Methanospirillum Hungatei GP1 As an S Layer MAX FIRTEL,1 GORDON SOUTHAM,1 GEORGE HARAUZ,2 and TERRY J
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Trace Elements in Anaerobic Biotechnologies
Trace Elements Biotechnologies in Anaerobic Trace Trace Elements in Anaerobic Biotechnologies Edited by Fernando G. Fermoso, Eric van Hullebusch, Gavin Collins, Jimmy Roussel, Ana Paula Mucha and Giovanni Esposito The use of trace elements to promote biogas production features prominently on the agenda for many biogas-producing companies. However, the application of the technique is often characterized by trial-and-error methodology due to the ambiguous and scarce basic knowledge on the impact of trace elements in anaerobic biotechnologies under different process conditions. This book describes and defines the broad landscape in the research area of trace elements in anaerobic biotechnologies, from the level of advanced chemistry and single microbial cells, through to engineering and bioreactor technology and to the fate of trace elements in the environment. The book results from the EU COST Action on ‘The ecological roles of trace metals in anaerobic biotechnologies’. Trace elements in anaerobic biotechnologies is a critical, exceptionally complex and technical Collins, Gavin Hullebusch, van Eric G. Fermoso, Fernando by Edited challenge. The challenging chemistry underpinning the availability of Esposito and Giovanni Mucha Roussel, Ana Paula Jimmy trace elements for biological uptake is very poorly understood, despite the importance of trace elements for successful anaerobic operations across the bioeconomy. This book discusses and places a common understanding of this challenge, with a strong focus on technological Trace Elements tools and solutions. The group of contributors brings together chemists with engineers, biologists, environmental scientists and mathematical modellers, as well as industry representatives, to show an up-to-date vision of the fate of trace elements on anaerobic biotechnologies. -
Taxonomy and Ecology of Methanogens
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Horizon / Pleins textes FEMS Microbiology Reviews 87 (1990) 297-308 297 Pubfished by Elsevier FEMSRE 00180 Taxonomy and ecology of methanogens J.L. Garcia Laboratoire de Microbiologie ORSTOM, Université de Provence, Marseille, France Key words: Methanogens; Archaebacteria; Taxonomy; Ecology 1. INTRODUCTION methane from CO2 using alcohols as hydrogen donors; 2-propanol is oxidized to acetone, and More fhan nine reviews on taxonomy of 2-butanol to 2-butanone. Carbon monoxide may methanogens have been published during the last also be converted into methane; most hydro- decade [l-91, after the discovery of the unique genotrophic species (60%) will also use formate. biochemical and genetic properties of these Some aceticlastic species are incapable of oxidiz- organisms led to the concept of Archaebacteria at ing H,. The aceticlastic species of the genus the end of the seventies. Moreover, important Methanosurcina are the most metabolically diverse economic factors have ,placed these bacteria in the methanogens, whereas the obligate aceticlastic limelight [5], including the need to develop alter- Methanosaeta (Methanothrix) can use only acetate. native forms of energy, xenobiotic pollution con- The taxonomy of the methanogenic bacteria trol, the enhancement of meat yields in the cattle has been extensively revised in the light of new industry, the distinction between biological and information based on comparative studies of 16 S thermocatalytic petroleum generation, and the rRNA oligonucleotide sequences, membrane lipid global distribution of methane in the earth's atmo- composition, and antigenic fingerprinting data. sphere. The phenotypic characteristics often do not pro- vide a sufficient means of distinguishing among taxa or determining the phylogenetic position of a 2. -
Archaea in Coastal Marine Environments (Achabaterla/Phyoey/Batwe Nt/N a Eclogu) EDWARD F
Proc. Natl. Acad. Sci. USA Vol. 89, pp. 5685-5689, June 1992 Ecology Archaea in coastal marine environments (achabaterla/phyoey/batwe nt/n a eclogU) EDWARD F. DELONG* Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA 02543 Communicated by George N. Somero, March 17, 1992 (receivedfor review February 4, 1992) ABSTRACT Archaea (archaebacteria) are a phenotypi- macroaggregate samples, eubacterial- or archaeal-biased cally diverse group of microorganisms that share a common PCR primers were routinely used to exclude the amplification evolutionary history. There are four general phenotypic groups of eukaryotic ribosomal RNA-encoding DNA (rDNA). Sur- of archaea: the methanogens, the extreme halophiles, the prisingly, archaeal rDNA was detected in many samples. sulfate-reducing archaea, and the extreme thermophiles. In the This report describes the detection of two marine archaeal marine environment, archaeal habitats are generally limited to lineages and their preliminary phylogenetic and ecological shallow or deep-sea anaerobic sediments (free-living and en- characterization. dosymbiotic methanogens), hot springs or deep-sea hydrother- mal vents (methanogens, sulfate reducers, and extreme ther- mophiles), and highly saline land-locked seas (halophiles). This METHODS report provides evidence for the widespread occurrence of Bacterioplankton Collection. Coastal water samples were unusual archaea in oxygenated coasl surface waters of North collected and screened through a 10-L&m Nytex mesh prefil- America. Quantitative mates indicated that up to 2% ofthe ter. Bacterioplankton were concentrated from these 10-pm- total ribosomal RNA extracted fom coastal bacterioplankton filtered water samples by using a CH2PR filtration unit assemblages was archaeal. Archaeal small-subunit ribosomal (Amicon) fitted with a polysulfone hollow-fiber filter (30-kDa RNA-encoding DNAs (rDNAs) were coned from mixed bac- cutoff). -
Methanogenic Microorganisms in Industrial Wastewater Anaerobic Treatment
processes Review Methanogenic Microorganisms in Industrial Wastewater Anaerobic Treatment Monika Vítˇezová 1 , Anna Kohoutová 1, Tomáš Vítˇez 1,2,* , Nikola Hanišáková 1 and Ivan Kushkevych 1,* 1 Department of Experimental Biology, Faculty of Science, Masaryk University, 62500 Brno, Czech Republic; [email protected] (M.V.); [email protected] (A.K.); [email protected] (N.H.) 2 Department of Agricultural, Food and Environmental Engineering, Faculty of AgriSciences, Mendel University, 61300 Brno, Czech Republic * Correspondence: [email protected] (T.V.); [email protected] (I.K.); Tel.: +420-549-49-7177 (T.V.); +420-549-49-5315 (I.K.) Received: 31 October 2020; Accepted: 24 November 2020; Published: 26 November 2020 Abstract: Over the past decades, anaerobic biotechnology is commonly used for treating high-strength wastewaters from different industries. This biotechnology depends on interactions and co-operation between microorganisms in the anaerobic environment where many pollutants’ transformation to energy-rich biogas occurs. Properties of wastewater vary across industries and significantly affect microbiome composition in the anaerobic reactor. Methanogenic archaea play a crucial role during anaerobic wastewater treatment. The most abundant acetoclastic methanogens in the anaerobic reactors for industrial wastewater treatment are Methanosarcina sp. and Methanotrix sp. Hydrogenotrophic representatives of methanogens presented in the anaerobic reactors are characterized by a wide species diversity. Methanoculleus -
Rare Horizontal Gene Transfer in a Unique Motility Structure Elie Desmond, Céline Brochier-Armanet, Simonetta Gribaldo
Phylogenomics of the archaeal flagellum: rare horizontal gene transfer in a unique motility structure Elie Desmond, Céline Brochier-Armanet, Simonetta Gribaldo To cite this version: Elie Desmond, Céline Brochier-Armanet, Simonetta Gribaldo. Phylogenomics of the archaeal flagel- lum: rare horizontal gene transfer in a unique motility structure. BMC Evolutionary Biology, BioMed Central, 2007, 7, pp.53-70. 10.1186/1471-2148-7-106. hal-00698404 HAL Id: hal-00698404 https://hal.archives-ouvertes.fr/hal-00698404 Submitted on 7 Apr 2020 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Distributed under a Creative Commons Attribution| 4.0 International License BMC Evolutionary Biology BioMed Central Research article Open Access Phylogenomics of the archaeal flagellum: rare horizontal gene transfer in a unique motility structure Elie Desmond1, Celine Brochier-Armanet2,3 and Simonetta Gribaldo*1 Address: 1Unite Biologie Moléculaire du Gène chez les Extremophiles, Institut Pasteur, 25 rue du Dr. Roux, 75724 Paris Cedex 15, France, 2Université de Provence Aix-Marseille -
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. -
Genome-Based Microbial Taxonomy Coming of Age
Downloaded from http://cshperspectives.cshlp.org/ on September 28, 2021 - Published by Cold Spring Harbor Laboratory Press Genome-Based Microbial Taxonomy Coming of Age Philip Hugenholtz, Adam Skarshewski, and Donovan H. Parks Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia QLD 4072, Australia Correspondence: [email protected] Reconstructing the complete evolutionary history of extant life on our planet will be one of the most fundamental accomplishments of scientific endeavor, akin to the completion of the periodic table, which revolutionized chemistry. The road to this goal is via comparative genomics because genomes are our most comprehensive and objective evolutionary docu- ments. The genomes of plant and animal species have been systematically targeted over the past decade to provide coverage of the tree of life. However, multicellular organisms only emerged in the last 550 million years of more than three billion years of biological evolution and thus comprise a small fraction of total biological diversity. The bulk of biodiversity, both past and present, is microbial. We have only scratched the surface in our understanding of the microbial world, as most microorganisms cannot be readily grown in the laboratory and remain unknown to science. Ground-breaking, culture-independent molecular techniques developed over the past 30 years have opened the door to this so-called microbial dark matter with an accelerating momentum driven byexponential increases in sequencing capacity. We are on the verge of obtaining representative genomes across all life for the first time. However, historical use of morphology, biochemical properties, behavioral traits, and single-marker genes to infer organismal relationships mean that the existing highly incomplete tree is riddled with taxonomic errors. -
Acetomicrobium Hydrogeniformans OS1 Is an Obligate Anaerobic Bacterial Species of the Phylum
UCLA UCLA Electronic Theses and Dissertations Title Hydrogen Metabolism in Syntrophic Microorganisms Permalink https://escholarship.org/uc/item/87b121vn Author Cook, Lauren Publication Date 2019 Peer reviewed|Thesis/dissertation eScholarship.org Powered by the California Digital Library University of California UNIVERSITY OF CALIFORNIA Los Angeles Hydrogen Metabolism in Syntrophic Microorganisms A dissertation submitted in partial satisfaction of the requirements for the degree Doctor of Philosophy in Microbiology, Immunology, and Molecular Genetics by Lauren Emma Cook 2019 © Copyright by Lauren Emma Cook 2019 ABSTRACT OF THE DISSERTATION Hydrogen Metabolism in Syntrophic Microorganisms by Lauren Emma Cook Doctor of Philosophy in Microbiology, Immunology, and Molecular Genetics University of California, Los Angeles, 2019 Professor Robert P. Gunsalus, Chair Acetomicrobium hydrogeniformans OS1 is an obligate anaerobic bacterial species of the phylum Synergistetes that generates an unusually high molar ratio of hydrogen from glucose, thus suggesting an undescribed metabolic ability relative to other hydrogen-forming bacteria. Here, the genomic, proteomic, and enzymatic basis of glucose fermentation in A. hydrogeniformans is examined. A modified Embden-Meyerhoff pathway was revealed that employs a glyceraldehyde-3-phosphate oxidoreductase enzyme (GAPOR) in place of glyceraldehyde-3- phosphate dehydrogenase (GapA) and glycerate kinase (Pkg). A. hydrogeniformans cell extracts exhibited GAPOR as well as pyruvate-ferredoxin oxidoreductase (PFOR) activity in place of GapA, Pgk, pyruvate dehydrogenase (Pdh), or pyruvate formate lyase (Pfl) activity that would generate acetyl-CoA and NADH. Proteomic and enzyme studies revealed that electrons derived from GAPOR and PFOR drive hydrogen formation by a soluble FeFe-type hydrogenase. These A. hydrogeniformans findings demonstrate the presence of an unconventional C6 metabolism that would explain the high hydrogen production. -
Extracellular Electron Uptake in Methanosarcinales Is Independent of Multiheme C-Type Cytochromes Mon Oo Yee & Amelia-Elena Rotaru*
www.nature.com/scientificreports OPEN Extracellular electron uptake in Methanosarcinales is independent of multiheme c-type cytochromes Mon Oo Yee & Amelia-Elena Rotaru* The co-occurrence of Geobacter and Methanosarcinales is often used as a proxy for the manifestation of direct interspecies electron transfer (DIET) in the environment. Here we tested eleven new co- culture combinations between methanogens and electrogens. Previously, only the most electrogenic Geobacter paired by DIET with Methanosarcinales methanogens, namely G. metallireducens and G. hydrogenophilus. Here we provide additional support, and show that fve additional Methanosarcinales paired with G. metallireducens, while a strict hydrogenotroph could not. We also show that G. hydrogenophilus, which is incapable to grow with a strict hydrogenotrophic methanogen, could pair with a strict non-hydrogenotrophic Methanosarcinales. Likewise, an electrogen outside the Geobacter cluster (Rhodoferrax ferrireducens) paired with Methanosarcinales but not with strict hydrogenotrophic methanogens. The ability to interact with electrogens appears to be conserved among Methanosarcinales, the only methanogens with c-type cytochromes, including multihemes (MHC). Nonetheless, MHC, which are often linked to extracellular electron transfer, were neither unique nor universal to Methanosarcinales and only two of seven Methanosarcinales tested had MHC. Of these two, one strain had an MHC-deletion knockout available, which we hereby show is still capable to retrieve extracellular electrons from G. metallireducens or an electrode suggesting an MHC- independent strategy for extracellular electron uptake. Direct interspecies electron transfer (DIET) was discovered in an artifcial co-culture of an ethanol-oxidizing Geobacter metallireducens with a fumarate-reducing Geobacter sulfurreducens where the possibility of hydrogen 1,2 gas (H2) or formate transfer was invalidated through genetic studies . -
Methanospirillum Hungatei</Italic>
ARTICLES PUBLISHED: 5 DECEMBER 2016 | VOLUME: 2 | ARTICLE NUMBER: 16222 CryoEM structure of the Methanospirillum hungatei archaellum reveals structural features distinct from the bacterial flagellum and type IV pilus Nicole Poweleit1,2,PengGe1,2,HongH.Nguyen3,RachelR.OgorzalekLoo3, Robert P. Gunsalus1,4 and Z. Hong Zhou1,2* Archaea use flagella known as archaella—distinct both in protein composition and structure from bacterial flagella—to drive cell motility, but the structural basis of this function is unknown. Here, we report an atomic model of the archaella, based on the cryo electron microscopy (cryoEM) structure of the Methanospirillum hungatei archaellum at 3.4 Å resolution. Each archaellum contains ∼61,500 archaellin subunits organized into a curved helix with a diameter of 10 nm and average length of 10,000 nm. The tadpole-shaped archaellin monomer has two domains, a β-barrel domain and a long, mildly kinked α-helix tail. Our structure reveals multiple post-translational modifications to the archaella, including six O-linked glycans and an unusual N-linked modification. The extensive interactions among neighbouring archaellins explain how the long but thin archaellum maintains the structural integrity required for motility-driving rotation. These extensive inter- subunit interactions and the absence of a central pore in the archaellum distinguish it from both the bacterial flagellum and type IV pili. rokaryotes use a variety of extracellular protein complexes to from images recorded on photographic films and is insufficient to interact with their surrounding environment. Both domains resolve the two domains of monomers within the filament18,19. Pof prokaryotes—archaea and bacteria—express extracellular Because the domains appeared to be a central α-helix and an exterior filaments (called archaella and flagella, respectively) that drive cellu- globular domain, it was hypothesized that the archaellin had a ‘type IV lar motility in the form of ‘swimming’. -
Supplementary Materials
SUPPLEMENTARY TABLE 1. Scientific names of free-living organisms sampled in this study along with taxonomic classification and GO coverage. # Organism Taxonomy Superkingdom GO coverage (%) 1 Aeropyrum pernix K1 Crenarchaeota-Desulfurococcales Archaea 56 2 Sulfolobus solfataricus P2 Crenarchaeota- Sulfolobales Archaea 52 3 Sulfolobus acidocaldarius DSM 639 Crenarchaeota-Sulfolobales Archaea 54 4 Thermofilum pendens Hrk 5 Crenarchaeota-Thermoproteales Archaea 53 5 Pyrobaculum islandicum DSM 4184 Crenarchaeota- Thermoproteales Archaea 52 6 Caldivirga maquilingensis IC-167 Crenarchaeota- Thermoproteales Archaea 58 7 Metallosphaera sedula DSM 5348 Crenarchaeota- Sulfolobales Archaea 55 8 Staphylothermus marinus F1 Crenarchaeota- Desulfurococcales Archaea 55 9 Pyrobaculum calidifontis JCM 11548 Crenarchaeota- Thermoproteales Archaea 52 10 Hyperthermus butylicus DSM 5456 Crenarchaeota- Desulfurococcales Archaea 54 11 Sulfolobus islandicus L.S.2.15 Crenarchaeota- Sulfolobales Archaea 54 12 Thermoproteus neutrophilus V24Sta Crenarchaeota- Thermoproteales Archaea 51 13 Desulfurococcus kamchatkensis 1221n Crenarchaeota- Desulfurococcales Archaea 55 14 Methanosphaerula palustris E1-9c Euryarchaeota- Methanomicrobia Archaea 57 15 Archaeoglobus fulgidus DSM 4304 Euryarchaeota-Archaeoglobi Archaea 56 16 Natronomonas pharaonis DSM 2160 Euryarchaeota-Halobacteria Archaea 52 17 Haloquadratum walsbyi DSM 16790 Euryarchaeota-Halobacteria Archaea 51 18 Halobacterium salinarum R1 Euryarchaeota-Halobacteria Archaea 51 19 Methanobacterium Euryarchaeota-Methanobacteria -
The Halobacterium Salinarum Taxis Signal Transduction Network: a Protein-Protein Interaction Study
Dissertation zur Erlangung des Doktorgrades der Fakultät für Chemie und Pharmazie der Ludwig-Maximilians-Universität München The Halobacterium salinarum Taxis Signal Transduction Network: a Protein-Protein Interaction Study Matthias Schlesner aus Kiel 2008 Erklärung Diese Dissertation wurde im Sinne von § 13 Abs. 3 bzw. 4 der Promotionsordnung vom 29. Januar 1998 von Herrn Prof. Dr. Dieter Oesterhelt betreut. Ehrenwörtliche Versicherung Diese Dissertation wurde selbständig und ohne unerlaubte Hilfe angefertigt. Martinsried, am 07.10.2008 Matthias Schlesner Dissertation eingereicht am: 14.10.2008 1. Gutachter: Prof. Dr. Dieter Oesterhelt 2. Gutachter: Prof. Dr. Wolfgang Marwan Mündliche Prüfung am: 9.12.2008 Meiner Familie Contents Summary xvii 1 Background 1 1.1 H. salinarum, an archaeal model organism ................ 1 1.1.1 Halobacterium salinarum ...................... 1 1.1.2 Archaea ............................... 2 1.1.3 Halophiles and their ecology .................... 3 1.1.4 Adaptation to hypersaline environments ............. 4 1.1.5 Bioenergetics ............................ 5 1.2 Signal transduction and taxis in prokaryotes ............... 7 1.2.1 Two-component systems ...................... 8 1.2.2 The principles of prokaryotic taxis ................ 9 1.3 Protein-protein interaction analysis .................... 10 1.4 Objectives .................................. 12 2 Materials and methods 15 2.1 General materials .............................. 15 2.1.1 Instruments ............................. 15 2.1.2 Chemicals and Kits ......................... 15 2.1.3 Enzymes ............................... 15 2.1.4 Strains ................................ 17 2.1.5 Software ............................... 17 2.2 General methods .............................. 17 2.2.1 Growth and storage of E. coli ................... 17 2.2.2 Growth and storage of H. salinarum ................ 18 2.2.3 Separation of DNA fragments by agarose gel electrophoresis .. 18 2.2.4 Purification of DNA fragments ..................