Microbial Ecology

, Volume 52, Issue 2, pp 311–321 | Cite as

Stability in a Denitrifying Fluidized Bed Reactor

  • M. Gentile
  • T. Yan
  • S. M. Tiquia
  • M. W. Fields
  • J. Nyman
  • J. Zhou
  • C. S. CriddleEmail author


This study evaluates changes in the microbial community structure and function of a pilot-scale denitrifying fluidized bed reactor during periods of constant operating conditions and periods of perturbation. The perturbations consisted of a shutdown period without feed, two disturbances in which biofilms were mechanically sheared from carrier particles, and a twofold step increase in feed nitrate concentration. In the absence of perturbations, nitrate removal was stable and consistently greater than 99%. The structure and dynamics of the microbial community were studied using cloning and sequencing techniques and terminal restriction fragment length polymorphism (T-RFLP) of the SSU rRNA gene. Under unperturbed operating conditions, stable function was accompanied by high constancy and low variability of community structure with the majority of terminal restriction fragments (T-RFs) appearing throughout operation at consistent relative abundances. Several of the consistently present T-RFs correlated with clone sequences closely related to Acidovorax (98% similarity), Dechloromonas (99% similarity), and Zoogloea (98% similarity), genera recently identified by molecular analyses of similar systems. Significant changes in community structure and function were not observed after the shutdown period. In contrast, following the increase in loading rate and the mechanical disturbances, new T-RFs appeared. After both mechanical disturbances, function and community structure recovered. However, function was much more resilient than community structure. The similarity of response to the mechanical disturbances despite differences in community structure and operating conditions suggests that flexible community structure and potentially the activity of minor members under nonperturbation conditions promotes system recovery.


Clone Library Terminal Restriction Fragment Length Polymorphism Mechanical Disturbance Carrier Particle Terminal Restriction Fragment Length Polymorphism Analysis 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.



We thank Qi Ye for assistance in 16S rRNA sequencing of bacterial isolates. This research was supported by the Natural and Accelerated Bioremediation Research program, Biological and Environmental Research, U.S. Department of Energy under grant number DE-F603-00ER63046. Margaret Gentile was supported by a Stanford Graduate Fellowship sponsored by James Clark and a fellowship from the U.S. Environmental Protection Agency Science to Achieve Results program.


  1. 1.
    Amann, R, Ludwig, W, Schulze, R, Spring, S, Moore, E, Schleifer, KH (1996) rRNA-targeted oligonucleotide probes for the identification of genuine and former pseudomonads. Syst Appl Microbiol 19: 501–509Google Scholar
  2. 2.
    Briones, A, Raskin, L (2003) Diversity and dynamics of microbial communities in engineered environments and their implications for process stability. Curr Opin Biotechnol 14: 270–276PubMedCrossRefGoogle Scholar
  3. 3.
    Cole, JR, Chai, B, Marsh, TL, Farris, RJ, Wang, Q, Kulam, SA, Chandra, S, Mcgarrell, DM, Schmidt, TM, Garrity, GM, Tiedje, JM (2003) The ribosomal database project (RDP-II): previewing a new autoaligner that allows regular updates and the new prokaryotic taxonomy. Nucleic Acids Res 31: 442–443PubMedCrossRefGoogle Scholar
  4. 4.
    Colwell, RK (2004) EstimateS: Statistical Estimation of Species Richness and Shared Species from Samples. Version 7 [Online.]. User's guide and application available at: http://Purl.Oclc.Org/Estimates
  5. 5.
    Crosby, LD, Criddle, CS (2003) Understanding bias in microbial community analysis techniques due to rrn operon copy number heterogeneity. Biotechniques 34: 790–802PubMedGoogle Scholar
  6. 6.
    Curtis, T, Head, I, Graham, D (2003) Theoretical ecology for engineering biology. Environ Sci Technol 37: 64A–70APubMedCrossRefGoogle Scholar
  7. 7.
    Doak, DF, Bigger, D, Harding, EK, Marvier, MA, O'Malley, RE, Thomson, D (1998) The statistical inevitability of stability–diversity relationships in community ecology. Am Natural 151: 264–276CrossRefGoogle Scholar
  8. 8.
    Dunbar, J, Ticknor, L, Kuske, C (2000) Assessment of microbial diversity in four southwestern United States soils by 16S rRNA gene terminal restriction fragment analysis. Appl Environ Microbiol 66: 2943–2950PubMedCrossRefGoogle Scholar
  9. 9.
    Egert, M, Friedrich, M (2003) Formation of pseudo-terminal restriction fragments, a PCR-related bias affecting terminal restriction fragment length polymorphism analysis of microbial community structure. Appl Environ Microbiol 69: 2555–2562PubMedCrossRefGoogle Scholar
  10. 10.
    Etchebehere, C, Errazquin, I, Barrandeguy, E, Dabert, P, Moletta, L, Muxi, L (2001) Evaluation of the denitrifying microbiota of anoxic reactors. FEMS Microbiol Ecol 35: 259–265PubMedCrossRefGoogle Scholar
  11. 11.
    Etchebehere, C, Errazquin, M, Dabert, P, Muxi, L (2002) Community analysis of a denitrifying reactor treating landfill leachate. FEMS Microbiol Ecol 40: 97–106CrossRefPubMedGoogle Scholar
  12. 12.
    Fernandez, A, Huang, SY, Seston, S, Xing, J, Hickey, R, Criddle, C, Tiedje, J (1999) How stable is stable? Function versus community composition. Appl Environ Microbiol 65: 3697–3704PubMedGoogle Scholar
  13. 13.
    Fernandez, AS, Hashsham, SA, Dollhopf, SL, Raskin, L, Glagoleva, O, Dazzo, O, Hickey, RF, Criddle, CS, Tiedje, JM (2000) Flexible community structure correlates with stable community function in methanogenic bioreactor communities perturbed by glucose. Appl Environ Microbiol 66: 4058–4067PubMedCrossRefGoogle Scholar
  14. 14.
    Fields, MW, Yan, T, Rhee, S-K, Carroll, SL, Jardine, PM, Watson, DB, Criddle, DB, Zhou, J (2005) Impacts on microbial communities and cultivable isolates from groundwater contaminated with high levels of nitric acid–uranium waste. FEMS Microbiol Ecol 53: 417–428PubMedCrossRefGoogle Scholar
  15. 15.
    Godon, JJ, Zumstein, E, Dabert, P, Habouzit, F, Moletta, R (1997) Molecular microbial diversity of an anaerobic digestor as determined by small-subunit rDNA sequence analysis. Appl Environ Microbiol 63: 2802–2813PubMedGoogle Scholar
  16. 16.
    Grimm, V, Schmidt, E, Wissel, C (1992) On the application of stability concepts in ecology. Ecol Model 63: 143–161CrossRefGoogle Scholar
  17. 17.
    Hashsham, S, Fernandez, A, Dollhopf, S, Dazzo, F, Hickey, R, Tiedje, J, Criddle, J (2000) Parallel processing of substrate correlates with greater functional stability in methanogenic bioreactor communities perturbed by glucose. Appl Environ Microbiol 66: 4050–4057PubMedCrossRefGoogle Scholar
  18. 18.
    Hiscock, K, Lloyd, J, Lerner, D (1991) Review of natural and artificial denitrification of groundwater. Water Res 25: 1099–1111CrossRefGoogle Scholar
  19. 19. Cited November 19, 2004
  20. 20.
    Hurt, RA, Qiu, XY, Wu, LY, Roh, Y, Palumbo, AV, Tiedje, JM, Zhou, JH (2001) Simultaneous recovery of RNA and DNA from soils and sediments. Appl Environ Microbiol 67: 4495–4503PubMedCrossRefGoogle Scholar
  21. 21.
    Janda, V, Rudovsky, J, Wanner, J, Marha, K (1988) In situ denitrification of drinking-water. Water Sci Technol 20: 215–219Google Scholar
  22. 22.
    Kaplan, C, Kitts, C (2003) Variation between observed and true terminal restriction fragment length is dependent on true TRF length and purine content. J Microbiol Methods 54: 121–125PubMedCrossRefGoogle Scholar
  23. 23.
    Kaplan, CW, Astaire, JC, Sanders, ME, Reddy, BS, Kitts, CL (2001) 16S ribosomal DNA terminal restriction fragment pattern analysis of bacterial communities in feces of rats fed lactobacillus acidophilus NCFM. Appl Environ Microbiol 67: 1935–1939PubMedCrossRefGoogle Scholar
  24. 24.
    Labbe, N, Juteau, P, Parent, S, Villemur, R (2003) Bacterial diversity in a marine methanol-fed denitrification reactor at the Montreal Biodome, Canada. Microbial Ecol 46: 12–21CrossRefGoogle Scholar
  25. 25.
    Lane, D (1991) 16S/23s rRNA sequencing. In: Stackebrant E, Goodfellow M (Eds.) Nucleic Acid Techniques in Bacterial Systematics. Wiley, New York, pp 115–175Google Scholar
  26. 26.
    Lee, H, Lee, S, Lee, J, Park, J, Choi, E, Park, Y (2002) Molecular characterization of microbial community in nitrate-removing activated sludge. FEMS Microbiol Ecol 41: 85–94CrossRefPubMedGoogle Scholar
  27. 27.
    Lehman, CL, Tilman, D (2000) Biodiversity, stability, and productivity in competitive communities. Am Nat 156: 534–552CrossRefGoogle Scholar
  28. 28.
    Loreau, M, Naeem, S, Inchausti, P, Bengtsson, J, Grime, J, Hector, A, Hooper, A, Huston, M, Raffaelli, D, Schmid, B, Tilman, D, Wardle, D (2001) Ecology—biodiversity and ecosystem functioning: current knowledge and future challenges. Science 294: 804–808PubMedCrossRefGoogle Scholar
  29. 29.
    Ludwig, W, Strunk, O, Westram, R, Richter, L, Meier, H, Kumar, Y, Buchner, A, Lai, T, Steppi, S, Jobb, G, Forster, W, Brettske, W, Gerber, S, Ginhart, AW, Gross, O, Grumann, S, Hermann, S, Jost, R, Konig, A, Liss, T, Lussmann, 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: 1363–1371PubMedCrossRefGoogle Scholar
  30. 30.
    Mcnaughton, SJ (1977) Diversity and stability of ecological communities a comment on the role of empiricism in ecology. Am Nat 111: 515–525CrossRefGoogle Scholar
  31. 31.
    Neubert, M, Caswell, H (1997) Alternatives to resilience for measuring the responses of ecological systems to perturbations. Ecology 78: 653–665CrossRefGoogle Scholar
  32. 32.
    Pimm, S (1984) The complexity and stability of ecosystems. Nature 307: 321–326CrossRefGoogle Scholar
  33. 33.
    Qiu, XY, Wu, LY, Huang, HS, McDonel, PE, Palumbo, AV, Tiedje, JM, Zhou, JM (2001) Evaluation of PCR-generated chimeras: mutations, and heteroduplexes with 16S rRNA gene-based cloning. Appl Environ Microbiol 67: 880–887PubMedCrossRefGoogle Scholar
  34. 34.
    Schulze, R, Spring, S, Amann, R, Huber, I, Ludwig, W, Schleifer, KH, Kampfer, KH (1999) Genotypic diversity of acidovorax strains isolated from activated sludge and description of Acidovorax defluvii sp nov. Syst Appl Microbiol 22: 205–214PubMedGoogle Scholar
  35. 35.
    Smith, N, Yu, Z, Mohn, W (2003) Stability of the bacterial community in a pulp mill effluent treatment system during normal operation and a system shutdown. Water Res 37: 4873–4884PubMedCrossRefGoogle Scholar
  36. 36.
    Smith, R, Miller, D, Brooks, M, Widdowson, M, Killingstad, M (2001) In situ stimulation of groundwater denitrification with formate to remediate nitrate contamination. Environ Sci Technol 35: 196–203PubMedCrossRefGoogle Scholar
  37. 37.
    Son, K, Hall, E (2003) Use of a similarity index based on microbial fatty acid (MFA) analysis to monitor biological wastewater treatment systems. Environ Technol 24: 1147–1156PubMedGoogle Scholar
  38. 38.
    Song, BK, Palleroni, NJ, Haggblom, MM (2000) Isolation and characterization of diverse halobenzoate-degrading denitrifying bacteria from soils and sediments. Appl Environ Microbiol 66: 3446–3453PubMedCrossRefGoogle Scholar
  39. 39.
    Stamper, D, Walch, M, Jacobs, R (2003) Bacterial population changes in a membrane bioreactor for graywater treatment monitored by denaturing gradient gel electrophoretic analysis of 16S rRNA gene fragments. Appl Environ Microbiol 69: 852–860PubMedCrossRefGoogle Scholar
  40. 40.
    Sundh, I, Carlsson, H, Nordberg, A, Hansson, M, Mathisen, B (2003) Effects of glucose overloading on microbial community structure and biogas production in a laboratory-scale anaerobic digester. Bioresour Technol 89: 237–243PubMedCrossRefGoogle Scholar
  41. 41.
    Thioulouse, J, Chessel, D, Doledec, S, Olivier, J-M (1997) Ade-4: a multivariate analysis and graphical display software. Stat Comput 7: 75–83CrossRefGoogle Scholar
  42. 42.
    Tilman, D (1996) Biodiversity: population versus ecosystem stability. Ecology 77: 350–363CrossRefGoogle Scholar
  43. 43.
    Tilman, D (1999) The ecological consequences of changes in biodiversity: a search for general principles. Ecology 80: 1455–1474Google Scholar
  44. 44.
    Von Canstein, H, Li, Y, Felske, A, Wagner-Dobler, I (2001) Long-term stability of mercury-reducing microbial biofilm communities analyzed by 16S-23s rDNA interspacer region polymorphism. Microbial Ecol 42: 624–634CrossRefGoogle Scholar
  45. 45.
    Wang, CC, Lee, CM (2001) Denitrification with acrylonitrile as a substrate using pure bacteria cultures isolated from acrylonitrile–butadiene–styrene wastewater. Environ Int 26: 237–241PubMedCrossRefGoogle Scholar
  46. 46.
    Yoshie, S, Noda, N, Miyano, T, Tsuneda, S, Hirata, A, Inamori, Y (2001) Microbial community analysis in the denitrification process of saline-wastewater by denaturing gradient gel electrophoresis of PCR-amplified 16S rDNA and the cultivation method. J Biosci Bioeng 92: 346–353PubMedCrossRefGoogle Scholar
  47. 47.
    Zhou, JZ, Bruns, MA, Tiedje, JM (1996) DNA recovery from soils of diverse composition. Appl Environ Microbiol 62: 316–322PubMedGoogle Scholar
  48. 48.
    Zumstein, E, Moletta, R, Godon, JJ (2000) Examination of two years of community dynamics in an anaerobic bioreactor using fluorescence polymerase chain reaction (PCR) single-strand conformation polymorphism analysis. Environ Microbiol 2: 69–78PubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media, Inc. 2006

Authors and Affiliations

  • M. Gentile
    • 1
  • T. Yan
    • 2
  • S. M. Tiquia
    • 2
    • 3
  • M. W. Fields
    • 4
  • J. Nyman
    • 1
  • J. Zhou
    • 2
  • C. S. Criddle
    • 1
    • 5
    Email author
  1. 1.Department of Civil and Environmental EngineeringStanford UniversityStanfordUSA
  2. 2.Environmental Science DivisionOak Ridge National LabOak RidgeUSA
  3. 3.Department of Natural SciencesThe University of MichiganDearbornUSA
  4. 4.Department of MicrobiologyMiami UniversityOxfordUSA
  5. 5.Department of Civil and Environmental EngineeringM11 Terman EngineeringStanfordUSA

Personalised recommendations