Identity and ecophysiology of filamentous bacteria in activated sludge

FEMS Microbiology Reviews

Volumn 33, Issue 6, 2009, Pages 969-998

  Nielsen, Per Halkjær ^a   Kragelund, Caroline ^a   Seviour, Robert J ^b   Nielsen, Jeppe Lund ^a  

^a AALBORG UNIVERSITY   (Denmark)

^b LA TROBE UNIVERSITY   (Australia)

Author keywords

Activated sludge; Bulking; Ecophysiology; Filamentous bacteria; FISH; Foaming

Indexed keywords

ACTINOBACTERIA; ACTIVATED SLUDGE; ALPHAPROTEOBACTERIA; BACTERIAL GROWTH; BACTERIAL METABOLISM; BACTERIAL STRAIN; BACTERIUM; BACTERIUM CULTURE; BACTERIUM IDENTIFICATION; BACTERIUM ISOLATION; BACTEROIDETES; BETAPROTEOBACTERIA; BIOMASS FERMENTATION; BIOREACTOR; CARBOHYDRATE METABOLISM; CHLOROFLEXI; ECOPHYSIOLOGY; EFFLUENT; ENVIRONMENTAL MONITORING; FILAMENTOUS BACTERIUM; FIRMICUTES; FLOCCULATION; FOAM; GAMMAPROTEOBACTERIA; GENETIC VARIABILITY; LIPID DEGRADATION; MICROBIAL BIOMASS; MICROTHRIX; MOLECULAR DYNAMICS; NONHUMAN; PHYLOGENY; PHYLUM; PROTEIN DEGRADATION; PROTEOBACTERIA; REVIEW; STRAIN DIFFERENCE; WASTE WATER TREATMENT PLANT;

ANIMALS; BACTERIA; BACTERIAL PHYSIOLOGICAL PHENOMENA; ECOSYSTEM; HUMANS; PHYLOGENY; SEWAGE; WASTE DISPOSAL, FLUID;

BACTERIA (MICROORGANISMS);

EID: 70349696156     PISSN: 01686445     EISSN: 15746976     Source Type: Journal    
DOI: 10.1111/j.1574-6976.2009.00186.x     Document Type: Review

References (160)

1. Amann RI, Krumholz L Stahl DA (1990) Fluorescent-oligonucleotide probing of whole cells for determinative, phylogenetic, and environmental studies in microbiology. J Bacteriol 172 : 762 770.
2. Andreasen K Nielsen PH (1997) Application of microautoradiography to the study of substrate uptake by filamentous microorganisms in activated sludge. Appl Environ Microb 63 : 3662 3668.
3. Andreasen K Nielsen PH (1998) In situ characterization of substrate uptake by Microthrix parvicella using microautoradiography. Water Sci Technol 37 : 19 26.
4. Andreasen K Nielsen PH (2000) Growth of Microthrix parvicella in nutrient removal activated sludge plants: studies of in situ physiology. Water Res 34 : 1559 1569.
5. Aruga S, Kamagata Y, Kohno T, Hanada S, Nakamura K Kanagawa T (2002) Characterization of filamentous Eikelboom Type 021N bacteria and description of Thiothrix disciformis sp. nov. and Thiothrix flexilis sp. nov. Int J Syst Evol Micr 52 : 1309 1316.
6. Beer M, Seviour EM, Kong Y, Cunningham M, Blackall LL Seviour RJ (2002) Phylogeny of the filamentous bacterium Eikelboom Type 1851, and design and application of a 16S rRNA targeted oligonucleotide probe for its fluorescence in situ identification in activated sludge. FEMS Microbiol Lett 207 : 179 183.
7. Beimfohr C, Krause A, Amann R, Ludwig W Schleifer KH (1993) In-situ identification of Lactococci, Enterococci and Streptococci. Syst Appl Microbiol 16 : 450 456.
8. Bjornsson L, Hugenholtz P, Tyson GW Blackall LL (2002) Filamentous Chloroflexi (green non-sulfur bacteria) are abundant in wastewater treatment processes with biological nutrient removal. Microbiology 148 : 2309 2318.
9. Blackall LL Marshall KC (1989) The mechanism of stabilization of actinomycete foams and the prevention of foaming under laboratory conditions. J Ind Microbiol Biot 4 : 181 187.
10. Blackall LL, Tandoi V Jenkins D (1991) Continuous culture studies with Nocardia amarae from activated sludge and their Implications for Nocardia foaming control. Res J Water Pollut C 63 : 44 49.
11. Blackall LL, Seviour EM, Cunningham MA, Seviour RJ Hugenholtz P (1994) Microthrix parvicella is a novel, deep branching member of the actinomycetes subphylum. Syst Appl Microbiol 17 : 513 518.
12. Blackall LL, Stratton H, Bradford D, delDot T, Sjorup C, Seviour EM Seviour RJ (1996) 'Candidatus Microthrix parvicella', a filamentous bacterium from activated sludge sewage treatment plants. Int J Syst Bacteriol 46 : 344 346.
13. Blackall LL, Seviour EM, Bradford D, Rossetti S, Tandoi V Seviour RJ (2000) 'Candidatus Nostocoida limicola', a filamentous bacterium from activated sludge. Int J Syst Evol Micr 50 : 703 709.
14. Boomer SM, Lodge DP, Dutton BE Pierson B (2002) Molecular characterization of novel red green nonsulfur bacteria from five distinct hot spring communities in Yellowstone National Park. Appl Environ Microb 68 : 346 355.
15. Bradford D (1997) Molecular biological studies of filamentous bacteria associated with activated sludge bulking and foaming. PhD thesis, University of Queensland, Australia.
16. Bradford D, Hugenholtz P, Seviour EM, Cunningham MA, Stratton H, Seviour RJ Blackall LL (1996) 16S rRNA analysis of isolates obtained from gram-negative, filamentous bacteria micromanipulated from activated sludge. Syst Appl Microbiol 19 : 334 343.
17. Carr EL, Eales KL, Soddell J Seviour RJ (2005) Improved permeabilization protocols for fluorescence in situ hybridization (FISH) of mycolic-acid- containing bacteria found in foams. J Microbiol Meth 61 : 47 54.
18. Carr EL, Eales KL Seviour RJ (2006) Substrate uptake by Gordonia amarae in activated foams by FISH-MAR. Water Sci Technol 54 : 39 45.
19. Chun J, Blackall LL, Kang SO, Hah YC Goodfellow M (1997) A proposal to reclassify Nocardia pinensis Blackall et al as Skermania piniformis gen. nov., comb. nov. Int J Syst Bacteriol 47 : 127 131.
20. Cole JR, Chai B, Farris RJ, Wang Q, Kulam SA, McGarrell DM, Garrity GM Tiedje JM (2005) The Ribosomal Database Project (RDP-II): sequences and tools for high-throughput rRNA analysis. Nucleic Acids Res 33 : D294 D296.
21. Crocetti GR, Hugenholtz P, Bond PL, Schuler A, Keller J, Jenkins D Blackall LL (2000) Identification of polyphosphate-accumulating organisms and design of 16S rRNA-directed probes for their detection and quantitation. Appl Environ Microb 66 : 1175 1182.
22. Daims H, Lucker S Wagner M (2006) daime, a novel image analysis program for microbial ecology and biofilm research. Environ Microbiol 8 : 200 213.
23. Davenport RJ, Curtis TP, Goodfellow M, Stainsby FM Bingley M (2000) Quantitative use of fluorescent in situ hybridization to examine relationships between mycolic acid-containing actinomycetes and foaming in activated sludge plants. Appl Environ Microb 66 : 1158 1166.
24. Dawes EA (1991) Prokaryotic Structure and Function (Mohan S, Dow C Coles JA, eds), pp. 81 122. Cambridge University Press, Cambridge.
25. de los Reyes FL, Ritter W Raskin L (1997) Group-specific small-subunit rRNA hybridization probes to characterize filamentous foaming in activated sludge systems. Appl Environ Microb 63 : 1107 1117.
26. de los Reyes FL, Oerther DB, los Reyes MF, Hernandez M Raskin L (1998) Characterization of filamentous foaming in activated sludge systems using oligonucleotide hybridization probes and antibody probes. Water Sci Technol 37 : 485 493.
27. Ding L Yokota A (2004) Proposals of Curvibacter gracilis gen. nov., sp. nov. and Herbaspirillum putei sp. nov. for bacterial strains isolated from well water and reclassification of [Pseudomonas] huttiensis, [Pseudomonas] lanceolata, [Aquaspirillum] delicatum and [Aquaspirillum] autotrophicum as Herbaspirillum huttiense comb. nov., Curvibacter lanceolatus comb. nov., Curvibacter delicatus comb. nov. and Herbaspirillum autotrophicum comb. nov. Int J Syst Evol Micr 54 : 2223 2230.
28. Eales KL, Nielsen JL, Kragelund C, Seviour RJ Nielsen PH (2005) The in situ physiology of pine tree like organisms (PTLO) in activated sludge foams. Acta hydroch hydrob 33 : 203 209.
29. Eales KL, Nielsen JL, Seviour EM, Nielsen PH Seviour RJ (2006) The in situ physiology of Skermania piniformis in foams in Australia activated sludge plants. Environ Microbiol 8 : 1712 1720.
30. Eikelboom DH (1975) Filamentous organisms observed in activated sludge. Water Res 9 : 365 388.
31. Eikelboom DH (2000) Process Control of Activated Sludge Plants by Microscopic Investigation. IWA Publishing, London.
32. Eikelboom DH (2006) Identification and Control of Filamentous Microorganisms in Industrial Wastewater Treatment Plants. IWA Publishing, London.
33. Eikelboom DH Geurkink B (2002) Filamentous micro-organisms observed in industrial activated sludge plants. Water Sci Technol 46 : 535 542.
34. Eilers H, Pernthaler J, Peplies J, Glöckner FO, Gerdts G Amann R (2001) Isolation of novel pelagic bacteria from the German bight and their seasonal contributions to surface picoplankton. Appl Environ Microb 67 : 5134 5142.
35. Erhart R, Bradford D, Seviour RJ, Amann R Blackall LL (1997) Development and use of fluorescent in situ hybridization probes for the detection and identification of 'Microthrix parvicella' in activated sludge. Syst Appl Microbiol 20 : 310 318.
36. Garrity GM Holt JG (2001) Phylum BVI. Chloroflexi Phy. Nov. Bergey's Manual of Systematic Bacteriology, Vol. 2 (Boone DR, Castenholz RW, eds), pp. 426 446. Springer-Verlag, New York.
37. Garrity GM, Johnson KL, Bells JA Searles DB (2002) Taxonomic outline of the prokaryotes. Bergey's Manual of Systematic Bacteriology, Vol. 2 (Boone DR, Castenholz RW, eds). Springer-Verlag, New York.
38. Gich F, Garcia-Gil J Overmann J (2001) Previously unknown and phylogenetically diverse members of the green nonsulfur bacteria are indigenous to freshwater lakes. Arch Microbiol 177 : 1 10.
39. Goodfellow M Maldonado LA (2006) The families Dietziaceae, Gordoniaceae, Nocardiaceae and Tsukamurellaceae. The Prokaryotes, A Handbook on the Biology of Bacteria, Vol 3: Archaea. Bacteria: Firmicutes, Actinomycetes 3 (Dworkin M, ed), pp. 843 888. Springer-Verlag, New York.
40. Goodfellow M, Stainsby FM, Davenport R, Chun JS Curtis T (1998) Activated sludge foaming: the true extent of actinomycete diversity. Water Sci Technol 37 : 511 519.
41. Hanada S Pierson B (2002) The Family Chloroflexaceae. The Prokaryotes 3, Electron Release 3,1. Springer-Verlag, New York.
42. Hanada S, Takaichi S, Matsuura K Nakamura K (2002) Roseiflexus castenholzii gen. nov., sp nov., a thermophilic, filamentous, photosynthetic bacterium that lacks chlorosomes. Int J Syst Evol Micr 52 : 187 193.
43. Hesselsoe M, Nielsen JL, Roslev P Nielsen PH (2005) Isotope labeling and microautoradiography of active heterotrophic bacteria assimilation of 14CO2 (HetCO2-MAR). Appl Environ Microb 71 : 646 655.
44. Howarth R, Head IM Unz RF (1998) Phylogenetic assessment of five filamentous bacteria isolated from bulking activated sludges. Water Sci Technol 37 : 303 306.
45. Howarth R, Unz RF, Seviour EM, Seviour RJ, Blackall LL, Pickup RW, Jones JG, Yaguchi J Head IM (1999) Phylogenetic relationships of filamentous sulfur bacteria (Thiothrix spp. and Eikelboom type 021N bacteria) isolated from wastewater-treatment plants and description of Thiothrix eikelboomii sp. nov., Thiothrix unzii sp. nov., Thiothrix fructosivorans sp. nov. and Thiothrix defluvii sp. nov. Int J Syst Bacteriol 49 : 1817 1827.
46. Hugenholtz P, Goebel BM Pace NR (1998) Impact of culture-independent studies on the emerging phylogenetic view of bacterial diversity. J Bacteriol 180 : 4765 4774.
47. Hugenholtz P, Tyson GW, Webb RI, Wagner AM Blackall LL (2001) Investigation of candidate division TM7, a recently recognized major lineage of the domain Bacteria with no known pure-culture representatives. Appl Environ Microb 67 : 411 419.
48. Jenkins D, Richard MG Daigger GT (2004) Manual on the Causes and Control of Activated Sludge Bulking, Foaming, and other Solids Separation Problems. 3rd edn. IWA Publishing, London.
49. Kämpfer P (1995) Physiological and chemotaxonomic characterization of filamentous bacteria belonging to the genus Haliscomenobacter. Syst Appl Microbiol 18 : 363 367.
50. Kämpfer P, Weltin D, Hoffmeister D Dott W (1995) Growth requirements of filamentous bacteria isolated from bulking and scumming sludge. Water Res 29 : 1585 1588.
51. Kanagawa T, Kamagata Y, Aruga S, Kohno T, Horn M Wagner M (2000) Phylogenetic analysis of and oligonucleotide probe development for eikelboom type 021N filamentous bacteria isolated from bulking activated sludge. Appl Environ Microb 66 : 5043 5052.
52. Kindaichi T, Ito T Okabe S (2004) Ecophysiological interaction between nitrifying bacteria and heterotrophic bacteria in autotrophic nitrifying biofilms as determined by microautoradiography-fluorescence in situ hybridization. Appl Environ Microb 70 : 1641 1650. (Pubitemid 38365148)
53. Kohno T, Sei K Mori K (2002) Characterization of Type 1851 organism isolated from activated sludge samples. Water Sci Technol 46 : 111 114.
54. Kong Y, Xia Y Nielsen PH (2008) Activity and identity of fermenting microorganisms in full-scale biological nutrient removing wastewater treatment plants. Environ Microbiol 10 : 2008 2019.
55. Kragelund C, Nielsen JL, Thomsen TR Nielsen PH (2005) Ecophysiology of the filamentous Alphaproteobacterium Meganema perideroedes in activated sludge. FEMS Microbiol Ecol 54 : 111 122.
56. Kragelund C, Kong Y, van der Waarde J, Thelen K, Eikelboom D, Tandoi V, Thomsen TR Nielsen PH (2006) Ecophysiology of different filamentous Alphaproteobacteria species from industrial waste water treatment plants. Microbiology 152 : 3003 3012.
57. Kragelund C, Levantesi C, Borger A et al 2007a) Identity, abundance and ecophysiology of filamentous Chloroflexi species from activated sludge treatment plants. FEMS Microbiol Ecol 59 : 671 682.
58. Kragelund C, Nilsson B, Eskildsson K, Fritzson K, Bøgh AM Nielsen PH (2007b) Control of filamentous foam formers by chemical addition. Chemical Water and Wastewater Treatment IX (Lindquist A, Hahn H Hoffmann E, eds), pp. 83 93. IWA Publishing, London.
59. Kragelund C, Remesova Z, Nielsen JL, Thomsen TR, Eales Kl, Seviour RJ, Wanner J Nielsen PH (2007c) Ecophysiology of mycolic acid containing Actinobacteria (Mycolata) in activated sludge foams. FEMS Microbiol Ecol 61 : 174 184.
60. Kragelund C, Levantesi C, Borger A et al 2008) Identity, abundance and ecophysiology of filamentous bacteria belonging to the Bacteroidetes present in activated sludge plants. Microbiology 154 : 886 894.
61. Kragelund C, Müller E, Schade M, Nguyen H, Lemmer H, Seviour RJ Nielsen PH (2009) FISH Handbook for Biological Wastewater Treatment (Nielsen PH, Daims H Lemmer H, eds), pp. 36 68. IWA Publishing, London.
62. Krul JM (1977) Experiments with Haliscomenobacter hydrossis in continuous culture without and with Zoogloea ramigera. Water Res 11 : 197 204.
63. Larsen P, Nielsen JL, Dueholm MS, Wetzel R, Otzen D Nielsen PH (2007) Amyloid adhesins are abundant in natural biofilms. Environ Microbiol 9 : 3077 3090.
64. Larsen P, Nielsen JL, Otzen D Nielsen PH (2008) Amyloid-like adhesins produced by floc-forming and filamentous bacteria in activated sludge. Appl Environ Microb 74 : 1517 1526.
65. Lee N, Nielsen PH, Andreasen KH, Juretschko S, Nielsen JL, Schleifer KH Wagner M (1999) Combination of fluorescent in situ hybridization and microautoradiography-a new tool for structure-function analyses in Microb Ecol. Appl Environ Microb 65 : 1289 1297.
66. Levantesi C, Beimfohr C, Geurkink B, Rossetti S, Thelen K, Krooneman J, Snaidr J, van der Waarde J Tandoi V (2004) Filamentous Alphaproteobacteria associated with bulking in industrial wastewater treatment plants. Syst Appl Microbiol 27 : 716 727.
67. Levantesi C, Rossetti S, Thelen K, Kragelund C, Krooneman J, Eikelboom D, Nielsen PH Tandoi V (2006) Phylogeny, physiology and distribution of 'Candidatus Microthrix calida', a new Microthrix species isolated from industrial activated sludge wastewater treatment plants. Environ Microbiol 8 : 1552 1563.
68. Liu JR Seviour RJ (2001) Design and application of oligonucleotide probes for fluorescent in situ identification of the filamentous bacterial morphotype Nostocoida limicola in activated sludge. Environ Microbiol 3 : 551 560.
69. Liu JR, Burrell P, Seviour EM, Soddell JA, Blackall LL Seviour RJ (2000) The filamentous bacterial morphotype 'Nostocoida limicola' I contains at least two previously described genera in the low G+C gram positive bacteria. Syst Appl Microbiol 23 : 528 534.
70. Liu JR, McKenzie CA, Seviour EM, Webb RI, Blackall LL, Saint CP Seviour RJ (2001) Phylogeny of the filamentous bacterium 'Nostocoida limicola' III from activated sludge. Int J Syst Evol Micr 51 : 195 202.
71. Liu JR, Tanner RS, Schumann P, Weiss N, McKenzie CA, Janssen PH, Seviour EM, Lawson PA, Allen TD Seviour RJ (2002) Emended description of the genus Trichococcus, description of Trichococcus collinsii sp. nov., and reclassification of Lactosphaera pasteurii as Trichococcus pasteurii comb. nov. and of Ruminococcus palustris as Trichococcus palustris comb. nov. in the low-G+C gram-positive bacteria. Int J Syst Evol Micr 52 : 1113 1126.
72. Loy A, Horn M Wagner M (2003) probeBase: an online resource for rRNA-targeted oligonucleotide probes. Nucleic Acids Res 31 : 514 516.
73. Loy A, Maixner F, Wagner M Horn M (2007) probeBase-an online resource for rRNA-targeted oligonucleotide probes: new features. Nucleic Acids Res 35 : D800 D804.
74. Lydell C, Dowell L, Sikaroodi M, Gillevet P Emerson D (2004) A population survey of members of the phylum Bacteroidetes isolated from salt marsh sediments along the East Coast of the United States. Microb Ecol 48 : 263 273.
75. 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.
76. Manz W, Amann R, Ludwig W, Vancanneyt M Schleifer KH (1996) Application of a suite of 16S rRNA-specific oligonucleotide probes designed to investigate bacteria of the phylum Cytophaga-Flavobacter-Bacteroides in the natural environment. Microbiology 142 : 1097 1106.
77. Martins AM, Pagilla K, Heijnen JJ Van Loosdrecht MC (2004) Filamentous bulking sludge - a critical review. Water Res 38 : 793 817.
78. McKenzie CM, Seviour EM, Schumann P, Maszenan AM, Liu JR, Webb RI, Monis P, Saint CP, Steiner U Seviour RJ (2006) Isolates of 'Candidatus Nostocoida limicola' Blackall et al. 2000 should be described as three novel species of the genus Tetrasphaera, as Tetrasphaera jenkinsii sp. nov., Tetrasphaera vanveenii sp. nov. and Tetrasphaera veronensis sp. nov. Int J Syst Evol Micr 56 : 2279 2290.
79. Meier H, Amann R, 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.
80. Miura Y Okabe S (2008) Quantification of cell specific uptake activity of microbial products by uncultured Chloroflexi by microautoradiography combined with fluorescence in situ hybridization. Environ Sci Technol 42 : 7380 7386.
81. Miura Y, Watanabe Y Okabe S (2007) Significance of Chloroflexi in performance of submerged membrane bioreactors (MBR) treating municipal wastewater. Environ Sci Technol 41 : 7787 7794.
82. Morgan-Sagastume F, Larsen P, Nielsen JL Nielsen PH (2008) Characterization of the loosely attached fraction of activated sludge bacteria. Water Res 42 : 843 854.
83. Mulder EG Deinema MH (1992) The sheathed bacteria. The Prokaryotes 'A Handbook on the Biology of Bacteria: Ecophysiology, Isolation, Identification, Application' (Balows A, ed), pp. 2612 2624. Springer-Verlag, New York.
84. Mussmann M, Schulz HN, Strotmann B, Kjaer T, Nielsen LP, Rossello-Mora RA, Amann RI Jorgensen BB (2003) Phylogeny and distribution of nitrate-storing Beggiatoa spp. in coastal marine sediments. Environ Microbiol 5 : 523 533.
85. Neef A (1997) Anwendung der in situ-einzelzell-identifizierung von bakterien zur populationsanalyse in komplesen mikrobiellen biozönose. PhD thesis, TU Munich, Germany.
86. Neef A, Amann R, Schlesner H Schleifer KH (1998) Monitoring a widespread bacterial group: in situ detection of planctomycetes with 16S rRNA-targeted probes. Microbiology 144 : 3257 3266.
87. Nelson DC (1992) The genus Beggiatoa. The Prokaryotes 'A Handbook on the Biology of Bacteria: Ecophysiology, Isolation, Identification, Application' (Balows A, ed), pp. 3171 3180. Springer-Verlag, New York.
88. Nielsen JL Nielsen PH (2005) Advances in microscopy: microautoradiography of single cells. Method Enzymol 397 : 237 256.
89. Nielsen JL, Mikkelsen LH Nielsen PH (2001) In situ detection of cell surface hydrophobicity of probe-defined bacteria in activated sludge. Water Sci Technol 43 : 97 103.
90. Nielsen JL, Aquino DM Nielsen PH (2003a) Evaluation of the redox dye 5-cyano-2,3-tolyl-tetrazolium chloride for activity studies by simultaneous use of microautoradiography and fluorescence in situ hybridization. Appl Environ Microb 69 : 641 643.
91. Nielsen JL, Christensen D, Kloppenborg M Nielsen PH (2003b) Quantification of cell-specific substrate uptake by probe-defined bacteria under in situ conditions by microautoradiography and fluorescence in situ hybridization. Environ Microbiol 5 : 202 211.
92. Nielsen PH, Andreasen K, Wagner M, Blackall LL, Lemmer H Seviour RJ (1998) Variability of type 021N in activated sludge as determined by in situ substrate uptake pattern and in situ hybridization with fluorescent rRNA targeted probes. Water Sci Technol 37 : 423 440.
93. Nielsen PH, de Muro MA Nielsen JL (2000) Studies on the in situ physiology of Thiothrix spp. present in activated sludge. Environ Microbiol 2 : 389 398.
94. Nielsen PH, Roslev P, Dueholm TE Nielsen JL (2002) Microthrix parvicella, a specialized lipid consumer in anaerobic-aerobic activated sludge plants. Water Sci Technol 46 : 73 80.
95. Nielsen PH, Kragelund C, Nielsen JL, Tiro S, Lebek M, Rosenwinkel KH Gessesse A (2005) Control of Microthrix parvicella in activated sludge plants by dosage of polyaluminium salts: possible mechanisms. Acta hydroch hydrob 33 : 255 261.
96. Nubel U, Bateson MM, Madigan MT, Kuhl M Ward DM (2001) Diversity and distribution in hypersaline microbial mats of bacteria related to Chloroflexus spp. Appl Environ Microb 67 : 4365 4371.
97. Nubel U, Bateson MM, Vandieken V, Wieland A, Kuhl M Ward DM (2002) Microscopic examination of distribution and phenotypic properties of phylogenetically diverse Chloroflexaceae-related bacteria in hot spring microbial mats. Appl Environ Microb 68 : 4593 4603.
98. Okabe S, Kindaichi T, Nakamura Y Ito T (2005) Eco-physiology of autotrophic nitrifying biofilms. Water Sci Technol 52 : 225 232.
99. Ouverney CC Fuhrman JA (1999) Combined microautoradiography-16S rRNA probe technique for determination of radioisotope uptake by specific microbial cell types in situ. Appl Environ Microb 65 : 1746 1752.
100. Polz MF, Odintsova EV Cavanaugh CM (1996) Phylogenetic relationships of the filamentous sulfur bacterium Thiothrix ramosa based on 16S rRNA sequence analysis. Int J Syst Bacteriol 46 : 94 97.
101. Reichenbach H (1992) The genus Herpetosiphon. The Prokaryotes 'A Handbook on the Biology of Bacteria: Ecophysiology, Isolation, Identification, Application' (Balows A, ed), pp. 3785 3805. Springer-Verlag, New York.
102. Reichenbach H (1999) The order Cytophagales. The Prokaryotes 'A Handbook on the Biology of Bacteria: Ecophysiology, Isolation, Identification, Application' (Balows A, ed), pp. 3785 3805. Springer-Verlag, New York.
103. Richard M, Jenkins D, Hao O Shimizu GP (1982) The Isolation and Characterization of Filamentous Micro-Organisms from Activated Sludge Bulking. University of California, Sanitary Engineering and Environmental Health Research Laboratory, Berkeley, CA.
104. Richard M, Hao O Jenkins D (1985a) Growth kinetics of Sphaerotilus species and their significance in activated sludge bulking. J Water Pollut Con F 57 : 68 81. (Pubitemid 16184789)
105. Richard M, Shimizu GP Jenkins D (1985b) The growth physiology of the filamentous organism Type 021N and its significance to activated sludge bulking. J Water Pollut Con F 57 : 1152 1162.
106. Roels T, Dauwe F, Van Damme S, De Wilde K Roelandt F (2002) The influence of PAX-14 on activated sludge systems and in particular on Microthrix parvicella. Water Sci Technol 46 : 487 490.
107. Roller C, Wagner M, Amann R, 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.
108. Rossetti S, Carucci A Rolle E (1994) Survey on the occurrence of filamentous organisms in municipal wastewater treatment plants related to their operating-conditions. Water Sci Technol 29 : 305 308.
109. Rossetti S, Hildisch D, Christensson C, del Dot T, Blackall LL Tandoi V (1997) Isolation and identification of an Eikelboom Type 1863 strain as Acinetobacter johnsonii. Water Res 31 : 657 660.
110. Rossetti S, Blackall LL, Levantesi C, Uccelletti D Tandoi V (2003) Phylogenetic and physiological characterization of a heterotrophic, chemolithoautotrophic Thiothrix strain isolated from activated sludge. Int J Syst Evol Micr 53 : 1271 1276.
111. Rossetti S, Tomei MC, Nielsen PH Tandoi V (2005) 'Microthrix parvicella', a filamentous bacterium causing bulking and foaming in activated sludge systems: a review of current knowledge. FEMS Microbiol Rev 29 : 49 64.
112. Roth A, Andrees S, Kroppenstedt RM, Harmsen D Mauch H (2003) Phylogeny of the genus Nocardia based on reassessed 16S rRNA gene sequences reveals underspeciation and division of strains classified as Nocardia asteroides into three established species and two unnamed taxons. J Clin Microbiol 41 : 851 856.
113. Schade M, Beimfohr C Lemmer H (2002) Phylogenetic and physiological characterization of a 'Nostocoida limicola'-like organism isolated from activated sludge. Water Sci Technol 46 : 91 97.
114. Schauer M Hahn MW (2005) Diversity and phylogenetic affiliations of morphologically conspicuous large filamentous bacteria occurring in the pelagic zones of a broad spectrum of freshwater habitats. Appl Environ Microb 71 : 1931 1940.
115. Schuppler M, Wagner M, Schön G Gobel UB (1998) In situ identification of nocardioform actinomycetes in activated sludge using fluorescent rRNA-targeted oligonucleotide probes. Microbiology 144 : 249 259.
116. 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 Microbiol 65 : 1280 1288.
117. Senghas E Lingens F (1985) Characterization of a new gram-negative filamentous bacterium isolated from bulking sludge. Appl Microbiol Biot 21 : 118 124.
118. Seviour EM, Williams C, Degrey B, Soddell JA, Seviour RJ Lindrea KC (1994) Studies on filamentous bacteria from Australian activated sludge plants. Water Res 28 : 2335 2342.
119. Seviour EM, Blackall LL, Christensson C, Hugenholtz P, Cunningham MA, Bradford D, Stratton HM Seviour RJ (1997) The filamentous morphotype Eikelboom Type 1863 is not a single genetic entity. J Appl Microbiol 82 : 411 421.
120. Seviour EM, Eales KL, Izzard L, Beer M, Carr EL Seviour RJ (2006) The in situ physiology of 'Nostocoida limicola' II, a filamentous bacterial morphotype in bulking activated sludge, using fluorescence in situ hybridization (FISH) and microautoradiography (MAR). Water Sci Technol 54 : 47 53.
121. Seviour RJ, Liu JR, Seviour EM, McKenzie CA, Blackall LL Saint CP (2002) The 'Nostocoida limicola' story: resolving the phylogeny of this morphotype responsible for bulking in activated sludge. Water Sci Technol 46 : 105 110.
122. Seviour RJ, Kragelund C, Kong Y, Eales K, Nielsen JL Nielsen PH (2008) Ecophysiology of the Actinobacteria in activated sludge systems. Antonie Van Leeuwenhoek 94 : 21 33.
123. Slijkhuis H (1983) Microthrix parvicella, a filamentous bacterium isolated from activated sludge - cultivation in a chemically defined medium. Appl Environ Microb 46 : 832 839.
124. Slijkhuis H Deinema MH (1982) The physiology of Microthrix parvicella, a filamentous bacterium from activated sludge. Bulking of Activated Sludge (Chambers B, Tomlinson EJ, eds), pp. 75 83. Ellis Horwood WRC Ltd, Chichester.
125. Slijkhuis H, Vangroenestijn JW Kylstra DJ (1984) Microthrix parvicella, a filamentous bacterium isolated from activated sludge - growth on tween 80 as carbon and energy source. J Gen Microbiol 130 : 2035 2042.
126. Snaidr J, Fuchs B, Wallner G, Wagner M, Schleifer KH Amann R (1999) Phylogeny and in situ identification of a morphologically conspicuous bacterium, Candidatus Magnospira bakii, present at very low frequency in activated sludge. Environ Microbiol 1 : 125 135.
127. Snaidr J, Beimfohr C, Levantesi C, Rossetti S, van der WJ, Geurkink B, Elkelboom D, Lemaitre M Tandoi V (2002) Phylogenetic analysis and in situ identification of 'Nostocoida limicola'-like filamentous bacteria in activated sludge from industrial wastewater treatment plants. Water Sci Technol 46 : 99 104.
128. Soddell J (1999) Foaming. The Microbiology of Activated Sludge (Seviour RJ, Blackall L, eds), pp. 161 202. Kluwer Academic Publishers, Dordrecht.
129. Soddell JA Seviour RJ (1990) Microbiology of foaming in activated sludge plants. J Appl Bacteriol 69 : 145 176.
130. Soddell JA Seviour RJ (1998) Numerical taxonomy of Skermania piniformis and related isolates from activated sludge. J Appl Microbiol 84 : 272 284.
131. Speirs L, Nittami T, McIlroy S, Schroeder S Seviour RJ (2009) Filamentous bacterium Eikelboom type 0092 in activated sludge plants in Australia is a member of the phylum Chloroflexi. Appl Environ Microb 75 : 2446 2452.
132. Stainsby FM, Soddell J, Seviour R, Upton J Goodfellow M (2002) Dispelling the 'Nocardia amarae' myth: a phylogenetic and phenotypic study of mycolic acid-containing actinomycetes isolated from activated sludge foam. Water Sci Technol 46 : 81 90.
133. Strom PF Jenkins D (1984) Identification and significance of filamentous microorganisms in activated sludge. J Water Pollut Con F 56 : 449 459. (Pubitemid 14108459)
134. Tandoi V, Caravaglio N, Balsamo DD, Majone M Tomei MC (1994) Isolation and physiological characterization of Thiothrix sp. Water Sci Technol 29 : 261 269.
135. Tandoi V, Rossetti S, Blackall LL Majone M (1998) Some physiological properties of an Italian isolate of 'Microthrix parvicella'. Water Sci Technol 37 : 1 8.
136. Tandoi V, Jenkins D Wanner J (2006) Activated Sludge Separation Problems. IWA Publishing, London.
137. Teske A, Ramsing NB, Kuver J Fossing H (1996) Phylogeny of Thioploca and related filamentous sulfide-oxidizing bacteria. Syst Appl Microbiol 18 : 517 526.
138. Thomsen TR, Kjellerup BV, Nielsen JL, Hugenholtz P Nielsen PH (2002) In situ studies of the phylogeny and physiology of filamentous bacteria with attached growth. Environ Microbiol 4 : 383 391.
139. Thomsen TR, Nielsen JL, Ramsing NB Nielsen PH (2004) Micromanipulation and further identification of FISH-labelled microcolonies of a dominant denitrifying bacterium in activated sludge. Environ Microbiol 6 : 470 479.
140. Thomsen TR, Blackall LL, de Muro MA, Nielsen JL Nielsen PH (2006a) Meganema perideroedes gen. nov., sp. nov., a new filamentous alphaproteobacterium from activated sludge. Int J Syst Evol Micr 56 : 1865 1868.
141. Thomsen TR, Kragelund C Nielsen PH (2006b) Identity, abundance and physiology of Aquaspirillum-related filamentous bacteria in activated sludge. Water Sci Technol 54 : 237 245 K, Leitritz L, Adler K, Schubert S, Autenrieth IB Heesemann J (2000) Culture independent and rapid identification of bacterial pathogens in necrotising fasciitis and streptococcal toxic shock syndrome by fluorescence in situ hybridisation. Med Microbiol Immun 188 : 169 175.
142. van der Waarde J, Krooneman J, Geurkink B, van der Werf A, Eikelboom D, Beimfohr C, Snaidr J, Levantesi C Tandoi V (2002) Molecular monitoring of bulking sludge in industrial wastewater treatment plants. Water Sci Technol 46 : 551 558.
143. Van Ommen Kloecke F Geesey GG (1999) Localization and identification of populations of phosphatase-active bacterial cells associated with activated sludge flocs. Microb Ecol 38 : 201 214.
144. Van Veen WL (1973) Bacteriology of activated-sludge, in particular filamentous bacteria. Antonie Van Leeuwenhoek 39 : 189 205.
145. Van Veen WL, Van der kooij D, Geuze ECWA Van der Vlies AW (1973) Investigations on sheathed bacterium Haliscomenobacter hydrossis gen. nov., sp. nov., isolated from activated sludge. Antonie Van Leeuwenhoek 39 : 207 216.
146. Van Veen WL, Mulder EG Deinema MH (1978) Sphaerotilus-Leptothrix group of bacteria. Microbiol Rev 42 : 329 356.
147. Wagner F (1982) Study of the cause and prevention of sludge bulking in Germany. Bulking of Activated Sludge: Preventative and Remedial Methods (Chambers B, Tomlinson EJ, eds), pp. 29 40. Ellis Horwood WRC Ltd, Chichester.
148. Wagner M, Amann R, Kämpfer P, Assmus B, Hartmann A, Hutzler P, Springer N Schleifer KH (1994a) Identification and in situ detection of Gram-negative filamentous bacteria in activated sludge. Syst Appl Microbiol 17 : 405 417.
149. Wagner M, Erhart R, Manz W, Amann R, Lemmer H, Wedi D Schleifer KH (1994b) Development of an rRNA-targeted oligonucleotide probe specific for the genus Acinetobacter and its application for in situ monitoring in activated sludge. Appl Environ Microb 60 : 792 800.
150. Wanner J (1994) Activated Sludge Bulking and Foaming Control. Technomic Publishing AG, Basel.
151. Wanner J Grau P (1989) Identification of filamentous microorganisms from activated sludge - a compromise between wishes, needs and possibilities. Water Res 23 : 883 891.
152. Wanner J, Ruzickova I, Krhutkova O Pribyl M (2000) Activated sludge population dynamics and wastewater treatment plant design and operation. Water Sci Technol 41 : 217 225.
153. Weller R, Glöckner FO Amann R (2000) 16S rRNA-targeted oligonucleotide probes for the in situ detection of members of the phylum
154. Williams TM Unz RF (1985a) Filamentous sulfur bacteria of activated sludge: characterization of Thiothrix, Beggiatoa, and Eikelboom Type 021N strains. Appl Environ Microb 49 : 887 898 TM Unz RF (1985b) Isolation and characterization of filamentous bacteria present in bulking activated sludge. Appl Microbiol Biot 22 : 273 282.
155. Williams TM Unz RF (1989) The nutrition of Thiothrix, Type 021N, Beggiatoa and Leucothrix strains. Water Res 23 : 15 22.
156. Xia Y, Kong Y Nielsen PH (2007) In situ detection of protein-hydrolysing microorganisms in activated sludge. FEMS Microbiol Ecol 60 : 156 165.
157. Xia Y, Kong Y, Thomsen TR Nielsen PH (2008) Identification and ecophysiological characterization of epiphytic protein-hydrolyzing Saprospiraceae ('Candidatus Epiflobacter' spp.) in activated sludge. Appl Environ Microb 74 : 2229 2238.
158. Ziegler M, Lange M Dott W (1990) Isolation and morphological and cytological characterization of filamentous bacteria from bulking sludge. Water Res 24 : 1437 1451.
159. Zita A Hermansson M (1997a) Determination of bacterial cell surface hydrophobicity of single cells in cultures and in wastewater in situ. FEMS Microbiol Lett 152 : 299 306.
160. Zita A Hermansson M (1997b) Effects of bacterial cell surface structures and hydrophobicity on attachment to activated sludge flocs. Appl Environ Microb 63 : 1168 1170.