Methane source strength and energy flow shape methanotrophic communities in oxygen-methane counter-gradients

Environmental Microbiology Reports

Volumn 4, Issue 2, 2012, Pages 203-208

  Krause, Sascha ^a,b   Lüke, Claudia ^a   Frenzel, Peter ^a  

^a MAX PLANCK INSTITUTE FOR TERRESTRIAL MICROBIOLOGY   (Germany)

^b NETHERLANDS INSTITUTE OF ECOLOGY NIOO KNAW   (Netherlands)

Author keywords

[No Author keywords available]

Indexed keywords

METHYLOBACTER;

EID: 84858588445     PISSN: None     EISSN: 17582229     Source Type: Journal    
DOI: 10.1111/j.1758-2229.2011.00322.x     Document Type: Article

References (43)

1. Belova, S.E., Baani, M., Suzina, N.E., Bodelier, P.L.E., Liesack, W., and Dedysh, S.N. (2011) Acetate utilization as a survival strategy of peat-inhabiting Methylocystis spp. Environ Microbiol Rep 3: 36-46.
2. Bodelier, P.L.E. (2011) Interactions between nitrogenous fertilizers and methane cycling in wetland and upland soils. Curr Opin Environ Sutainability 3: 379-388.
3. + oxidation in the rice rhizosphere using new methods for discrimination. Appl Environ Microbiol 65: 1826-1833.
4. Bodelier, P.L.E., and Laanbroek, H.J. (2004) Nitrogen as a regulatory factor of methane oxidation in soils and sediments. FEMS Microbiol Ecol 47: 265-277.
5. Bodelier, P.L.E., Roslev, P., Henckel, T., and Frenzel, P. (2000) Stimulation by ammonium-based fertilizers of methane oxidation in soil around rice roots. Nature 403: 421-424.
6. Bodrossy, L., Stralis-Pavese, N., Murrell, J.C., Radajewski, S., Weilharter, A., and Sessitsch, A. (2003) Development and validation of a diagnostic microbial microarray for methanotrophs. Environ Microbiol 5: 566-582.
7. Bodrossy, L., Stralis-Pavese, N., Konrad-Koszler, M., Weilharter, A., Reichenauer, T.G., Schofer, D., and Sessitsch, A. (2006) mRNA-based parallel detection of active methanotroph populations by use of a diagnostic microarray. Appl Environ Microbiol 72: 1672-1676.
8. Costello, A.M., and Lidstrom, M.E. (1999) Molecular characterization of functional and phylogenetic genes from natural populations of methanotrophs in lake sediments. Appl Environ Microbiol 65: 5066-5074.
9. Dedysh, S.N., Liesack, W., Khmelenina, V.N., Suzina, N.E., Trotsenko, Y.A., Semrau, J.D., etal. (2000) Methylocella palustris gen. nov., sp. nov., a new methane-oxidizing acidophilic bacterium from peat bogs, representing a novel subtype of serine-pathway methanotrophs. Int J Syst Evol Microbiol 50: 955-969.
10. Degelmann, D.M., Borken, W., Drake, H.L., and Kolb, S. (2010) Different atmospheric methane-oxidizing communities in European Beech and Norway spruce soils. Appl Environ Microbiol 76: 3228-3235.
11. Dufrene, M., and Legendre, P. (1997) Species assemblages and indicator species: the need for a flexible asymmetrical approach. Ecol Monogr 67: 345-366.
12. Eller, G., Krüger, M., and Frenzel, P. (2005) Comparing field and microcosm experiments: a case study on methano- and methylotrophic bacteria in paddy soil. FEMS Microbiol Ecol 51: 279-291.
13. Frenzel, P., Bosse, U., and Janssen, P.H. (1999) Rice roots and methanogenesis in a paddy soil: ferric iron as an alternative electron acceptor in the rooted soil. Soil Biol Biochem 31: 421-430.
14. 4 oxidation: the activity of bacteria, their distribution and the microenvironment. Soil Biol Biochem 30: 1903-1916.
15. Graham, D.W., Chaudhary, J.A., Hanson, R.S., and Arnold, R.G. (1993) Factors affecting competition between type I and type II methanotrophs in two-organism, continuous-flow reactors. Microb Ecol 25: 1-17.
16. Ho, A., Lüke, C., and Frenzel, P. (2011) Recovery of methanotrophs from disturbance: population dynamics, evenness, and functioning. ISME J 5: 750-758.
17. Holmes, A.J., Costello, A., Lidstrom, M.E., and Murrell, J.C. (1995) Evidence that particulate methane monooxygenase and ammonia monooxygenase may be evolutionarily related. FEMS Microbiol Lett 132: 203-208.
18. Intergovernmental Panel on Climate Change (2007) Climate Change 2007: The Physical Science Basis. Summary for Policymakers. Contribution of Working Group I to the Fourth Assessment Report of the Intergovernmental Panel on Climate Change. Summary for Policymakers Formally Approved at the 10th Session of Working Group I of the IPCC. Geneva, Switzerland: IPCC Secretariat.
19. Knief, C., and Dunfield, P.F. (2005) Response and adaptation of different methanotrophic bacteria to low methane mixing ratios. Environ Microbiol 7: 1307-1131.
20. Krause, S., Lüke, C., and Frenzel, P. (2010) Succession of methanotrophs in oxygen-methane counter-gradients of flooded rice paddies. ISME J 4: 1603-1607.
21. Krüger, M., Frenzel, P., and Conrad, R. (2001) Microbial processes influencing methane emission from rice fields. Glob Chang Biol 7: 49-63.
22. Lennon, J.T., and Jones, S.E. (2011) Microbial seed banks: the ecological and evolutionary implications of dormancy. Nat Rev Micro 9: 119-130.
23. Lüke, C., and Frenzel, P. (2011) The potential of pmoA amplicon pyrosequencing for methanotroph diversity studies. Appl Environ Microbiol 77: 6305-6309.
24. Lüke, C., Krause, S., Cavigioli, S., Greppi, D., Lupotto, E., and Frenzel, P. (2010) Biogeography of wetland rice methanotrophs. Environ Microbiol 12: 862-872.
25. McDonald, I.R., and Murrell, J.C. (1997) The particulate methane monooxygenase gene pmoA and its use as a functional gene probe for methanotrophs. FEMS Microbiol Lett 156: 205-210.
26. Miller, L.G., and Oremland, R.S. (1998) Difluoromethane, a new and improved inhibitor of methanotrophy. Appl Environ Microbiol 64: 4357-4362.
27. Mohanty, S.R., Bodelier, P.L.E., Floris, V., and Conrad, R. (2006) Differential effects of nitrogenous fertilizers on methane-consuming microbes in rice field and forest soils. Appl Environ Microbiol 72: 1346-1354.
28. Murase, J., and Frenzel, P. (2007) A methane-driven microbial food web in a wetland rice soil. Environ Microbiol 9: 3025-3034.
29. Murase, J., and Frenzel, P. (2008) Selective grazing of methanotrophs by protozoa in a rice field soil. FEMS Microbiol Ecol 65: 408-414.
30. Nazaries, L., Tate, K.R., Ross, D.J., Singh, J., Dando, J., Saggar, S., etal. (2011) Response of methanotrophic communities to afforestation and reforestation in New Zealand. ISME J 5: 1832-1836.
31. Noll, M., Frenzel, P., and Conrad, R. (2008) Selective stimulation of type I methanotrophs in a rice paddy soil by urea fertilization revealed by RNA-based stable isotope probing. FEMS Microbiol Ecol 65: 125-132.
32. Nyerges, G., and Stein, L.Y. (2009) Ammonia cometabolism and product inhibition vary considerably among species of methanotrophic bacteria. FEMS Microbiol Lett 297: 131-136.
33. Oksanen, J., Blanchet, F.G., Kindt, R., Legendre, P., O'Hara, R.G., Simpson, G.L., etal. (2010) vegan: Community Ecology Package, ver. 1.17-3. URL
34. Priemé, A., Christensen, S., Dobbie, K.E., and Smith, K.A. (1997) Slow increase in rate of methane oxidation in soils with time following land use change from arable agriculture to woodland. Atmos Environ 29: 1269-1273.
35. R Development Core Team (2010) R: a language and environment for statistical computing, ver. 2.11.1. URL ISBN 3-900051-07-0.
36. Rahman, M.T., Crombie, A., Chen, Y., Stralis-Pavese, N., Bodrossy, L., Meir, P., etal. (2011) Environmental distribution and abundance of the facultative methanotroph Methylocella. ISME J 5: 1061-1066.
37. Semrau, J.D., DiSpirito, A.A., and Yoon, S. (2010) Methanotrophs and copper. FEMS Microbiol Rev 34: 496-531.
38. Semrau, J.D., DiSpirito, A.A., and Vuilleumier, S. (2011) Facultative methanotrophy: false leads, true results, and suggestions for future research. FEMS Microbiol Lett 323: 1-12.
39. Stralis-Pavese, N., Abell, G.C.J., Sessitsch, A., and Bodrossy, L. (2011) Analysis of methanotroph community composition using a pmoA-based microbial diagnostic microarray. Nat Protoc 6: 609-624.
40. Trotsenko, Y.A., and Murrell, J.C. (2008) Metabolic aspects of aerobic obligate methanotrophy. Adv Appl Microbiol 63: 183-229.
41. Vorobev, A.V., Baani, M., Doronina, N.V., Brady, A.L., Liesack, W., Dunfield, P.F., and Dedysh, S.N. (2010) Methyloferula stellata gen. nov., sp. nov., an acidophilic, obligately methanotrophic bacterium possessing only a soluble methane monooxygenase. Int J Syst Evol Microbol 61: 2456-2463.
42. Whittenbury, R., Davies, S.L., and Davey, J.F. (1970a) Exospores and cysts formed by methane-utilizing bacteria. J Gen Microbiol 61: 219-226.
43. Whittenbury, R., Philips, K.C., and Wilkinson, J.F. (1970b) Enrichment, isolation, and some properties of methane-utilizing bacteria. J Gen Microbiol 61: 205-218.