Skip to main content
Article thumbnail
Location of Repository

Molecular ecology of methanotrophs in a landfill cover soil

By Deepak Kumaresa


Landfills are a major anthropogenic source of methane and understanding the factors influencing the activity and diversity of methane oxidizing bacteria (methanotrophs) in landfill cover soil is critical to devise better landfill cover soil management strategies. A detailed study was carried out to investigate the effect of earthworms on soil methane oxidation potential and community structure of active methanotrophs in a landfill cover soil. Earthworms were found increase soil methane oxidation potential by 15% ± 7%. However, no substantial shifts in the community structure of active methanotrophs were observed. A Bacteroidetes-related bacterium was identified only in active bacterial community of earthworm-incubated landfill cover soil. However, its role in methane cycling is uncertain. In a subsequent study, a larger experimental system was used to simulate in situ landfill conditions and also to mimic the in situ environmental heterogeneity. A mRNA-based microarray analysis revealed that earthworm activity in landfill cover soil stimulates activity and diversity of Type I methanotrophs compared to Type II methanotrophs. \ud Understanding spatio-temporal distribution pattern of microorganisms and the factors influencing their distribution pattern are integral for a better understanding of microbial functions in ecosystems. A pmoA-based microarray analysis of methanotroph community structure in a landfill cover soil revealed a temporal shift in methanotroph populations across different seasons. In the case of spatial distribution, only minor differences in methanotroph community structure were observed with no recognizable patterns. Correlation analysis between soil abiotic parameters (total C, N, NH4 +, NO3 - and water content) and distribution of methanotrophs revealed a lack of conclusive evidence for any distinct correlation pattern between measured abiotic parameters and methanotroph community structure, suggesting that complex interactions of several physic-chemical parameters shape methanotroph diversity and activity in landfill cover soils. A study was designed to investigate the shift in functional diversity of methanotrophs when microniches created by soil aggregates are physically altered. mRNA-based analysis of the bacterial transcription activity revealed an effect of physical disruption on active methanotrophs. The result emphasized that a change in a particular microbial niche need not be accompanied by an immediate change to the bacterial functional diversity and it depends on the ability of the bacterial communities to respond to the perturbation and perform the ecosystem function. \ud DNA-SIP and mRNA based microarray techniques were compared for the assessment of active methanotroph community structure. Results from this study indicated that assessment of active methanotroph community structure by both the techniques were congruent. This suggested that the mRNA based microarray technique could be used to study active methanotroph community structure in situations where SIP experiments are not practical. However, both DNA-SIP and mRNA-microarray have their advantages and limitations and the selection of appropriate technique to assess active community structure depends on the nature of the study

Topics: QR
OAI identifier:

Suggested articles


  1. (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. doi
  2. (1992). Adsorption of DNA on clay minerals: protection against DNaseI and influence on gene transfer. doi
  3. (1987). An evaluation of the relative robustness of techniques for ecological ordination. doi
  4. (2008). Analysis of methanotrophic communities in landfill biofilters using diagnostic microarray. doi
  5. (1986). Applying metric and non8 doi
  6. (1995). Capacity for methane oxidation in landfill cover soils measured in laboratory-scale soil microcosms.
  7. (1998). Changing concentration, lifetime and climate forcing of atmospheric methane. doi
  8. (2003). Characterization of methanogenic and methanotrophic assemblages in landfill samples. doi
  9. (2003). Development and validation of a diagnostic microbial microarray for methanotrophs. doi
  10. (1997). Distribution of bacterioplankton in meromictic Lake Saelenvannet, as determined by denaturing gradient gel electrophoresis of PCR-amplified gene fragments coding for 16S rRNA.
  11. (2003). Diversity and activity of methanotrophic bacteria in different upland soils. doi
  12. (1995). Effect of CH4 concentrations and soil conditions on the induction of CH4 oxidation activity. doi
  13. (2008). Effect of earthworms on the community structure of active methanotrophic bacteria in a landfill cover soil. doi
  14. (2000). Effects of O2 and CH4 on presence and activity of the indigenous methanotrophic community in rice field soil. doi
  15. (1993). Emission of methane into the atmosphere from landfills in the former USSR. doi
  16. (2002). Estimating prokaryotic diversity and its limits. doi
  17. (1970). Exospores and cysts formed by methane-utilizing bacteria. doi
  18. (1993). Factors affecting competition between type I and type II methanotrophs in two-organism, continuousflow reactors. doi
  19. (2000). Geostatistical analysis of the distribution of NH4 + and NO2 --oxidizing bacteria and serotypes at the millimeter scale along a soil transect. doi
  20. (1995). Growth of methanotrophs in methane and oxygen counter gradients. doi
  21. (2007). Identification of active methanotrophs in a landfill cover soil through detection of expression of 16S rRNA and functional genes. doi
  22. (2002). In situ spatial patterns of soil bacterial populations, mapped at multiple scales, in an arable soil. doi
  23. (1993). Instability and decay of the primary structure of DNA. doi
  24. (2009). Mapping field-scale spatial patterns of size and activity of the denitrifier community. doi
  25. (2008). Metabolic aspects of aerobic obligate methanotrophy. doi
  26. (1993). Methane emission and methane oxidation in land-fill cover soil. doi
  27. (2008). Methane oxidation at 55 degrees C and pH 2 by a thermoacidophilic bacterium belonging to the Verrucomicrobia phylum. doi
  28. (2007). Methane oxidation by an extremely acidophilic bacterium of the phylum Verrucomicrobia. doi
  29. (1999). Methane oxidation in simulated landfill cover soil environments. doi
  30. (1999). Methanotroph diversity in landfill soil: isolation of novel type I and type II methanotrophs whose presence was suggested by culture-independent 16S ribosomal DNA analysis.
  31. (1996). Methanotrophic bacteria. doi
  32. (2007). Methanotrophy below p H1b yan e wVerrucomicrobia species. doi
  33. (2005). Methylocella species are facultatively methanotrophic. doi
  34. (2004). Microbial biogeography along an estuarine salinity gradient: combined influences of bacterial growth and residence time. doi
  35. (2008). Microbial biogeography: from taxonomy to traits. doi
  36. (2006). Microbial biogeography: putting microorganisms on the map. doi
  37. (2002). Microbial diversity and function in soil: from genes to ecosystems. doi
  38. (2004). Microbial oxidation of CH4 at different temperatures in landfill cover soils. doi
  39. (2001). Microbial population structures in soil particle size fractions of a long-term fertilizer field experiment. doi
  40. (2008). Molecular ecology techniques for the study of aerobic methanotrophs. doi
  41. (2006). mRNA-based parallel detection of active methanotroph populations by use of a diagnostic microarray. doi
  42. (2003). Multi-scale variation in spatial heterogeneity for microbial community structure in an eastern Virginia agricultural field. doi
  43. (2004). Nitrogen as a regulatory factor of methane oxidation in soils and sediments. doi
  44. (2004). Optimization of diagnostic microarray for application in analysing landfill methanotroph communities under different plant covers. doi
  45. (2001). Quantitative and qualitative microscale distribution of bacteria in soil. doi
  46. (2006). Rebuilding community ecology from functional traits. doi
  47. (2008). Selective stimulation of type I methanotrophs in a rice paddy soil by urea fertilization revealed by RNA-based stable isotope probing. doi
  48. (2001). Simultaneous recovery of RNA and DNA from soils and sediments. doi
  49. (2009). Society for Applied Microbiology and Blackwell Publishing Ltd, Environmental Microbiology Reportsmetric multidimensional scaling to ecological studies: some new results.
  50. (1996). Soft spots’ in the global methane budget. doi
  51. (2003). Spatial and temporal variability of bacterial 16S rRNA-based T-RFLP patterns derived from soil of two Wyoming grassland ecosystems. doi
  52. (1998). Spatial homogeneity of abundant bacterial 16S rRNA molecules in grassland soils. doi
  53. (2006). Spatial scaling of microbial biodiversity. doi
  54. (2004). Spatial structure in soil chemical and microbiological properties in an upland grassland. doi
  55. (2004). Stable isotope pulse-chasing and compound specific stable carbon isotope analysis of phospholipid fatty acids to assess methane oxidizing bacterial populations in landfill cover soils. doi
  56. (2000). Stimulation by ammonium-based fertilizers of methane oxidation in soil around rice roots.
  57. (2002). Stratification and seasonal stability of diverse bacterial communities in a Pinus merkusii (pine) forest soil in central Java, doi
  58. (1999). The distribution of microbial communities in anaerobic and aerobic zones of a shallow coastal plain aquifer. doi
  59. (2006). The diversity and biogeography of soil bacterial communities. doi

To submit an update or takedown request for this paper, please submit an Update/Correction/Removal Request.