Analysis of intergenic spacer region length polymorphisms to investigate the halophilic archaeal diversity of stromatolites and microbial mats

Extremophiles

Volumn 11, Issue 1, 2007, Pages 203-210

  Leuko, S ^a   Goh, F ^b   Allen, M A ^b   Burns, B P ^a,b   Walter, M R ^a   Neilan, B A ^a,b  

^a MACQUARIE UNIVERSITY   (Australia)

^b UNIVERSITY OF NEW SOUTH WALES   (Australia)

Author keywords

ARISA; Diversity; Hypersaline environment; Intergenic spacer region; Shark Bay; Stromatolites

Indexed keywords

ARCHAEAL DNA; PRIMER DNA; RIBOSOMAL SPACER DNA; SEA WATER;

ARCHAEBACTERIUM; ARTICLE; AUSTRALIA; CLINICAL TRIAL; DNA SEQUENCE; ECOSYSTEM; GENETIC POLYMORPHISM; GENETIC VARIABILITY; GENETICS; METHODOLOGY; MICROBIOLOGY; MOLECULAR CLONING; MULTICENTER STUDY; PHYLOGENY; POLYMERASE CHAIN REACTION; SEDIMENT;

ARCHAEA; CLONING, MOLECULAR; DNA PRIMERS; DNA, ARCHAEAL; DNA, RIBOSOMAL SPACER; ECOSYSTEM; GEOLOGIC SEDIMENTS; PHYLOGENY; POLYMERASE CHAIN REACTION; POLYMORPHISM, GENETIC; SEAWATER; SEQUENCE ANALYSIS, DNA; VARIATION (GENETICS); WESTERN AUSTRALIA;

ARCHAEA; BACTERIA (MICROORGANISMS); CHONDRICHTHYES; CYANOBACTERIA;

EID: 33846127844     PISSN: 14310651     EISSN: 14334909     Source Type: Journal    
DOI: 10.1007/s00792-006-0028-z     Document Type: Article

References (42)

1. Acinas SG, Antón J, Rodríguez-Valera F (1999) Diversity of free-living and attached bacteria in offshore western Mediterranean waters as depicted by analysis of genes encoding 16S rRNA. Appl Environ Microbiol 65:514-522
2. Amann G, Stetter KO, Llobet-Brossa E, Amann R, Antón J (2000) Direct proof for the presence and expression of two 5% different 16S rRNA genes in individual cells of Haloarcula marismortui. Extremophiles 4:373-376
3. Arp G, Reimer A, Reitner J (2001) Photosynthesis-induced biofilm calcification and calcium concentrations in phanerozoic oceans. Science 292:1701-1704
4. Benlloch S, Acinas SG, Antón J, López-López A, Luz SP, Rodríguez-Valera F (2001) Archaeal biodiversity in crystallizer ponds from a solar saltern: culture versus PCR. Microb Ecol 41:12-19
5. Boucher Y, Douady CJ, Sharma AK, Kamekura M, Doolittle WF (2004) Intragenomic heterogeneity and intergenomic recombination among haloarchaeal rRNA genes. J Bacteriol 186:3980-3990
6. Briones C, Amils R (2000) Nucleotide sequence of the 23s rRNA from Haloferax mediterranei and phylogenetic analysis of halophilic archaea based on LSU rRNA. Syst Appl Microbiol 23:124-131
7. Burns BP, Goh F, Allen MA, Neilan BA (2004) Microbial diversity of extant stromatolites in the hypersaline marine environment of Shark Bay, Australia. Environ Microbiol 6:1096-1101
8. Cardinale M, Brusetti L, Quatrini P, Borin S, Puglia AM, Rizzi A, Zanardini E, Sorlini C, Corselli C, Daffonchio D (2004) Comparison of different primer sets for use in automated ribosomal intergenic spacer analysis of complex bacterial communities. Appl Environ Microbiol 70:6147-6156
9. DasSarma S, Fleischmann EM, Rodríguez-Valera F (1995) Halophiles. In: Robb FT (ed) Archaea: a laboratory manual. CSHL Press, Cold Spring Harbor, pp 225-230
10. DeLong EF (1992) Archaea in coastal marine environments. Proc Natl Acad Sci USA 89:5685-5689
11. Dennis PP, Ziesche S, Mylvaganam S (1998) Transcription analysis of two disparate rRNA operons in the halophilic Archaeon Haloarcula marismortui. J Bacteriol 180:4804-4813
12. Elshahed MS, Najar FZ, Roe BA, Oren A, Dewers TA, Krumholz LR (2004) Survey of archaeal diversity reveals an abundance of halophilic archaea in a low-salt, sulfide- and sulfur-rich spring. Appl Environ Microbiol 70:2230-2239
13. Fisher MM, Triplett EW (1999) Automated approach for ribosomal intergenic spacer analysis of microbial diversity and its application to freshwater bacterial communities. Appl Environ Microbiol 65:4630-4636
14. García-Martínez J, Rodríguez-Valera F (2000) Microdiversity of uncultured marine prokaryotes: the SAR11 cluster and the marine Archaea of group I. Mol Ecol 9:935-948
15. García-Martínez J, Bescós I, Rodríguez-Sala J, Rodríguez-Valera (2001) RISSC: a novel database for ribosomal 16S-23S RNA genes spacer regions. Nucleic Acid Res 29:178-180
16. Goh F, Leuko S, Allen MA, Bowman JP, Kamekura M, Neilan BA, Burns BP (2006) Halococcus hamelinensis sp. nov., a novel halophilic archaeon isolated from stromatolites in Shark Bay, Australia. Int J Syst 56:1323-1329
17. González N, Romero J, Espejo RT (2003) Comprehensive detection of bacterial populations by PCR amplification of the 16S-23S rRNA spacer region. J Microbiol Meth 55:91-97
18. Grant WD, Gemmell RT, McGenity TJ (1998) Halobacteria: the evidence for longevity. Extremophiles 2:279-287
19. Kushner DJ, Kamekura M (1988) Physiology of halophilic eubacteria. In: Rodríguez-Valera F (ed) Halophilic bacteria, vol I. CRC Press, Boca Raton, pp 109-140
20. Leuko S, Weidler G, Radax C, Legat A, Koemle NI, Kargl G, Stan-Lotter H (2002) Examining the physico-chemical resistance of halobacteria with the LIFE-DEAD kit, following exposure to simulated Martian atmospheric conditions and heat. ESA Special Publication (ESA-SP-518)
21. Martin-Laurent F, Philippot L, Hallet S, Chaussod R, Germon JC, Soulas G, Catroux G (2001) DNA extraction from soils: old bias for new microbial diversity analysis methods. Appl Environ Microbiol 67:2354-2359
22. McGenity TJ, Gemmell RT, Grant WD, Stan-Lotter H (2000) Origins of halophilic microorganisms in ancient salt deposits. Environ Microbiol 2:243-250
23. Monty C (1977) Evolving concepts on the nature and the ecological significance of stromatolites. In: Flügel E (ed) Fossil algae, recent results and developments. Springer, Berlin Heidelberg New York, pp 15-35
24. Mormile MR, Biesen MA, Gutierrez MC, Ventosa A, Pavlovich JB, Onstott TC, Fredrickson JK (2003) Isolation of Halobacterium salinarum retrieved directly from halite brine inclusion. Environ Microbiol 5(11):1094-1102
25. Ng WV, Kennedy SP, Mahairas GG, Berquist B, Pan M, Shukla HD, Lasky SR, Baliga NS, Thorsson V, Sbrogna J, Swartzell S, Weir D, Hall J, Dahl TA, Welti R, Goo YA, Leithauser B, Keller K, Cruz R, Danson MJ, Hough DW, Maddocks DG, Jablonksi PE, Krebs MP, Angevine CM, Dale H, Isenbarger TA, Peck RF, Pohlschroder M, Spudich JL, Jung KH, Alam M, Freitas T, Hou S, Daniels CJ, Dennis PP, Omer AD, Ebhardt H, Lowe TM, Liang P, Riley M, Hood L, DasSarma S (2000) Genome sequence of Halobacterium species NRC-1. PNAS 97:12176-12181
26. Oren A (2001) The order Halobacteriales. In: Dworkin M, Falkow S, Rosenberg E, Schleifer K-H, Stackebrand E (eds) The prokaryotes: an evolving electronic resource for the microbiological community, 3rd ed., release 3.2, 25 July 2001. Springer, Berlin Heidelberg New York
27. Oren A, Gurevich P, Gemmell RT, Teske A (1995) Halobaculum gomorrense gen. nov., sp. nov., a novel extremely halophilic archaeon from the Dead Sea. Int J Syst Bacteriol 45:747-754
28. Øvreås L, Daae FL, Torsvik V, Rodríguez-Valera F (2003) Characterization of microbial diversity in hypersaline environments by melting profiles and reassociation kinetics in combination with terminal restriction fragment length polymorphism (T-RFLP). Microb Ecol 46:291-301
29. Palmisano AC, Summons RE, Cronin SE, Des Marias DJ (1989) Lipophilic pigments from cyanobacterial (blue-green algal) and diatom mats in Hamelin pool, Shark Bay, Western Australia. J Phycol 25:655-661
30. Papineau D, Walker JJ, Mojzsis SJ, Pace NR (2005) Composition and structure of microbial communities from stromatolites of Hamelin Pool in Shark Bay, Western Australia. Appl Environ Microbiol 71:4822-4832
31. Petrisor AI, Decho AW (2004) Using geographical information techniques to quantify the spatial structure of endolithic boring processes within sediment grains of marine stromatolites. J Micro Meth 56:173-180
32. Polz MF, Cavanaugh CM (1998) Bias in template to product ratios in multitemplate PCR. Appl Environ Microbiol 64:3724-3730
33. Purdy KJ, Cresswell-Maynard TD, Nedwell DB, McGenity TJ, Grant WD, Timmis KN Embley TM (2004) Isolation of haloarchaea that grow at low salinities. Environ Microbiol 6:591-595
34. Radax C, Gruber C, Stan-Lotter H (2001) Novel haloarchaeal 16S rRNA gene sequences from alpine Permo-Triassic rock salt. Extremophiles 5:221-228
35. Ranjard L, Brothier E, Nazaret S (2000) Sequencing bands of ribosomal intergenic spacer analysis fingerprints for characterization and microscale distribution of soil bacterium populations responding to mercury spiking. Appl Environ Microbiol 66:5334-5339
36. Reid RP, James NP, Macintyre IG, Dupraz CP, Burne RV (2003) Shark Bay stromatolites: microfabrics and reinterpretation of origins. Facies 49:299-324
37. Rodríguez-Valera F, Ruiz-Berraquero F, Ramos-Cormenzana A (1979) Isolation of extreme halophiles from Seawater. Appl Environ Microbiol 38:164-165
38. Stan-Lotter H, Pfaffenhuemer M, Legat A, Busse HJ, Gruber C (2002) Halococcus dombrowskii sp. nov., an archaeal isolate from a Permian alpine salt deposit. Int J Syst Evol Microbiol 52:1807-1814
39. Tillett D, Neilan BA (2000) Xanthogenate nucleic acid isolation from cultured and environmental cyanobacteria. J Phycol 36:251-258
40. Wilson K (1990) Preparation of genomic DNA from bacteria. In: Ausubel FM, Brent R, Kingston RE, Moore DD, Seidman JG, Smith JA, Struhl K (eds) Current protocols in molecular biology. Wiley, New York, pp 2.4.1-2.4.2
41. von Wintzingerode F, Goebel UB, Stackebrandt E (1997) Determination of microbial diversity in environmental samples: pitfalls of PCR-based rRNA analysis. FEMS Microbiol Rev 21:213-229
42. Yannarell AC, Triplett EW (2005) Geographic and environmental sources of variation in lake bacterial community composition. Appl Environ Microbiol 71:227-239