Methylocella palustris gen. nov., sp. nov., a new methane-oxidizing acidophilic bacterium from peat bogs, representing a novel subtype of serine-pathway methanotrophs.

Dedysh, Svetlana N.; Liesack, Werner; Khmelenina, V. N.; Сузина, Н. Е.; Trotsenko, Yu. A.; Semrau, Jeremy D.; Bares, Amy M.; Panikov, N. S.; Tiedje, James M.

doi:10.1099/00207713-50-3-955

Cited by 370 publications

(361 citation statements)

References 46 publications

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“…The MOB community of peat bogs or acidic forest soils, for example, was restricted to members of type II MOB [39,40,43]. Besides, all known acidophilic isolates belong to the genera Methylocapsa and Methylocella, both type II MOB [9][10][11][12]. The MOB community capable of the consumption of atmospheric methane was studied in different forest and grassland soils and was found to exclude members of the type I group.…”

Section: Discussionmentioning

confidence: 99%

“…The microbial conversion of methane into carbon dioxide was estimated to account for 30% to 90% in flooded rice fields [1,2], for 13% to 38% of the methane produced in temperate and subarctic peat soils [13], and for 15% to more than 90% of the diffusive methane flux in wetlands [36,47]. The group of MOB comprises the three families Methylococcaceae, Methylocystaceae, and Beijerinckiaceae [5,[9][10][11][12]. The only exception is Crenothrix polyspora, a filamentous, sheathed microorganism recently discovered to be methanotrophic [52].…”

Section: Introductionmentioning

confidence: 99%

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Diversity of Aerobic Methanotrophic Bacteria in a Permafrost Active Layer Soil of the Lena Delta, Siberia

et al. 2008

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With this study, we present first data on the diversity of aerobic methanotrophic bacteria (MOB) in an Arctic permafrost active layer soil of the Lena Delta, Siberia. Applying denaturing gradient gel electrophoresis and cloning of 16S ribosomal ribonucleic acid (rRNA) and pmoA gene fragments of active layer samples, we found a general restriction of the methanotrophic diversity to sequences closely related to the genera Methylobacter and Methylosarcina, both type I MOB. In contrast, we revealed a distinct species-level diversity. Based on phylogenetic analysis of the 16S rRNA gene, two new clusters of MOB specific for the permafrost active layer soil of this study were found. In total, 8 out of 13 operational taxonomic units detected belong to these clusters. Members of these clusters were closely related to Methylobacter psychrophilus and Methylobacter tundripaludum, both isolated from Arctic environments. A dominance of MOB closely related to M. psychrophilus and M. tundripaludum was confirmed by an additional pmoA gene analysis. We used diversity indices such as the Shannon diversity index or the Chao1 richness estimator in order to compare the MOB community near the surface and near the permafrost table. We determined a similar diversity of the MOB community in both depths and suggest that it is not influenced by the extreme physical and geochemical gradients in the active layer.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Diversity of Aerobic Methanotrophic Bacteria in a Permafrost Active Layer Soil of the Lena Delta, Siberia

et al. 2008

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“…The key enzyme of all MOB is methane monooxygenase (MMO), and the overwhelming majority of cultivated MOB possess a membranebound MMO (particulate MMO). Only the genera Methylocella and Methyloferula lack this enzyme and instead have a soluble MMO (sMMO) (Dedysh et al, 2000;Dedysh, 2009;Vorobev et al, 2011). The pmoA gene, which encodes the b-subunit of particulate MMO, is an excellent functional marker for studying MOB in most environments (McDonald and Murrell, 1997;Dumont and Murrell, 2005;McDonald et al, 2008).…”

Section: Introductionmentioning

confidence: 99%

One millimetre makes the difference: high-resolution analysis of methane-oxidizing bacteria and their specific activity at the oxic–anoxic interface in a flooded paddy soil

et al. 2012

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Aerobic methane-oxidizing bacteria (MOB) use a restricted substrate range, yet >30 species-equivalent operational taxonomical units (OTUs) are found in one paddy soil. How these OTUs physically share their microhabitat is unknown. Here we highly resolved the vertical distribution of MOB and their activity. Using microcosms and cryosectioning, we sub-sampled the top 3-mm of a water-saturated soil at near in situ conditions in 100-μm steps. We assessed the community structure and activity using the particulate methane monooxygenase gene pmoA as a functional and phylogenetic marker by terminal restriction fragment length polymorphism (t-RFLP), a pmoA-specific diagnostic microarray, and cloning and sequencing. pmoA genes and transcripts were quantified using competitive reverse transcriptase PCR combined with t-RFLP. Only a subset of the methanotroph community was active. Oxygen microprofiles showed that 89% of total respiration was confined to a 0.67-mm-thick zone immediately above the oxic–anoxic interface, most probably driven by methane oxidation. In this zone, a Methylobacter-affiliated OTU was highly active with up to 18 pmoA transcripts per cell and seemed to be adapted to oxygen and methane concentrations in the micromolar range. Analysis of transcripts with a pmoA-specific microarray found a Methylosarcina-affiliated OTU associated with the surface zone. High oxygen but only nanomolar methane concentrations at the surface suggested an adaptation of this OTU to oligotrophic conditions. No transcripts of type II methanotrophs (Methylosinus, Methylocystis) were found, which indicated that this group was represented by resting stages only. Hence, different OTUs within a single guild shared the same microenvironment and exploited different niches.

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“…These are distributed among Gammaproteobacteria (type I methanotrophs), Alphaproteobacteria (type II methanotrophs) (reviewed in Trotsenko and Murrell, 2008), filamentous methane oxidizers (Stoecker et al, 2006;Vigliotta et al, 2007) and Verrucomicrobia (Dunfield et al, 2007;Pol et al, 2007;Islam et al, 2008). Methanotrophs oxidize methane to methanol by the enzyme methane monooxygenase (MMO), present either as the particulate form (pMMO) in all characterized methanotrophs (except in the genus Methylocella (Dedysh et al, 2000)) or as the soluble form (sMMO) in some methanotrophs (Trotsenko and Murrell, 2008). Methanol dehydrogenase (MDH) catalyzes the conversion of methanol to formaldehyde in methylotrophs Murrell, 2008, Chistoserdova et al, 2009).…”

Section: Introductionmentioning

confidence: 99%

Active methylotrophs in the sediments of Lonar Lake, a saline and alkaline ecosystem formed by meteor impact

et al. 2010

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Lonar Lake is a unique saline and alkaline ecosystem formed by meteor impact in the Deccan basalts in India around 52 000 years ago. To investigate the role of methylotrophy in the cycling of carbon in this unusual environment, stable-isotope probing (SIP) was carried out using the onecarbon compounds methane, methanol and methylamine. Denaturing gradient gel electrophoresis fingerprinting analyses performed with heavy 13 C-labelled DNA retrieved from sediment microcosms confirmed the enrichment and labelling of active methylotrophic communities. Clone libraries were constructed using PCR primers targeting 16S rRNA genes and functional genes. Methylomicrobium, Methylophaga and Bacillus spp. were identified as the predominant active methylotrophs in methane, methanol and methylamine SIP microcosms, respectively. Absence of mauA gene amplification in the methylamine SIP heavy fraction also indicated that methylamine metabolism in Lonar Lake sediments may not be mediated by the methylamine dehydrogenase enzyme pathway. Many gene sequences retrieved in this study were not affiliated with extant methanotrophs or methylotrophs. These sequences may represent hitherto uncharacterized novel methylotrophs or heterotrophic organisms that may have been cross-feeding on methylotrophic metabolites or biomass. This study represents an essential first step towards understanding the relevance of methylotrophy in the soda lake sediments of an unusual impact crater structure.

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Methylocella palustris gen. nov., sp. nov., a new methane-oxidizing acidophilic bacterium from peat bogs, representing a novel subtype of serine-pathway methanotrophs.

Cited by 370 publications

References 46 publications

Diversity of Aerobic Methanotrophic Bacteria in a Permafrost Active Layer Soil of the Lena Delta, Siberia

Diversity of Aerobic Methanotrophic Bacteria in a Permafrost Active Layer Soil of the Lena Delta, Siberia

One millimetre makes the difference: high-resolution analysis of methane-oxidizing bacteria and their specific activity at the oxic–anoxic interface in a flooded paddy soil

Active methylotrophs in the sediments of Lonar Lake, a saline and alkaline ecosystem formed by meteor impact

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