW, Whyte LG (2007) Characterization of the microbial diversity in a permafrost sample from the Canadian high Arctic using culturedependent and culture-independent methods. FEMS Microbiol Ecol 59:513–523

    Article  CAS  Google Scholar 

  • Subbiah BH, Asija GL (1956) A rapid procedure for determination of available nitrogen in soils. Curr Sci 25:259–260

    CAS  Google Scholar 

  • Suzuki K, Sasaki J, Uramoto M, Nakase T, Komagata K (1997) Cryobacterium psychrophilum gen. nov., sp. nov., nom. rev., comb. nov., an obligately psychrophilic actinomycete to accommodate ‘‘Curtobacterium psychrophilum’’ Inoue and Komagata 1976. Int J Syst Bacteriol 47:474–478

    Article  CAS  Google Scholar 

  • Tamura K, Dudley J, Nei M, Kumar S (2007) MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol Biol Evol 24:1596–1599

    Article  CAS  Google Scholar 

  • Thompson JD, Higgins DG, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG (1997) The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25:4876–4882

    Article  CAS  Google Scholar 

  • Tindall BJ (2004) Prokaryotic diversity in the Antarctic: the tip of the iceberg. Microb Ecol 47:271–283

    Article  CAS  Google Scholar 

  • Treves DS, **a B, Tiedje JM (2003) A two-species test of the hypothesis that spatial isolation influences microbial diversity in soil. Microbiol Ecol 45:20–28

    Article  CAS  Google Scholar 

  • Tsai YL, Olson BH (1991) Rapid method for direct extraction of DNA from soil and sediments. Appl Environ Microbiol 57:1070–1074

    CAS  Google Scholar 

  • Tsai YL, Olson BH (1992) Rapid method for seperation of bacterial DNA from humic substances in sediments for polymerase chain reaction. Appl Environ Microbiol 58:2292–2295

    CAS  Google Scholar 

  • Wagner D, Kobabe S, Liebner S (2009) Bacterial community structure and carbon turnover in permafrost-affected soils of the Lena Delta, northeastern Siberia. Can J Microbiol 55:77–83

    Article  Google Scholar 

  • Walkley A, Black CA (1934) An examination of Degtjareff methods for determining soil organic matter and a proposed modification of chromic acid titration method. Soil Sci 37:29–38

    Article  CAS  Google Scholar 

  • **ang SR, Yao TD, An LZ, Xu BQ, Li Z, Wu GJ, Wang YQ, Ma S, Chen XR (2004) Bacterial diversity in Malan ice core from the Tibetan Plateau. Folia Microbiol 49:269–275

    Article  CAS  Google Scholar 

  • **ang S, Yao T, An L, Xu B, Wang J (2005) 16S rRNA sequences and differences in bacteria isolated from the Muztag Ata glacier at increasing depths. Appl Environ Microbiol 71:4619–4627

    Article  CAS  Google Scholar 

  • Yergeau E, Newsham KK, Pearce DA, Kowalchuk GA (2007) Patterns of bacterial diversity across a range of Antarctic terrestrial habitats. Environ Microbiol 9:2670–2682

    Article  CAS  Google Scholar 

  • Zhang X, Tandong Y, Lizhe A, Lide T, Shijian X (2006) A study on the vertical profile of bacterial DNA structure in the Puruogangri (Tibetan Plateau) ice core using denaturing gradient gel electrophoresis. Ann Glaciol 43:160–166

    Article  CAS  Google Scholar 

  • Zhang X, Yao T, Tian L, Xu S, An L (2008) Phylogenetic and physiological diversity of bacteria isolated from Puruogangri ice core. Microbiol Ecol 55:476–488

    Article  CAS  Google Scholar 

  • Zhou J, Davey ME, Figueras JB, Rivkina E, Gilichinsky D, Tiedje JM (1997) Phylogenetic diversity of a bacterial community determined from Siberian tundra soil DNA. Microbiology 143:3913–3919

    Article  CAS  Google Scholar 

  • Zhou J, **a B, Treves DS, Wu L-Y, Marsh TL, O’Neill RV, Palumbo AV, Tiedje JM (2002) Spatial and resource factors influencing high microbial diversity in soil. Appl Environ Microbiol 68:326–334

    Article  CAS  Google Scholar 

Download references

Acknowledgments

We would like to thank the Department of Biotechnology and Council of Scientific and Industrial Research, Government of India for financial support to Dr. S. Shivaji. TNRS acknowledges the CSIR, Government of India, for the award of Research Associateship. We would like to thank Dr. M. K. Reddy, Scientist and Head and Dr. M. Kalita, Scientist from National Environmental Engineering Research Institute, Zonal Laboratory, Hyderabad, and Dr. M. K. Singh, Scientist from National Centre for Antarctic Ocean Research, Goa, for providing the data of the soil chemical characteristics.

Author information

Authors and Affiliations

  1. Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, 500 007, India

    Suman Pradhan, T. N. R. Srinivas, Pavan Kumar Pindi, K. Hara Kishore, Z. Begum, Pawan Kumar Singh, Ashish Kumar Singh, M. S. Pratibha, Arun K. Yasala, G. S. N. Reddy & S. Shivaji

Authors
  1. Suman Pradhan
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. T. N. R. Srinivas
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Pavan Kumar Pindi
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. K. Hara Kishore
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Z. Begum
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Pawan Kumar Singh
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Ashish Kumar Singh
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. M. S. Pratibha
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. Arun K. Yasala
    View author publications

    You can also search for this author in PubMed Google Scholar

  10. G. S. N. Reddy
    View author publications

    You can also search for this author in PubMed Google Scholar

  11. S. Shivaji
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to S. Shivaji.

Additional information

Communicated by A. Oren.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary material 1 (DOC 394 kb)

Rights and permissions

Reprints and permissions

About this article

Cite this article

Pradhan, S., Srinivas, T.N.R., Pindi, P.K. et al. Bacterial biodiversity from Roopkund Glacier, Himalayan mountain ranges, India. Extremophiles 14, 377–395 (2010). https://doi.org/10.1007/s00792-010-0318-3

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00792-010-0318-3

Keywords

Search

Navigation