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.
Similar content being viewed by others
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
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
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
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
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
Blok HJ, Gohlke AM & Akkermans ADL (1997) Quantitative analysis of 16S rDNA using competitive PCR and the QPCR System 5000. Biotechniques 22: 700–702
Böttger EC (1996) Approaches for identification of microorganisms. ASM News 62: 247–250
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
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
DeLong EF, Wickham GS & Pace NR (1989) Phylogenetic strains: ribosomal RNA-based probes for the identification of single cells. Science 243: 1360–1363
Doddema HJ & Vogels GD (1978) Improved identification of methanogenic bacteria by fluorescence microscopy. Appl. Environ. Microbiol. 36: 752–754
Dolfing J, Griffioen A, van Neerven ARW & Zevenhuizen LPTM (1985) Chemical and bacteriological composition of granular methanogenic sludge. Can. J. Microbiol. 31: 744–750
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
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
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
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
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
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
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
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
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
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
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
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
Hugenholtz P & Pace NR (1996) Identifying microbial diversity in the natural environment: a molecular phylogenetic approach. Tibtech 14: 190–197
Jürgens G, Lindstrom K & Saano A (1997) Novel group within the kingdom Crenarchaeota from boreal forest soil. Appl. Environ. Microbiol. 63: 803–805
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
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
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
Lettinga G (1995) Anaerobic digestion and wastewater treatment systems. Antonie van Leeuwenhoek 67: 3–28
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
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
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
Martin CS, Butler L & Bronstein I (1995) Quantification of PCR products with chemiluminescence. Biotechnol. 18: 908–912
Muyzer G & Ramsing NB (1995) Molecular methods to study the organization of microbial communities. Water Sci. Technol. 31: 1–9
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
Ng A, Melvin WT & Hobson PN (1994) Identification of anaerobic digester bacteria using a polymerase chain reaction method. Bioresource Technol. 47: 73-80
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
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
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
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
Oude Elferink SJWH (1998) Sulfate-reducing bacteria in anaerobic bioreactors. PhD Thesis. Wageningen Agricultural University, the Netherlands
Oude Elferink SJWH, Visser A, Hulshoff Pol LW, & Stams AJM (1994) Sulfate reduction in methanogenic bioreactors. FEMS Microbiol. Rev. 15: 119–136
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
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
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
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
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
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
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
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
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
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
Robinson RW & Erdos GW (1985) Immuno-electron microscopic identification of Methanosarcina spp. in anaerobic digester fluid. Can. J. Microbiol. 31: 839–844
Singleton Jr R, Denis J & Campbell LL (1985) Whole-cell antigens of members of the sulfate-reducing genus Desulfovibrio. Arch. Microbiol. 141: 195–197
Smith AD (1982) Immunofluorescence of sulphate-reducing bacteria. Arch. Microbiol. 133: 118–121
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.
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
Stahl DA (1995) Application of phylogenetically based hybridization probes to microbial ecology. Molec. Ecol. 4: 535–542
Stams AJM (1994) Metabolic interactions between anaerobic bacteria in methanogenic environments. Antonie van Leeuwenhoek 66: 271–294
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
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
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
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
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
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
Woese CR (1987) Bacterial evolution. Microbiol. Rev. 51: 221–271
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
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
Author information
Authors and Affiliations
Rights and permissions
About this article
Cite this article
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
Issue Date:
DOI: https://doi.org/10.1023/A:1008300423935