Methanol Consumption Drives the Bacterial Chloromethane Sink in a Forest Soil
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Asaia Bogorensis Gen. Nov., Sp. Nov., an Unusual Acetic Acid Bacterium in the Α-Proteobacteria
International Journal of Systematic and Evolutionary Microbiology (2000) 50, 823–829 Printed in Great Britain Asaia bogorensis gen. nov., sp. nov., an unusual acetic acid bacterium in the α-Proteobacteria Yuzo Yamada,1 Kazushige Katsura,1 Hiroko Kawasaki,2 Yantyati Widyastuti,3 Susono Saono,3 Tatsuji Seki,2 Tai Uchimura1 and Kazuo Komagata1 Author for correspondence: Yuzo Yamada. Tel\Fax: j81 54 635 2316. 1 Laboratory of General and Eight Gram-negative, aerobic, rod-shaped and peritrichously flagellated strains Applied Microbiology, were isolated from flowers of the orchid tree (Bauhinia purpurea) and of Department of Applied Biology and Chemistry, plumbago (Plumbago auriculata), and from fermented glutinous rice, all Faculty of Applied collected in Indonesia. The enrichment culture approach for acetic acid bacteria Bioscience, Tokyo was employed, involving use of sorbitol medium at pH 35. All isolates grew University of Agriculture, Sakuragaoka 1-1-1, well at pH 30 and 30 SC. They did not oxidize ethanol to acetic acid except for Setagaya-ku, one strain that oxidized ethanol weakly, and 035% acetic acid inhibited their Tokoyo 156-8502, Japan growth completely. However, they oxidized acetate and lactate to carbon 2 The International Center dioxide and water. The isolates grew well on mannitol agar and on glutamate for Biotechnology, Osaka agar, and assimilated ammonium sulfate for growth on vitamin-free glucose University, Yamadaoka 2-1, Suita, Osaka 565-0871, medium. The isolates produced acid from D-glucose, D-fructose, L-sorbose, Japan dulcitol and glycerol. The quinone system was Q-10. DNA base composition 3 Research and ranged from 593to610 mol% GMC. -
Chemical Structures of Some Examples of Earlier Characterized Antibiotic and Anticancer Specialized
Supplementary figure S1: Chemical structures of some examples of earlier characterized antibiotic and anticancer specialized metabolites: (A) salinilactam, (B) lactocillin, (C) streptochlorin, (D) abyssomicin C and (E) salinosporamide K. Figure S2. Heat map representing hierarchical classification of the SMGCs detected in all the metagenomes in the dataset. Table S1: The sampling locations of each of the sites in the dataset. Sample Sample Bio-project Site depth accession accession Samples Latitude Longitude Site description (m) number in SRA number in SRA AT0050m01B1-4C1 SRS598124 PRJNA193416 Atlantis II water column 50, 200, Water column AT0200m01C1-4D1 SRS598125 21°36'19.0" 38°12'09.0 700 and above the brine N "E (ATII 50, ATII 200, 1500 pool water layers AT0700m01C1-3D1 SRS598128 ATII 700, ATII 1500) AT1500m01B1-3C1 SRS598129 ATBRUCL SRS1029632 PRJNA193416 Atlantis II brine 21°36'19.0" 38°12'09.0 1996– Brine pool water ATBRLCL1-3 SRS1029579 (ATII UCL, ATII INF, N "E 2025 layers ATII LCL) ATBRINP SRS481323 PRJNA219363 ATIID-1a SRS1120041 PRJNA299097 ATIID-1b SRS1120130 ATIID-2 SRS1120133 2168 + Sea sediments Atlantis II - sediments 21°36'19.0" 38°12'09.0 ~3.5 core underlying ATII ATIID-3 SRS1120134 (ATII SDM) N "E length brine pool ATIID-4 SRS1120135 ATIID-5 SRS1120142 ATIID-6 SRS1120143 Discovery Deep brine DDBRINP SRS481325 PRJNA219363 21°17'11.0" 38°17'14.0 2026– Brine pool water N "E 2042 layers (DD INF, DD BR) DDBRINE DD-1 SRS1120158 PRJNA299097 DD-2 SRS1120203 DD-3 SRS1120205 Discovery Deep 2180 + Sea sediments sediments 21°17'11.0" -
Hydrogen and Carbon Isotope Fractionation During Degradation Of
ORIGINAL RESEARCH Hydrogen and carbon isotope fractionation during degradation of chloromethane by methylotrophic bacteria Thierry Nadalig1, Markus Greule2, Francßoise Bringel1,Stephane Vuilleumier1 & Frank Keppler2 1Equipe Adaptations et Interactions Microbiennes dans l’Environnement, UMR 7156 Universite de Strasbourg - CNRS, 28 rue Goethe, Strasbourg, 67083, France 2Max Planck Institute for Chemistry, Hahn-Meitner-Weg 1, 55128 Mainz, Germany Keywords Abstract Carbon isotope fractionation, chloromethane biodegradation, hydrogen isotope Chloromethane (CH3Cl) is a widely studied volatile halocarbon involved in the fractionation, methylotrophic bacteria. destruction of ozone in the stratosphere. Nevertheless, its global budget still remains debated. Stable isotope analysis is a powerful tool to constrain fluxes Correspondence of chloromethane between various environmental compartments which involve Thierry Nadalig, Universite de Strasbourg, a multiplicity of sources and sinks, and both biotic and abiotic processes. In UMR 7156 UdS-CNRS, 28 rue Goethe, this study, we measured hydrogen and carbon isotope fractionation of the 67083 Strasbourg Cedex, France. Tel: +33 3 68851973; Fax: +33 3 68852028; remaining untransformed chloromethane following its degradation by methylo- Methylobacterium extorquens Hyphomicrobium E-mail: [email protected] trophic bacterial strains CM4 and sp. MC1, which belong to different genera but both use the cmu pathway, the Funding Information only pathway for bacterial degradation of chloromethane characterized so far. Financial support for the acquisition of Hydrogen isotope fractionation for degradation of chloromethane was deter- GC-FID equipment by REALISE (http://realise. mined for the first time, and yielded enrichment factors (e)ofÀ29& and unistra.fr), the Alsace network for research À27& for strains CM4 and MC1, respectively. In agreement with previous and engineering in environmental sciences, is studies, enrichment in 13C of untransformed CH Cl was also observed, and gratefully acknowledged. -
Polyamine Profiles of Some Members of the Alpha Subclass of the Class Proteobacteria: Polyamine Analysis of Twenty Recently Described Genera
Microbiol. Cult. Coll. June 2003. p. 13 ─ 21 Vol. 19, No. 1 Polyamine Profiles of Some Members of the Alpha Subclass of the Class Proteobacteria: Polyamine Analysis of Twenty Recently Described Genera Koei Hamana1)*,Azusa Sakamoto1),Satomi Tachiyanagi1), Eri Terauchi1)and Mariko Takeuchi2) 1)Department of Laboratory Sciences, School of Health Sciences, Faculty of Medicine, Gunma University, 39 ─ 15 Showa-machi 3 ─ chome, Maebashi, Gunma 371 ─ 8514, Japan 2)Institute for Fermentation, Osaka, 17 ─ 85, Juso-honmachi 2 ─ chome, Yodogawa-ku, Osaka, 532 ─ 8686, Japan Cellular polyamines of 41 newly validated or reclassified alpha proteobacteria belonging to 20 genera were analyzed by HPLC. Acetic acid bacteria belonging to the new genus Asaia and the genera Gluconobacter, Gluconacetobacter, Acetobacter and Acidomonas of the alpha ─ 1 sub- group ubiquitously contained spermidine as the major polyamine. Aerobic bacteriochlorophyll a ─ containing Acidisphaera, Craurococcus and Paracraurococcus(alpha ─ 1)and Roseibium (alpha-2)contained spermidine and lacked homospermidine. New Rhizobium species, including some species transferred from the genera Agrobacterium and Allorhizobium, and new Sinorhizobium and Mesorhizobium species of the alpha ─ 2 subgroup contained homospermidine as a major polyamine. Homospermidine was the major polyamine in the genera Oligotropha, Carbophilus, Zavarzinia, Blastobacter, Starkeya and Rhodoblastus of the alpha ─ 2 subgroup. Rhodobaca bogoriensis of the alpha ─ 3 subgroup contained spermidine. Within the alpha ─ 4 sub- group, the genus Sphingomonas has been divided into four clusters, and species of the emended Sphingomonas(cluster I)contained homospermidine whereas those of the three newly described genera Sphingobium, Novosphingobium and Sphingopyxis(corresponding to clusters II, III and IV of the former Sphingomonas)ubiquitously contained spermidine. -
Oleomonas Sagaranensis Gen. Nov., Sp. Nov., Represents a Novel Genus in the K-Proteobacteria
FEMS Microbiology Letters 217 (2002) 255^261 www.fems-microbiology.org Oleomonas sagaranensis gen. nov., sp. nov., represents a novel genus in the K-Proteobacteria Takeshi Kanamori a, Naeem Rashid a, Masaaki Morikawa b, Haruyuki Atomi a, a;Ã Tadayuki Imanaka Downloaded from https://academic.oup.com/femsle/article/217/2/255/502948 by guest on 01 October 2021 a Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Yoshida-Honmachi, Sakyo-ku, Kyoto 606-8501, Japan, and Core Research for Evolutional Science and Technology Program of Japan Science and Technology Corporation (CREST-JST), Kawaguchi, Saitama 332-0012, Japan b Department of Material and Life Science, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan Received 13 July 2002; received in revised form 7 October 2002; accepted 21 October 2002 First published online 7 November 2002 Abstract A Gram-negative bacterium was previously isolated from an oil field in Shizuoka, Japan, and designated strain HD-1. Here we have performed detailed characterization of the strain, and have found that it represents a novel genus. The 16S rRNA sequence of strain HD-1 displayed highest similarity to various uncultured species (86.7V99.7%), along with 86.2V88.2% similarity to sequences from Azospirillum, Methylobacterium, Rhizobium, and Hyphomicrobium, all members of the K-Proteobacteria. Phylogeneticanalysis revealed that HD-1 represented a deep-branched lineage among the K-Proteobacteria. DNA^DNA hybridization analysis with Azospirillum lipoferum and Hyphomicrobium vulgare revealed low levels of similarity among the strains. We further examined the biochemical properties of the strain under aerobic conditions. -
Chemosynthetic Symbiont with a Drastically Reduced Genome Serves As Primary Energy Storage in the Marine Flatworm Paracatenula
Chemosynthetic symbiont with a drastically reduced genome serves as primary energy storage in the marine flatworm Paracatenula Oliver Jäcklea, Brandon K. B. Seaha, Målin Tietjena, Nikolaus Leischa, Manuel Liebekea, Manuel Kleinerb,c, Jasmine S. Berga,d, and Harald R. Gruber-Vodickaa,1 aMax Planck Institute for Marine Microbiology, 28359 Bremen, Germany; bDepartment of Geoscience, University of Calgary, AB T2N 1N4, Canada; cDepartment of Plant & Microbial Biology, North Carolina State University, Raleigh, NC 27695; and dInstitut de Minéralogie, Physique des Matériaux et Cosmochimie, Université Pierre et Marie Curie, 75252 Paris Cedex 05, France Edited by Margaret J. McFall-Ngai, University of Hawaii at Manoa, Honolulu, HI, and approved March 1, 2019 (received for review November 7, 2018) Hosts of chemoautotrophic bacteria typically have much higher thrive in both free-living environmental and symbiotic states, it is biomass than their symbionts and consume symbiont cells for difficult to attribute their genomic features to either functions nutrition. In contrast to this, chemoautotrophic Candidatus Riegeria they provide to their host, or traits that are necessary for envi- symbionts in mouthless Paracatenula flatworms comprise up to ronmental survival or to both. half of the biomass of the consortium. Each species of Paracate- The smallest genomes of chemoautotrophic symbionts have nula harbors a specific Ca. Riegeria, and the endosymbionts have been observed for the gammaproteobacterial symbionts of ves- been vertically transmitted for at least 500 million years. Such icomyid clams that are directly transmitted between host genera- prolonged strict vertical transmission leads to streamlining of sym- tions (13, 14). Such strict vertical transmission leads to substantial biont genomes, and the retained physiological capacities reveal and ongoing genome reduction. -
Catalytic Conversion of Chloromethane to Methanol and Dimethyl Ether Over Two Catalytic Beds: a Study of Acid Strength
BRAZILIAN JOURNAL OF PETROLEUM AND GAS | v. 4 n. 3 | p. 083-089 | 2010 | ISSN 1982-0593 CATALYTIC CONVERSION OF CHLOROMETHANE TO METHANOL AND DIMETHYL ETHER OVER TWO CATALYTIC BEDS: A STUDY OF ACID STRENGTH a a a 1 Fernandes, D. R.; Leite, T. C. M., Mota, C. J. A. a Universidade Federal do Rio de Janeiro, Instituto de Química ABSTRACT The catalytic hydrolysis of chloromethane to methanol and dimethyl ether (DME) was studied over metal- exchanged Beta and Mordenite zeolites, acidic MCM-22 and SAPO-5. The use of a second catalytic bed with HZSM-5 zeolite increased the selectivity to DME, due to methanol dehydration on the acid sites. The effect was more significant on catalysts presenting medium and weak acid site distribution, showing that dehydration of methanol to DME is accomplished over sites of higher acid strength. KEYWORDS natural gas conversion; chloromethane; zeolites; methanol; dimethyl ether 1 To whom all correspondence should be addressed. Address: Universidade Federal do Rio de Janeiro, Instituto de Química. Av Athos da Silveira Ramos 149, CT Bloco A, 21941-909, Rio de Janeiro, Brazil |e-mail: [email protected] doi:10.5419/bjpg2010-0009 83 BRAZILIAN JOURNAL OF PETROLEUM AND GAS | v. 4 n. 3 | p. 083-089 | 2010 | ISSN 1982-0593 1. INTRODUCTION derivatives, either through direct reaction of natural gas with the halogens, or through The production of methanol and dimethyl ether oxyhalogenation processes, using HCl or HBr and (DME) from natural gas has been the subject of air. In addition, the electrophilic halogenation of great industrial interest. These oxygenates have methane can be performed with the use of Lewis high commercial value, because they can be used acid catalysts, yielding monohalomethane as liquid fuels and raw material for petrochemicals. -
List of Lists
United States Office of Solid Waste EPA 550-B-10-001 Environmental Protection and Emergency Response May 2010 Agency www.epa.gov/emergencies LIST OF LISTS Consolidated List of Chemicals Subject to the Emergency Planning and Community Right- To-Know Act (EPCRA), Comprehensive Environmental Response, Compensation and Liability Act (CERCLA) and Section 112(r) of the Clean Air Act • EPCRA Section 302 Extremely Hazardous Substances • CERCLA Hazardous Substances • EPCRA Section 313 Toxic Chemicals • CAA 112(r) Regulated Chemicals For Accidental Release Prevention Office of Emergency Management This page intentionally left blank. TABLE OF CONTENTS Page Introduction................................................................................................................................................ i List of Lists – Conslidated List of Chemicals (by CAS #) Subject to the Emergency Planning and Community Right-to-Know Act (EPCRA), Comprehensive Environmental Response, Compensation and Liability Act (CERCLA) and Section 112(r) of the Clean Air Act ................................................. 1 Appendix A: Alphabetical Listing of Consolidated List ..................................................................... A-1 Appendix B: Radionuclides Listed Under CERCLA .......................................................................... B-1 Appendix C: RCRA Waste Streams and Unlisted Hazardous Wastes................................................ C-1 This page intentionally left blank. LIST OF LISTS Consolidated List of Chemicals -
Downloaded from Genbank
Methylotrophs and Methylotroph Populations for Chloromethane Degradation Françoise Bringel1*, Ludovic Besaury2, Pierre Amato3, Eileen Kröber4, Stefen Kolb4, Frank Keppler5,6, Stéphane Vuilleumier1 and Thierry Nadalig1 1Université de Strasbourg UMR 7156 UNISTR CNRS, Molecular Genetics, Genomics, Microbiology (GMGM), Strasbourg, France. 2Université de Reims Champagne-Ardenne, Chaire AFERE, INR, FARE UMR A614, Reims, France. 3 Université Clermont Auvergne, CNRS, SIGMA Clermont, ICCF, Clermont-Ferrand, France. 4Microbial Biogeochemistry, Research Area Landscape Functioning – Leibniz Centre for Agricultural Landscape Research – ZALF, Müncheberg, Germany. 5Institute of Earth Sciences, Heidelberg University, Heidelberg, Germany. 6Heidelberg Center for the Environment HCE, Heidelberg University, Heidelberg, Germany. *Correspondence: [email protected] htps://doi.org/10.21775/cimb.033.149 Abstract characterized ‘chloromethane utilization’ (cmu) Chloromethane is a halogenated volatile organic pathway, so far. Tis pathway may not be representa- compound, produced in large quantities by terres- tive of chloromethane-utilizing populations in the trial vegetation. Afer its release to the troposphere environment as cmu genes are rare in metagenomes. and transport to the stratosphere, its photolysis con- Recently, combined ‘omics’ biological approaches tributes to the degradation of stratospheric ozone. A with chloromethane carbon and hydrogen stable beter knowledge of chloromethane sources (pro- isotope fractionation measurements in microcosms, duction) and sinks (degradation) is a prerequisite indicated that microorganisms in soils and the phyl- to estimate its atmospheric budget in the context of losphere (plant aerial parts) represent major sinks global warming. Te degradation of chloromethane of chloromethane in contrast to more recently by methylotrophic communities in terrestrial envi- recognized microbe-inhabited environments, such ronments is a major underestimated chloromethane as clouds. -
4. Production, Import/Export, Use, and Disposal
CHLOROMETHANE 149 4. PRODUCTION, IMPORT/EXPORT, USE, AND DISPOSAL 4.1 PRODUCTION Table 4-1 lists the facilities in each state that manufacture or process chloromethane, the intended use, and the range of maximum amounts of chloromethane that are stored on site. The data listed in Table 4-l are derived from the Toxics Release Inventory (TRI96 1998). Only certain types of facilities were required to report. Therefore, this is not an exhaustive list. Based on the most current TRI information, there are currently 96 facilities that produce or process chloromethane in the United States. Chloromethane (also commonly known as methyl chloride) is both an anthropogenic and naturally occurring chemical. Anthropogenic sources include industrial production, polyvinyl chloride burning, and wood burning; natural sources include the oceans, microbial fermentation, and biomass fires (e.g., forest fires, grass fires). Chloromethane is produced industrially by reaction of methanol and hydrogen chloride (HCl) or by chlorination of methane (Edwards et al. 1982a; Holbrook 1992; Key et al. 1980). While the reaction of methanol with HCl is the most common method, the choice of process depends, in part, on the HCl balance at the site (the methane route produces HCl, the methanol route uses it) (Edwards et al. 1982a; Holbrook 1992). Typically, manufacturing plants that produce chloromethane also produce higher chlorinated methanes (methylene chloride, chloroform, and carbon tetrachloride). The methanol-HCl process involves combining vapor-phase methanol and HCl at 180-200 °C, followed by passage over a catalyst where the reaction occurs (Holbrook 1992; Key et al. 1980). Catalysts include alumina gel, gamma alumina, and cuprous or zinc chloride on pumice or activated carbon. -
Determination of Chloromethane and Dichloromethane in a Tropical T Terrestrial Mangrove Forest in Brazil by Measurements and Modelling
Atmospheric Environment 173 (2018) 185–197 Contents lists available at ScienceDirect Atmospheric Environment journal homepage: www.elsevier.com/locate/atmosenv Determination of chloromethane and dichloromethane in a tropical T terrestrial mangrove forest in Brazil by measurements and modelling ∗ S.R. Kolusua,c, , K.H. Schlünzena, D. Grawea, R. Seifertb a Meteorological Institute, CEN, University of Hamburg, Hamburg, Germany b Institute for Geology and Marine Chemistry, University of Hamburg, Hamburg, Germany c Department of Geography, School of Global Studies, University of Sussex, Brighton, UK ARTICLE INFO ABSTRACT Keywords: Chloromethane (CH3Cl) and dichloromethane (CH2Cl2) are known to have both natural and anthropogenic Chloromethane sources to the atmosphere. From recent studies it is known that tropical and sub tropical plants are primary Dichloromethane sources of CH3Cl in the atmosphere. In order to quantify the biogenic emissions of CH3Cl and CH2Cl2 from Mangrove mangroves, field measurement were conducted in a tropical mangrove forest on the coast of Brazil. To the best of Emission our knowledge these field measurements were the first of its kind conducted in the tropical mangrove ecosystem METRAS of Braganca. A mesoscale atmospheric model, MEsoscale TRAnsport and fluid (Stream) model (METRAS), was used to simulate passive tracers concentrations and to study the dependency of concentrations on type of emission function and meteorology. Model simulated concentrations were normalized using the observed field data. With the help of the mesoscale model results and the observed data the mangrove emissions were estimated at the local scale. By using this bottom-up approach the global emissions of CH3Cl and CH2Cl2 from mangroves were quantified. The emission range obtained with different emission functions and different meteorology are −1 4–7Ggyr for CH3Cl and 1–2Ggyr2 for CH2Cl2. -
Mxaf Gene, a Gene Encoding Alpha Subunit of Methanol Dehydrogenase in and False Growth of Acetic Acid Bacteria on Methanol
J. Gen. Appl. Microbiol., 55, 101‒110 (2009) Full Paper MxaF gene, a gene encoding alpha subunit of methanol dehydrogenase in and false growth of acetic acid bacteria on methanol Rei Suzuki, Puspita Lisdiyanti†, Kazuo Komagata, and Tai Uchimura* Laboratory of General and Applied Microbiology, Department of Applied Biology and Chemistry, Faculty of Applied Bioscience, Tokyo University of Agriculture, Setagaya-ku, Tokyo 156‒8502, Japan (Received September 30, 2008; Accepted November 21, 2008) MxaF gene, a gene encoding alpha subunit of methanol dehydrogenase, was investigated for acetic acid bacteria, and growth on methanol was examined for the bacteria by using various media. Of 21 strains of acetic acid bacteria studied, Acidomonas methanolica strains showed the presence of mxaF gene exclusively, and grew on a defi ned medium containing methanol. Further, none of the strains tested of which the growth on methanol had been previously reported, except for Acidomonas methanolica, showed the presence of mxaF gene or the growth on methanol. Precautions were taken against false growth on compounds used for identifi cation of bacteria. Key Words—acetic acid bacteria; Acidomonas; growth on methanol; mxaF gene Introduction grow on methanol (Gosselé et al., 1983b), but this fi nding was rejected by using the same strains as Acetic acid bacteria grow on a variety of sugars, theirs (Uhlig et al., 1986; Urakami et al., 1989). Further, sugar alcohols, and alcohols, and produce corre- Acetobacter pomorum LTH 2458T was described to sponding oxidation products by incomplete oxidation grow on methanol (Sokollek et al., 1998), but it was of the compounds. However, confl icting data have not recognized (Cleenwerck et al., 2002).