Seasonal population changes in the restriction fragment length polymorphism (RFLP) patterns from PCR-amplified 16S rRNA genes of predominant ribotypes in microbial mat samples from the Ebro Delta (Spain)

Current Microbiology

Volumn 46, Issue 3, 2003, Pages 190-198

  Ramírez Moreno, Sergio ^a   Martínez Alonso, María Ramos ^a   Méndez Álvarez, Sebastián ^b   Esteve, Isabel ^a   Gaju, Núria ^a  

^a UNIVERSITAT AUTÒNOMA DE BARCELONA   (Spain)

^b UNIVERSIDAD DE LA LAGUNA   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

RNA 16S; PIGMENT;

ARTICLE; GENE AMPLIFICATION; GENETIC ANALYSIS; MICROBIAL MAT; NONHUMAN; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; RESTRICTION FRAGMENT LENGTH POLYMORPHISM; RIBOTYPING; SEASONAL VARIATION; SPAIN; ARCHAEBACTERIUM; BACTERIAL GENE; BACTERIUM; BIOMASS; CLASSIFICATION; ECOSYSTEM; GENE; GENETICS; ISOLATION AND PURIFICATION; METHODOLOGY; SEASON;

ARCHAEA; BACTERIA (MICROORGANISMS);

ARCHAEA; BACTERIA; BIOMASS; ECOSYSTEM; GENES, ARCHAEAL; GENES, BACTERIAL; PIGMENTS, BIOLOGICAL; POLYMERASE CHAIN REACTION; POLYMORPHISM, RESTRICTION FRAGMENT LENGTH; RIBOTYPING; RNA, RIBOSOMAL, 16S; SEASONS; SPAIN;

EID: 0037507357     PISSN: 03438651     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00284-002-3854-y     Document Type: Article

References (46)

1. Acinas S, Rodriguez-Valera F, Pedrós-Alió C (1997) Spatial and temporal variation in marine bacterioplankton diversity as shown by RFLP fingerprinting of PCR amplified 16S rDNA. FEMS Microbiol Ecol 24:27-40
2. Amann R, Ludwig W, Schleifer K (1995) Phylogenetic identification and in-situ detection of individual microbial cells without cultivation. Microbiol Rev 59:143-169
3. Bebout B, Garcia-Pichel F (1995) UV B-induced vertical migrations of cyanobacteria in a microbial mat. Appl Environ Microbiol 61:4215-4222
4. Blanc M, Marilley L, Beffa T, Aragno M (1997) Rapid identification of heterotrophic, thermophilic, spore-forming bacteria isolated from hot composts. Int J Syst Bacteriol 47:1246-1248
5. Castenholz R, Garcia-Pichel F (1999) Cyanobacterial responses to UV-radiation. In: Whitton B, Potts M (eds) Ecology of Cyanobacteria: their diversity in time and space. Dordrecht: Kluwer, pp 591-611
6. Chandler D, Fredrickson K, Brockman F (1997) Effect of PCR template concentration on the composition and distribution of total community 16S rDNA clone libraries. Mol Ecol 6:475-482
7. Esteve I, Martínez-Alonso M, Mir J, Guerrero R (1992) Distribution, typology and structure of microbial mat communities in Spain: a preliminary study. Limnetica 8:185-195
8. Esteve I, Ceballos D, Martínez-Alonso M, Gaju N, Guerrero R (1994) Development of versicoloured microbial mats: succession of microbial communities. In: Stal LJ, Caumette P (eds) Structure, development and environmental significance. NATO ASI Series, Vol G 35. Heidelberg: Springer-Verlag, pp 415-420
9. Farrelly V, Rainey A, Stackebrandt E (1995) Effect of genome size and rm gene copy number on PCR amplification of 16S rRNA genes from a mixture of bacterial species. Appl Environ Microbiol 61:2798-2801
10. Garcia-Pichel F, Mechling M, Castenholz R (1994) Diel migrations of microorganisms within a benthic, hypersaline mat community. Appl Environ Microbiol 60:1500-1511
11. Giuliano L, Domenico M, Domenico E, Höfle M, Yakimov M (1999) Identification of culturable oligotrophic bacteria within naturally occurring bacterioplankton communities of the Ligurian sea by 16S rRNA sequencing and probing. Microb Ecol 37:77-85
12. Hansen M, Tolker-Nielsen T, Givskov M, Molin S (1998) Biased 16S rDNA PCR amplification caused by interference from flanking the template region. FEMS Microbiol Ecol 26:141-149
13. Jorgensen B, Cohen Y, Revsbech N (1986) Transition from anoxygenic to oxygenic photosynthesis in a Microcoleus chthonoplastes cyanobacterial mat. Appl Environ Microbiol 51:408-417
14. Kehrmeyer S, Applegate B, Pinkart H, Hedrick D, White D, Sayler G (1996) Combined lipid/DNA extraction method for environmental samples. J Microbiol Methods 25:153-163
15. Krekeler D, Teske A, Cypionka H (1998) Strategies of sulphate-reducing bacteria to scape oxygen stress in a cyanobacterial mat. FEMS Microbiol Ecol 25:89-96
16. Kruschel C, Castenholz R (1998) The effect of solar UV and visible irradiance on the vertical movements of cyanobacteria in microbial mats of hypersaline waters. FEMS Microbiol Ecol 27: 53-72
17. Kuske C, Barns S, Busch J (1997) Diverse uncultivated bacterial groups from soils of the and southwestern United States that are present in many geographic regions. Appl Environ Microbiol 63: 3614-3621
18. Lessa E (1990) Multidimensional analysis of geographic genetic structure. Syst Zool 39:242-252
19. Macarrón B (1998) Utilización de marcadores lipídicos en el estudio de la biomasa, la estructura y el estado nutricional de las comunidades de los tapices microbianos del Delta del Ebro. PhD thesis, Autonomous University of Barcelona, Barcelona, Spain
20. Martínez-Alonso M (1997) Estudio comparativo de los ecosistemas bentónicos estratificados de la zona mediterránea de la Península Ibérica. Caracterización ecofisiológica de los tapetes microbianos del Delta del Ebro. PhD thesis, Autonomous University of Barcelona, Barcelona, Spain
21. Martínez-Murcia A, Acinas S, Rodriguez-Valera F (1995) Evaluation of prokaryotic diversity by restrictase digestion of 16S rDNA directly amplified from hypersaline environments. FEMS Microbiol Ecol 17:247-256
22. Méndez-Alvarez S, Esteve I, Guerrero R, Gaju N (1998) RAPD fingerprinting of Chlorobium strains. Syst Appl Microbiol 21:274-278
23. Mir J, Martínez-Alonso M, Esteve I, Guerrero R (1991) Vertical stratification and microbial assemblage of a microbial mat in the Ebro Delta (Spain). FEMS Microbiol Ecol 86:59-68
24. Moore DD (1998) Purification and concentration of DNA from aqueous solutions. Current protocols in molecular ecology. New York: John Wiley and Sons, Inc., pp 2.1.1-2.1.10
25. Navarrete A, Peacock A, Macnaughton SJ, Urmeneta J, Mas-Castella J, White DC, Guerrero R (2000) Physiological status and community composition of microbial mats of the Ebro Delta, Spain, by signature lipid biomarkers. FEMS Microbiol Ecol 39: 92-99
26. Pavón V, Gaju N (1997) Genomic relationship of five species of the genus Chromatium by analysis of large restriction fragments (macrorestriction analysis) using pulsed-field gel electrophoresis. Int J Syst Bacteriol 47:586-589
27. Pfenning N, Trüper H (1981) Isolation of members of the families Chromatiaceae and Chlorobiaceae. In: Starr MP, Stolz H, Trüper HG, Ballows A, Schlegel HG (eds) The prokaryotes, 1st ed. Berlin: Springer-Verlag, pp 279-289
28. Pfennig N, Trüper H (1992) The family Chlorobiaceae. In: Ballows A, Trüper H, Dworkin M, Harder W, Schleifer K (eds) The prokaryotes. Berlin: Springer-Verlag, 4:3583-3592
29. Redecker D, Thierfelder H, Walker C, Werner D (1997) Restriction analysis of PCR-amplified internal transcribed spacers of ribosomal DNA as a tool for species identification in different genera of the order glomales. Appl Environ Microbiol 63:1756-1761
30. Reysenbach A, Giver L, Wickham G, Pace N (1992) Differential amplification of rRNA genes by polymerase chain reaction. Appl Environ Microbiol 58:3417-3418
31. Rodríguez-Valera F, Ruiz-Berraquero F, Ramos-Cormenzana A (1981) Characteristics of the heterotrophic bacterial populations in hypersaline environments of different salt concentrations. Microbiol Ecol 7:235-243
32. Saiki R, Gelfand D, Stoffel S, Scharf S, Higuchi R, Horn G, Mullis K, Erlich H (1988) Primer-directed enzymatic amplification of DNA with a thermostable DNA polymerase. Science 239:487-494
33. Sambrook J, Fritsch E, Maniatis T (1989) Molecular cloning: a laboratory manual. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press
34. Sass H, Cypionka H, Babenzien H (1997) Vertical distribution of sulfate-reducing bacteria at the oxic-anoxic interface in sediments of the oligotrophic lake Stechlin. FEMS Microbiol Ecol 22:245-255
35. Smalla K, Cresswell N, Mendonca-Hagler L, Wolters A, Van Elsas J (1993) Rapid DNA extraction protocol from soil for polymerase chain reaction-mediated amplification. J Syst Bacteriol 74:78-85
36. Smit E, Leeflang P, Wernars K (1997) Detection of shifts in microbial community structure and diversity in soil by copper contamination using amplified ribosomal DNA restriction analysis. FEMS Microbiol Ecol 23:249-261
37. Suzuki M, Giovannoni S (1996) Bias caused template annealing in the amplification of mixtures of 16S rRNA genes by PCR. Appl Environ Microbiol 62:625-630
38. Urakawa H, Kita-Tsukamoto K, Ohwada K (1997) 16S rDNA genotyping using PCR/RFLP (restriction fragment length polymorphism) analysis among the family Vibrionaceae. FEMS Microbiol Lett 152:125-132
39. Urakawa H, Kita-Tsukamoto K, Ohwada K (1998) A new approach to separate the genus Photobacterium from Vibrio with RFLP pattern by Hha1 digestion of PCR-amplified 16S rDNA. Curr Microbiol 36:171-174
40. Van Gemerden H, Beeftink H (1983) Ecology of phototrophic bacteria. In: Ormerod JG (ed) The phototrophic bacteria: anaerobic life in the light. Studies in microbiology. Oxford: Blackwell Scientific Publications, 4:146-185
41. Van Hannen E, Mooij W, Van Agterveld M, Gons H, Laanbroek H (1999) Detritus-dependent development of the microbial community in a experimental system: qualitative analysis by denaturing gradient gel electrophoresis. Appl Environ Microbiol 65:2478-2484
42. Ward D, Weller R, Bateson M (1990) 16S rRNA sequences reveal numerous uncultured microorganisms in a natural community. Nature 344:137-141
43. Wilson I (1997) Minireview: Inhibition and facilitation of nucleic acid amplification. Appl Environ Microbiol 63:3741-3751
44. Wood J, Scott K, Avgustin G, Newbold C, Flint H (1998) Estimation of the relative abundance of different Bacteroides and Prevotella ribotypes in gut samples by restriction enzyme profiling of PCR-amplified 16S rRNA gene sequences. Appl Environ Microbiol 64:3683-3689
45. Yeates C, Gillings M, Davison A, Altavilla N, Veal D (1997) PCR amplification of crude microbial DNA extracted from soil. Lett Appl Microbiol 25:303-307
46. Zhou J, Bruns M, Tiedje J (1996) DNA recovery from soils of diverse composition. Appl Environ Microbiol 62:316-322