Molecular sequence analysis of prokaryotic diversity in the anoxic sediments underlying cyanobacterial mats of two hypersaline ponds in Mediterranean salterns

FEMS Microbiology Ecology

Volumn 44, Issue 1, 2003, Pages 117-130

  Mouné, Sophie ^a,b   Caumette, Pierre ^b   Matheron, Robert ^c   Willison, John C ^a  

^a CEA GRENOBLE   (France)

^b UNIVERSITÉ DE PAU ET DES PAYS DE L'ADOUR   (France)

^c AVIGNON UNIVERSITÉ   (France)

Author keywords

Anoxic sediment; Archaeon; Halophilic bacterium; Mediterranean saltern; Microbial mat; Prokaryotic diversity

Indexed keywords

NUCLEIC ACID; SMALL SUBUNIT RIBOSOMAL DNA; SODIUM CHLORIDE; UNCLASSIFIED DRUG;

ANOXIC CONDITIONS; BACTERIUM; HYPERSALINE ENVIRONMENT; MICROBIAL ECOLOGY; MOLECULAR ANALYSIS;

ANAEROBIC FERMENTATION; ARCHAEBACTERIUM; ARTICLE; BACTERIAL FLORA; BACTERIUM; BACTERIUM CULTURE; BACTEROIDES; CRENARCHAEOTA; CYANOBACTERIUM; DNA LIBRARY; FLAVOBACTERIUM; FLEXIBACTERACEAE; FRANCE; GENE CONSTRUCT; GENE ISOLATION; GRAM NEGATIVE BACTERIUM; HALOBACTERIALES; METHANOBACTERIALES; METHANOCOCCUS; MICROBIAL DIVERSITY; MICROFLORA; MOLECULAR BIOLOGY; MOLECULAR CLONING; MOLECULAR GENETICS; NONHUMAN; NUCLEOTIDE SEQUENCE; ORDO; PHYLUM; PHYSICAL CHEMISTRY; POND; PRIORITY JOURNAL; PROKARYOTE; SALINITY; SAMPLING; SEDIMENT; SEQUENCE ANALYSIS; SPIROCHETE; SULFATE REDUCING BACTERIUM; UNINDEXED SEQUENCE;

FRANCE; PROVENCE-ALPES-COTE D'AZUR; SALIN-DE-GIRAUD;

ARCHAEA; BACTERIA (MICROORGANISMS); BACTEROIDES; BACTEROIDETES; CRENARCHAEOTA; CYANOBACTERIA; CYTOPHAGA; DELTAPROTEOBACTERIA; EURYARCHAEOTA; FIRMICUTES; FLAVOBACTERIUM; GAMMAPROTEOBACTERIA; HALOBACTERIA; HALOBACTERIALES; METHANOBACTERIA; METHANOCOCCI; PROKARYOTA; PROTEOBACTERIA; SPIROCHAETA;

EID: 0041380947     PISSN: 01686496     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0168-6496(03)00017-5     Document Type: Article

References (49)

1. Ollivier B., Caumette P., Garcia J.-L., Mah R.A. Anaerobic bacteria from hypersaline environments. Microbiol. Rev. 58:1994;27-38.
2. Caumette P., Matheron R., Raymond N., Relexans J.-C. Microbial mats in the hypersaline ponds of Mediterranean salterns (Salins-de-Giraud, France). FEMS Microbiol. Ecol. 13:1994;273-286.
3. Caumette P., Baulaigue R., Matheron R. Characterization of Chromatium salexigens sp. nov., a halophilic Chromatiaceae isolated from Mediterranean salinas. Syst. Appl. Microbiol. 10:1988;284-292.
4. Caumette P., Baulaigue R., Matheron R. Thiocapsa halophila sp. nov., a new halophilic phototrophic purple sulfur bacterium. Arch. Microbiol. 155:1991;170-176.
5. Mouné S., Manac'h N., Hirschler A., Caumette P., Willison J.C., Matheron R. Haloanaerobacter salinarius sp. nov., a novel halophilic fermentative bacterium that reduces glycine-betaine to trimethylamine with hydrogen or serine as electron donors; emendation of the genus Haloanaerobacter. Int. J. Syst. Bacteriol. 49:1999;103-112.
6. Mouné S., Eatock C., Matheron R., Willison J.C., Hirschler A., Herbert R., Caumette P. Orenia salinaria sp. nov., a fermentative bacterium isolated from anaerobic sediments of Mediterranean salterns. Int. J. Syst. Evol. Microbiol. 50:2000;721-729.
7. Hirschler-Réa A., Matheron R., Riffaud C., Mouné S., Eatock C., Herbert R., Willison J.C., Caumette P. Isolation and characterization of spirilloid purple phototrophic bacteria forming red layers in microbial mats of Mediterranean salterns; description of Halorhodospira neutrophila sp. nov., and emendation of the genus Halorhodospira. Int. J. Syst. Evol. Microbiol. 53:2003;153-163.
8. Pace N.R., Stahl D.A., Lane D.L., Olsen G.J. The analysis of natural microbial populations by rRNA sequences. Adv. Microb. Ecol. 9:1986;1-55.
9. Amann R.I., Ludwig W., Schleifer K.-H. Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol. Rev. 59:1995;143-169.
10. Hugenholtz P., Pitulle C., Hershberger K.L., Pace N.R. Novel division level bacterial diversity in a Yellowstone hot spring. J. Bacteriol. 180:1998;366-376.
11. Bowman J.P., McCammon S.A., Brown M.V., Nichols D.S., McMeekin T.A. Diversity and association of psychrophilic bacteria in Antarctic sea ice. Appl. Environ. Microbiol. 63:1997;3068-3078.
12. Benlloch S., Lopez-Lopez A., Casamayor E.O., Ovreas L., Goddard V., Daae F.L., Smerdon G., Massana R., Joint I., Thingstad F., Pedros-Allo C., Rodriguez-Valera F. Prokaryotic genetic diversity throughout the salinity gradient of a coastal solar saltern. Environ. Microbiol. 4:2002;349-360.
13. Fuhrman J.A., McCallum K., Davis A.A. Phylogenetic diversity of subsurface marine microbial communities from the Atlantic and Pacific oceans. Appl. Environ. Microbiol. 59:1993;1294-1302.
14. Rehnstam A.-S., Bäckman S., Smith D., Azam F., Hagström A. Blooms of sequence-specific culturable bacteria in the sea. FEMS Microbiol. Ecol. 102:1993;161-166.
15. Benlloch S., Martinez-Murcia A.J., Rodriguez-Valera F. Sequencing of bacterial and archaeal 16S rRNA genes directly amplified from a hypersaline environment. Syst. Appl. Microbiol. 18:1995;574-581.
16. Eder W., Ludwig W., Huber R. Novel 16S rRNA sequences retrieved from highly saline brine sediments of Kebrit Deep, Red Sea. Arch. Microbiol. 172:1999;213-218.
17. Holben W.E., Jansson J.K., Chelm B.K., Tiedje J.M. DNA probe method for the detection of specific microorganisms in the soil bacterial community. Appl. Environ. Microbiol. 54:1988;703-711.
18. Tsai Y.-L., Olson B. Rapid method for direct extraction of DNA from soil and sediments. Appl. Environ. Microbiol. 57:1991;1070-1074.
19. Rochelle P.A., Fry J.C., Parkes R.J., Weightman A.J. DNA extraction for 16S rRNA gene analysis to determine genetic diversity in deep sediment communities. FEMS Microbiol. Lett. 100:1992;59-66.
20. Chirgwin J.M., Przybyla A.E., MacDonald R.J., Ritter W.J. Isolation of biologically active ribonucleic acid from sources enriched in ribonuclease. Biochemistry. 18:1979;5294-5299.
21. Felsenstein, J. (1993) Phylogeny Inference Package, version 3.5c. Department of Genetics, University of Washington, Seattle, WA.
22. Anton J., Oren A., Benlloch S., Rodriguez-Valera F., Amann R., Rossello-Mora R. Salinibacter ruber gen. nov., sp. nov., a novel, extremely halophilic member of the Bacteria from saltern crystallizer ponds. Int. J. Syst. Evol. Microbiol. 52:2002;485-491.
23. Alfredsson G.A., Kristjansson J.K., Hjörleifsdottir S., Stetter K.O. Rhodothermus marinus, gen. nov., sp. nov., a thermophilic, halophilic bacterium from submarine hot springs in Iceland. J. Gen. Microbiol. 134:1988;299-306.
24. Jurgens G., Glockner F., Amann R., Saano A., Montonen L., Likolammi M., Munster U. Identification of novel Archaea in bacterioplankton of a boreal forest lake by phylogenetic analysis and fluorescent in situ hybridization (1). FEMS Microbiol. Ecol. 34:2000;45-56.
25. Li L., Kato C., Horikoshi K. Microbial diversity in sediments collected from the deepest cold-seep area, the Japan Trench. Mar. Biotechnol. 1:1999;391-400.
26. Jurgens G., Lindström K., Saano A. Novel group within the kingdom Crenarchaeota from boreal forest soil. Appl. Environ. Microbiol. 63:1997;803-805.
27. Barns S.M., Delwiche C.F., Palmer J.D., Pace N.R. Perspectives on archaeal diversity, thermophily and monophyly from environmental rRNA sequences. Proc. Natl. Acad. Sci. USA. 93:1996;9188-9193.
28. Clayton R.A., Sutton G., Hinkle P.S., Bult C., Fields C. Intraspecific variation in small-subunit rRNA in GenBank: why single sequences may not adequately represent prokaryotic taxa. Int. J. Syst. Bacteriol. 45:1995;595-599.
29. Nübel U., Engelen B., Felske A., Snaidr J., Wieshuber A., Amann R.I., Ludwig W., Backhaus H. Sequence heterogeneities of genes encoding 16S rRNAs in Paenibacillus polymyxa detected by temperature gradient gel electrophoresis. J. Bacteriol. 178:1996;5636-5643.
30. Benlloch S., Acinas S.G., Martinez-Murcia A.J., Rodriguez-Valera F. Description of prokaryotic diversity along the salinity gradient of a multipond solar saltern by direct PCR amplification of 16S rDNA. Hydrobiologia. 329:1996;19-31.
31. Benlloch S., Acinas S.G., Anton J., Lopez-Lopez A., Luz S.P., Rodriguez-Valera F. Archaeal biodiversity in crystallizer ponds from a solar saltern: culture versus PCR. Microbiol. Ecol. 41:2001;12-19.
32. Cytryn E., Minz D., Oremland R.S., Cohen Y. Distribution and diversity of Archaea corresponding to the limnological cycle of a hypersaline stratified lake (Solar Lake, Sinai, Egypt). Appl. Environ. Microbiol. 66:2000;3269-3276.
33. de Souza M.P., Amini A., Dojka M.A., Pickering I.J., Dawson S.C., Pace N.R., Terry N. Identification and characterization of bacteria in a selenium-contaminated hypersaline evaporation pond. Appl. Environ. Microbiol. 67:2001;3785-3794.
34. Anton J., Rossello-Mora R., Rodriguez-Valera F., Amann R. Extremely halophilic Bacteria in crystallizer ponds from solar salterns. Appl. Environ. Microbiol. 66:2000;3052-3057.
35. Hartmann R., Sickinger H.-D., Oesterhelt D. Anaerobic growth of halobacteria. Proc. Natl. Acad. Sci. USA. 77:1980;3821-3825.
36. Oren A., Trüper H.G. Anaerobic growth of halophilic archaeobacteria by reduction of dimethylsulfoxide and trimethylamine N-oxide. FEMS Microbiol. Lett. 70:1990;33-36.
37. Caumette P., Cohen Y., Matheron R. Isolation and characterization of Desulfovibrio halophilus sp. nov., a halophilic sulfate-reducing bacterium isolated from Solar lake (Sinai). Syst. Appl. Microbiol. 14:1991;33-38.
38. Caumette P. Ecology and physiology of phototrophic bacteria and sulfate-reducing bacteria in marine salterns. Experientia. 49:1993;473-481.
39. Imhoff J.F., Süling J. The phylogenetic relationship among Ectothiorhodospiraceae: a reevaluation of their taxonomy on the basis of 16S rDNA sequences. Arch. Microbiol. 165:1996;106-113.
40. Minz D., Fishbain S., Green S.J., Muyzer G., Cohen Y., Rittmann B.E., Stahl D.A. Unexpected population distribution in a microbial mat community: sulfate-reducing bacteria localized to the highly oxic chemocline in contrast to a eukaryotic preference for anoxia. Appl. Environ. Microbiol. 65:1999;4659-4665.
41. Oren A. Formation and breakdown of glycine betaine and trimethylamine in hypersaline environments. Antonie van Leeuwenhoek. 58:1990;291-298.
42. Welsh D.T., Lindsay Y.E., Caumette P., Herbert R.A., Hannan J. Identification of trehalose and glycine betaine as compatible solutes in the moderately halophilic sulfate reducing bacterium, Desulfovibrio halophilus. FEMS Microbiol. Lett. 140:1996;203-207.
43. Bintrim S.B., Donohue T.J., Handelsman J., Roberts G.P., Goodman R. Molecular phylogeny of Archaea from soil. Proc. Natl. Acad. Sci. USA. 94:1997;277-282.
44. Buckley D.H., Graber J.R., Schmidt T.M. Phylogenetic analysis of nonthermophilic members of the kingdom Crenarchaeota and their diversity and abundance in soils. Appl. Environ. Microbiol; 64:1998;4333-4339.
45. Greenberg E.P., Canale-Parola E. Spirochaeta halophila sp. nov., a fermentative anaerobic bacterium from a high-salinity pond. Arch. Microbiol. 110:1976;185-194.
46. Magot M., Fradeau M.-L., Arnauld O., Lanau C., Ollivier B., Thomas P., Patel B.K.C. Spirochaeta smaragdinae sp. nov., a new mesophilic strictly anaerobic spirochete from an oil field. FEMS Microbiol. Lett. 155:1997;185-191.
47. Rainey F.A., Zhilina T.N., Boulygina E.S., Stackebrandt E., Tourova T.P., Zavarin G.A. The taxonomic status of the fermentative halophilic anaerobic bacteria: description of Haloanaerobiales ord. nov., Halobacteroidiaceae fam. nov., Orenia gen. nov. and further taxonomic rearrangements at the genus and species level. Anaerobe. 1:1995;185-199.
48. Patel B.K.C., Andrews K.T., Ollivier B., Mah R.A., Garcia J.L. Reevaluating the classification of Halobacteroides and Haloanaerobacter species based on sequence comparisons of the 16S ribosomal RNA gene. FEMS Microbiol. Lett. 134:1995;115-119.
49. Stackebrandt E., Rainey F.A., Ward-Rainey N. Anoxygenic phototrophy across the phylogenetic spectrum: current understanding and future perspectives. Arch. Microbiol. 166:1996;211-223.