Skip to main content
SpringerLink
Log in

Phylogenetic and functional diversity of propionate-oxidizing bacteria in an anaerobic digester sludge

  • Environmental Biotechnology
  • Published:
Applied Microbiology and Biotechnology Aims and scope Submit manuscript

Abstract

The phylogenetic and functional diversity of syntrophic propionate-oxidizing bacteria (POB) present in an anaerobic digester was investigated by microautoradiography combined with fluorescent in situ hybridization (MAR–FISH) that can directly link 16S rRNA phylogeny with in situ metabolic function. The syntrophic POB community in the anaerobic digester sludge consisted of at least four phylogenetic groups: Syntrophobacter, uncultured short rod Smithella (Smithella sp. SR), uncultured long rod Smithella (Smithella sp. LR), and an unidentified group. The activities of these POB groups were dependent on the propionate concentrations. The uncultured Smithella sp. SR accounted for 52–62% of the total active POB under all the propionate concentrations tested (0.5–15 mM). In contrast, uncultured Smithella sp. LR was active only at lower propionate concentrations and became a dominant active POB at 0.5 mM of propionate. Syntrophobacter accounted for 16–31% of the total active POB above 2.5 mM propionate, whereas the active Syntrophobacter population became low (ca. 6%) at 0.5 mM of propionate. The anaerobic digester was operated in a fill and draw mode, resulting in periodical changes in propionate concentration ranging from 0 to 10 mM. These phylogenetically and functionally diverse, to some extent functionally redundant, active POB communities were dynamically responding to the periodical changes in propionate concentration.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5

Similar content being viewed by others

References

  • Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ (1997) Gapped BLAST and PSI–BLAST: a new generation of protein database search programs. Nucleic Acids Res 25:3389–3402

    CAS  PubMed  PubMed Central  Google Scholar 

  • Amann RI (1995) In situ identification of micro-organism by whole cell hybridization with rRNA-targeted nucleic probes. In: Akkerman ADC, van Elsas JD, de Bruijn FJ (eds) Molecular microbial ecology manual. Kluwer, The Netherlands, pp 1–15

    Google Scholar 

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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • American Public Health Association, American Water Works Association, and Water Environment Federation (1995) Standard methods for the examination of water and wastewater, 19th edn. American Public Health Association, American Water Works Association, and Water Environment Federation, Washington, D.C., USA

  • Ariesyady HD, Ito T, Okabe S (2007) Functional bacterial and archaeal community structures of major trophic groups in a full-scale anaerobic sludge digester. Water Res DOI https://doi.org/10.1016/j.watres.2006.12.036

  • Boone DR, Bryant MP (1980) Propionate-degrading bacterium, Syntrophobacter wolinii sp. nov. gen. nov. from methanogenic ecosystems. Appl Environ Microbiol 40:626–632

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Chen S, Liu X, Dong X (2005) Syntrophobacter sulfatireducens sp. nov., a novel syntrophic, propionate-oxidizing bacterium isolated from UASB reactors. Int J Syst Evol Microbiol 55:1319–1324

    Article  CAS  PubMed  Google Scholar 

  • 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

    Article  CAS  PubMed  Google Scholar 

  • Daims H, Bruhl A, Amann R, Schleifer KH, Wagner M (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

    Article  CAS  PubMed  Google Scholar 

  • Daims H, Nielsen JL, Nielsen PH, Schleifer KH, Wagner M (2001) In situ characterization of Nitrospira-like nitrite-oxidizing bacteria active in wastewater treatment plants. Appl Environ Microbiol 67:5273–5284

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • de Bok FAM, Stams ALM, Dijkema C, Boone DR (2001) Pathway of propionate oxidation by a syntrophic culture of Smithellapropionica and Methanospirillum hungatei. Appl Environ Microbiol 67:1800–1804

    Article  PubMed  PubMed Central  Google Scholar 

  • de Bok FA, Harmsen HJ, Plugge CM, de Vries MC, Akkermans AD, de Vos WM, Stams AJ (2005) The first true obligatory syntrophic propionate-oxidizing bacterium, Pelotomaculum schinkii sp. nov., co-cultured with Methanospirillum hungatei, and emended description of the genus Pelotomaculum. Int J Syst Evol Microbiol 55:1697–1703

    Article  CAS  PubMed  Google Scholar 

  • Fernández A, Huang S, Seston S, Xing J, Hickey R, Criddle C, Tiedje J (1999) How stable is stable? Function versus community composition. Appl Environ Microbiol 65:3697–3704

    Article  PubMed  PubMed Central  Google Scholar 

  • Fukuzaki S, Nishio N, Shobayashi M, Nogai S (1990) Inhibition of the fermentation of propionate to methane by hydrogen, acetate and propionate. Appl Environ Microbiol 56:719–723

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Hansen KH, Ahring BK, Raskin L (1999) Quantification of syntrophic fatty acid-beta-oxidizing bacteria in a mesophilic biogas reactor by oligonucleotide probe hybridization. Appl Environ Microbiol 65:4767–4774

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • 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

    Article  CAS  PubMed  PubMed Central  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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Harmsen HJM, van Kuijk BLM, Plugge CM, Akkermans ADL, de Vos WM, Stams AJM (1998) Syntrophobacter fumaroxidans sp. nov., a syntrophic propionate-degrading sulfate-reducing bacterium. Int J Syst Bacteriol 48:1383–1387

    Article  CAS  PubMed  Google Scholar 

  • Heyes RH, Hall RJ (1983) Kinetics of two subgroups of propionate-using organisms in anaerobic digestion. Appl Environ Microbiol 46:710–715

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Houwen FP, Plokker J, Stams AJM, Zehnder AJB (1990) Enzymatic evidence for involvement of the methyl-malonyl-CoA pathway in propionate oxidation by Syntrophobacter wolinii. Arch Microbiol 155:52–55

    Article  CAS  Google Scholar 

  • Imachi H, Sekiguchi Y, Kamagata Y, Hanada S, Ohashi A, Harada H (2002) Pelotomaculum thermopropionicum gen. nov., sp. nov., an anaerobic, thermophilic, syntrophic propionate-oxidizing bacterium. Int J Syst Evol Microbiol 52:1729–1735

    CAS  PubMed  Google Scholar 

  • Kaspar HF, Wuhrnann K (1978) Kinetic parameters and relative turnovers of some important catabolic reactions in digesting sludge. Appl Environ Microbiol 36:1–7

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kindaichi T, Ito T, Okabe S (2004) Eco-physiological interaction between nitrifying bacteria and heterotrophic bacteria in autotrophic nitrifying biofilms as determined by MAR–FISH. Appl Environ Microbiol 70:1641–1650

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kong YH, Nielsen JL, Nielsen PH (2004) Microautoradiographic study of Rhodocyclus-related polyphosphate-accumulating bacteria in full-scale EBPR plants. Appl Environ Microbiol 70:5383–5390

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kumar S, Tamura K, Nei M (2004) MEGA3: integrated software for molecular evolutionary genetics analysis and sequence alignment. Brief Bioinform 5:150–163

    Article  CAS  PubMed  Google Scholar 

  • Kus F, Wiesmann U (1995) Degradation kinetics of acetate and propionate by immobilized anaerobic mixed cultures. Water Res 29:1437–1443

    Article  CAS  Google Scholar 

  • Lane DJ (1991) 16S/23S rRNA sequencing. In: Stackebrandt E, Goodfellow M (eds) Nucleic acid techniques in bacterial systematics. Wiley, Chichester, England, pp 115–175

    Google Scholar 

  • Lawrence AW, McCarty PL (1969) Kinetics of methane fermentation in anaerobic treatment. Res J Water Pollut Control Fed 41:R1–R17

    CAS  Google Scholar 

  • 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 microbial ecology. Appl Environ Microbiol 65:1289–1297

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Liu Y, Balkwill DL, Aldrich HC, Drake GR, Boone DR (1999) Characterization of the anaerobic propionate-degrading syntrophs Smithella propionica gen. nov. sp. nov. and Syntrophobacter wolinii. Int J Syst Bacteriol 49:545–556

    Article  CAS  PubMed  Google Scholar 

  • Loreau M, Naeem S, Inchausti P, Bengtsson J, Grime JP, Hector A, Hooper DU, Huston MA, Raffaelli D, Schmid B, Tilman D, Wardle DA (2001) Biodiversity and ecosystem functioning: current knowledge and future challenges. Science 294:804–808

    Article  CAS  PubMed  Google Scholar 

  • Lowe SE, Jain MK, Zeikus JG (1993) Biology, ecology, and biotechnological applications of anaerobic bacteria adapted to environmental stresses in temperature, pH, salinity, or substrates. Microbiol Rev 57:451–509

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Loy A, Horn M, Wagner M (2003) ProbeBase: an online resource for rRNA-targeted oligonucleotide probes. Nucleic Acids Res 31:514–516

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ludwig W, Strunk O, Westram R, Richter L, Meier H, Yadhukumar, Buchner A, Lai T, Steppi S, Jobb G, Förster W, Brettske I, Gerber S, Ginhart AW, Gross O, Grumann S, Hermann S, Jost R, König A, Liss T, Lüβmann 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 32:1363–1371

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Lueders T, Pommerenke B, Friedrich MW (2004) Stable-isotope probing of microorganisms thriving at thermodynamic limits: syntrophic propionate oxidation in flooded soil. Appl Environ Microbiol 70:5778–5786

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Maillacheruvu KY, Parkin GF (1996) Kinetics of growth, substrate utilization and sulfide toxicity for propionate, acetate, and hydrogen utilizers in anaerobic systems. Water Environ Res 68:1099–1106

    Article  CAS  Google Scholar 

  • Manefield M, Whiteley AS, Griffiths RI, Bailey MJ (2002) RNA stable isotope probing, a novel means of linking microbial community function to phylogeny. Appl Environ Microbiol 68:5367–5373

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • McCarty PL, Smith DP (1986) Anaerobic wastewater treatment. Environ Sci Technol 20:1200–1206

    Article  CAS  Google Scholar 

  • McMahon KD, Stroot PG, Mackie RI, Raskin L (2001) Anaerobic codigestion of municipal solid waste and biosolids under various mixing conditions, II: microbial population dynamics. Water Res 35:1817–1827

    Article  CAS  PubMed  Google Scholar 

  • McMahon KD, Zheng D, Stams AJM, Mackie RI, Raskin L (2004) Microbial population dynamics during start-up and overload conditions of anaerobic digesters treating municipal solid waste and sewage sludge. Biotechnol Bioeng 87:823–834

    Article  CAS  PubMed  Google Scholar 

  • Okabe S, Satoh H, Watanabe Y (1999) In situ analysis of nitrifying biofilms as determined by in situ hybridization and the use of microelectrodes. Appl Environ Microbiol 65:3182–3191

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Okabe S, Kindaichi T, Ito T (2005) Fate of 14C-labeled microbial products derived from nitrifying bacteria in autotrophic nitrifying biofilms. Appl Environ Microbiol 71:3987–3994

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Plugge CM, Balk M, Stams AJM (2002) Desulfotomaculum thermobenzoicum subsp. thermosyntrophicum subsp. nov., a thermophilic, syntrophic, propionate oxidizing, spore-forming bacterium. Int J Syst Evol Microbiol 52:391–399

    Article  CAS  PubMed  Google Scholar 

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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • 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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Stoecker K, Bendinger B, Schöning B, Nielsen PH, Nielsen JL, Baranyi C, Toenshoff ER, Daims H, Wagner M (2006) Cohn’s Crenothrix is a filamentous methane oxidizer with an unusual methane monooxygenase. Proc Natl Acad Sci USA 103:2363–2367

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Thompson JD, Higgins DG, Gibson TJ (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22:4673–4680

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wallrabenstein C, Hauschild E, Schink B (1994) Pure culture and cytological properties of Syntrophobacter wolinii. FEMS Microbiol Lett 123:249–254

    Article  CAS  Google Scholar 

  • Wallrabenstein C, Hauschild E, Schink B (1995) Syntrophobacter pfennigii sp. nov., new syntrophically propionate-oxidizing anaerobe growing in pure culture with propionate and sulfate. Arch Microbiol 164:346–352

    Article  CAS  Google Scholar 

Download references

Acknowledgment

We gratefully thank the Central Institute of Isotope Science, Hokkaido University, for providing the facilities for the isotope experiments. This study was carried out as a part of “The Project for Development of Technologies for Analyzing and Controlling the Mechanism of Biodegrading and Processing,” which was entrusted by the New Energy and Industrial Technology Development Organization (NEDO), Japan.

Author information

Authors and Affiliations

  1. Department of Urban and Environmental Engineering, Graduate School of Engineering, Hokkaido University, North-13, West-8, Kita-ku, Sapporo, 060-8628, Japan

    Herto Dwi Ariesyady, Kazumi Yoshiguchi & Satoshi Okabe

  2. Department of Civil Engineering, Faculty of Engineering, Gunma University, 1-5-1 Tenjin-cho, Kiryu, 376-8515, Japan

    Tsukasa Ito

Authors
  1. Herto Dwi Ariesyady
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Tsukasa Ito
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Kazumi Yoshiguchi
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Satoshi Okabe
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Satoshi Okabe.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Ariesyady, H.D., Ito, T., Yoshiguchi, K. et al. Phylogenetic and functional diversity of propionate-oxidizing bacteria in an anaerobic digester sludge. Appl Microbiol Biotechnol 75, 673–683 (2007). https://doi.org/10.1007/s00253-007-0842-y

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00253-007-0842-y

Keywords

Search

Navigation