Methanogenic archaea database containing physiological and biochemical characteristics

Jabłoński, Sławomir; Rodowicz, Paweł; Łukaszewicz, Marcin

doi:10.1099/ijs.0.000065

Cited by 84 publications

(59 citation statements)

References 61 publications

(64 reference statements)

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“…Taxonomies of these high-quality sequences were assigned via the greengenes database using the RDP classifier55 with a minimum confidence threshold of 50%. Sequences of known methanogens were extracted from all sequences according to recent methanogen databases5657. The sequences that did not match any taxonomic Class were also removed.…”

Section: Methodsmentioning

confidence: 99%

Stability of peatland carbon to rising temperatures

et al. 2016

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Peatlands contain one-third of soil carbon (C), mostly buried in deep, saturated anoxic zones (catotelm). The response of catotelm C to climate forcing is uncertain, because prior experiments have focused on surface warming. We show that deep peat heating of a 2 m-thick peat column results in an exponential increase in CH4 emissions. However, this response is due solely to surface processes and not degradation of catotelm peat. Incubations show that only the top 20–30 cm of peat from experimental plots have higher CH4 production rates at elevated temperatures. Radiocarbon analyses demonstrate that CH4 and CO2 are produced primarily from decomposition of surface-derived modern photosynthate, not catotelm C. There are no differences in microbial abundances, dissolved organic matter concentrations or degradative enzyme activities among treatments. These results suggest that although surface peat will respond to increasing temperature, the large reservoir of catotelm C is stable under current anoxic conditions.

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Section: Methodsmentioning

confidence: 99%

Stability of peatland carbon to rising temperatures

et al. 2016

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“…Sequences not aligning within the expected region flanked by the PCR primers were removed from further analysis. Methanogen taxonomic lineages were classified into different physiological categories depending on their presumed substrate preference (Canfield et al, 2005; Jabłoński et al, 2015): hydrogenotrophic (H 2 ) using H 2 /CO 2 , acetoclastic (Acetate) using acetate, methylotrophic (Methyl) using non-competitive methylated substrates (MAs, methanol, etc. ), mixotrophic (Mix) using more than one type of substrates, and unclassified (N).…”

Section: Methodsmentioning

confidence: 99%

Concurrent Methane Production and Oxidation in Surface Sediment from Aarhus Bay, Denmark

et al. 2017

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Marine surface sediments, which are replete with sulfate, are typically considered to be devoid of endogenous methanogenesis. Yet, methanogenic archaea are present in those sediments, suggesting a potential for methanogenesis. We used an isotope dilution method based on sediment bag incubation and spiking with 13C-CH4 to quantify CH4 turnover rates in sediment from Aarhus Bay, Denmark. In two independent experiments, highest CH4 production and oxidation rates (>200 pmol cm-3 d-1) were found in the top 0–2 cm, below which rates dropped below 100 pmol cm-3 d-1 in all other segments down to 16 cm. This drop in overall methane turnover with depth was accompanied by decreasing rates of organic matter mineralization with depth. Molecular analyses based on quantitative PCR and MiSeq sequencing of archaeal 16S rRNA genes showed that the abundance of methanogenic archaea also peaked in the top 0–2 cm segment. Based on the community profiling, hydrogenotrophic and methylotrophic methanogens dominated among the methanogenic archaea in general, suggesting that methanogenesis in surface sediment could be driven by both CO2 reduction and fermentation of methylated compounds. Our results show the existence of elevated methanogenic activity and a dynamic recycling of CH4 at low concentration in sulfate-rich marine surface sediment. Considering the common environmental conditions found in other coastal systems, we speculate that such a cryptic methane cycling can be ubiquitous.

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“…The public mcrA data set allows for extracting general ecological patterns and investigating the shaping environmental gradients at global and regional scales. Additionally, a database summarizing the physiological properties of 152 methanogenic isolates is available 1 (Jabłoński et al, 2015). Recently, genome binning revealed unusual mcrA sequences in the new class of Methanofastidiosa (Nobu et al, 2016) and the new phyla of Bathyarchaeota (Evans et al, 2015) and Verstraetearchaeota (Vanwonterghem et al, 2016).…”

Section: Introductionmentioning

confidence: 99%

Global Biogeographic Analysis of Methanogenic Archaea Identifies Community-Shaping Environmental Factors of Natural Environments

Yang

Horn

et al. 2017

Front. Microbiol.

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Methanogenic archaea are important for the global greenhouse gas budget since they produce methane under anoxic conditions in numerous natural environments such as oceans, estuaries, soils, and lakes. Whether and how environmental change will propagate into methanogenic assemblages of natural environments remains largely unknown owing to a poor understanding of global distribution patterns and environmental drivers of this specific group of microorganisms. In this study, we performed a meta-analysis targeting the biogeographic patterns and environmental controls of methanogenic communities using 94 public mcrA gene datasets. We show a global pattern of methanogenic archaea that is more associated with habitat filtering than with geographical dispersal. We identify salinity as the control on methanogenic community composition at global scale whereas pH and temperature are the major controls in non-saline soils and lakes. The importance of salinity for structuring methanogenic community composition is also reflected in the biogeography of methanogenic lineages and the physiological properties of methanogenic isolates. Linking methanogenic alpha-diversity with reported values of methane emission identifies estuaries as the most diverse methanogenic habitats with, however, minor contribution to the global methane budget. With salinity, temperature and pH our study identifies environmental drivers of methanogenic community composition facing drastic changes in many natural environments at the moment. However, consequences of this for the production of methane remain elusive owing to a lack of studies that combine methane production rate with community analysis.

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Methanogenic archaea database containing physiological and biochemical characteristics

Cited by 84 publications

References 61 publications

Stability of peatland carbon to rising temperatures

Stability of peatland carbon to rising temperatures

Concurrent Methane Production and Oxidation in Surface Sediment from Aarhus Bay, Denmark

Global Biogeographic Analysis of Methanogenic Archaea Identifies Community-Shaping Environmental Factors of Natural Environments

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