Effect of earthworms on the community structure of active methanotrophic bacteria in a landfill cover soil

Abstract

In the United Kingdom, landfills are the primary anthropogenic source of methane emissions. Methanotrophic bacteria present in landfill biocovers can significantly reduce methane emissions via their capacity to oxidize up to 100% of the methane produced. Several biotic and abiotic parameters regulate methane oxidation in soil, such as oxygen, moisture, methane concentration and temperature. Earthworm-mediated bioturbation has been linked to an increase in methanotrophy in a landfill biocover soil (AC Singer et al., unpublished), but the mechanism of this trophic interaction remains unclear. The aims of this study were to determine the composition of the active methanotroph community and to investigate the interactions between earthworms and bacteria in this landfill biocover soil where the methane oxidation activity was significantly increased by the earthworms. Soil microcosms were incubated with 13 C-CH 4 and with or without earthworms. DNA and RNA were extracted to characterize the soil bacterial communities, with a particular emphasis on methanotroph populations, using phylogenetic (16S ribosomal RNA) and functional methane monooxygenase (pmoA and mmoX) gene probes, coupled with denaturing gradient-gel electrophoresis, clone libraries and pmoA microarray analyses. Stable isotope probing (SIP) using 13 C-CH 4 substrate allowed us to link microbial function with identity of bacteria via selective recovery of 'heavy' 13 C-labelled DNA or RNA and to assess the effect of earthworms on the active methanotroph populations. Both types I and II methanotrophs actively oxidized methane in the landfill soil studied. Results suggested that the earthworm-mediated increase in methane oxidation rate in the landfill soil was more likely to be due to the stimulation of bacterial growth or activity than to substantial shifts in the methanotroph community structure. A Bacteroidetes-related bacterium was identified only in the active bacterial community of earthworm-incubated soil but its capacity to actually oxidize methane has to be proven.

Environmental distribution and abundance of the facultative methanotroph Methylocella

“…Detection of a certain level of non-target sequences by primers designed to target a particular bacterial genus has earlier been observed (Fierer et al, 2005) , and by detecting the mmoX copies from the spiked soil (Figure 1b). Ufton landfill cover soil was chosen for the spiking study because we did not detect any Methylocella-related 16S rRNA genes from this soil, which supports the earlier observation of Héry et al (2008), who also did not detect Methylocella spp. from this location.…”

Impact of Peat Mining and Restoration on Methane Turnover Potential and Methane-Cycling Microorganisms in a Northern Bog

“…Structural genes appear to correlate well to the activity catalyzed by the respective encoded enzymes, as has been shown for methanogenesis and methane oxidation (41)(42)(43)(44), as well as other microbe-mediated processes, e.g., 2-methyl-4-chlorophenoxyacetic acid, an herbicide, degradation (45), and N-cycling processes (46). Determining the gene abundances before and after incubation, we relate the magnitude change in the mcrA and pmoA genes to the total methane produced and oxidized, respectively (Fig.…”

Diversity and methane oxidation of active epibiotic methanotrophs on live Shinkaia crosnieri

“…Furthermore, the detection of 16S rRNA gene sequences closely related to gammaproteobacterial type I methanotrophs and the 16S rRNA-targeting FISH analyses do not ensure the presence of methanotrophic activity. An adequate level of certainty requires the combined use of nanoscale secondary ion mass spectrometry or stable isotope probing to specify the cellular level of uptake of labeled CH 4 (Hery et al, 2008;Watsuji et al, 2012).…”