DOCSLIB.ORG

Hydrolytic Enzymes

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Hydrolytic Enzymes Revista de Microbiologia (1999) 30:287-298 Extremely thermophilic microorganisms ISSN 0001-3714 EXTREMELY THERMOPHILIC MICROORGANISMS AND THEIR POLYMER- HYDROLYTIC ENZYMES Carolina M.M.C. Andrade1*; Nei Pereira Jr.1; Garo Antranikian2 1Departamento de Engenharia Bioquímica, Escola de Química, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brasil. 2Department of Technical Microbiology, Technical University Hamburg- Harburg, Hamburg, Germany Submitted: May 25, 1999; Returned to authors for corrections: July 29, 1999; Approved: August 26, 1999 MINI-REVIEW ABSTRACT Thermophilic and hyperthermophilic microorganisms are found as normal inhabitants of continental and submarine volcanic areas, geothermally heated sea-sediments and hydrothermal vents and thus are considered extremophiles. Several present or potential applications of extremophilic enzymes are reviewed, especially polymer-hydrolysing enzymes, such as amylolytic and hemicellulolytic enzymes. The purpose of this review is to present the range of morphological and metabolic features among those microorganisms growing from 70oC to 100°C and to indicate potential opportunities for useful applications derived from these features. Key words: Archaea, extremophiles, amylases, xylanases, pullulanases, thermostability INTRODUCTION especially the thermophiles, is an area that is receiving increasing attention. In general, moderate In recent years it became obvious that thermophiles are primarily bacteria and display extremophilic microorganisms differ from eucaryotic optimal growth temperature between 60°C and 80°C. cells because they have adapted to grow under Hyperthermophiles are primarily archaea and growth extreme conditions such as high temperature optimally at 80°C or above, being unable to grow (>100°C), high salinity (saturated NaCl), extremes below 60°C (47). of pH (<2.0, >10.0), and substrate stress. These kinds The hyperthermophiles are now well characterised of extreme microbial growth conditions are found taxonomically at the DNA-DNA hybridisation level, in exotic environments which were more widespread and their evolutionary relatedness has been examined. on primitive Earth. Extreme environments include By using 16S rRNA sequence comparison, an archaeal also high pressure (> 50 MPa) and the presence of phylogenetic tree has been proposed (54), with a organic solvents (e.g. > 1% toluene) or heavy metals. tripartite division of the living world consisting of the The evolution and taxonomy of extremophiles, domains Eucarya, Bacteria, and Archaea. In this * Corresponding author. Mailing address: Universidade Federal do Rio de Janeiro, Ilha do Fundão Centro de Tecnologia, Bloco E, Escola de Química, Departamento de Engenharia Bioquímica, Laboratório de Engenharia Bioquímica, CEP 21949-900, Rio de Janeiro, RJ, Brasil. Fax: (+5521) 590-4991, E-mail: [email protected] 287 C.M.M.C. Andrade et al. division Sulfolobales and Thermoproteales form one Thermophiles and hyperthermophiles: branch (the Crenarchaeota) and the remaining physiological and morphological aspects. Most of thermophiles form another branch containing the anaerobic thermophilic bacteria are methanogens, and extreme halophiles (the chemoorganotrophic in their metabolism. The Euryarchaeota). Currently, the only hyperthermophilic bacterial thermophilic thermoanaerobes, for organisms within the Bacterial domain are members example, belong to nearly the same range of of the genus Thermotoga and Aquifex (47). Until now, nutritional categories as do mesophilic bacteria. The no hyperthermophilic microorganisms in the domain hyperthermophilic bacteria Thermotoga are able to Eucarya have been reported. ferment various carbohydrates like glucose, starch Hyperthermophiles are represented at the deepest and xylans, forming acetate, L-lactate, H2 and CO2 and shortest lineages, including both genera of as end product (47), while the hyperthermophilic hyperthermophilic bacteria and the genus Aquifex is strictly chemolithoautotrophic, using Pyrodictium, Pyrobaculum, Desulfurococcus, molecular hydrogen, thiosulfate and elemental Sulfolobus, Methanopyrus, Thermococcus, sulphur as electron donors and oxygen (at low Methanothermus, Archaeoglobus within the concentrations) and nitrate as electron acceptors (22). Archaea. Recently, genetic elements, e.g. viruses and In general, the physiological processes for plasmids (excluding IS elements and transposons) adaptation to environmental stress in anaerobic have been described in the kingdom Crenarcheota bacteria seem to have involved different factors from (Thermoproteales and Sulfolobales) and in the those in aerobic bacteria. First, anaerobes are energy kingdom Euryarchaeota (Thermococcales and limited during the chemoorganotrophic growth Thermoplasmales) of the archaeal domain (57). because they can not couple dehydrogenation Some similarities between the archaeal virus FH and reaction to oxygen reduction and gain a high level the bacterial phage P1 strongly indicate that this of chemical free energy. Second, growth of most temperate phage type already existed before the chemoorganotrophic anaerobes (except for separation of the Archaea from the Bacteria, which methanogens) is naturally associated with the was the first documented lineage diversion in cellular generation of toxic end products (e.g., organic acids evolution (57). Based on these observations, or alcohols, HS-), which requires that anaerobic hyperthermophiles may still be rather primitive and species develop some sort of dynamic adaptation the last common ancestor, the progenota, may have mechanism or tolerance to their catabolic end been a hyperthermophile (47, 54). products. In the last decades thermophilic and The most interesting group of thermophiles is the hyperthermophilic anaerobes have been isolated hyperthermophiles, since the isolation of these from continental and submarine volcanic areas, such organisms has caused a revaluation of the possible as solfatar fields, geothermal power plants, habitats for microorganisms and has increased the geothermally heated sea sediments and hydrothermal high-temperature limits at which life is known to vents (14, 18, 47, 50). Sites from which exist. The hyperthermophilic anaerobic archaea have hyperthermophilic organisms have been isolated almost the same size as one typical procaryotic cell, comprises solfataric fields; steam-heated soils, mud about 0.5 - 2.0µm, although some of them have holes, surface waters; deep hot springs; geothermal unusual morphological features (47). power plants as well as submarine hot springs and Hyperthermophiles are rather diverse with respect fumaroles; hot sediments and vents,black smokers to their metabolism, since they include methanogens, or chimneys; and active sea-mounts. sulphate-reducers, nitrate-reducers and also the It is interesting that some organisms have been aerobic respirers. However the majority of the species isolated from areas with temperatures much higher know at the present are strictly anaerobic than their maximum growth temperature, e.g., heterotrophic S0 reducers (24). Among the terrestrial Hyperthermus butilicus (56) and Pyrococcus abyssi Archaea, three groups can be distinguished. (18), which suggests that in these environments the Acidophilic extremethermophiles, which are found organisms may not be actively growing. The same exclusively within continental solfataric fields. The could be true for the organisms isolated from organisms are coccoid-shaped, strict and facultative temperatures much below their growth temperature aerobes, and require acidic pH (opt. approx. pH 3.0) optimum, such as Archaeoglobus profundus (7). to grow. Phylogenetically, they belong to the archaeal 288 Extremely thermophilic microorganisms genera Sulfolobus, Metallosphaera, Acidianus, and cells are connected by a network of ultra thin hollow Desulfurolobus (47). On the other hand, the slightly tubules (47). Strains of Pyrodictium are usually acidophilic and neutrophilic thermophiles are found chemolitoautotrophs gaining energy by reduction of 0 both in continental solfataric fields and in submarine S by H2. Although growth is stimulated by yeast hydrothermal systems. All of them are strict extract, both species of Pyrodictium are strictly anaerobes. Solfataric fields contain members of the dependent upon H2. genera Thermoproteus, Pyrobaculum, As an exception, Pyrodictium abyssi is a Thermophilum, Desulfurococcus, and heterotroph growing by fermentation of peptides and Methanothermus. Pyrobaculum islandicum is able is unable to grow chemolitotrophically on H2/CO2 0 -2 to grow autotrophically by anaerobic reduction of either in the presence of S or S2O3 . Similar to the 0 S with H2 as electron donor (35), but is also able to other members of the genus, the cells of Pyrodictium grow heterotrophically by sulphur respiration (47). abyssi are highly polymorphous, often disk-shaped, Strains of Thermophilum and Pyrobaculum and display ultra flat areas. The cell envelope consists organotrophum are obligate heterotrophs. They grow of the cytoplasmic membrane, a periplasmic space, by sulphur respiration using different organic and a surface layer protein. The ultra thin sections substrates. Interestingly, Thermophilum pendens also reveal a zigzag structure of the S-layer (40). shows an obligate requirement for a lipid fraction of Usually S-layer proteins are highly stable, maintain Thermoproteux tenax (117). the structural integrity of bacterial cells under The variety of hyperthermophilic archaea that are extreme environmental
Load more

Recommended publications
  • 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.
    [Show full text]
  • Genome-Resolved Meta-Analysis of the Microbiome in Oil Reservoirs Worldwide
    microorganisms Article Genome-Resolved Meta-Analysis of the Microbiome in Oil Reservoirs Worldwide Kelly J. Hidalgo 1,2,* , Isabel N. Sierra-Garcia 3 , German Zafra 4 and Valéria M. de Oliveira 1 1 Microbial Resources Division, Research Center for Chemistry, Biology and Agriculture (CPQBA), University of Campinas–UNICAMP, Av. Alexandre Cazellato 999, 13148-218 Paulínia, Brazil; [email protected] 2 Graduate Program in Genetics and Molecular Biology, Institute of Biology, University of Campinas (UNICAMP), Rua Monteiro Lobato 255, Cidade Universitária, 13083-862 Campinas, Brazil 3 Biology Department & CESAM, University of Aveiro, Aveiro, Portugal, Campus de Santiago, Avenida João Jacinto de Magalhães, 3810-193 Aveiro, Portugal; [email protected] 4 Grupo de Investigación en Bioquímica y Microbiología (GIBIM), Escuela de Microbiología, Universidad Industrial de Santander, Cra 27 calle 9, 680002 Bucaramanga, Colombia; [email protected] * Correspondence: [email protected]; Tel.: +55-19981721510 Abstract: Microorganisms inhabiting subsurface petroleum reservoirs are key players in biochemical transformations. The interactions of microbial communities in these environments are highly complex and still poorly understood. This work aimed to assess publicly available metagenomes from oil reservoirs and implement a robust pipeline of genome-resolved metagenomics to decipher metabolic and taxonomic profiles of petroleum reservoirs worldwide. Analysis of 301.2 Gb of metagenomic information derived from heavily flooded petroleum reservoirs in China and Alaska to non-flooded petroleum reservoirs in Brazil enabled us to reconstruct 148 metagenome-assembled genomes (MAGs) of high and medium quality. At the phylum level, 74% of MAGs belonged to bacteria and 26% to archaea. The profiles of these MAGs were related to the physicochemical parameters and recovery management applied.
    [Show full text]
  • Marsarchaeota Are an Aerobic Archaeal Lineage Abundant in Geothermal Iron Oxide Microbial Mats
    Marsarchaeota are an aerobic archaeal lineage abundant in geothermal iron oxide microbial mats Authors: Zackary J. Jay, Jacob P. Beam, Mansur Dlakic, Douglas B. Rusch, Mark A. Kozubal, and William P. Inskeep This is a postprint of an article that originally appeared in Nature Microbiology on May 14, 2018. The final version can be found at https://dx.doi.org/10.1038/s41564-018-0163-1. Jay, Zackary J. , Jacob P. Beam, Mensur Dlakic, Douglas B. Rusch, Mark A. Kozubal, and William P. Inskeep. "Marsarchaeota are an aerobic archaeal lineage abundant in geothermal iron oxide microbial mats." Nature Microbiology 3, no. 6 (May 2018): 732-740. DOI: 10.1038/ s41564-018-0163-1. Made available through Montana State University’s ScholarWorks scholarworks.montana.edu Marsarchaeota are an aerobic archaeal lineage abundant in geothermal iron oxide microbial mats Zackary J. Jay1,4,7, Jacob P. Beam1,5,7, Mensur Dlakić2, Douglas B. Rusch3, Mark A. Kozubal1,6 and William P. Inskeep 1* The discovery of archaeal lineages is critical to our understanding of the universal tree of life and evolutionary history of the Earth. Geochemically diverse thermal environments in Yellowstone National Park provide unprecedented opportunities for studying archaea in habitats that may represent analogues of early Earth. Here, we report the discovery and character- ization of a phylum-level archaeal lineage proposed and herein referred to as the ‘Marsarchaeota’, after the red planet. The Marsarchaeota contains at least two major subgroups prevalent in acidic, microaerobic geothermal Fe(III) oxide microbial mats across a temperature range from ~50–80 °C. Metagenomics, single-cell sequencing, enrichment culturing and in situ transcrip- tional analyses reveal their biogeochemical role as facultative aerobic chemoorganotrophs that may also mediate the reduction of Fe(III).
    [Show full text]
  • Thermococcus Piezophilus Sp. Nov., a Novel Hyperthermophilic And
    1 Systematic and Applied Microbiology Achimer October 2016, Volume 39, Issue 7, Pages 440-444 http://dx.doi.org/10.1016/j.syapm.2016.08.003 http://archimer.ifremer.fr http://archimer.ifremer.fr/doc/00348/45949/ © 2016 Elsevier GmbH. All rights reserved. Thermococcus piezophilus sp. nov., a novel hyperthermophilic and piezophilic archaeon with a broad pressure range for growth, isolated from a deepest hydrothermal vent at the Mid-Cayman Rise ✯ Dalmasso Cécile 1, 2, 3, Oger Philippe 4, Selva Gwendoline 1, 2, 3, Courtine Damien 1, 2, 3, L'Haridon Stéphane 1, 2, 3, Garlaschelli Alexandre 1, 2, 3, Roussel Erwan 1, 2, 3, Miyazaki Junichi 5, Reveillaud Julie 1, 2, 3, Jebbar Mohamed 1, 2, 3, Takai Ken 5, Maignien Lois 1, 2, 3, Alain Karine 1, 2, 3, * 1 Université de Bretagne Occidentale (UBO, UEB), Institut Universitaire Européen de la Mer (IUEM) − UMR 6197, Laboratoire de Microbiologie des Environnements Extrêmes (LM2E), Place Nicolas Copernic, F-29280 Plouzané, France 2 CNRS, IUEM − UMR 6197, Laboratoire de Microbiologie des Environnements Extrêmes (LM2E), Place Nicolas Copernic, F-29280 Plouzané, France 3 Ifremer, UMR 6197, Laboratoire de Microbiologie des Environnements Extrêmes (LM2E), Technopôle Pointe du diable, F-29280 Plouzané, France 4 Université de Lyon, INSA Lyon, CNRS UMR 5240, 11 Avenue Jean Capelle, F-69621 Villeurbanne, France 5 Department of Subsurface Geobiological Analysis and Research (D-SUGAR), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka 237-0061, Japan * Corresponding author : Karine Alain, email address : [email protected] ✯ Note: The EMBL/GenBank/DDBJ 16S rRNA gene sequence accession number of strain CDGST is LN 878294.
    [Show full text]
  • A Proposal to Rename the Hyperthermophile Pyrococcus Woesei As Pyrococcus Furiosus Subsp
    Archaea 1, 277–283 © 2004 Heron Publishing—Victoria, Canada A proposal to rename the hyperthermophile Pyrococcus woesei as Pyrococcus furiosus subsp. woesei WIROJNE KANOKSILAPATHAM,1 JUAN M. GONZÁLEZ,1,2 DENNIS L. MAEDER,1 1,3 1,4 JOCELYNE DIRUGGIERO and FRANK T. ROBB 1 Center of Marine Biotechnology, University of Maryland Biotechnology Institute, Baltimore, MD 21202, USA 2 Present address: IRNAS-CSIC, P.O. Box 1052, 41080 Sevilla, Spain 3 Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20274, USA 4 Corresponding author ([email protected]) Received April 8, 2004; accepted July 28, 2004; published online August 31, 2004 Summary Pyrococcus species are hyperthermophilic mem- relatively rapidly at temperatures above 90 °C and produce ° bers of the order Thermococcales, with optimal growth tem- H2S from elemental sulfur (S ) (Zillig et al. 1987). Two Pyro- peratures approaching 100 °C. All species grow heterotrophic- coccus species, P. furiosus (Fiala and Stetter 1986) and ° ally and produce H2 or, in the presence of elemental sulfur (S ), P. woesei (Zillig et al. 1987), were isolated from marine sedi- H2S. Pyrococcus woesei and P.furiosus were isolated from ma- ments at a Vulcano Island beach site in Italy. They have similar rine sediments at the same Vulcano Island beach site and share morphological and physiological characteristics: both species many morphological and physiological characteristics. We re- are cocci and move by means of a tuft of polar flagella. They port here that the rDNA operons of these strains have identical are heterotrophic and grow optimally at 95–100 °C, utilizing sequences, including their intergenic spacer regions and part of peptides as major carbon and nitrogen sources.
    [Show full text]
  • Functionalized Membrane Domains: an Ancestral Feature of Archaea? Maxime Tourte, Philippe Schaeffer, Vincent Grossi, Phil Oger
    Functionalized Membrane Domains: An Ancestral Feature of Archaea? Maxime Tourte, Philippe Schaeffer, Vincent Grossi, Phil Oger To cite this version: Maxime Tourte, Philippe Schaeffer, Vincent Grossi, Phil Oger. Functionalized Membrane Domains: An Ancestral Feature of Archaea?. Frontiers in Microbiology, Frontiers Media, 2020, 11, pp.526. 10.3389/fmicb.2020.00526. hal-02553764 HAL Id: hal-02553764 https://hal.archives-ouvertes.fr/hal-02553764 Submitted on 20 May 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. fmicb-11-00526 March 30, 2020 Time: 21:44 # 1 ORIGINAL RESEARCH published: 31 March 2020 doi: 10.3389/fmicb.2020.00526 Functionalized Membrane Domains: An Ancestral Feature of Archaea? Maxime Tourte1†, Philippe Schaeffer2†, Vincent Grossi3† and Phil M. Oger1*† 1 Université de Lyon, INSA Lyon, CNRS, MAP UMR 5240, Villeurbanne, France, 2 Université de Strasbourg-CNRS, UMR 7177, Laboratoire de Biogéochimie Moléculaire, Strasbourg, France, 3 Université de Lyon, ENS Lyon, CNRS, Laboratoire de Géologie de Lyon, UMR 5276, Villeurbanne, France Bacteria and Eukarya organize their plasma membrane spatially into domains of distinct functions. Due to the uniqueness of their lipids, membrane functionalization in Archaea remains a debated area.
    [Show full text]
  • High-Fidelity Amplification Using a Thermostable DNA Polymerase Isolated from P’~Ococcusfuriosus
    Gette, 108 (1991) 1-6 8 1991 Elsevier Science Publishers B.V. All rights reserved. 0378-l 119/91/SO3.50 GENE 06172 High-fidelity amplification using a thermostable DNA polymerase isolated from P’~OCOCCUSfuriosus (Polymerase chain reaction; mutation frequency; lack; proofreading; 3’40-5 exonuclease; recombinant DNA; archaebacteria) Kelly S. Lundberg”, Dan D. Shoemaker*, Michael W.W. Adamsb, Jay M. Short”, Joseph A. Serge* and Eric J. Mathur” “ Division of Research and Development, Stratagene, Inc., La Jolla, CA 92037 (U.S.A.), and h Centerfor Metalloen~~vme Studies, University of Georgia, Athens, GA 30602 (U.S.A.) Tel. (404/542-2060 Received by M. Salas: 16 May 1991 Revised/Accepted: 11 August/l3 August 1991 Received at publishers: 17 September 1991 -.-- SUMMARY A thermostable DNA polymerase which possesses an associated 3’-to-5’ exonuclease (proofreading) activity has been isolated from the hyperthermophilic archaebacterium, Pyrococcus furiosus (Pfu). To test its fidelity, we have utilized a genetic assay that directly measures DNA polymerase fidelity in vitro during the polymerase chain reaction (PCR). Our results indicate that PCR performed with the DNA polymerase purified from P. furiosus yields amplification products containing less than 10s.~ of the number of mutations obtained from similar amplifications performed with Tuq DNA polymerase. The PCR fidelity assay is based on the ampli~cation and cloning of lad, lac0 and IacZor gene sequences (IcrcIOZa) using either ffil or 7ii~irqDNA poIymerase. Certain mutations within the lucf gene inactivate the Lac repressor protein and permit the expression of /?Gal. When plated on a chromogenic substrate, these Lacl - mutants exhibit a blue-plaque phenotype.
    [Show full text]
  • Representatives of a Novel Archaeal Phylum Or a Fast-Evolving
    Open Access Research2005BrochieretVolume al. 6, Issue 5, Article R42 Nanoarchaea: representatives of a novel archaeal phylum or a comment fast-evolving euryarchaeal lineage related to Thermococcales? Celine Brochier*, Simonetta Gribaldo†, Yvan Zivanovic‡, Fabrice Confalonieri‡ and Patrick Forterre†‡ Addresses: *EA EGEE (Evolution, Génomique, Environnement) Université Aix-Marseille I, Centre Saint-Charles, 3 Place Victor Hugo, 13331 Marseille, Cedex 3, France. †Unite Biologie Moléculaire du Gène chez les Extremophiles, Institut Pasteur, 25 rue du Dr Roux, 75724 Paris Cedex ‡ 15, France. Institut de Génétique et Microbiologie, UMR CNRS 8621, Université Paris-Sud, 91405 Orsay, France. reviews Correspondence: Celine Brochier. E-mail: [email protected]. Simonetta Gribaldo. E-mail: [email protected] Published: 14 April 2005 Received: 3 December 2004 Revised: 10 February 2005 Genome Biology 2005, 6:R42 (doi:10.1186/gb-2005-6-5-r42) Accepted: 9 March 2005 The electronic version of this article is the complete one and can be found online at http://genomebiology.com/2005/6/5/R42 reports © 2005 Brochier et al.; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Placement<p>Anteins from analysis 25of Nanoarcheumarchaeal of the positiongenomes equitans of suggests Nanoarcheum in the that archaeal N. equitans phylogeny inis likethe lyarchaeal to be the phylogeny representative using aof large a fast-evolving dataset of concatenatedeuryarchaeal ribosomalineage.</p>l pro- deposited research Abstract Background: Cultivable archaeal species are assigned to two phyla - the Crenarchaeota and the Euryarchaeota - by a number of important genetic differences, and this ancient split is strongly supported by phylogenetic analysis.
    [Show full text]
  • Open Dissertation 4-7-09.Pdf
    The Pennsylvania State University The Graduate School Department of Civil and Environmental Engineering IMPROVED ANAEROBIC DIGESTER STABILITY TO ORGANIC LOADING RATE SHOCKS WITH THE USE OF AN ENVIRONMENTALLY DERIVED INOCULUM A Dissertation in Environmental Engineering and Biogeochemistry by Lisa Marie Steinberg © 2009 Lisa Marie Steinberg Submitted in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy May 2009 The dissertation of Lisa Marie Steinberg was reviewed and approved* by the following: John Regan Associate Professor of Environmental Engineering Dissertation Advisor Chair of Committee Christopher House Associate Professor of Geosciences Bruce Logan Kappe Professor of Environmental Engineering Jenn Macalady Assistant Professor of Geosciences Peggy Johnson Department Head and Professor of Civil Engineering *Signatures are on file in the Graduate School ABSTRACT Anaerobic digestion broadly describes technology that utilizes microorganisms to break down organic matter under anaerobic conditions through the coordinated efforts of several trophic groups of microorganisms. The last step is catalyzed by methanogens which produce primarily methane, carbon dioxide, and water as products of metabolism. Anaerobic digestion occurs naturally in a variety of water-saturated sediments, but is also used to treat waste in constructed reactors. There are a number of advantages to treating waste with anaerobic digestion, but perhaps the greatest is that waste treatment can be coupled to energy generation by the production of a methane-rich biogas. Despite the advantages, anaerobic digestion is severely under-utilized in waste treatment mainly due to the belief that anaerobic digesters are less stable than aerobic treatment processes. Anaerobic digesters are typically operated under warm temperatures and circumneutral pH, with operation outside of these conditions leading to instability and potential reactor failure.
    [Show full text]
  • A Brief Journey to the Microbial World
    2 A Brief Journey to the Microbial World Green sulfur bacteria are I Seeing the Very Small 25 phototrophic microorganisms 2.1 Some Principles of Light Microscopy 25 that form their own phyloge- 2.2 Improving Contrast in Light Microscopy 26 netic lineage and were some 2.3 Imaging Cells in Three Dimensions 29 of the first phototrophs to 2.4 Electron Microscopy 30 evolve on Earth. II Cell Structure and Evolutionary History 31 2.5 Elements of Microbial Structure 31 2.6 Arrangement of DNA in Microbial Cells 33 2.7 The Evolutionary Tree of Life 34 III Microbial Diversity 36 2.8 Metabolic Diversity 36 2.9 Bacteria 38 2.10 Archaea 41 2.11 Phylogenetic Analyses of Natural Microbial Communities 43 2.12 Microbial Eukarya 43 CHAPTER 2 • A Brief Journey to the Microbial World 25 for which resolution is considerably greater than that of the light I Seeing the Very Small microscope. UNIT 1 istorically, the science of microbiology blossomed as the The Compound Light Microscope ability to see microorganisms improved; thus, microbiology H The light microscope uses visible light to illuminate cell struc- and microscopy advanced hand-in-hand. The microscope is the tures. Several types of light microscopes are used in microbiol- microbiologist’s most basic tool, and every student of microbiol- ogy: bright-field, phase-contrast, differential interference contrast, ogy needs some background on how microscopes work and how dark-field, and fluorescence. microscopy is done. We therefore begin our brief journey to the With the bright-field microscope, specimens are visualized microbial world by considering different types of microscopes because of the slight differences in contrast that exist between and the applications of microscopy to imaging microorganisms.
    [Show full text]
  • Tackling the Methanopyrus Kandleri Paradox Céline Brochier*, Patrick Forterre† and Simonetta Gribaldo†
    View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by PubMed Central Open Access Research2004BrochieretVolume al. 5, Issue 3, Article R17 Archaeal phylogeny based on proteins of the transcription and comment translation machineries: tackling the Methanopyrus kandleri paradox Céline Brochier*, Patrick Forterre† and Simonetta Gribaldo† Addresses: *Equipe Phylogénomique, Université Aix-Marseille I, Centre Saint-Charles, 13331 Marseille Cedex 3, France. †Institut de Génétique et Microbiologie, CNRS UMR 8621, Université Paris-Sud, 91405 Orsay, France. reviews Correspondence: Céline Brochier. E-mail: [email protected] Published: 26 February 2004 Received: 14 November 2003 Revised: 5 January 2004 Genome Biology 2004, 5:R17 Accepted: 21 January 2004 The electronic version of this article is the complete one and can be found online at http://genomebiology.com/2004/5/3/R17 reports © 2004 Brochier et al.; licensee BioMed Central Ltd. This is an Open Access article: verbatim copying and redistribution of this article are permitted in all media for any purpose, provided this notice is preserved along with the article's original URL. ArchaealPhylogeneticsequencedusingrespectively). two phylogeny concatenated genomes, analysis based it of is datasetsthe now on Archaea proteinspossible consisting has ofto been thetest of transcription alternative mainly14 proteins established approach involv and translationed byes in 16S bytranscription rRNAusing machineries: largesequence andsequence 53comparison.tackling ribosomal datasets. the Methanopyrus Withproteins We theanalyzed accumulation(3,275 archaealkandleri and 6,377 of phyparadox comp positions,logenyletely Abstract deposited research Background: Phylogenetic analysis of the Archaea has been mainly established by 16S rRNA sequence comparison. With the accumulation of completely sequenced genomes, it is now possible to test alternative approaches by using large sequence datasets.
    [Show full text]
  • Hyperthermophilic Archae- and Eubacteria Occurring Within Indonesian Hydrothermal Areas
    Mitt. Geol.-Paläont. Inst. Univ. Hamburg The Sea off Mount Tambora S. 161-172 Hamburg Heft 70 October 1992 Hyperthermophilic Archae- and Eubacteria occurring within Indonesian Hydrothermal Areas by G. HUBER, R. HUBER, B. JONES G. LAUERER, A. NEUNER, A. SEGERER, K. O. STETTER & E. T. DEGENS*) With 3 Figures and 6 Tables Contents Abstract 162 1. Introduction ^2 2. Results and Discussion 163 2.1 Sampling 163 2.2 Archaebacterial Isolates from Sea Sediments and Sea Water Samples from the Sumbawa and Komodo-Rinja Areas 164 2.3 Hyperthermophilic Archaebacterial and Eubacterial Isolates from the Shallow Submarine Hot Springs at the Beach of Sangeang Island 165 2.4 Methanogenic Isolates from the Toye Bungkah Hot Springs, Bali 167 2.5 Hyperthermophilic and Thermophilic Archae- and Eubacteria Isolated from Solfatara Fields at the Dieng Plateau and Tangkuban Prahu, Java 167 3. Acknowledgements 17C References 171 *) Addresses of the authors: B. JONES, Gist-Brocades, Delft, The Netherlands; G. HUBER, R. HUBER, G. LAUERER, A. NEUNER, A. SEGERER, Prof. Dr. K. O. STETTER, University of Regensburg, Institute of Microbiology, Universitätsstr. 31, D-8400 Regensburg, Federal Republic of Germany; Prof. Dr. E. T. DEGENS, SCOPE/UNEP International Carbon Unit, Institute of Biogeochemistry and Marine Chemistry, University of Hamburg, Bundesstraße 55, D-2000 Hamburg 13, Federal Republic of Germany. Abstract From 85 samples taken during cruise 45B of the R/V SONNE within the Sunda Arc subduction zone and from solfatara fields in Java, thermophilic and hyperthermophilic archae- and eubacteria were isolated. The archaebacteria belong to the genera Methanobacterium, Methanolobus, Methanosarcina, Acidianus, Thermoproteus, Desulfurococcus, Thermoplasma and to two up to now unknown genera of hyperthermophilic marine heterotrophs and continental metal mobilizers.
    [Show full text]