Identification of and spatio-temporal differences between microbial assemblages from two neighboring sulfurous lakes: Comparison by microscopy and denaturing gradient gel electrophoresis

Applied and Environmental Microbiology

Volumn 66, Issue 2, 2000, Pages 499-508

  Casamayor, Emilio O ^a   Schäfer, Hendrik ^b,d   Bañeras, Lluis ^c   Pedrós Alió, Carlos ^a   Muyzer, Gerard ^b,d  

^a INSTITUT DE CIÈNCIES DEL MAR   (Spain)

^b MAX PLANCK INSTITUTE FOR MARINE MICROBIOLOGY   (Germany)

^c UNIVERSITY OF GIRONA   (Spain)

^d ROYAL NETHERLANDS INSTITUTE FOR SEA RESEARCH   (Netherlands)

Author keywords

[No Author keywords available]

Indexed keywords

LAKE WATER; RNA 16S; SULFUR;

COMMUNITY DYNAMICS; ENVIRONMENTAL CONDITIONS; GENETIC ANALYSIS; MICROBIAL COMMUNITY; MICROSCOPY; PHYLOGENETICS; SPATIOTEMPORAL ANALYSIS;

ARTICLE; BACTEROIDES; CLIMATE; DENATURING GRADIENT GEL ELECTROPHORESIS; EURYARCHAEOTA; FLAVOBACTERIUM; FLEXIBACTERACEAE; LAKE; MICROBIAL GROWTH; MICROSCOPY; NONHUMAN; NUCLEOTIDE SEQUENCE; PHOTOTROPHIC BACTERIUM; PHYLOGENY; PHYTOPLANKTON; POLYMERASE CHAIN REACTION; RNA GENE; SEQUENCE ANALYSIS; SULFUR BACTERIUM;

ARCHAEA; BACTERIA; DNA, BACTERIAL; DNA, RIBOSOMAL; ECOSYSTEM; ELECTROPHORESIS; FRESH WATER; MICROSCOPY; MOLECULAR SEQUENCE DATA; PHYLOGENY; POLYMERASE CHAIN REACTION; RNA, RIBOSOMAL, 16S; SEQUENCE ANALYSIS, DNA; SULFIDES; WATER MICROBIOLOGY;

SPAIN;

ARCHAEA; BACTERIA (MICROORGANISMS); BACTEROIDES; BACTEROIDES PHYLUM; CHLOROBI; CRENARCHAEOTA; CYANOBACTERIA; CYTOPHAGA; EURYARCHAEOTA; FLAVOBACTERIUM; FLEXIBACTERACEAE; PHOTOBACTERIA; POSIBACTERIA; PROKARYOTA; PROTEOBACTERIA; THERMOPLASMA;

EID: 17544390961     PISSN: 00992240     EISSN: None     Source Type: Journal    
DOI: 10.1128/AEM.66.2.499-508.2000     Document Type: Article

References (58)

1. Altschul, S. F., W. Gish, W. Miller, E. W. Myers, and D. J. Lipman. 1990. Basic local alignment search tool. J. Mol. Biol. 215:403-410.
2. Amann, R. I., W. Ludwig, and K. H. Schleifer. 1995. Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol. Rev. 59:143-169.
3. Andreasen, K., and P. H. Nielsen. 1997. Application of microautoradiography to the study of substrate uptake by filamentous microorganisms in activated sludge. Appl. Environ. Microbiol. 63:3662-3668.
4. Aravalli, R. N., Q. X. She, and R. A. Garrett. 1998. Archaea and the new age of microorganisms. Trends Ecol. Evol. 13:190-194.
5. Brock, T. D. 1987. The study of microorganisms in situ: progress and problems. Symp. Soc. Gen. Microbiol. 41:1-17.
6. Brosius, J., T. J. Dull, D. D. Sleeter, and H. F. Noller. 1981. Gene organization and primary structure of a ribosomal RNA operon from Escherichia coli. J. Bacteriol. 148:107-127.
7. Casamayor, E. O., J. I. Calderón-Paz, J. Mas, and C. Pedrós-Alió. 1998. Identification of phototrophic sulfur bacteria through the analysis of ImwRNA band patterns. Arch. Microbiol. 170:269-278.
8. Casamitjana, C., and E. Roget. 1993. Resuspension of sediment by focused groundwater in Lake Banyoles. Limnol. Oceanogr. 38:643-656.
9. Chen, F., J. M. González, W. A. Dustman, M. A. Moran, and R. E. Hodson. 1997. In situ reverse transcription, an approach to characterize genetic diversity and activities of prokaryotes. Appl. Environ. Microbiol. 63:4907-4913.
10. Delwart, E. L., B. Herring, A. G. Rodrigo, and J. I. Mullins. 1995. Genetic subtyping of human immunodeficiency virus using a heteroduplex mobility assay. Genome Res. 4:216.
11. Farrelly, V., F. A. Rainey, and E. Stackebrandt. 1995. Effect of genome size and rrn gene copy number on PCR amplification of 16S rRNA genes from a mixture of bacterial species. Appl. Environ. Microbiol. 61:2798-2801.
12. Fenchel, T., and B. J. Finlay. 1991. Synchronous division of an endosymbiotic methanogenic bacterium in the anaerobic ciliate Plagiopyla frontata Kahl. J. Protozool. 38:22-28.
13. Ferris, M. J., and D. M. Ward. 1997. Seasonal distributions of dominant 16S rRNA-defined populations in a hot spring microbial mat examined by denaturing gradient gel electrophoresis. Appl. Environ. Microbiol. 63:1375-1381.
14. Figueras, J. B., L. J. García-Gil, and C. A. Abellà. 1997. Phylogeny of the genus Chlorobium based on 16S rDNA sequence. FEMS Microhiol. Lett. 152:31-36.
15. García-Cantizano, J., J. I. Calderón-Paz, and C. Pedrós-Alió. 1994. Thymidine incorporation in Lake Cisó: problems in estimating bacterial secondary production across oxic-anoxic interfaces. FEMS Microbiol. Ecol. 14:53-64.
16. Gasol, J. M., R. Guerrero, and C. Pedrós-Alió. 1991. Seasonal variations in size structure and procaryotic dominance in sulfurous Lake Cisó. Limnol. Oceanogr. 36:860-872.
17. Golterman, H. L., R. S. Clymo, and M. A. M. Ohnstad. 1978. Methods for physical and chemical analysis of fresh waters. IBP Handbook no. 8. Scientific Publications, Oxford, United Kingdom.
18. Guerrero, R., E. Montesinos, I. Esteve, and C. Abellà. 1980. Physiological adaptation and growth of purple and green sulfur bacteria in a meromictic lake (Vilà) as compared to a holomictic lake (Sisó), p. 161-171. In M. Dokulil, H. Metz, and D. Jewson (ed.), Shallow lakes. Contribution to their limnology. Developments in hydrobiology, vol. 3. Dr. W. Junk Publishers, The Hague, The Netherlands.
19. Guerrero, R., E. Montesinos, C. Pedrós-Alió, I. Esteve, J. Mas, H. van Gemerden, P. A. G. Hofman, and J. F. Bakker. 1985. Phototrophic sulfur bacteria in two Spanish lakes: vertical distribution and limiting factors. Limnol. Oceanogr. 30:919-931.
20. Guerrero, R., C. Pedrós-Alió, I. Esteve, and J. Mas. 1987. Communities of phototrophic sulfur bacteria in lakes of the Spanish Mediterranean region. Acta Acad. Abo. 47:125-151.
21. Hansen, M. C., T. Tolkernielsen, M. Givskov, and S. Molin. 1998. Biased 16S rDNA PCR amplification caused by interference from DNA flanking the template region. FEMS Microbiol. Ecol. 26:141-149.
22. Hugenholtz, P., and N. R. Pace. 1996. Identifying microbial diversity in the natural environment: a molecular phylogenetic approach. Trends Biotechnol. 14:190-197.
23. Kirchman, D., J. Sigda, R. Kapuscinski, and R. Mitchell. 1982. Statistical analysis of the direct count method for enumerating bacteria. Appl. Environ. Microbiol. 44:376-82.
24. Liu, W. T., T. L. Marsh, H. Cheng, and L. J. Forney. 1997. Characterization of microbial diversity by determining terminal restriction fragment length polymorphisms of genes encoding 16S rRNA. Appl. Environ. Microbiol. 63:4516-4522.
25. Llobet-Brossa, E., R. Rosselló-Mora, and R. Amann. 1998. Microbial community composition of Wadden Sea sediments as revealed by fluorescence in situ hybridization. Appl. Environ. Microbiol. 64:2691-2696.
26. Ludwig, W., and K. H. Schleifer. 1994. Bacterial phylogeny based on 16S and 23S rDNA sequence analysis. FEMS Microbiol. Rev. 15:155-173.
27. Ludwig, W., O. Strunk, S. Klugbauer, N. Klugbauer, M. Weizenegger, J. Neumaier, M. Bachleitner, and K. H. Schleifer. 1998. Bacterial phylogeny based on comparative sequence analysis. Electrophoresis 19:554-568.
28. Maidak, B. L., G. J. Olsen, N. Larsen, R. Overbeek, M. J. McCaughey, and C. R. Woese. 1997. The RDP (Ribosomal Database Project). Nucleic Acids Res. 25:109-110.
29. Massana, R., J. García-Cantizano, and C. Pedrós-Alió. 1996. Components, structure and fluxes of the microbial food web in a small, stratified lake. Aquat. Microb. Ecol. 11:279-288.
30. Massana, R., and C. Pedrós-Alió. 1994. Role of anaerobic ciliates in planktonic food webs: abundance, feeding, and impact on bacteria in the field. Appl. Environ. Microhiol. 60:1325-1334.
31. Montesinos, E., R. Guerrero, C. Abellà, and I. Esteve. 1983. Ecology and physiology of the competition between Chlorobium limicola and Chlorobium phaeobacteroides. Appl. Environ. Microhiol. 46:1007-1016.
32. Murray, A. E., J. T. Hollibaugh, and C. Orrego. 1996. Phylogenetic compositions of bacterioplankton from two California estuaries compared by denaturing gradient gel electrophoresis of 16S rDNA fragments. Appl. Environ. Microbiol. 62:2676-2680.
33. Muyzer, G. 1998. Structure, function and dynamics of microbial communities: the molecular biological approach, p. 87-117. In G R. Carvalho (ed.), Advances in molecular ecology. NATO Science Series. IOS Press, Amsterdam, The Netherlands.
34. Muyzer, G., T. Brinkhoff, U. Nübel, C. Santegoeds, H. Schäfer, and C. Wawer, 1998. Denaturing gradient gel electrophoresis (DGGE) in microbial ecology, p. 1-27. In A. D. L. Akkermans, J. D. van Elsas, and F. J. de Bruijn (ed.), Molecular microbial ecology manual, vol. 3.4.4. Kluwer Academic Publishers, Dordrecht, The Netherlands.
35. Muyzer, G., E. D. De Waal, and A. G. Uitterlinden. 1993. Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA. Appl. Environ. Microbiol. 59:695-700.
36. Muyzer, G., and K. Smalla. 1998. Application of denaturing gradient gel electrophoresis (DGGE) and temperature gradient gel electrophoresis (TGGE) in microbial ecology. Antonie Leeuwenhoek 73:127-141.
37. Muyzer, G., A. Teske, C. O. Wirsen, and H. W. Jannasch. 1995. Phylogenetic relationship of Thiomicrospira species and their identification in deep-sea hydrothermal vent samples by denaturing gradient gel electrophoresis of 16S rDNA fragments. Arch. Microbiol. 164:165-172.
38. Nübel, U., F. García-Pichel, M. Kühl, and G. Muyzer. 1999 Quantifying microbial diversity: morphotypes, 16S rRNA genes, and carotenoids from oxygenic phototrophs in microbial mats. Appl. Environ. Microbiol. 65:422-430.
39. Nübel, U., F. García-Pichel, and G. Muyzer. 1997. PCR primers to amplify 16S rRNA genes from cyanobacteria. Appl. Environ. Microbiol. 63:3327-3332.
40. Oelmüller, U., N. Krüger, A. Steinbüchel, and C. G. Friedrich. 1990. Isolation of prokaryotic RNA and detection of specific mRNA with biotinylated probes. J. Microbiol. Methods 11:73-84.
41. Overmann, J., and C. Tuschak. 1997. Phylogeny and molecular fingerprinting of green sulfur bacteria. Arch. Microbiol. 167:302-309.
42. Øvreas, L., L. Forney, F. L. Daae, and V. Torsvik. 1997. Distribution of bacterioplankton in meromictic Lake Saelenvannet, as determined by denaturing gradient gel electrophoresis of PCR-amplified gene fragments coding for 16S rRNA. Appl. Environ. Microbiol. 63:3367-3373.
43. Pace, N. R. 1997. A molecular view of microbial diversity and the biosphere. Science 276:734-740.
44. Pedrós-Alió, C. 1993. Diversity of bacterioplankton. Trends Ecol. Evol. 8:86-90.
45. Pedrós-Alió, C., J. García-Cantizano, and J. I. Calderón-Paz. 1993. Bacterial production in anaerobic water columns, p. 519-530. In P. F. Kemp, B. F. Sherr, E. B. Sherr, and J. J. Cole (ed.), Current methods in aquatic microbial ecology. Lewis Publishers, Boca Raton, Fla.
46. Pedrós-Alió, C., and R. Guerrero. 1993. Microbial ecology in Lake Cisó. Adv. Microb. Ecol. 13:155-209.
47. Pfennig, N., and H. G. Trüper. 1989. Anoxygenic phototrophic bacteria, p. 1635-1653. In J. T. Staley, M. P. Bryant, N. Pfennig, and J. G. Holt (ed.), Bergey's manual of systematic bacteriology, vol. 3. Williams and Wilkins, Baltimore, Md.
48. Porter, K. G., and Y. S. Feig. 1980. The use of DAPI for identifying and counting aquatic microflora. Limnol. Oceanogr. 25:943-948.
49. Raskin, L., J. M. Stromley, B. E. Rittmann, and D. A. Stahl. 1994. Group-specific 16S rRNA hybridization probes to describe natural communities of methanogens. Appl. Environ. Microbiol. 60:1232-1240.
50. Reisenbach, H. 1991. The order Cytophagales, p. 3631-3675. In A. Balows, H. G. Trüper, M. Dworkin, W. Harder, and K.-H. Schleifer (ed.), The prokaryotes, vol. 4. Springer-Verlag, Berlin, Germany.
51. Reysenbach, A. L., L. J. Giver, G. S. Wickham, and N. R. Pace. 1992. Differential amplification of rRNA genes by polymerase chain reaction. Appl. Environ. Microbiol. 58:3417-3418.
52. Rosselló-Mora, R., B. Thamdrup, H. Schäfer, R. Weller, and R. Amann. 1999. The response of the microbial community of marine sediment to organic carbon input under anaerobic conditions. Syst. Appl. Microbiol. 22:237-248.
53. Santegoeds, C. M., S. C. Nold, and D. M. Ward. 1996. Denaturing gradient gel electrophoresis used to monitor the enrichment culture of aerobic chemoorganotrophic bacteria from a hot spring cyanobacterial mat. Appl. Environ. Microbiol. 62:3922-3928.
54. Stackebrandt, E., and F. A. Rainey. 1995. Partial and complete 16S rDNA sequences, their use in generation of 16S rDNA phylogenetic trees and their implications in molecular ecological studies, p. 1-17. In A. D. L. Akkermans, J. D. van Elsas, and F. J. de Bruijn (ed.), Molecular microbial ecology manual, vol. 3.1.1. Kluwer Academic Publishers, Dordrecht, The Netherlands.
55. Stahl, D. A., and R. I. Amann. 1991. Development and application of nucleic acid probes, p. 205-248. In E. Stackebrandt and M. Goodfellow (ed.), Nucleic acid techniques in bacterial systematics. Wiley, New York, N. Y.
56. Suzuki, M. T., and S. J. Giovannoni. 1996. Bias caused by template annealing in the amplification of mixtures of 16S rRNA genes by PCR. Appl. Environ. Microbiol. 62:625-630.
57. Teske, A., P. Sigalevich, Y. Cohen, and G. Muyzer. 1996. Molecular identification of bacteria from a coculture by denaturing gradient gel electrophoresis of 16S ribosomal DNA fragments as a tool for isolation in pure cultures. Appl. Environ. Microbiol. 62:4210-4215.
58. Wintzingerode, F. V., U. B. Goebel, and E. Stackebrandt. 1997. Determination of microbial diversity in environmental samples: pitfalls of PCR-based rRNA analysis. FEMS Microbiol. Rev. 21:213-229.