Molecular analysis of temporal changes of a bacterial community structure in activated sludge using denaturing gradient gel electrophoresis (DGGE) and fluorescent in situ hybridization (FISH)

Polish Journal of Microbiology

Volumn 56, Issue 2, 2007, Pages 119-127

  Ziembińska, Aleksandra ^a   Raszka, Anna ^a   Truu, Jaak ^b   Surmacz Górska, Joanna ^a   Miksch, Korneliusz ^a  

^a SILESIAN UNIVERSITY OF TECHNOLOGY   (Poland)

^b UNIVERSITY OF TARTU   (Estonia)

Author keywords

Activated sludge; Ammonia nitrogen removal effectiveness; FISH; PCR DGGE

Indexed keywords

AMMONIA; GENE PRODUCT; NITROGEN; RIBOSOME RNA;

ACTIVATED SLUDGE; ARTICLE; BACTERIAL FLORA; BIOREACTOR; FLUORESCENCE IN SITU HYBRIDIZATION; GEL ELECTROPHORESIS; GENE PROBE; METHODOLOGY; MOLECULAR WEIGHT; NITRIFICATION; NITROSOMONAS; NONHUMAN; POLYMERASE CHAIN REACTION; SPECIES IDENTIFICATION; WASTE WATER MANAGEMENT;

AMMONIA; BACTERIA; BIODIVERSITY; BIOREACTORS; DNA, BACTERIAL; DNA, RIBOSOMAL; ELECTROPHORESIS, POLYACRYLAMIDE GEL; IN SITU HYBRIDIZATION, FLUORESCENCE; NUCLEIC ACID DENATURATION; NUCLEIC ACID HYBRIDIZATION; RNA, RIBOSOMAL, 16S; SEWAGE; TIME FACTORS; WATER; WATER MICROBIOLOGY; WATER PURIFICATION;

BACTERIA (MICROORGANISMS); NITROSOMONAS OLIGOTROPHA;

EID: 34447502003     PISSN: 17331331     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Article

References (40)

1. Adamczyk J., M. Hesselsoe, N. Iversen, M. Horn, A. Lehner, P.H. Nielsen, M. Schloter, P. Roslev. and M. Wagner. 2003. The isotope array, a new tool that employs substrate-mediated labeling of rRNA for determination of microbial community structure and function. Appl. Environ. Microbiol. 69: 6875-6887.
2. Amann R.I., B.J. Binder, R.J. Olson, S.W. Chisholm, R. Devereux and D.A. Stahl. 1990. Combination of 16S rRNA-targeted oligonucleotide probes with flow cytometry for analyzing mixed microbial populations. Appl. Environ. Microbiol. 56: 1919-1925.
3. Amann R. and M. Kuhl. 1998. In situ methods for assessment of microorganisms and their activities. Curr Opin Microbiol. 1: 352-358.
4. Blackall L.L., S. Rossetti, C. Christenson, M. Cunningham, P. Hartman, P. Hugenholtz and V. Tandoi. 1997. The characterization and description of representatives of 'G' bacteria from activated sludge plants. Lett. Appl. Microbiol. 25: 63-69.
5. Bodzek M., J. Bohdziewicz and K. Konieczny. 1997. Membrane techniques in the environmental protection (in Polish). Wydawnictwo Politechniki Śla̧skiej, Gliwice.
6. Chain P., J. Lamerdin, F. Larimer, W. Regala, V. Lao V., M. Land, L. Hauser, A. Hooper, M. Klotz, J. Norton, L. Sayavedra-Soto, D. Arciero, N. Hommes, M. Whittaker and D. Arp. 2003. Complete genome sequence of the ammonia-oxidizing bacterium and obligate chemolithoautotroph Nitrosomonas europaea. J. Bacteriol. 85: 2759-2773.
7. Charcosset C. 2006. Membrane process in biotechnology: an overview. Biotechnol. Adv. 24: 482-492.
8. Curtis T.P. and N.G. Craine. 1998. The comparison of the diversity of activated sludge plants. Wat. Sci. Technol. 37: 71-78.
9. Daims H., J.L. Nielsen, P.H. Nielsen, K.H. Schleifer and M. Wagner. 2001a. In situ characterization of Nitrospira-like nitrite-oxidizing bacteria active in wastewater treatment plants. Appl. Environ. Microbiol. 67: 5273-5284.
10. Daims H., A. Brühl, R. Amann, K.H. Schleife and M. Wagner. 1999. The domain-specific probe EUB338 is insufficient for the detection of all Bacteria: Development and evaluation of a more comprehensive probe set. Syst. Appl. Microbiol. 22: 434-444.
11. Daims H., U. Purkhold, L. Bjerrum, E. Arnold, P.A. Wilderer. and M. Wagner. 2001b. Nitrification in sequencing batch biofilm reactors: lessons from molecular approach. Wat. Sci. Technol. 43:9-18.
12. Daims H., K. Stoecker. and M. Wagner. 2005. Fluorescence in situ hybridization for the detection of prokaryotes, pp: 213-239. In: Osborn A.M. and C.J. Smith (eds), Advanced Methods in Molecular Microbial ecology. Bios-Garland. Abingdon, UK.
13. Duddleston K.N., P.J. Bottomley, A. Porter and D.J. Arp. 2000. Effects of soil and water content on methyl bromide oxidation by the ammonia-oxidizing bacterium Nitrosomonas europaea. Appl. Environ. Microbiol. 66: 2636-2640.
14. Eichner C.A., R.W. Erb, K.N. Timmis. and I. Wagner-Döbler. 1999. Thermal gradient gel electrophoresis analysis of bioprotection from pollutant shock in the activated sludge microbial community. Appl Environ. Microbiol. 65: 102-109.
15. Felske A., B. Engelen., U. Nübel and H. Backhaus. 1996. Direct ribosome isolation from soil to extract bacterial rRNA for community analysis. Appl. Environ. Microbiol. 62: 4162-4167.
16. Hermanowicz W. and J. Dojlido. 1999. Physical and Chemical Methods in Water and Wastewater Analysis (in Polish). Arkady, Warszawa.
17. Holben W.E, K. Noto, T. Sumino. and Y. Suwa. 1998. Molecular analysis of bacterial communities in a three-compartment granular activated sludge system indicates community-level control by compatible nitrification processes. Appl. Environ. Microbiol. 64: 2528-2532.
18. Hommes N.G., L.A. Sayavedra-Soto and D.J. Arp. 2001. Transcript analysis of multiple copies of amo (encoding ammonia monooxygenase) and hao (encoding hydroxylamine oxidoreductase) in Nitrosomonas europaea. FEMS Microbiol. Ecol. 43: 195-206.
19. ISO regulation: ISO 7890-1.
20. Juretschko S., G. Timmermann, M. Schmid, K.H. Schleifer, A. Pommerening-Röser, H.P. Koops and M. Wagner. 1998. Combined molecular and conventional analyses of nitrifying bacterium diversity in activated sludge: Nitrosococcus mobilis and Nitrospira-like bacteria as dominant populations. Appl Environ Microbiol. 64: 3042-3051.
21. Kelly J.J., S. Siripong., J. McCormack, L.R. Janus, H. Urakawa, S. El Fantroussi, P.A. Noble, L. Sappelsa., B.E. Rittmann and D.A. Stahl. 2005. DNA microarray detection of nitrifying bacterial 16S rRNA in wastewater treatment plant samples. Water Res. 39: 3229-3238.
22. Kowalchuk G.A., J.R. Stephen, W. De Boer, J.I. Prosser, T.M. Embley. and J.W. Woldendorp. 1997. Analysis of ammonia-oxidizing bacteria of the β subdivision of the class Proteobacteria in coastal sand dunes by denaturing gradient gel electrophoresis and sequencing of PCR-amplified 16S ribosomal DNA fragments. Appl. Environ. Microbiol. 63: 1489-1497.
23. Loy A., M. Horn and M. Wagner. 2003. ProbeBase - an online resource for rRNA-targeted oligonucleotide probes. Nucleic Acids Res. 31: 514-516.
24. Luxmy B.S., F. Nakajima and K. Yamamoto. 2000. Analysis of bacterial community in membrane-separation bioreactors by fluorescent in situ hybridization (FISH) and denaturing gradient gel electrophoresis (DGGE) techniques. Wat. Sci. Technol. 41: 259-268.
25. Metcalf and Eddy inc. 1991. Wastewater Engineering: Treatment, Disposal and Reuse, 3rd ed. McGrow - Hill Inc., New York.
26. Mobarry B.K., M. Wagner, V. Urbain, B.E. Rittmann and D.A. Stahl. 1996. Phylogenetic probes for analyzing abundance and spatial organization of nitrifying bacteria. Appl. Environ. Microbiol. 62: 2156-2162.
27. Nübel U., F. Garcia-Pichel, M. Kuhl and G. Muyzer. 1999. Quantify microbial diversity: morphotypes, 16S rRNA genes and carotenoids of oxygenic phototrophs in microbial mats, Appl. Environ. Microbiol. 62: 422-430.
28. Polish regulation: PN-C-04576-4:1994.
29. Pommerening-Roser A., G. Rath and H.P. Koops. 1996. Phylogenetic diversity within the genus Nitrosomonas. Syst. Appl. Microbiol. 19: 344-351.
30. Possemiers S.,K. Verthe, S. Uyttendaele and W. Verstraete. 2004. PCR-DGGE-based quantification of stability of the microbial community in a simulator of the human intestinal microbial ecosystem. FEMS Microbiol. Ecol. 49: 495-507.
31. Rowan A.K., J.R. Snape, D. Fearnside, M.R. Barer, T.P. Curtis and I.M. Head. 2003. Composition and diversity of ammonia-oxidising bacterial communities in wastewater treatment reactors of different design treating identical wastewater. FEMS Microbiol. Ecol., 43: 195-206.
32. Schramm A., D. de Beer., M. Wagner and R. Amman. 1998 Identification and activity in situ of Nitrosospira and Nitrospira sp. as dominant populations in a nitrifying fluidized bed reactor. Appl. Environ. Microbiol. 67: 1351-1362.
33. Schuppler M., M. Wagner, G. Schon and U.B. Gobel. 1998. In situ identification of nocardioform actinomycetes in activated sludge using fluorescent rRNA-targeted oligonucleotide probes. Microbiology 144: 249-259.
34. Snaidr J., R. Amann, I. Huber, W. Ludwig. and K.H. Schleifer. 1997. Phylogenetic analysis and in situ identification of bacteria in activated sludge. Appl Environ Microbiol. 63: 2884-2889.
35. Sponza D.T. 2002. Extracellular polymer substances and physicochemical properties of floes in steady- and unsteady-state activated sludge systems. Process Biochem. 37: 983-998.
36. Sponza D.T. 2003. Investigation of extracellular polymer substances (EPS) and physicochemical properties of different activated sludge floes under steady-state conditions. Enzyme Microb. Technol. 32: 375-385.
37. Van der Gast Ch.J., B. Jefferson, E. Reid, T. Robinson, M.J. Bailey, S.J. Judd and I.P. Thompson. 2006. Bacterial diversity is determined by volume in membrane bioreactors. Environ. Microbiol. 8: 1048-1055.
38. Wagner M., G. Rath, R. Amann, H.P. Koops and H.K. Schleifer. 1995. In situ identification of ammonia-oxidizing bacteria. Syst. Appl. Microbiol. 18: 251-264.
39. Wagner M., G. Rath, H.P. Koops and H.K. Schleifer. 1996. In situ identification of nitrifying bacteria in sewage treatment plants. Wat. Sci. Tech. 34: 237-244.
40. Wittebolle L., N. Boon, B. Vanparys, K. Heylen K., P. De Vos. and W. Verstraete. 2005. Failure of the ammonia oxidation process in two pharmaceutical wastewater treatment plants is linked to shifts in the bacterial communities. J. Appl. Microbiol. 99: 997-1006.