Skip to main content
SpringerLink
Log in

Effect of nutrient and selective inhibitor amendments on methane oxidation, nitrous oxide production, and key gene presence and expression in landfill cover soils: characterization of the role of methanotrophs, nitrifiers, and denitrifiers

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

Abstract

Methane and nitrous oxide are both potent greenhouse gasses, with global warming potentials approximately 25 and 298 times that of carbon dioxide. A matrix of soil microcosms was constructed with landfill cover soils collected from the King Highway Landfill in Kalamazoo, Michigan and exposed to geochemical parameters known to affect methane consumption by methanotrophs while also examining their impact on biogenic nitrous oxide production. It was found that relatively dry soils (5% moisture content) along with 15 mg NH +4 (kg soil)−1 and 0.1 mg phenylacetylene∙(kg soil)−1 provided the greatest stimulation of methane oxidation while minimizing nitrous oxide production. Microarray analyses of pmoA showed that the methanotrophic community structure was dominated by Type II organisms, but Type I genera were more evident with the addition of ammonia. When phenylacetylene was added in conjunction with ammonia, the methanotrophic community structure was more similar to that observed in the presence of no amendments. PCR analyses showed the presence of amoA from both ammonia-oxidizing bacteria and archaea, and that the presence of key genes associated with these cells was reduced with the addition of phenylacetylene. Messenger RNA analyses found transcripts of pmoA, but not of mmoX, nirK, norB, or amoA from either ammonia-oxidizing bacteria or archaea. Pure culture analyses showed that methanotrophs could produce significant amounts of nitrous oxide, particularly when expressing the particulate methane monooxygenase (pMMO). Collectively, these data suggest that methanotrophs expressing pMMO played a role in nitrous oxide production in these microcosms.

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

Similar content being viewed by others

References

  • Amaral JA, Knowles R (1995) Growth of methanotrophs in methane and oxygen counter gradients. FEMS Microbiol Lett 126:215–220

    CAS  Google Scholar 

  • Balasubramanian R, Rosenzweig AA (2008) Copper methanobactin: a molecule whose time has come. Curr Opin Chem Biol 12:1–5

    Google Scholar 

  • Barlaz MA, Green RB, Chanton JP, Goldsmith CD, Hater GR (2004) Evaluation of a biologically active cover for mitigation of landfill gas emissions. Environ Sci Technol 38:4891–4899

    CAS  PubMed  Google Scholar 

  • Bender M, Conrad R (1995) Effect of CH4 concentrations and soil conditions on the induction of CH4 oxidation activity. Soil Biol Biochem 27:1517–1527

    CAS  Google Scholar 

  • Bodelier PLE, Roslev P, Henckel T, Frenzel P (2000) Stimulation by ammonium-based fertilizers of methane oxidation in soil around rice plants. Nature 403:421–424

    CAS  PubMed  Google Scholar 

  • Bodrossy L, Stralis-Pavese N, Murrell JC, Radajewski S, Weilharter A, Sessitsch A (2003) Development and validation of a diagnostic microbial microarray for methanotrophs. Environ Microbiol 5:566–582

    CAS  PubMed  Google Scholar 

  • Boeckx P, Van Cleemput O (1996) Methane oxidation in a neutral cover soil: influence of moisture content, temperature, and nitrogen-turnover. J Environ Qual 25:178–183

    CAS  Google Scholar 

  • Boeckx P, Van Cleemput O, Villaralvo I (1996) Methane emission from a landfill and the methane oxidising capacity of its cover soil. Soil Biol Biochem 28:1397–1405

    CAS  Google Scholar 

  • Bogner JE, Spokas KA, Burton EA (1997) Kinetics of methane oxidation in cover soil: temporal variations, a whole-landfill oxidation experiment, and modeling of net CH4 emissions. Environ Sci Technol 31:2504–2514

    CAS  Google Scholar 

  • Braker G, Tiedje JM (2003) Nitric oxide reductases (norB) genes from pure cultures and environmental samples. Appl Environ Microbiol 69:3476–3483

    CAS  PubMed  PubMed Central  Google Scholar 

  • Braker G, Fesefeldt A, Witzel K-P (1998) Development of PCR primer systems for amplification of nitrite reductases genes (nirK and nirS) to detect denitrifying bacteria in environmental samples. Appl Environ Microbiol 64:3769–3775

    Google Scholar 

  • Brusseau GA, Tsien H-C, Hanson RS, Wackett LP (1990) Optimization of trichloroethylene oxidation by methanotrophs and the use of a colorimetric assay to detect soluble methane monooxygenase activity. Biodeg 1:19–29

    CAS  PubMed  Google Scholar 

  • Casciotti KL, Ward BB (2005) Phylogenetic analysis of nitric oxide reductases gene homologues from aerobic ammonia-oxidizing bacteria. FEMS Microb Ecol 52:197–205

    CAS  Google Scholar 

  • Cebron A, Bodrossy L, Chen Y, Singer AC, Thompson IP, Prosser JI, Murrell JC (2007) Identity of active methanotrophs in landfill cover soil as revealed by DNA-stable isotope probing. FEMS Microbiol Ecol 62:12–23

    CAS  PubMed  Google Scholar 

  • Chan SI, Yu SSF (2008) Controlled oxidation of hydrocarbons by the membrane-bound methane monooxygenase: a case for a tricopper cluster. Acc Chem Res 41:969–979

    CAS  PubMed  Google Scholar 

  • Chen M, Ma LQ (2001) Comparison of three aqua regia digestion methods for twenty Florida soils. Soil Sci Soc Am J 65:491–499

    CAS  Google Scholar 

  • Chen Y, Dumont MG, Cebron A, Murrell JC (2007) Identification of active methanotrophs in a landfill cover soil through detection of expression of 16S rRNA and functional genes. Environ Microbiol 9:2855–2869

    CAS  PubMed  Google Scholar 

  • Choi D-W, Kunz RC, Boyd ES, Semrau JD, Antholine WA, Han J-I et al (2003) The membrane-associated methane monooxygenase (pMMO) and pMMO-NADH:quinone oxidoreductase from Methylococcus capsulatus Bath. J Bacteriol 185:5755–5764

    CAS  PubMed  PubMed Central  Google Scholar 

  • Choi D-W, Antholine WE, Do YS, Semrau JD, Kisting CJ, Kunz RC et al (2005) Effect of methanobactin on activity and electron paramagnetic resonance spectra of the methane oxidation by the membrane-associated methane monooxygenase in Methylococcus capsulatus Bath. Microbiology 151:3417–3426

    CAS  PubMed  Google Scholar 

  • Choi D-W, Zea CJ, Do YS, Semrau JD, Antholine WA, Hargrove MS et al (2006) Spectral, kinetic and thermodynamic properties of Cu(I)- and Cu(II)-binding by methanobactin from Methylosinus trichosporium OB3b. Biochemistry 45:1142–1153

    Google Scholar 

  • Costello AM, Lidstrom ME (1999) Molecular characterization of functional and phylogenetic genes from natural populations of methanotrophs in lake sediments. Appl Environ Microbiol 65:5066–5074

    CAS  PubMed  PubMed Central  Google Scholar 

  • Coyne MS, Tiedje JM (1990) Induction of denitrifying enzymes in oxygen-limited Achromobacter cyclolastes continuous culture. FEMS Microbiol Ecol 73:263–270

    CAS  Google Scholar 

  • Czepiel PM, Mosher B, Crill PM, Hariss RC (1996) Quantifying the effect of oxidation on landfill emissions. J Geophys Res 101:16721–16729

    CAS  Google Scholar 

  • Dantata N, Touran A, Wang J (2005) An analysis of cost and duration for deconstruction and demolition of residential buildings in Massachusetts. Resour Conserv Recycl 44:1–15

    Google Scholar 

  • De Visscher A, Van Cleemput O (2003) Induction of enhanced CH4 oxidation in soils: NH +4 inhibition patterns. Soil Biol Biochem 35:907–913

    Google Scholar 

  • Dedysh SN, Liesack W, Khmelenina VN, Suzina NE, Trotsenko YA, Semrau JD, Bares AM, Panikov NS, Tiedje JM (2000) Methylocella palustris gen. nov., sp. nov., a new methane-oxidizing acidophilic bacterium from peat bogs, representing a novel subtype of serine-pathway methanotrophs. Intl J Syst Evol Microbiol 50:955–969

    CAS  Google Scholar 

  • DeVisscher A, Boeckx P, van Cleemput O (2007) Artificial methane sinks. In: Reay DS, Hewitt CN, Grace J (eds) Greenhouse gas sinks. Wallingford, Oxfordshire, pp 184–200

    Google Scholar 

  • El Masri AM, Smith JN, Williams RT (1958) Studies in detoxication, 73. The metabolism of alkylbenzenes: phenylacetylene and phenylethylene (styrene). Biochem J 68:199–204

    CAS  PubMed  Google Scholar 

  • Energy Information Administration (2008) Emission of greenhouse gases in the United States 2007. Office of Integrated Analysis and Forecasting, US Department of Energy, Washington DC 20585. Available at http://www.eia.doe.gov/oiaf/1605/ggrpt/pdf/0573(2007).pdf

  • Francis CA, Roberts KJ, Beman JM, Santoro AE, Oakley BB (2005) Ubiquity and diversity of ammonia-oxidizing archaea in water columns and sediments of the ocean. Proc Nat Acad Sci 102:14683–14688

    CAS  PubMed  PubMed Central  Google Scholar 

  • Hakemian AS, Kondapalli KC, Tesler J, Hoffman BM, Stemmler TL, Rosenzweig AC (2008) The metal centers of particulate methane monooxygenase from Methylosinus trichosporium OB3b. Biochemistry 47:6793–6801

    CAS  PubMed  Google Scholar 

  • Hallin S, Lindgren P-E (1999) PCR detection of genes encoding nitrite reductases in denitrifying bacteria. Appl Environ Microbiol 65:1652–1657

    CAS  PubMed  PubMed Central  Google Scholar 

  • Han JI, Semrau JD (2004) Quantification of gene expression in methanotrophs by competitive reverse transcription-polymerase chain reaction. Environ Microbiol 6:388–399

    CAS  PubMed  Google Scholar 

  • Hilger H, Barlaz M, Wollum A (2000) Landfill CH4 oxidation: response to vegetation, fertilization and liming. J Environ Qual 29:324–334

    CAS  Google Scholar 

  • Holmes AJ, Costello A, Lidstrom ME, Murrell JC (1995) Evidence that particulate methane monooxygenase and ammonia monooxygenase may be evolutionary related. FEMS Microbiol Lett 132:203–208

    CAS  PubMed  Google Scholar 

  • Hooper AB, Terry KR (1979) Hydroxylamine oxidoreductase of Nitrosomonas production of nitric oxide from hydroxylamine. Biochim Biophys Acta 571:12–20

    CAS  PubMed  Google Scholar 

  • Hou AX, Chen GX, Wang ZP, Van Cleemput O, Patrick WH (2000) Methane and nitrous oxide emissions from a rice field in relation to soil redox and microbiological processes. Soil Sci Am J 64:2180–2186

    CAS  Google Scholar 

  • Hutchens E, Radajewski S, Dumont MG, McDonald IR, Murrell JC (2004) Analysis of methanotrophic bacteria in Movile Cave by stable isotope probing. Environ Microbiol 6:111–120

    CAS  PubMed  Google Scholar 

  • IPCC (2007) Climate change 2007: synthesis report. Cambridge University Press, Cambridge

    Google Scholar 

  • Jiang Q-Q, Bakken LR (1999) Nitrous oxide production and methane oxidation by different ammonia-oxidizing bacteria. Appl Environ Microbiol 65:2679–2684

    CAS  PubMed  PubMed Central  Google Scholar 

  • Jones HA, Nedwell DB (1993) Methane emission and methane oxidation in land-fill cover soil. FEMS Microbiol Ecol 102:185–195

    CAS  Google Scholar 

  • Kightley D, Nedwell DB, Cooper M (1995) Capacity for methane oxidation in landfill cover soils measured in laboratory-scale soil microcosms. Appl Environ Microbiol 61:592–601

    CAS  PubMed  PubMed Central  Google Scholar 

  • Knapp WC, Fowle DA, Kulcycki E, Roberts JA, Graham DW (2007) Methane monooxygenase gene expression mediated by methanobactin in the presence of mineral copper sources. Proc Natl Acad Sci USA 104:12040–12045

    CAS  PubMed  PubMed Central  Google Scholar 

  • Krämer M, Baumgartner M, Bender M, Conrad R (1990) Consumption of NO by methanotrophic bacteria in pure culture and in soil. FEMS Microbiol Ecol 73:345–350

    Google Scholar 

  • Kreader CA (1996) Relief of amplification inhibition in PCR with bovine serum albumin or T4 gene 32 protein. Appl Environ Microbiol 62:1102–1106

    CAS  PubMed  PubMed Central  Google Scholar 

  • Kucera I (2006) Interference of chlorate and chlorite with nitrate reduction in resting cells of Paracoccus denitrificans. Microbiol-SGM 152:3529–3534

    CAS  Google Scholar 

  • Kulczycki E, Fowle DA, Knapp C, Graham DW, Roberts JA (2007) Methanobactin-promoted dissolution of Cu-substituted borsilicate glass. Geobiology 5:251–263

    CAS  Google Scholar 

  • Lee S-W, Keeney DR, Lim D-H, DiSpirito AA, Semrau JD (2006) Mixed pollutant degradation by Methylosinus trichosporium OB3b expressing either soluble or particulate methane monooxygenase: can the tortoise beat the hare? Appl Environ Microbiol 72:7503–7509

    CAS  PubMed  PubMed Central  Google Scholar 

  • Leiberman RL, Rosenzweig AC (2005) Crystal structure of a membrane-bound metalloenzyme that catalyzes the biological oxidation of methane. Nature 434:177–182

    Google Scholar 

  • Leininger S, Urich T, Schloter M, Schwark L, Qi J, Nicol GW et al (2006) Archaea predominate among ammonia-oxidizing prokaryotes in soils. Nature 442:806–809

    CAS  PubMed  Google Scholar 

  • Lontoh S, Semrau JD (1998) Trichloroethylene and methane oxidation by the particulate methane monooxygenase of Methylosinus trichosporium OB3b. Appl Environ Microbiol 64:1106–1114

    CAS  PubMed  PubMed Central  Google Scholar 

  • Lontoh S, DiSpirito AA, Krema CL, Whittaker MR, Hooper AB, Semrau JD (2000) Differential inhibition in vivo of ammonia monooxygenase, soluble methane monooxygenase and membrane-associated methane monooxygenase by phenylacetylene. Environ Microbiol 2:485–494

    CAS  PubMed  Google Scholar 

  • Majumdar D (2003) Methane and nitrous oxide emission from irrigated rice fields: proposed mitigation strategies. Curr Sci 84:1317–1326

    CAS  Google Scholar 

  • Martinho M, Choi DW, DiSpirito AA, Antholine WE, Semrau JD, Münck (2007) Mössbauer studies of the membrane-associated methane monooxygenase from Methylococcus capsulatus Bath: evidence or a diiron center. J Am Chem Soc 129:15783–15785

    CAS  PubMed  PubMed Central  Google Scholar 

  • McBride MB, Richards BK, Steenhuis T (2004) Bioavailability and crop uptake of trace elements in soil columns amended with sewage sludge products. Plant Soil 262:71–84

    CAS  Google Scholar 

  • Nishimura S, Sawamoto T, Akiyama H, Sudo S, Yagi K (2004) Methane and nitrous oxide emissions from a paddy field with Japanese conventional water management and fertilizer application. Global Biogeochem Cycles 18:2207–2216

    Google Scholar 

  • Poth M, Focht DD (1985) 15N kinetic analysis of N2O production by Nitrosomonas europaea: an examination of nitrifier denitrification. Appl Environ Microbiol 49:1134–1141

    CAS  PubMed  PubMed Central  Google Scholar 

  • Prior SD, Dalton H (1985) The effect of copper ions on the membrane content and methane monooxygenase activity in methanol grown cells of Methylococcus capsulatus (Bath). J Gen Microbiol 131:155–163

    CAS  Google Scholar 

  • Qian X, Koerner RM, Gray DH (2002) Geotechnical aspects of landfill design and construction. Prentice-Hall, Inc, Upper Saddle River

    Google Scholar 

  • Reay DS, Smith KA, Hewitt CN (2007) Methane: importance, source and sinks. In: Reay DS, Hewitt CN, Grace J (eds) Greenhouse gas sinks. Wallingford, Oxfordshire, pp 143–151

    Google Scholar 

  • Ren T, Roy R, Knowles R (2000) Production and consumption of nitric oxide by three methanotrophic bacteria. Appl Environ Microbiol 66:3891–3897

    CAS  PubMed  PubMed Central  Google Scholar 

  • Rinne J, Pihlatie M, Lohila A, Thum T, Aurela M, Tuovinen J-P, Laurila T, Vesala T (2005) Nitrous oxide emissions from a municipal landfill. Env Sci Technol 39:7790–7793

    CAS  Google Scholar 

  • Ritchie GA, Nicholas DJD (1972) Identification of the sources of nitrous oxide produced by oxidative and reductive processes in Nitrosomonas europaea. Biochem J 126:1181–1191

    CAS  PubMed  PubMed Central  Google Scholar 

  • Rotthauwe JH, Witzel KP, Liesack W (1997) The ammonia monooxygenase structural gene amoA as a functional marker, molecular fine scale analysis of natural ammonia oxidizing populations. Appl Environ Microbiol 63:4704–4712

    CAS  PubMed  PubMed Central  Google Scholar 

  • Rusmana I, Nedwell DB (2004) Use of chlorate as a selective inhibitor to distinguish membrane-bound nitrate reductases (Nar) and periplasmic nitrate reductases (Nap of dissimilative nitrate reducing bacteria in sediment. FEMS Micobiol Ecol 48:379–386

    CAS  Google Scholar 

  • Seghers D, Siciliano SD, Top EM, Verstraete W (2005) Combined effect of fertilizer and herbicide applications on the abundance, community structure and performance of the soil methanotrophic community. Soil Biol Biochem 37:187–193

    CAS  Google Scholar 

  • Shaw LJ, Nicol GW, Smith Z, Fear J, Prosser JI, Baggs EM (2006) Nitrosospira spp. can produce nitrous oxide via a nitrifier denitrification pathway. Environ Microbiol 8:214–222

    CAS  PubMed  Google Scholar 

  • Soil Survey Division Staff (1993) Soil survey manual. U.S. Department of Agriculture Handbook 18. U.S. Government Printing Office, Washington DC

    Google Scholar 

  • Stanley SH, Dalton H (1983) Copper stress underlies the fundamental change in intracellular location of methane mono-oxygenase in methane utilizing organisms: studies in batch and continuous cultures. Biotechnol Lett 5:487–492

    CAS  Google Scholar 

  • Stralis-Pavese N, Sessitsch S, Weilharter A, Reichenauer T, Riesing J, Csontos J et al (2004) Optimization of diagnostic microarray for application in analysing landfill methanotrophic communities under different plant covers. Environ Microbiol 6:347–363

    CAS  PubMed  Google Scholar 

  • Sutka RL, Ostrom NE, Ostrom PH, Gandhi H, Breznak JA (2003) Nitrogen isotopomer site preference of N2O produced by Nitrosomonas europaea and Methylococcus capsulatus Bath. Rapid Commun Mass Spectrom 17:738–745

    CAS  PubMed  Google Scholar 

  • Sutka RL, Ostrom NE, Ostrom PH, Breznak JA, Gandhi H, Pitt AJ, Li F (2006) Distinguishing nitrous oxide production from nitrification and denitrification on the basis of isotopomer abundances. Appl Environ Microbiol 72:638–644

    CAS  PubMed  PubMed Central  Google Scholar 

  • US EPA (1996) Standards of performance for new stationary sources and guidelines for control of existing sources: municipal solid waste landfills. Code of Federal Regulations, Title 40, Sections 9, 51, 52, and 60; Fed Regist 61 (49)

  • Whalen SC, Reeburgh WS (1990) Consumption of atmospheric methane by tundra soils. Nature 346:160–162

    CAS  Google Scholar 

  • Whalen SC, Reeburgh WS, Sandbeck KA (1990) Rapid methane oxidation in a landfill cover soil. Appl Environ Microbiol 56:3405–3411

    CAS  PubMed  PubMed Central  Google Scholar 

  • Whittenbury RK, Philips KD, Wilkinson JF (1970) Enrichment, isolation, and characterization of methane-utilizing bacteria. J Gen Microbiol 61:205–218

    CAS  PubMed  Google Scholar 

  • Yoshinari T (1985) Nitrite and nitrous oxide production by Methylosinus trichosporium. Can J Microbiol 31:139–144

    CAS  PubMed  Google Scholar 

  • Zahn JA, DiSpirito AA (1996) Membrane-associated methane monooxygenase from Methylococcus capsulatus Bath. J Bacteriol 178:1018–1029

    CAS  PubMed  PubMed Central  Google Scholar 

Download references

Acknowledgements

We thank George Wells and Craig Criddle for providing an amoA amplicon from ammonia-oxidizing archaea. Support from the Department of Energy (DE-FC26-05NT42431) to JDS is also gratefully acknowledged.

Author information

Author notes

  1. Sung-Woo Lee

    Present address: Oregon Graduate Institute, Department of Environmental and Biomolecular Systems, Oregon Health and Sciences University, 20000 NW Walker Road, Beaverton, OR, 97006, USA

Authors and Affiliations

  1. Department of Civil and Environmental Engineering, The University of Michigan, 1351 Beal Avenue, Ann Arbor, MI, 48109-2125, USA

    Sung-Woo Lee, Jeongdae Im & Jeremy D. Semrau

  2. Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, 50011-3211, USA

    Alan A. DiSpirito

  3. Department of Biotechnology, ARC Seibersdorf Research GmbH, A-2444, Seibersdorf, Austria

    Levente Bodrossy

  4. Department of Chemistry, Western Michigan University, 1903 W. Michigan, Kalamazoo, MI, 49008-5413, USA

    Michael J. Barcelona

Authors
  1. Sung-Woo Lee
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Jeongdae Im
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Alan A. DiSpirito
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Levente Bodrossy
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Michael J. Barcelona
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Jeremy D. Semrau
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Jeremy D. Semrau.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Lee, SW., Im, J., DiSpirito, A.A. et al. Effect of nutrient and selective inhibitor amendments on methane oxidation, nitrous oxide production, and key gene presence and expression in landfill cover soils: characterization of the role of methanotrophs, nitrifiers, and denitrifiers. Appl Microbiol Biotechnol 85, 389–403 (2009). https://doi.org/10.1007/s00253-009-2238-7

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00253-009-2238-7

Keywords

Search

Navigation