DOCSLIB.ORG

Isolation, Physiology and Preservation of Methane-Oxidizing Bacteria

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Isolation, Physiology and Preservation of Methane-Oxidizing Bacteria From Nature to Nurture: Isolation, Physiology and Preservation of Methane-Oxidizing Bacteria Sven Hoefman Promotor Prof. Dr. Paul De Vos Co-Promotors Prof. Dr. Peter Vandamme Dr. Kim Heylen Dissertation submitted in fulfillment of the requirements for the degree of Doctor (Ph.D.) in Sciences, Biotechnology Sven Hoefman – From Nature to Nurture: Isolation, Physiology and Preservation of Methane-Oxidizing Bacteria Copyright ©2013 Sven Hoefman ISBN-number: 978-9-4619711-8-0 No part of this thesis protected by its copyright notice may be reproduced or utilized in any form, or by any means, electronic or mechanical, including photocopying, recording or by any information storage or retrieval system without written permission of the author and promotors. Printed by University Press | www.universitypress.be Ph.D. thesis, Faculty of Sciences, Ghent University, Ghent, Belgium. This Ph.D. work was financially supported by a project of the Geconcerteerde Onderzoeksacties of Ghent University (BOF09/GOA/005) Publicly defended in Ghent, Belgium, May 27th, 2013 Examination committee Prof. Dr. Savvas Savvides (Chairman) L-Probe: Laboratory for protein Biochemistry and Biomolecular Engineering, Faculty of Sciences, Ghent University, Belgium Prof. Dr. Paul De Vos (Promotor) LM-UGent: Laboratory of Microbiology, Faculty of Science, Ghent University, Belgium BCCM-LMG Bacteria Collection, Ghent, Belgium Prof. Dr. Peter Vandamme (Co-promotor) LM-UGent: Laboratory of Microbiology, Faculty of Science, Ghent University, Belgium Dr. Kim Heylen (Co-promotor) LM-UGent: Laboratory of Microbiology, Faculty of Science, Ghent University, Belgium Prof. Dr. Nico Boon LabMET: Laboratory of Microbial Ecology and Technology, Faculty of Bioscience Engineering, Ghent University, Belgium Dr. Huub Op den Camp Institute for Water and Wetland Research, Faculty of Science, Radboud University Nijmegen, The Netherlands Prof. Dr. Hendrikus Laanbroek NIOO-KNAW: Netherlands Institute of Ecology, Wageningen, The Netherlands Prof. Dr. Stéphane Declerck Faculty of Biological, Agricultural and Environmental Engineering, Université catholique de Louvain, Louvain-la-Neuve, Belgium i List of abbreviations AMO ammonia monooxygenase ANOVA analysis of variance AOB ammonia-oxidizing bacteria AUC area under the curve BLAST basic local alignment search tool CBB Calvin-Benson-Bassham cycle CFU colony forming units CPA cryoprotectant (d)AMS (diluted) ammonium mineral salts DGGE denaturing gradient gel electrophoresis DMSO dimethyl sulfoxide (d)NMS (diluted) nitrate mineral salts DO dissolved oxygen EM expectation maximization FCM flow cytometry GC gas chromatography GTR general time reversible HAO hydroxylamine oxidoreductase HRT hydraulic retention time ICM intracytoplasmic membrane LPA lyoprotectant MALDI TOF matrix assisted laser desorption ionisation time of flight MS mass spectrometry ML maximum likelihood MOB methane-oxidizing bacteria MOR methane oxidation rate MPN most probable number NOB nitrite-oxidizing bacteria iii OD optical density PAR photosynthetic active range PFP primary facultative pond PI propidium iodide PLFA phospholipid-derived fatty acids (P)PCA (probabilistic) principle component analysis (p/s)MMO (particulate/soluble) methane monooxygenase rep-PCR repetitive element sequence based polymerase chain reaction ROC receiver operating characteristic RuMP ribulose monophosphate (s)COD (soluble) chemical oxygen demand SRT sludge retention time T-RFLP terminal-restriction fragment length polymorphism TSA trypticase soy agar TSB trypticase soy broth UPGMA unweighted pair group method with arithmetic averages VBNC viable but non-culturable VSS volatile suspended solids WSP waste stabilization pond WWTP waste water treatment plant iv Table of contents Examination committee i List of abbreviations iii Table of contents v Part A: General Introduction 1 Background & Scope 3 An introduction to aerobic methane-oxidizing bacteria 5 Aims & Outline 29 References 33 Part B: Isolation of methane-oxidizing bacteria 41 Chapter I: Miniaturized extinction culturing for rapid isolation of methane-oxidizing bacteria 43 Chapter II: Facultative ponds harbor methane oxidizing communities supported by algae 69 Reflection & Discussion 89 Part C: Physiology of methane-oxidizing bacteria 95 Chapter III: Customized media based on miniaturized screening improve growth rate and cell yield of Methylomonas strains 97 Chapter IV: Versatile and strain-dependent nitrogen metabolism within the genus Methylomonas 121 Chapter V: Exploration and prediction of interactions between methanotrophs and heterotrophs 145 Chapter VI: Methyloparacoccus murrellii, a novel methanotroph isolated from pond water in South Africa and Japan 171 v Chapter VII: Methylomonas lenta, a novel methanotroph isolated from manure and a denitrification tank in Belgium 189 Reflection & Discussion 205 Part D: Preservation of methane-, ammonia- and nitrite-oxidizing bacteria 215 Chapter VIII: Survival or Revival: Long-term preservation induces a reversible viable but non-culturable state in methane-oxidizing bacteria 217 Chapter IX: Efficient cryopreservation protocol enables accessibility of a broad range of ammonia-oxidizing bacteria 241 Chapter X: Influence of carbon and DMSO concentration on the successful preservation of nitrite-oxidizing bacteria 253 Reflection & Discussion 269 Concluding remarks 273 Summary 275 Samenvatting 277 Dankwoord 281 Curriculum vitae 285 vi Part A: General Introduction Part A - General Introduction Background & Scope The surface of our planet is warming up. Iconic to this fact is the melting of the polar ice caps, but other direct major implications are observed that affect us all, including extreme drought, loss of biodiversity and an increase in weather extremities, to name a few. The temperature on Earth is governed by a balance of greenhouse gases, such as water vapor, carbon dioxide, methane and nitrous oxide, which absorb solar energy and reradiate it in the form of heat into the atmosphere. For ages, these gases are continuously being produced and broken down by a variety of chemical and biological processes. However, since the industrial revolution the atmospheric greenhouse gas concentration has gone up due to an increase in human-induced emissions. For example, extensive methane emissions are detected from rice paddies, animal husbandry and landfills. All around the world, microbes, termed methanotrophs, are found that can consume this greenhouse gas, and are thus viewed as gatekeepers preventing excessive methane emissions from escaping to the atmosphere. It is of vital importance to understand what factors may positively or negatively impact the methane consuming activity of these organisms. Therefore, tools are needed to efficiently bring and keep these organisms into culture and to catalog and safeguard the methane-oxidizing biodiversity. In the future, this might allow us to manage these human-related methane emissions, by stimulating these organisms to consume methane, which can potentially be coupled to the degradation of groundwater pollutants or the production of high-value biomass. The work in this thesis describes (i) the successful long-term preservation of methane- utilizing bacteria and confirms the broad applicability of the applied methodology for fastidious bacteria in general, (ii) advocates the use of miniaturized tools for rapid isolation, screening and characterization of these methanotrophs, (iii) discusses the large variability and its implications of important physiological features between closely related strains and (iv) validates the research by depositing all characterized strains in public culture collections and describing several novel methanotrophic taxa. 3 Part A - General Introduction The research was performed between May 2009 and March 2013 at the Laboratory of Microbiology (LM-UGent), Faculty of Science, Ghent University. The central research themes of this lab are diversity, classification and identification of a wide variety of bacteria, including food-associated, animal and human-associated and environmental strains. In 2009, a project of the Geconcerteerde Onderzoeksacties of Ghent University (BOF09/GOA/005) was initiated in collaboration with the Laboratory of Microbial Ecology and Technology (LabMET), Ghent University. The aim of this project, named “Sustainable methanotrophs: from ecology to microbial resource management”, is to develop the concept of managing microbial methanotrophic communities by (i) the transposition and selection of natural methane-oxidizing inocula in diverse conditions, (ii) identifying, isolating and preserving the key microbial partners in these consortia and (iii) exploring methanotroph applications relevant to the society. As LM-UGent had no prior experience or expertise in working with these organisms, several tools had to be implemented initially in order to perform the experiments described throughout the thesis and to initiate this exciting new research line at the lab. 4 Part A - General Introduction An introduction to aerobic methane-oxidizing bacteria METHANE-OXIDIZING BACTERIA Definition Methanotrophs are microorganisms defined by their ability to generate energy via the oxidation of the greenhouse gas methane (Semrau et al., 2010). In this way, all methanotrophs fully oxidize CH4 to CO2 (Chistoserdova, 2011; Joye, 2012). The organisms that fulfill this definition are remarkably diverse. In anaerobic environments, both archaea and bacteria can oxidize methane. Anaerobic methanotrophic archaea couple methane oxidation
Load more

Recommended publications
  • Isolation and Characterisation of Methylocystis Spp. for Poly-3
    Rumah et al. AMB Expr (2021) 11:6 https://doi.org/10.1186/s13568-020-01159-4 ORIGINAL ARTICLE Open Access Isolation and characterisation of Methylocystis spp. for poly-3-hydroxybutyrate production using waste methane feedstocks Bashir L. Rumah† , Christopher E. Stead† , Benedict H. Claxton Stevens , Nigel P. Minton , Alexander Grosse‑Honebrink and Ying Zhang* Abstract Waste plastic and methane emissions are two anthropogenic by‑products exacerbating environmental pollution. Methane‑oxidizing bacteria (methanotrophs) hold the key to solving these problems simultaneously by utilising otherwise wasted methane gas as carbon source and accumulating the carbon as poly‑3‑hydroxybutyrate, a biode‑ gradable plastic polymer. Here we present the isolation and characterisation of two novel Methylocystis strains with the ability to produce up to 55.7 1.9% poly‑3‑hydroxybutyrate of cell dry weight when grown on methane from diferent waste sources such as landfll± and anaerobic digester gas. Methylocystis rosea BRCS1 isolated from a recrea‑ tional lake and Methylocystis parvus BRCS2 isolated from a bog were whole genome sequenced using PacBio and Illumina genome sequencing technologies. In addition to potassium nitrate, these strains were also shown to grow on ammonium chloride, glutamine and ornithine as nitrogen source. Growth of Methylocystis parvus BRCS2 on Nitrate Mineral Salt (NMS) media with 0.1% methanol vapor as carbon source was demonstrated. The genetic tractability by conjugation was also determined with conjugation efciencies up to 2.8 10–2 and 1.8 10–2 for Methylocystis rosea BRCS1 and Methylocystis parvus BRCS2 respectively using a plasmid with ColE1× origin of ×replication. Finally, we show that Methylocystis species can produce considerable amounts of poly‑3‑hydroxybutyrate on waste methane sources without impaired growth, a proof of concept which opens doors to their use in integrated bio‑facilities like landflls and anaerobic digesters.
    [Show full text]
  • Iguchi, Hiroyuki; Yurimoto, Hiroya; Sakai, Yasuyoshi
    View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Kyoto University Research Information Repository Methylovulum miyakonense gen. nov., sp. nov., a type I Title methanotroph isolated from forest soil. Author(s) Iguchi, Hiroyuki; Yurimoto, Hiroya; Sakai, Yasuyoshi International journal of systematic and evolutionary Citation microbiology (2011), 61(4): 810-815 Issue Date 2011-04 URL http://hdl.handle.net/2433/197236 This is an author accepted manuscript (AAM) that has been accepted for publication in International Journal of Systematic and Evolutionary Microbiology that has not been copy-edited, typeset or proofed. The Society for General Microbiology (SGM) does not permit the posting Right of AAMs for commercial use or systematic distribution. SGM disclaims any responsibility or liability for errors or omissions in this version of the manuscript or in any version derived from it by any other parties. The final version is available athttp://dx.doi.org/10.1099/ijs.0.019604-0 Type Journal Article Textversion author Kyoto University 1 Methylovulum miyakonense gen. nov., sp. nov., a novel 2 type I methanotroph from a forest soil in Japan 3 4 5 6 Hiroyuki Iguchi, Hiroya Yurimoto and Yasuyoshi Sakai 7 8 9 Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto 10 University, Kitashirakawa-Oiwake, Sakyo-ku, Kyoto 606-8502, Japan. 11 12 Author for correspondence: Yasuyoshi Sakai. Tel: +81 75 753 6385. Fax: +81 13 75 753 6454. E-mail: [email protected] 14 15 16 Subject category: Proteobacteria. 17 Runnning title: Methylovulum miyakonense gen. nov., sp.
    [Show full text]
  • Fatty Acid 13C-Fingerprinting in Mytilid-Bacteria Symbiosis
    Discussion Paper | Discussion Paper | Discussion Paper | Discussion Paper | Biogeosciences Discuss., 7, 3453–3475, 2010 Biogeosciences www.biogeosciences-discuss.net/7/3453/2010/ Discussions BGD doi:10.5194/bgd-7-3453-2010 7, 3453–3475, 2010 © Author(s) 2010. CC Attribution 3.0 License. Fatty acid This discussion paper is/has been under review for the journal Biogeosciences (BG). 13C-fingerprinting in Please refer to the corresponding final paper in BG if available. Mytilid-bacteria symbiosis Tracing carbon assimilation in V. Riou et al. endosymbiotic deep-sea hydrothermal vent Mytilid fatty acids by Title Page 13 C-fingerprinting Abstract Introduction Conclusions References V. Riou1,2, S. Bouillon1,3, R. Serrao˜ Santos2, F. Dehairs1, and A. Colac¸o2 Tables Figures 1Department of Analytical and Environmental Chemistry, Vrije Universiteit Brussel, Brussels, Belgium J I 2Department of Oceanography and Fisheries, IMAR-University of Azores, Horta, Portugal 3Department of Earth and Environmental Sciences, Katholieke Universiteit Leuven, J I Leuven, Belgium Back Close Received: 4 May 2010 – Accepted: 5 May 2010 – Published: 10 May 2010 Full Screen / Esc Correspondence to: V. Riou (virginie [email protected]) Published by Copernicus Publications on behalf of the European Geosciences Union. Printer-friendly Version Interactive Discussion 3453 Discussion Paper | Discussion Paper | Discussion Paper | Discussion Paper | Abstract BGD Bathymodiolus azoricus mussels thrive at Mid-Atlantic Ridge hydrothermal vents, where part of their energy requirements
    [Show full text]
  • Large Scale Biogeography and Environmental Regulation of 2 Methanotrophic Bacteria Across Boreal Inland Waters
    1 Large scale biogeography and environmental regulation of 2 methanotrophic bacteria across boreal inland waters 3 running title : Methanotrophs in boreal inland waters 4 Sophie Crevecoeura,†, Clara Ruiz-Gonzálezb, Yves T. Prairiea and Paul A. del Giorgioa 5 aGroupe de Recherche Interuniversitaire en Limnologie et en Environnement Aquatique (GRIL), 6 Département des Sciences Biologiques, Université du Québec à Montréal, Montréal, Québec, Canada 7 bDepartment of Marine Biology and Oceanography, Institut de Ciències del Mar (ICM-CSIC), Barcelona, 8 Catalunya, Spain 9 Correspondence: Sophie Crevecoeur, Canada Centre for Inland Waters, Water Science and Technology - 10 Watershed Hydrology and Ecology Research Division, Environment and Climate Change Canada, 11 Burlington, Ontario, Canada, e-mail: [email protected] 12 † Current address: Canada Centre for Inland Waters, Water Science and Technology - Watershed Hydrology and Ecology Research Division, Environment and Climate Change Canada, Burlington, Ontario, Canada 1 13 Abstract 14 Aerobic methanotrophic bacteria (methanotrophs) use methane as a source of carbon and energy, thereby 15 mitigating net methane emissions from natural sources. Methanotrophs represent a widespread and 16 phylogenetically complex guild, yet the biogeography of this functional group and the factors that explain 17 the taxonomic structure of the methanotrophic assemblage are still poorly understood. Here we used high 18 throughput sequencing of the 16S rRNA gene of the bacterial community to study the methanotrophic 19 community composition and the environmental factors that influence their distribution and relative 20 abundance in a wide range of freshwater habitats, including lakes, streams and rivers across the boreal 21 landscape. Within one region, soil and soil water samples were additionally taken from the surrounding 22 watersheds in order to cover the full terrestrial-aquatic continuum.
    [Show full text]
  • Technologies for the Bioconversion of Methane Into More Valuable Products
    Revised manuscript_ COBIOT_2017 Technologies for the bioconversion of methane into more valuable products S. Cantera, R. Muñoz, R, Lebrero, J.C López, Y. Rodríguez, P A. García-Encina* Department of Chemical Engineering and Environmental Technology, Valladolid University, Dr. Mergelina, s/n, Valladolid, Spain, Tel. +34 983186424, Fax: 983423013. [email protected] Abstract Methane, with a global warming potential twenty five times higher than that of CO2 is the second most important greenhouse gas emitted nowadays. Its bioconversion into microbial molecules with a high retail value in the industry offers a potential cost-efficient and environmentally friendly solution for mitigating anthropogenic diluted CH4-laden streams. Methane bio-refinery for the production of different compounds such as ectoine, feed proteins, biofuels, bioplastics and polysaccharides, apart from new bioproducts characteristic of methanotrophic bacteria, has been recently tested in discontinuous and continuous bioreactors with promising results. This review constitutes a critical discussion about the state-of-the-art of the potential and research niches of biotechnologies applied in a CH4 biorefinery approach. Keywords: CH4 bio-refinery, methane treatment, bio-products, industrial approach Graphical_abstract_COBIOT_2017 Highlights_COBIOT_2017 • Methanotrophs as a competitive platform for the generation of valuable products • CH4 emissions used as a feedstock in biorefinery reduces GHGs environmental impact • Current biotechnological limitations and potential improvements are reviewed • Environmental and economic analysis supports the feasibility of CH4 revalorization Manuscript_COBIOT_2017 Technologies for the bioconversion of methane into more valuable products S. Cantera, R. Muñoz, R, Lebrero, J.C López, Y. Rodríguez, P A. García-Encina* Department of Chemical Engineering and Environmental Technology, Valladolid University, Dr. Mergelina, s/n, Valladolid, Spain, Tel.
    [Show full text]
  • Characterizing Methanogen and Methanotroph Diversity, Abundance and Activity Within the Hampshire-Avon Catchment
    Characterizing methanogen and methanotroph diversity, abundance and activity within the Hampshire-Avon catchment A thesis submitted for the degree of PhD G. Leung Supervisors: Dr. C. Whitby, Prof. D. Nedwell (University of Essex) 1 Summary: Methane (CH4) is an important greenhouse gas and research into its production and oxidation by microbial communities is crucial in predicting their impact in future climate change. Here, potential rate measurements, quantitative real-time polymerase chain reactions (Q-PCR) of pmoA, mcrA genes and next generation sequencing, were applied to characterize methanogen and methanotroph community structure, abundance and activity in the Hampshire-Avon catchment, UK. Soil and river sediments were taken from sites across different underlying geologies based on their baseflow index (BFI); from low (chalk) to medium (greensand) to high BFI (clay). In general, methane oxidation potentials (MOP) and methane production potentials (MPP) were greater in river sediments compared to soils (particularly higher in clays). Sequence analysis identified Methanococcoides, Methanosarcina and Methanocorpusculum as candidates driving methanogenesis across all river geologies. Methylocystis was also found to predominate in all the river sediments and may be a key methane oxidiser. In soils microcosms, MOP doubled when temperature was increased from 4oC to 30oC (in greensand soils sampled in summer but not winter). In long-term in-situ field warming experiments, MOP was unaffected by temperature in the clay and chalk soils, whereas MOP increased by two-fold in the greensand soils. In both microcosms and field warming experiments pmoA abundance was unchanged. In soil microcosms amended with nitrogen (N) and phosphate (P), high N and low P concentrations had the greatest inhibition on methane oxidation in clay soils, whilst chalk and greensand soils were unaffected.
    [Show full text]
  • Denitrification and the Hypoxic Response in Obligate Aerobic Methane-Oxidizing Bacteria
    Denitrification and the hypoxic response in obligate aerobic methane-oxidizing bacteria By Kerim Dimitri Kits A thesis submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy In Microbiology and Biotechnology Department of Biological Sciences University of Alberta Kerim Dimitri Kits, 2016 Abstract Aerobic methanotrophic bacteria lessen the impact of the greenhouse gas methane (CH4) not only because they are a sink for atmospheric methane but also because they oxidize it before it is emitted to the atmospheric reservoir. Aerobic methanotrophs, unlike anaerobic methane oxidizing archaea, have a dual need for molecular oxygen (O2) for respiration and CH4 oxidation. Nevertheless, methanotrophs are highly abundant and active in environments that are extremely hypoxic and even anaerobic. While the O2 requirement in these organisms for CH4 oxidation is inflexible, recent genome sequencing efforts have uncovered the presence of putative denitrification genes in many aerobic methanotrophs. Being able to use two different terminal electron acceptors – hybrid respiration – would be massively advantageous to aerobic methanotrophs as it would allow them to halve their O2 requirement. But, the function of these genes that hint at an undiscovered respiratory anaerobic metabolism is unknown. Moreover, past work on pure cultures of aerobic methanotrophs ruled out the possibility that these organisms - denitrify. An organism that can couple CH4 oxidation to NO3 respiration so far does not exist in pure culture. So while the role of aerobic methanotrophs in the carbon cycle is appreciated, the hypoxic metabolism and contribution of these specialized microorganisms to the nitrogen cycle is not understood. Here we demonstrate using cultivation dependent approaches, microrespirometry, and whole genome, transcriptome, and proteome analysis that an aerobic - methanotroph – Methylomonas denitrificans FJG1 – couples CH4 oxidation to NO3 respiration - with N2O as the terminal product via the intermediates NO2 and NO.
    [Show full text]
  • 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.
    [Show full text]
  • 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.
    [Show full text]
  • International Journal of Systematic and Evolutionary Microbiology
    International Journal of Systematic and Evolutionary Microbiology Methylovulum psychrotolerans sp. nov., a cold-adapted methanotroph from low- temperature terrestrial environments and emended description of the genus Methylovulum --Manuscript Draft-- Manuscript Number: IJSEM-D-15-00727R2 Full Title: Methylovulum psychrotolerans sp. nov., a cold-adapted methanotroph from low- temperature terrestrial environments and emended description of the genus Methylovulum Short Title: Methylovulum psychrotolerans sp. nov. Article Type: Note Section/Category: New taxa - Proteobacteria Keywords: Methylovulum psychrotolerans sp. nov.; cold-adapted methanotrophs; methane oxidation at low temperatures; West Siberian methane seeps; subarctic freshwater lakes Corresponding Author: Svetlana N. Dedysh, Doctor of Sciences Winogradsky Institute of Microbiology, Russian Academy of Sciences Moscow, RUSSIAN FEDERATION First Author: Igor Y. Oshkin Order of Authors: Igor Y. Oshkin Svetlana E. Belova, PhD Olga V. Danilova, PhD Kirill K. Miroshnikov W. Irene C. Rijpstra Jaap S. Sinninghe Damste, Prof. Werner Liesack, Prof. Svetlana N. Dedysh, Doctor of Sciences Manuscript Region of Origin: RUSSIAN FEDERATION Abstract: Two isolates of aerobic methanotrophic bacteria, strains Sph1T and Sph2, were obtained from cold methane seeps in a floodplain of the river Mukhrinskaya, Irtysh basin, West Siberia. Another morphologically and phenotypically similar methanotroph, strain OZ2, was isolated from a sediment of a subarctic freshwater lake, Archangelsk region, Northern Russia. Cells of these three strains were Gram-stain-negative, light- pink-pigmented, non-motile, encapsulated, large cocci that contained an intracytoplasmic membrane system typical of type I methanotrophs. They possessed a particulate methane monooxygenase enzyme and utilized only methane and methanol. Strains Sph1T, Sph2, and OZ2 were able to grow at a pH range of 4.0-8.9 (optimum at 6.0-7.0) and at temperatures between 2 and 36°C.
    [Show full text]
  • 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.
    [Show full text]
  • Iguchi, Hiroyuki; Yurimoto, Hiroya; Sakai, Yasuyoshi
    Methylovulum miyakonense gen. nov., sp. nov., a type I Title methanotroph isolated from forest soil. Author(s) Iguchi, Hiroyuki; Yurimoto, Hiroya; Sakai, Yasuyoshi International journal of systematic and evolutionary Citation microbiology (2011), 61(4): 810-815 Issue Date 2011-04 URL http://hdl.handle.net/2433/197236 This is an author accepted manuscript (AAM) that has been accepted for publication in International Journal of Systematic and Evolutionary Microbiology that has not been copy-edited, typeset or proofed. The Society for General Microbiology (SGM) does not permit the posting of AAMs for commercial use or systematic distribution. SGM disclaims any Right responsibility or liability for errors or omissions in this version of the manuscript or in any version derived from it by any other parties. The final version is available at http://dx.doi.org/10.1099/ijs.0.019604-0; This is not the published version. Please cite only the published version.; この 論文は出版社版でありません。引用の際には出版社版を ご確認ご利用ください。 Type Journal Article Textversion author Kyoto University 1 Methylovulum miyakonense gen. nov., sp. nov., a novel 2 type I methanotroph from a forest soil in Japan 3 4 5 6 Hiroyuki Iguchi, Hiroya Yurimoto and Yasuyoshi Sakai 7 8 9 Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto 10 University, Kitashirakawa-Oiwake, Sakyo-ku, Kyoto 606-8502, Japan. 11 12 Author for correspondence: Yasuyoshi Sakai. Tel: +81 75 753 6385. Fax: +81 13 75 753 6454. E-mail: [email protected] 14 15 16 Subject category: Proteobacteria. 17 Runnning title: Methylovulum miyakonense gen. nov., sp. nov. 18 Abbreviations: pMMO, particulate methane monooxygenase; sMMO, soluble 19 methane monooxygenase; NMS, nitrate mineral salt.
    [Show full text]