DOCSLIB.ORG

Environmentalmicrobiology

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
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. Early Earth was inhospitable from time to time because space rocks crushed into the Earth’s surface. Some impacts were powerful enough to vaporize oceans and create clouds of steam which sterilized the Earth’s surface. Nonetheless, some microorganisms were able to survive this period deep underground while some may have had the capacity of modern microorganism to produce survival forms called endospores. Early in the planet’s history conditions were harsh. The Earth’s surface was exposed to strong ultraviolet (UV) radiation because the ozone layer was not yet formed in the atmosphere. Nevertheless, the prokaryotic microorganisms began to develop. The first prokaryotic microor- ganisms lived in anaerobic environment because atmosphere was a mixture of CO2,N2, and H2O vapour and in traces H2.O2 gas began to appear in significant amount in the Earth’s atmosphere between 2.5 and 2 billion years ago as a result of microbial metabolic process called oxygenic photosynthesis. Oxygenic photosynthesis which started around 3 billion years ago differed from earlier forms of photosynthesis and the bacteria respon- sible for this type of photosynthesis are called cyanobacteria. Cyanobacteria brought the O2 level of the Earth’s from River Valley Technologies Ltd atmosphere up to 10 % of today’s level and due to it the formation of ozone layer started. O2 level was high enough to enable evolution of oxygen-utilizing organisms [1, 2]. An approximate timeline of the development of life on Earth is presented in Figure 1. Since many eukaryotes are O2 dependent, researchers had theorized ProofCheck that protists first appeared around 2 billion years ago but according to recent evidence the first protistsap- peared about 3 billion years ago. Although bacteria and archaea are older than protists, an early appearance of the first eukaryotes is evidenced with a high degree of diversity in this group. Algae appeared after cyanobac- teria within the last 2 billion years, because their chloroplasts were derived from cyanobacteria. Fungi appeared during the last several hundred million years. Marija Vuković Domanovac is the corresponding author. © 2017 Walter de Gruyter GmbH, Berlin/Boston. Automatically generated rough PDF by This content is free. 1 Briški and Vuković Domanovac DE GRUYTER Figure 1: Approximate timeline in the history of life on Earth [1]. 2 The microbial world: classification, metabolism and growth Microorganisms are the foundation for all life on Earth. They vary in their appearance, ability to carry out differ- ent biochemical transformations, ability to grow in wide variety of environments and in their interactions with other organisms. Due to a great variety of different organisms on Earth, a systematic approach to classifying these organisms is necessary. The science of classifying organisms is called taxonomy and the groups making up the classification hierarchy are called taxa. Nomenclature refers to the actual naming of organisms. The binominal system of nomenclature is used for microorganisms. The names are given in Latin or are Latinized. The first word in the name is the genus, with the first letter always capitalized; the second isthe species name, which is not capitalized. Both words are always italicized. Classification of well-known bacterium Escherichia coli is presented in Example 1. Example 1. Classification of bacterium Escherichia coli E. coli is a member of genus Escherichia. It was named after the person who first isolated and described it, Theodor Escherich. The species name comes from the location where it was found, in this case in human intestinal tract. Its classification is as follows: Domain: Bacteria, Phylum: Proteobacteria, Class: Gammaproteobacteria, Order: Enterobacteriales, Family: Enterobacteriaceae, Genus: Escherichia, Species: E. coli. Traditional classification of living organisms was based on morphological differences like shape, colouring or appendages (flagella) extending from the cells. In the 1970s, a research by Woese and others suggested that life on Earth evolved along three evolutionary lineages. Analysis of 16S rRNA (ribosomal ribonucleic acid) has led to the modern phylogenetic classification of living organisms in three domains: Archaea, Bacteria and Eukarya. Phylogenetic information along with other taxonomic information has been used to construct the phylogenetic tree (Figure 2). from River Valley Technologies Ltd ProofCheck Figure 2: Schematics of universal phylogenetic tree evolved from a common ancestor. Using the rRNA gene sequences of many different organisms resulted in formation of a tree with longer and shorter branches; the longer the branches lengths, the greater the diversity in the group. The branches lengths are shorter for newly evolved organisms such as fungi, plants and animals in comparison with the branches lengths for prokaryotic and lower eukaryotic microorganisms [1, 3]. Members of microbial world consist of two major cell types: the simple prokaryotic and the complex eu- Automatically generated rough PDF by karyotic cells. Microscopically, the cells in domains Bacteria and Archaea look similar. They do not contain 2 DE GRUYTER Briški and Vuković Domanovac a membrane-bound nucleus or other intracellular lipid-bound organelles. Their genetic information is stored in a circular strand of deoxyribonucleic acid (DNA) in the nucleotide and cytoplasm is surrounded by a rigid cell wall. Due to structural similarities bacteria and archaea are prokaryotes but they differ in their chemical composition and therefore they are in different domains. The domain Eukarya is comprised of four kingdoms: Animalia, Fungi, Plantae and Protista. All members in this domain contain eukaryotic cells and this microbial world is composed of single-celled and multicellular organisms. The cells contain a membrane-bound nucleus and other internal organelles (mitochondria, chloroplast and cytoskeleton) that make eukaryotes more com- plex than the simple prokaryotes. Term microorganism is used to describe an organism that is so small that it cannot be seen without the use of microscope. Microscopy plays an integral role in the study of microorganisms and can provide extremely useful information about them. Even today, one of the most important tools for studying microorganisms is the bright- field light microscope that can magnify images 1000×. Most living microorganisms are nearly transparent and move rapidly about the slide. Consequently, cells must be immobilised and stained with dyes. Simple staining employs one dye to stain the cells. Differential staining is used to distinguish one group of bacteria from another. One of most frequently used staining procedures is the Gram stain (Example 2). Example 2. Gram staining is the procedure (Figure 3) by which bacteria can be separated in two major groups: Gram positive and Gram negative. Difference in the staining properties of these two groups isdueto the difference in the chemical structure of their cell walls. This procedure was developed over a century agoby Dr. Hans Christian Gram. Figure 3: Staining bacteria for microscopic observation. The bacteria are the smallest prokaryotic cells and the least structurally complex unicellular microorgan- isms. They possess the greatest metabolic flexibility. Typical shapes of common bacteria are: (a) sphere (coccus), (b) rod (bacillus) and (c) spiral (spirillum). Diameter of a typical cell is 1 µm. A representative of rod-shaped bac- teria is presented in Figure 4(a). The cell wall contains chemical compound peptidoglycan, which is not found in organisms in other domains. They multiply by binary fission in which one cell divides in two cells, and many can move using flagella. The archaea are a group of ancient organisms
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]
  • 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.
    [Show full text]
  • 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.
    [Show full text]
  • 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.
    [Show full text]
  • 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.
    [Show full text]
  • 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.
    [Show full text]
  • Validation of the Publication of New Names and New Combinations Previously Effectively Published Outside the IJSB List No
    INTERNATIONAL JOURNAL OF SYSTEMATIC BACTERIOLOGY, OCt. 1986, p. 573-576 Vol. 36, No. 4 0020-7713/86/040573-04$~2.OO/O Copyright 0 1986, International Union of Microbiological Societies Validation of the Publication of New Names and New Combinations Previously Effectively Published Outside the IJSB List No. 22t The purpose of this announcement is to effect the valid publication of the following new names and new combinations under the procedufe described previously (Int. J. Syst. Bacteriol. 27(3):iv, 1977). Authors and other individuals wishing to have new names and/or combinations included in future lists should send the pertinent reprint or a photocopy thereof to the IJSB for confirmation that all of the other requirements for valid publication have been met. It should be noted that the date of valid publication of these new names and combinations is the date of publication of this list, not the date of the original publication of the names and combinations. The authors of the new names and combinations are as given below, arid these authors’ names will be included in the author index of the present issue and in the volume author index in this issue of the IJSB. Inclusion of a name on these lists validates the name and thereby makes it available in bacteriological nomenclature. The, inclusion of a name on this list is not to be construed as taxonomic acceptance of the taxon to which the name is applied. Indeed, some of these names may, in time, be shown to be synonyms, or the organism may be transferred to another genus, thus necessitating the creation of a new combination.
    [Show full text]
  • First Insights Into the Microbiology of Three Antarctic Briny Systems of the Northern Victoria Land
    diversity Review First Insights into the Microbiology of Three Antarctic Briny Systems of the Northern Victoria Land Maria Papale 1,† , Carmen Rizzo 1,2,† , Gabriella Caruso 1 , Rosabruna La Ferla 1, Giovanna Maimone 1, Angelina Lo Giudice 1,* , Maurizio Azzaro 1,‡ and Mauro Guglielmin 3,‡ 1 Institute of Polar Sciences, National Research Council (CNR-ISP), Spianata San Raineri 86, 98122 Messina, Italy; [email protected] (M.P.); [email protected] (C.R.); [email protected] (G.C.); [email protected] (R.L.F.); [email protected] (G.M.); [email protected] (M.A.) 2 Stazione Zoologica Anton Dohrn, Department BIOTECH, National Institute of Biology, Villa Pace, Contrada Porticatello 29, 98167 Messina, Italy 3 Dipartimento di Scienze Teoriche e Applicate, University of Insubria, Via J.H. Dunant 3, 21100 Varese, Italy; [email protected] * Correspondence: [email protected]; Tel.: +39-090-6015-414 † Equal contribution as first author. ‡ Equal contribution as last author. Abstract: Different polar environments (lakes and glaciers), also in Antarctica, encapsulate brine pools characterized by a unique combination of extreme conditions, mainly in terms of high salinity and low temperature. Since 2014, we have been focusing our attention on the microbiology of brine pockets from three lakes in the Northern Victoria Land (NVL), lying in the Tarn Flat (TF) and Boulder Clay (BC) areas. The microbial communities have been analyzed for community structure by next generation sequencing, extracellular enzyme activities, metabolic potentials, and microbial abundances. In this Citation: Papale, M.; Rizzo, C.; study, we aim at reconsidering all available data to analyze the influence exerted by environmental Caruso, G.; La Ferla, R.; Maimone, G.; parameters on the community composition and activities.
    [Show full text]
  • 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
    [Show full text]
  • Complete Genome Sequence of Methanobacterium Thermoautotrophicum ⌬H: Functional Analysis and Comparative Genomics DOUGLAS R
    JOURNAL OF BACTERIOLOGY, Nov. 1997, p. 7135–7155 Vol. 179, No. 22 0021-9193/97/$04.0010 Copyright © 1997, American Society for Microbiology Complete Genome Sequence of Methanobacterium thermoautotrophicum DH: Functional Analysis and Comparative Genomics DOUGLAS R. SMITH,1* LYNN A. DOUCETTE-STAMM,1 CRAIG DELOUGHERY,1 HONGMEI LEE,1 JOANN DUBOIS,1 TYLER ALDREDGE,1 ROMINA BASHIRZADEH,1 DERRON BLAKELY,1 ROBIN COOK,1 KATIE GILBERT,1 DAWN HARRISON,1 LIEU HOANG,1 PAMELA KEAGLE,1 WENDY LUMM,1 BRYAN POTHIER,1 DAYONG QIU,1 ROB SPADAFORA,1 RITA VICAIRE,1 YING WANG,1 JAMEY WIERZBOWSKI,1 RENE GIBSON,1 NILOFER JIWANI,1 ANTHONY CARUSO,1 DAVID BUSH,1 1 1 1 1 HERSHEL SAFER, DONIVAN PATWELL, SHASHI PRABHAKAR, STEVE MCDOUGALL, GEORGE SHIMER,1 ANIL GOYAL,1 SHMUEL PIETROKOVSKI,2 GEORGE M. CHURCH,3 4 1 1 1 4 CHARLES J. DANIELS, JEN-I MAO, PHIL RICE, JO¨ RK NO¨ LLING, AND JOHN N. REEVE Genome Therapeutics Corporation, Collaborative Research Division, Waltham, Massachusetts 02154,1 Howard Hughes Medical Institute, Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115,3 Fred Hutchinson Cancer Research Center, Seattle, Washington 98109,2 and Department of Microbiology, The Ohio State University, Columbus, Ohio 432104 Received 2 July 1997/Accepted 3 September 1997 The complete 1,751,377-bp sequence of the genome of the thermophilic archaeon Methanobacterium thermo- autotrophicum DH has been determined by a whole-genome shotgun sequencing approach. A total of 1,855 open reading frames (ORFs) have been identified that appear to encode polypeptides, 844 (46%) of which have been assigned putative functions based on their similarities to database sequences with assigned functions.
    [Show full text]
  • 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.
    [Show full text]
  • Methanogenesis and Methane Oxidation in Wetlands. Implications in the Global Carbon Cycle
    TORRES OK 09 11/11/05 5:39 PM Page 327 Hidrobiológica 15 (3): 327-349 ARTÍCULO DE REVISIÓN Diciembre 2005 Methanogenesis and methane oxidation in wetlands. Implications in the global carbon cycle Metanogénesis y metano-oxidación en humedales. Implicaciones en el ciclo del carbono global Rocio Torres-Alvarado1, Florina Ramírez-Vives2, Francisco José Fernández 2 e Irene Barriga-Sosa1 1Departamento de Hidrobiología y 2Departamento de Biotecnología. Universidad Autónoma Metropolitana-Iztapalapa (UAM-I). Av. San Rafael Atlixco # 186.Col. Vicentina. A. P. 55 535. Ciudad de México. 09430, México. Torres-Alvarado R., F. Ramírez-Vives, F. J. Fernández e I. Barriga-Sosa. 2005. Methanogenesis and Methane Oxidation in Wetlands. Implications in the Global Carbon Cycle. Hidrobiológica 15 (3): 327-349. ABSTRACT Wetlands are important ecosystems on the Earth. They are distinguished by the presence of water, saturated anoxic soils, and different kinds of vegetation adapted to this conditions. Organic matter in these environments is mineralized mainly in the sediments throughout anaerobic processes where sulfate reduction is one of the most important terminal stages of anaerobic decomposition in coastal wetlands, whereas methanogenesis is important in freshwater wetlands. In this environments, methane, a greenhouse gas, is produced as a result of the activity of a large and diverse group of methanogenic bacteria (Domain Archaea). The generated methane can be diffused to the atmosphere or can be oxidized by several microorganisms under aerobic and anaerobic conditions, such microorganisms intercept and consume this gas diminishing its emission to the atmosphere. The production and consumption of methane in wetlands involve complex physiological processes of plants and microorganisms, which are regulated by climatic and edaphic factors, mainly soil temperature and water table level.
    [Show full text]