Potential of
            <i>pmoA</i>
            Amplicon Pyrosequencing for Methanotroph Diversity Studies

Lüke, Claudia; Frenzel, Peter

doi:10.1128/aem.05355-11

Cited by 132 publications

(113 citation statements)

References 30 publications

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“…Two of the 59 pmoA OTUs made up 96.8 % of all sequences, while all other OTUs individually represented ≤ 1 % of the pmoA sequences. The most abundant OTU (71.0 % of all sequences) clustered with two uncultured isolates from methane seeps (NCBI accession: HQ738559, EU444875) in the deep sea-3/OPU3 subgroup of γ -Proteobacteria Type I MOB (Hansman et al, 2017;Knief, 2015;Lüke and Frenzel, 2011). The second most abundant (25.8 %) OTU was related to Methyloprofundus sedimentii, another Type I MOB.…”

Section: Particulate Methane Monooxygenase (Pmoa) Sequencesmentioning

confidence: 99%

“…De novo chimera filtration was run with the UCHIME (Edgar et al, 2011) wrapper in mothur. A similarity of 93 % between pmoA sequences was defined to match the 97 % cutoff as species definition for the 16S gene (Lüke and Frenzel, 2011). PmoA OTUs were built at a maximal distance of 7 % between the furthest neighbors to maximize resolution between OTUs due to the short read length and limited number of unique sequences (Table S1 in the Supplement).…”

Section: Particulate Methane Monooxygenase: Pmoamentioning

confidence: 99%

“…In the first step, methane is oxidized to methanol catalyzed by the enzyme methane monooxygenase. Since methane monooxygenase is characteristic of nearly all aerobic MOB (Knief, 2015), pmoA, the gene encoding for a subunit of the membrane-bound particulate methane monooxygenase, has been used as a specific molecular marker for detection and characterization of aerobic MOB (Knief, 2015;Lüke and Frenzel, 2011;reviewed by McDonald et al, 2008;Tavormina et al, 2008). Methanol is further metabolized to formaldehyde, from which it is either mineralized to carbon dioxide (CO 2 ) or assimilated into organic compounds and finally biomass (reviewed by Hanson and Hanson, 1996; reviewed by Strong et al, 2015).…”

Section: Introductionmentioning

confidence: 99%

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Methane-oxidizing seawater microbial communities from an Arctic shelf

et al. 2018

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Abstract. Marine microbial communities can consume dissolved methane before it can escape to the atmosphere and contribute to global warming. Seawater over the shallow Arctic shelf is characterized by excess methane compared to atmospheric equilibrium. This methane originates in sediment, permafrost, and hydrate. Particularly high concentrations are found beneath sea ice. We studied the structure and methane oxidation potential of the microbial communities from seawater collected close to Utqiagvik, Alaska, in April 2016. The in situ methane concentrations were 16.3 ± 7.2 nmol L −1 , approximately 4.8 times oversaturated relative to atmospheric equilibrium. The group of methaneoxidizing bacteria (MOB) in the natural seawater and incubated seawater was > 97 % dominated by Methylococcales (γ -Proteobacteria). Incubations of seawater under a range of methane concentrations led to loss of diversity in the bacterial community. The abundance of MOB was low with maximal fractions of 2.5 % at 200 times elevated methane concentration, while sequence reads of non-MOB methylotrophs were 4 times more abundant than MOB in most incubations. The abundances of MOB as well as non-MOB methylotroph sequences correlated tightly with the rate constant (k ox ) for methane oxidation, indicating that non-MOB methylotrophs might be coupled to MOB and involved in community methane oxidation. In sea ice, where methane concentrations of 82 ± 35.8 nmol kg −1 were found, Methylobacterium (α-Proteobacteria) was the dominant MOB with a relative abundance of 80 %. Total MOB abundances were very low in sea ice, with maximal fractions found at the icesnow interface (0.1 %), while non-MOB methylotrophs were present in abundances similar to natural seawater communities. The dissimilarities in MOB taxa, methane concentrations, and stable isotope ratios between the sea ice and water column point toward different methane dynamics in the two environments.

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Section: Particulate Methane Monooxygenase (Pmoa) Sequencesmentioning

confidence: 99%

Section: Particulate Methane Monooxygenase: Pmoamentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Methane-oxidizing seawater microbial communities from an Arctic shelf

et al. 2018

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“…Next to this, the special C1 metabolism distinguishes MOB from the activity of other bacteria, which in combination with the possession of unique PLFAs (Bodelier et al, 2009) facilitates the use of stable isotope labeling approaches (Boschker et al, 1998;Bodelier et al, 2012) to capture the active MOB in the environment. The molecular detection of MOB is facilitated by the use of a functional marker gene (particulate methane monooxygenase (pmoA)) that is strongly linked to the phylogeny of aerobic proteobacterial MOB (Holmes et al, 1995;Kolb et al, 2003;Lü ke and Frenzel, 2011). The phylogeny of the methaneoxidizing guild has been changed substantially in the last decade.…”

Section: Introductionmentioning

confidence: 99%

Microbial minorities modulate methane consumption through niche partitioning

et al. 2013

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Microbes catalyze all major geochemical cycles on earth. However, the role of microbial traits and community composition in biogeochemical cycles is still poorly understood mainly due to the inability to assess the community members that are actually performing biogeochemical conversions in complex environmental samples. Here we applied a polyphasic approach to assess the role of microbial community composition in modulating methane emission from a riparian floodplain. We show that the dynamics and intensity of methane consumption in riparian wetlands coincide with relative abundance and activity of specific subgroups of methane-oxidizing bacteria (MOB), which can be considered as a minor component of the microbial community in this ecosystem. Microarray-based community composition analyses demonstrated linear relationships of MOB diversity parameters and in vitro methane consumption. Incubations using intact cores in combination with stable isotope labeling of lipids and proteins corroborated the correlative evidence from in vitro incubations demonstrating c-proteobacterial MOB subgroups to be responsible for methane oxidation. The results obtained within the riparian flooding gradient collectively demonstrate that niche partitioning of MOB within a community comprised of a very limited amount of active species modulates methane consumption and emission from this wetland. The implications of the results obtained for biodiversity-ecosystem functioning are discussed with special reference to the role of spatial and temporal heterogeneity and functional redundancy.

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“…Moreover, sample sequencing costs tend to decrease through the application of new sequencing technologies, which are more efficient, and with higher competition between companies that provide such services 70 . Next-Generation Sequencing (NGS) methods, such as pyrosequencing, Ion Torrent, Illumina and SOLiD Systems, bring a large-scale information about the diversity of microorganisms, starting a new path in microbial ecology 71 . The challenge today is how to interpret that amount of results and information generated by these new technologies 70 .…”

Section: Techniques For the Identification Of Functional Groupsmentioning

confidence: 99%

Functional Genes of Microorganisms, Comprehending the Dynamics of Agricultural Ecosystems

Reali

Júnior

Meile

et al. 2017

Braz. arch. biol. technol.

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The microbial composition of different types,in ecosystems (including agro-ecosystems), has been investigated in a rapidly growing number of studies in the past few years. The importance of microorganisms, regarding the maintenance and stability of nutrients in agroecosystems, is a key to maintain the sustainability of a crop. Molecular tools to study microbial communities are possible through many methods such as RISA, DGGE, TGGE, clone libraries, T-RFLP, RAPD, SSCP and more recently NGS (Next-Generation Sequencing). DGGE is widely employed to characterize the diversity and the community dynamics of microorganisms in the environment

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Potential of pmoA Amplicon Pyrosequencing for Methanotroph Diversity Studies

Cited by 132 publications

References 30 publications

Methane-oxidizing seawater microbial communities from an Arctic shelf

Methane-oxidizing seawater microbial communities from an Arctic shelf

Microbial minorities modulate methane consumption through niche partitioning

Functional Genes of Microorganisms, Comprehending the Dynamics of Agricultural Ecosystems

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