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Methanothermus Fervidus Type Strain (V24S)
UC Davis UC Davis Previously Published Works Title Complete genome sequence of Methanothermus fervidus type strain (V24S). Permalink https://escholarship.org/uc/item/9367m39j Journal Standards in genomic sciences, 3(3) ISSN 1944-3277 Authors Anderson, Iain Djao, Olivier Duplex Ngatchou Misra, Monica et al. Publication Date 2010-11-20 DOI 10.4056/sigs.1283367 Peer reviewed eScholarship.org Powered by the California Digital Library University of California Standards in Genomic Sciences (2010) 3:315-324 DOI:10.4056/sigs.1283367 Complete genome sequence of Methanothermus fervidus type strain (V24ST) Iain Anderson1, Olivier Duplex Ngatchou Djao2, Monica Misra1,3, Olga Chertkov1,3, Matt Nolan1, Susan Lucas1, Alla Lapidus1, Tijana Glavina Del Rio1, Hope Tice1, Jan-Fang Cheng1, Roxanne Tapia1,3, Cliff Han1,3, Lynne Goodwin1,3, Sam Pitluck1, Konstantinos Liolios1, Natalia Ivanova1, Konstantinos Mavromatis1, Natalia Mikhailova1, Amrita Pati1, Evelyne Brambilla4, Amy Chen5, Krishna Palaniappan5, Miriam Land1,6, Loren Hauser1,6, Yun-Juan Chang1,6, Cynthia D. Jeffries1,6, Johannes Sikorski4, Stefan Spring4, Manfred Rohde2, Konrad Eichinger7, Harald Huber7, Reinhard Wirth7, Markus Göker4, John C. Detter1, Tanja Woyke1, James Bristow1, Jonathan A. Eisen1,8, Victor Markowitz5, Philip Hugenholtz1, Hans-Peter Klenk4, and Nikos C. Kyrpides1* 1 DOE Joint Genome Institute, Walnut Creek, California, USA 2 HZI – Helmholtz Centre for Infection Research, Braunschweig, Germany 3 Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA 4 DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany 5 Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, California, USA 6 Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA 7 University of Regensburg, Archaeenzentrum, Regensburg, Germany 8 University of California Davis Genome Center, Davis, California, USA *Corresponding author: Nikos C. -
Insights Into Archaeal Evolution and Symbiosis from the Genomes of a Nanoarchaeon and Its Inferred Crenarchaeal Host from Obsidian Pool, Yellowstone National Park
University of Tennessee, Knoxville TRACE: Tennessee Research and Creative Exchange Microbiology Publications and Other Works Microbiology 4-22-2013 Insights into archaeal evolution and symbiosis from the genomes of a nanoarchaeon and its inferred crenarchaeal host from Obsidian Pool, Yellowstone National Park Mircea Podar University of Tennessee - Knoxville, [email protected] Kira S. Makarova National Institutes of Health David E. Graham University of Tennessee - Knoxville, [email protected] Yuri I. Wolf National Institutes of Health Eugene V. Koonin National Institutes of Health See next page for additional authors Follow this and additional works at: https://trace.tennessee.edu/utk_micrpubs Part of the Microbiology Commons Recommended Citation Biology Direct 2013, 8:9 doi:10.1186/1745-6150-8-9 This Article is brought to you for free and open access by the Microbiology at TRACE: Tennessee Research and Creative Exchange. It has been accepted for inclusion in Microbiology Publications and Other Works by an authorized administrator of TRACE: Tennessee Research and Creative Exchange. For more information, please contact [email protected]. Authors Mircea Podar, Kira S. Makarova, David E. Graham, Yuri I. Wolf, Eugene V. Koonin, and Anna-Louise Reysenbach This article is available at TRACE: Tennessee Research and Creative Exchange: https://trace.tennessee.edu/ utk_micrpubs/44 Podar et al. Biology Direct 2013, 8:9 http://www.biology-direct.com/content/8/1/9 RESEARCH Open Access Insights into archaeal evolution and symbiosis from the genomes of a nanoarchaeon and its inferred crenarchaeal host from Obsidian Pool, Yellowstone National Park Mircea Podar1,2*, Kira S Makarova3, David E Graham1,2, Yuri I Wolf3, Eugene V Koonin3 and Anna-Louise Reysenbach4 Abstract Background: A single cultured marine organism, Nanoarchaeum equitans, represents the Nanoarchaeota branch of symbiotic Archaea, with a highly reduced genome and unusual features such as multiple split genes. -
Nitrate Decreases Ruminal Methane Production with Slight Changes To
Zhao et al. BMC Microbiology (2018) 18:21 https://doi.org/10.1186/s12866-018-1164-1 RESEARCH ARTICLE Open Access Nitrate decreases ruminal methane production with slight changes to ruminal methanogen composition of nitrate- adapted steers Liping Zhao, Qingxiang Meng, Yan Li, Hao Wu, Yunlong Huo, Xinzhuang Zhang and Zhenming Zhou* Abstract Background: This study was conducted to examine effects of nitrate on ruminal methane production, methanogen abundance, and composition. Six rumen-fistulated Limousin×Jinnan steers were fed diets supplemented with either 0% (0NR), 1% (1NR), or 2% (2NR) nitrate (dry matter basis) regimens in succession. Rumen fluid was taken after two-week adaptation for evaluation of in vitro methane production, methanogen abundance, and composition measurements. Results: Results showed that nitrate significantly decreased in vitro ruminal methane production at 6 h, 12 h, and 24 h (P < 0.01; P < 0.01; P = 0.01). The 1NR and 2NR regimens numerically reduced the methanogen population by 4.47% and 25.82% respectively. However, there was no significant difference observed between treatments. The alpha and beta diversity of the methanogen community was not significantly changed by nitrate either. However, the relative abundance of the methanogen genera was greatly changed. Methanosphaera (PL = 0.0033) and Methanimicrococcus (PL = 0.0113) abundance increased linearly commensurate with increasing nitration levels, while Methanoplanus abundance was significantly decreased (PL = 0.0013). The population of Methanoculleus, the least frequently identified genus in this study, exhibited quadratic growth from 0% to 2% when nitrate was added (PQ = 0.0140). Conclusions: Correlation analysis found that methane reduction was significantly related to Methanobrevibacter and Methanoplanus abundance, and negatively correlated with Methanosphaera and Methanimicrococcus abundance. -
In: Microbial Growth on Compounds. Proceedings of the 5Th International Symposium. / (H.W. Van Verseveld, J.A. Duine Eds.) Pp. 44-51, Nijhoff Publ., Dordrecht (1987)
In: Microbial Growth on Compounds. Proceedings of the 5th International Symposium. / (H.W. van Verseveld, J.A. Duine eds.) pp. 44-51, Nijhoff Publ., Dordrecht (1987). AEROBIC AND ANAEROBIC EXTREMELY THERMOPHILIC AUTOTROPHS R. HUBER G HUBS*. A. SEGERER J. SEGER and K.O. STETTER Lehrstuhl für MkrobJoiogie, Urwers/iát Regensburg, 8400 Regensburg, Federal Repubßc of Germany. 1. INTRODUCTION During the last years, various extremely themioprÄ badend 80X rwe been i»latedfTOT 15,17}.Alof these organisms belong to the archaebacteria, the third kingdom of Be[19]. The mode of nutrition is Hthoautotrophlc or organotrophic, depenolng on the isolates. In this paper, limoautotrophic extreme thermophlles including some very recent isolates are described which are the primary producers of organic matter at high temperatures. 2. BIOTOPES Up ta now, aft extremely therrnophfe autotrophic b^ fieWs and submarine hydPotherinalsysteni& about 400 to 2000 m wM the floor (10]. From tf^^ mainly C02. SO2 and H^S. escape and are heal the sol and surface water. The examination of so* profiles wiminsotfatarlcfields showed^ the top, there is an oxypen^ntaioing strongly aocfcs lay er of about 15 to 30 cm in thickness, which shows an ochre cotoir due to the presence of feró to neutraJ btoish-Wack 20m. which contains ferrous suTxJe. Submarine hydrcmermaJ syalems contain seawater of neutral to sfigMy acxScpH which remains Squid even above 100*C due to the prevenfion of boHmg by the hydros!^ sulfur which ts formed by the oxidation of H^S ana by the reaction of H2S with S02- Seawaler contains atwutjfnmotes of sufate per fitre. 3. -
Environmentalmicrobiology
DE GRUYTER Physical Sciences Reviews. 2017; 20160118 Felicita Briški1 / Marija Vuković Domanovac1 Environmental microbiology 1 Faculty of Chemical Engineering and Technology, University of Zagreb, Marulićev trg 19, HR-10000 Zagreb, Croatia, E-mail: [email protected] Abstract: For most people, microorganisms are out of sight and therefore out of mind but they are large, extremely di- verse group of organisms, they are everywhere and are the dominant form of life on planet Earth. Almost every surface is colonized by microorganisms, including our skin; however most of them are harmless to humans. Some microorganisms can live in boiling hot springs, whereas others form microbial communities in frozen sea ice. Among their many roles, microorganisms are necessary for biogeochemical cycling, soil fertility, decom- position of dead plants and animals and biodegradation of many complex organic compounds present in the environment. Environmental microbiology is concerned with the study of microorganisms in the soil, water and air and their application in bioremediation to reduce environmental pollution through the biological degra- dation of pollutants into non-toxic or less toxic substances. Field of environmental microbiology also covers the topics such as microbially induced biocorrosion, biodeterioration of constructing materials and microbiological quality of outdoor and indoor air. Keywords: microorganisms, environment, indicator microorganisms, biodegradation, bioremediation DOI: 10.1515/psr-2016-0118 Gentlemen, it is the microbes who will have the last word. (Louis Pasteur) 1 Evolution of microorganisms Earth is about 4.5 billion years old and scientists estimate that life first emerged at least 3.8 billion years ago after the surface of crust had cooled enough to allow liquid water to form. -
Implantation Du Microbiote Et Mise En Place Des Fonctions Du Rumen Chez Le Veau De Race Laitière Et Effet De La Supplémentation En Levures Vivantes
En vue de l’obtention du DOCTORAT DE L’UNIVERSITÉ DE TOULOUSE Délivré par : Institut National Polytechnique de Toulouse (INP Toulouse) Discipline ou spécialité : Pathologie, Toxicologie, Génétique et Nutrition Présentée et soutenue par : Mickael Rey Le : 15 novembre 2012 Titre : Implantation du microbiote et mise en place des fonctions du rumen chez le veau de race laitière et effet de la supplémentation en levures vivantes Ecole doctorale : Sciences Ecologiques, Vétérinaires, Agronomiques et Bioingénieries (SEVAB) Unité de recherche : UMR 1289 INRA-INP/ENSAT-ENVT ‘TANDEM’ Directeur(s) de Thèse : Valérie Monteils Francis Enjalbert Rapporteurs : Evelyne Forano Véronique Julliand Membre(s) du jury: Evelyne Forano Véronique Julliand Gérard Fonty Valérie Monteils Francis Enjalbert 1 2 REMERCIEMENTS Ce manuscrit de thèse vient clôturer une belle expérience scientifique et humaine qui a été réalisée au sein de l’UMR 1289 TANDEM (Tissus Animaux, Nutrition, Digestion, Ecosystème, Métabolisme). Pour cela, je souhaiterai remercier toutes les personnes ayant contribué de près ou de loin à l’aboutissement de ce projet. Je tiens à remercier les personnes qui ont accepté de participer à mon jury de thèse : Evelyne Forano (Unité de Microbiologie, INRA, Clermont-Ferrand-Theix), Véronique Julliand (AgroSup Dijon, D2A2E, URANIE-USC INRA Nutrition du cheval athlète, Dijon), pour m’avoir fait l’honneur d’être rapporteurs de cette thèse. Mais aussi Gérard Fonty (Microorganismes : Génome et Environnement, CNRS, Aubière Cedex. France) pour avoir accepté de participer à ce jury et m’avoir fait l’honneur d’en être le président. Je tiens à remercier mes directeurs de thèse, Francis Enjalbert et Valérie Monteils pour leurs encadrements et leurs qualités scientifiques et pédagogiques qui m’ont permis de structurer mon travail au cours de ces trois années. -
Diversity of Archaea Domain in Cuatro Cienegas Basin: Archaean Domes
bioRxiv preprint doi: https://doi.org/10.1101/766709; this version posted September 12, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 1 Diversity of Archaea Domain in Cuatro Cienegas Basin: Archaean Domes 2 3 Medina-Chávez Nahui Olin1, Viladomat-Jasso Mariette2, Olmedo-Álvarez Gabriela3, Eguiarte Luis 4 E2, Souza Valeria2, De la Torre-Zavala Susana1,4 5 6 1Universidad Autónoma de Nuevo León, Facultad de Ciencias Biológicas, Instituto de 7 Biotecnología. Av. Pedro de Alba S/N Ciudad Universitaria. San Nicolás de los Garza, Nuevo León, 8 México. C.P. 66455. 9 2Instituto de Ecología, UNAM, Circuito Exterior S/N anexo Jardín Botánico exterior. Ciudad 10 Universitaria, Ciudad de México, C.P. 04500 11 3Departamento de Ingeniería Genética, Centro de Investigación y de Estudios Avanzados del I.P.N. 12 Campus Guanajuato, AP 629 Irapuato, Guanajuato 36500, México 13 14 4Correspondence should be addressed to Susana De la Torre-Zavala; 15 [email protected]. 16 17 18 19 20 21 22 1 bioRxiv preprint doi: https://doi.org/10.1101/766709; this version posted September 12, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 23 Abstract 24 Herein we describe the Archaea diversity in a shallow pond in the Cuatro Ciénegas Basin (CCB), 25 Northeast Mexico, with fluctuating hypersaline conditions containing elastic microbial mats that 26 can form small domes where their anoxic inside reminds us of the characteristics of the Archaean 27 Eon, rich in methane and sulfur gases; thus, we named this site the Archaean Domes (AD). -
4 Metabolic and Taxonomic Diversification in Continental Magmatic Hydrothermal Systems
Maximiliano J. Amenabar, Matthew R. Urschel, and Eric S. Boyd 4 Metabolic and taxonomic diversification in continental magmatic hydrothermal systems 4.1 Introduction Hydrothermal systems integrate geological processes from the deep crust to the Earth’s surface yielding an extensive array of spring types with an extraordinary diversity of geochemical compositions. Such geochemical diversity selects for unique metabolic properties expressed through novel enzymes and functional characteristics that are tailored to the specific conditions of their local environment. This dynamic interaction between geochemical variation and biology has played out over evolu- tionary time to engender tightly coupled and efficient biogeochemical cycles. The timescales by which these evolutionary events took place, however, are typically in- accessible for direct observation. This inaccessibility impedes experimentation aimed at understanding the causative principles of linked biological and geological change unless alternative approaches are used. A successful approach that is commonly used in geological studies involves comparative analysis of spatial variations to test ideas about temporal changes that occur over inaccessible (i.e. geological) timescales. The same approach can be used to examine the links between biology and environment with the aim of reconstructing the sequence of evolutionary events that resulted in the diversity of organisms that inhabit modern day hydrothermal environments and the mechanisms by which this sequence of events occurred. By combining molecu- lar biological and geochemical analyses with robust phylogenetic frameworks using approaches commonly referred to as phylogenetic ecology [1, 2], it is now possible to take advantage of variation within the present – the distribution of biodiversity and metabolic strategies across geochemical gradients – to recognize the extent of diversity and the reasons that it exists. -
Deep Conservation of Histone Variants in Thermococcales Archaea
bioRxiv preprint doi: https://doi.org/10.1101/2021.09.07.455978; this version posted September 7, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. 1 Deep conservation of histone variants in Thermococcales archaea 2 3 Kathryn M Stevens1,2, Antoine Hocher1,2, Tobias Warnecke1,2* 4 5 1Medical Research Council London Institute of Medical Sciences, London, United Kingdom 6 2Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, 7 United Kingdom 8 9 *corresponding author: [email protected] 10 1 bioRxiv preprint doi: https://doi.org/10.1101/2021.09.07.455978; this version posted September 7, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. 1 Abstract 2 3 Histones are ubiquitous in eukaryotes where they assemble into nucleosomes, binding and 4 wrapping DNA to form chromatin. One process to modify chromatin and regulate DNA 5 accessibility is the replacement of histones in the nucleosome with paralogous variants. 6 Histones are also present in archaea but whether and how histone variants contribute to the 7 generation of different physiologically relevant chromatin states in these organisms remains 8 largely unknown. Conservation of paralogs with distinct properties can provide prima facie 9 evidence for defined functional roles. -
Variations in the Two Last Steps of the Purine Biosynthetic Pathway in Prokaryotes
GBE Different Ways of Doing the Same: Variations in the Two Last Steps of the Purine Biosynthetic Pathway in Prokaryotes Dennifier Costa Brandao~ Cruz1, Lenon Lima Santana1, Alexandre Siqueira Guedes2, Jorge Teodoro de Souza3,*, and Phellippe Arthur Santos Marbach1,* 1CCAAB, Biological Sciences, Recoˆ ncavo da Bahia Federal University, Cruz das Almas, Bahia, Brazil 2Agronomy School, Federal University of Goias, Goiania,^ Goias, Brazil 3 Department of Phytopathology, Federal University of Lavras, Minas Gerais, Brazil Downloaded from https://academic.oup.com/gbe/article/11/4/1235/5345563 by guest on 27 September 2021 *Corresponding authors: E-mails: [email protected]fla.br; [email protected]. Accepted: February 16, 2019 Abstract The last two steps of the purine biosynthetic pathway may be catalyzed by different enzymes in prokaryotes. The genes that encode these enzymes include homologs of purH, purP, purO and those encoding the AICARFT and IMPCH domains of PurH, here named purV and purJ, respectively. In Bacteria, these reactions are mainly catalyzed by the domains AICARFT and IMPCH of PurH. In Archaea, these reactions may be carried out by PurH and also by PurP and PurO, both considered signatures of this domain and analogous to the AICARFT and IMPCH domains of PurH, respectively. These genes were searched for in 1,403 completely sequenced prokaryotic genomes publicly available. Our analyses revealed taxonomic patterns for the distribution of these genes and anticorrelations in their occurrence. The analyses of bacterial genomes revealed the existence of genes coding for PurV, PurJ, and PurO, which may no longer be considered signatures of the domain Archaea. Although highly divergent, the PurOs of Archaea and Bacteria show a high level of conservation in the amino acids of the active sites of the protein, allowing us to infer that these enzymes are analogs. -
Nov., Isolated from an Oil-Producing Well
International Journal of Systematic Bacteriology (1998), 48, 821-828 Printed in Great Britain Methanocalculus halotolerans gen. nov., sp. nov., isolated from an oil-producing well Bernard Ollivier,’ Marie-Laure Fardeau,l Jean-Luc Cayol,’ Michel Magot,’ Bharat K. C. Patel,3 Gerard Prensiep and Jean-Louis Garcia’ Author for correspondence: Bernard Ollivier. Tel: + 33 4 91 82 85 76. Fax: + 33 4 91 82 85 70. e-mail : [email protected] 1 Laboratoire ORSTOM de Two irregular coccoid methanogens designated SEBR 4845Tand FRlT were Microbiologie des isolated from an oilfield in Alsace, France. Strain SEBR 4845l (T = type strain) is AnaCrobies, UniversitC de Provence, 13288 Marseille a hydrogenotrophic halotolerant methanogen, which grows optimally at 5 O/O Cedex 9, France NaCl (whr) and tolerates up to 12O/0 NaCI. It does not use methylated * Sanofi Recherche, Groupe compounds and therefore cannot be ascribed to any of the known genera of Elf-Aquitaine, Unit6 de the halophilic methylotrophic methanogens. It differs from hydrogenotrophic Microbiologie, 31 676 members of the orders Methanococcales and Methanomicrobiales in the NaCl La b&ge Cedex, France growth range (0-12% NaCI), which is the widest reported to date for any 3 School of Biomolecular hydrogenotrophic methanogen. 165 rRNA gene sequence analysis indicated and Biomedical Sciences, Griffith University, Nathan that strain SEBR 4845l is a novel isolate for which a new genus is proposed, 41 11, Brisbane, Methanocalculus halotolerans gen. nov., sp. nov. (= OCM 4703 that might be Queensland, Australia indigenous to the oilfield ecosystem. Strain FRlT (= OCM 471) is a moderately 4 Laboratoire de halophilic methanogen which grows optimally at 10% NaCl and tolerates up to Microbiologie, UniversitC 20% NaCI. -
Biotechnology of Archaea- Costanzo Bertoldo and Garabed Antranikian
BIOTECHNOLOGY– Vol. IX – Biotechnology Of Archaea- Costanzo Bertoldo and Garabed Antranikian BIOTECHNOLOGY OF ARCHAEA Costanzo Bertoldo and Garabed Antranikian Technical University Hamburg-Harburg, Germany Keywords: Archaea, extremophiles, enzymes Contents 1. Introduction 2. Cultivation of Extremophilic Archaea 3. Molecular Basis of Heat Resistance 4. Screening Strategies for the Detection of Novel Enzymes from Archaea 5. Starch Processing Enzymes 6. Cellulose and Hemicellulose Hydrolyzing Enzymes 7. Chitin Degradation 8. Proteolytic Enzymes 9. Alcohol Dehydrogenases and Esterases 10. DNA Processing Enzymes 11. Archaeal Inteins 12. Conclusions Glossary Bibliography Biographical Sketches Summary Archaea are unique microorganisms that are adapted to survive in ecological niches such as high temperatures, extremes of pH, high salt concentrations and high pressure. They produce novel organic compounds and stable biocatalysts that function under extreme conditions comparable to those prevailing in various industrial processes. Some of the enzymes from Archaea have already been purified and their genes successfully cloned in mesophilic hosts. Enzymes such as amylases, pullulanases, cyclodextrin glycosyltransferases, cellulases, xylanases, chitinases, proteases, alcohol dehydrogenase,UNESCO esterases, and DNA-modifying – enzymesEOLSS are of potential use in various biotechnological processes including in the food, chemical and pharmaceutical industries. 1. Introduction SAMPLE CHAPTERS The industrial application of biocatalysts began in 1915 with the introduction of the first detergent enzyme by Dr. Röhm. Since that time enzymes have found wider application in various industrial processes and production (see Enzyme Production). The most important fields of enzyme application are nutrition, pharmaceuticals, diagnostics, detergents, textile and leather industries. There are more than 3000 enzymes known to date that catalyze different biochemical reactions among the estimated total of 7000; only 100 enzymes are being used industrially.