Draft Genome Sequence of Uncultured Upland Soil Cluster
            <i>Gammaproteobacteria</i>
            Gives Molecular Insights into High-Affinity Methanotrophy

Edwards, Collin R.; Onstott, Tullis C.; Miller, Jennifer M.; Wiggins, Jessica B.; We, Wang; Lee, Charles K.; Cary, S. Craig; Pointing, Stephen B.; Lau, Maggie C. Y.

doi:10.1128/genomea.00047-17

Cited by 24 publications

(40 citation statements)

References 16 publications

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“…We also found the presence of the specific 16S rRNA gene sequence related to the upland soil cluster gamma (USCγ) in a large number of the same cave datasets. USCγ was just very recently identified to belong to the Chromatiales , based on a draft genome (Edwards et al ., ).…”

Section: Resultsmentioning

confidence: 97%

“…We also found the presence of the specific 16S rRNA gene sequence related to the upland soil cluster gamma (USCg) in a large number of the same cave datasets. USCg was just very recently identified to belong to the Chromatiales, based on a draft genome (Edwards et al, 2017). All of these findings strongly suggest a potential unrecognized role of these previously unnoticed environments in the biological sink for atmospheric methane and might lead to a reassessment of methane sinks around the globe.…”

Section: First Environmental Survey Of Usca Methanotrophs Based On 16mentioning

confidence: 95%

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Unravelling the Identity, Metabolic Potential and Global Biogeography of the Atmospheric Methane‐Oxidizing Upland Soil Cluster α

Pratscher

Vollmers

Wiegand

et al. 2018

Environmental Microbiology

110

102

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Summary Understanding of global methane sources and sinks is a prerequisite for the design of strategies to counteract global warming. Microbial methane oxidation in soils represents the largest biological sink for atmospheric methane. However, still very little is known about the identity, metabolic properties and distribution of the microbial group proposed to be responsible for most of this uptake, the uncultivated upland soil cluster α (USCα). Here, we reconstructed a draft genome of USCα from a combination of targeted cell sorting and metagenomes from forest soil, providing the first insights into its metabolic potential and environmental adaptation strategies. The 16S rRNA gene sequence recovered was distinctive and suggests this crucial group as a new genus within the Beijerinckiaceae, close to Methylocapsa. Application of a fluorescently labelled suicide substrate for the particulate methane monooxygenase enzyme (pMMO) coupled to 16S rRNA fluorescence in situ hybridisation (FISH) allowed for the first time a direct link of the high‐affinity activity of methane oxidation to USCα cells in situ. Analysis of the global biogeography of this group further revealed its presence in previously unrecognized habitats, such as subterranean and volcanic biofilm environments, indicating a potential role of these environments in the biological sink for atmospheric methane.

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Section: Resultsmentioning

confidence: 97%

Section: First Environmental Survey Of Usca Methanotrophs Based On 16mentioning

confidence: 95%

Unravelling the Identity, Metabolic Potential and Global Biogeography of the Atmospheric Methane‐Oxidizing Upland Soil Cluster α

Pratscher

Vollmers

Wiegand

et al. 2018

Environmental Microbiology

110

102

View full text Add to dashboard Cite

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“…B42 genome from deep-sea hydrothermal vents ( 12 ), the OPU3 genome from marine oxygen minimum zones ( 10 ), Crenothrix sp. D3 genome from lacustrine waters ( 11 ), and Upland Soil Cluster γ from Antarctic cryosols ( 31 ). Although Methylococcales species have been cultivated for decades, genomes reconstructed from metagenomes continue to illuminate the methanotroph genome diversity present across terrestrial and marine ecosystems.…”

Section: Resultsmentioning

confidence: 99%

Members of the Genus Methylobacter Are Inferred To Account for the Majority of Aerobic Methane Oxidation in Oxic Soils from a Freshwater Wetland

Smith

Angle

Solden

et al. 2018

mBio

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Here we used soil metagenomics and metatranscriptomics to uncover novel members within the genus Methylobacter. We denote these closely related genomes as members of the lineage OWC Methylobacter. Despite the incredibly high microbial diversity in soils, here we present findings that unexpectedly showed that methane cycling was primarily mediated by a single genus for both methane production (“Candidatus Methanothrix paradoxum”) and methane consumption (OWC Methylobacter). Metatranscriptomic analyses revealed that decreased methanotrophic activity rather than increased methanogenic activity possibly contributed to the greater methane emissions that we had previously observed in summer months, findings important for biogeochemical methane models. Although members of this Methylococcales order have been cultivated for decades, multi-omic approaches continue to illuminate the methanotroph phylogenetic and metabolic diversity harbored in terrestrial and marine ecosystems.

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“…Notably, both groups have also been observed in arctic upland soils (28). During the last years, information on their distribution, abundance, and activity was supplemented with first insights into their genomic repertoire as obtained from metagenomics (25, 29–31), but no complete genome sequence of a USC member has yet been reported.…”

mentioning

confidence: 99%

Widespread soil bacterium that oxidizes atmospheric methane

Tveit

Hestnes

Robinson

et al. 2019

Proc. Natl. Acad. Sci. U.S.A.

181

177

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The global atmospheric level of methane (CH4), the second most important greenhouse gas, is currently increasing by ∼10 million tons per year. Microbial oxidation in unsaturated soils is the only known biological process that removes CH4from the atmosphere, but so far, bacteria that can grow on atmospheric CH4have eluded all cultivation efforts. In this study, we have isolated a pure culture of a bacterium, strain MG08 that grows on air at atmospheric concentrations of CH4[1.86 parts per million volume (p.p.m.v.)]. This organism, namedMethylocapsa gorgona, is globally distributed in soils and closely related to uncultured members of the upland soil cluster α. CH4oxidation experiments and13C-single cell isotope analyses demonstrated that it oxidizes atmospheric CH4aerobically and assimilates carbon from both CH4and CO2. Its estimated specific affinity for CH4(a0s) is the highest for any cultivated methanotroph. However, growth on ambient air was also confirmed forMethylocapsa acidiphilaandMethylocapsa aurea, close relatives with a lower specific affinity for CH4, suggesting that the ability to utilize atmospheric CH4for growth is more widespread than previously believed. The closed genome ofM. gorgonaMG08 encodes a single particulate methane monooxygenase, the serine cycle for assimilation of carbon from CH4and CO2, and CO2fixation via the recently postulated reductive glycine pathway. It also fixes dinitrogen and expresses the genes for a high-affinity hydrogenase and carbon monoxide dehydrogenase, suggesting that atmospheric CH4oxidizers harvest additional energy from oxidation of the atmospheric trace gases carbon monoxide (0.2 p.p.m.v.) and hydrogen (0.5 p.p.m.v.).

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Draft Genome Sequence of Uncultured Upland Soil Cluster Gammaproteobacteria Gives Molecular Insights into High-Affinity Methanotrophy

Cited by 24 publications

References 16 publications

Unravelling the Identity, Metabolic Potential and Global Biogeography of the Atmospheric Methane‐Oxidizing Upland Soil Cluster α

Unravelling the Identity, Metabolic Potential and Global Biogeography of the Atmospheric Methane‐Oxidizing Upland Soil Cluster α

Members of the Genus Methylobacter Are Inferred To Account for the Majority of Aerobic Methane Oxidation in Oxic Soils from a Freshwater Wetland

Widespread soil bacterium that oxidizes atmospheric methane

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