Analysis of microbial community during biofilm development in an anaerobic wastewater treatment reactor

Microbial Ecology

Volumn 56, Issue 1, 2008, Pages 121-132

  Fernández, Nuria ^a   Díaz, Emiliano Enrique ^a   Amils, Ricardo ^a   Sanz, José L ^a  

^a UNIVERSIDAD AUTÓNOMA DE MADRID   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

RNA 16S;

ANAEROBIC GROWTH; ARCHAEBACTERIUM; ARTICLE; BACTERIUM; BIOFILM; BIOREACTOR; CLASSIFICATION; CONFOCAL MICROSCOPY; DNA SEQUENCE; ECOSYSTEM; ELECTROPHORESIS; FLUORESCENCE IN SITU HYBRIDIZATION; GENETICS; GROWTH, DEVELOPMENT AND AGING; METHODOLOGY; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PHYLOGENY; PROTEOBACTERIA; SCANNING ELECTRON MICROSCOPY; SEWAGE; ULTRASTRUCTURE; WATER MANAGEMENT;

ANAEROBIOSIS; ARCHAEA; BACTERIA; BIOFILMS; BIOREACTORS; ECOSYSTEM; ELECTROPHORESIS; IN SITU HYBRIDIZATION, FLUORESCENCE; MICROSCOPY, CONFOCAL; MICROSCOPY, ELECTRON, SCANNING; MOLECULAR SEQUENCE DATA; PHYLOGENY; PROTEOBACTERIA; RNA, RIBOSOMAL, 16S; SEQUENCE ANALYSIS, DNA; WASTE DISPOSAL, FLUID; WATER PURIFICATION;

ALPHAPROTEOBACTERIA; ARCHAEA; ARCOBACTER; ARCOBACTER SP. SOLAR LAKE; AZOSPIRILLUM; BACTERIA (MICROORGANISMS); FIRMICUTES; METHANOSAETA CONCILII; METHANOSARCINA; METHANOSPIRILLUM; OLEOMONAS; PROTEOBACTERIA; THERMOTOGAE; THERMOTOGAE (CLASS);

EID: 44949146472     PISSN: 00953628     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00248-007-9330-2     Document Type: Article

References (61)

1. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215:403-410
2. Alphenaar PA (1994) Anaerobic granular sludge: characterization, and factors affecting its functioning. Ph.D. thesis, Landbouwuniversiteit, Wageningen, The Netherlands
3. Amann RI, Krumholz I, Stahl DA (1990) Fluorescent oligonucleotide probing of whole cells for determinative, phylogenetic, and environmental studies in microbiology. J Bateriol 172:762-770
4. Amann RI, Binder BJ, Olson BJ, Chisholm SW, Devereux R, Stahl DA (1990) Combination of 16S rRNA-targeted oligonucleotide probes with flow cytometry for analyzing mixed microbial populations. Appl Environ Microbiol 56:1919-1925
5. Amann RI, Ludwig W, Schleifer KH (1995) Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol Rev 59:143-169
6. Amann RI (1995) In situ identification of microorganisms by whole cell hybridization with rRNA-targeted nucleic acid probes. In: Akkermans ADL, van Elsas JK (eds) Molecular microbial ecology manual, section 3.3.6. Kluwer Academic Publishers, London, pp 3.3.6/1-3.3.6/15
7. Amann RI, Fuchs BM, Behrens S (2001) The identification of microorganisms by fluorescence in situ hybridisation. Curr Opin Biotech 12:231-236
8. Araujo JC, Brucha G, Campos JR, Vazoller RF (2000) Monitoring the development of anaerobic biofilms using fluorescent in situ hybridization and confocal laser scanning microscopy. Water Sci Technol 41:69-77
9. Boetius A, Ravenschlag K, Schubert C, Rickert D, Widdel F, Gieseke A, Amann RI, Jørgesen B, Witte U, Pfannkuche O (2000) A marine microbial consortium apparently mediating anaerobic oxidation of methane. Nature 407:623-626
10. Bergey's manual of systematic bacteriology, 2nd edn (2005). In: Brenner DJ, Krieg NR, Staley JT (eds) The proteobacteria, Springer.
11. Brosius J, Dull TJ, Sleeter DD, Noller HF (1981) Gene organization and primary structure of a ribosomal RNA operon from Escherichia coli. J Mol Biol 148:107-127
12. Chan O-C, Liu W-T, Fang HHP (2001) Study of microbial community of brewery-treating granular sludge by denaturing gradient gel electrophoresis of 16S rRNA gene. Water Sci Technol 43:77-82
13. Costerton JW, Llewandowski Z, DeBeer D, Caldwell D, Korber D, James G (1994) Biofilms, the customized microniche. J. Bacteriol 176:2137-2142
14. Costerton JW, Stewart PS, Greenberg EP (1999) Bacterial biofilms: a common cause of persistent infections. Science 284:1318-1322
15. Díaz EE, Amils R, Sanz JL (2003) Molecular ecology of anaerobic granular sludge grown at different conditions. Water Sci Technol 48:57-64
16. Díaz EE, Stams AJ, Amils R, Sanz JL (2006) Phenotypic properties and microbial diversity of methanogenic granules from a full-scale upflow anaerobic sludge bed reactor treating brewery wastewater. Appl Environ Microbiol 72:4942-4949
17. Doré J, Sghir A, Hannequart-Gramet G, Corthier G, Pochart P (1998) Design and evaluation of a 16S rRNA-targeted oligonucleotide probe for specific detention and quantification of human faecal Bacteroides populations. Syst Appl Microbiol 21:65-71
18. Dunne WM (2002) Bacterial adhesion: seen any good biofilms lately? Clin Microbiol Rev 15:155-166
19. Egli D, Bosshard G, Werlen C, Lais P, Siegrist H, Zehnder AJB, Van der Meer JR (2003) Microbial composition and structure of a rotating biological contactor biofilm treating ammonium-rich wastewater without organic carbon. Microbial Ecol 45:419-432
20. Fang HHP (2000) Microbial distribution in UASB granules and its resulting effects. Water Sci Technol 42:201-208
21. Fang HHP, Chan K-Y, Xu L-C (2000) Quantification of bacterial adhesion forces using atomic force microscopy (AFM). J Microbiol Meth 40:89-97
22. García Encina PA, Hidalgo MD (2005) Influence of substrate feed patterns on biofilm development in anaerobic fluidized bed reactors (AFBR). Process Biochem 40:2509-2516
23. Gonzalez-Gil G, Lens PNL, van Aelst A, van As H, Versprille AI, Lettinga G (2001) Cluster structure of anaerobic aggregates of an expanded granular sludge bed reactor. Appl Environm Microb 678:3683-3692
24. Harmsen HJM, Kengen HMP, Akkermans ADL, Stams AJM, De Vos WM (1996) Detection and localization of syntrophic propionate-oxidizing bacteria in granular sludge by in situ hybridization using 16S rRNA-based oligonucleotide probes. Appl Environ Microb 62:1656-1663
25. Hentzer M, Teitzel GM, Balzer GJ, Heydorn A, Molin S, Givskov M, Parsek MR (2001) Alginate overproduction affects Pseudomonas aeruginosa biofilm structure and function. J Bacteriol 183:5395-5401
26. Hidalgo MD, García-Encina PA (2002) Biofilm development and bed segregation in a methanogenic fluidized bed reactor. Water Res 36:3083-3091
27. Kanamori T, Rashid N, Morikawa M, Haruyuki A, Imanaka T (2002) Oleomonas sagaranensis gen. nov., sp. nov., represents a novel genus in the α-Proteobacteria. FEMS Microbiol Lett 217:255-261
28. Lane DJ (1991) 16S/23S rRNA sequencing. In: Stackebrandt E, Goodfellow M (eds) Nucleic acid techniques in bacterial systematic. Wiley, New York, NY, pp 115-175
29. Lehtola MJ, Miettinen IT, Keinänen MM, Kekki TK, Laine O, Hirvonen A, Vartiainen T, Martikanen PJ (2004) Microbiology, chemistry and biofilm development in a pilot drinking water distribution system with copper and plastic pipes. Water Res 38:3769-3779
30. Liu Y, Tay J-H (2002) The essential role of hydrodynamic shear force in the formation of biofilm and granular sludge. Water Res 36:1653-1665
31. Ludwig W, Strunk O, Westram R, Richter L, Meier H, Yadhukumar, Buchner A, Lai T, Steppi S, Jobb G, Förster W, Brettske I, Gerber S, Ginhart AW, Gross O, Grumann S, Hermann S, Jost R, König A, Liss T, Lüßmann R, May M, Nonhoff B, Reichel B, Strehlow R, Stamatakis A, Stuckmann N, Vilbig A, Lenke M, Ludwig T, Bode A, Schleifer KH (2004) ARB: a software environment for sequence data. Nucleic Acids Res 32:1363-1371
32. Manz W, Amann R, Ludwig W, Wagner M, Schleifer KH (1992) Phylogenetic oligodeoxynucleotide probes for the major subclasses of proteobacteria: problems and solutions. Syst Appl Microbiol 15:593-600
33. Manz W, Eisenbrecher M, Neu TR, Szewzyk U (1998) Abundance and spatial organization of gram-negative sulfate-reducing bacteria in activated sludge investigated by in situ probing with specific 16S rRNA targeted oligonucleotides. FEMS Microbiol Ecol 25:43-61
34. Manz W, Wendt-Potthoff K, Neu TR, Szewzyk U, Lawrence JR (1999) Phylogenetic composition, spatial structure, and dynamics of lotic bacterial biofilms investigated by fluorescent in situ hybridization and confocal laser scanning microscopy. Microbial Ecol 37:225-237
35. McLeod ES, MacDonald R, Brözel VS (2002) Distribution of Shewanella putrefaciens and Desulfovibrio vulgaris in sulphidogenic biofilms of industrial cooling water systems determined by fluorescent in situ hybridisation. Water SA 28:123-128
36. Meier H, Amann RI, Ludwig W, Schleifer KH (1999) Specific oligonucleotide probes for in situ detection of a major group of gram-positive bacteria with low DNA G + C content. Syst Appl Microbiol 22:186-196
37. Miranda-Tello E, Fardeau M-L, Thomas P, Ramirez F, CAsalot L, Cayol J-L, Garcia J-L, Ollivier B (2004) Petrotoga mexicana sp. nov., a novel thermophilic, anaerobic and xylanolytic bacterium isolated from an oil-producing well in the Gulf of Mexico. Int J Sys Evo Microbiol 54:169-174
38. Mujer W, Zehnder AJB (1983) Conversion. processes in anaerobic digestion. Water Sci Technol 15:127-167
39. Muyzer G, Hottenträger S, Teske A, Wawer C (1996) Denaturing gradient gel electrophoresis of PCR-amplified 16S rDNA - A new molecular approach to analyse the genetic diversity of mixed microbial communities. In: Akkermans ADL, van Elsas JK (eds) Molecular microbial ecology manual, Section 3.4.4. Kluiwer Academic Publishers, London, pp 3.4.4./1-3.4.4./23
40. Muyzer G, Smalla K (1998) Application of denaturing gradient gel electrophoresis (DGGE) and temperature gradient gel electrophoresis (TGGE) in microbial ecology. Mini review. Anton Leeuw Int J G 73:127-141
41. Nakagawa T, Sato S, Yamamoto Y, Fukui M (2002) Successive changes in community structure of an ethylbenzene-degrading sulfate-reducing consortium. Water Res 36:2813-2823
42. Neef A, (1997) An wendug der in situ-Einzelzell-Identifizierung von Bakterien zur populations analyse in Komplexen Mikrobiellen biozönsen. Doctoral thesis, Faculty of Biology, Chemistry and Geosciences, Technische Universität München.
43. Raskin L, Strinmley J, Rittmann BE, Stahl DA (1994) Group specific 16S RNA hybridization probes to describe natural communities of methanogens. Appl Environ Microb 60:1232-1240
44. Roller E, Wagner M, Amann RI, Ludwig W, Schleifer KH (1994) In situ probing of gram-positive bacteria with high DNA G + C content using 23S rRNA targeted oligonucleotides. Microbiology 140:2849-2858
45. Roselló-Mora R, Thamdrup B, Schäfer H, Weller R, Amann R (1999) The response of the microbial community of marine sediments to organic carbon input under anaerobic conditions. Sist Appl Microbiol 22:237-248
46. Sanz JL, Köchling T (2007) Molecular. biology techniques used in wastewater treatment: An overview. Process Biochem 42:119-133
47. Schmidt JE, Ahring BK (1995) Granular sludge formation in upflow anaerobic sludge blanket (UASB) reactors. Biotechnol Bioeng 49:229-246
48. Sekiguchi Y, Kamagata Y, Nakamura K, Ohashi A, Harada H (1999) Fluorescence in situ hybridization using 16S rRNA-targeted oligonucleotides reveals localization of methanogens and selected uncultured bacteria in mesophilic and thermophilic sludge granules. Appl Environ Microb 65:1280-1288
49. Silyn-Roberts G, Lewis G (2003) Substrata effects on bacterial biofilm development in a subsurface flow dairy waste treatment wetland. Water Sci Technol 48:261-269
50. Stahl DA, Amann RI (1991) Development and application of nucleic acid probes. In: Stackebrandt E, Goodfellow M (eds) Nucleic acid techniques in bacterial systematics. Wiley Inc, New York, pp 205-247
51. Tolker-Nielsen T, Brinch UC, Ragas PC, Andersen JB, Jacobsen CS, Molin S (2000) Development and dynamics of Pseudomonas sp. biofilms. J Bacteriol 182:6482-6489
52. Thörn M, Mattsson A, Sörensson F (1996) Biofilm development in a nitrifying trickling filter. Water Sci Tech 34:83-89
53. Tsuneda S, Aikawa H, Hayashi H, Yuasa A, Hirata A (2003) Extracellular polymeric substances responsible for bacterial adhesion onto solid surface. FEMS Microbiol Lett 223:287-292
54. Wagner M, Horn M, Daims H (2003) Fluorescence in situ hybridisation for the identification and characterization of prokaryotes. Curr Opin Microbiol 6:302-309
55. Wallner G, Amann R, Beisker W (1993) Optimizing fluorescent in situ hybridization with rRNA-targeted oligonucleotide probes for flow cytometric identification of microorganisms. Cytometry 14:136-143
56. Wäsche S, Horn H, Hempel DC (2002) Influence of growth conditions on biofilm development and mass transfer at the bulk/biofilm interface. Water Res 36:4775-4784
57. Watnick PI, Kolter R (1999) Steps in the development of a Vibrio cholerae biofilm. Mol Microbiol 34:586-595
58. Watnick P, Kolter R (2000) Minireview. biofilm, city of Microbes. J Bacteriol 182:2675-2679
59. Wery N, Lesongeur F, Pignet P, Derennes V, Cambon-Bonavita M-A, Godfroy A, Barbier G (2001) Marinitoga camini gen. nov., sp. nov., a rod-shaped bacterium belonging to the order Thermotogales, isolated from a deep-sea hydrothermal vent. Int J Sys Evo Microbiol 51:495-504
60. Wimpenny J, Manz W, Szewzyk U (2000) Heterogeneity in biofilms. FEMS Microbiol Rev 24:661-671
61. Wu W-M, Hickey RF, Zeikus JG (1991) Characterization of metabolic performance of methanogenic granules treating brewery wastewater: role of sulphate-reducing bacteria. Appl Environm Microb 57:3438-3449