16S rDNA diversity of cultured and uncultured prokaryotes of a mat sample from Lake Fryxell, McMurdo Dry Valleys, Antarctica

Extremophiles

Volumn 5, Issue 1, 2001, Pages 23-33

  Brambilla, Evelyne ^a   Hippe, Hans ^a   Hagelstein, Anja ^a   Tindall, Brian J ^a   Stackebrandt, Erko ^a  

^a LEIBNIZ INSTITUTE DSMZ GERMAN COLLECTION OF MICROORGANISMS AND CELL CULTURES   (Germany)

Author keywords

Antarctica; Biodiversity; Lake Fryxell mat; Psychrophiles

Indexed keywords

ARCHAEAL DNA; BACTERIAL DNA; FRESH WATER; RIBOSOME DNA; RNA 16S;

AEROBIC BACTERIUM; ANAEROBIC BACTERIUM; ANTARCTICA; ARCHAEBACTERIUM; ARTICLE; CLASSIFICATION; DNA SEQUENCE; ECOSYSTEM; GENETICS; ISOLATION AND PURIFICATION; MICROBIOLOGY; MOLECULAR CLONING; PHYLOGENY; POLYMERASE CHAIN REACTION; RNA GENE;

ANTARCTIC REGIONS; ARCHAEA; BACTERIA, AEROBIC; BACTERIA, ANAEROBIC; CLONING, MOLECULAR; DNA, ARCHAEAL; DNA, BACTERIAL; DNA, RIBOSOMAL; ECOSYSTEM; FRESH WATER; GENES, RRNA; PHYLOGENY; POLYMERASE CHAIN REACTION; RNA, RIBOSOMAL, 16S; SEQUENCE ANALYSIS, DNA;

EID: 0035257574     PISSN: 14310651     EISSN: None     Source Type: Journal    
DOI: 10.1007/s007920000169     Document Type: Article

References (63)

1. Abyzov SS, Mitskevich IN, Poglazova MN (1998) Microflora of the deep glacier horizons of central Antarctica. Microbiology 67:451-458
2. Ashbolt NJ (1990) Antarctic biotechnology-what is the potential? Aust J Biotechnol 4:103-105
3. Bowman JP (1998) Pseudoalteromonas prydzensis sp. nov., a psychrotrophic, halotolerant bacterium from Antarctic sea ice. Int J Syst Bacteriol 43:1037-1041
4. Bowman JP, Cavanagh J, Austin J, Sanderson K (1996) Novel Psychrobacter species from Antarctic ornithogenic soils. Int J Syst Bacteriol 46:841-848
5. Bowman JP, McCammon SA, Brown JL, Nichols PD, McMeekin TA (1997a) Psychroserpens burtonensis gen. nov., sp. nov., and Gelidibacter algens gen. nov., sp. nov., psychrophilic bacteria isolated from antarctic lacustrine and sea ice habitats. Int J Syst Bacteriol 47:670-677
6. Bowman JP, McCammon SA, Brown MV, Nichols DS McMeekin TA (1997b) Diversity and association of psychrophilic bacteria in Antarctic sea ice. Appl Environ Microbiol 63:3068-3078
7. Bowman JP, McCammon SA, Lewis T, Skerratt JH, Brown JL, Nichols DS, McMeekin TA (1998) Psychroflexus torquis gen. nov., sp. nov., a psychrophilic species from Antarctic sea ice, and reclassification of Flavobacterium gondwanense (Dobson et al. 1993) as Psychroflexus gondwanense gen. nov., comb. nov. Microbiology 144:1601-1609
8. Bowman JP, McCammon SA, Nichols DS, Skerratt JH, Rea SM, Nicols PD, McMeekin TA (1997c) Shewanella gelidimarina sp. nov. and Shewanella frigidimarina sp. nov., novel Antarctic species with the ability to produce eicosapentaenoic acid (20:5ω3) and grow anaerobically by dissimilatory Fe(III) reduction. Int J Syst Bacteriol 47:1040-1047
9. Bowman JP, McCammon SA, Skerratt JH (1997d) Methylosphaera hansonii gen. nov., sp. nov., a psychrophilic, group I methanotroph from Antarctic marine-salinity, meromictic lakes. Microbiology 143:1451-1459
10. Bowman, JP, Nichols DS, McMeekinTA (1997e) Psychrobacter glacincola sp. nov., a halotolerant, psychrophilic bacterium isolated from Antarctic sea ice. Syst Appl Microbiol 20:209-215
11. 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
12. Bozal N, Tudela E, Roselló-Mora R, Lalucat J Guinea J (1997) Pseudoalteromonas antarctica sp. nov., isolated from an Antarctic coastal environment. Int J Syst Bacteriol 47:345-351
13. Brosius JM, Palmer L, Kennedy P, Noller HF (1978) Complete nucleotide sequence of the 16S ribosomal RNA gene from Escherichia coli. Proc Natl Acad Sci USA 75:4801-4805
14. Cambell R, Greaves MP (1990) Methods for studying the microbial ecology of the rhizosphere. Methods Microbiol 22:447-477
15. Chinn TH (1993) Physical hydrology of the Dry Valley Lakes. In: Green WJ, Friedman EI (eds) Physical and biogeochemical processes in Antarctic lakes. Antarctic research series 59. American Geophysical Union, Washington, DC, pp 1-52
16. Choi B-K, Paster BJ, Dewhirst FE, Göbel UB (1994) Diversity of cultivable and uncultivable oral spirochetes from a patient with severe destructive periodontitis. Infect Immun 62:1889-1895
17. Collins MD, Rodrigues UM, Dainty RH, Edwards RA, Roberts TA (1992) Taxonomic studies on a psychrophilic Clostridium from vacuum-packed beef: description of Clostridium estertheticum sp. nov. FEMS Microbiol Lett 96:235-240
18. Conovitz PA, McKnight D, MacDonald LH, Fountain AGM, House HR (1998) Hydrologic processes influencing streamflow variation in Fryxell Basin, Antarctica. In: Priscu JC (ed) Ecosystem dynamics in a polar desert. The McMurdo Dry Valleys, Antarctica. Antarctic research series 72. American Geophysical Union, Washington, DC, pp 93-108
19. DeSoete G (1983) A least squares algorithm for fitting additive trees to proximity data. Psychometrika 48:621-626
20. Dobson SJ, Colwell RR, McMeekin TA, Franzmann PD (1993) Direct sequencing of the polymerase chain reaction-amplified 16S rRNA gene of Flavobacterium gondwanense sp. nov. and Flavobacterium salegens sp. nov., two new species from a hypersaline Antarctic lake. Int J Syst Bacteriol 43:77-83
21. DSMZ (1998) Catalogue of strains, 6th edn. Deutsche Sammlung von Mikroorganismen und Zellkulturen, Braunschweig
22. Franzmann PD, Höpfl P, Weiss N, Tindall BJ (1991) Psychrotrophic, lactic acid-producing bacteria from anoxic waters in Ace Lake, Antarctica; Carnobacterium funditum sp. nov. and Carnobacterium alterfunditum sp. nov. Arch Microbiol 156:255-262
23. 2-using methanogen from Ace Lake, Antarctica. Int J Syst Bacteriol 47:1068-1072
24. Friedmann EI (1980) Endolithic microbial life in hot and cold deserts. Origins Life 10:223-235
25. Gosink JJ, Staley JT (1995) Biodiversity of gas vacuolate bacteria from Antarctic sea ice and water. Appl Environ Microbiol 61:3486-3489
26. Gosink JJ, Woese CR, Staley JT (1998) Polaribacter gen. nov., with three new species, P. irgensii sp. nov., P. franzmannii sp. nov. and P. filamentus sp. nov., gas vacuolate polar marine bacteria of the Cytophaga-Flavobacterium-Bacteroides group and reclassification of 'Flectobacillus glomeratus' as Polaribacter glomeratus comb. nov. Int J Syst Bacteriol 48:223-235
27. Griepenburg U, Ward-Rainey N, Mohamed S, Schlesner H, Marxsen H, Rainey FA, Stackebrandt E, Auling G (1996) Phylogenetic diversity, polyamine pattern and DNA base composition of members of the order Planctomycetales. Int J Syst Bacteriol 49:689-696
28. Hawes I, Howard-Williams C (1998) Primary production processes in streams of the McMurdo Dry Valleys, Antarctica. In: Priscu JC (ed) Ecosystem dynamics in a polar desert. The McMurdo Dry Valleys, Antarctica. Antarctic research series 72. American Geophysical Union, Washington, DC, pp 129-140
29. Hirsch P, Ludwig W, Hethke C, Sittig M, Hoffmann B, Gallikowski CA (1998) Hymenobacter roseosalivarius gen. nov., sp. nov. from continental Antartica soils and sandstone: bacteria of the Cytophaga/Flavobacterium/Bacteroides line of phylogenetic descent. Syst Appl Microbiol 21:374-383
30. Irgens RL, Gosink JJ, Staley JT (1996) Polaromonas vacuolata gen. nov., sp. nov., a psychrophilic, marine, gas vacuolate bacterium from Antarctica. Int J Syst Bacteriol 46:822-826
31. James MR, Hall JA, Laybourn-Parry J (1998) Protozooplankton and microzooplankton ecology in lakes of the Dry Valleys, Southern Victoria Land. In: Priscu JC (ed) Ecosystem dynamics in a polar desert. The McMurdo Dry Valleys, Antarctica. Antarctic research series 72. American Geophysical Union, Washington, DC, pp 255-267
32. Jay JM (1979) Comparison of homogenizing, shaking and blending on the recovery of microorganisms and endotoxins from fresh and frozen ground beef. Appl Environ Microbiol 38:879-884
33. Jukes TH, Cantor CR (1969) Evolution of protein molecules. In: Munro HN (ed) Mammalian protein metabolism. Academic Press, New York, pp 21-132
34. Junge K, Gosink JJ, Hoppe H-G, Staley JT (1998) Arthrobacter, Brachybacterium and Planococcus isolates identified from antarctic sea ice brine. Description of Planococcus mcmeekinii, sp. nov. Syst Appl Microbiol 21:306-314
35. Kriss AE (1976) Microbiological studies of the Wanda Lake. Mikrobiologia 45:1075-1081
36. Labrenz M, Collins MD, Lawson PA, Tindall BJ, Braker G, Hirsch P (1998) Antarctobacter heliothermus gen. nov., sp. nov., a budding bacterium from hypersaline and heliothermal Ekho Lake. Int J Syst Bacteriol 48:1363-1372
37. Laybourn-Parry J, James MR, McKnight D, Priscu J, Spaulding S, Shiel R (1997) The microbial plankton of Lake Fryxell, Southern Victoria land, Antarctica. Polar Biol 17:54-61
38. Liesack W, Stackebrandt E (1992) Occurrence of novel groups of the domain Bacteria as revealed by analysis of genetic material isolated from an Australian terrestrial environment. J Bacteriol 174:5072-5078
39. Lyons WB, Welch KA, Neumann K, Toxey JK, McArthur R, Williams C, McKnight DM, Moorhead D (1998) Geochemical linkages among glaciers, streams and lakes within the Taylor Valley, Antarctica. In: Priscu JC (ed) Ecosystem dynamics in a polar desert. The McMurdo Dry Valleys, Antarctica. Antarctic research series 72. American Geophysical Union,Washington, DC, pp 77-92
40. Marshall BJ (1966) Bacillus macquariensis n. sp., a psychrotrophic bacterium from sub-antarctic soil. J Gen Microbiol 44:41-46
41. Maugeri TL, Gugliandolo C, Bruni V (1996) Heterotrophic bacteria in the Ross Sea (Terra Nova Bay, Antarctica). Microbiologica 19:67-76
42. McCammon SA, Innes BH, Bowman J, Franzmann PD, Dobson SJ, Holloway PE, Skeratt JH, Nichols PD, Rankin LM (1998) Flavobacterium hibernum sp. nov., a lactose-utilizing bacterium from a freshwater Antarctic lake. Int J Syst Bacteriol 48:1405-1412
43. McKnight D, Alger A, Tate CM, Shupe G, Spaulding S (1998) Longitudinal patterns in algal abundance and species distribution in meltwater streams in Taylor Valley, Southern Victoria Land, Antarctica. In: Priscu JC (ed) Ecosystem dynamics in a polar desert. The McMurdo Dry Valleys, Antarctica. Antarctic research series 72. American Geophysical Union,Washington, DC, pp 109-127
44. Mountfort DO, Rainey FA, Burghardt J, Kaspar HF, Stackebrandt E (1998) Clostridium vincentii sp. nov., a new obligately anaerobic, saccharolytic, psychrophilic bacterium isolated from low-salinity pond sediment of the McMurdo Ice Shelf, Antarctica. Arch Microbiol 167:54-60
45. Murray AE (1998) Seasonal and spatial variability of bacterial and archaeal assemblages in the coastal waters near Anvers Island, Antarctica. Appl Environ Microbiol 64:2585-2595
46. Osnitskaia LK (1978) Photosynthesizing bacteria from the Wanda Lake. Mikrobiologia 47:131-137
47. Pfister RM (1965) Numerical taxonomy of some bacteria isolated from antarctic and tropical seawaters. J Bacteriol 90:863-872
48. Priscu JC (1998) Perennial Antarctic lake ice: an oasis for life in a polar desert. Science 280:2095-2098
49. Pukall R, Päuker O, Buntefuß D, Ulrichs G, Lebaron P, Bernhard L, Guindulain T, Vives-Rego J, Stackebrandt E (1998) High sequence diversity of Alteromonas macleodii-related cloned and cellular 16S rDNAs from a Mediterranean seawater mesocosm experiment. FEMS Microb Ecol 28:335-344
50. Rainey FA, Ward-Rainey N, Kroppenstedt RM, Stackebrandt E (1996) The genus Nocardiopsis represents a phylogenetically coherent taxon and a distinct actinomycete lineage: proposal of Nocardiopsaceae fam. nov. Int J Syst Bacteriol 46:1088-1092
51. Reddy GSN, Aggarwal RK, Matsumoto GI, Shivaji S (2000) Arthrobacter flavus sp. nov., a psychrophilic bacterium isolated from a pond in McMurdo Dry Valley, Antarctica. Int J Syst Evol Microbiol 50:1553-1561
52. Rheims H, Stackebrandt E (1998) Application of nested PCR for the detection of as yet uncultured organisms of the class Actinobacteria in environmental samples. Mol Ecol 1:137-143
53. Rheims H, Felske A, Seufert S, Stackebrandt E (1998) Molecular monitoring of an uncultured group of the class Actinobacteria in two terrestrial environments. J Microbiol Methods 36:65-75
54. Sambrook J, Fritsch EF, Maniatis T (1989) Molecular cloning. A laboratory manual, 2nd edn. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York
55. Schumann P, Prauser H, Rainey FA, Stackebrandt E, Hirsch P (1997) Friedmanniella antarctica gen. nov., sp. nov., an LL-diaminopimelic acid-containing actinomycete from Antarctic sandstone. Int J Syst Bacteriol 47:278-283
56. Stackebrandt E, Goebel BM (1994) A place for DNA-DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. Int J Syst Bacteriol 44:846-849
57. Stackebrandt E, Hippe H (2000) Taxonomy and systematics. In: Bahl H, Dürre P (eds) Clostridia: biotechnology and medical applications. Wiley-VCH, Weinheim (in press)
58. Stackebrandt E, Rainey FA (1995) Partial and complete 16S rDNA sequences, their use in generation of 16S rDNA phylogenetic trees and their implications in molecular ecological studies. In: Akkermans ADL, van Elsas JD, de Bruijn FJ (eds) Molecular microbial ecology manual, vol 3.1.1. Kluwer, Dordrecht, pp 1-17
59. Suzuki K-I, 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 47:474-447
60. Tindall BJ, Brambilla E, Steffen M, Neumann R, Pukall R, Kroppenstedt RM, Stackebrandt E (2000) Cultivatable microbial diversity: gnawing at the Gordian knot. Environ Microbiol 2:310-318
61. Tsyganov VA (1970) Detection and morphological-cultural characteristics of actinomyces from the Antarctic. Mikrobiologia 39:821-826
62. von Wintzingerode F, Göbel U, Stackebrandt E (1997) Determination of microbial diversity in environmental samples: pitfalls of PCR-based rRNA analysis. FEMS Microbiol Rev 21:213-229
63. Voytek MA, Ward BB, Pricu JC (1998) The abundance of ammonium-oxidizing bacteria in Lake Bonney, Antarctica, determined by immunofluorescence, PCR, and in situ hybridization. In: Priscu JC (ed) Ecosystem dynamics in a polar desert. The McMurdo Dry Valleys, Antarctica. Antarctic research series 72. American Geophysical Union, Washington, DC, pp 217-228