Molecular ecology of methanotrophs in a landfill cover soil

Abstract

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. 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. 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