Characterization of Microbial Diversity in Hypersaline Environments by Melting Profiles and Reassociation Kinetics in Combination with Terminal Restriction Fragment Length Polymorphism (T-RFLP)

Microbial Ecology

Volumn 46, Issue 3, 2003, Pages 291-301

  Ovreas L ^a   Daae, F L ^a   Torsvik, V ^a   Rodriguez Valera F ^b  

^a UNIVERSITY OF BERGEN   (Norway)

^b MIGUEL HERNÁNDEZ UNIVERSITY   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIUM; DNA FINGERPRINTING; HYPERSALINE ENVIRONMENT; MICROBIAL COMMUNITY; PROKARYOTE; SALINITY; SPECIES DIVERSITY;

BACTERIA; BIOMASS; DNA FINGERPRINTING; DNA PRIMERS; DNA, BACTERIAL; KINETICS; MICROSCOPY, ELECTRON; POLYMORPHISM, RESTRICTION FRAGMENT LENGTH; POPULATION DYNAMICS; SODIUM CHLORIDE; VARIATION (GENETICS); WATER MICROBIOLOGY;

ARCHAEA; BACTERIA (MICROORGANISMS); BACTEROIDETES; ESCHERICHIA COLI; PROKARYOTA; SALINIBACTER RUBER;

EID: 0346816538     PISSN: 00953628     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00248-003-3006-3     Document Type: Article

References (35)

1. Amann RI, Ludwig W, Schleifer KH (1995) Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol Rev 59:143-169
2. Antón J, Llobet-Brossa E, Rodríguez-Valera F, Amann RI (1999) Fluorescence in situ hybridization analysis of the prokaryotic community inhabiting crystallizer ponds. Environ Microbiol 1:517-525
3. Antón J, Rosselló-Mora R, Rodríguez-Valera F, Amann RI (2000) Extremely halophilic Bacteria in crystallizer ponds from solar salterns. Appl Environ Microbiol 66:3052-3057
4. Antón J, Oren A, Benlloch S, Rodríguez-Valera F, Amann R, Roselló-Mora R (2001) Salinibacter ruber gen. nov., sp. nov., a new species of extremely halophilic Bacteria from saltern crystallizer ponds. Int J Syst Evol Microbiol 52: 485-491
5. Benlloch S, Martínez-Murcia AJ, Rodríguez-Valera F (1995) Sequencing of bacterial and archaeal 16S rRNA genes directly amplified from a hypersaline environment. Syst Appl Microbiol 18:574-581
6. Benlloch S, López-López A, Casamayor E, Øvreås L, Goddard V, Daae FL, Smerdon G, Massana R, Joint I, Thingstad TF, Pedrós-Alió C, Rodríguez-Valera F (2002) Prokaryotic diversity throughout the salinity gradient of a coastal solar saltern. Environ Microbiol 4:349-360
7. Bratbak G, Heldal M (1993) Total counts of viruses in aquatic environments. In: Kemp PF, Sherr BF, Sherr EB, Cole JJ (Eds.) Handbook of Methods in Aquatic Microbial Ecology. Lewis Publishers, Boca Raton, FL, pp 135-138
8. Casamayor EO, Schäfer H, Bañeras L, Pedrós-Alió C, Muyzer G (2000) Identification and spatiotemporal differences between microbial assemblages from two neighboring sulforous lakes: comparison by microscopy and denaturant gradient gel electrophoresis. Appl Environ Microbiol 66:499-508
9. Casamayor EO, Calderón-Paz JI, Pedrós-Alió C (2000) 5S rRNA fingerprints of marine bacteria, halophilic archaea and natural procaryotic assemblages along a salinity gradient. FEMS Microbiol Ecol 34:113-119
10. Casamayor EO, Massana R, Benlloch S, Øvreås L, Díez B, Goddard VJ, Gasol JM, Joint I, Rodríguez-Valera F, Pedrós-Alió C (2002) Changes in archaeal, bacterial and eucaryal assemblages along a salinity gradient by comparison of genetic fingerprint methods in a multipond solar saltern. Environ Microbiol 4:338-348
11. DeLong EF (1992) Archaea in coastal marine environments. Proc Nat-Acad Sci USA 89:5685-5689
12. Espejo RT, Feijoo CJ, Romero J, Vásquez M (1998) PAGE separation of the heteroduplex formed between PCR amplified 16S ribosomal RNA genes allows estimation of phylogenetic relatedness between isolates and assessment of bacterial diversity. Microbiology 144:1611-1617
13. Felske A, Akkermans ADL, Devos WM (1998) Quantification of 16S rRNAs in complex bacterial communities by multiple competitive reverse transcription PCR in temperature gradient gel electrophoresis fingerprints. Appl Environ Microbiol 64:4581-4587
14. Guixa-Boixareu N, Calderón-Paz JI, Heldal M, Bratbak G, Pedrós-Alió C (1996) Viral lysis and bacterivory as prokaryotic loss factors along a salinity gradient. Aquat Microb Ecol 11:215-227
15. Harper JL, Hawksworth DL (1994) Biodiversity: Measurements and estimation. Preface. Phil Trans R Soc Lond B 345:5-12
16. Liu W-T, Marsh TL, Cheng H, Forney L (1997) Characterization of microbial diversity by determining terminal restriction fragment length polymorphisms of genes encoding 16S rRNA. Appl Environ Microbiol 63:4516-4522
17. Mandel M, Igambi L, Bergendahl J, Dodson ML, Scheltgen E (1970) Correlation of melting temperature and cesium chloride boyant density of bacterial deoxyribonucleic acid. J Bacteriol 101:333-338
18. Muyzer G, Brinkhoff T, Nübel U, Santegoeds C, Schäfer H, Wawer C (1998) Denaturing gradient gel electrophoresis (DGGE) in microbial ecology. In: Akkermans ADL, van Elsas JD, de Bruijn FJ (Eds.) Molecular Microbial Ecology Manual. Kluwer Academic Publishers, Dordrecht, pp 1-27
19. Ng WV, Kennedy SP, Mahairas GG, Bergquist 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, Jablonski PE, Krebs MP, Angevine CM, Dale H, Isenbarger TA, Peck RF, Pohlschroder M, Spudich JL, Jung KW, 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. Proc Natl Acad Sci USA, pp 12176-12181
20. Oren A (1994) The ecology of the extremely halophilic archaea. FEMS Microbiol Rev 13:415-430
21. Pedrós-Alió C, Calderón-Paz JI, MacLean MH, Medina G, Marassé C, Gasol JM, Guixa-Boixereu N (2000) The microbial foodweb along salinity gradients. FEMS Microbiol Ecol 32:143-155
22. Perna NT, Plunkett 3rd G, Burland V, Mau B, Glasner JD, Rose DJ, Mayhew GF, Evans PS, Gregor J, Kirkpatrick HA, Posfai G, Hackett J, Klink S, Boutin A, Shao Y, Miller L, Grotbeck EJ, Davis NW, Lim A, Dimalanta ET, Potamousis KD, Apodaca J, Anantharaman TS, Lin J, Yen G, Schwartz DC, Welch RA, Blattner FR (2001) Genome sequence of enterohaemorrhagic Escherichia coli O157:H7. Nature 463:465-466
23. Riemann L, Steward GF, Fandino LB, Campbell L, Landry MR, Azam F (1999) Bacterial community composition during two consecutive NE Monsoon periods in the Arabian sea studied by denaturing gradient gel electrophoresis (DGGE) of rRNA genes. Deep Sea Res II 46:1791-1811
24. Ritz K, Griffiths BS, Torsvik VL, Hendriksen NB (1997) Analysis of soil and bacterioplanktoncommunity DNA by melting profiles and reassociation kinetics. FEMS Microbiol Lett 149:151-156
25. Rodríguez-Valera F, Ventosa A, Juez G, Imhoff JF (1985) Variation of environmental features and microbial populations with salt concentrations in a multi-pond saltern. Microb Ecol 11:107-115
26. Rodríguez-Valera F, Acinas SG, Antón J (1999) Contribution of molecular techniques to the study of microbial diversity in hypersaline environments. In: Oren A (Ed.) Microbiology and Biogeochemistry of Hypersaline Environments. CRC Press, Boca Raton, FL, pp 27-38
27. Stetter KO (1998) Hyperthermophiles: Isolation, classification and properties. In: Horikoshi K, Grant WD (Eds.) Extremophiles - Microbial Life in Extreme Environments. Wiley, New York, pp 1-24
28. Torsvik V, Goksøyr J, Daae FL (1990) High diversity in DNA of soil bacteria. Appl Environ Microbiol 56:782-787
29. Torsvik V, Sørheim R, Goksøyr J (1996) Total bacterial diversity in soil and sediment communities - a review. J Indust Microbiol 17:170-178
30. Torsvik V, Øvreås L, Thingstad TF (2002) Procaryotic diversity - magnitude, dynamics, and controlling factors. Science 296:1064-1066
31. van der, Maarel MJEC, Artz RRE, Haanstra R, Forney LJ (1998) Association of marine Archaea with the digestive tracts of two marine fish species. Appl Environ Microbiol 64:2894-2898
32. Walsby AE (1980) A square bacterium. Nature 283:69-71
33. Ward DM, Ferris MJ, Nold SC, Bateson MM, Kopczynski ED, Ruff-Roberts AL (1994) Species diversity in hot spring microbial mats as revealed by both molecular and enrichment culture approaches - relationship between biodiversity and community structure. In: Stahl LJ, Caumette P (Eds.) Microbial Mats: Structure, Development and Environmental Significance. Springer Verlag, Heidelberg, pp 33-44
34. Wayne LG, Brenner DJ, Colwell RR, Grimont PAD, Kandler O, Krichevsky MI, Moore LH, Moore WEC, Murray RGE, Stackebrandt E, Starr MP, Truper HG (1987) Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Bacteriol 37:463-464
35. Øvreås L (2000) population and community level approaches for analysing microbial diversity in natural environments. Ecol Lett 3:236-251