Faculty Opinions recommendation of Methane metabolism in the archaeal phylum Bathyarchaeota revealed by genome-centric metagenomics.

Microbial communities of methane producing methanogens and consuming methanotrophs play an important role for the earths atmospheric methane budget. Despite their global significance, the functional potential of these communities is poorly understood. To investigate this, we applied the molecular technique, captured metagenomics, to identify the variability in functional diversity of microorganisms involved in the metabolism of methanein an environmentally controlled laboratory study. Nine plant-peat mesocosms dominated by the sedge Eriophorum vaginatum, with varying coverage, were collected from a temperate natural wetland is Sweden and subjected to a simulated growing season. Samples for analysis of captured metagenomes were taken from the top, bottom and root adjacent zone at the end of the experiment. In addition, over the simulated season, measured gas fluxes of carbon dioxide (CO2) and CH4, &#948;13C of emitted CH4 and the pore water concentration of dissolved methane and low molecular weight organic acids were recorded. The functional genes resulting from the captured metagenomes had a higher Shannon &#945;-diversity in the root zone when compared to the bottom and top. Sequences coding for methane metabolism were significantly more diverse in the root and bottom zones when compared to the top. However, the frequency of Acetyl-CoA decarbonylase and methane monooxygenase subunit A were significantly higher in the high emitting methane flux category when compared to the medium and low emitting mesocosms. We conclude that captured metagenomic analyses of functional genes provides a good measure of the functional potential methanogenic and methanotrophic microbial communities. This technique can be used to investigate how methanogens and methanotrophs function in peatlands and thus, contribute to the concentration of atmospheric methane.

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Metatranscriptomic insights into microbial consortia driving methane metabolism in paddy soils

Soil Science & Plant Nutrition ◽

10.1080/00380768.2018.1457409 ◽

2018 ◽

Vol 64 (4) ◽

pp. 455-464 ◽

Cited By ~ 6

Author(s):

Yoko Masuda ◽

Hideomi Itoh ◽

Yutaka Shiratori ◽

Keishi Senoo

Keyword(s):

Paddy Soils ◽

Microbial Consortia ◽

Methane Metabolism

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Comparison between wild and related cultivated rice species reveals strong impacts of crop domestication on methane metabolism of the rhizomicrobiome

10.21203/rs.3.rs-28865/v1 ◽

2020 ◽

Author(s):

Lei Tian ◽

Jingjing Chang ◽

Shaohua Shi ◽

Li Ji ◽

Jianfeng Zhang ◽

...

Keyword(s):

Microbial Communities ◽

Carbon Metabolism ◽

Methane Production ◽

Wild Rice ◽

Nucleotide Metabolism ◽

Cultivated Rice ◽

Wild Rice Species ◽

Methane Metabolism ◽

First Time ◽

Rice Domestication

Abstract Background Rice root-inhabited microbial communities are seriously affected by domestication as evidenced by comparing the rhizomicrobiomes of wild and related cultivated rice species. While earlier studies focused on the structures of the rhizomicrobiomes, here, we compared the functioning of the microbial communities in the rhizosphere of wild versus that of related cultivated rice species, which were originated from Africa and Asia. Results The microbial functions involved in carbon metabolism and nucleotide metabolism were found to be enriched in wild rice species, whereas those involved in nitrogen metabolism, lipid metabolism, metabolism of cofactors and vitamins, and xenobiotic biodegradation were more enriched in cultivated rice species. Among the overall carbon metabolism, specifically, methane metabolism of the rhizomicrobiomes clearly differed between wild and cultivated rice. The key enzymes in methane production and utilization were overrepresented in wild rice species, suggesting that the rhizomicrobiome of wild rice maintained a better ecological balance for methane production and utilization than the related cultivated rice species. Conclusions For the first time, the impacts of rice domestication on the main metabolic pathways of the rhizomicrobiome were assessed, which revealed the strong impacts of rice domestication on methane metabolism that is one of the most critical functions of the microbial community of the rhizosphere of rice. The results provide important guidelines for future breeding and cultivation of rice in the framework of more sustainable rice production.

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The Genomic Capabilities of Microbial Communities Track Seasonal Variation in Environmental Conditions of Arctic Lagoons

Frontiers in Microbiology ◽

10.3389/fmicb.2021.601901 ◽

2021 ◽

Vol 12 ◽

Author(s):

Kristina D. Baker ◽

Colleen T. E. Kellogg ◽

James W. McClelland ◽

Kenneth H. Dunton ◽

Byron C. Crump

Keyword(s):

Organic Matter ◽

Microbial Communities ◽

Seasonal Variability ◽

Carbon Fixation ◽

Light Availability ◽

Open Water ◽

Ice Cover ◽

Energy Inputs ◽

Methane Metabolism ◽

Extreme Seasonality

In contrast to temperate systems, Arctic lagoons that span the Alaska Beaufort Sea coast face extreme seasonality. Nine months of ice cover up to ∼1.7 m thick is followed by a spring thaw that introduces an enormous pulse of freshwater, nutrients, and organic matter into these lagoons over a relatively brief 2–3 week period. Prokaryotic communities link these subsidies to lagoon food webs through nutrient uptake, heterotrophic production, and other biogeochemical processes, but little is known about how the genomic capabilities of these communities respond to seasonal variability. Replicate water samples from two lagoons and one coastal site near Kaktovik, AK were collected in April (full ice cover), June (ice break up), and August (open water) to represent winter, spring, and summer, respectively. Samples were size fractionated to distinguish free-living and particle-attached microbial communities. Multivariate analysis of metagenomes indicated that seasonal variability in gene abundances was greater than variability between size fractions and sites, and that June differed significantly from the other months. Spring (June) gene abundances reflected the high input of watershed-sourced nutrients and organic matter via spring thaw, featuring indicator genes for denitrification possibly linked to greater organic carbon availability, and genes for processing phytoplankton-derived organic matter associated with spring blooms. Summer featured fewer indicator genes, but had increased abundances of anoxygenic photosynthesis genes, possibly associated with elevated light availability. Winter (April) gene abundances suggested low energy inputs and autotrophic bacterial metabolism, featuring indicator genes for chemoautotrophic carbon fixation, methane metabolism, and nitrification. Winter indicator genes for nitrification belonged to Thaumarchaeota and Nitrosomonadales, suggesting these organisms play an important role in oxidizing ammonium during the under-ice period. This study shows that high latitude estuarine microbial assemblages shift metabolic capabilities as they change phylogenetic composition between these extreme seasons, providing evidence that these communities may be resilient to large hydrological events in a rapidly changing Arctic.

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Genomic remnants of ancestral hydrogen and methane metabolism in Archaea drive anaerobic carbon cycling

10.1101/2021.08.02.454722 ◽

2021 ◽

Author(s):

Panagiotis S. Adam ◽

George E. Kolyfetis ◽

Till L.V. Bornemann ◽

Constantinos E. Vorgias ◽

Alexander J. Probst

Keyword(s):

Carbon Cycling ◽

Unknown Function ◽

Membrane Association ◽

Selective Pressures ◽

Anoxic Environments ◽

Metabolic States ◽

Methane Metabolism

Methane metabolism is among the hallmarks of Archaea, originating very early in their evolution. Other than its two main complexes, methyl-CoM reductase (Mcr) and tetrahydromethanopterin-CoM methyltransferase (Mtr), there exist other genes called "methanogenesis markers" that are believed to participate in methane metabolism. Many of them are Domains of Unknown Function. Here we show that these markers emerged together with methanogenesis. Even if Mcr is lost, the markers and Mtr can persist resulting in intermediate metabolic states related to the Wood-Ljungdahl pathway. Beyond the markers, the methanogenic ancestor was hydrogenotrophic, employing the anaplerotic hydrogenases Eha and Ehb. The selective pressures acting on Eha, Ehb, and Mtr partially depend on their subunits' membrane association. Integrating the evolution of all these components, we propose that the ancestor of all methane metabolizers was an autotrophic H2/CO2 methanogen that could perhaps use methanol but not oxidize alkanes. Hydrogen-dependent methylotrophic methanogenesis has since emerged multiple times independently, both alongside a vertically inherited Mcr or from a patchwork of ancient transfers. Through their methanogenesis genomic remnants, Thorarchaeota and two newly reconstructed order-level lineages in Archaeoglobi and Bathyarchaeota act as metabolically versatile players in carbon cycling of anoxic environments across the globe.

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Effects of Methane Metabolism on Nitrification and Nitrous Oxide Production in Polluted Freshwater Sediment

Applied and Environmental Microbiology ◽

10.1128/aem.60.9.3307-3314.1994 ◽

1994 ◽

Vol 60 (9) ◽

pp. 3307-3314 ◽

Cited By ~ 35

Author(s):

Réal Roy ◽

Roger Knowles

Keyword(s):

Nitrous Oxide ◽

Freshwater Sediment ◽

Oxide Production ◽

Nitrous Oxide Production ◽

Methane Metabolism

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Monodeuterated Methane, an Isotopic Tool To Assess Biological Methane Metabolism Rates

mSphere ◽

10.1128/mspheredirect.00309-17 ◽

2017 ◽

Vol 2 (4) ◽

Cited By ~ 3

Author(s):

Jeffrey J. Marlow ◽

Joshua A. Steele ◽

Wiebke Ziebis ◽

Silvan Scheller ◽

David Case ◽

...

Keyword(s):

Methane Oxidation ◽

Type I ◽

Hydrogen Atoms ◽

Natural Systems ◽

Methane Consumption ◽

Oxidation Rates ◽

Carbon Isotopic ◽

Wide Range ◽

Methane Metabolism ◽

Aerobic And Anaerobic

ABSTRACTBiological methane oxidation is a globally relevant process that mediates the flux of an important greenhouse gas through both aerobic and anaerobic metabolic pathways. However, measuring these metabolic rates presents many obstacles, from logistical barriers to regulatory hurdles and poor precision. Here we present a new approach for investigating microbial methane metabolism based on hydrogen atom dynamics, which is complementary to carbon-focused assessments of methanotrophy. The method uses monodeuterated methane (CH3D) as a metabolic substrate, quantifying the aqueous D/H ratio over time using off-axis integrated cavity output spectroscopy. This approach represents a nontoxic, comparatively rapid, and straightforward approach that supplements existing radiotopic and stable carbon isotopic methods; by probing hydrogen atoms, it offers an additional dimension for examining rates and pathways of methane metabolism. We provide direct comparisons between the CH3D procedure and the well-established14CH4radiotracer method for several methanotrophic systems, including type I and II aerobic methanotroph cultures and methane-seep sediment slurries and carbonate rocks under anoxic and oxic incubation conditions. In all applications tested, methane consumption values calculated via the CH3D method were directly and consistently proportional to14C radiolabel-derived methane oxidation rates. We also employed this method in a nontraditional experimental setup, using flexible, gas-impermeable bags to investigate the role of pressure on seep sediment methane oxidation rates. Results revealed an 80% increase over atmospheric pressure in methanotrophic rates the equivalent of ~900-m water depth, highlighting the importance of this parameter on methane metabolism and exhibiting the flexibility of the newly described method.IMPORTANCEMicrobial methane consumption is a critical component of the global carbon cycle, with wide-ranging implications for climate regulation and hydrocarbon exploitation. Nonetheless, quantifying methane metabolism typically involves logistically challenging methods and/or specialized equipment; these impediments have limited our understanding of methane fluxes and reservoirs in natural systems, making effective management difficult. Here, we offer an easily implementable, precise method using monodeuterated methane (CH3D) that advances three specific aims. First, it allows users to directly compare methane consumption rates between different experimental treatments of the same inoculum. Second, by empirically linking the CH3D procedure with the well-established14C radiocarbon approach, we determine absolute scaling factors that facilitate rate measurements for several aerobic and anaerobic systems of interest. Third, CH3D represents a helpful tool in evaluating the relationship between methane activation and full oxidation in methanotrophic metabolisms. The procedural advantages, consistency, and novel research questions enabled by the CH3D method should prove useful in a wide range of culture-based and environmental microbial systems to further elucidate methane metabolism dynamics.

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A Metabolic Study on Colon Cancer Using1H Nuclear Magnetic Resonance Spectroscopy

Biochemistry Research International ◽

10.1155/2014/348712 ◽

2014 ◽

Vol 2014 ◽

pp. 1-7 ◽

Cited By ~ 14

Author(s):

Zahra Zamani ◽

Mohammad Arjmand ◽

Farideh Vahabi ◽

Seyed Mahmood Eshaq Hosseini ◽

Sadegh Mohammad Fazeli ◽

...

Keyword(s):

Colon Cancer ◽

Metabolic Pathways ◽

Vitamin B6 ◽

Screening Tests ◽

Glutathione Metabolism ◽

Resonance Spectroscopy ◽

Metabolic Study ◽

Acid Biosynthesis ◽

Noninvasive Test ◽

Methane Metabolism

Background. Colorectal carcinoma is the third cause of cancer deaths in the world. For diagnosis, invasive methods like colonoscopy and sigmoidoscopy are used, and noninvasive screening tests are not very accurate. We decided to study the potential of1HNMR spectroscopy with metabolomics and chemometrics as a preliminary noninvasive test. We obtained a distinguishing pattern of metabolites and metabolic pathways between colon cancer patient and normal.Methods. Sera were obtained from confirmed colon cancer patients and the same number of healthy controls. Samples were sent for1HNMR spectroscopy and analysis was carried out Chenomex and MATLAB software. Metabolites were identified using Human Metabolic Data Base (HDMB) and the main metabolic cycles were identified using Metaboanalyst software.Results. 15 metabolites were identified such as pyridoxine, orotidine, and taurocholic acid. Main metabolic cycles involved were the bile acid biosynthesis, vitamin B6 metabolism, methane metabolism, and glutathione metabolism.Discussion. The main detected metabolic cycles were also reported earlier in different cancers. Our observations corroborated earlier studies that suggest the importance of lowering serum LCA/DCA and increasing vitamin B6 intake to help prevent colon cancer. This work can be looked upon as a preliminary step in using1HNMR analysis as a screening test before invasive procedures.

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