Spatial Distribution of Dimethylsulfide and Dimethylsulfoniopropionate In
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Regeneration of Unconventional Natural Gas by Methanogens Co
www.nature.com/scientificreports OPEN Regeneration of unconventional natural gas by methanogens co‑existing with sulfate‑reducing prokaryotes in deep shale wells in China Yimeng Zhang1,2,3, Zhisheng Yu1*, Yiming Zhang4 & Hongxun Zhang1 Biogenic methane in shallow shale reservoirs has been proven to contribute to economic recovery of unconventional natural gas. However, whether the microbes inhabiting the deeper shale reservoirs at an average depth of 4.1 km and even co-occurring with sulfate-reducing prokaryote (SRP) have the potential to produce biomethane is still unclear. Stable isotopic technique with culture‑dependent and independent approaches were employed to investigate the microbial and functional diversity related to methanogenic pathways and explore the relationship between SRP and methanogens in the shales in the Sichuan Basin, China. Although stable isotopic ratios of the gas implied a thermogenic origin for methane, the decreased trend of stable carbon and hydrogen isotope value provided clues for increasing microbial activities along with sustained gas production in these wells. These deep shale-gas wells harbored high abundance of methanogens (17.2%) with ability of utilizing various substrates for methanogenesis, which co-existed with SRP (6.7%). All genes required for performing methylotrophic, hydrogenotrophic and acetoclastic methanogenesis were present. Methane production experiments of produced water, with and without additional available substrates for methanogens, further confrmed biomethane production via all three methanogenic pathways. Statistical analysis and incubation tests revealed the partnership between SRP and methanogens under in situ sulfate concentration (~ 9 mg/L). These results suggest that biomethane could be produced with more fexible stimulation strategies for unconventional natural gas recovery even at the higher depths and at the presence of SRP. -
Isolation and Characterization of Methanohalophilus Portucalensis Sp
INTERNATIONALJOURNAL OF SYSTEMATICBACTERIOLOGY, July 1993, p. 430-437 Vol. 43, No. 3 0020-7713/93/030430-08$02.00/0 Copyright 0 1993, International Union of Microbiological Societies Isolation and Characterization of Methanohalophilus portucalensis sp. nov. and DNA Reassociation Study of the Genus Methanohalophilus DAVID R. BOONE,ly2* INDRA M. MATHRLWI,~?YITAT LIU,l JOSE A. G. F. MENAIA,1-4 ROBERT A. AND JANE E. BOONE' Departments of Environmental Science and Engineering' and Chemical and Biological Sciences, Oregon Graduate Institute of Science & Technology, 19600 N. W. von Neumann Drive, Beaverton, Oregon 97006- 1999; School of Public Health, University of California, Los Angeles, California 900243; and Laboratbrio Nacional de Engenharia e Tecnologia Industrial, Estrada das Palmeiras, 2745 Queluz, Portugal4 Six strains of coccoid, halophilic methanogens were isolated from various salinaria and natural hypersaline environments. These isolates (strains FDF-lT [T = type strain], FDF-2, SF-2, Ret-1, SD-1, and Cas-1) grew on media containing methanol and mono-, di-, and trimethylamines as catabolic substrates, but not on media containing dimethyl sulfide, methane thiol, H,, formate, or acetate; when cells were provided with H, in addition to methanol or trimethylamine, they grew on the medium containing a methyl substrate but did not catabolize H,. All of the strains were capable of growth in mineral medium to which trimethylamine was added as a catabolic substrate, although some strains were greatly stimulated by biotin or p-aminobenzoate. DNA reassociation and denaturing electrophoresis of whole-cell proteins indicated that strains FDF-lT, FDF-2, SF-2, and Ret-1, together with previously described strains SF-1, 2-7302, 2-7401, 2-7404, and 2-7405, belong to a new taxon named Methunohalophilzuportucalensis sp. -
Supporting Information
Supporting Information Lozupone et al. 10.1073/pnas.0807339105 SI Methods nococcus, and Eubacterium grouped with members of other Determining the Environmental Distribution of Sequenced Genomes. named genera with high bootstrap support (Fig. 1A). One To obtain information on the lifestyle of the isolate and its reported member of the Bacteroidetes (Bacteroides capillosus) source, we looked at descriptive information from NCBI grouped firmly within the Firmicutes. This taxonomic error was (www.ncbi.nlm.nih.gov/genomes/lproks.cgi) and other related not surprising because gut isolates have often been classified as publications. We also determined which 16S rRNA-based envi- Bacteroides based on an obligate anaerobe, Gram-negative, ronmental surveys of microbial assemblages deposited near- nonsporulating phenotype alone (6, 7). A more recent 16S identical sequences in GenBank. We first downloaded the gbenv rRNA-based analysis of the genus Clostridium defined phylo- files from the NCBI ftp site on December 31, 2007, and used genetically related clusters (4, 5), and these designations were them to create a BLAST database. These files contain GenBank supported in our phylogenetic analysis of the Clostridium species in the HGMI pipeline. We thus designated these Clostridium records for the ENV database, a component of the nonredun- species, along with the species from other named genera that dant nucleotide database (nt) where 16S rRNA environmental cluster with them in bootstrap supported nodes, as being within survey data are deposited. GenBank records for hits with Ͼ98% these clusters. sequence identity over 400 bp to the 16S rRNA sequence of each of the 67 genomes were parsed to get a list of study titles Annotation of GTs and GHs. -
Evidence of Active Methanogen Communities in Shallow Sediments
Evidence of active methanogen communities in shallow sediments of the Sonora Margin cold seeps Adrien Vigneron, St´ephaneL'Haridon, Anne Godfroy, Erwan Roussel, Barry A Cragg, R. John Parkes, Laurent Toffin To cite this version: Adrien Vigneron, St´ephaneL'Haridon, Anne Godfroy, Erwan Roussel, Barry A Cragg, et al.. Evidence of active methanogen communities in shallow sediments of the Sonora Margin cold seeps. Applied and Environmental Microbiology, American Society for Microbiology, 2015, 81 (10), pp.3451-3459. <10.1128/AEM.00147-15>. <hal-01144705> HAL Id: hal-01144705 http://hal.univ-brest.fr/hal-01144705 Submitted on 23 Apr 2015 HAL is a multi-disciplinary open access L'archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destin´eeau d´ep^otet `ala diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publi´esou non, lished or not. The documents may come from ´emanant des ´etablissements d'enseignement et de teaching and research institutions in France or recherche fran¸caisou ´etrangers,des laboratoires abroad, or from public or private research centers. publics ou priv´es. Distributed under a Creative Commons Attribution - NonCommercial 4.0 International License Evidence of Active Methanogen Communities in Shallow Sediments of the Sonora Margin Cold Seeps Adrien Vigneron,a,b,c,e Stéphane L’Haridon,b,c Anne Godfroy,a,b,c Erwan G. Roussel,a,b,c,d Barry A. Cragg,d R. John Parkes,d Downloaded from Laurent Toffina,b,c Ifremer, Laboratoire de Microbiologie -
Insights Into Archaeal Evolution and Symbiosis from the Genomes of a Nanoarchaeon and Its Inferred Crenarchaeal Host from Obsidian Pool, Yellowstone National Park
University of Tennessee, Knoxville TRACE: Tennessee Research and Creative Exchange Microbiology Publications and Other Works Microbiology 4-22-2013 Insights into archaeal evolution and symbiosis from the genomes of a nanoarchaeon and its inferred crenarchaeal host from Obsidian Pool, Yellowstone National Park Mircea Podar University of Tennessee - Knoxville, [email protected] Kira S. Makarova National Institutes of Health David E. Graham University of Tennessee - Knoxville, [email protected] Yuri I. Wolf National Institutes of Health Eugene V. Koonin National Institutes of Health See next page for additional authors Follow this and additional works at: https://trace.tennessee.edu/utk_micrpubs Part of the Microbiology Commons Recommended Citation Biology Direct 2013, 8:9 doi:10.1186/1745-6150-8-9 This Article is brought to you for free and open access by the Microbiology at TRACE: Tennessee Research and Creative Exchange. It has been accepted for inclusion in Microbiology Publications and Other Works by an authorized administrator of TRACE: Tennessee Research and Creative Exchange. For more information, please contact [email protected]. Authors Mircea Podar, Kira S. Makarova, David E. Graham, Yuri I. Wolf, Eugene V. Koonin, and Anna-Louise Reysenbach This article is available at TRACE: Tennessee Research and Creative Exchange: https://trace.tennessee.edu/ utk_micrpubs/44 Podar et al. Biology Direct 2013, 8:9 http://www.biology-direct.com/content/8/1/9 RESEARCH Open Access Insights into archaeal evolution and symbiosis from the genomes of a nanoarchaeon and its inferred crenarchaeal host from Obsidian Pool, Yellowstone National Park Mircea Podar1,2*, Kira S Makarova3, David E Graham1,2, Yuri I Wolf3, Eugene V Koonin3 and Anna-Louise Reysenbach4 Abstract Background: A single cultured marine organism, Nanoarchaeum equitans, represents the Nanoarchaeota branch of symbiotic Archaea, with a highly reduced genome and unusual features such as multiple split genes. -
Halophilic Methylotrophic Methanogens May Contribute to the High Ammonium Concentrations Found in Shale Oil and Shale Gas Reservoirs
ORIGINAL RESEARCH published: 07 March 2019 doi: 10.3389/fenrg.2019.00023 Halophilic Methylotrophic Methanogens May Contribute to the High Ammonium Concentrations Found in Shale Oil and Shale Gas Reservoirs Biwen Annie An 1,2*, Yin Shen 2, Johanna Voordouw 2 and Gerrit Voordouw 2 1 Division 4.1 Biodeterioration and Reference Organisms, Federal Institute for Materials Research and Testing, Berlin, Germany, 2 Petroleum Microbiology Research Group, Department of Biological Sciences, University of Calgary, Calgary, AB, Canada Flow-back and produced waters from shale gas and shale oil fields contain high ammonium, which can be formed by methanogenic degradation of methylamines Edited by: into methane and ammonium. Methylamines are added to fracturing fluid to prevent Claire Dumas, clay swelling or can originate from metabolism of the osmolyte triglycinebetaine (GB). Institut National de la Recherche We analyzed field samples from a shale gas reservoir in the Duvernay formation Agronomique (INRA), France Reviewed by: and from a shale oil reservoir in the Bakken formation in Canada to determine the Qaisar Mahmood, origin of high ammonium. Fresh waters used to make fracturing fluid, early flow-back COMSATS University Islamabad, waters, and late flow back waters from the shale gas reservoir had increasing salinity Pakistan Mohanakrishna Gunda, of 0.01, 0.58, and 2.66 Meq of NaCl, respectively. Microbial community analyses Qatar University, Qatar reflected this fresh water to saline transition with halophilic taxa including Halomonas, Jorge Gonzalez-Estrella, Halanaerobium, and Methanohalophilus being increasingly present. Early and late University of New Mexico, United States flow-back waters had high ammonium concentrations of 32 and 15 mM, respectively. -
Fermentation and Anaerobic Decomposition in a Hot Spring
Fermentation and anaerobic decomposition in a hot spring microbial mat by Karen Leigh Anderson A thesis submitted in partial fulfillment of requirements for the degree of Master of Science in Microbiology Montana State University © Copyright by Karen Leigh Anderson (1984) Abstract: Fermentation was investigated in a low sulfate hot spring microbial mat (Octopus Spring) according to current models on anaerobic decomposition. The mat was studied to determine what fermentation products accumulated, where in the mat they accumulated, and what factors affected their accumulation. Mat samples were incubated under dark anaerobic conditions to measure accumulation of fermentation products. Acetate and propionate (ca. 3:1) were the major products to accumulate in a 55°,C mat. Other products accumulated to a much lesser extent. Incubation of mat samples of varying thickness showed that fermentation occurred in the top 4mm of the mat. This has interesting implications for fermentative organisms in the mat due to the diurnal changes in mat oxygen concentrations. Fermentation measured in mat samples collected at various temperatures (50°,-70°C) showed acetate and propionate to be the major accumulation products. According to the interspecies hydrogen transfer model, the hydrogen concentration in a system affects the types of fermentation products produced. At a 65° C site, with natural high hydrogen levels, and at a 55°C site, with active methanogenesis, fermentation product accumulation was compared. There was a greater ratio of reduced fermentation products to acetate, with the exception of propionate, at 65°C. Ethanol accumulated at the 65°C site, as did lactate, though to a lesser extent. -
Representatives of a Novel Archaeal Phylum Or a Fast-Evolving
Open Access Research2005BrochieretVolume al. 6, Issue 5, Article R42 Nanoarchaea: representatives of a novel archaeal phylum or a comment fast-evolving euryarchaeal lineage related to Thermococcales? Celine Brochier*, Simonetta Gribaldo†, Yvan Zivanovic‡, Fabrice Confalonieri‡ and Patrick Forterre†‡ Addresses: *EA EGEE (Evolution, Génomique, Environnement) Université Aix-Marseille I, Centre Saint-Charles, 3 Place Victor Hugo, 13331 Marseille, Cedex 3, France. †Unite Biologie Moléculaire du Gène chez les Extremophiles, Institut Pasteur, 25 rue du Dr Roux, 75724 Paris Cedex ‡ 15, France. Institut de Génétique et Microbiologie, UMR CNRS 8621, Université Paris-Sud, 91405 Orsay, France. reviews Correspondence: Celine Brochier. E-mail: [email protected]. Simonetta Gribaldo. E-mail: [email protected] Published: 14 April 2005 Received: 3 December 2004 Revised: 10 February 2005 Genome Biology 2005, 6:R42 (doi:10.1186/gb-2005-6-5-r42) Accepted: 9 March 2005 The electronic version of this article is the complete one and can be found online at http://genomebiology.com/2005/6/5/R42 reports © 2005 Brochier et al.; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Placement<p>Anteins from analysis 25of Nanoarcheumarchaeal of the positiongenomes equitans of suggests Nanoarcheum in the that archaeal N. equitans phylogeny inis likethe lyarchaeal to be the phylogeny representative using aof large a fast-evolving dataset of concatenatedeuryarchaeal ribosomalineage.</p>l pro- deposited research Abstract Background: Cultivable archaeal species are assigned to two phyla - the Crenarchaeota and the Euryarchaeota - by a number of important genetic differences, and this ancient split is strongly supported by phylogenetic analysis. -
Exploring the Nutritional Values of Hydrogenotrophic Bacteria As Space Food
ISSN: 2455-2631 © December 2018 IJSDR | Volume 3, Issue 12 Exploring the Nutritional Values of Hydrogenotrophic Bacteria as Space Food 1M.GIRISH, 2S.ABIRAMI, 3Dr.V.MAHALAKSHMI 1,2Research scholar, 3Professor 1,3Madras Christian College, 2V.R.R Institute of Biomedical Sciences. Abstract: Hydrogenotrophs are organisms that are capable of metabolizing molecular hydrogen as source of energy and hence hydrogenotrophy is performed by carbon dioxide reducing organism to produce methane. Methanogens are diverse group of strict anaerobes where methanogenesis is a major route in the anaerobic mineralization of organic matter. They have very unique enzyme and cofactors involved in this metabolic pathway. The anaerobic chamber provides a convenient culture system for large-scale studies of strictly anaerobic and/or facultative anaerobic bacteria. In this study, the Hydrogenotrophic organism isolated was characterized as Methanosarcina sp. Though these hydrogenotrophs utilise carbon dioxide and grow in a minimal growth requirement, they were found to be rich in carbohydrates and protein content. Therefore, Hydrogenotroph being a good food source, can be used for future space travel where the astronauts could carry them aboard and synthesis their own food. The by-products produced by these organisms can be used to produce a protein rich meal. This system can be incorporated on to space craft where this works as a closed loop between astronauts and hydrogenotrophs, where carbon dioxide released by astronauts can be captured and filtered through a system and supplied for the growth of these microbes which in turn synthesis carbohydrates. Keywords: Hydrogenotrophs, space food, anaerobes. I. INTRODUCTION Hydrogenotrophs are organisms that are capable of metabolizing molecular hydrogen as source of energy. -
Supplementary Information
Retroconversion of estrogens into androgens by bacteria via a cobalamin-mediated methylation Po-Hsiang Wang, Yi-Lung Chen, Sean Ting-Shyang Wei, Kan Wu, Tzong-Huei Lee, Tien-Yu Wu, and Yin-Ru Chiang Supplementary Information Table of Contents Dataset Dataset S1. Genome annotation of strain DHT3 and transcriptomic analysis (RNA-Seq) of bacterial cells grown anaerobically with testosterone or estradiol. SI Tables Table S1. Oligonucleotides used in this study. Table S2. Selection of housekeeping genes of strain DHT3 used for constructing the linear regression line in the global gene expression profiles (RNA-Seq). Table S3. Selection of the cobalamin-dependent methyltransferases used for the un-rooted maximum likelihood tree construction. Table S4. UPLC–APCI–HRMS data of the intermediates involved in anaerobic estrone catabolism by strain DHT3. Table S5. 1H- (600 MHz) and 13C-NMR (150 MHz) spectral data of the HPLC-purified metabolite (AND2) and the authentic standard 5-androstan-3,17-diol Table S6. Selection of the bacteria used for comparative analysis of the gene organization for HIP degradation. SI Figures Fig. S1 Scanning electron micrographs of strain DHT3 cells. Fig. S2 Cobalamin as an essential vitamin during the anaerobic growth of strain DHT3 on estradiol. Fig. S3 Arrangement and expression analysis of the emt genes in strain DHT3. Fig. S4 The anaerobic growth of the wild type (A) and the emtA-disrupted mutant (B) of strain DHT3 with testosterone and estradiol. Fig. S5 APCI–HRMS spectrum of the HIP produced by estrone-fed strain DHT3. 1 Fig. S6 UPLC–APCI–HRMS spectra of two TLC-purified androgen metabolites, 17β-hydroxyandrostan-3-one (A) and 3β,17β-dihydroxyandrostane (B). -
An Evolutionary Approach to Bibliographic Classification
University of Tennessee, Knoxville TRACE: Tennessee Research and Creative Exchange Doctoral Dissertations Graduate School 8-2018 AN EVOLUTIONARY APPROACH TO BIBLIOGRAPHIC CLASSIFICATION David Linn Sims University of Tennessee Follow this and additional works at: https://trace.tennessee.edu/utk_graddiss Recommended Citation Sims, David Linn, "AN EVOLUTIONARY APPROACH TO BIBLIOGRAPHIC CLASSIFICATION. " PhD diss., University of Tennessee, 2018. https://trace.tennessee.edu/utk_graddiss/5006 This Dissertation is brought to you for free and open access by the Graduate School at TRACE: Tennessee Research and Creative Exchange. It has been accepted for inclusion in Doctoral Dissertations by an authorized administrator of TRACE: Tennessee Research and Creative Exchange. For more information, please contact [email protected]. To the Graduate Council: I am submitting herewith a dissertation written by David Linn Sims entitled "AN EVOLUTIONARY APPROACH TO BIBLIOGRAPHIC CLASSIFICATION." I have examined the final electronic copy of this dissertation for form and content and recommend that it be accepted in partial fulfillment of the requirements for the degree of Doctor of Philosophy, with a major in Communication and Information. Suzanne L. Allard, Major Professor We have read this dissertation and recommend its acceptance: David G. Anderson, Bradley Wade Bishop, Stuart N. Brotman Accepted for the Council: Dixie L. Thompson Vice Provost and Dean of the Graduate School (Original signatures are on file with official studentecor r ds.) AN EVOLUTIONARY APPROACH TO BIBLIOGRAPHIC CLASSIFICATION A Dissertation Presented for the Doctor of Philosophy Degree The University of Tennessee, Knoxville David Linn Sims August 2018 Copyright © 2018 by David L. Sims All rights reserved. ii ACKNOWLEDGEMENTS If it had not been for my dissertation chair, Suzie Allard, I may not have completed this degree. -
Carbon Nanotubes Accelerate Acetoclastic Methanogenesis
Carbon nanotubes accelerate acetoclastic methanogenesis: From pure cultures to anaerobic soils Leilei Xiao, Shiling Zheng, Eric Lichtfouse, Min Luo, Yang Tan, Fanghua Liu To cite this version: Leilei Xiao, Shiling Zheng, Eric Lichtfouse, Min Luo, Yang Tan, et al.. Carbon nanotubes accelerate acetoclastic methanogenesis: From pure cultures to anaerobic soils. Soil Biology and Biochemistry, Elsevier, 2020, 150, 10.1016/j.soilbio.2020.107938. hal-02930808 HAL Id: hal-02930808 https://hal.archives-ouvertes.fr/hal-02930808 Submitted on 4 Sep 2020 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Carbon nanotubes accelerate acetoclastic methanogenesis: From pure cultures to anaerobic soils Leilei Xiao a,e,f, Shiling Zheng a,f, Eric Lichtfouse c, Min Luo d, Yang Tan f, Fanghua Liu a,b,e,f,* a Key Laboratory of Coastal Biology and Biological Resources Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264003, PR China b Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science