Skip to main content
SpringerLink
Log in

Molecular analysis of methanogens involved in methanogenic degradation of tetramethylammonium hydroxide in full-scale bioreactors

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

Abstract

This study investigated methanogenic communities involved in degradation of tetramethylammonium hydroxide (TMAH) in three full-scale bioreactors treating TMAH-containing wastewater. Based on the results of terminal-restriction fragment-length polymorphism (T-RFLP) and quantitative PCR analyses targeting the methyl-coenzyme M reductase alpha subunit (mcrA) genes retrieved from three bioreactors, Methanomethylovorans and Methanosarcina were the dominant methanogens involved in the methanogenic degradation of TMAH in the bioreactors. Furthermore, batch experiments were conducted to evaluate mcrA messenger RNA (mRNA) expression during methanogenic TMAH degradation, and the results indicated that a higher level of TMAH favored mcrA mRNA expression by Methansarcina, while Methanomethylovorans could only express considerable amount of mcrA mRNA at a lower level of TMAH. These results suggest that Methansarcina is responsible for methanogenic TMAH degradation at higher TMAH concentrations, while Methanomethylovorans may be important at a lower TMAH condition.

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

  • Angelidaki I, Ahring BK (1993) Thermophilic anaerobic digestion of livestock waste: the effect of ammonia. Appl Microbiol Biotechnol 38:560–564

    Article  CAS  Google Scholar 

  • APHA (1995) Standard methods for the examination of water and wastewater, 19th edn. APHA American Public Health Association, Washington, DC

    Google Scholar 

  • Asakawa S, Sauer K, Liesack W, Thauer RK (1998) Tetramethylammonium: coenzyme M methyltransferase system from Methanococcoides sp. Arch Microbiol 170:220–226

    Article  CAS  PubMed  Google Scholar 

  • Chang KF, Yang SY, You HS, Pan JR (2008) Anaerobic treatment of tetramethylammonium hydroxide (TMAH) containing wastewater. IEEE Trans Semicond Manuf 21:486–491

    Article  Google Scholar 

  • Chaudhary PP, Brablcová L, Buriánková I, Rulík M (2013) Molecular diversity and tools for deciphering the methanogen community structure and diversity in freshwater sediments. Appl Microbiol Biotechnol 97:7553–7562

    Article  CAS  PubMed  Google Scholar 

  • Collins RE, Rocap G (2007) REPK: an analytical Web server to select restriction endonucleases for terminal restriction fragment length polymorphism analysis. Nucleic Acids Res 35:W58–W62

    Article  PubMed Central  PubMed  Google Scholar 

  • Deppenmeier U, Johann A, Hartsch T, Merkl R, Schmitz RA, Martinez-Arias R, Henne A, Wiezer A, Ba¨umer S, Jacobi C, Brüggemann H, Lienard T, Christmann A, Bo¨meke M, Steckel S, Bhattacharyya A, Lykidis A, Overbeek R, Klenk HP, Gunsalus RP, Fritz HJ, Gottschalk G (2002) The genome of Methanosarcina mazei: evidence for lateral gene transfer between bacteria and archaea. J Mol Microbiol Biotechnol 4:453–461

    CAS  PubMed  Google Scholar 

  • Ferry JG (1993) Methanogenesis, ecology, physiology, biochemistry and genetics. Springer, New York

    Google Scholar 

  • Ferry JG (1999) Enzymology of one-carbon metabolism in methanogenic pathways. FEMS Microbiol Rev 23:13–38

    Article  CAS  PubMed  Google Scholar 

  • Freitag TE, Prosser JI (2009) Correlation of methane production and functional gene transcriptional activity in a peat soil. Appl Environ Microbiol 75:6679–6687

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Galagan JE, Nusbaum C, Roy A, Endrizzi MG, Macdonald P, FitzHugh W, Calvo S, Engels R, Smirnov S, Atnoor D, Brown A, Allen N, Naylor J, Stange-Thomann N, DeArellano K, Johnson R, Linton L, Mc-Ewan P, McKernan K, Talamas J, Tirrell A, Ye W, Zimmer A, Barber RD, Cann I, Graham DE, Graham DA, Guss AM, Hedderich R, Ingram-Smith C, Kuettner HC, Krzycki JA, Leigh JA, Li W, Liu J, Mukhopadhyay B, Reeve JN, Smith K, Springer TA, Umayam LA, White O, White RH, Conway de Macario E, Ferry FG, Jarrell KF, Jing H, Macario AJ, Paulsen I, Pritchett M, Sowers KR, Swanson RV, Zinder SH, Lander E, Metcalf WW, Birren B (2002) The genome of Methanosarcina acetivorans reveals extensive metabolic and physiological diversity. Genome Res 12:532–542

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Hales BA, Edwards C, Ritchie DA, Hall G, Pickup RW, Saunders JR (1996) Isolation and identification of methanogen-specific DNA from blanket bog feat by PCR amplification and sequence analysis. Appl Environ Microbiol 62:668–675

    CAS  PubMed Central  PubMed  Google Scholar 

  • Hallam SJ, Girguis PR, Preston CM, Richardson PM, DeLong EF (2003) Identification of methyl coenzyme M reductase A (mcrA) genes associated with methane-oxidizing Archaea. Appl Environ Microbiol 69(9):5483–5491

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Hippe H, Caspari D, Fiebig K, Gottschalk G (1979) Utilization of trimethylamine and other N-methyl compounds for growth and methane formation by Methanosarcina barkeri. Proc Natl Acad Sci 76:494–498

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Hirano K, Okamura J, Taira T, Sano K, Toyoda A, Ikeda M (2001) An efficient treatment technique for TMAH wastewater by catalytic oxidation. IEEE Trans Semicond Manuf 14:202–206

    Article  Google Scholar 

  • Hu TH, Whang LM, Liu PWG, Hung YC, Chen HW, Lin LB, Chen CF, Chen SK, Hsu SF, Shen W, Fu R, Hsu R (2012) Biological treatment of TMAH (tetra-methyl ammonium hydroxide) in a full-scale TFT-LCD wastewater treatment plant. Bioresour Technol 113:303–310

    Article  CAS  PubMed  Google Scholar 

  • Jiang B, Parshina S, van Doesburg W, Lomans B, Stams A (2005) Methanomethylovorans thermophila sp. nov., a thermophilic, methylotrophic methanogen from an anaerobic reactor fed with methanol. Int J Syst Evol Microbiol 55:2465–2470

    Article  CAS  PubMed  Google Scholar 

  • Karakashev D, Batstone DJ, Angelidaki I (2005) Influence of environmental conditions on methanogenic compositions in anaerobic biogas reactors. Appl Environ Microbiol 71:331–338

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Karakashev D, Batstone DJ, Trably E, Angelidaki I (2006) Acetate oxidation is the dominant methanogenic pathway from acetate in the absence of Methanosaetaceae. Appl Environ Microbiol 72:5138–5141

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Konig H, Stetter K (1982) Isolation and characterization of Methanolobus tindarius sp. nov., a coccoid methanogen growing only on methanol and methylamines. Zentralbl Bakteriol Parasitenkd Infektionskr Hyg Abt 1:478–490

    Google Scholar 

  • Lei CN, Whang LM, Chen PC (2010) Biological treatment of thin-film transistor liquid crystal display (TFT-LCD) wastewater using aerobic and anoxic/oxic sequencing batch reactors. Chemosphere 81:57–64

    Article  CAS  PubMed  Google Scholar 

  • Liu Y, Boone DR, Sleat R, Mah RA (1985) Methanosarcina mazei LYC, a new methanogenic isolate which produces a disaggregating enzyme. Appl Environ Microbiol 49:608–613

    CAS  PubMed Central  PubMed  Google Scholar 

  • Lomans BP, Maas R, Luderer R, Op den Camp HJM, Pol A, van der Drift C, Vogels GD (1999) Isolation and characterization of Methanomethylovorans hollandica gen. nov., sp. nov., isolated from freshwater sediment, a methylotrophic methanogen able to grow on dimethyl sulfide and methanethiol. Appl Environ Microbiol 65:3641–3650

    CAS  PubMed Central  PubMed  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, Lüßmann 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 Central  PubMed  Google Scholar 

  • Lueders T, Friedrich MW (2003) Evaluation of PCR amplification bias by terminal restriction fragment length polymorphism analysis of small-subunit rRNA and mcrA genes by using defined template mixtures of methanogenic pure cultures and soil DNA extracts. Appl Environ Microbiol 69:320–326

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Lueders T, Chin KJ, Conrad R, Friedrich M (2001) Molecular analyses of methyl-coenzyme M reductase alpha-subunit (mcrA) genes in rice field soil and enrichment cultures reveal the methanogenic phenotype of a novel archaeal lineage. Environ Microbiol 3:194–204

    Article  CAS  PubMed  Google Scholar 

  • Luton PE, Wayne JM, Sharp RJ, Riley PW (2002) The mcrA gene as an alternative to 16S rRNA in the phylogenetic analysis of methanogen populations in landfill. Microbiology 148:3521–3530

    CAS  PubMed  Google Scholar 

  • Lyimo TJ, Pol A, Jetten MSM, den Camp HJMO (2009) Diversity of methanogenic archaea in a mangrove sediment and isolation of a new Methanococcoides strain. FEMS Microbiol Lett 291:247–253

    Article  CAS  PubMed  Google Scholar 

  • Maeder DL, Anderson I, Brettin TS, Bruce DC, Gilna P, Han CS, Lapidus A, Metcalf WW, Saunders E, Tapia R, Sowers KR (2006) The Methanosarcina barkeri genome: comparative analysis with Methanosarcina acetivorans and Methanosarcina mazei reveals extensive rearrangement within methanosarcinal genomes. J Bacteriol 188:7922–7931

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Mrklas O, Chu A, Lunn S (2003) Determination of ethanolamine, ethylene glycol and triethylene glycol by ion chromatography for laboratory and field biodegradation studies. J Environ Monitor 5:336–340

    Article  CAS  Google Scholar 

  • Patel G, Sprott G (1990) Methanosaeta concilii gen nov., sp. nov.,(Methanothrix concilii) and Methanosaeta thermoacetophila nom. rev., comb. nov. Int J Syst Bacteriol 40:79–82

    Article  Google Scholar 

  • Peck JE (2010) Multivariate analysis for community ecologists: step-by-step using PC-ORD. MjM Software Design, Oregon

    Google Scholar 

  • Pruesse E, Quast C, Knittel K, Fuchs B, Ludwig W, Peplies J, Glöckner FO (2007) SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucleic Acids Res 35:7188–7196

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Simankova MV, Kotsyurbenko OR, Lueders T, Nozhevnikova AN, Wagner B, Conrad R, Friedrich MW (2003) Isolation and characterization of new strains of methanogens from cold terrestrial habitats. Syst Appl Microbiol 26:312–318

    Article  PubMed  Google Scholar 

  • Singh N, Kendall MM, Liu Y, Boone DR (2005) Isolation and characterization of methylotrophic methanogens from anoxic marine sediments in Skan Bay, Alaska: description of Methanococcoides alaskense sp. nov., and emended description of Methanosarcina baltica. Int J Syst Bacteriol 55:2531–2538

    Article  CAS  Google Scholar 

  • Sowers KR, Ferry JG (1983) Isolation and characterization of a methylotrophic marine methanogen, Methanococcoides methylutens gen. nov., sp. nov. Appl Environ Microbiol 45:684–690

    CAS  PubMed Central  PubMed  Google Scholar 

  • Sowers KR, Baron SF, Ferry JG (1984) Methanosarcina acetivorans sp. nov., an acetotrophic methane-producing bacterium isolated from marine sediments. Appl Environ Microbiol 47:971–978

    CAS  PubMed Central  PubMed  Google Scholar 

  • Springer E, Sachs MS, Woese CR, Boone DR (1995) Partial gene sequences for the A subunit of methyl-coenzyme M reductase (mcrI) as a phylogenetic tool for the family Methanosarcinaceae. Int J Syst Bacteriol 45:554–559

    Article  CAS  PubMed  Google Scholar 

  • Steinberg LM, Regan JM (2008) Phylogenetic comparison of the methanogenic communities from an acidic, oligotrophic fen and an anaerobic digester treating municipal wastewater sludge. Appl Environ Microbiol 74:6663–6671

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Steinberg LM, Regan JM (2009) mcrA-Targeted real-time quantitative PCR method to examine methanogen communities. Appl Environ Microbiol 75(13):4435–4442

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Tanaka K (1994) Anaerobic degradation of tetramethylammonium by a newly isolated marine methanogen. J Ferment Bioeng 78:386–388

    Article  CAS  Google Scholar 

  • Urakami T, Araki H, Kobayashi H (1990) Isolation and identification of tetramethylammonium-biodegrading bacteria. J Ferment Bioeng 70:41–44

    Article  CAS  Google Scholar 

  • Watanabe T, Kimura M, Asakawa S (2009) Distinct members of a stable methanogenic archaeal community transcribe mcrA genes under flooded and drained conditions in Japanese paddy field soil. Soil Biol Biochem 41:276–285

    Article  CAS  Google Scholar 

  • Woese CR, Kandler O, Wheelis ML (1990) Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. Proc Natl Acad Sci 87:4576–4579

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Wu CL, Su SB, Chen JL, Lin HJ, Guo HR (2008) Mortality from dermal exposure to tetramethylammonium hydroxide. J Occup Health 50:99–102

    Article  CAS  PubMed  Google Scholar 

  • Yuan YL, Conrad R, Lu YH (2011) Transcriptional response of methanogen mcrA genes to oxygen exposure of rice field soil. Environ Microbiol Rep 3:320–328

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgments

The authors would like to acknowledge the financial support from the Bureau of Energy, Ministry of Economic Affairs Energy Technology Program for Academia under grant no. 102-D0613, the Ministry of Education of Taiwan under grant for the Top University Project to the National Cheng Kung University, and partially financial support from the Innolux Corporation.

Author information

Authors and Affiliations

  1. Department of Environmental Engineering, National Cheng Kung University, No. 1, University Road, Tainan, 701, Taiwan, Republic of China

    Liang-Ming Whang, Tai-Ho Hu, Yu-Ching Hung, Toshikazu Fukushima, Yi-Ju Wu & Shao-Hsiung Chang

  2. Sustainable Environment Research Laboratory (SERL), National Cheng Kung University, No. 1, University Road, Tainan, 701, Taiwan, Republic of China

    Liang-Ming Whang

  3. Research Center for Energy Technology and Strategy (RCETS), National Cheng Kung University, No. 1, University Road, Tainan, 701, Taiwan, Republic of China

    Liang-Ming Whang

  4. Department of Safety Health and Environmental Engineering, Chung Hwa University of Medical Technology, Tainan, Taiwan, Republic of China

    Pao-Wen Grace Liu

Authors
  1. Liang-Ming Whang
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Tai-Ho Hu
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Pao-Wen Grace Liu
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Yu-Ching Hung
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Toshikazu Fukushima
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Yi-Ju Wu
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Shao-Hsiung Chang
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Liang-Ming Whang.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Whang, LM., Hu, TH., Liu, PW.G. et al. Molecular analysis of methanogens involved in methanogenic degradation of tetramethylammonium hydroxide in full-scale bioreactors. Appl Microbiol Biotechnol 99, 1485–1497 (2015). https://doi.org/10.1007/s00253-014-6058-z

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00253-014-6058-z

Keywords

Search

Navigation