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Supplementary Material 16S Rrna Clone Library
Kip et al. Biogeosciences (bg-2011-334) Supplementary Material 16S rRNA clone library To investigate the total bacterial community a clone library based on the 16S rRNA gene was performed of the pool Sphagnum mosses from Andorra peat, next to S. magellanicum some S. falcatulum was present in this pool and both these species were analysed. Both 16S clone libraries showed the presence of Alphaproteobacteria (17%), Verrucomicrobia (13%) and Gammaproteobacteria (2%) and since the distribution of bacterial genera among the two species was comparable an average was made. In total a 180 clones were sequenced and analyzed for the phylogenetic trees see Fig. A1 and A2 The 16S clone libraries showed a very diverse set of bacteria to be present inside or on Sphagnum mosses. Compared to other studies the microbial community in Sphagnum peat soils (Dedysh et al., 2006; Kulichevskaya et al., 2007a; Opelt and Berg, 2004) is comparable to the microbial community found here, inside and attached on the Sphagnum mosses of the Patagonian peatlands. Most of the clones showed sequence similarity to isolates or environmental samples originating from peat ecosystems, of which most of them originate from Siberian acidic peat bogs. This indicated that similar bacterial communities can be found in peatlands in the Northern and Southern hemisphere implying there is no big geographical difference in microbial diversity in peat bogs. Four out of five classes of Proteobacteria were present in the 16S rRNA clone library; Alfa-, Beta-, Gamma and Deltaproteobacteria. 42 % of the clones belonging to the Alphaproteobacteria showed a 96-97% to Acidophaera rubrifaciens, a member of the Rhodospirullales an acidophilic bacteriochlorophyll-producing bacterium isolated from acidic hotsprings and mine drainage (Hiraishi et al., 2000). -
Novel Facultative Methylocella Strains Are Active Methane Consumers at Terrestrial Natural Gas Seeps Muhammad Farhan Ul Haque1,2* , Andrew T
Farhan Ul Haque et al. Microbiome (2019) 7:134 https://doi.org/10.1186/s40168-019-0741-3 RESEARCH Open Access Novel facultative Methylocella strains are active methane consumers at terrestrial natural gas seeps Muhammad Farhan Ul Haque1,2* , Andrew T. Crombie3* and J. Colin Murrell1 Abstract Background: Natural gas seeps contribute to global climate change by releasing substantial amounts of the potent greenhouse gas methane and other climate-active gases including ethane and propane to the atmosphere. However, methanotrophs, bacteria capable of utilising methane as the sole source of carbon and energy, play a significant role in reducing the emissions of methane from many environments. Methylocella-like facultative methanotrophs are a unique group of bacteria that grow on other components of natural gas (i.e. ethane and propane) in addition to methane but a little is known about the distribution and activity of Methylocella in the environment. The purposes of this study were to identify bacteria involved in cycling methane emitted from natural gas seeps and, most importantly, to investigate if Methylocella-like facultative methanotrophs were active utilisers of natural gas at seep sites. Results: The community structure of active methane-consuming bacteria in samples from natural gas seeps from Andreiasu Everlasting Fire (Romania) and Pipe Creek (NY, USA) was investigated by DNA stable isotope probing (DNA- SIP) using 13C-labelled methane. The 16S rRNA gene sequences retrieved from DNA-SIP experiments revealed that of various active methanotrophs, Methylocella was the only active methanotrophic genus common to both natural gas seep environments. We also isolated novel facultative methanotrophs, Methylocella sp. -
Title Stimulation of Methanotrophic Growth in Cocultures by Cobalamin
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Kyoto University Research Information Repository Stimulation of methanotrophic growth in cocultures by Title cobalamin excreted by rhizobia. Author(s) Iguchi, Hiroyuki; Yurimoto, Hiroya; Sakai, Yasuyoshi Applied and environmental microbiology (2011), 77(24): 8509- Citation 8515 Issue Date 2011-12 URL http://hdl.handle.net/2433/152321 Right © 2011, American Society for Microbiology. Type Journal Article Textversion author Kyoto University 1 Stimulation of methanotrophic growth in co-cultures by 2 cobalamin excreted by rhizobia 3 4 Hiroyuki Iguchi,1 Hiroya Yurimoto,1 and Yasuyoshi Sakai1,2* 5 6 Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto 7 University, Kyoto,1 and Research Unit for Physiological Chemistry, the 8 Center for the Promotion of Interdisciplinary Education and Research, 9 Kyoto,2 Japan 10 11 Corresponding author: Yasuyoshi Sakai, Ph.D. Professor 12 Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto 13 University, Kitashirakawa-Oiwake, Sakyo-ku, Kyoto 606-8502, Japan. 14 Tel: +81 75 753 6385. Fax: +81 75 753 6454 15 E-mail: [email protected] 16 17 Running title: Cobalamin stimulates methanotrophic growth 18 19 1 20 ABSTRACT 21 Methanotrophs play a key role in the global carbon cycle, in which they 22 affect methane emissions and help to sustain diverse microbial communities 23 through the conversion of methane to organic compounds. To investigate the 24 microbial interactions that caused positive effects on the methanotroph, co-cultures 25 were constructed using Methylovulum miyakonense HT12 and each of nine 26 non-methanotrophic bacteria, which were isolated from a methane-utilizing 27 microbial consortium culture established from forest soil. -
B.CCH.1013 Final Report
final report Project code: B.CCH.1013 Prepared by: Damien Finn, Diane Ouwerkerk, Athol Klieve The University of Queensland and Department of Employment, Economic Development and Innovation Date published: September 2012 PUBLISHED BY Meat & Livestock Australia Limited Locked Bag 991 NORTH SYDNEY NSW 2059 Methanotrophs from natural ecosystems as biocontrol agents for ruminant methane emissions Meat & Livestock Australia acknowledges the matching funds provided by the Australian Government to support the research and development detailed in this publication. This publication is published by Meat & Livestock Australia Limited ABN 39 081 678 364 (MLA). Care is taken to ensure the accuracy of the information contained in this publication. However MLA cannot accept responsibility for the accuracy or completeness of the information or opinions contained in the publication. You should make your own enquiries before making decisions concerning your interests. Reproduction in whole or in part of this publication is prohibited without prior written consent of MLA. B.CCH.1013 Final Report 1 Abstract In ruminant cattle, the anaerobic fermentation of ingested plant biomass results in the production of methane (CH4). This CH4 is subsequently eructated to the environment, where it acts as a potent greenhouse gas and is one of the leading sources of anthropogenic CH4 in Australia. Methane oxidising microorganisms are an important environmental sink for CH4; however the possibility that methanotrophs are native to the rumen has received little attention. This project aimed to characterise methanotrophs from a range of environments, and to subsequently determine the metabolic activity of these microorganisms under in vitro rumen-like conditions. This study is the first to characterise rumen methanotrophs using molecular methodology. -
Diversity of Aerobic Methanotrophic Bacteria in a Permafrost Active Layer Soil of the Lena Delta, Siberia
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Electronic Publication Information Center Microb Ecol (2009) 57:25–35 DOI 10.1007/s00248-008-9411-x SOIL MICROBIOLOGY Diversity of Aerobic Methanotrophic Bacteria in a Permafrost Active Layer Soil of the Lena Delta, Siberia Susanne Liebner & Katja Rublack & Torben Stuehrmann & Dirk Wagner Received: 15 November 2007 /Accepted: 20 May 2008 /Published online: 1 July 2008 # The Author(s) 2008 Abstract With this study, we present first data on the Introduction diversity of aerobic methanotrophic bacteria (MOB) in an Arctic permafrost active layer soil of the Lena Delta, Aerobic methanotrophic bacteria (MOB) of the phylum Siberia. Applying denaturing gradient gel electrophoresis Proteobacteria primarily contribute to the consumption of and cloning of 16S ribosomal ribonucleic acid (rRNA) and methane in terrestrial environments. The microbial conver- pmoA gene fragments of active layer samples, we found a sion of methane into carbon dioxide was estimated to general restriction of the methanotrophic diversity to account for 30% to 90% in flooded rice fields [1, 2], for sequences closely related to the genera Methylobacter and 13% to 38% of the methane produced in temperate and Methylosarcina, both type I MOB. In contrast, we revealed subarctic peat soils [13], and for 15% to more than 90% of a distinct species-level diversity. Based on phylogenetic the diffusive methane flux in wetlands [36, 47]. The group analysis of the 16S rRNA gene, two new clusters of MOB of MOB comprises the three families Methylococcaceae, specific for the permafrost active layer soil of this study Methylocystaceae,andBeijerinckiaceae [5, 9–12]. -
Application for Approval to Import Into Containment Any New Organism That
ER-AN-02N 10/02 Application for approval to import into FORM 2N containment any new organism that is not genetically modified, under Section 40 of the Page 1 Hazardous Substances and New Organisms Act 1996 FORM NO2N Application for approval to IMPORT INTO CONTAINMENT ANY NEW ORGANISM THAT IS NOT GENETICALLY MODIFIED under section 40 of the Hazardous Substances and New Organisms Act 1996 Application Title: Importation of extremophilic microorganisms from geothermal sites for research purposes Applicant Organisation: Institute of Geological & Nuclear Sciences ERMA Office use only Application Code: Formally received:____/____/____ ERMA NZ Contact: Initial Fee Paid: $ Application Status: ER-AN-02N 10/02 Application for approval to import into FORM 2N containment any new organism that is not genetically modified, under Section 40 of the Page 2 Hazardous Substances and New Organisms Act 1996 IMPORTANT 1. An associated User Guide is available for this form. You should read the User Guide before completing this form. If you need further guidance in completing this form please contact ERMA New Zealand. 2. This application form covers importation into containment of any new organism that is not genetically modified, under section 40 of the Act. 3. If you are making an application to import into containment a genetically modified organism you should complete Form NO2G, instead of this form (Form NO2N). 4. This form, together with form NO2G, replaces all previous versions of Form 2. Older versions should not now be used. You should periodically check with ERMA New Zealand or on the ERMA New Zealand web site for new versions of this form. -
Biological Conversion Process of Methane Into Methanol Using Mixed Culture Methanotrophic Bacteria Enriched from Activated Sludge System
BIOLOGICAL CONVERSION PROCESS OF METHANE INTO METHANOL USING MIXED CULTURE METHANOTROPHIC BACTERIA ENRICHED FROM ACTIVATED SLUDGE SYSTEM Ahmed Mohamed AlSayed Mahmoud A THESIS SUBMITTED TO THE FACULTY OF GRADUATE STUDIES IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF MASTER OF APPLIED SCIENCE GRADUATE PROGRAM IN CIVIL ENGINEERING YORK UNIVERSITY, TORONTO, ONTARIO AUGUST 2017 © Ahmed AlSayed, 2017 Abstract Wastewater treatment plants contribute to the global warming phenomena not only by GHG emissions, but also, by consuming enormous amount of fossil fuel based energy. Therefore, methane bio-hydroxylation has attracted the attention as methanol is an efficient substitute for methane (GHG) due to its transportability and higher energy yield. This work is destined to investigate and optimize the factors affecting the microbial activity within methane bio-hydroxylation system using type I methanotrophs enriched from activated sludge system. The optimization resulted in a notable enhancement of the growth kinetics. The -1 attained maximum specific growth rate (µmax) (0.358 hr ) and maximum specific methane -1 biodegradation rate (qmax) (0.605 g-CH4,Total/g-DCW/hr ) were the highest reported in mixed cultures. Furthermore, the maximum methanol productivity achieved is comparable with pure cultures and equal to 2115±81 mg/L/day. Whereas, methanol concentration of 485±21 mg/L was attained which is two times higher than the reported using mixed culture. ii Dedication " Bountiful is your life, full and complete. Or so you think, until someone comes along and makes you realize what you have been missing all this time. Like a mirror that reflects what is absent rather than present, he shows you the void in your soul—the void you have resisted seeing. -
Reduced Methane Oxidizing Activity by Sediment Methanotrophs in Shallow Coastal Zones with High Methane Emissions
Reduced methane oxidizing activity by sediment methanotrophs in shallow coastal zones with high methane emissions Elias Broman ( [email protected] ) Stockholm University https://orcid.org/0000-0001-9005-5168 Xiaole Sun Stockholm University Christian Stranne Stockholm University Marco G Salgado Stockholm University Stefano Bonaglia Stockholm University Marc Geibel Stockholm University Alf Norkko University of Helsinki Christoph Humborg Stockholm University Francisco J.A Nascimento Stockholm University Research Keywords: oceanic methane emissions, coastal zone, sediment methanotrophs Posted Date: February 13th, 2020 DOI: https://doi.org/10.21203/rs.2.17360/v2 License: This work is licensed under a Creative Commons Attribution 4.0 International License. Read Full License Version of Record: A version of this preprint was published on July 7th, 2020. See the published version at https://doi.org/10.3389/fmicb.2020.01536. Page 1/32 Abstract Background Coastal zones are transitional areas between land and sea where large amounts of organic and inorganic carbon compounds are recycled by microbes. Especially shallow zones near land have been shown to be the main source for oceanic methane (CH4) emissions. Water depth has been predicted as the best explanatory variable, which is related to CH4 ebullition, but exactly how sediment methanotrophic bacteria mediates these emissions along water depth is unknown. Here, we investigated the activity of methanotrophs in the sediment of shallow coastal zones with high CH4 emissions within a depth gradient from 10–45 m. Field sampling consisted of collecting sediment slices from eight stations along a coastal gradient (0–4 km from land) in the coastal Baltic Sea. We combined real-time measurements of surface water CH4 concentrations, acoustic detection of CH4 seeps in the bottom water, and sediment DNA plus RNA sequencing. -
Biogeochemical Constraints on the Origin of Methane in an Alluvial Aquifer: Evidence for the Upward Migration of Methane from Underlying Coal Measures
Biogeosciences, 14, 215–228, 2017 www.biogeosciences.net/14/215/2017/ doi:10.5194/bg-14-215-2017 © Author(s) 2017. CC Attribution 3.0 License. Biogeochemical constraints on the origin of methane in an alluvial aquifer: evidence for the upward migration of methane from underlying coal measures Charlotte P. Iverach1,2, Sabrina Beckmann3, Dioni I. Cendón1,2, Mike Manefield3, and Bryce F. J. Kelly1 1Connected Waters Initiative Research Centre, UNSW Australia, UNSW Sydney, NSW, 2052, Australia 2Australian Nuclear Science and Technology Organisation, New Illawarra Rd, Lucas Heights, NSW, 2234, Australia 3School of Biotechnology and Biomolecular Sciences, UNSW Australia, UNSW Sydney, NSW, 2052, Australia Correspondence to: Charlotte P. Iverach ([email protected]) Received: 26 August 2016 – Published in Biogeosciences Discuss.: 5 September 2016 Revised: 12 December 2016 – Accepted: 24 December 2016 – Published: 17 January 2017 Abstract. Geochemical and microbiological indicators of 1 Introduction methane (CH4/ production, oxidation and migration pro- cesses in groundwater are important to understand when at- Interest in methane (CH4/ production and degradation pro- tributing sources of gas. The processes controlling the natural cesses in groundwater is driven by the global expansion of occurrence of CH4 in groundwater must be understood, es- unconventional-gas production. There is concern regarding pecially when considering the potential impacts of the global the potential impacts of gas and fluid movement, as well as expansion of coal seam gas (CSG) production on ground- depressurisation, on groundwater quality and quantity in ad- water quality and quantity. We use geochemical and micro- jacent aquifers used to support other industries (Atkins et al., biological data, along with measurements of CH4 isotopic 2015; Heilweil et al., 2015; Iverach et al., 2015; Moritz et al., 13 composition (δ C-CH4/, to determine the processes acting 2015; Owen et al., 2016; Zhang and Soeder, 2016). -
High Throughput Sequencing to Detect Differences In
Microorganisms 2015, 3, 113-136; doi:10.3390/microorganisms3020113 OPEN ACCESS microorganisms ISSN 2076-2607 www.mdpi.com/journal/microorganisms Article High Throughput Sequencing to Detect Differences in Methanotrophic Methylococcaceae and Methylocystaceae in Surface Peat, Forest Soil, and Sphagnum Moss in Cranesville Swamp Preserve, West Virginia, USA Evan Lau *, Edward J. Nolan IV, Zachary W. Dillard, Ryan D. Dague, Amanda L. Semple and Wendi L. Wentzell Department of Natural Sciences and Mathematics, West Liberty University, 208 University Drive, CUB#139, West Liberty, WV 26074, USA; E-Mails: [email protected] (E.J.N.); [email protected] (Z.W.D.); [email protected] (R.D.D.); [email protected] (A.L.S.); [email protected] (W.L.W.) * Author to whom correspondence should be addressed; E-Mail: [email protected] or [email protected]; Tel.: +1-304-336-8529. Academic Editors: Marina G. Kalyuzhnaya and Ludmila Chistoserdova Received: 25 January 2015/ Accepted: 26 March 2015 / Published: 2 April 2015 Abstract: Northern temperate forest soils and Sphagnum-dominated peatlands are a major source and sink of methane. In these ecosystems, methane is mainly oxidized by aerobic methanotrophic bacteria, which are typically found in aerated forest soils, surface peat, and Sphagnum moss. We contrasted methanotrophic bacterial diversity and abundances from the (i) organic horizon of forest soil; (ii) surface peat; and (iii) submerged Sphagnum moss from Cranesville Swamp Preserve, West Virginia, using multiplex sequencing of bacterial 16S rRNA (V3 region) gene amplicons. From ~1 million reads, >50,000 unique OTUs (Operational Taxonomic Units), 29 and 34 unique sequences were detected in the Methylococcaceae and Methylocystaceae, respectively, and 24 potential methanotrophs in the Beijerinckiaceae were also identified. -
Pan-Genome-Based Analysis As a Framework for Demarcating Two Closely Related Methanotroph Genera Methylocystis and Methylosinus
microorganisms Article Pan-Genome-Based Analysis as a Framework for Demarcating Two Closely Related Methanotroph Genera Methylocystis and Methylosinus Igor Y. Oshkin 1,*, Kirill K. Miroshnikov 1, Denis S. Grouzdev 2 and Svetlana N. Dedysh 1 1 Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia; [email protected] (K.K.M.); [email protected] (S.N.D.) 2 Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia; [email protected] * Correspondence: [email protected]; Tel.: +7-(499)-135-0591; Fax: +7-(499)-135-6530 Received: 16 April 2020; Accepted: 17 May 2020; Published: 20 May 2020 Abstract: The Methylocystis and Methylosinus are two of the five genera that were included in the first taxonomic framework of methanotrophic bacteria created half a century ago. Members of both genera are widely distributed in various environments and play a key role in reducing methane fluxes from soils and wetlands. The original separation of these methanotrophs in two distinct genera was based mainly on their differences in cell morphology. Further comparative studies that explored various single-gene-based phylogenies suggested the monophyletic nature of each of these genera. Current availability of genome sequences from members of the Methylocystis/Methylosinus clade opens the possibility for in-depth comparison of the genomic potentials of these methanotrophs. Here, we report the finished genome sequence of Methylocystis heyeri H2T and compare it to 23 currently available genomes of Methylocystis and Methylosinus species. The phylogenomic analysis confirmed that members of these genera form two separate clades. -
Isolation and Characterization of a Metsulfuron-Methyl Degrading Bacterium Methylopila Sp
See discussions, stats, and author profiles for this publication at: https://www.researchgate.net/publication/223473143 Isolation and characterization of a metsulfuron-methyl degrading bacterium Methylopila sp. S113 Article in International Biodeterioration & Biodegradation · December 2007 DOI: 10.1016/j.ibiod.2007.02.005 CITATIONS READS 37 201 6 authors, including: Xing Huang Jian He Nanjing Agricultural University 236 PUBLICATIONS 3,700 CITATIONS 61 PUBLICATIONS 776 CITATIONS SEE PROFILE SEE PROFILE Ji-Quan Sun Inner Mongolia University 57 PUBLICATIONS 572 CITATIONS SEE PROFILE Some of the authors of this publication are also working on these related projects: Xenobiotic compound degradation View project Bacterial resource of alkaline-saline soil View project All content following this page was uploaded by Xing Huang on 04 March 2020. The user has requested enhancement of the downloaded file. ARTICLE IN PRESS International Biodeterioration & Biodegradation 60 (2007) 152–158 www.elsevier.com/locate/ibiod Isolation and characterization of a metsulfuron-methyl degrading bacterium Methylopila sp. S113 Xing Huang, Jian He, Jiquan Sun, Jijie Pan, Xiaofei Sun, Shunpeng Lià Key Laboratory of Microbiological Engineering of Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, PR China Received 14 September 2006; received in revised form 29 January 2007; accepted 12 February 2007 Available online 12 April 2007 Abstract The bacterium S113, capable of degrading metsulfuron-methyl, was isolated from metsulfuron-methyl-treated soil. The isolate was identified as Methylopila sp. according to its phenotypic features and 16S rDNA phylogenetic analysis. This strain could utilize metsulfuron-methyl as the sole carbon or nitrogen source. More than 97% of the 50 mg lÀ1 initially added metsulfuron-methyl was depleted after 72 h when a culture was inoculated with 104 cells lÀ1 of strain S113.