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Detection and quantification of microorganisms in anaerobic bioreactors

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Abstract

The presence of sulfate in anaerobic reactors can trigger competitive and syntrophic interactions between various groups of microorganisms, such as sulfate reducers, methanogens and acetogens. In order to steer the reactor process in the direction of sulfidogenesis or methanogenesis, it is essential to get insight into the population dynamics of these groups of microorganisms upon changes in the reactor operating conditions. Several methods exist to characterize and quantify the microbial sludge composition. Combining classical microbiological and modern molecular-based sludge characterization methods has proven to be a powerful approach to study the microbial composition of the anaerobic sludge.

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References

  • Akkermans ADL, van Elsas JD & de Bruijn FJ (1995; 1996; 1998) Molecular Microbial Ecology Manual + supplements 1,2 (1996) and 3 (1998). Kluwer Academic Publishers, Dordrecht

    Google Scholar 

  • Amann RI, Stromley J, Key R & Stahl DA (1992) Molecular and microscopic identification of sulfate-reducing bacteria in multispecies biofilms. Appl. Environ. Microbiol. 58: 614–623

    Google Scholar 

  • Amann RI, Ludwig W & Schleifer K-H (1995) Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol. Rev. 59: 143–169

    Google Scholar 

  • Amann RI, Snaidr J, Wagner M, Ludwig W & Schleifer K-H (1996) In situ visualization of high genetic diversity in a natural microbial community. J. Bacteriol. 178: 3496–3500

    Google Scholar 

  • Bauer-Kreisel P, Eisenbeis M & Scholz-Muramatsu H (1996) Quantification of Dehalospirillum multivorans in mixed-culture biofilms with an enzyme-linked immunosorent assay. Appl Environ. Microbiol. 62: 3050–3052

    Google Scholar 

  • Blok HJ, Gohlke AM & Akkermans ADL (1997) Quantitative analysis of 16S rDNA using competitive PCR and the QPCR System 5000. Biotechniques 22: 700–702

    Google Scholar 

  • Böttger EC (1996) Approaches for identification of microorganisms. ASM News 62: 247–250

    Google Scholar 

  • Boschker HTS, Nold SC, Wellbury P, Bos D, de Graaf W, Pel R, Parkes RJ & Cappenberg TE (1998) Direct linking of microbial populations to specific biogeochemical processes by 13C-labelling of biomarkers. Nature 392: 801–805

    Google Scholar 

  • Davey HM & Kell DB (1996) Flow cytometry and cell sorting of heterogeneous microbial populations: the importance of single-cell analyses. Microbiol. Rev. 60: 641–696

    Google Scholar 

  • DeLong EF, Wickham GS & Pace NR (1989) Phylogenetic strains: ribosomal RNA-based probes for the identification of single cells. Science 243: 1360–1363

    Google Scholar 

  • Doddema HJ & Vogels GD (1978) Improved identification of methanogenic bacteria by fluorescence microscopy. Appl. Environ. Microbiol. 36: 752–754

    Google Scholar 

  • Dolfing J, Griffioen A, van Neerven ARW & Zevenhuizen LPTM (1985) Chemical and bacteriological composition of granular methanogenic sludge. Can. J. Microbiol. 31: 744–750

    Google Scholar 

  • Dowling NJE, Nichols PD & White DC (1988) Phospholipid fatty acid and infra-red spectroscopic analysis of a sulphate-reducing consortium. FEMS Microbiol. Ecol. 53: 325–334

    Google Scholar 

  • Edlund A, Nichols PD, Roffey R & White DC (1985) Extractable and lipopolysaccharide fatty acid and hydroxy acid profiles from Desulfovibrio species. J. Lipid Res. 26: 982–988

    Google Scholar 

  • Felske A, Rheims H, Wolterink A, Stackebrandt E & Akkermans ADL (1997) Ribosome analysis reveals prominent activity of an uncultured member of the class Actinobacteria in grassland soils. Microbiol. 143: 2983–2989

    Google Scholar 

  • Ferré F, Marchese A, Pezzoli P, Griffin S, Buxton E & Boyer V (1994) Quantitative PCR: An overview. In: Mullis KB, Ferré F & Gibbs RA (Eds) The polymerase chain reaction. Brinkhauser, Boston

    Google Scholar 

  • Fukui M, Suwa Y & Urushigawa Y (1996) High survival efficiency and ribosomal RNA decaying pattern of Desulfobacter latus, a highly specific acetate-utilizing organism during starvation. FEMS Microb. Ecol. 19: 17–25

    Google Scholar 

  • Gausing K (1977) Regulation of ribosome production in Escherichia coli: Synthesis and stability of ribosomal RNA and of ribosomal protein messenger RNA at different growth rates. J. Molec. Biol. 115: 335–354

    Google Scholar 

  • Giovannoni S (1991) The polymerase chain reaction. In: Stackebrandt E & Goodfellow M (Eds) Nucleic acid techniques in bacterial systems (pp 177–203). John Wiley & Sons, Chichester

    Google Scholar 

  • Grotenhuis JTC, Smit M, Plugge CM, Xu Y, van Lammeren AAM, Stams AJM & Zehnder AJB (1991) Bacteriological composition and structure of granular sludge adapted to different substrates. Appl. Environ. Microbiol. 57: 1942–1949

    Google Scholar 

  • Guckert JB, Antworth CP, Nichols PD & White DC (1985) Phopholipid ester-linked fatty acid profiles as reproducible assays for changes in prokaryotic community structure of estuarine sediments. FEMS Microbiol. Ecol. 31: 147–158

    Google Scholar 

  • Harlow E & Lane D (1988) Antibodies: A laboratory manual. Cold Spring Harbor Laboratory

  • Harmsen HJM, Akkermans ADL, Stams AJM & de Vos WM (1996a) Population dynamics of propionate-oxidizing bacteria under methanogenic and sulfidogenic conditions in anaerobic granular sludge. Appl. Environ. Microbiol. 62: 2163–2168

    Google Scholar 

  • Harmsen HJM, Kengen HMP, Akkermans ADL, Stams AJM & de Vos WM (1996b) Detection and localization of syntrophic propionate-oxidizing bacteria in granular sludge by in situ hybridization using 16S rRNA-based oligonucleotide probes. Appl. Environ. Microbiol. 62: 1656–1663

    Google Scholar 

  • Hiraishi A, Kamagata Y & Nakamura K (1995) Polymerase chain reaction amplification and restriction fragment length polymorphism analysis of 16S rRNA genes from methanogens. J. Ferment. Bioeng. 79: 523–529

    Google Scholar 

  • Hugenholtz P & Pace NR (1996) Identifying microbial diversity in the natural environment: a molecular phylogenetic approach. Tibtech 14: 190–197

    Google Scholar 

  • Jürgens G, Lindstrom K & Saano A (1997) Novel group within the kingdom Crenarchaeota from boreal forest soil. Appl. Environ. Microbiol. 63: 803–805

    Google Scholar 

  • Kane MD, Poulsen LK & Stahl DA (1993) Monitoring the enrichment and isolation of sulfate-reducing bacteria by using oligonucleotide hybridization probes designed form environmentally derived 16S rRNA sequences. Appl. Environ. Microbiol. 59: 682–686

    Google Scholar 

  • Kohring LL, Ringelberg DB, Devereux R, Stahl DA, Mittelman MW & White DC (1994) Comparison of phylogenetic relationships based on phospholipid fatty acid profiles and ribosomal RNA sequence similarities among dissimilatory sulfate-reducing bacteria. FEMS Microbiol. Lett. 119: 303–308

    Google Scholar 

  • Koornneef E, Macario AJL, Grotenhuis JTC & Conway de Macario E (1990) Methanogens revealed immunologically in granules from five upflow anaerobic sludge blanket (UASB) bioreactors grown on different substrates. FEMS microbiol. Ecol. 73: 225–230

    Google Scholar 

  • Lettinga G (1995) Anaerobic digestion and wastewater treatment systems. Antonie van Leeuwenhoek 67: 3–28

    Google Scholar 

  • Lillebaek R (1995) Application of antisera raised against sulfate-reducing bacteria for indirect immunofluorescent detection of immunoreactive bacteria in sediment from the German Baltic Sea. Appl. Environ. Microbiol. 61: 3436–3442

    Google Scholar 

  • Macario AJL, Peck MW, Conway de Macario E & Chynoweth DP (1991a) Unusual methanogenic flora of a wood-fermenting anaerobic bioreactor. J. Appl. Bacteriol. 71: 31–37

    Google Scholar 

  • Macario AJL, Visser FA, van Lier JB & Conway de Macario E (1991b) Topography of methanogenic subpopulatons in a microbial consortium adapting to thermophile conditions. J. Gen. Microbiol. 137: 2179–2189

    Google Scholar 

  • Martin CS, Butler L & Bronstein I (1995) Quantification of PCR products with chemiluminescence. Biotechnol. 18: 908–912

    Google Scholar 

  • Muyzer G & Ramsing NB (1995) Molecular methods to study the organization of microbial communities. Water Sci. Technol. 31: 1–9

    Google Scholar 

  • Muyzer G, de Waal EC & Uitterlinden AG (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

    Google Scholar 

  • Ng A, Melvin WT & Hobson PN (1994) Identification of anaerobic digester bacteria using a polymerase chain reaction method. Bioresource Technol. 47: 73-80

    Google Scholar 

  • Nishihara M, Akagawa-Matsushita M, Togo Y & Koga Y (1995) Inference of methanogenic bacteria in wastewater digestor sludges by lipid component analysis. J. Ferment. Bioeng. 79: 400–402

    Google Scholar 

  • Nübel U, Engelen B, Felske A, Snaidr J, Woeshuber A, Amann RI, Ludwig W & Backhaus H (1996) Sequence heterogeneities of genes encoding 16S rRNAs in Paenibacillus polymixa by temperature gradient gel electrophoresis. J. Bacteriol. 178: 5636–5643

    Google Scholar 

  • Ohtsubo S, Kanno M, Miyahara H, Kohno S, Koga Y & Miura I (1993) A sensitive method for quantification of aceticlastic methanogens and estimation of total methanogenic cells in natural environments based on an analysis of ether-linked glycerolipids. FEMS Microbiol. Ecol. 12: 39–50

    Google Scholar 

  • Omil F, Oude Elferink SJWH, Lens P, Hulshoff Pol LW & Lettinga G (1997) Effect of the inoculation with Desulforhabdus amnigenus and pH or O2 shocks on the competition between sulphate reducing and methanogenic bacteria in an acetate fed UASB reactor. Biores. Technol. 60: 113–122

    Google Scholar 

  • Oude Elferink SJWH (1998) Sulfate-reducing bacteria in anaerobic bioreactors. PhD Thesis. Wageningen Agricultural University, the Netherlands

    Google Scholar 

  • Oude Elferink SJWH, Visser A, Hulshoff Pol LW, & Stams AJM (1994) Sulfate reduction in methanogenic bioreactors. FEMS Microbiol. Rev. 15: 119–136

    Google Scholar 

  • Oude Elferink SJWH, Rinia HA, Bruins ME, de Vos WM & Stams AJM (1997) Detection and quantification of Desulforhabdus amnigenus in anaerobic granular sludge by dot blot hybridization and PCR amplification. J. Appl. Bacteriol. 83: 102–110

    Google Scholar 

  • Oude Elferink SJWH, Boschker HTS & Stams AJM (1998) Identification of sulfate reducers and Syntrophobacter sp. in anaerobic granular sludge by fatty acid biomarkers and 16S rRNA probing. Geomicrobiol. J. 15: 3–17

    Google Scholar 

  • Pace NR, Stahl DA, Lane DJ & Olson GJ (1986) The analysis of natural microbial populations by ribosomal RNA sequences. Adv. Microb. Ecol. 9: 1–55

    Google Scholar 

  • Parkes RJ (1987) Analysis of microbial communities within sediments using biomarkers. In: Fletcher M, Gray TRG & Jones JG (Eds) Ecology of microbial communities (pp 147–177) Cambridge University Press, Cambridge

    Google Scholar 

  • Raskin L, Amann RI, Poulsen LK, Rittmann BE & Stahl DA (1995a) Use of ribosomal RNA-based molecular probes for characterization of complex microbial communities in anaerobic biofilms. Water Sci. Technol. 31: 261–272

    Google Scholar 

  • Raskin L, Poulsen LK, Noguera DR, Rittmann BE & Stahl DA (1994a) Quantification of methanogenic groups in anaerobic biological reactors by oligonucleotide probe hybridization. Appl. Environ. Microbiol. 60: 1241–1248

    Google Scholar 

  • Raskin L, Rittmann BE & Stahl DA (1996) Competition and coexistence of sulfate-reducing and methanogenic populations in anaerobic biofilms. Appl. Environ. Microbiol. 62: 3847–3857

    Google Scholar 

  • Raskin L, Stromly JM, Rittmann BE & Stahl DA (1994b) Group-specific 16S rRNA hybridization probes to describe natural communities of methanogens. Appl. Environ. Microbiol. 60: 1232–1240

    Google Scholar 

  • Raskin L, Zheng D, Griffin ME, Stroot PG & Misra P (1995b) Characterization of microbial communities in anaerobic bioreactors using molecular probes. Antonie van Leeuwenhoek 68: 297–308

    Google Scholar 

  • Ringelberg DB, Townsend GT, DeWeerd KA, Suflita JM & White DC (1994) Detection of the anaerobic dechlorinating microorganism Desulfomonile tiedjei in environmental matrices by its signature lipopolysaccaride branched-long-chain hydroxy fatty acids. FEMS Microbiol. Ecol. 14: 9–18

    Google Scholar 

  • Robinson RW & Erdos GW (1985) Immuno-electron microscopic identification of Methanosarcina spp. in anaerobic digester fluid. Can. J. Microbiol. 31: 839–844

    Google Scholar 

  • Singleton Jr R, Denis J & Campbell LL (1985) Whole-cell antigens of members of the sulfate-reducing genus Desulfovibrio. Arch. Microbiol. 141: 195–197

    Google Scholar 

  • Smith AD (1982) Immunofluorescence of sulphate-reducing bacteria. Arch. Microbiol. 133: 118–121

    Google Scholar 

  • Sørensen AH & Ahring BK (1997) An improved enzyme-linked immunosorbent assay for whole-cell determination of methanogens in samples from anaerobic reactors. Appl. Environ. Microbiol. 63: 2001–2006.

    Google Scholar 

  • Sørensen AH, Torsvik VL, Torsvik T, Poulsen LK & Ahring BK (1997) Whole-cell hybridization of Methanosarcina cells with two new oligonucleotide probes. Appl. Environ. Microbiol. 63: 3043–3050

    Google Scholar 

  • Stahl DA (1995) Application of phylogenetically based hybridization probes to microbial ecology. Molec. Ecol. 4: 535–542

    Google Scholar 

  • Stams AJM (1994) Metabolic interactions between anaerobic bacteria in methanogenic environments. Antonie van Leeuwenhoek 66: 271–294

    Google Scholar 

  • Surman SB, Walker JT, Goddard DT, Morton LHG, Keevil CW, Weaver W, Skinner A, Hanson K, Caldwell D & Kurtz J (1996) Comparison of microscope techniques for the examination of biofilms. J. Microbiol. Meth. 25: 57–70

    Google Scholar 

  • Suzuki MT & Giovannoni SJ (1996) Bias caused by template annealing in the amplification of mixtures of 16S rRNA genes by PCR. Appl. Environ. Microbiol. 62: 625–630

    Google Scholar 

  • Taylor J & Parkes RJ (1983) The cellular fatty acids of the sulfate-reducing bacteria, Desulfobacter sp., Desulfobulbus sp. and Desulfovibrio desulfuricans. J. Gen. Microbiol. 129: 3303–3309

    Google Scholar 

  • Vainshtein M, Hippe H & Kroppenstedt RM (1992) Cellular fatty acid composition of Desulfovibrio species and its use in classification of sulfate-reducing bacteria. Syst. Appl. Microbiol. 15: 554–566

    Google Scholar 

  • Visser A, Beeksma I, van der Zee F, Stams AJM & Lettinga G (1993) Anaerobic degradation of volatile fatty acids at different sulfate concentrations. Appl. Microbiol. Biotechnol. 40: 549–556

    Google Scholar 

  • Whitman WB, Bowen TL & Boone DR (1992) The methanogenic bacteria. In: Balows A, Trüper, Dworkin M, Harder W & Schleifer K-H (Eds) The Prokaryotes, 2nd edn. (pp 719–767). Springer-Verlag, New York

    Google Scholar 

  • Woese CR (1987) Bacterial evolution. Microbiol. Rev. 51: 221–271

    Google Scholar 

  • Wu W-M, Jain M, Conway de Macario E, Thiele JH & Zeikus JG (1992) Microbial composition and characterization of prevalent methanogens and acetogens isolated from syntrophic methanogenic granules. Appl. Microbiol. Biotechnol. 38: 282–290

    Google Scholar 

  • Zellner G, Diekmann H, Austermann-Haun U, Baumgarten G & Seyfried C-F (1993) Biofilm formation on polypropylene during start-up of anaerobic fixed-bed reactors. Biofouling 6: 345–361

    Google Scholar 

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Oude Elferink, S., van Lis, R., Heilig, H. et al. Detection and quantification of microorganisms in anaerobic bioreactors. Biodegradation 9, 169–177 (1998). https://doi.org/10.1023/A:1008300423935

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