DOCSLIB.ORG

Methanotrophs: Promising Bacteria for Environmental Remediation

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Methanotrophs: Promising Bacteria for Environmental Remediation Int. J. Environ. Sci. Technol. (2014) 11:241–250 DOI 10.1007/s13762-013-0387-9 REVIEW Methanotrophs: promising bacteria for environmental remediation V. C. Pandey • J. S. Singh • D. P. Singh • R. P. Singh Received: 13 October 2011 / Revised: 16 June 2012 / Accepted: 1 December 2012 / Published online: 7 November 2013 Ó Islamic Azad University (IAU) 2013 Abstract Methanotrophs are unique and ubiquitous bac- Introduction teria that utilize methane as a sole source of carbon and energy from the atmosphere. Besides, methanotrophs may There is a growing concern about global warming world- also be targeted for bioremediation of diverse type of heavy wide. Methane (CH4) is one of the greenhouse gases metals and organic pollutants owing to the presence of (GHGs), which contributes to global warming. Methane is broad-spectrum methane monooxygenases enzyme. They about 23 times more effective as a greenhouse gas than are highly specialized group of aerobic bacteria and have a carbon dioxide (CO2) (Hasin et al. 2010). Methanotrophs unique capacity for oxidation of certain types of organic are the only known significant biological sink for atmo- pollutants like alkanes, aromatics, halogenated alkenes, etc. spheric CH4 and play a crucial role in reducing CH4 load Oxidation reactions are initiated by methane monooxyge- up to 15 % to the total global CH4 destruction (Singh et al. nases enzyme, which can be expressed by methanotrophs in 2010). Methanotrophs exist in a variety of habitats due to the absence of copper. The present article describes briefly having physiologically versatile nature and found in a wide the concerns regarding the unusual reactivity and broad range of pH, temperature, oxygen concentrations, salinity, substrate profiles of methane monooxygenases, which indi- heavy metal concentrations, and radiation (Barcena et al. cate many potential applications in bioremediation of heavy 2010; Dubey 2005; Durisch-Kaiser et al. 2005; Lindner metals and toxic organic compounds. Research is needed to et al. 2007; Tsubota et al. 2005). Broad-spectrum methane- develop understanding in plant–methanotrophs interactions oxidizing methane monooxygenase (MMO) enzyme is that optimize methanotrophs utilization in the field of envi- found only in methanotrophs, which possess two forms, ronmental remediation, while supporting other ecosystem namely membrane-associated or particulate form (pMMO) services. and soluble or cytoplasmic form (sMMO). The pMMO is found in all known methanotrophs except for the genus Keywords Bioremediation Á Heavy metals Á Methylocella (acidophilic) (Theisen et al. 2005), while the Methanotrophs Á Organic pollutants sMMO is present only in a few methanotroph strains (Murrell et al. 2000a, b). There are several sources that generate huge amount of V.C. Pandey and J.S. Singh contributed equally as first author. toxic heavy metals/metalloids (Cr, Cd, Pb, As, Cu, Zn, Ni, Hg, etc.) and organic pollutants into the environment V. C. Pandey (&) Á D. P. Singh Á R. P. Singh (Wijnhoven et al. 2007). Soils contaminated with heavy Department of Environmental Science, Babasaheb Bhimrao metals and/or organic pollutants are generally left aban- Ambedkar (Central) University, Lucknow 226025, Uttar Pradesh, India doned for several years and therefore may not be safe for e-mail: [email protected] agricultural production. Recently, microbial bioremedia- tion techniques have been found to alleviate the metal/ J. S. Singh organic pollutant toxicity of contaminated soils (Hasin Department of Environmental Microbiology, Babasaheb Bhimrao Ambedkar (Central) University, Lucknow 226025, et al. 2010; Shukla et al. 2009). Methanotrophs may be Uttar Pradesh, India promising bacteria for environmental bioremediation 123 242 Int. J. Environ. Sci. Technol. (2014) 11:241–250 (Jiang et al. 2010). Methanotrophs have been shown to methanotrophs (Jiang et al. 2010; Kikuchi et al. 2002; degrade/co-oxidize diverse type of heavy metals and Shukla et al. 2009). The majority of methanotrophs are organic pollutants due to the presence of broad-spectrum known to produce particulate methane monooxygenase MMO (Lindner et al. 2005; McFarland et al. 1992; Smith (pMMO) except few strains like Methylcella palustris and Dalton 2004). The MMO has been shown to oxidize a (Dedysh et al. 2000)—a known producer of soluble wide range of substrates, including aromatic compounds methane monooxygenase (sMMO). The sMMO-expressing viz. halogenated benzenes, toluene, and styrene as well as methanotrophs, due to their relatively broad substrate range aliphatic hydrocarbons with up to eight carbons (Burrows (Shigematsu et al. 1999) and fast turnover kinetics, exhibit et al. 1984; Colby et al. 1977; Green and Dalton 1989). fast decline in the level of pollutants than that calculated Some of the comprehensive review articles provide for pMMO-expressing methanotrophs. In contrast to basic status and different perspectives of methanotrophs pMMO, which works on a very narrow spectrum of carbon viz. research history (Dalton 2005), extremophilic met- substrate (alkanes and alkenes), the sMMO is capable of hanotrophs (Trotsenko and Khmelenina 2002), taxonomy oxidizing a wider range of organic compounds including and ecology (Hanson and Hanson 1996), methanotrophs aliphatic, aromatic hydrocarbons, and their halogenated and CH4 oxidation related to wetlands (Chowdhury and derivatives (Trotsenko and Murrell 2008). Dick 2013), properties of methane monooxygenase (MMO) In contrast to other microbes that are recognized to (Lieberman and Rosenzweig 2005), metabolic aspects degrade halogenated hydrocarbons via reductive pathways (Trotsenko and Murrell 2008), biochemistry (Anthony (Maymo-Gatell et al. 1999), the biodegradation of chlori- 1982; Hakemian and Rosenzweig 2007), gene regulation nated hydrocarbons by methanotrophs occurs in an oxida- (Murrell et al. 2000a, b), biotechnological applications tive manner (Lontoh et al. 2000). The oxidative (Dalton 2005; Trotsenko and Khmelenina 2005), molecular biodegradation carried out by MMO appears more signif- marker (Dumont and Murrell 2005; McDonald et al. 2007). icant than the reductive dechlorination of chlorinated eth- None of them paid attention to explain about bioremedia- enes, such as TCE and tetrachloroethylene, which often tion potential of methanotrophs. So, there is an urgent need results into accumulation of more toxic intermediates, e.g., to re-tabulate the real involvement and benefits of this vinyl chloride, a known potent carcinogen (Maymo-Gatell unique microbe in bioremediation of toxic pollutants. et al. 1999). On the contrary, the MMO-mediated oxidative Broad substrate profiles of MMOs and its unusual reac- mechanisms of degradation of halogenated compounds by tivity indicate diverse potential applications of methano- the methanotrophs do not accumulate hazardous interme- trophs in bioremediation. Advancement in our knowledge diates (McCue et al. 2002). Thus, the applicability of about methanotrophic bioremediation may facilitate their methanotrophic degradation of halogenated hydrocarbons wide applications for safe and sustainable environmental for in situ bioremediation of contaminated soil and water development. This article has been aimed to highlight the system can be a safer remediation technique for sustainable bioremediation potential of methanotrophs and provides a development of the environment. moderate review on the progress made in methanotrophic Earlier it has been reported that trichloroethylene research related to bioremediation and identifying the (haloalkenes), a volatile chlorinated organic pollutant, is critical research needs for developing and implementing generally resistant to biodegradation by microorganisms successful methanotrophic bioremediation as a model (Wilson and Wilson 1985), but methanotrophs have been worldwide. The possible ways to maximize its multiple shown to co-metabolize trichloroethylene by the potent uses for mitigating the various pollutants are also MMO enzyme (Van Hylckama Vlieg and Janssen 2001). suggested. Stockholm Convention banned the use of persistent organic pollutants (POPs) like lindane, which are highly carcino- genic, persistent, bio-accumulative and endocrine disruptor Remediation of hazardous organic pollutants (ATSDR 2005). Under aerobic conditions, the degradation by methanotrophs of lindane [c-hexachlorocyclohexane (C6H6Cl6)] by bac- teria occurs through repeated steps of dehydrochlorination Methanotrophs synthesize both particulate and soluble and dechlorination, and it gets converted to chlorobenzenes forms of methane monooxygenases (pMMO and sMMO, and the end-product is carbon dioxide, which can be taken respectively), which can co-metabolize diverse type of up by plants (Mathur and Saha 1975; Vonk and Quirijns hydrocarbons and halogenated organic compounds 1979). New, low cost and rapid screening tool for the including aromatics. The priority pollutants like trichloro- detection of microbes capable of degrading lindane has ethylene (TCE) can be easily degraded by application of been discovered (Phillips et al. 2001). The same assay 123 Int. J. Environ. Sci. Technol. (2014) 11:241–250 243 technique may be used for identifying lindane-degrading trichlorohydroquinone and dichlorohydroquinone, because methanotrophs. Thus, there is an urgent need to examine the activity of monooxygenase and dioxygenase was degradation of lindane by the potent MMO enzyme of the inhibited by the substituted chlorine (Rasul and Chapala- methanotrophs. Similarly, the methanotrophs-mediated
Load more

Recommended publications
  • Downloaded from the Fungene Database (
    bioRxiv preprint doi: https://doi.org/10.1101/2020.09.21.307504; this version posted September 22, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Enhancement of nitrous oxide emissions in soil microbial consortia via copper competition between proteobacterial methanotrophs and denitrifiers Jin Chang,a,b Daehyun Daniel Kim,a Jeremy D. Semrau,b Juyong Lee,a Hokwan Heo,a Wenyu Gu,b* Sukhwan Yoona# aDepartment of Civil and Environmental Engineering, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Korea bDepartment of Civil and Environmental Engineering, University of Michigan, Ann Arbor, MI, 48109 Running Title: Methanotrophic influence on N2O emissions #Address correspondence to Sukhwan Yoon, [email protected]. *Present address: Department of Civil & Environmental Engineering, Stanford University, Palo Alto CA, 94305 bioRxiv preprint doi: https://doi.org/10.1101/2020.09.21.307504; this version posted September 22, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Abstract Unique means of copper scavenging have been identified in proteobacterial methanotrophs, particularly the use of methanobactin, a novel ribosomally synthesized post-translationally modified polypeptide that binds copper with very high affinity. The possibility that copper sequestration strategies of methanotrophs may interfere with copper uptake of denitrifiers in situ and thereby enhance N2O emissions was examined using a suite of laboratory experiments performed with rice paddy microbial consortia. Addition of purified methanobactin from Methylosinus trichosporium OB3b to denitrifying rice paddy soil microbial consortia resulted in substantially increased N2O production, with more pronounced responses observed for soils with lower copper content.
    [Show full text]
  • Global Molecular Analyses of Methane Metabolism in Methanotrophic Alphaproteobacterium, Methylosinus Trichosporium Ob3b
    ORIGINAL RESEARCH ARTICLE published: 03 April 2013 doi: 10.3389/fmicb.2013.00070 Global molecular analyses of methane metabolism in methanotrophic Alphaproteobacterium, Methylosinus trichosporium OB3b. Part II. metabolomics and 13C-labeling study SongYang 1, Janet B. Matsen1, Michael Konopka1, Abigail Green-Saxena2, Justin Clubb1, Martin Sadilek 3, Victoria J. Orphan4, David Beck 1,5 and Marina G. Kalyuzhnaya6* 1 Department of Chemical Engineering, University of Washington, Seattle, WA, USA 2 Division of Biology, California Institute of Technology, Pasadena, CA, USA 3 Department of Chemistry, University of Washington, Seattle, WA, USA 4 Division of Geological and Planetary Sciences; California Institute of Technology, Pasadena, CA, USA 5 eScience Institute, University of Washington, Seattle, WA, USA 6 Department of Microbiology, University of Washington, Seattle, WA, USA Edited by: In this work we use metabolomics and 13C-labeling data to refine central metabolic Amy V. Callaghan, University of pathways for methane utilization in Methylosinus trichosporium OB3b, a model alphapro- Oklahoma, USA teobacterial methanotrophic bacterium. We demonstrate here that similar to non-methane Reviewed by: Alan A. DiSpirito, Ohio State utilizing methylotrophic alphaproteobacteria the core metabolism of the microbe is rep- University, USA resented by several tightly connected metabolic cycles, such as the serine pathway, the Amy V. Callaghan, University of ethylmalonyl-CoA (EMC) pathway, and the citric acid (TCA) cycle. Both in silico estimations Oklahoma, USA and stable isotope labeling experiments combined with single cell (NanoSIMS) and bulk *Correspondence: biomass analyses indicate that a significantly larger portion of the cell carbon (over 60%) is Marina G. Kalyuzhnaya, Department 13 of Microbiology, University of derived from CO2 in this methanotroph.
    [Show full text]
  • Specialized Metabolites from Methylotrophic Proteobacteria Aaron W
    Specialized Metabolites from Methylotrophic Proteobacteria Aaron W. Puri* Department of Chemistry and the Henry Eyring Center for Cell and Genome Science, University of Utah, Salt Lake City, UT, USA. *Correspondence: [email protected] htps://doi.org/10.21775/cimb.033.211 Abstract these compounds and strategies for determining Biosynthesized small molecules known as special- their biological functions. ized metabolites ofen have valuable applications Te explosion in bacterial genome sequences in felds such as medicine and agriculture. Con- available in public databases as well as the availabil- sequently, there is always a demand for novel ity of bioinformatics tools for analysing them has specialized metabolites and an understanding of revealed that many bacterial species are potentially their bioactivity. Methylotrophs are an underex- untapped sources for new molecules (Cimerman- plored metabolic group of bacteria that have several cic et al., 2014). Tis includes organisms beyond growth features that make them enticing in terms those traditionally relied upon for natural product of specialized metabolite discovery, characteriza- discovery, and recent studies have shown that tion, and production from cheap feedstocks such examining the biosynthetic potential of new spe- as methanol and methane gas. Tis chapter will cies indeed reveals new classes of compounds examine the predicted biosynthetic potential of (Pidot et al., 2014; Pye et al., 2017). Tis strategy these organisms and review some of the specialized is complementary to synthetic biology approaches metabolites they produce that have been character- focused on activating BGCs that are not normally ized so far. expressed under laboratory conditions in strains traditionally used for natural product discovery, such as Streptomyces (Rutledge and Challis, 2015).
    [Show full text]
  • Evolution of Methanotrophy in the Beijerinckiaceae&Mdash
    The ISME Journal (2014) 8, 369–382 & 2014 International Society for Microbial Ecology All rights reserved 1751-7362/14 www.nature.com/ismej ORIGINAL ARTICLE The (d)evolution of methanotrophy in the Beijerinckiaceae—a comparative genomics analysis Ivica Tamas1, Angela V Smirnova1, Zhiguo He1,2 and Peter F Dunfield1 1Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada and 2Department of Bioengineering, School of Minerals Processing and Bioengineering, Central South University, Changsha, Hunan, China The alphaproteobacterial family Beijerinckiaceae contains generalists that grow on a wide range of substrates, and specialists that grow only on methane and methanol. We investigated the evolution of this family by comparing the genomes of the generalist organotroph Beijerinckia indica, the facultative methanotroph Methylocella silvestris and the obligate methanotroph Methylocapsa acidiphila. Highly resolved phylogenetic construction based on universally conserved genes demonstrated that the Beijerinckiaceae forms a monophyletic cluster with the Methylocystaceae, the only other family of alphaproteobacterial methanotrophs. Phylogenetic analyses also demonstrated a vertical inheritance pattern of methanotrophy and methylotrophy genes within these families. Conversely, many lateral gene transfer (LGT) events were detected for genes encoding carbohydrate transport and metabolism, energy production and conversion, and transcriptional regulation in the genome of B. indica, suggesting that it has recently acquired these genes. A key difference between the generalist B. indica and its specialist methanotrophic relatives was an abundance of transporter elements, particularly periplasmic-binding proteins and major facilitator transporters. The most parsimonious scenario for the evolution of methanotrophy in the Alphaproteobacteria is that it occurred only once, when a methylotroph acquired methane monooxygenases (MMOs) via LGT.
    [Show full text]
  • Methanotrophic Bacterial Biomass As Potential Mineral Feed Ingredients for Animals
    International Journal of Environmental Research and Public Health Article Methanotrophic Bacterial Biomass as Potential Mineral Feed Ingredients for Animals Agnieszka Ku´zniar 1,*, Karolina Furtak 2 , Kinga Włodarczyk 1, Zofia St˛epniewska 1 and Agnieszka Woli ´nska 1 1 Department of Biochemistry and Environmental Chemistry, The John Paul II Catholic University of Lublin, Konstantynów St. 1 I, 20-708 Lublin, Poland 2 Department of Agriculture Microbiology, Institute of Soil Sciences and Plant Cultivation State Research Institute, Czartoryskich St. 8, 24-100 Puławy, Poland * Correspondence: [email protected]; Tel.: +48-81-454-5461 Received: 14 June 2019; Accepted: 23 July 2019; Published: 26 July 2019 Abstract: Microorganisms play an important role in animal nutrition, as they can be used as a source of food or feed. The aim of the study was to determine the nutritional elements and fatty acids contained in the biomass of methanotrophic bacteria. Four bacterial consortia composed of Methylocystis and Methylosinus originating from Sphagnum flexuosum (Sp1), S. magellanicum (Sp2), S. fallax II (Sp3), S. magellanicum IV (Sp4), and one composed of Methylocaldum, Methylosinus, and Methylocystis that originated from coalbed rock (Sk108) were studied. Nutritional elements were determined using the flame atomic absorption spectroscopy technique after a biomass mineralization stage, whereas the fatty acid content was analyzed with the GC technique. Additionally, the growth of biomass and dynamics of methane consumption were monitored. It was found that the methanotrophic biomass 1 contained high concentrations of K, Mg, and Fe, i.e., approx. 9.6–19.1, 2.2–7.6, and 2.4–6.6 g kg− , respectively.
    [Show full text]
  • Revised Taxonomy of the Methanotrophs: Description of Methylobacter Gen
    INTERNATIONALJOURNAL OF SYSTEMATICBACTERIOLOGY, Oct. 1993, p. 735-753 Vol. 43, No. 4 0020-7713/93/040735-19$02.00/0 Revised Taxonomy of the Methanotrophs: Description of Methylobacter gen. nov., Emendation of Methylococcus, Validation of Methylosinus and Methylocystis Species, and a Proposal that the Family Methylococcaceae Includes Only the Group I Methanotrophs JOHN P. BOWMAN,’?” LINDSAY I. SLY,l PETER D. NICHOLS,2 AND A. C. HAYWARD’ Center for Bacterial Diversity and Identification, Department of Microbiology, The University of Queensland, Brisbane, Queensland 4072, and CSIRO Marine Laboratories, Division of Oceanography, Hobart, Tasmania 7001, Australia Numerical taxonomic, DNA-DNA hybridization, and phospholipid fatty acid composition analyses were performed on an extensive range of methanotrophic strains, including reference strains and environmental isolates obtained from sites throughout eastern Australia. When the results of these studies were related to the results of a study based on genomic physicochemical properties, they clarified group I and I1 methanotroph genus and species interrelationships. The group I methanotrophs were found to be made up of three broadly phenotypically and genotypically homologous clusters of species. The first group I methanotroph cluster included the carotenoid-containing species Methylomonas methanica, Methylomonas fodinarum, and Methy- lomonas aurantiucu. These species represent the true members of the genus Methylomonas. The second group I methanotroph cluster was made up of two subclusters of strains. One subcluster included species not capable of producing resting cells and consisted of the species “Methylomonas ugile,” “Methylomonas alba,” and Methylomonas pelagica. The other subcluster included species capable of forming desiccation-resistant cysts and included Methylococcus luteus, marine Methylomonas-like strains, and Methylococcus whittenburyi.
    [Show full text]
  • Pyani Documentation Release 0.2.9
    pyani Documentation Release 0.2.9 Leighton Pritchard Sep 08, 2021 Contents: 1 Build information 1 2 PyPI version and Licensing 3 3 conda version 5 4 Description 7 5 Reporting problems and requesting improvements9 5.1 Citing pyani ..............................................9 5.2 About pyani .............................................. 29 5.3 QuickStart Guide............................................. 29 5.4 Requirements............................................... 33 5.5 Installation Guide............................................ 37 5.6 Basic Use................................................. 42 5.7 Examples................................................. 51 5.8 pyani subcommands.......................................... 51 5.9 Use With a Scheduler.......................................... 55 5.10 Testing.................................................. 57 5.11 Contributing to pyani .......................................... 58 5.12 Licensing................................................. 59 5.13 pyani package.............................................. 60 5.14 Indices and tables............................................ 114 Python Module Index 115 Index 117 i ii CHAPTER 1 Build information 1 pyani Documentation, Release 0.2.9 2 Chapter 1. Build information CHAPTER 2 PyPI version and Licensing 3 pyani Documentation, Release 0.2.9 4 Chapter 2. PyPI version and Licensing CHAPTER 3 conda version If you’re feeling impatient, please head over to the QuickStart Guide 5 pyani Documentation, Release 0.2.9 6 Chapter 3. conda
    [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]
  • Combined Effects of Carbon and Nitrogen Source to Optimize Growth of Proteobacterial Methanotrophs
    fmicb-09-02239 September 22, 2018 Time: 17:4 # 1 ORIGINAL RESEARCH published: 25 September 2018 doi: 10.3389/fmicb.2018.02239 Combined Effects of Carbon and Nitrogen Source to Optimize Growth of Proteobacterial Methanotrophs Catherine Tays1,2, Michael T. Guarnieri3, Dominic Sauvageau2 and Lisa Y. Stein1* 1 Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada, 2 Department of Chemical and Materials Engineering, University of Alberta, Edmonton, AB, Canada, 3 National Renewable Energy Laboratory, Golden, CO, United States Methane, a potent greenhouse gas, and methanol, commonly called wood alcohol, are common by-products of modern industrial processes. They can, however, be consumed as a feedstock by bacteria known as methanotrophs, which can serve as useful vectors for biotransformation and bioproduction. Successful implementation in industrial settings relies upon efficient growth and bioconversion, and the optimization Edited by: Obulisamy Parthiba Karthikeyan, of culturing conditions for these bacteria remains an ongoing effort, complicated by University of Michigan, United States the wide variety of characteristics present in the methanotroph culture collection. Here, Reviewed by: we demonstrate the variable growth outcomes of five diverse methanotrophic strains – Mariusz Cycon,´ Medical University of Silesia, Poland Methylocystis sp. Rockwell, Methylocystis sp. WRRC1, Methylosinus trichosporium Muhammad Farhan Ul Haque, OB3b, Methylomicrobium album BG8, and Methylomonas denitrificans FJG1 – grown University of East Anglia, on either methane or methanol, at three different concentrations, with either ammonium United Kingdom or nitrate provided as nitrogen source. Maximum optical density (OD), growth rate, *Correspondence: Lisa Y. Stein and biomass yield were assessed for each condition. Further metabolite and fatty [email protected] acid methyl ester (FAME) analyses were completed for Methylocystis sp.
    [Show full text]
  • Entwicklung Eines Datenbank-Gestützten Computerprogramms Zur Taxonomischen Identifizierung Von Mikrobiellen Populationen Auf Molekularbiologischer Basis
    Entwicklung eines Datenbank-gestützten Computerprogramms zur taxonomischen Identifizierung von mikrobiellen Populationen auf molekularbiologischer Basis Anwendung dieses Programms auf die Charakterisierung der Diversität stickstofffixierender und denitrifzierender Mikroorganismen in Abhängigkeit einer Stickstoffdüngung Inaugural-Dissertation zur Erlangung des Doktorgrades der Mathematisch-Naturwissenschaftlichen Fakultät der Universität zu Köln vorgelegt von Christopher Rösch aus München Hundt Druck Köln, 2005 Berichterstatter: Prof. Dr. H. Bothe Prof. Dr. D. Schomburg Tag der mündlichen Prüfung: 11. Juli 2005 Meinen Eltern Abstract The present work aimed at developing a novel method which allows to characterize microbial communities from environmental samples in a comprehensive and rapid way. Approaches tried so far either supplied information about the identity of a small fraction of organisms within the total community (e. g. by sequencing of clone libraries), or demonstrated the diversity of organisms without identifying them (e. g. community profiling). In the approach presented here, a method for determining such profiles (by tRFLP analysis) was combined with an automatic analysis by a computer program (TReFID) newly developed for the current study. For the characterization of microorganisms, three different data bases have been constructed: (1) for denitrifying bacteria: a nosZ data base with 607 entries (2) for dinitrogen fixing bacteria: a nifH data base with 1,318 entries (3) for bacteria in general: a 16S rDNA data base with 22,145 entries Thus a comprehensive data set has been developed particularly for the 16S rRNA gene. The use of the TReFID program now allows investigators to characterize bacterial communities from any environmental sample in a rather comprehensive way. Several control analyses showed that the TReFID program is suited for the analysis of environmental samples.
    [Show full text]
  • Global Molecular Analyses of Methane Metabolism in Methanotrophic Alphaproteobacterium, Methylosinus Trichosporium Ob3b
    View metadata, citation and similar papers at core.ac.uk brought to you by CORE ORIGINAL RESEARCH ARTICLE published:provided 03 April by 2013 Frontiers - Publisher Connector doi: 10.3389/fmicb.2013.00040 Global molecular analyses of methane metabolism in methanotrophic alphaproteobacterium, Methylosinus trichosporium OB3b. Part I: transcriptomic study Janet B. Matsen1, SongYang 1, LisaY. Stein2, David Beck 1,3 and Marina G. Kalyuzhnaya4* 1 Department of Chemical Engineering, University of Washington, Seattle, WA, USA 2 Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada 3 eScience Institute, University of Washington, Seattle, WA, USA 4 Department of Microbiology, University of Washington, Seattle, WA, USA Edited by: Methane utilizing bacteria (methanotrophs) are important in both environmental and Amy V. Callaghan, University of biotechnological applications, due to their ability to convert methane to multicarbon com- Oklahoma, USA pounds. However, systems-level studies of methane metabolism have not been carried out Reviewed by: Svetlana N. Dedysh, Russian in methanotrophs. In this work we have integrated genomic and transcriptomic information Academy of Sciences, Russia to provide an overview of central metabolic pathways for methane utilization in Methylosi- Jeremy Semrau, The University of nus trichosporium OB3b, a model alphaproteobacterial methanotroph. Particulate methane Michigan, USA monooxygenase, PQQ-dependent methanol dehydrogenase, the H4MPT-pathway, and *Correspondence: NAD-dependent formate dehydrogenase are involved in methane oxidation to CO2. All Marina G. Kalyuzhnaya, Department of Microbiology, University of genes essential for operation of the serine cycle, the ethylmalonyl-CoA (EMC) pathway, Washington, Benjamin Hall IRB RM and the citric acid (TCA) cycle were expressed. PEP-pyruvate-oxaloacetate interconversions 455, 616 NE Northlake Place, Seattle, may have a function in regulation and balancing carbon between the serine cycle and the WA 98105, USA.
    [Show full text]
  • Genomic and Physiological Properties of a Facultative Methane-Oxidizing Bacterial Strain of Methylocystis Sp
    microorganisms Article Genomic and Physiological Properties of a Facultative Methane-Oxidizing Bacterial Strain of Methylocystis sp. from a Wetland Gi-Yong Jung 1,2, Sung-Keun Rhee 2, Young-Soo Han 3 and So-Jeong Kim 1,* 1 Geologic Environment Research Division, Korea Institute of Geoscience and Mineral Resources, Daejeon 34132, Korea; [email protected] 2 Department of Microbiology, Chungbuk National University, Cheongju 28644, Korea; [email protected] 3 Department of Environmental Engineering, Chungnam National University, Daejeon 34134, Korea; [email protected] * Correspondence: [email protected]; Tel.: +82-42-868-3311; Fax: +82-42-868-3414 Received: 2 September 2020; Accepted: 30 October 2020; Published: 2 November 2020 Abstract: Methane-oxidizing bacteria are crucial players in controlling methane emissions. This study aimed to isolate and characterize a novel wetland methanotroph to reveal its role in the wetland environment based on genomic information. Based on phylogenomic analysis, the isolated strain, designated as B8, is a novel species in the genus Methylocystis. Strain B8 grew in a temperature range of 15 ◦C to 37 ◦C (optimum 30–35 ◦C) and a pH range of 6.5 to 10 (optimum 8.5–9). Methane, methanol, and acetate were used as carbon sources. Hydrogen was produced under oxygen-limited conditions. The assembled genome comprised of 3.39 Mbp and 59.9 mol% G + C content. The genome contained two types of particulate methane monooxygenases (pMMO) for low-affinity methane oxidation (pMMO1) and high-affinity methane oxidation (pMMO2). It was revealed that strain B8 might survive atmospheric methane concentration. Furthermore, the genome had various genes for hydrogenase, nitrogen fixation, polyhydroxybutyrate synthesis, and heavy metal resistance.
    [Show full text]