Hyperthermophiles: Optimum for Them Is Extreme for the Rest 1,2,3I
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Geomicrobiological Processes in Extreme Environments: a Review
202 Articles by Hailiang Dong1, 2 and Bingsong Yu1,3 Geomicrobiological processes in extreme environments: A review 1 Geomicrobiology Laboratory, China University of Geosciences, Beijing, 100083, China. 2 Department of Geology, Miami University, Oxford, OH, 45056, USA. Email: [email protected] 3 School of Earth Sciences, China University of Geosciences, Beijing, 100083, China. The last decade has seen an extraordinary growth of and Mancinelli, 2001). These unique conditions have selected Geomicrobiology. Microorganisms have been studied in unique microorganisms and novel metabolic functions. Readers are directed to recent review papers (Kieft and Phelps, 1997; Pedersen, numerous extreme environments on Earth, ranging from 1997; Krumholz, 2000; Pedersen, 2000; Rothschild and crystalline rocks from the deep subsurface, ancient Mancinelli, 2001; Amend and Teske, 2005; Fredrickson and Balk- sedimentary rocks and hypersaline lakes, to dry deserts will, 2006). A recent study suggests the importance of pressure in the origination of life and biomolecules (Sharma et al., 2002). In and deep-ocean hydrothermal vent systems. In light of this short review and in light of some most recent developments, this recent progress, we review several currently active we focus on two specific aspects: novel metabolic functions and research frontiers: deep continental subsurface micro- energy sources. biology, microbial ecology in saline lakes, microbial Some metabolic functions of continental subsurface formation of dolomite, geomicrobiology in dry deserts, microorganisms fossil DNA and its use in recovery of paleoenviron- Because of the unique geochemical, hydrological, and geological mental conditions, and geomicrobiology of oceans. conditions of the deep subsurface, microorganisms from these envi- Throughout this article we emphasize geomicrobiological ronments are different from surface organisms in their metabolic processes in these extreme environments. -
Extreme Organisms on Earth Show Us Just How Weird Life Elsewhere Could Be. by Chris Impey Astrobiology
Astrobiology Extreme organisms on Earth show us just how weird life elsewhere could be. by Chris Impey How life could thrive on hostile worlds Humans have left their mark all over Earth. We’re proud of our role as nature’s generalists — perhaps not as swift as the gazelle or as strong as the gorilla, but still pretty good at most things. Alone among all species, technology has given us dominion over the planet. Humans are endlessly plucky and adaptable; it seems we can do anything. Strain 121 Yet in truth, we’re frail. From our safe living rooms, we may admire the people who conquer Everest or cross deserts. But without technology, we couldn’t live beyond Earth’s temperate zones. We cannot survive for long in temperatures below freezing or above 104° Fahrenheit (40° Celsius). We can stay underwater only as long as we can hold our breath. Without water to drink we’d die in 3 days. Microbes, on the other hand, are hardy. And within the microbial world lies a band of extremists, organisms that thrive in conditions that would cook, crush, smother, and dissolve most other forms of life. Collectively, they are known as extremophiles, which means, literally, “lovers of extremes.” Extremophiles are found at temperatures above the boiling point and below the freezing point of water, in high salinity, and in strongly acidic conditions. Some can live deep inside rock, and others can go into a freeze-dried “wait state” for tens of thousands of years. Some of these microbes harvest energy from meth- ane, sulfur, and even iron. -
Dominio Archaea
FILOGENIA DE LOS SERES VIVOS: DOMINIO ARCHAEA Nuria Garzón Pinto Facultad de Farmacia Universidad de Sevilla Septiembre de 2017 FILOGENIA DE LOS SERES VIVOS: DOMINIO ARCHAEA TRABAJO FIN DE GRADO Nuria Garzón Pinto Tutores: Antonio Ventosa Ucero y Cristina Sánchez-Porro Álvarez Tipología del trabajo: Revisión bibliográfica Grado en Farmacia. Facultad de Farmacia Departamento de Microbiología y Parasitología (Área de Microbiología) Universidad de Sevilla Sevilla, septiembre de 2017 RESUMEN A lo largo de la historia, la clasificación de los seres vivos ha ido variando en función de las diversas aportaciones científicas que se iban proponiendo, y la historia evolutiva de los organismos ha sido durante mucho tiempo algo que no se lograba conocer con claridad. Actualmente, gracias sobre todo a las ideas aportadas por Carl Woese y colaboradores, se sabe que los seres vivos se clasifican en 3 dominios (Bacteria, Eukarya y Archaea) y se conocen las herramientas que nos permiten realizar estudios filogenéticos, es decir, estudiar el origen de las especies. La herramienta principal, y en base a la cual se ha realizado la clasificación actual es el ARNr 16S. Sin embargo, hoy día sedispone de otros métodos que ayudan o complementan los análisis de la evolución de los seres vivos. En este trabajo se analiza cómo surgió el dominio Archaea, se describen las características y aspectos más importantes de las especies este grupo y se compara con el resto de dominios (Bacteria y Eukarya). Las arqueas han despertado un gran interés científico y han sido investigadas sobre todo por su capacidad para adaptarse y desarrollarse en ambientes extremos. -
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a 50 40 DSB 30 DSS HSB OTUs 20 10 HSS 0 REB 0 20406080RES Number of clones 20 DSB b 15 DSS 10 HSB OTUs 5 HSS 0 REB 0 204060 RES Number of clones Fig. S1. Rarefaction curves for bacterial (a) and archaeal (b) clone libraries. 1 Fig. S2. Communities clustered using normalized weighted-UniFrac PCA for bacterial communities (a). Each point represents an individual sample. 2 a b Jaccard Chao cd Jaccard Chao Fig. S3. Communities clustered using multidimensional scaling method for bacterial (a and b, Jaccard- and Chao-indices, respectively) and archaeal communities (c and d, Jaccard- and Chao-indices, respectively). Each point represents an individual sample. 3 Table S1. Summary of archaeal 16S rRNA gene clone sequences identified from the Yamagawa coastal hydrothermal field. Number of clones Pylogenetic group Representative clone Closest match (NCBI BLAST) Source Accession no. Similarity (%) HSS HSB DSS DSB RES REB Crenarchaeota Desulfurococcacae DSB_A38 1 Aeropyrum camini strain SY1 deep-sea hydrothermal vent chimney NR_040973 95 HSB_A50 1 Aeropyrum camini strain SY1 deep-sea hydrothermal vent chimney NR_040973 95 HSB_A77 6 Aeropyrum camini strain SY1 deep-sea hydrothermal vent chimney NR_040973 96 HSS_A02 1 10 Aeropyrum camini strain SY1 deep-sea hydrothermal vent chimney NR_040973 97 HSB_A38 2 clone HTM1036Pn-A124 microbial mats on polychaete nests at the Hatoma Knoll AB611454 99 HSB_A68 1 clone HTM1036Pn-A124 microbial mats on polychaete nests at the Hatoma Knoll AB611454 93 Pyrodictiaceae HSB_A20 2 Geogemma indica strain 296 deep-sea hydrothermal vent sulfide chimney DQ492260 98 HSB_A46 1 clone TOTO-A1-15 Pacific Ocean, Mariana Volcanic Arc AB167480 95 HSB_A23 1 clone F99a113 nascent hydrothermal chimney DQ228527 99 Thermoproteaceae HSB_A18 3 Pyrobaculum aerophilum str. -
The Thermal Limits to Life on Earth
International Journal of Astrobiology 13 (2): 141–154 (2014) doi:10.1017/S1473550413000438 © Cambridge University Press 2014. The online version of this article is published within an Open Access environment subject to the conditions of the Creative Commons Attribution licence http://creativecommons.org/licenses/by/3.0/. The thermal limits to life on Earth Andrew Clarke1,2 1British Antarctic Survey, Cambridge, UK 2School of Environmental Sciences, University of East Anglia, Norwich, UK e-mail: [email protected] Abstract: Living organisms on Earth are characterized by three necessary features: a set of internal instructions encoded in DNA (software), a suite of proteins and associated macromolecules providing a boundary and internal structure (hardware), and a flux of energy. In addition, they replicate themselves through reproduction, a process that renders evolutionary change inevitable in a resource-limited world. Temperature has a profound effect on all of these features, and yet life is sufficiently adaptable to be found almost everywhere water is liquid. The thermal limits to survival are well documented for many types of organisms, but the thermal limits to completion of the life cycle are much more difficult to establish, especially for organisms that inhabit thermally variable environments. Current data suggest that the thermal limits to completion of the life cycle differ between the three major domains of life, bacteria, archaea and eukaryotes. At the very highest temperatures only archaea are found with the current high-temperature limit for growth being 122 °C. Bacteria can grow up to 100 °C, but no eukaryote appears to be able to complete its life cycle above *60 °C and most not above 40 °C. -
Microbial Extremophiles in Aspect of Limits of Life. Elena V. ~Ikuta
Source of Acquisition NASA Marshall Space Flight Centel Microbial extremophiles in aspect of limits of life. Elena V. ~ikuta',Richard B. ~oover*,and Jane an^.^ IT LF " '-~ationalSpace Sciences and Technology CenterINASA, VP-62, 320 Sparkman Dr., Astrobiology Laboratory, Huntsville, AL 35805, USA. 3- Noblis, 3 150 Fairview Park Drive South, Falls Church, VA 22042, USA. Introduction. During Earth's evolution accompanied by geophysical and climatic changes a number of ecosystems have been formed. These ecosystems differ by the broad variety of physicochemical and biological factors composing our environment. Traditionally, pH and salinity are considered as geochemical extremes, as opposed to the temperature, pressure and radiation that are referred to as physical extremes (Van den Burg, 2003). Life inhabits all possible places on Earth interacting with the environment and within itself (cross species relations). In nature it is very rare when an ecotope is inhabited by a single species. As a rule, most ecosystems contain the functionally related and evolutionarily adjusted communities (consortia and populations). In contrast to the multicellular structure of eukaryotes (tissues, organs, systems of organs, whole organism), the highest organized form of prokaryotic life in nature is the benthic colonization in biofilms and microbial mats. In these complex structures all microbial cells of different species are distributed in space and time according to their functions and to physicochemical gradients that allow more effective system support, self- protection, and energy distribution. In vitro, of course, the most primitive organized structure for bacterial and archaeal cultures is the colony, the size, shape, color, consistency, and other characteristics of which could carry varies specifics on species or subspecies levels. -
Post-Genomic Characterization of Metabolic Pathways in Sulfolobus Solfataricus
Post-Genomic Characterization of Metabolic Pathways in Sulfolobus solfataricus Jasper Walther Thesis committee Thesis supervisors Prof. dr. J. van der Oost Personal chair at the laboratory of Microbiology Wageningen University Prof. dr. W. M. de Vos Professor of Microbiology Wageningen University Other members Prof. dr. W.J.H. van Berkel Wageningen University Prof. dr. V.A.F. Martins dos Santos Wageningen University Dr. T.J.G. Ettema Uppsala University, Sweden Dr. S.V. Albers Max Planck Institute for Terrestrial Microbiology, Marburg, Germany This research was conducted under the auspices of the Graduate School VLAG Post-Genomic Characterization of Metabolic Pathways in Sulfolobus solfataricus Jasper Walther Thesis Submitted in fulfilment of the requirements for the degree of doctor at Wageningen University by the authority of the Rector Magnificus Prof. dr. M.J. Kropff, in the presence of the Thesis Committee appointed by the Academic Board to be defended in public on Monday 23 January 2012 at 11 a.m. in the Aula. Jasper Walther Post-Genomic Characterization of Metabolic Pathways in Sulfolobus solfataricus, 164 pages. Thesis, Wageningen University, Wageningen, NL (2012) With references, with summaries in Dutch and English ISBN 978-94-6173-203-3 Table of contents Chapter 1 Introduction 1 Chapter 2 Hot Transcriptomics 17 Chapter 3 Reconstruction of central carbon metabolism in Sulfolobus solfataricus using a two-dimensional gel electrophoresis map, stable isotope labelling and DNA microarray analysis 45 Chapter 4 Identification of the Missing -
Exploring the Cell Cycle of Archaea
Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology 300 Exploring the Cell Cycle of Archaea MAGNUS LUNDGREN ACTA UNIVERSITATIS UPSALIENSIS ISSN 1651-6214 UPPSALA ISBN 978-91-554-6881-1 2007 urn:nbn:se:uu:diva-7848 ! " # ! $%%& '( ) * * * + , - . , #, $%%&, / / * 0 , 0 , '%%, & , , 123 4&!54 5))657!! 5 , 0 * * , 1 * . , * * , - * * , . 5 * , " * . * 8 * 5 , 2 . 0 . . , 2 * 0 9 . * 5 , 0 * . , . * * . . , 0 , /7 . . 0 , -. /7 * . * , : . . * , 0 * ; . * / , 0 . . , < ; . * , - . . . 8 * , 1 , ! " 0 / : # / #$ % $ & $ ' ( )* $ $ %+,-./ $ ! = # $%%& 122 7) 57$ 6 123 4&!54 5))657!! 5 ( ((( 5&!6! > (?? ,,? @ A ( ((( 5&!6!B List of papers This thesis is based on the following papers, which are referred to in the text by their roman numerals. I Robinson NP, Dionne I*, Lundgren M*, Marsh VL, Bernander R, Bell SD. Identification of two origins of replication in the single chromosome of the archaeon Sulfolobus solfataricus. Cell, -
Eukarya Archaea Bacteria Euryarchaeota
or collective redistirbution of any portion of this article by photocopy machine, reposting, or other means is permitted only with the approval of Th e Oceanography Society. Send all correspondence to: [email protected] or Th eOceanography PO Box 1931, Rockville, USA.Society, MD 20849-1931, or e to: [email protected] Oceanography correspondence all Society. Send of Th approval portionthe ofwith any articlepermitted only photocopy by is of machine, reposting, this means or collective or other redistirbution articleis has been published in Th SPECIAL ISSUE FEATURE Oceanography , Volume 20, Number 1, a quarterly journal of Th e Oceanography Society. Copyright 2007 by Th e Oceanography Society. All rights reserved. Permission is granted to copy this article for use in teaching and research. Republication, systemmatic reproduction, Threproduction, Republication, systemmatic research. for this and teaching article copy to use in reserved. e is rights granted All OceanographyPermission Society. by 2007 eCopyright Oceanography Society. journal of Th 20, Number 1, a quarterly , Volume Th e Emergence of Life on Earth BY MITCHELL SCHULTE 42 Oceanography Vol. 20, No. 1 AMONG THE MOST enduring and perplexing questions pondered by humankind are why, how, and when life began on Earth, and whether life exists elsewhere in the solar system or the universe. Attempts to answer these questions have fallen under the purview of a number of areas of inquiry, including philosophy, religion, and, more recently, dedicated scientifi c inquiry. Scien- tifi c study of life’s beginnings necessarily draws from a wide variety of disciplines. Because of the complexity of the problem, geologists, chemists, biologists, and physicists, as well as engineers and Th e Emergence of mathematicians, have all been involved in origin-of-life research. -
Microbiology and Geochemistry of Smith Creek and Grass Valley Hot
Journal of Earth Science, Vol. 21, Special Issue, p. 315–318, June 2010 ISSN 1674-487X Printed in China Microbiology and Geochemistry of Smith Creek and Grass Valley Hot Springs: Emerging Evidence for Wide Distribution of Novel Thermophilic Lineages in the US Great Basin Jeremy A Dodsworth, Brian P Hedlund* School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV, 89154, USA INTRODUCTION the Southern Smith Creek Valley springs region and The endorheic Great Basin (GB) region in the GVS1 is just southeast of Hot Spring Point, as desig- western US is host to a variety of non-acidic geother- nated by the Nevada Bureau of Mines and Geology mal spring systems. Heating of the majority of these website (http://www.nbmg.unr.edu/geothermal/ systems is due to their association with range-front gthome. tm). Sample collection, DNA extraction, field faults, in contrast to caldera-associated hot springs in measurements and water chemistry analysis were per- systems such as Yellowstone National Park and formed with source pool samples essentially as de- Kamchatka (Faulds et al., 2006). Previous characteri- scribed (Vick et al., 2010). 16S rRNA gene libraries zation of two geothermal systems in the GB, Great were constructed using PCR forward primers 9bF Boiling/Mud Hot springs (Costa et al., 2009) and Lit- (specific for Bacteria; L2) or 8aF (specific for Ar- tle Hot Creek (Vick et al., 2010), indicated that they chaea; L4) in conjunction with reverse primer 1406uR host several novel deep lineages of potentially abun- as described in Costa et al. (2009). 48 clones from dant Bacteria and Archaea. -
Characterizing and Classifying Prokaryotes
PowerPoint® Lecture Presentations prepared by Mindy Miller-Kittrell, North Carolina State University C H A P T E R 11 Characterizing and Classifying Prokaryotes © 2014 Pearson Education, Inc. Bacteria as Plastic Recyclers http://www.cnn.com/2016/03/11/world/b acteria-discovery-plastic/index.html http://www.the- scientist.com/?articles.view/articleNo/4 5556/title/Microbial-Recycler-Found/ © 2014 Pearson Education, Inc. General Characteristics of Prokaryotic Organisms • Reproduction of Prokaryotic Cells • All reproduce asexually • Three main methods • Binary fission (most common) • Snapping division • Budding © 2014 Pearson Education, Inc. Figure 11.3 Binary fission. 1 Cell replicates its DNA. Cell wall Cytoplasmic Nucleoid membrane Replicated DNA 2 The cytoplasmic membrane elongates, separating DNA molecules. 3 Cross wall forms; membrane invaginates. 4 Cross wall forms completely. 5 Daughter cells may separate. © 2014 Pearson Education, Inc. Figure 11.4 Snapping division, a variation of binary fission. Older, outer portion of cell wall Newer, inner portion of cell wall Rupture of older, outer wall Hinge © 2014 Pearson Education, Inc. Figure 11.6 Budding Parent cell retains its identity © 2014 Pearson Education, Inc. General Characteristics of Prokaryotic Organisms • Arrangements of Prokaryotic Cells • Result from two aspects of division during binary fission • Planes in which cells divide • Separation of daughter cells © 2014 Pearson Education, Inc. Figure 11.7 Arrangements of cocci. Plane of division Diplococci Streptococci Tetrads Sarcinae Staphylococci © 2014 Pearson Education, Inc. Figure 11.8 Arrangements of bacilli. Single bacillus Diplobacilli Streptobacilli Palisade V-shape © 2014 Pearson Education, Inc. Modern Prokaryotic Classification • Currently based on genetic relatedness of rRNA sequences • Three domains • Archaea • Bacteria • Eukarya © 2014 Pearson Education, Inc. -
Downloaded from Appl
University of Massachusetts Amherst From the SelectedWorks of Derek Lovley November 2, 2007 Growth of Thermophilic and Hyperthermophilic Fe(III)-Reducing Microorganisms on a Ferruginous Smectite as the Sole Electron Acceptor Derek Lovley, University of Massachusetts - Amherst Kazem Kashefi Evgenya S Shelobolina W. Crawford Elliott Available at: https://works.bepress.com/derek_lovley/100/ Growth of Thermophilic and Hyperthermophilic Fe(III)-Reducing Microorganisms on a Ferruginous Smectite as the Sole Electron Acceptor Kazem Kashefi, Evgenya S. Shelobolina, W. Crawford Elliott and Derek R. Lovley Downloaded from Appl. Environ. Microbiol. 2008, 74(1):251. DOI: 10.1128/AEM.01580-07. Published Ahead of Print 2 November 2007. Updated information and services can be found at: http://aem.asm.org/ http://aem.asm.org/content/74/1/251 These include: REFERENCES This article cites 53 articles, 28 of which can be accessed free at: http://aem.asm.org/content/74/1/251#ref-list-1 on March 14, 2013 by Univ of Massachusetts Amherst CONTENT ALERTS Receive: RSS Feeds, eTOCs, free email alerts (when new articles cite this article), more» Information about commercial reprint orders: http://journals.asm.org/site/misc/reprints.xhtml To subscribe to to another ASM Journal go to: http://journals.asm.org/site/subscriptions/ APPLIED AND ENVIRONMENTAL MICROBIOLOGY, Jan. 2008, p. 251–258 Vol. 74, No. 1 0099-2240/08/$08.00ϩ0 doi:10.1128/AEM.01580-07 Copyright © 2008, American Society for Microbiology. All Rights Reserved. Growth of Thermophilic and Hyperthermophilic Fe(III)-Reducing Microorganisms on a Ferruginous Smectite as the Sole Electron Acceptorᰔ Kazem Kashefi,1* Evgenya S.