Archaeal Viruses from Yellowstone's High Temperature Environments
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CRISPR Loci Reveal Networks of Gene Exchange in Archaea Avital Brodt, Mor N Lurie-Weinberger and Uri Gophna*
Brodt et al. Biology Direct 2011, 6:65 http://www.biology-direct.com/content/6/1/65 RESEARCH Open Access CRISPR loci reveal networks of gene exchange in archaea Avital Brodt, Mor N Lurie-Weinberger and Uri Gophna* Abstract Background: CRISPR (Clustered, Regularly, Interspaced, Short, Palindromic Repeats) loci provide prokaryotes with an adaptive immunity against viruses and other mobile genetic elements. CRISPR arrays can be transcribed and processed into small crRNA molecules, which are then used by the cell to target the foreign nucleic acid. Since spacers are accumulated by active CRISPR/Cas systems, the sequences of these spacers provide a record of the past “infection history” of the organism. Results: Here we analyzed all currently known spacers present in archaeal genomes and identified their source by DNA similarity. While nearly 50% of archaeal spacers matched mobile genetic elements, such as plasmids or viruses, several others matched chromosomal genes of other organisms, primarily other archaea. Thus, networks of gene exchange between archaeal species were revealed by the spacer analysis, including many cases of inter-genus and inter-species gene transfer events. Spacers that recognize viral sequences tend to be located further away from the leader sequence, implying that there exists a selective pressure for their retention. Conclusions: CRISPR spacers provide direct evidence for extensive gene exchange in archaea, especially within genera, and support the current dogma where the primary role of the CRISPR/Cas system is anti-viral and anti- plasmid defense. Open peer review: This article was reviewed by: Profs. W. Ford Doolittle, John van der Oost, Christa Schleper (nominated by board member Prof. -
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. -
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). -
Changes to Virus Taxonomy 2004
Arch Virol (2005) 150: 189–198 DOI 10.1007/s00705-004-0429-1 Changes to virus taxonomy 2004 M. A. Mayo (ICTV Secretary) Scottish Crop Research Institute, Invergowrie, Dundee, U.K. Received July 30, 2004; accepted September 25, 2004 Published online November 10, 2004 c Springer-Verlag 2004 This note presents a compilation of recent changes to virus taxonomy decided by voting by the ICTV membership following recommendations from the ICTV Executive Committee. The changes are presented in the Table as decisions promoted by the Subcommittees of the EC and are grouped according to the major hosts of the viruses involved. These new taxa will be presented in more detail in the 8th ICTV Report scheduled to be published near the end of 2004 (Fauquet et al., 2004). Fauquet, C.M., Mayo, M.A., Maniloff, J., Desselberger, U., and Ball, L.A. (eds) (2004). Virus Taxonomy, VIIIth Report of the ICTV. Elsevier/Academic Press, London, pp. 1258. Recent changes to virus taxonomy Viruses of vertebrates Family Arenaviridae • Designate Cupixi virus as a species in the genus Arenavirus • Designate Bear Canyon virus as a species in the genus Arenavirus • Designate Allpahuayo virus as a species in the genus Arenavirus Family Birnaviridae • Assign Blotched snakehead virus as an unassigned species in family Birnaviridae Family Circoviridae • Create a new genus (Anellovirus) with Torque teno virus as type species Family Coronaviridae • Recognize a new species Severe acute respiratory syndrome coronavirus in the genus Coro- navirus, family Coronaviridae, order Nidovirales -
A Virus That Infects a Hyperthermophile Encapsidates A-Form
RESEARCH | REPORTS we observe sets of regulatory sites that exhibit Illumina, Inc. One or more embodiments of one or more patents SUPPLEMENTARY MATERIALS patterns of coordinated regulation (e.g., LYN, and patent applications filed by Illumina may encompass the www.sciencemag.org/content/348/6237/910/suppl/DC1 encoding a tyrosine kinase involved in B cell methods, reagents, and data disclosed in this manuscript. All Materials and Methods methods for making the transposase complexes are described in signaling) (Fig. 4B), although reproducibility of Figs. S1 to S22 (18); however, Illumina will provide transposase complexes in Tables S1 and S2 these patterns across biological replicates was response to reasonable requests from the scientific community References (24–39) modest (fig. S22). Given the sparsity of the data, subject to a material transfer agreement. Some work in this study identifying pairs of coaccessible DNA elements is related to technology described in patent applications 19 March 2015; accepted 24 April 2015 WO2014142850, 2014/0194324, 2010/0120098, 2011/0287435, Published online 7 May 2015; within individual loci is statistically challenging 2013/0196860, and 2012/0208705. 10.1126/science.aab1601 and merits further development. We report chromatin accessibility maps for >15,000 single cells. Our combinatorial cellular indexing scheme could feasibly be scaled to col- VIROLOGY lect data from ~17,280 cells per experiment by using 384-by-384 barcoding and sorting 100 nu- clei per well (assuming similar cell recovery and A virus that infects a collision rates) (fig. S1) (19). Particularly as large- scale efforts to build a human cell atlas are con- templated (23), it is worth noting that because hyperthermophile encapsidates DNA is at uniform copy number, single-cell chro- matin accessibility mapping may require far fewer A-form DNA reads per single cell to define cell types, relative to single-cell RNA-seq. -
Archaeology of Eukaryotic DNA Replication
Downloaded from http://cshperspectives.cshlp.org/ on September 25, 2021 - Published by Cold Spring Harbor Laboratory Press Archaeology of Eukaryotic DNA Replication Kira S. Makarova and Eugene V. Koonin National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894 Correspondence: [email protected] Recent advances in the characterization of the archaeal DNA replication system together with comparative genomic analysis have led to the identification of several previously un- characterized archaeal proteins involved in replication and currently reveal a nearly com- plete correspondence between the components of the archaeal and eukaryotic replication machineries. It can be inferred that the archaeal ancestor of eukaryotes and even the last common ancestor of all extant archaea possessed replication machineries that were compa- rable in complexity to the eukaryotic replication system. The eukaryotic replication system encompasses multiple paralogs of ancestral components such that heteromeric complexes in eukaryotes replace archaeal homomeric complexes, apparently along with subfunctionali- zation of the eukaryotic complex subunits. In the archaea, parallel, lineage-specific dupli- cations of many genes encoding replication machinery components are detectable as well; most of these archaeal paralogs remain to be functionally characterized. The archaeal rep- lication system shows remarkable plasticity whereby even some essential components such as DNA polymerase and single-stranded DNA-binding protein are displaced by unrelated proteins with analogous activities in some lineages. ouble-stranded DNA is the molecule that Okazaki fragments (Kornberg and Baker 2005; Dcarries genetic information in all cellular Barry and Bell 2006; Hamdan and Richardson life-forms; thus, replication of this genetic ma- 2009; Hamdan and van Oijen 2010). -
The Stability of Lytic Sulfolobus Viruses
The Stability of Lytic Sulfolobus Viruses A thesis submitted to the Graduate School of the University of Cincinnati In partial fulfillment of The requirements for the degree of Master of Sciences in the Department of Biological Sciences of the College of Arts and Sciences 2017 Khaled S. Gazi B.S. Umm Al-Qura University, 2011 Committee Chair: Dennis W. Grogan, Ph.D. i Abstract Among the three domains of cellular life, archaea are the least understood, and functional information about archaeal viruses is very limited. For example, it is not known whether many of the viruses that infect hyperthermophilic archaea retain infectivity for long periods of time under the extreme conditions of geothermal environments. To investigate the capability of viruses to Infect under the extreme conditions of geothermal environments. A number of plaque- forming viruses related to Sulfolobus islandicus rod-shaped viruses (SIRVs), isolated from Yellowstone National Park in a previous study, were evaluated for stability under different stress conditions including high temperature, drying, and extremes of pH. Screening of 34 isolates revealed a 95-fold range of survival with respect to boiling for two hours and 94-fold range with respect to drying for 24 hours. Comparison of 10 viral strains chosen to represent the extremes of this range showed little correlation of stability with respect to different stresses. For example, three viral strains survived boiling but not drying. On the other hand, five strains that survived the drying stress did not survive the boiling temperature, whereas one strain survived both treatments and the last strain showed low survival of both. -
A Korarchaeal Genome Reveals Insights Into the Evolution of the Archaea
A korarchaeal genome reveals insights into the evolution of the Archaea James G. Elkinsa,b, Mircea Podarc, David E. Grahamd, Kira S. Makarovae, Yuri Wolfe, Lennart Randauf, Brian P. Hedlundg, Ce´ line Brochier-Armaneth, Victor Kunini, Iain Andersoni, Alla Lapidusi, Eugene Goltsmani, Kerrie Barryi, Eugene V. Koonine, Phil Hugenholtzi, Nikos Kyrpidesi, Gerhard Wannerj, Paul Richardsoni, Martin Kellerc, and Karl O. Stettera,k,l aLehrstuhl fu¨r Mikrobiologie und Archaeenzentrum, Universita¨t Regensburg, D-93053 Regensburg, Germany; cBiosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831; dDepartment of Chemistry and Biochemistry, University of Texas, Austin, TX 78712; eNational Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894; fDepartment of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520; gSchool of Life Sciences, University of Nevada, Las Vegas, NV 89154; hLaboratoire de Chimie Bacte´rienne, Unite´ Propre de Recherche 9043, Centre National de la Recherche Scientifique, Universite´de Provence Aix-Marseille I, 13331 Marseille Cedex 3, France; iU.S. Department of Energy Joint Genome Institute, Walnut Creek, CA 94598; jInstitute of Botany, Ludwig Maximilians University of Munich, D-80638 Munich, Germany; and kInstitute of Geophysics and Planetary Physics, University of California, Los Angeles, CA 90095 Communicated by Carl R. Woese, University of Illinois at Urbana–Champaign, Urbana, IL, April 2, 2008 (received for review January 7, 2008) The candidate division Korarchaeota comprises a group of uncul- and sediment samples from Obsidian Pool as an inoculum. The tivated microorganisms that, by their small subunit rRNA phylog- cultivation system supported the stable growth of a mixed commu- eny, may have diverged early from the major archaeal phyla nity of hyperthermophilic bacteria and archaea including an or- Crenarchaeota and Euryarchaeota. -
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. -
Lipids of Archaeal Viruses
Hindawi Publishing Corporation Archaea Volume 2012, Article ID 384919, 8 pages doi:10.1155/2012/384919 Review Article Lipids of Archaeal Viruses Elina Roine and Dennis H. Bamford Department of Biosciences and Institute of Biotechnology, University of Helsinki, P.O. Box 56, Viikinkaari 5, 00014 Helsinki, Finland Correspondence should be addressed to Elina Roine, elina.roine@helsinki.fi Received 9 July 2012; Accepted 13 August 2012 Academic Editor: Angela Corcelli Copyright © 2012 E. Roine and D. H. Bamford. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Archaeal viruses represent one of the least known territory of the viral universe and even less is known about their lipids. Based on the current knowledge, however, it seems that, as in other viruses, archaeal viral lipids are mostly incorporated into membranes that reside either as outer envelopes or membranes inside an icosahedral capsid. Mechanisms for the membrane acquisition seem to be similar to those of viruses infecting other host organisms. There are indications that also some proteins of archaeal viruses are lipid modified. Further studies on the characterization of lipids in archaeal viruses as well as on their role in virion assembly and infectivity require not only highly purified viral material but also, for example, constant evaluation of the adaptability of emerging technologies for their analysis. Biological membranes contain proteins and membranes of archaeal viruses are not an exception. Archaeal viruses as relatively simple systems can be used as excellent tools for studying the lipid protein interactions in archaeal membranes. -
Fernanda , A. Metal Corrosion and Biological H2S Cycling in Closed
Metal corrosion and biological H2S cycling in closed systems Fernanda Abreu* Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil; [email protected]* Abstract Sulfate reducing bacteria produce H2S during growth. This gas is toxic and is associated with corrosion in industrial systems. In the environment purple sulfur bacteria, green sulfur bacteria and sulfur oxidizing bacteria use the H2S produced by sulfate reducing bacteria as electron donors. The major aim of this project is to evaluate the possibility of using H2S consuming bacteria to lower H2S concentration and prevent corrosion. Introduction In metal corrosion process the surface of the metal is destroyed due to certain external factors that lead to its chemical or electrochemical change to form more stable compounds. The simplified explanation of the corrosion process is the oxidation of at an anode (corroded end releasing electrons) and the reduction of a substance at a cathode. Corrosion mechanisms are very diverse and can be based on inorganic physicochemical reactions and/or biologically influenced. Microbiologically influenced corrosion (MIC) is a natural process that occurs in the environment as a result of metabolic activity of microorganisms. Microbial colonization and biofilm formation on metal surfaces modify the electrochemical conditions at the metal–solution interface, which usually have positive influence on corrosion process. MIC of steel generates approximately US$ 100 million financial losses per annum in the United States (Muyzer and Stams, 2008). In industrial settings, especially in petroleum, gas and shipping industries, sulfate reducing bacteria (SRB) are a major concern. SRB are ubiquitous in anoxic habitats and have an important role in both the sulfur and carbon cycles (Muyzer and Stams, 2008). -
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.