DOCSLIB.ORG

Methylotrophic Methanogenesis Governs the Biogenic Coal Bed Methane Formation in Eastern Ordos Basin, China

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Methylotrophic Methanogenesis Governs the Biogenic Coal Bed Methane Formation in Eastern Ordos Basin, China Appl Microbiol Biotechnol (2012) 96:1587–1597 DOI 10.1007/s00253-012-3889-3 ENVIRONMENTAL BIOTECHNOLOGY Methylotrophic methanogenesis governs the biogenic coal bed methane formation in Eastern Ordos Basin, China Hongguang Guo & Zhisheng Yu & Ruyin Liu & Hongxun Zhang & Qiding Zhong & Zhenghe Xiong Received: 23 October 2011 /Revised: 29 December 2011 /Accepted: 2 January 2012 /Published online: 28 January 2012 # Springer-Verlag 2012 Abstract To identify the methanogenic pathways present in a biodegradation of coal by methylotrophic methanogens and deep coal bed methane (CBM) reservoir associated with East- syntrophic bacteria, as well as thermogenic CBM production, ern Ordos Basin in China, a series of geochemical and micro- contributed to the Liulin CBM reserves associated with the biological studies was performed using gas and water samples Eastern Ordos Basin. produced from the Liulin CBM reservoir. The composition and stable isotopic ratios of CBM implied a mixed biogenic Keywords Coal bed methane . Methanogenesis . Deep and thermogenic origin of the methane. Archaeal 16S rRNA subsurface environment . Ordos Basin gene analysis revealed the dominance of the methylotrophic methanogen Methanolobus in the water produced. The high potential of methane production by methylotrophic methano- Introduction gens was found in the enrichments using the water samples amended with methanol and incubated at 25 and 35 °C. Coal bed methane (CBM) is a major clean energy resource Methylotrophic methanogens were the dominant archaea in worldwide and which is being intensively developed in many both enrichments as shown by polymerase chain reaction countries. CBM is generally understood to be formed by (PCR)–denaturing gradient gel electrophoresis (DGGE). Bac- microbial degradation of coal (biogenic origin) or thermal terial 16S rRNA gene analysis revealed that fermentative, decomposition of coal (thermogenic origin), which is typically sulfate-reducing, and nitrate-reducing bacteria inhabiting the analyzed by such standard geochemical technologies as plot- water produced were a factor in coal biodegradation to fuel ting hydrocarbon gas composition C1/(C2+C3)(C1–C3,meth- methanogens. These results suggested that past and ongoing ane, ethane, propane) versus stable carbon isotope ratios of 13 methane δ C–CH4 (Bernard et al. 1978). Biogenic CBM has been reported to be present in various reservoirs with mixed H. Guo : Z. Yu (*) : R. Liu : H. Zhang College of Resources and Environment, biogenic and thermogenic CBM or predominantly biogenic Graduate University of Chinese Academy of Sciences, CBM, e.g., in the San Juan Basin (Scott et al. 1994), in the 19 A Yuquan Road, Illinois Basin (Strapoć et al. 2007), and in the Powder River ’ Beijing 100049, People s Republic of China Basin (Flores et al. 2008). It is generally accepted that bio- e-mail: [email protected] genic CBM is the end product of coal biodegradation by H. Zhang methanogenic archaea and syntrophic bacteria inhabiting coal Research Center for Eco-Environmental Sciences, beds. These microorganisms are essential for artificially stim- Chinese Academy of Sciences, ulating the regeneration of biogenic CBM (Green et al. 2008; 18 Shuangqing Road, Beijing 100085, People’s Republic of China Harris et al. 2008; Pfeiffer et al. 2010). Thus, it is essential : to explore the existence of biogenic CBM to more fully Q. Zhong Z. Xiong understand the microorganisms involved in the formation of Food Analysis using Isotope Technology Lab, China National biogenic CBM. Research Institute of Food and Fermentation Industries, 32 Xiaoyun Road, Some systemic studies have evaluated the microbial com- Beijing 100027, People’s Republic of China munities inhabiting the CBM reservoirs containing biogenic 1588 Appl Microbiol Biotechnol (2012) 96:1587–1597 CBM. Sampling gas and water produced in the Illinois The Ordos Basin, situated in central China within the Basin, Strapoć et al. (2007, 2008) demonstrated the predom- Yellow River drainage basin (Fig. 1), is one of the largest inance of biogenic CBM formed via hydrogentrophic meth- CBM reservoirs and a principal target area for CBM explo- anogenesis by a population of Methanocorpusculum using ration and development in China. However, there is limited geochemical and microbiological methods. It was found that understanding on the origin of CBM and of the microbial methanogens were also present in water produced from communities related to CBM in the Ordos Basin. In this other reservoirs, e.g., the Powder River Basin (Green et al. study, we sought preliminary identification of the origin of 2008), the Gippsland Basin (Midgley et al. 2010), and CBM using the chemical and stable isotopic signatures of the Alberta Basin (Penner et al. 2010). Furthermore, CBM. Culture-independent and culture-dependent methods enrichment studies demonstrated that native methanogens were also used to explore the pathway of biogenic CBM indicated the production of methane by supplementing formation in a deep CBM reservoir associated with the water samples with nutrients and substrates for methano- Ordos Basin. gens (Green et al. 2008; Midgley et al. 2010). It has been reported that acetotrophic and hydrogenotrophic methanogen- eses were the dominant pathways for the production of meth- Materials and methods ane in CBM reservoirs (Strapoć et al. 2011). However, as one of the pathways for producing methane by methanogens, Study site and sample collection methylotrophic methanogenesis was rarely reported in CBM formation (Shimizu et al. 2007;Strapoć et al. Water and gas samples were collected from deep wells in the 2010). Liulin District which is located in the middle part of the Fig. 1 Location of the Liulin District in China. The map is modified from Ding et al. (2011) Appl Microbiol Biotechnol (2012) 96:1587–1597 1589 Eastern Ordos Basin (Fig. 1). It is the first experimental base The PCR products of the archaeal and bacterial 16S of CBM exploration and development in China (Su et al. rRNA genes were cloned and transformed into competent 2003). The wells were drilled down to about 700 m below Escherichia coli DH5α cells using pGEM-T Easy Vector the ground surface and constructed with tight steel pipes. (Promega Corporation, Madison, WI, USA). Recombinant Water samples were collected from five CBM-producing pGEM-T Easy vectors were checked for 16S rRNA ampli- wells (SXLL-2, SXLL-3, SXLL-4, SXLL-6, and SXLL-9). con inserts by PCR using M13 primers. For the archaeal To prevent contamination by air and steel pipes, the water library, the right-inserted recombinant clones were se- produced was continuously pumped for more than 5 days quenced. For the bacterial library, the correct clones were before sampling. Water samples were collected into au- analyzed by amplified ribosomal DNA restriction analysis toclaved glass bottles, carefully maintaining air in the (ARDRA) using restriction enzyme Msp I (NEB) as de- headspaces clean. Bottles were then tightly sealed and scribed by Steven et al. (2007). For each restriction fragment immediately transported on ice to the laboratory. The gas length polymorphism (RFLP) type, one representative clone samples from four CBM-producing wells (SXLL-2, SXLL-3, was chosen at random and sequenced. SXLL-6, and SXLL-9) were collected at the well sites through water displacement into inverted bottles. The bottles were Sequencing and phylogenetic analyses tightly sealed with butyl rubber stoppers underwater to prevent air contamination. The sequences of inserted PCR products selected from recombinant colonies were determined on an Applied Bio- Physical and chemical analysis systems 3730xl (Applied Biosytems, Darmstadt, Germany) using M13 primers. The operational taxonomic units Cations were determined by utilizing an inductively coupled (OTUs) for the archaeal clone library were determined using plasma optical emission spectrometer (Spectro Analytical Mothur software (Schloss et al. 2009). A 3% distance level Instruments, Kleve, Germany). Anions were determined by between sequences was used as the cutoff to define distinct ion chromatography (Metrohm Ltd, Herisau, Switzerland), ex- OTUs. Sequences for each archaeal OTU and bacterial + cept that NH4 was analyzed by utilizing a colorimetrical RFLP type were then compared with NCBI nucleotide se- method. Concentrations of H2,O2,CO2,N2,CH4,C2H6,and quence database using NCBI BLAST (http://www.ncbi.nlm. C3H8 in the gas samples were determined using the Agilent nih.gov/BLAST/). Sequences were aligned by Clustal X 3000A Micro gas chromatograph (GC) (Agilent Technologies). (Thompson et al. 1997). A phylogenetic tree was con- 13 13 The stable isotopic ratios of the C(δ C) of the CH4 structed in the MEGA 4 software using the neighbor- and CO2 in the gas samples were measured by an online joining method and bootstrap resampling analysis for CH4 extraction system, Trace GC Ultra™ (Thermo Electron 1,000 repeats (Tamura et al. 2007). Corporation, Austin, TX, USA), a combustion furnace (ce- ramic tube packed with CuO, NiO, and Pt wires), and Real-time PCR analysis ThermoQuest DeltaplusXL isotope ratio mass spectrometer (Thermo Finnigan). The δ13C derived was determined with The 16S rRNA genes from Methanolobus species and Clos- reference to Vienna PeeDee Belemnite samples. The preci- tridium species were respectively amplified using primer sets sion of the determination was ±0.1‰. AR-8F and AR-958R (DeLong 1992) and BAC-27F and BAC-1492R (Lane 1991) to construct the plasmids to be used Archaeal and bacterial 16S rRNA gene analysis
Load more

Recommended publications
  • Cryptic Inoviruses Are Pervasive in Bacteria and Archaea Across Earth's
    bioRxiv preprint doi: https://doi.org/10.1101/548222; this version posted February 15, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. Cryptic inoviruses are pervasive in bacteria and archaea across Earth’s biomes Simon Roux1*, Mart Krupovic2, Rebecca A. Daly3, Adair L. Borges4, Stephen Nayfach1, Frederik Schulz1, Jan-Fang Cheng1, Natalia N. Ivanova1, Joseph Bondy-Denomy4,5, Kelly C. Wrighton3, Tanja Woyke1, Axel Visel1, Nikos C. Kyrpides1, Emiley A. Eloe-Fadrosh1* 1 5 DOE Joint Genome Institute, Walnut Creek, CA 94598, USA 2Institut Pasteur, Unité Biologie Moléculaire du Gène chez les Extrêmophiles, Paris, 75015, France 3Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO 80521, USA 4Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA 5 10 Quantitative Biosciences Institute, University of California, San Francisco, San Francisco, CA 94143, USA *Correspondence to: EAE-F [email protected], SR [email protected] Abstract 15 Bacteriophages from the Inoviridae family (inoviruses) are characterized by their unique morphology, genome content, and infection cycle. To date, a relatively small number of inovirus isolates have been extensively studied, either for biotechnological applications such as phage display, or because of their impact on the toxicity of known bacterial pathogens including Vibrio cholerae and Neisseria meningitidis. Here we show that the current 56 members of the Inoviridae family represent a minute 20 fraction of a highly diverse group of inoviruses.
    [Show full text]
  • Biology, Ecology, and Biotechnological Applications of Anaerobic Bacteria Adapted to Environmental Stresses in Temperature, Ph, Salinity, Or Substrates SUSAN E
    MICROBIOLOGIcAL REVIEWS, June, 1993, p. 451-509 Vol. 57, No. 2 0146-0749/93/020451-59$02.00/0 Copyright X) 1993, American Society for Microbiology Biology, Ecology, and Biotechnological Applications of Anaerobic Bacteria Adapted to Environmental Stresses in Temperature, pH, Salinity, or Substrates SUSAN E. LOWE,lt* MAHENDRA K. JAIN,2 AND J. GREGORY ZEIKUS1'2'3 Department ofBiochemistry' and Department ofMicrobiology and Public Health,3 Michigan State University, East Lansing, Michigan 48824, and Michigan Biotechnology Institute, Lansing, Michigan 489092 INTRODUCTION ........................................................................... 453 THERMOPHILES .......................................................................... 454 Ecology, Diversity, and Taxonomy........................................................................... 454 Physiology, Biochemistry, and Genetics ........................................................................... 461 Downloaded from Overview.......................................................................... 461 Catabolism and autotrophy of methanogens and acetogens.......................................................461 (i) Methanogenesis and autotrophy........................................................................... 461 (ii) Acetogenesis and autotrophy of C. thermoaceticum .........................................................462 (iii) Novel properties of sulfur/sulfate/thiosulfate reducers and other species..............................462 Ethanolic fermentation of saccharides..........................................................................
    [Show full text]
  • Characterization of Methanosarcina Mazei JL01 Isolated from Holocene
    Proceedings Characterization of Methanosarcina mazei JL01 Isolated from Holocene Arctic Permafrost and Study of the Archaeon Cooperation with Bacterium Sphaerochaeta associata GLS2T † Viktoriia Oshurkova 1,*, Olga Troshina 1, Vladimir Trubitsyn 1, Yana Ryzhmanova 1, Olga Bochkareva 2 and Viktoria Shcherbakova 1 1 Skryabin Institute of Biochemistry and Physiology of Microorganisms, Federal Research Center Pushchino Center for Biological Research of the Russian Academy of Sciences, prospect Nauki 5, Pushchino, 142290 Moscow, Russia; [email protected] (O.T.); [email protected] (V.T.); [email protected] (Y.R.); [email protected] (V.S.) 2 Institute of Science and Technology (IST Austria), Am Campus 1, 3400 Klosterneuburg, Austria; [email protected] * Correspondence: [email protected] † Presented at the 1st International Electronic Conference on Microbiology, 2–30 November 2020; Available online: https://ecm2020.sciforum.net/. Published: 18 December 2020 Abstract: A mesophilic methanogenic culture, designated JL01, was isolated from Holocene permafrost in the Russian Arctic. After long-term extensive cultivation at 15 °C, it turned out to be a tied binary culture of archaeal (JL01) and bacterial (Sphaerochaeta associata GLS2) strains. Strain JL01 was a strict anaerobe and grew on methanol, acetate, and methylamines as energy and carbon sources. Cells were irregular coccoid, non-motile, non-spore-forming, and Gram-stain-positive. Optimum conditions for growth were 24–28 °C, pH 6.8–7.3, and 0.075–0.1 M NaCl. Phylogenetic tree reconstructions based on 16S rRNA and concatenated alignment of broadly conserved protein- coding genes revealed 16S rRNA’s close relation to Methanosarcina mazei S-6T (similarity 99.5%).
    [Show full text]
  • View This Section Focuses on the Genomic and Proteomic Analyses That Were Performed on Methanolobus Vulcani B1d
    MIAMI UNIVERSITY The Graduate School Certificate for Approving the Dissertation We hereby approve the Dissertation of Adam John Creighbaum Candidate for the Degree Doctor of Philosophy ______________________________________ Dr. Donald J. Ferguson Jr, Director ______________________________________ Dr. Annette Bollmann, Reader ______________________________________ Dr. Xin Wang, Reader ______________________________________ Dr. Rachael Morgan-Kiss ______________________________________ Dr. Richard Page, Graduate School Representative ABSTRACT EXAMINATION AND RECONSTITUTION OF THE GLYCINE BETAINE- DEPENDENT METHANOGENESIS PATHWAY FROM THE OBLIGATE METHYLOTROPHIC METHANOGEN METHANOLOBUS VULCANI B1D by Adam J. Creighbaum Recent studies indicate that environmentally abundant quaternary amines (QAs) are a primary source for methanogenesis, yet the catabolic enzymes are unknown. We hypothesized that the methanogenic archaeon Methanolobus vulcani B1d metabolizes glycine betaine through a corrinoid-dependent glycine betaine:coenzyme M (CoM) methyl transfer pathway. The draft genome sequence of M. vulcani B1d revealed a gene encoding a predicted non- pyrrolysine MttB homolog (MV8460) with high sequence similarity to the glycine betaine methyltransferase encoded by Desulfitobacterium hafniense Y51. MV8460 catalyzes glycine betaine-dependent methylation of free cob(I)alamin indicating it is an authentic MtgB enzyme. Proteomic analysis revealed that MV8460 and a corrinoid binding protein (MV8465) were highly abundant when M. vulcani B1d was grown
    [Show full text]
  • The Genome Sequence of Methanohalophilus Mahii SLPT
    Hindawi Publishing Corporation Archaea Volume 2010, Article ID 690737, 16 pages doi:10.1155/2010/690737 Research Article TheGenomeSequenceofMethanohalophilus mahii SLPT Reveals Differences in the Energy Metabolism among Members of the Methanosarcinaceae Inhabiting Freshwater and Saline Environments Stefan Spring,1 Carmen Scheuner,1 Alla Lapidus,2 Susan Lucas,2 Tijana Glavina Del Rio,2 Hope Tice,2 Alex Copeland,2 Jan-Fang Cheng,2 Feng Chen,2 Matt Nolan,2 Elizabeth Saunders,2, 3 Sam Pitluck,2 Konstantinos Liolios,2 Natalia Ivanova,2 Konstantinos Mavromatis,2 Athanasios Lykidis,2 Amrita Pati,2 Amy Chen,4 Krishna Palaniappan,4 Miriam Land,2, 5 Loren Hauser,2, 5 Yun-Juan Chang,2, 5 Cynthia D. Jeffries,2, 5 Lynne Goodwin,2, 3 John C. Detter,3 Thomas Brettin,3 Manfred Rohde,6 Markus Goker,¨ 1 Tanja Woyke, 2 Jim Bristow,2 Jonathan A. Eisen,2, 7 Victor Markowitz,4 Philip Hugenholtz,2 Nikos C. Kyrpides,2 and Hans-Peter Klenk1 1 DSMZ—German Collection of Microorganisms and Cell Cultures GmbH, 38124 Braunschweig, Germany 2 DOE Joint Genome Institute, Walnut Creek, CA 94598-1632, USA 3 Los Alamos National Laboratory, Bioscience Division, Los Alamos, NM 87545-001, USA 4 Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA 5 Oak Ridge National Laboratory, Oak Ridge, TN 37830-8026, USA 6 HZI—Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany 7 Davis Genome Center, University of California, Davis, CA 95817, USA Correspondence should be addressed to Stefan Spring, [email protected] and Hans-Peter Klenk, [email protected] Received 24 August 2010; Accepted 9 November 2010 Academic Editor: Valerie´ de Crecy-Lagard´ Copyright © 2010 Stefan Spring et al.
    [Show full text]
  • Predictedmethylators 20130327.Pdf
    Predicted Methylators Experimental Locus Tag Strain Phylum Taxonomic Class Gold Card ID Verification hgcA hgcB Desulfovibrio desulfuricans ND132 (1) Proteobacteria Deltaproteobacteria Gi03061 DND132_1056 DND132_1057 Desulfovibrio aespoeensis Aspo-2 (2) Proteobacteria Deltaproteobacteria Gc01651 Daes_2662 Daes_2663 Desulfovibrio africanus str. Walvis Bay ATCC 19997 (3) Proteobacteria Deltaproteobacteria Gi03062 Desaf_0117 Desaf_0115 Desulfomicrobium baculatum X DSM 4028 Proteobacteria Deltaproteobacteria Gc01026 Dbac_0376 Dbac_0375 Desulfonatronospira thiodismutans ASO3-1 Proteobacteria Deltaproteobacteria Gi02999 Dthio_PD1043 Dthio_PD1042 Desulfonatronum lacustre Z-7951 DSM 10312 Proteobacteria Deltaproteobacteria Gi03017 DeslaDRAFT_0127 DeslaDRAFT_0126 Desulfovibrio oxyclinae DSM 11498 Proteobacteria Deltaproteobacteria Gi11435 B149DRAFT_02526 B149DRAFT_02527 Desulfobulbus propionicus 1pr3 DSM 2032 (4) Proteobacteria Deltaproteobacteria Gc01599 Despr_0439 Despr_0438 uncultured Desulfobacterium sp. Proteobacteria Deltaproteobacteria N47_A07900 N47_A07910 Geobacter sulfurreducens PCA DSM 12127 ATCC 51573 (5) Proteobacteria Deltaproteobacteria Gc00166 GSU1440 GSU1441 Geobacter sulfurreducens DL-1 / KN400 Proteobacteria Deltaproteobacteria Gc01305 KN400_1466 KN400_1468 Geobacter metallireducens GS-15 (5) Proteobacteria Deltaproteobacteria Gc00314 Gmet_1240 Gmet_1241 Geobacter metallireducens RCH3 Proteobacteria Deltaproteobacteria Gi06445 GeomeDRAFT_0749 GeomeDRAFT_0748 Geobacter sp. daltonii FRC-32 Proteobacteria Deltaproteobacteria Gc00945
    [Show full text]
  • PDF Hosted at the Radboud Repository of the Radboud University Nijmegen
    PDF hosted at the Radboud Repository of the Radboud University Nijmegen The following full text is a publisher's version. For additional information about this publication click this link. http://hdl.handle.net/2066/113308 Please be advised that this information was generated on 2017-12-06 and may be subject to change. METHANOGENIC BACTERIA AS ENDOSYMBIONTS OF SAPROPELIC PROTOZOA HANS VAN BRUGGEN METHANOGENIC BACTERIA AS ENDOSYMBIONTS OF SAPROPELIC PROTOZOA METHANOGENIC BACTERIA AS ENDOSYMBIONTS OF SAPROPELIC PROTOZOA PROEFSCHRIFT ter verkrijging van de graad van doctor in de wiskunde en natuurwetenschappen aan de Katholieke Universiteit te Nijmegen op gezag van de Rector Magnificus Prof. Dr. J.H.G.I. Giesbers volgens besluit van het College van Dekanen in het openbaar te verdedigen op vrijdag 14 maart 1986 des namiddags te 2 uur precies door JOHAN JACOBUS ALBERT VAN BRUGGEN geboren te Meppel 1986 DRUK: STICHTING STUDENTENPERS NIJMEGEN Promotor : Prof. Dr. Ir. G.D. Vogels Co-referent : Dr. CK. Stumm in dankbare herinnering aan mijn moeder aan mijn vader voor Zwanetta en Nina CONTENTS Chapter 1 Introduction. Chapter 2 Symbiosis of methanogenic bacteria and sapropelic protozoa. Arch Uiavobiol 136:89-95 (1983) Chapter 3 Methanobaateriim formioioim, an endosymbiont of the anaerobic ciliate Metopus stviatus McMurrich. Arab. Microbiol 139:1-7 (1984) Chapter 4 Isolation of a methanogenic endosymbiont of the sapropelic amoeba Petomyxa palustris Greeff. J Protozool, submitted Chapter 5 Endosymbiotic methanogenic bacteria of the sapropelic amoeba Mastige lia. FEMS Microbiol Ecol 31:187-192 (1985) Chapter 6 Isolation and characterization of Methanaplanus endosymbiosus sp. nov., an endosymbiont of the marine sapropelic ciliate Metopus contortus.
    [Show full text]
  • Cryptic Inoviruses Revealed As Pervasive in Bacteria and Archaea
    Cryptic inoviruses revealed as pervasive in bacteria and archaea across Earth’s biomes Simon Roux, M Krupovic, Rebecca Daly, Adair Borges, Stephen Nayfach, Frederik Schulz, Allison Sharrar, Paula Matheus Carnevali, Jan-Fang Cheng, Natalia Ivanova, et al. To cite this version: Simon Roux, M Krupovic, Rebecca Daly, Adair Borges, Stephen Nayfach, et al.. Cryptic inoviruses revealed as pervasive in bacteria and archaea across Earth’s biomes. Nature Microbiology, Nature Publishing Group, 2019, 4 (11), pp.1895-1906. 10.1038/s41564-019-0510-x. pasteur-02557242 HAL Id: pasteur-02557242 https://hal-pasteur.archives-ouvertes.fr/pasteur-02557242 Submitted on 28 Apr 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. Distributed under a Creative Commons Attribution| 4.0 International License ARTICLES https://doi.org/10.1038/s41564-019-0510-x Cryptic inoviruses revealed as pervasive in bacteria and archaea across Earth’s biomes Simon Roux 1*, Mart Krupovic 2, Rebecca A. Daly3, Adair L. Borges4, Stephen Nayfach1, Frederik Schulz 1, Allison Sharrar5, Paula B. Matheus Carnevali 5, Jan-Fang Cheng1, Natalia N. Ivanova 1, Joseph Bondy-Denomy4,6, Kelly C. Wrighton3, Tanja Woyke 1, Axel Visel 1, Nikos C.
    [Show full text]
  • Taxonomy and Ecology of Methanogens
    View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Horizon / Pleins textes FEMS Microbiology Reviews 87 (1990) 297-308 297 Pubfished by Elsevier FEMSRE 00180 Taxonomy and ecology of methanogens J.L. Garcia Laboratoire de Microbiologie ORSTOM, Université de Provence, Marseille, France Key words: Methanogens; Archaebacteria; Taxonomy; Ecology 1. INTRODUCTION methane from CO2 using alcohols as hydrogen donors; 2-propanol is oxidized to acetone, and More fhan nine reviews on taxonomy of 2-butanol to 2-butanone. Carbon monoxide may methanogens have been published during the last also be converted into methane; most hydro- decade [l-91, after the discovery of the unique genotrophic species (60%) will also use formate. biochemical and genetic properties of these Some aceticlastic species are incapable of oxidiz- organisms led to the concept of Archaebacteria at ing H,. The aceticlastic species of the genus the end of the seventies. Moreover, important Methanosurcina are the most metabolically diverse economic factors have ,placed these bacteria in the methanogens, whereas the obligate aceticlastic limelight [5], including the need to develop alter- Methanosaeta (Methanothrix) can use only acetate. native forms of energy, xenobiotic pollution con- The taxonomy of the methanogenic bacteria trol, the enhancement of meat yields in the cattle has been extensively revised in the light of new industry, the distinction between biological and information based on comparative studies of 16 S thermocatalytic petroleum generation, and the rRNA oligonucleotide sequences, membrane lipid global distribution of methane in the earth's atmo- composition, and antigenic fingerprinting data. sphere. The phenotypic characteristics often do not pro- vide a sufficient means of distinguishing among taxa or determining the phylogenetic position of a 2.
    [Show full text]
  • Methylotrophic Methanogenesis in Hydraulically Fractured Shales
    Methylotrophic Methanogenesis in Hydraulically Fractured Shales Master’s Thesis Presented in Partial Fulfillment of the Requirements for the Degree Master of Science in the Graduate School of The Ohio State University By: Daniel Nimmer Marcus, B.S. Graduate Program in Microbiology The Ohio State University 2016 Thesis Committee: Kelly Wrighton PhD, Advisor Joseph Krzycki PhD Charles Daniels PhD Matthew Sullivan PhD Copyright by Daniel Nimmer Marcus 2016 ABSTRACT Over the last decade shale gas obtained from hydraulic fracturing of deep shale formations has become a sizeable component of the US energy portfolio. There is a growing body of evidence indicating that methanogenic archaea are both present and active in hydraulically fractured shales. However, little is known about the genomic architecture of shale derived methanogens. Here we leveraged natural gas extraction activities in the Appalachian region to gain access to fluid samples from two geographically and geologically distinct shale formations. Samples were collected over a time series from both shales for a period of greater than eleven months. Using assembly based metagenomics, two methanogen genomes from the genus Methanohalophilus were recovered and estimated to be near complete (97.1 and 100%) by 104 archaeal single copy genes. Additionally, a Methanohalophilus isolate was obtained which yielded a genome estimated to be 100% complete by the same metric. Based on metabolic reconstruction, it is inferred that these organisms utilize C-1 methyl substrates for methanogenesis. The ability to utilize monomethylamine, dimethylamine and methanol was experimentally confirmed with the Methanohalophilus isolate. In situ concentrations of C-1 methyl substrates, osmoprotectants, and Cl- were measured in parallel with estimates of community membership.
    [Show full text]
  • Study on Two Methylotrophic and Halophilic Methanogens, Methanosarcina Siciliae HI350 and Methanolobus Taylorii GS-16" By
    Study on Two Methylotrophic and Halophilic Methanogens, Methanosarcina siciliae HI350 and Methanolobus taylorii GS-16 Shuisong Ni M.S. (1987), Zhejiang Agricultural University, Hangzhou, China A dissertation submitted to the faculty of the Oregon Graduate Institute of Science & Technology in partial fulfillment of the requirements for the degree of Doctor of Philosophy in Biochemistry and Molecular Biology April 1994 The dissertation "Physiological study on two methylotrophic and halophilic methanogens, Methanosarcina siciliae HI350 and Methanolobus taylorii GS-16" by Shuisong Ni has been examined and approved by the following Examination Committee: - Y Avid #.I~oone Professor Thesis Advisor ) - I Joann S anders-Loehr Professor - Keith D. Garlid Professor 7 - - V ~onaldx.Orernland ( Project Chief/ U.S. Geological Survey, California To Professor Zhe-shu Qian, Who introduced me to the wonderful world of science ACKNOWLEDGEMENTS I would like to acknowledge all the people who contributed to the work which led to this dissertation. I am especially grateful to my advisor, Dr. David R. Boone. Without his brilliant ideas, warm encouragement and unwavering support, this work would not have been completed. I am thankful to other members of my thesis committee, Drs. Joann Sanders-Loehr, Keith D. Garlid, Wesley M. Jarrell, and Ronald S. Oremland for their advice. I would also like to thank Dr. William B. Whitman (University of Georgia, Athens) for measuring the G+C content of DNA of strain HI350, Dr. Carl R. Woese (University of Illinois, Urbana) for sequencing 16s rRNA of strain T4/M and providing 16s rRNA sequences of other methanogens, Dr. Henry C. Aldrich (University of Florida, Gainesville) for preparing thin-section electron micrographs of strain HI350, and Mr.
    [Show full text]
  • Isolation and Characterization of a Dimethyl Sulfide-Degrading Methanogen, Methanolobus Siciliae HI350, from an Oil Well, Characterization of M
    INTERNATIONALJOURNAL OF SYSTEMATICBACTERIOLOGY, July 1991, p. 410416 Vol. 41, No. 3 0020-771319 1IO30410-07$02.00/0 Copyright 0 1991, International Union of Microbiological Societies Isolation and Characterization of a Dimethyl Sulfide-Degrading Methanogen, Methanolobus siciliae HI350, from an Oil Well, Characterization of M. siciliae T4/MT, and Emendation of M. siciliae SHUISONG NI AND DAVID R. BOONE" Department of Environmental Science and Engineering and Department of Chemical and Biological Sciences, Oregon Graduate Institute, 19600 N.W. von Neumann Drive, Beaverton, Oregon 97006-1999 We isolated strain HI350 from a gas and oil well in the Gulf of Mexico, characterized it, and found that it is closely related to Methanolobus siciliae T4/MT(T = type strain), which we also characterized. The previously published characterization of the type strain of M. siciliae was limited to the optimum temperature for growth, and our characterization suggested the species description given below. Cells are irregular, nonmotile, coccoid, and 1.5 to 3 pm in diameter. The catabolic substrates used include methanol, trimethylamine, and dimethyl sulfide, but not H,-CO,, formate, or acetate. Growth is fastest in the presence of 0.4 to 0.6 M Na+, in the presence of 60 to 200 mM Mg2+,at pH 6.5 to 6.8, and at 40°C. Growth on trimethylamine is stimulated by yeast extract. An electrophoretic analysis confirmed that strain HI350 is closely related to strain T4/MT and indicated that major changes in the intracellular proteins of M. siciZiae HI350 occur when the growth substrate is switched between dimethyl sulfide and trimethylamine.
    [Show full text]