Discovery of a novel methanogen prevalent in thawing permafrost

Mondav, Rhiannon; Woodcroft, Ben J.; Kim, Eun Hae; McCalley, C. K.; Hodgkins, S. B.; Crill, Patrick; Chanton, Jeffrey P.; Hurst, Gregory B.; VerBerkmoes, Nathan C.; Saleska, S. R.; Hugenholtz, Philip; Rich, V. I.; Tyson, Gene W.

doi:10.1038/ncomms4212

Cited by 181 publications

(208 citation statements)

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“…-Omics studies showed that many of these processes are highly expressed and active when permafrost thaws (Hultman et al 2015). In contrast, at high elevations, oxygenation of deep soils promotes aerobic metabolism and abundance clearly are not uniform between sites (Hultman et al 2015, Mackelprang et al 2011, Mondav et al 2014, Rivkina et al 2007). …”

Section: Figurementioning

confidence: 99%

“…These studies show that communities may utilize a highly diverse and complex set of biochemical processes involved in carbon processing, organic matter decomposition, methane generation and oxidation, and nitrogen cycling (Hultman et al 2015, Lipson et al 2013, Mackelprang et al 2011, Mondav et al 2014, Yergeau et al 2010 (Figure 1).…”

Section: Application Of Multi-omics Strategies To Permafrost Environmmentioning

confidence: 99%

“…Mondav et al (2014) combined metagenomics and focused proteomic data to characterize the importance of a dominant methanogen in methane production in thawing permafrost. Tveit et al (2015) combined metagenomics, metatranscriptomics, and targeted metabolic profiling of permafrost communities to elucidate the temperature dependence of methane metabolism therein.…”

Section: Total Community Activity: Other -Omics Strategiesmentioning

confidence: 99%

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Permafrost Meta-Omics and Climate Change

Mackelprang

Saleska²,

Jacobsen

et al. 2016

Annu. Rev. Earth Planet. Sci.

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Permanently frozen soil, or permafrost, covers a large portion of the Earth's terrestrial surface and represents a unique environment for cold-adapted microorganisms. As permafrost thaws, previously protected organic matter becomes available for microbial degradation. Microbes that decompose soil carbon produce carbon dioxide and other greenhouse gases, contributing substantially to climate change. Next-generation sequencing and other -omics technologies offer opportunities to discover the mechanisms by which microbial communities regulate the loss of carbon and the emission of greenhouse gases from thawing permafrost regions. Analysis of nucleic acids and proteins taken directly from permafrost-associated soils has provided new insights into microbial communities and their functions in Arctic environments that are increasingly impacted by climate change. In this article we review current information from various molecular -omics studies on permafrost microbial ecology and explore the relevance of these insights to our current understanding of the dynamics of permafrost loss due to climate change.

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Section: Figurementioning

confidence: 99%

Section: Application Of Multi-omics Strategies To Permafrost Environmmentioning

confidence: 99%

Section: Total Community Activity: Other -Omics Strategiesmentioning

confidence: 99%

See 1 more Smart Citation

Permafrost Meta-Omics and Climate Change

Mackelprang

Saleska²,

Jacobsen

et al. 2016

Annu. Rev. Earth Planet. Sci.

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“…DNA from selected samples was extracted using a modified phenol:chloroform:isoamyl alcohol method, as described in Suzuki et al (2001). The 16S rRNA gene was PCR amplified using the universal primers 926F and 1392R under the reaction conditions described in Mondav and Woodcroft et al (2014). Amplicons were sequenced on the Roche 454 GS-FLX Titanium platform.…”

Section: Analysis Of Microbial Communitymentioning

confidence: 99%

Biogenic methane in Indonesian coal : assessing the potential using culture enrichment, molecular phylogenetic and isotopic analysis

Susilawati¹

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Biogenic coal bed methane (CBM) has gained considerable interest because of its potential to be regenerated. The research reported in this thesis evaluated the potential to develop Indonesian coals as CH 4 bioreactors using culture enrichment, molecular phylogenetic and isotopic composition analysis methods. The results increase the current understanding on microbial methanogenesis in coal, with a specific focus on Indonesian coals.Indonesian coals range in rank from lignite to bituminous, with anthracites occurring in specific areas. The coals are low in ash yield and dominated by vitrinite group macerals, with abundant liptinite group macerals, which is thought to make them good targets for methanogenesis.Stable isotope analysis of gas from pilot production wells confirmed the hypothesis that Indonesian CBM is partly biogenic in origin. Culture enrichment studies of formation water from these CBM pilot wells also indicated the presence of active coal to CH 4 consortia that has the capability for degrading native South Sumatra Basin (SSB) coals and foreign Surat Basin coal from Australia. Among the Indonesian coal basins, the SSB currently has the greatest CBM potential and good accessibility for gas, water, and coal sampling that is required to assess the biogenic CH 4 potential of Indonesian coal. Therefore, SSB was targeted for the experiments conducted in this thesis. The investigation of the microbial methanogen community structure grown on different coal substrates showed temporal changes in community structure over time, and suggested some influence of coal substrate on the microbial community composition. The community structure exhibited greater similarity when grown on coal from the same seam but of different ranks (Mangus iii sub-bituminous (SB) Rv 0.5% and Mangus Anthracite (A) Rv 2.2%) than for coal of similar types (Mangus SB Rv 0.5% and Burung SB Rv 0.39%). The obligate acetoclastic Methanosaeta members favor Burung SB coal, while metabolically versatile Methanosarcina members favor the Mangus coals and the obligate hydrogenotrophic methanogens are significant in the control cultures without coal. Regardless of the community structure similarities across all coal cultures, more CH 4 was generated from the lower rank sub-bituminous coal cultures relative to the one high-rank semi anthracite coal. These results suggest a potential relationship between coal type and rank, microbial community composition and CH 4 production, which warrants further investigation.While CH 4 measurements and molecular phylogenetic analysis confirmed the production of biogenic CH 4 in the cultures, the gas sampled from the culture headspace had δ 13 C-CH 4 values ( 52.2‰ to 22.6‰) that mostly fell outside the range currently considered to indicate a biogenic origin. In this study, the apparent carbon fractionation factor (α c =1.02±0.006) and isotope effect (ε c = 20.1‰±15.3) were found to be more useful indicators of methanogenic pathways than the absolute δ 13 C-CH 4 values. Both values agreed with the calculat...

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“…DNA from selected samples was extracted using a modified phenol:chloroform:isoamyl alcohol method, as described in Suzuki et al (2001). The 16S rRNA gene was PCR amplified using the universal primers 926F and 1392R under the reaction conditions described in Mondav et al (2014). Amplicons were sequenced on the Roche 454 GS-FLX Titanium platform.…”

Section: Analysis Of Microbial Communitymentioning

confidence: 99%

Carbon and hydrogen isotope fractionation during methanogenesis: A laboratory study using coal and formation water

Susilawati

Golding

Baublys

et al. 2016

International Journal of Coal Geology

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Carbon and hydrogen isotope compositions of CH 4 generated via methanogenesis in cultures of South Sumatra Basin (SSB) coalbed methane (CBM) formation waters grown on coal, acetate and H 2 +CO 2 were investigated. CH 4 production and molecular analysis confirmed the presence of active microbial communities that are able to convert coal into CH 4 using both acetoclastic and hydrogenotrophic pathways. The representative bacterial sequences were dominated by Bacteroidetes, Firmicutes and Deltaproteobacteria, while Methanosaeta and Methanosarcina were the most prevalent archaeal methanogens present in the cultures.CH 4 produced in this study's culturing experiments has δ 13 C values in the range of -50 ‰ to -20 ‰, with most values falling outside the current understanding of the carbon isotopic boundaries for biogenic CH 4 (-110 ‰ to -30 ‰). However, the corresponding apparent carbon isotopic α factor (α c = 1.02±0.006), and isotopic effect (ε c = -20.1 ‰ ±15.3) showed that CH 4 in SSB cultures was predominantly produced by acetoclastic methanogenesis, which is consistent with the results of molecular DNA analysis. In addition, the calculated contribution of CO 2 reduction from the δ 13 C values of coaltreated cultures was overall < 50 %, further confirming the high contribution of the acetoclastic pathway to CH 4 production in the SSB cultures. The outcome of this experimental study also suggests that δ 2 H-CH 4 values may not provide a reliable basis for distinguishing methanogenic pathways, while apparent carbon isotopic fractionation factor (α c ) and isotope effect (ε c ) are considered more useful indicators of the methanogenic pathway.The high δ 13 C-CH 4 values (>-30 ‰) and the dominance of Methanosaeta over Methanosarcina indicate that methanogens within the SSB cultures were operating at low substrate concentrations. An unusually positive δ 13 C-CH 4 suggests a substrate depletion effect, which is thought to be related to a decrease in the relative abundance of key bacterial coal degraders with formation water inoculum storage time. Closer observation of δ 13 C-CH 4 values during the growth of cultures within a single experiment also showed a 13 C-enrichment trend over time. At log phase of growth, the CH 4 produced was 13 C-depleted when compared to the stationary phase that also indicates substrate depletion effects. Finally, the δ 13 C-CH 4 values encountered in this study (as high as -20 ‰) highlight the possible positive extension of δ 13 C-CH 4 values of acetoclastic methanogenesis from those currently reported in the literature for natural and experimental samples (as high as -30 ‰).Keywords: Biogenic gas, coal, culture experiment, isotopic composition INTRODUCTIONArchaeal methanogens are the only known microorganisms capable of forming CH 4 . These strictly anaerobic microbes are restricted to utilizing simple compounds that contain no more than two carbon atoms. As such, complex organic compounds in anoxic environments (e.g., marine sediments, rice paddies, subsurface shales and coalbeds) ...

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Discovery of a novel methanogen prevalent in thawing permafrost

Cited by 181 publications

References 58 publications

Permafrost Meta-Omics and Climate Change

Permafrost Meta-Omics and Climate Change

Biogenic methane in Indonesian coal : assessing the potential using culture enrichment, molecular phylogenetic and isotopic analysis

Carbon and hydrogen isotope fractionation during methanogenesis: A laboratory study using coal and formation water

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