Publikationsserver der Universitätsbibliothek Marburg

Titel:Response and resilience of methanotrophs to disturbances
Autor:Ho, Adrian Kah Wye
Weitere Beteiligte: Frenzel, Peter (Prof. Dr.)
Veröffentlicht:2011
URI:https://archiv.ub.uni-marburg.de/diss/z2011/0047
DOI: https://doi.org/10.17192/z2011.0047
URN: urn:nbn:de:hebis:04-z2011-00472
DDC: Biowissenschaften, Biologie
Titel (trans.):Reaktion und Widerstandsfähigkeit methanotropher Bakterien gegenüber Störungen
Publikationsdatum:2011-01-20
Lizenz:https://rightsstatements.org/vocab/InC-NC/1.0/

Dokument

Schlagwörter:
pmoA, Biodiversity, Methan, Methanotrophs, Paddy soil, Biodiversität, pmoA, Reisfeldboden, Methanotrophe Bakterien, Ecosystem functioning

Summary:
Methanotrophic bacteria are the only known biological sink for the greenhouse gas methane. Therefore, methanotrophs play a key function in carbon cycling, an important biogeochemical process that affects global climate change. Yet, little is known of their vulnerability and resilience to disturbances. Driven by the gap of knowledge, this PhD thesis is a seminal study focusing on the recovery of methanotrophs from disturbances with respect to population dynamics, diversity and functioning. Two model disturbances were tested; disturbance-induced mortality and heat shock. While the former model disturbance represents a non-selective form of disturbance, the heat shock treatment may select for sub-populations of thermo-tolerant methanotrophs. Overall, methanotrophs are shown to be remarkably resilient to induced disturbances, compensating and even over-compensating for methane uptake during recovery. Type II methanotrophs, known to be present in high abundance as resting cells, appear to become more important during disturbances. Furthermore, the establishment and subsequent development of the methanotrophic community and activity were studied along a rice paddy chronosequence. With the influx of anthropogenic influences once a rice paddy is formed, the methanotrophic community structure is anticipated to undergo a dramatic change which in turn, may affect the activity. It appears that the young and ancient rice paddies do not show clear divergence, suggesting that the methane oxidizing community was soon established after a rice paddy is formed. However, the selection of the best adapted sub-population needs time. Accordingly, long term rice agriculture allows for higher methane uptake, and may select for a methanotroph sub-population that remains active. The predominant methanotrophs found in the Chinese rice paddies are type II, mainly Methylocystis species, and type Ib (RPC-1). However, type Ib seems to be the active dominant sub-population. This and previous studies suggest specific adaptation of type Ib to rice paddy environments. Interestingly, novel sequences phylogenetically grouped between pmoA and amoA were detected. Overall, paddy soil methanotrophs are not only able to recover from disturbances, but are apparently showing specific adaptation to rice paddy environments, demonstrating their resilience in face of perturbation.

Bibliographie / References

  1. Dörr, N., Glaser, B. and Kolb, S. (2010) Methanotrophic communities in Brazilian ferralsols from naturally forested, afforested, and agricultural sites. Appl Environ Microbiol 76: 1307-1310.
  2. Trotsenko, Y.A. and Murrell, J.C. (2008) Metabolic aspects of aerobic obligate methanotrophy. Adv Appl Microbiol 63: 183-229.
  3. 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.
  4. Shrestha, M., Abraham, W.R., Shrestha, P.M., Noll, M. and Conrad, R. (2008) Activity and composition of methanotrophic bacterial communities in planted rice soil studied by flux measurements, analyses of pmoA gene and stable isotope probing of phospholipid fatty acids. Environ Microbiol 10: 400-412.
  5. 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.
  6. Conrad, R. (2009) The global methane cycle: recent advances in understanding the microbial processes involved. Environ Microbiol Reports 1: 285-292.
  7. 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.
  8. Holmes, A.J., Costello, A., Lindstrom, M.E., and Murrell, J.C. (1995) Evidence that particulate methane monooxygenase and ammonia monooxygenase may be evolutionarily related. FEMS Microbiol Letters 132: 203-208.
  9. Prieme, 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.
  10. Jia Z., Kikuchi, K., Watanabe, T., Asakawa, S. and Kimura, M. (2007) Molecular identification of methane oxidizing bacteria in a Japanese rice field soil. Biol Fertil Soils 44: 121-130.
  11. Lüke, C., Krause, S., Cavigiolo, S., Greppi, D., Lupotto, E. and Frenzel, P. (2010) Biogeography pf wetland rice methanotrophs. Environ Microbiol 12: 862-872.
  12. Gelwicks, J.T., Risatti, J.B. and Hayes, J.M. (1994) Carbon isotope effects associated with acetoclastic methanogenesis. Appl Environ Microbiol 60: 467-472.
  13. Eller, G., Krüger, M. and Frenzel, P. (2005) Comparing field and microcosm experiments: a case study on methano-and methylo-trophic bacteria in paddy soil. FEMS Microbiol Ecol 51: 279-291.
  14. Miller, L.G., Sasson, E.M. and Oremland, R.S. (1998) Difluromethane, a new and improved inhibitor of methanotrophy. Appl Environ Microbiol 64: 4357-4362.
  15. Hoffmann, T., Horz, H.P., Kemnitz, D. and Conrad, R. (2002) Diversity of the particulate methane monooxygenase gene in methanotrophic samples from different rice field soils in China and the Philippines. System Appl Microbiol 25: 267-274.
  16. Krüger, M. and Frenzel, P. (2003) Effects of N-fertilization on CH 4 oxidation and production, and consequences for CH 4 emissions from microcosms and rice fields. Global Change Biol 9: 773-784.
  17. Neue, H.U. (1997) Fluxes of methane from rice fields and potential for mitigation. Soil Use Management 13: 258-267.
  18. Steudler, P.A., Bowden, R.D., Mellilo, J.M. and Aber, J.D. (1989) Influence of nitrogen fertilization on methane uptake in temperate forest soil. Nature 341: 314-316.
  19. Bosse, U. and Frenzel, P. (1998) Methane emissions from rice microcosms: The balance of production, accumulation and oxidation. Biogeochem 41: 199-214.
  20. Dedysh, S.N., Liesack, W., Khmelenina, V.N., Suzina, N.E., Trotsenko, Y.A., Semrau, J.D., Bares, A.M., Panikov, N.S. and Tiedje, J.M. (2000) Methylocella palustris gen. nov., sp. nov., a new methane-oxidizing acidophilic bacterium from peat bogs, representing a novel subtype of serine-pathway methanotrophs. IJSEM 50: 955-969.
  21. Epstein, S.S. (2009) Microbial awakenings. Nature 457: 1083.
  22. Liesack, W., Schnell, S. and Revsbech, N.P. (2000) Microbiology of flooded rice paddies. FEMS Microbiol Rev 24: 625-645.
  23. Lüke, C. (2009) Molecular ecology and biogeography of methanotrophic bacteria in wetland rice fields. PhD thesis, Marburg Universitat, Germany.
  24. Frenzel, P., Rothfuss, F. and Conrad, R. (1992) Oxygen profiles and methane turnover in a flooded rice microcosm. Biol Fertil Soils 14: 84-89.
  25. Macalady, J.L., McMillan, A.M.S., Dickens, A.F., Tyler, S.C. and Scow, K.M. (2002) Population dynamics of type I and II methanotrophic bacteria in rice soils. Environ Microbiol 4: 148-157.
  26. Kolb, S., Knief, C., Stubner, S. and Conrad, R. (2003) Quantitative detection of methanotrophs in soil by novel pmoA-targeted real-time PCR assays. Appl Environ Microbiol 69: 2423-2429.
  27. Ho, A., Lüke, C. and Frenzel, P. (2010) Recovery of methanotrophs from disturbance: population dynamics, evenness, and functioning. ISME J. Accepted.
  28. Krause, S., Luke, C. and Frenzel, P. (2009) Spatial heterogeneity of methanotrophs: a geostatistical analysis of pmoA-based T-RFLP patterns in a paddy soil. Environ Microbiol Reports 1: 393-397.
  29. Krause, S., Lüke, C. and Frenzel, P. (2010) Succession of methanotrophs in oxygen-methane counter-gradients of flooded rice paddies. ISME J: in press.
  30. Kajan, R. and Frenzel, P. (1999) The effect of chironomid larvae on production, oxidation and fluxes of methane in a flooded rice soil. FEMS Microbiology Ecology 28: 121-129.
  31. Bowman, J. (2000) The methanotrophs – the families Methylococcaceae and Methylocystaceae. In The Prokaryotes. Dworkin, M. (ed). New York: Springer.
  32. Ludwig, W., Strunk, O., Westram, R., Richter, L., Meier, H.,Yadhukumar, et al. (2004) ARB: a software environment for sequence data. Nucleic acids Res 32: 1363-1371.
  33. Chen, Y., Dumont, M.G., Cebron, A. and Murrell, J.C. (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.
  34. Chen, Y., Dumont, M.G., McNamara, N.P., Chamberlain, P.M., Bodrossy, L., Stralis-Pavese, N. and Murrell, J.C. (2008) Diversity of the active methanotrophic community in acidic peatlands as assessed by mRNA and SIP-PLFA analyses. Environ Microbiol 10: 446- 459.
  35. Luke, C., Krause, S., Cavigiolo, S., Greppi, D., Lupotto, E. And Frenzel, P. (2010) Biogeography of wetland rice methanotrophs. Environ Microbiol 12: 862-872.
  36. Bourne, D.G., McDonald, I.R. and Murrell, C. (2001) Comparison of pmoA primer sets as tools for investigating methanotroph diversity in three Danish soils. Appl Environ Microbiol 67: 3802-3809.
  37. Bodrossy, L., Stralis-Pavese, N., Murrell, J.C., Radajewski, S., Weiharter, A. and Sessitsch, A. (2003) Development and validation of a diagnostic microbial microarray for methanotrophs. Environ Microbiol 5: 566-582.
  38. Lueders, T. and Friedrich, M.W. (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.
  39. Murase, J., Noll, M. and Frenzel, P. (2006) Impact of protists on the activity and structure of the bacterial community in a rice field soil. Appl Environ Microbiol 72: 5436-5444.
  40. Islam, T., Jensen, S., Reigstad, L.J., Larsen, O. and Birkeland, N.K. (2008) Methane oxidation at 55°C and pH 2 by a thermoacidophilic bacterium belonging to the Verrucomicrobia phylum. PNAS 105: 300-304.
  41. Holmes, A.J., Roslev, P., McDonald, I.R., Iversen, N., Henriksen, K. and Murrell, C.J. (1999) Characterization of methanotrophic bacterial populations in soils showing atmospheric methane uptake. Appl Environ Microbiol 65: 3312-3318.
  42. Eller, G. and Frenzel, P. (2001) Changes in activity and community structure of methane- oxidizing bacteria over the growth period of rice. Appl Environ Microbiol 67: 2395-2403.
  43. Horz, H.P., Yimga, M.T. and Liesack, W. (2001) Detection of methanotroph diversity on roots of submerged rice plants by molecular retrieval of pmoA, mmoX, mxaF, and 16S rRNA and ribosomal DNA, including pmoA-based terminal restriction fragment length polymorphism profiling. Appl Environ Microbiol 67: 4177-4185.
  44. Cheng , Y.Q., Yang, L.Z., Cao, Z.H., Ci, E. and Yin, S. (2009) Chronosequential changes of selected pedogenic properties in paddy soils as compared with non-paddy soils. Geoderma 151: 31-41.
  45. Kolb, K., Knief, C., Dunfield, P.F. and Conrad, R. (2005) Abundance and activity of uncultured methanotrophic bacteria involved in the consumption of atmospheric methane in two forest soils. Environ Microbiol 7: 1150-1161.
  46. Bodelier, P.L.E., Gillisen, M-J.B., Hordijk, K., Damste, J.S.S., Rijpstra, W.I.C. Geenevasen, J.A. and Dunfield, P.F. (2009) A reanalysis of phospholipid fatty acids as ecological biomarkers for methanotrophic bacteria. ISME J 3: 606-617.
  47. 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.


* Das Dokument ist im Internet frei zugänglich - Hinweise zu den Nutzungsrechten