Extremophiles2016
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Efficient Genome Editing of an Extreme Thermophile, Thermus
www.nature.com/scientificreports OPEN Efcient genome editing of an extreme thermophile, Thermus thermophilus, using a thermostable Cas9 variant Bjorn Thor Adalsteinsson1*, Thordis Kristjansdottir1,2, William Merre3, Alexandra Helleux4, Julia Dusaucy5, Mathilde Tourigny4, Olafur Fridjonsson1 & Gudmundur Oli Hreggvidsson1,2 Thermophilic organisms are extensively studied in industrial biotechnology, for exploration of the limits of life, and in other contexts. Their optimal growth at high temperatures presents a challenge for the development of genetic tools for their genome editing, since genetic markers and selection substrates are often thermolabile. We sought to develop a thermostable CRISPR-Cas9 based system for genome editing of thermophiles. We identifed CaldoCas9 and designed an associated guide RNA and showed that the pair have targetable nuclease activity in vitro at temperatures up to 65 °C. We performed a detailed characterization of the protospacer adjacent motif specifcity of CaldoCas9, which revealed a preference for 5′-NNNNGNMA. We constructed a plasmid vector for the delivery and use of the CaldoCas9 based genome editing system in the extreme thermophile Thermus thermophilus at 65 °C. Using the vector, we generated gene knock-out mutants of T. thermophilus, targeting genes on the bacterial chromosome and megaplasmid. Mutants were obtained at a frequency of about 90%. We demonstrated that the vector can be cured from mutants for a subsequent round of genome editing. CRISPR-Cas9 based genome editing has not been reported previously in the extreme thermophile T. thermophilus. These results may facilitate development of genome editing tools for other extreme thermophiles and to that end, the vector has been made available via the plasmid repository Addgene. -
The 2014 Golden Gate National Parks Bioblitz - Data Management and the Event Species List Achieving a Quality Dataset from a Large Scale Event
National Park Service U.S. Department of the Interior Natural Resource Stewardship and Science The 2014 Golden Gate National Parks BioBlitz - Data Management and the Event Species List Achieving a Quality Dataset from a Large Scale Event Natural Resource Report NPS/GOGA/NRR—2016/1147 ON THIS PAGE Photograph of BioBlitz participants conducting data entry into iNaturalist. Photograph courtesy of the National Park Service. ON THE COVER Photograph of BioBlitz participants collecting aquatic species data in the Presidio of San Francisco. Photograph courtesy of National Park Service. The 2014 Golden Gate National Parks BioBlitz - Data Management and the Event Species List Achieving a Quality Dataset from a Large Scale Event Natural Resource Report NPS/GOGA/NRR—2016/1147 Elizabeth Edson1, Michelle O’Herron1, Alison Forrestel2, Daniel George3 1Golden Gate Parks Conservancy Building 201 Fort Mason San Francisco, CA 94129 2National Park Service. Golden Gate National Recreation Area Fort Cronkhite, Bldg. 1061 Sausalito, CA 94965 3National Park Service. San Francisco Bay Area Network Inventory & Monitoring Program Manager Fort Cronkhite, Bldg. 1063 Sausalito, CA 94965 March 2016 U.S. Department of the Interior National Park Service Natural Resource Stewardship and Science Fort Collins, Colorado The National Park Service, Natural Resource Stewardship and Science office in Fort Collins, Colorado, publishes a range of reports that address natural resource topics. These reports are of interest and applicability to a broad audience in the National Park Service and others in natural resource management, including scientists, conservation and environmental constituencies, and the public. The Natural Resource Report Series is used to disseminate comprehensive information and analysis about natural resources and related topics concerning lands managed by the National Park Service. -
Genomics and Energy and Environmental Science Poster 2011
Omics: Exploring the Molecular Universe within Biological Systems Instead of studying one or a few genes or proteins at a time, “omics” collectively Proteomics is the analysis of the proteome—the complete set describes the comprehensive analysis of genes, RNA transcripts, proteins, of proteins expressed by a cell or population of cells. Proteins, metabolites, and other molecules present in a biological system. Ongoing the workhorse molecules of life, catalyze biochemical reactions; advances in computing power and automated technologies for DNA sequencing provide structural support; and recognize, bind, or transport and experiments continue to improve our ability to analyze increasing numbers other molecules throughout the cell. Hundreds of dierent types of molecules and how they function as a system. Systems biology integrates the of proteins can be expressed at a time, and most are part of large data from various omic analyses using computational tools to build predictive complexes made up of models of biological systems. many proteins and other molecules. Transcriptomics is the analysis of the transcriptome—the complete set of RNA Hundreds to molecules present in a cell or population of thousands of different cells. RNA, which is much less stable than protein types exist within DNA, is constantly being synthesized and a cell. This large subunit of a ribosome contains about then broken down to facilitate rapid 3,000 RNA nucleotides changes in paerns of protein expression (gray) and 30 protein that occur as an organism dynamically chains (gold). responds to its environment. In addition to the three major classes of RNA (mRNA, tRNA, and ribosomal RNA), single- stranded RNA is very exible and can fold into complex shapes that carry out specic functions. -
Biological Diversity in the Patent System
Biological Diversity in the Patent System Paul Oldham1,2*, Stephen Hall1,3, Oscar Forero1,4 1 ESRC Centre for Economic and Social Aspects of Genomics (Cesagen), Lancaster University, Lancaster, United Kingdom, 2 Institute of Advanced Studies, United Nations University, Yokohama, Japan, 3 One World Analytics, Lancaster, United Kingdom, 4 Centre for Development, Environment and Policy, SOAS, University of London, London, United Kingdom Abstract Biological diversity in the patent system is an enduring focus of controversy but empirical analysis of the presence of biodiversity in the patent system has been limited. To address this problem we text mined 11 million patent documents for 6 million Latin species names from the Global Names Index (GNI) established by the Global Biodiversity Information Facility (GBIF) and Encyclopedia of Life (EOL). We identified 76,274 full Latin species names from 23,882 genera in 767,955 patent documents. 25,595 species appeared in the claims section of 136,880 patent documents. This reveals that human innovative activity involving biodiversity in the patent system focuses on approximately 4% of taxonomically described species and between 0.8–1% of predicted global species. In this article we identify the major features of the patent landscape for biological diversity by focusing on key areas including pharmaceuticals, neglected diseases, traditional medicines, genetic engineering, foods, biocides, marine genetic resources and Antarctica. We conclude that the narrow focus of human innovative activity and ownership of genetic resources is unlikely to be in the long term interest of humanity. We argue that a broader spectrum of biodiversity needs to be opened up to research and development based on the principles of equitable benefit-sharing, respect for the objectives of the Convention on Biological Diversity, human rights and ethics. -
18Th EANA Conference European Astrobiology Network Association
18th EANA Conference European Astrobiology Network Association 24-28 September 2018 Freie Universität Berlin, Germany Sponsors: Scientific Organizing Committee (EANA Council): Daniela Billi, Italy Oleg Kotsyurbenko, Russia Alexis Brandeker, Sweden Helmut Lammer, Austria John Brucato, Italy Harry Lehto, Finland Barbara Cavalazzi, Italy Kirsi Lehto, Finland Elias Chatzitheodoridis, Greece Zita Martins, Portugal Charles Cockell, UK Nigel Mason, UK Hervé Cottin, France Ralf Möller, Germany Rosa De la Torre, Spain Christine Moissl-Eichinger, Austria Jean-Pierre De Vera, Germany Lena Noack, Germany René Demets, ESA Karen Olsson-Francis, UK Cristina Dobrota, Romania François Raulin, France Pascale Ehrenfreund, The Netherlands Petra Rettberg, Germany Franco Ferrari, Poland Séverine Robert, Belgium Kai Finster, Denmark Gyorgyi Ronto, Hungary Muriel Gargaud, France Dirk Schulze-Makuch, Germany Beda Hofmann, Switzerland Alan Schwartz, The Netherlands Nils Holm, Sweden Ewa Szuszkiewicz, Poland Jan Jehlicka, Czech Republic Ruth-Sophie Taubner, Austria Jean-Luc Josset, Switzerland Jorge Vago, The Netherlands Kensei Kobayashi, Japan Frances Westall, France Local Organizing Committee: Lena Noack (FU) Lutz Hecht (MfN, FU) Jean-Pierre de Vera (DLR, DAbG) Jacob Heinz (TU) Dirk Schulze-Makuch (TU, DAbG) Dennis Höning (VU Amsterdam) Alessandro Airo (TU) Deborah Maus (TU) Felix Arens (FU) Ralf Möller (DLR) Alexander Balduin Carolin Rabethge (FU) Mickael Baqué (DLR) Heike Rauer (DLR, TU, FU) Doris Breuer -
Sulfur Metabolism Pathways in Sulfobacillus Acidophilus TPY, a Gram-Positive Moderate Thermoacidophile from a Hydrothermal Vent
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Frontiers - Publisher Connector ORIGINAL RESEARCH published: 18 November 2016 doi: 10.3389/fmicb.2016.01861 Sulfur Metabolism Pathways in Sulfobacillus acidophilus TPY, A Gram-Positive Moderate Thermoacidophile from a Hydrothermal Vent Wenbin Guo 1, Huijun Zhang 1, 2, Wengen Zhou 1, 2, Yuguang Wang 1, Hongbo Zhou 2 and Xinhua Chen 1, 3* 1 Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, State Oceanic Administration, Xiamen, China, 2 Department of Bioengineering, School of Minerals Processing and Bioengineering, Central South University, Changsha, China, 3 Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory forMarine Science and Technology, Qingdao, China Sulfobacillus acidophilus TPY, isolated from a hydrothermal vent in the Pacific Ocean, is a moderately thermoacidophilic Gram-positive bacterium that can oxidize ferrous iron or Edited by: sulfur compounds to obtain energy. In this study, comparative transcriptomic analyses of Jake Bailey, University of Minnesota, USA S. acidophilus TPY were performed under different redox conditions. Based on these Reviewed by: results, pathways involved in sulfur metabolism were proposed. Additional evidence M. J. L. Coolen, was obtained by analyzing mRNA abundance of selected genes involved in the sulfur Curtin University, Australia Karen Elizabeth Rossmassler, metabolism of sulfur oxygenase reductase (SOR)-overexpressed S. acidophilus TPY Colorado State University, USA recombinant under different redox conditions. Comparative transcriptomic analyses of *Correspondence: S. acidophilus TPY cultured in the presence of ferrous sulfate (FeSO4) or elemental Xinhua Chen sulfur (S0) were employed to detect differentially transcribed genes and operons involved [email protected] in sulfur metabolism. -
Genomic Analysis of Family UBA6911 (Group 18 Acidobacteria)
bioRxiv preprint doi: https://doi.org/10.1101/2021.04.09.439258; this version posted April 10, 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 2 Genomic analysis of family UBA6911 (Group 18 3 Acidobacteria) expands the metabolic capacities of the 4 phylum and highlights adaptations to terrestrial habitats. 5 6 Archana Yadav1, Jenna C. Borrelli1, Mostafa S. Elshahed1, and Noha H. Youssef1* 7 8 1Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, 9 OK 10 *Correspondence: Noha H. Youssef: [email protected] bioRxiv preprint doi: https://doi.org/10.1101/2021.04.09.439258; this version posted April 10, 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. 11 Abstract 12 Approaches for recovering and analyzing genomes belonging to novel, hitherto unexplored 13 bacterial lineages have provided invaluable insights into the metabolic capabilities and 14 ecological roles of yet-uncultured taxa. The phylum Acidobacteria is one of the most prevalent 15 and ecologically successful lineages on earth yet, currently, multiple lineages within this phylum 16 remain unexplored. Here, we utilize genomes recovered from Zodletone spring, an anaerobic 17 sulfide and sulfur-rich spring in southwestern Oklahoma, as well as from multiple disparate soil 18 and non-soil habitats, to examine the metabolic capabilities and ecological role of members of 19 the family UBA6911 (group18) Acidobacteria. -
Extremely Thermophilic Microorganisms As Metabolic Engineering Platforms for Production of Fuels and Industrial Chemicals
REVIEW published: 05 November 2015 doi: 10.3389/fmicb.2015.01209 Extremely thermophilic microorganisms as metabolic engineering platforms for production of fuels and industrial chemicals Benjamin M. Zeldes 1, Matthew W. Keller 2, Andrew J. Loder 1, Christopher T. Straub 1, Michael W. W. Adams 2 and Robert M. Kelly 1* 1 Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, USA, 2 Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA Enzymes from extremely thermophilic microorganisms have been of technological interest for some time because of their ability to catalyze reactions of industrial significance at elevated temperatures. Thermophilic enzymes are now routinely produced in recombinant mesophilic hosts for use as discrete biocatalysts. Genome and metagenome sequence data for extreme thermophiles provide useful information for putative biocatalysts for a wide range of biotransformations, albeit involving at most a few enzymatic steps. However, in the past several years, unprecedented progress has been made in establishing molecular genetics tools for extreme thermophiles to the point Edited by: that the use of these microorganisms as metabolic engineering platforms has become Bettina Siebers, University of Duisburg-Essen, possible. While in its early days, complex metabolic pathways have been altered or Germany engineered into recombinant extreme thermophiles, such that the production of fuels and Reviewed by: chemicals at elevated temperatures has become possible. Not only does this expand the Haruyuki Atomi, thermal range for industrial biotechnology, it also potentially provides biodiverse options Kyoto University, Japan Phillip Craig Wright, for specific biotransformations unique to these microorganisms. The list of extreme University of Sheffield, UK thermophiles growing optimally between 70 and 100◦C with genetic toolkits currently *Correspondence: available includes archaea and bacteria, aerobes and anaerobes, coming from genera Robert M. -
Perspectives
Copyright 1999 by the Genetics Society of America Perspectives Anecdotal, Historical and Critical Commentaries on Genetics Edited by James F. Crow and William F. Dove What Archaea Have to Tell Biologists William B. Whitman,* Felicitas Pfeifer,² Paul Blum³ and Albrecht Klein§ *Department of Microbiology, University of Georgia, Athens Georgia 30602-2605, ²Institut fuer Mikrobiologie und Genetik, Technischen Universitaet, D-64287 Darmstadt Germany, ³School of Biological Sciences, University of Nebraska, Lincoln, Nebraska 68588-0666 and §Fachbereich Biologie-Genetik, Universitaet Marburg, D-35043 Marburg, Germany E are excited to present the following review and While the study of fascinating microorganisms needs W research articles on archaeal research, and we no special justi®cation, the archaea provide unique op- thank the Genetics Society of America for this opportu- portunities to gain insight into a number of fundamen- nity. In addition, we recognize the contributions of our tal problems in biology. As one of the most ancient colleagues, Charles Daniels (Ohio State University) and lineages of living organisms, the archaea set a boundary Michael Thomm (Universitaet Kiel), who along with for evolutionary diversity and have the potential to offer the authors served as coeditors of papers on archaea in key insights into the early evolution of life, including this volume. the origin of the eukaryotes. Many archaea are also More than two decades after the initial proposal, the extremophiles that ¯ourish at high temperature, low or archaeal hypothesis remains the best explanation for high pH, or high salt and delineate another boundary the unexpected diversity of molecular and biochemical for life, the biochemical and geochemical boundary, properties found in the prokaryotes. -
ELBA BIOFLUX Extreme Life, Biospeology & Astrobiology International Journal of the Bioflux Society
ELBA BIOFLUX Extreme Life, Biospeology & Astrobiology International Journal of the Bioflux Society A short review on tardigrades – some lesser known taxa of polyextremophilic invertebrates 1Andrea Gagyi-Palffy, and 2Laurenţiu C. Stoian 1Faculty of Environmental Sciences and Engineering, Babeş-Bolyai University, Cluj- Napoca, Romania; 2Faculty of Geography, Babeş-Bolyai University, Cluj-Napoca, Romania. Corresponding author: A. Gagyi-Palffy, [email protected] Abstract. Tardigrades are polyextremophilic small organisms capable to survive in a variety of extreme conditions. By reversibly suspending their metabolism (cryptobiosis – tun state) tardigrades can dry or freeze and, thus, survive the extreme conditions like very high or low pressure and temperatures, changes in salinity, lack of oxygen, lack of water, some noxious chemicals, boiling alcohol, even the vacuum of the outer space. Despite their peculiar morphology and amazing diversity of habitats, relatively little is known about these organisms. Tardigrades are considered some lesser known taxa. Studying tardigrades can teach us about the evolution of life on our planet, can help us understand what extremophilic evolution and adaptation means and they can show us what forms of life may develop on other planets. Key Words: tardigrades, extremophiles, extreme environments, adaptation. Rezumat. Tardigradele sunt mici organisme poliextremofile capabile să supraviețuiască într-o varietate de condiţii extreme. Suspendandu-şi reversibil metabolismul (criptobioză) tardigradele pot să se usuce sau să îngheţe şi, astfel, să supravieţuiască unor condiţii extreme precum presiuni şi temperaturi foarte scăzute sau crescute, variaţii de salinitate, lipsă de oxygen, lipsă de apă, unele chimicale toxice, alcool în fierbere, chiar şi vidul spaţiului extraterestru. În ciuda morfologiei lor deosebite şi a diversittii habitatelor lor, se cunosc relativ puţine aspecte se despre aceste organisme. -
MIAMI UNIVERSITY the Graduate School Certificate for Approving The
MIAMI UNIVERSITY The Graduate School Certificate for Approving the Dissertation We hereby approve the Dissertation of Qiuyuan Huang Candidate for the Degree: Doctor of Philosophy _______________________________________ Hailiang Dong, Director ________________________________________ Yildirim Dilek, Reader ________________________________________ Jonathan Levy, Reader ______________________________________ Chuanlun Zhang, External examiner ______________________________________ Annette Bollmann, Graduate School Representative ABSTRACT GEOMICROBIAL INVESTIGATIONS ON EXTREME ENVIRONMENTS: LINKING GEOCHEMISTRY TO MICROBIAL ECOLOGY IN TERRESTRIAL HOT SPRINGS AND SALINE LAKES by Qiuyuan Huang Terrestrial hot springs and saline lakes represent two extreme environments for microbial life and constitute an important part of global ecosystems that affect the biogeochemical cycling of life-essential elements. Despite the advances in our understanding of microbial ecology in the past decade, important questions remain regarding the link between microbial diversity and geochemical factors under these extreme conditions. This dissertation first investigates a series of hot springs with wide ranges of temperature (26-92oC) and pH (3.72-8.2) from the Tibetan Plateau in China and the Philippines. Within each region, microbial diversity and geochemical conditions were studied using an integrated approach with 16S rRNA molecular phylogeny and a suite of geochemical analyses. In Tibetan springs, the microbial community was dominated by archaeal phylum Thaumarchaeota -
Counts Metabolic Yr10.Pdf
Advanced Review Physiological, metabolic and biotechnological features of extremely thermophilic microorganisms James A. Counts,1 Benjamin M. Zeldes,1 Laura L. Lee,1 Christopher T. Straub,1 Michael W.W. Adams2 and Robert M. Kelly1* The current upper thermal limit for life as we know it is approximately 120C. Microorganisms that grow optimally at temperatures of 75C and above are usu- ally referred to as ‘extreme thermophiles’ and include both bacteria and archaea. For over a century, there has been great scientific curiosity in the basic tenets that support life in thermal biotopes on earth and potentially on other solar bodies. Extreme thermophiles can be aerobes, anaerobes, autotrophs, hetero- trophs, or chemolithotrophs, and are found in diverse environments including shallow marine fissures, deep sea hydrothermal vents, terrestrial hot springs— basically, anywhere there is hot water. Initial efforts to study extreme thermo- philes faced challenges with their isolation from difficult to access locales, pro- blems with their cultivation in laboratories, and lack of molecular tools. Fortunately, because of their relatively small genomes, many extreme thermo- philes were among the first organisms to be sequenced, thereby opening up the application of systems biology-based methods to probe their unique physiologi- cal, metabolic and biotechnological features. The bacterial genera Caldicellulosir- uptor, Thermotoga and Thermus, and the archaea belonging to the orders Thermococcales and Sulfolobales, are among the most studied extreme thermo- philes to date. The recent emergence of genetic tools for many of these organ- isms provides the opportunity to move beyond basic discovery and manipulation to biotechnologically relevant applications of metabolic engineering.