Bacterial diversity of soil in the vicinity of Pindari glacier, Himalayan mountain ranges, India, using culturable bacteria and soil 16S rRNA gene clones

Extremophiles

Volumn 15, Issue 1, 2011, Pages 1-22

  Shivaji, S ^a   Pratibha, M S ^a   Sailaja, B ^a   Hara Kishore, K ^a   Singh, Ashish K ^a   Begum, Z ^a   Anarasi, Uttam ^a   Prabagaran, S R ^a   Reddy, G S N ^a   Srinivas, T N R ^a  

^a CENTRE FOR CELLULAR AND MOLECULAR BIOLOGY   (India)

Author keywords

16S rRNA gene clone library; Cellular fatty acids; Himalayan glacier; Pindari glacier; Psychrophiles; Psychrophilic enzymes

Indexed keywords

ACIDOBACTERIA; ACTINOBACTERIA; BACTERIA (MICROORGANISMS); BACTEROIDETES; CANDIDATE DIVISION SPAM; CHLAMYDIAE; CHLOROBI; CHLOROFLEXI; CHLOROFLEXI (CLASS); DICTYOGLOMI; FIBROBACTERES; FIRMICUTES; GEMMATIMONADETES; NITROSPIRAE; OTUS; PLANCTOMYCETES; PROTEOBACTERIA; VERRUCOMICROBIA;

EID: 78651252306     PISSN: 14310651     EISSN: 14334909     Source Type: Journal    
DOI: 10.1007/s00792-010-0333-4     Document Type: Article

References (76)

1. Abyzov SS, Mitskevich IN, Poglazova MN (1998) Microflora of the deep glacier horizons of central Antarctica. Microbiology 67: 66-73.
2. Ageta Y, Kadota T (1992) Predictions of changes of glacier mass balance in the Nepal Himalaya and Tibetan Plateau: a case study of air temperature increase for three glaciers. Ann Glaciol 16: 89-94.
3. Blakemore LC, Searle PL, Daly BK (1987) Methods for chemical analysis of soils. NZ Soil Bureau Scientific Report 80.
4. Booth C (1978) Introduction to general methods. In: Booth C (ed) Methods Microbiol. Academic Press, New York, pp 57-91.
5. 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.
6. Brinkmeyer R, Knittel K, Jürgens J, Weyland H, Amann R, Helmke E (2003) Diversity and community structure of bacterial communities in Arctic versus Antarctic sea ice. Appl Environ Microbiol 69: 6610-6619.
7. 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.
8. Chaturvedi P, Shivaji S (2006) Exiguobacterium indicum sp. nov., a psychrophilic bacterium from the Hamta glacier of the Himalayan mountain ranges of India. Int J Syst Evol Microbiol 56: 2765-2770.
9. Chaturvedi P, Reddy GSN, Shivaji S (2005) Dyadobacter hamtensis sp. nov., from Hamta glacier, located in the Himalayas, India. Int J Syst Evol Microbiol 55: 2113-2117.
10. Cheng SM, Foght JM (2007) Cultivation-independent and -dependent characterization of bacteria resident beneath John Evans glacier. FEMS Microbiol Ecol 59: 318-330.
11. Chintalapati S, Kiran MD, Shivaji S (2004) Role of membrane lipid fatty acids in cold adaptation. Cell Mol Biol 50: 631-642.
12. 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.
13. Christner BC, Mosley-Thompson E, Thompson LG, Reeve JN (2003) Bacterial recovery from ancient glacial ice. Environ Microbiol 5: 433-436.
14. 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.
15. 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.
16. Dong H, Zhang G, Jiang H, Yu B, Chapman LR, Lucas CR, Fields MW (2006) Microbial diversity in sediments of saline Qinghai Lake, China: linking geochemical controls to microbial ecology. Microbiol Ecol 51: 65-82.
17. Dyurgerov MB, Meier MF (1997) Mass balance of mountain and subpolar glaciers: a new global assessment for 1961-1990. Arct Alp Res 29: 379-391.
18. 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.
19. Feller G, Gerday C (2003) Psychrophilic enzymes: hot topics in cold adaptation. Nat Rev Microbiol 1: 200-208.
20. 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.
21. Fushimi H, Ikegami K, Higuchi K, Shankar K (1985) Nepal case study: catastrophic floods. In: Young GJ (ed) Techniques for prediction of runoff from glacierized areas (publication 149). International Association of Hydrological Sciences, Wallingford, UK, pp 125-130.
22. 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.
23. Gomes J, Steiner W (2004) The biocatalytic potential of extremophiles and extremozymes. Food Technol Biotechnol 42: 223-235.
24. Good IJ (1954) The population frequencies of species and the estimation of population parameters. Biometrica 40: 237-264.
25. Hur I, Chun J (2004) A method for comparing multiple bacterial community structures from 16S rDNA clone library sequences. J Microbiol 42: 9-13.
26. Jackson ML (1967) Soil chemical analysis. Prentice-Hall of India, New Delhi.
27. 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.
28. Kishore KH, Begum Z, Pathan AA, Shivaji S (2010) Paenibacillus glacialis sp. nov., isolated from Kafni glacier of Himalayas, India. Int J Syst Evol Microbiol (in press).
29. 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.
30. Lefauconnier B, Hagen JO, Rudant JP (1994) Flow speed and calving rate of Kongsbreen glacier, Svalbard, using SPOT images. Pol Res 10: 56-65.
31. 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.
32. Lipson DA, Schmidt SK (2004) Seasonal changes in an alpine soil bacterial community in the Colorado Rocky Mountains. Appl Environ Microbiol 70: 2867-2879.
33. 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.
34. 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.
35. 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.
36. Magurran AE (1996) (ed) Ecological diversity and its measurement. Chapman-Hall, London, pp 274-286.
37. 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.
38. Mayilraj S, Prasad GS, Suresh K, Saini HS, Shivaji S, Chakrabarti T (2005) Planococcus stackebrandtii sp. nov., isolated from a cold desert of the Himalayas, India. Int J Syst Evol Microbiol 55: 91-94.
39. 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.
40. Miteva VI, Sheridan PP, Brenchley JE (2004) Phylogenetic and physiological diversity of microorganisms isolated from a deep Greenland glacier ice core. Appl Environ Microbiol 70: 202-213.
41. Mosier AC, Murray AE, Fritsen CH (2007) Microbiota within the perennial ice cover of Lake Vida, Antarctica. FEMS Microbiol Ecol 59: 274-288.
42. Nemergut DR, Anderson SP, Cleveland CC, Martin AP, Miller AE, Seimon A, Schmidt SK (2007) Microbial community succession in an unvegetated, recently deglaciated soil. Microbiol Ecol 53: 110-122.
43. Nishida I, Murata N (1996) Chilling sensitivity in plants and cyanobacteria: the crucial contribution of membrane lipids. Annu Rev Plant Physiol Plant Mol Biol 47: 541-568.
44. Pindi PK, Kishore HK, Reddy GSN, Shivaji S (2009) Description of Leifsonia kafniensis sp. nov. and Leifsonia antarctica sp. nov. Int J Syst Evol Microbiol 59: 1348-1352.
45. Pradhan S, Srinivas TNR, Pindi PK, Kishore KH, Begum Z, Singh PK, Singh AK, Pratibha MS, Yasala AK, Reddy GS, Shivaji S (2010) Bacterial biodiversity from Roopkund glacier, Himalayan mountain ranges, India. Extremophiles 14: 377-395.
46. Priest FG (1977) Extracellular enzyme synthesis in the genus Bacillus. Bacteriol Rev 41: 711-753.
47. Priscu JC, Christner BC (2003) Microbial diversity and bioprocessing. In: Bull AT (ed) Earth's icy biosphere. ASM Press, Washington DC, pp 130-145.
48. 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.
49. Reddy GSN, Prabagaran SR, Shivaji S (2008a) Leifsonia pindariensis sp. nov., isolated from the Pindari glacier of the Indian Himalayas, and emended description of the genus Leifsonia. Int J Syst Evol Microbiol 58: 2229-2234.
50. Reddy GSN, Uttam A, Shivaji S (2008b) Bacillus cecembensis sp. nov., isolated from the Pindari glacier of the Indian Himalayas. Int J Syst Evol Microbiol 58: 2330-2335.
51. Reddy GSN, Pradhan S, Manorama R, Shivaji S (2010) Cryobacterium Pindariense sp. nov., a psychrophilic bacterium from a Himalayan glacier. Int J Syst Evol Microbiol 60: 866-870.
52. 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.
53. Rhoades JD (1982) Soluble salts. In: Page AL (ed) Methods of soil analysis. Part 2, 2nd edn. Agronomy monograph No. 9. American Society of Agronomy, Madison, WI, pp 167-179.
54. Russell NJ (1998) Molecular adaptations in psychrophilic bacteria: potential for biotechnological applications. Adv Biochem Eng Biotechnol 61: 1-21.
55. 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.
56. Shivaji S, Shyamala Rao N, Saisree L, Sheth V, Reddy GSN, Bhargava PM (1989) Isolation and identification of Pseudomonas species from Schirmacher Oasis, Antarctica. Appl Environ Microbiol 55: 767-771.
57. 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.
58. Shivaji S, Kiran MD, Chintalapati S (2007) Perception and transduction of low temperature in bacteria. In: Gerday C, Glansdorff N (eds) Physiology and biochemistry of extremophiles. ASM Press, Washington, DC, pp 194-207.
59. 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.
60. Srinivas TNR, Nageswara Rao SSS, Vishnu Vardhan Reddy P, Pratibha MS, Sailaja B, Kavya B, Hara Kishore K, Begum Z, Singh SM, Shivaji S (2009) Bacterial diversity and bioprospecting for cold-active lipases, amylases and proteases, from culturable bacteria of Kongsfjorden and Ny-Ålesund, Svalbard, Arctic. Curr Microbiol 59: 537-547.
61. 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 culture-dependent and culture-independent methods. FEMS Microbiol Ecol 59: 513-523.
62. Treves DS, Xia B, Tiedje JM (2003) A two-species test of the hypothesis that spatial isolation influences microbial diversity in soil. Microbiol Ecol 45: 20-28.
63. Tsai YL, Olson BH (1991) Rapid method for direct extraction of DNA from soil and sediments. Appl Environ Microbiol 57: 1070-1074.
64. Tsai YL, Olson BH (1992) Rapid method for separation of bacterial DNA from humic substances in sediments for polymerase chain reaction. Appl Environ Microbiol 58: 2292-2295.
65. Vardhan Reddy VP, Nageswara SSS, Pratibha MS, Sailaja B, Kavya B, Ruth Manorama R, Singh SM, Srinivas TNR, Shivaji S (2009) Bacterial diversity and bioprospecting for cold-active enzymes from culturable bacteria associated with sediment of melt water stream of Midtre Lov′enbreen glacier, an Arctic glacier. Res Microbiol 160: 538-546.
66. 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.
67. Xiang 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.
68. Xiang 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.
69. Xiang SR, Yao TD, Wu GJ, Chen Y, Shang TC, Pu LL, An LZ (2006) Deposition properties of bacterial populations in the Muztag Ata ice core. Quat Sci 26: 185-191.
70. Xiang SR, Shang TC, Chen Y, Jing ZF, Yao T (2009) Dominant bacteria and biomass in the Kuytun 51 glacier. Appl Environ Microbiol 75: 7287-7290.
71. Yamada T (1991) Preliminary report on glacier lake outburst flood in the Nepal Himalayas, Report 4/1/291191/1/l, Seq. No. 387. Water and Energy secretariat, HMG, Kathmandu, Nepal.
72. Yamada T, Shiraiwa T, Iida H, Kadota T, Watanabe T, Rana B, Ageta Y, Fushimi H (1992) Fluctuations of the glaciers from the 1970s to 1989 in the Khumbu, Shorong and Langtang regions, Nepal Himalayas. Bull Glaciol Res 10: 11-19.
73. 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.
74. Zhang S, Hou S, Ma X, Qin D, Chen T (2007) Culturable bacteria in Himalayan glacial ice in response to atmospheric circulation. Biogeoscience 4: 1-9.
75. 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.
76. 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. Microbiol 143: 3913-3919.