Skip to main content

Advertisement

SpringerLink
Log in

Microbial population in the biomass adhering to supporting material in a packed-bed reactor degrading organic solid waste

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

Abstract

An anaerobic packed-bed reactor using carbon fiber textiles (CFT) as the supporting material was continuously operated using an artificial garbage slurry. 16S rRNA gene analysis showed that many bacteria in the biomass adhering to CFT were closely related to those observed from other anaerobic environments, although a wide variety of unidentified bacteria were also found. Dot blot hybridization results clarified that 16S rRNA levels of methanogens in the adhering biomass were higher than those in the effluent. Based on microscopic observation, the adhering biomass consisted of microorganisms, organic material, and void areas. Bacteria and Archaea detected by fluorescence in situ hybridization were distributed from the surface to the inner regions of the adhering biomass. Methanosarcina sp. tended to be more abundant in the inner part of the adhering biomass than at the surface. This is the first report to elucidate the structure of the microbial community on CFT in a packed-bed reactor.

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

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

    Google Scholar 

  • Boone DR, Mah RA (2001) Genus I Methanosarcina. In: Boone DR, Castenholz RW (eds) Bergey’s manual of systematic bacteriology, vol. 1. Springer, New York, pp 269–276

    Google Scholar 

  • Bryant MP, Boone DR (1987) Isolation and characterization of Methanobacterium formicicum MF. Int J Syst Bacteriol 37:171

    Google Scholar 

  • Chouari R, Paslier DL, Daegelen P, Ginestet P, Weissenbach J, Sghir A (2005) Novel predominant archaeal and bacterial groups revealed by molecular analysis of an anaerobic sludge digestor. Environ Microbiol 7:1104–1115

    CAS  PubMed  Google Scholar 

  • Collins MD, Lawson PA, Willems A, Cordoba JJ, Fernandez-Garayzabal J, Garcia P, Cai J, Hippe H, Farrow JAE (1994) The phylogeny of the genus Clostridium: proposal of five new genera and eleven new species combinations. Int J Syst Bacteriol 44:812–826

    CAS  PubMed  Google Scholar 

  • Daims H, Brühl 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

    CAS  PubMed  Google Scholar 

  • Delong EF (1992) Archaea in coastal marine environments. Proc Natl Acad Sci USA 89:5685–5689

    CAS  PubMed  Google Scholar 

  • Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783–791

    Google Scholar 

  • Großkopf R, Stubner S, Liesack W (1998) Novel Euryarchaeota lineages detected on rice roots and in the anoxic bulk soil of flooded rice microcosms. Appl Environ Microbiol 64:4983–4989

    PubMed Central  Google Scholar 

  • Haruta S, Kondo M, Nakamura K, Aiba H, Ueno S, Ishii M, Igarashi Y (2002) Microbial community changes during organic solid waste treatment analyzed by double gradient-denaturing gradient gel electrophoresis and fluorescence in situ hybridization. Appl Microbiol Biotechnol 60:224–231

    CAS  PubMed  Google Scholar 

  • Haruta S, Nakamura T, Nakamura K, Hemmi H, Ishii M, Igarashi Y, Nishino T (2005) Microbial diversity in biodegradation and reutilization processes of garbage. J Biosci Bioeng 99:1–11

    CAS  PubMed  Google Scholar 

  • Hori T, Haruta S, Ueno Y, Ishii M, Igarashi Y (2006) Direct comparison of single-strand conformation polymorphism (SSCP) and denaturing gradient gel electrophoresis (DGGE) to characterize a microbial community on the basis of 16S rRNA gene fragments. J Microbiol Methods 66:165–169

    CAS  PubMed  Google Scholar 

  • Huang LN, Zhu S, Zhou H, Qu LH (2005) Molecular phylogenetic diversity of bacteria associated with the leachate of a closed municipal solid waste landfill. FEMS Microbiol Lett 242:297–303

    CAS  PubMed  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 

  • Japanese Industrial Standards Committee (1986) Organic matter. In: Namiki H (ed) Testing methods for industrial wastewater, JIS K 0102-1986. Japanese Standards Association, Tokyo, pp 32–33

    Google Scholar 

  • Kersters I, Maestrojuan GM, Torck U, Vancanneyt M, Kersters K, Verstraete W (1994) Isolation of Coprothermobacter proteolyticus from an anaerobic digest and further characterization of the species. Syst Appl Microbiol 17:289–295

    CAS  Google Scholar 

  • Kumar S, Tamura K, Jakobsen IB, Nei M (2001) MEGA2: molecular evolutionary genetics analysis software. Bioinformatics 17:1244–1245

    CAS  PubMed  Google Scholar 

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

    Google Scholar 

  • Lanthier M, Juteau P, Lépine F, Beaudet R, Villemur R (2005) Desulfitobacterium hafniense is present in a high proportion within the biofilms of a high-performance pentachlorophenol-degrading methanogenic fixed-film reactor. Appl Environ Microbiol 71:1058–1065

    CAS  PubMed  PubMed Central  Google Scholar 

  • Maidak B, Cole JR, Lilburn TG, Parker CT, Saxman PR, Farris RJ, Garrity GM, Olsen GJ, Schmidt TM, Tiedje JM (2001) The RDP-II (Ribosomal Database Project). Nucleic Acids Res 29:173–174

    CAS  PubMed  PubMed Central  Google Scholar 

  • Menes RJ, Muxi L (2002) Anaerobaculum mobile sp. nov., a novel anaerobic, moderately thermophilic, peptide-fermenting bacterium that uses crotonate as an electron acceptor, and emended description of the genus Anaerobaculum. Int J Syst Evol Microbiol 52:157–164

    CAS  PubMed  Google Scholar 

  • Muyzer G, de Waal ECD, Uitterlinder 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

    CAS  PubMed  PubMed Central  Google Scholar 

  • Myers RM, Scheffield VC, Cox DR (1989) Mutation detection by PCR, GC-clamps, and denaturing gradient gel electrophoresis. In: Erlich HA (ed) PCR-technology—principles and applications for DNA amplification. Stocken Press, New York, pp 71–88

    Google Scholar 

  • Nakamura K, Terada T, Sekiguchi Y, Shinzato N, Meng XY, Enoki M, Kamagata Y (2006) Application of pseudomurein endoisopeptidase to fluorescence in situ hybridization of methanogens within the family Methanobacteriaceae. Appl Environ Microbiol 72:6907–6913

    CAS  PubMed  PubMed Central  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

    CAS  PubMed  PubMed Central  Google Scholar 

  • Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425

    CAS  Google Scholar 

  • Sasaki K, Haruta S, Tatara M, Yamazawa A, Ueno Y, Ishii M, Igarashi Y (2006a) Microbial community in methanogenic packed-bed reactor successfully operating at short hydraulic retention time. J Biosci Bioeng 101:271–273

    CAS  PubMed  Google Scholar 

  • Sasaki K, Haruta S, Ueno Y, Ishii M, Igarashi Y (2006b) Archaeal population on supporting material in a methanogenic packed-bed reactor. J Biosci Bioeng 102:244–246

    CAS  PubMed  Google Scholar 

  • Sekiguchi Y, Kamagata Y, Syutsubo K, Ohashi A, Harada H, Nakamura K (1998) Phylogenetic diversity of mesophilic and thermophilic granular sludges determined by 16S rRNA analysis. Microbiology 144:2655–2665

    CAS  PubMed  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

    CAS  PubMed  PubMed Central  Google Scholar 

  • Sekiguchi Y, Yamada T, Hanada S, Ohashi A, Harada H, Kamagata Y (2003) Anaerolinea thermophila gen. nov., sp. nov. and Caldinea aerophila gen. nov., sp. nov., novel filamentous thermophiles that represent a previously uncultured lineage of the domain Bacteria at the subphylum level. Int J Syst Evol Microbiol 53:1843–1851

    CAS  PubMed  Google Scholar 

  • Shiratori H, Ikeno H, Ayame S, Kataoka N, Miya A, Hosono K, Beppu T, Ueda K (2006) Isolation and characterization of a new Clostridium sp. that performs effective cellulosic waste digestion in a thermophilic methanogenic bioreactor. Appl Environ Microbiol 72:3702–3709

    CAS  PubMed  PubMed Central  Google Scholar 

  • Stahl DA, Amann R (1991) Development and application of nucleic acid probes in bacterial systematics. In: Stackebrandt E, Goodfellow M (eds) Nucleic acid techniques in bacterial systematics. Wiley, New York, pp 205–248

    Google Scholar 

  • Tang Y, Shigematsu T, Ikbal, Morimura S, Kida K (2004) The effects of micro-aeration on the phylogenetic diversity of microorganisms in a thermophilic anaerobic municipal solid-waste digester. Water Res 38:2537–2550

    CAS  PubMed  Google Scholar 

  • Tang Y, Shigematsu T, Morimura S, Kida K (2005) Microbial community analysis of mesophilic anaerobic protein degrading process using bovine serum albumin (BSA)-fed continuous cultivation. J Biosci Bioeng 99:150–164

    CAS  PubMed  Google Scholar 

  • Tatara M, Yamazawa A, Ueno Y, Fukui H, Goto M, Sode K (2004) High-rate thermophilic methane fermentation on short-chain fatty acids in a down-flow anaerobic packed-bed reactor. Bioprocess Biosyst Eng 27:105–113

    PubMed  Google Scholar 

  • Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG (1997) The clustal_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25:4876–4882

    CAS  PubMed  PubMed Central  Google Scholar 

  • Ueno Y, Haruta S, Ishii M, Igarashi Y (2001) Changes in product formation and bacterial community by dilution rate on carbohydrate fermentation by methanogenic microflora in continuous flow stirred tank reactor. Appl Microbiol Biotechnol 57:65–73

    CAS  PubMed  Google Scholar 

  • Williams ME (1994) Integrated solid waste management. In: Kreith F (ed) Handbook of solid waste management. McGraw-Hill, New York

    Google Scholar 

  • Yamada T, Sekiguchi Y, Imachi H, Kamagata Y, Ohashi A, Harada H (2005) Diversity, localization, and physiological properties of filamentous microbes belonging to Chloroflexi subphylum I in mesophilic and thermophilic methanogenic sludge granules. Appl Environ Microbiol 71:7493–7503

    CAS  PubMed  PubMed Central  Google Scholar 

  • Zeikus JG, Wolfe RS (1972) Methanobacterium thermoautotrophicus sp. n., an anaerobic, autotrophic, extreme thermophiles. J Bacteriol 109:707–713

    CAS  PubMed  PubMed Central  Google Scholar 

  • Zeller G, Messner P, Winter J, Stackebandt E (1998) Methanoculleus palmolei sp. nov., an irregularly coccoid methanogen from an anaerobic digester treating wastewater of a palm oil plant in north-Sumatra, Indonesia. Int J Syst Bacteriol 48:1111–1117

    Google Scholar 

  • Zheng D, Alm EW, Stahl DA, Raskin L (1996) Characterization of universal small-subunit rRNA hybridization probes for quantitative molecular ecology studies. Appl Environ Microbiol 62:4504–4513

    CAS  PubMed  PubMed Central  Google Scholar 

  • Zhu H, Qu F, Zhu LH (1993) Isolation of genomic DNAs from plants, fungi and bacteria using benzyl chrolide. Nucleic Acids Res 21:5279–5280

    CAS  PubMed  PubMed Central  Google Scholar 

  • Zinder SH, Robert AM (1979) Isolation and characterization of a thermophilic strain of Methanosarcina unable to use H2–CO2 for methanogenesis. Appl Environ Microbiol 38:996–1008

    CAS  PubMed  PubMed Central  Google Scholar 

Download references

Acknowledgements

We thank E. Kumano and T. Kuroiwa of Micro-edge Instruments for the technical advice on cryosectioning. This work was supported by the New Energy and Industrial Technology Development Organization (NEDO).

Author information

Authors and Affiliations

  1. Department of Biotechnology, Graduate School of Agricultural and Life Science, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo, 113-8657, Japan

    Kengo Sasaki, Shin Haruta, Masaharu Ishii & Yasuo Igarashi

  2. Environmental and Bioengineering Group, Kajima Technical Research Institute, Tobitakyu 2-19-1, Chofu-shi, Tokyo, 182-0036, Japan

    Yoshiyuki Ueno

Authors
  1. Kengo Sasaki
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Shin Haruta
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Yoshiyuki Ueno
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Masaharu Ishii
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Yasuo Igarashi
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Kengo Sasaki.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Sasaki, K., Haruta, S., Ueno, Y. et al. Microbial population in the biomass adhering to supporting material in a packed-bed reactor degrading organic solid waste. Appl Microbiol Biotechnol 75, 941–952 (2007). https://doi.org/10.1007/s00253-007-0888-x

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00253-007-0888-x

Keywords

Search

Navigation