Regulation of methane oxidation in the facultative methanotroph <i>Methylocella silvestris</i> BL2

Theisen, Andreas R.; Ali, M. Hanif; Radajewski, Stefan; Dumont, Marc G.; Dunfield, Peter F.; McDonald, Ian R.; Dedysh, Svetlana N.; Míguez, Carlos B.; Murrell, J. Colin

doi:10.1111/j.1365-2958.2005.04861.x

Cited by 134 publications

(95 citation statements)

References 40 publications

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“…Since pMMO is present in all known methanotrophs with the exception of Methylocella (Dedysh et al, 2000;Theisen et al, 2005) and the phylogeny of pmoA is congruent with 16S rRNA phylogeny (Kolb et al, 2003), pmoA is the most frequent target in molecular ecology studies of methanotrophs (see Dumont and Murrell, 2005 for a review). Recently, a pmoA microarray has been developed by Bodrossy and colleagues, which has proved to be particularly suitable for characterizing the diversity within methanotroph communities (Bodrossy et al, 2003(Bodrossy et al, , 2006Stralis-Pavese et al, 2004).…”

Section: Introductionmentioning

confidence: 99%

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

et al. 2007

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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bioturbation has been linked to an increase in methanotrophy in a landfill biocover soil (AC Singer et al., unpublished), but the mechanism of this trophic interaction remains unclear.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.

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Section: Introductionmentioning

confidence: 99%

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

et al. 2007

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“…are aerobic facultative methanotrophs (Alphaproteobacteria), with three validated species, M. palustris, M. silvestris and M. tundrae, isolated from acidic soils (Dunfield et al, 2003;Dedysh et al, 2000Dedysh et al, , 2004. M. silvestris BL2, which can grow on a variety of multicarbon substrates (Dedysh et al, 2005;Theisen et al, 2005), oxidizes methane using the soluble methane monooxygenase encoded by the operon mmoXYBZDC. Methylocella spp.…”

Section: Introductionmentioning

confidence: 99%

Environmental distribution and abundance of the facultative methanotroph Methylocella

et al. 2010

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Methylocella spp. are facultative methanotrophs, which are able to grow not only on methane but also on multicarbon substrates such as acetate, pyruvate or malate. Methylocella spp. were previously thought to be restricted to acidic soils such as peatlands, in which they may have a key role in methane oxidation. There is little information on the abundance and distribution of Methylocella spp. in the environment. New primers were designed, and a real-time quantitative PCR method was developed and validated targeting Methylocella mmoX (encoding the a-subunit of the soluble methane monooxygenase) that allowed the quantification of Methylocella spp. in environmental samples. We also developed and validated specific PCR assays, which target 16S rRNA genes of known Methylocella spp. These were used to investigate the distribution of Methylocella spp. in a variety of environmental samples. It was revealed that Methylocella species are widely distributed in nature and not restricted to acidic environments.

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“…Type IIa was used for the primary pmoA sequences of the Methylocystaceae . Type IIb was used to group all other Type II-related (i.e., Alphaproteobacteria ) sequences, including those from the Beijerinckiaceae (Theisen et al, 2005; Dunfield et al, 2010; Vorobev et al, 2011) and the alternate pMMO2 identified in some Methylocystis species (Dunfield et al, 2002; Baani and Liesack, 2008). …”

Section: Pmoa Taxonomymentioning

confidence: 99%

Classification of pmoA amplicon pyrosequences using BLAST and the lowest common ancestor method in MEGAN

et al. 2014

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The classification of high-throughput sequencing data of protein-encoding genes is not as well established as for 16S rRNA. The objective of this work was to develop a simple and accurate method of classifying large datasets of pmoA sequences, a common marker for methanotrophic bacteria. A taxonomic system for pmoA was developed based on a phylogenetic analysis of available sequences. The taxonomy incorporates the known diversity of pmoA present in public databases, including both sequences from cultivated and uncultivated organisms. Representative sequences from closely related genes, such as those encoding the bacterial ammonia monooxygenase, were also included in the pmoA taxonomy. In total, 53 low-level taxa (genus-level) are included. Using previously published datasets of high-throughput pmoA amplicon sequence data, we tested two approaches for classifying pmoA: a naïve Bayesian classifier and BLAST. Classification of pmoA sequences based on BLAST analyses was performed using the lowest common ancestor (LCA) algorithm in MEGAN, a software program commonly used for the analysis of metagenomic data. Both the naïve Bayesian and BLAST methods were able to classify pmoA sequences and provided similar classifications; however, the naïve Bayesian classifier was prone to misclassifying contaminant sequences present in the datasets. Another advantage of the BLAST/LCA method was that it provided a user-interpretable output and enabled novelty detection at various levels, from highly divergent pmoA sequences to genus-level novelty.

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Regulation of methane oxidation in the facultative methanotroph Methylocella silvestris BL2

Cited by 134 publications

References 40 publications

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

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

Environmental distribution and abundance of the facultative methanotroph Methylocella

Classification of pmoA amplicon pyrosequences using BLAST and the lowest common ancestor method in MEGAN

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