Characteristics of Predominant Microorganisms in Foods
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(Gid ) Genes Coding for Putative Trna:M5u-54 Methyltransferases in 355 Bacterial and Archaeal Complete Genomes
Table S1. Taxonomic distribution of the trmA and trmFO (gid ) genes coding for putative tRNA:m5U-54 methyltransferases in 355 bacterial and archaeal complete genomes. Asterisks indicate the presence and the number of putative genes found. Genomes Taxonomic position TrmA Gid Archaea Crenarchaea Aeropyrum pernix_K1 Crenarchaeota; Thermoprotei; Desulfurococcales; Desulfurococcaceae Cenarchaeum symbiosum Crenarchaeota; Thermoprotei; Cenarchaeales; Cenarchaeaceae Pyrobaculum aerophilum_str_IM2 Crenarchaeota; Thermoprotei; Thermoproteales; Thermoproteaceae Sulfolobus acidocaldarius_DSM_639 Crenarchaeota; Thermoprotei; Sulfolobales; Sulfolobaceae Sulfolobus solfataricus Crenarchaeota; Thermoprotei; Sulfolobales; Sulfolobaceae Sulfolobus tokodaii Crenarchaeota; Thermoprotei; Sulfolobales; Sulfolobaceae Euryarchaea Archaeoglobus fulgidus Euryarchaeota; Archaeoglobi; Archaeoglobales; Archaeoglobaceae Haloarcula marismortui_ATCC_43049 Euryarchaeota; Halobacteria; Halobacteriales; Halobacteriaceae; Haloarcula Halobacterium sp Euryarchaeota; Halobacteria; Halobacteriales; Halobacteriaceae; Haloarcula Haloquadratum walsbyi Euryarchaeota; Halobacteria; Halobacteriales; Halobacteriaceae; Haloquadra Methanobacterium thermoautotrophicum Euryarchaeota; Methanobacteria; Methanobacteriales; Methanobacteriaceae Methanococcoides burtonii_DSM_6242 Euryarchaeota; Methanomicrobia; Methanosarcinales; Methanosarcinaceae Methanococcus jannaschii Euryarchaeota; Methanococci; Methanococcales; Methanococcaceae Methanococcus maripaludis_S2 Euryarchaeota; Methanococci; -
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. -
Adaptations of Methanococcus Maripaludis to Its Unique Lifestyle
ADAPTATIONS OF METHANOCOCCUS MARIPALUDIS TO ITS UNIQUE LIFESTYLE by YUCHEN LIU (Under the Direction of William B. Whitman) ABSTRACT Methanococcus maripaludis is an obligate anaerobic, methane-producing archaeon. In addition to the unique methanogenesis pathway, unconventional biochemistry is present in this organism in adaptation to its unique lifestyle. The Sac10b homolog in M. maripaludis, Mma10b, is not abundant and constitutes only ~ 0.01% of the total cellular protein. It binds to DNA with sequence-specificity. Disruption of mma10b resulted in poor growth of the mutant in minimal medium. These results suggested that the physiological role of Mma10b in the mesophilic methanococci is greatly diverged from the homologs in thermophiles, which are highly abundant and associate with DNA without sequence-specificity. M. maripaludis synthesizes lysine through the DapL pathway, which uses diaminopimelate aminotransferase (DapL) to catalyze the direct transfer of an amino group from L-glutamate to L-tetrahydrodipicolinate (THDPA), forming LL-diaminopimelate (LL-DAP). This is different from the conventional acylation pathway in many bacteria that convert THDPA to LL-DAP in three steps: succinylation or acetylation, transamination, and desuccinylation or deacetylation. The DapL pathway eliminates the expense of using succinyl-CoA or acetyl-CoA and may represent a thriftier mode for lysine biosynthesis. Methanogens synthesize cysteine primarily on tRNACys via the two-step SepRS/SepCysS pathway. In the first step, tRNACys is aminoacylated with O-phosphoserine (Sep) by O- phosphoseryl-tRNA synthetase (SepRS). In the second step, the Sep moiety on Sep-tRNACys is converted to cysteine with a sulfur source to form Cys-tRNACys by Sep-tRNA:Cys-tRNA synthase (SepCysS). -
Hyperthermophilic Methanogenic Archaea Act As High-Pressure CH4 Cell Factories
ARTICLE https://doi.org/10.1038/s42003-021-01828-5 OPEN Hyperthermophilic methanogenic archaea act as high-pressure CH4 cell factories Lisa-Maria Mauerhofer1, Sara Zwirtmayr2, Patricia Pappenreiter2, Sébastien Bernacchi 3, Arne H. Seifert3, Barbara Reischl1,3, Tilman Schmider1, Ruth-Sophie Taubner 1,2, Christian Paulik 2 & ✉ Simon K.-M. R. Rittmann 1 Bioprocesses converting carbon dioxide with molecular hydrogen to methane (CH4) are currently being developed to enable a transition to a renewable energy production system. In this study, we present a comprehensive physiological and biotechnological examination of 80 methanogenic archaea (methanogens) quantifying growth and CH4 production kinetics at 1234567890():,; hyperbaric pressures up to 50 bar with regard to media, macro-, and micro-nutrient supply, specific genomic features, and cell envelope architecture. Our analysis aimed to system- atically prioritize high-pressure and high-performance methanogens. We found that the hyperthermophilic methanococci Methanotorris igneus and Methanocaldococcoccus jannaschii are high-pressure CH4 cell factories. Furthermore, our analysis revealed that high- performance methanogens are covered with an S-layer, and that they harbour the amino acid motif Tyrα444 Glyα445 Tyrα446 in the alpha subunit of the methyl-coenzyme M reduc- tase. Thus, high-pressure biological CH4 production in pure culture could provide a purpo- seful route for the transition to a carbon-neutral bioenergy sector. 1 Archaea Physiology & Biotechnology Group, Department Functional and Evolutionary Ecology, Universität Wien, Wien, Austria. 2 Institute for Chemical ✉ Technology of Organic Materials, Johannes Kepler Universität Linz, Linz, Austria. 3 Krajete GmbH, Linz, Austria. email: [email protected] COMMUNICATIONS BIOLOGY | (2021) 4:289 | https://doi.org/10.1038/s42003-021-01828-5 | www.nature.com/commsbio 1 ARTICLE COMMUNICATIONS BIOLOGY | https://doi.org/10.1038/s42003-021-01828-5 26 ethane (CH4) is an energy carrier of worldwide growth and CH4 production . -
Systematic Bacteriology Second Edition
BERGEY'S MANUAL® OF Systematic Bacteriology Second Edition Volume One The Archaea and the Deeply Branching and Phototrophic Bacteria Springer New York Berlin Heidelberg Barcelona HongKong London Milan Paris Singapore Tokyo BERGEY'S MANUAL® OF Systematic Bacteriology Second Edition Volume One The Archaea and the Deeply Branching and Phototrophic Bacteria David R. Boone Richard W. Castenholz EDITORS, VOLUME ONE George M. Garrity EDITOR-IN-CHIEF EDITORIAL BOARD James T. Staley, Chairman, David R. Boone, Vice Chairman, Don J. Brenner, Richard W. Castenholz, George M. Garrity, Michael Goodfellow, Noel R. Krieg, Fred A. Rainey, Karl-Heinz Schleifer WITH CONTRIBUTIONS FROM 105 COLLEAGUES Springer George M. Garrity Department of Microbiology and Molecular Genetics Bergey's Manual Trust Michigan State University East Lansing, MI 48824-1101 USA Library of Congress Cataloging-in-Publication Data Bergey's manual of systematic bacteriology / David R. Boone, Richard W. Castenholz, editors, volume 1 ; George M. Garrity, editor-in-chief.-2nd ed. p.cm. Includes bibliographical references and index. Contents: v.I. The archaea and the deeply branching and phototrophic bacteria. ISBN 0-387-98771-1 (alk. paper) 1. Bacteria-Classification. I. Title: Systematic bacteriology. II. Boone, David R. III. Castenholz, Richard W. IV. Garrity, George M. QR81.B462001 579.3'01 '2-dc21 2001020400 With 330 illustrations The following proprietary names of products are used in this volume: Casamino@ acids; Vector NTI®; XLI0-Gold®; Gelrite®; Tryptone@l; Phytagel@; bio-Trypcasew; Trypticasev; Oxoid® purified agar. Printed on acid-free paper. First edition published 1984-1989 by Bergey's Manual Trust and Williams & Wilkins, Baltimore. © 2001 Bergey's Manual Trust All rights reserved. -
Contents Topic 1. Introduction to Microbiology. the Subject and Tasks
Contents Topic 1. Introduction to microbiology. The subject and tasks of microbiology. A short historical essay………………………………………………………………5 Topic 2. Systematics and nomenclature of microorganisms……………………. 10 Topic 3. General characteristics of prokaryotic cells. Gram’s method ………...45 Topic 4. Principles of health protection and safety rules in the microbiological laboratory. Design, equipment, and working regimen of a microbiological laboratory………………………………………………………………………….162 Topic 5. Physiology of bacteria, fungi, viruses, mycoplasmas, rickettsia……...185 TOPIC 1. INTRODUCTION TO MICROBIOLOGY. THE SUBJECT AND TASKS OF MICROBIOLOGY. A SHORT HISTORICAL ESSAY. Contents 1. Subject, tasks and achievements of modern microbiology. 2. The role of microorganisms in human life. 3. Differentiation of microbiology in the industry. 4. Communication of microbiology with other sciences. 5. Periods in the development of microbiology. 6. The contribution of domestic scientists in the development of microbiology. 7. The value of microbiology in the system of training veterinarians. 8. Methods of studying microorganisms. Microbiology is a science, which study most shallow living creatures - microorganisms. Before inventing of microscope humanity was in dark about their existence. But during the centuries people could make use of processes vital activity of microbes for its needs. They could prepare a koumiss, alcohol, wine, vinegar, bread, and other products. During many centuries the nature of fermentations remained incomprehensible. Microbiology learns morphology, physiology, genetics and microorganisms systematization, their ecology and the other life forms. Specific Classes of Microorganisms Algae Protozoa Fungi (yeasts and molds) Bacteria Rickettsiae Viruses Prions The Microorganisms are extraordinarily widely spread in nature. They literally ubiquitous forward us from birth to our death. Daily, hourly we eat up thousands and thousands of microbes together with air, water, food. -
Quantitative Detection of Culturable Methanogenic Archaea Abundance in Anaerobic Treatment Systems Using the Sequence-Specific Rrna Cleavage Method
The ISME Journal (2009) 3, 522–535 & 2009 International Society for Microbial Ecology All rights reserved 1751-7362/09 $32.00 www.nature.com/ismej ORIGINAL ARTICLE Quantitative detection of culturable methanogenic archaea abundance in anaerobic treatment systems using the sequence-specific rRNA cleavage method Takashi Narihiro1, Takeshi Terada1, Akiko Ohashi1, Jer-Horng Wu2,4, Wen-Tso Liu2,5, Nobuo Araki3, Yoichi Kamagata1,6, Kazunori Nakamura1 and Yuji Sekiguchi1 1Institute for Biological Resources and Functions, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, Japan; 2Division of Environmental Science and Engineering, National University of Singapore, Singapore and 3Department of Civil Engineering, Nagaoka National College of Technology, Nagaoka, Japan A method based on sequence-specific cleavage of rRNA with ribonuclease H was used to detect almost all known cultivable methanogens in anaerobic biological treatment systems. To do so, a total of 40 scissor probes in different phylogeny specificities were designed or modified from previous studies, optimized for their specificities under digestion conditions with 32 methanogenic reference strains, and then applied to detect methanogens in sludge samples taken from 6 different anaerobic treatment processes. Among these processes, known aceticlastic and hydrogenotrophic groups of methanogens from the families Methanosarcinaceae, Methanosaetaceae, Methanobacter- iaceae, Methanothermaceae and Methanocaldococcaceae could be successfully detected and -
1E6v Lichtarge Lab 2006
Pages 1–18 1e6v Evolutionary trace report by report maker July 11, 2009 4.4.1 Clustering of residues at 25% coverage. 9 4.4.2 Overlap with known functional surfaces at 25% coverage. 10 4.4.3 Possible novel functional surfaces at 25% coverage. 15 5 Notes on using trace results 16 5.1 Coverage 16 5.2 Known substitutions 16 5.3 Surface 16 5.4 Number of contacts 16 5.5 Annotation 16 5.6 Mutation suggestions 16 6 Appendix 16 6.1 File formats 16 6.2 Color schemes used 16 6.3 Credits 17 6.3.1 Alistat 17 6.3.2 CE 17 6.3.3 DSSP 17 6.3.4 HSSP 17 CONTENTS 6.3.5 LaTex 17 6.3.6 Muscle 17 1 Introduction 1 6.3.7 Pymol 17 6.4 Note about ET Viewer 17 2 Chain 1e6vC 1 6.5 Citing this work 17 2.1 Q49604 overview 1 6.6 About report maker 17 2.2 Multiple sequence alignment for 1e6vC 1 6.7 Attachments 17 2.3 Residue ranking in 1e6vC 1 2.4 Top ranking residues in 1e6vC and their position on 1 INTRODUCTION the structure 2 2.4.1 Clustering of residues at 25% coverage. 2 From the original Protein Data Bank entry (PDB id 1e6v): 2.4.2 Overlap with known functional surfaces at Title: Methyl-coenzyme m reductase from methanopyrus kandleri 25% coverage. 2 Compound: Mol id: 1; molecule: methyl-coenzyme m reductase i alpha subunit; chain: a, d; mol id: 2; molecule: methyl-coenzyme m 3 Chain 1e6vA 6 reductase i beta subunit; chain: b, e; mol id: 3; molecule: methyl- 3.1 Q49605 overview 6 coenzyme m reductase i gamma subunit; chain: c, f 3.2 Multiple sequence alignment for 1e6vA 7 Organism, scientific name: Methanopyrus Kandleri; 3.3 Residue ranking in 1e6vA 7 1e6v contains unique chains 1e6vC (248 residues), 1e6vA (545 3.4 Top ranking residues in 1e6vA and their position on residues), and 1e6vB (436 residues) 1e6vF is a homologue of chain the structure 7 1e6vC. -
Metabolic Roles of Uncultivated Bacterioplankton Lineages in the Northern Gulf of Mexico 2 “Dead Zone” 3 4 J
bioRxiv preprint doi: https://doi.org/10.1101/095471; this version posted June 12, 2017. 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 4.0 International license. 1 Metabolic roles of uncultivated bacterioplankton lineages in the northern Gulf of Mexico 2 “Dead Zone” 3 4 J. Cameron Thrash1*, Kiley W. Seitz2, Brett J. Baker2*, Ben Temperton3, Lauren E. Gillies4, 5 Nancy N. Rabalais5,6, Bernard Henrissat7,8,9, and Olivia U. Mason4 6 7 8 1. Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, USA 9 2. Department of Marine Science, Marine Science Institute, University of Texas at Austin, Port 10 Aransas, TX, USA 11 3. School of Biosciences, University of Exeter, Exeter, UK 12 4. Department of Earth, Ocean, and Atmospheric Science, Florida State University, Tallahassee, 13 FL, USA 14 5. Department of Oceanography and Coastal Sciences, Louisiana State University, Baton Rouge, 15 LA, USA 16 6. Louisiana Universities Marine Consortium, Chauvin, LA USA 17 7. Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille Université, 18 13288 Marseille, France 19 8. INRA, USC 1408 AFMB, F-13288 Marseille, France 20 9. Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia 21 22 *Correspondence: 23 JCT [email protected] 24 BJB [email protected] 25 26 27 28 Running title: Decoding microbes of the Dead Zone 29 30 31 Abstract word count: 250 32 Text word count: XXXX 33 34 Page 1 of 31 bioRxiv preprint doi: https://doi.org/10.1101/095471; this version posted June 12, 2017. -
Supplementary Material For: Undinarchaeota Illuminate The
Supplementary Material for: Undinarchaeota illuminate the evolution of DPANN archaea Nina Dombrowski1, Tom A. Williams2, Benjamin J. Woodcroft3, Jiarui Sun3, Jun-Hoe Lee4, Bui Quang MinH5, CHristian Rinke5, Anja Spang1,5,# 1NIOZ, Royal NetHerlands Institute for Sea ResearcH, Department of Marine Microbiology and BiogeocHemistry, and UtrecHt University, P.O. Box 59, NL-1790 AB Den Burg, THe NetHerlands 2 ScHool of Biological Sciences, University of Bristol, Bristol, BS8 1TQ, UK 3Australian Centre for Ecogenomics, ScHool of CHemistry and Molecular Biosciences, THe University of Queensland, QLD 4072, Australia 4Department of Cell- and Molecular Biology, Science for Life Laboratory, Uppsala University, SE-75123, Uppsala, Sweden 5ResearcH ScHool of Computer Science and ResearcH ScHool of Biology, Australian National University, ACT 2601, Australia #corresponding autHor. Postal address: Landsdiep 4, 1797 SZ 't Horntje (Texel). Email address: [email protected]. PHone number: +31 (0)222 369 526 Table of Contents Table of Contents 2 General 3 Evaluating CHeckM completeness estimates 3 Screening for contaminants 3 Phylogenetic analyses 4 Informational processing and repair systems 7 Replication and cell division 7 Transcription 7 Translation 8 DNA-repair and modification 9 Stress tolerance 9 Metabolic features 10 Central carbon and energy metabolism 10 Anabolism 13 Purine and pyrimidine biosyntHesis 13 Amino acid degradation and biosyntHesis 14 Lipid biosyntHesis 15 Vitamin and cofactor biosyntHesis 16 Host-symbiont interactions 16 Genes potentially -
Coexistance of Acetogens, Methanogens and Sulfate Reducing Bacteria in Enrichments from Trunk River
Coexistance of acetogens, methanogens and sulfate reducing bacteria in enrichments from Trunk River María Consuelo Gazitúa Center for Genomics and Bioinformatics University Mayor - Chile [email protected] Introduction In the absence of oxygen, chemotrophic growth depends on alternative electron acceptors such as nitrate, iron, manganese, sulfate and CO2. In the presence of sulfate, such as in seawater, sulfate reduction is highly favorable, coupling the reduction of sulfate with the oxidation of H2 or simple organic compounds. In the absence of sulfate, methanogenic archaea are able to cleave acetate, producing CO2 and CH4, as well as reduce or disproportionate C1 compounds such as CO2, CO, formate and methanol, using H2 and formate as the main electron donor. Homoacetogenic bacteria use C-1 compounds as electron acceptors, catalyzing the reduction of two CO2 molecules to acetate. This is a highly variable group of strictly anaerobic bacteria, able to grow on a variety of substrates. In most anaerobic environments, hydrogen is present as an intermediate for which sulfate reducing bacteria (SRB), hydrogenotrophic methanogens and homoacetogens will compete. Under standard conditions, sulfate reduction and methanogenesis are thermodynamically more favorable than homoacetogenesis. However, Weijma et al. (2002) reported that when H2/CO2 is added as the sole substrate in sludge bioreactores, heterotrophic SRB and homoacetogens can coexist, suggesting the SRB growth depends on the growth kinetics of the homoacetogens. During the isolation of chemolithotrophic microorganisms during the course, specifically for SRB, homoacetogens and methanogens, the enrichment for SRB showed the coexistence of these three groups, based on measurements of methane, hydrogen sulfide and acetate. Some of the organisms growing in the enrichment formed aggregates, where the presence of methanogens could be inferred based on the blue autofluorescence, after excitation with AF430 (Doddema and Vogels 1978). -
Microbial Community of Recently Discovered Auka
bioRxiv preprint doi: https://doi.org/10.1101/2021.08.02.454472; this version posted August 2, 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 Microbial community of recently discovered Auka vent field sheds light on vent 2 biogeography and evolutionary history of thermophily 3 4 Daan R. Speth1,2 *, Feiqiao B. Yu3,4, Stephanie A. Connon2, Sujung Lim2, John S. Magyar2, 5 Manet E. Peña5, Stephen R. Quake3,4 , and Victoria J. Orphan1,2 6 7 1 Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, 8 CA, USA 9 2 Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, 10 CA, USA 11 3 Department of Bioengineering, Stanford University, Stanford, CA, USA 12 4 Chan Zuckerberg Biohub, San Francisco, CA, USA 13 5 Facultad de Ciencias Marinas, Universidad Autónoma de Baja California, Ensenada, Mexico 14 * Present address: Max Planck Institute for Marine Microbiology, Bremen, Germany 15 16 17 Correspondence: 18 [email protected] or [email protected] 19 20 1 bioRxiv preprint doi: https://doi.org/10.1101/2021.08.02.454472; this