Hyperthermophilic Microorganisms
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New Opportunities Revealed by Biotechnological Explorations of Extremophiles - Mircea Podar and Anna-Louise Reysenbach
BIOTECHNOLOGY – Vol .III – New Opportunities Revealed by Biotechnological Explorations of Extremophiles - Mircea Podar and Anna-Louise Reysenbach NEW OPPORTUNITIES REVEALED BY BIOTECHNOLOGICAL EXPLORATIONS OF EXTREMOPHILES Mircea Podar and Anna-Louise Reysenbach Department of Biology, Portland State University, Portland, OR 97201, USA. Keywords: extremophiles, genomics, biotechnology, enzymes, metagenomics. Contents 1. Introduction 2. Extremophiles and Biomolecules 3. Extremophile Genomics Exposing the Biotechnological Potential 4. Tapping into the Hidden Biotechnological Potential through Metagenomics 5. Unexplored Frontiers and Future Prospects Acknowledgements Glossary Bibliography Biographical Sketches Summary Over the past few decades the extremes at which life thrives has continued to challenge our understanding of biochemistry, biology and evolution. As more new extremophiles are brought into laboratory culture, they have provided a multitude of new potential applications for biotechnology. Furthermore, more recently, innovative culturing approaches, environmental genome sequencing and whole genome sequencing have provided new opportunities for biotechnological exploration of extremophiles. 1. Introduction Organisms that live at the extremes of pH (>pH 8.5,< pH 5.0), temperature (>45°C, <15°C), pressure (>500 atm), salinity (>1.0M NaCl) and in high concentrations of recalcitrant substances or heavy metals (extremophiles) represent one of the last frontiers for biotechnological and industrial discovery. As we learn more about the -
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). -
A Web Tool for Hydrogenase Classification and Analysis Dan Søndergaard1, Christian N
www.nature.com/scientificreports OPEN HydDB: A web tool for hydrogenase classification and analysis Dan Søndergaard1, Christian N. S. Pedersen1 & Chris Greening2,3 H2 metabolism is proposed to be the most ancient and diverse mechanism of energy-conservation. The Received: 24 June 2016 metalloenzymes mediating this metabolism, hydrogenases, are encoded by over 60 microbial phyla Accepted: 09 September 2016 and are present in all major ecosystems. We developed a classification system and web tool, HydDB, Published: 27 September 2016 for the structural and functional analysis of these enzymes. We show that hydrogenase function can be predicted by primary sequence alone using an expanded classification scheme (comprising 29 [NiFe], 8 [FeFe], and 1 [Fe] hydrogenase classes) that defines 11 new classes with distinct biological functions. Using this scheme, we built a web tool that rapidly and reliably classifies hydrogenase primary sequences using a combination of k-nearest neighbors’ algorithms and CDD referencing. Demonstrating its capacity, the tool reliably predicted hydrogenase content and function in 12 newly-sequenced bacteria, archaea, and eukaryotes. HydDB provides the capacity to browse the amino acid sequences of 3248 annotated hydrogenase catalytic subunits and also contains a detailed repository of physiological, biochemical, and structural information about the 38 hydrogenase classes defined here. The database and classifier are freely and publicly available at http://services.birc.au.dk/hyddb/ Microorganisms conserve energy by metabolizing H2. Oxidation of this high-energy fuel yields electrons that can be used for respiration and carbon-fixation. This diffusible gas is also produced in diverse fermentation and 1 anaerobic respiratory processes . H2 metabolism contributes to the growth and survival of microorganisms across the three domains of life, including chemotrophs and phototrophs, lithotrophs and heterotrophs, aerobes and 1,2 anaerobes, mesophiles and extremophiles alike . -
The Genome of Nanoarchaeum Equitans: Insights Into Early Archaeal Evolution and Derived Parasitism
The genome of Nanoarchaeum equitans: Insights into early archaeal evolution and derived parasitism Elizabeth Waters†‡, Michael J. Hohn§, Ivan Ahel¶, David E. Graham††, Mark D. Adams‡‡, Mary Barnstead‡‡, Karen Y. Beeson‡‡, Lisa Bibbs†, Randall Bolanos‡‡, Martin Keller†, Keith Kretz†, Xiaoying Lin‡‡, Eric Mathur†, Jingwei Ni‡‡, Mircea Podar†, Toby Richardson†, Granger G. Sutton‡‡, Melvin Simon†, Dieter So¨ ll¶§§¶¶, Karl O. Stetter†§¶¶, Jay M. Short†, and Michiel Noordewier†¶¶ †Diversa Corporation, 4955 Directors Place, San Diego, CA 92121; ‡Department of Biology, San Diego State University, 5500 Campanile Drive, San Diego, CA 92182; §Lehrstuhl fu¨r Mikrobiologie und Archaeenzentrum, Universita¨t Regensburg, Universita¨tsstrasse 31, D-93053 Regensburg, Germany; ‡‡Celera Genomics Rockville, 45 West Gude Drive, Rockville, MD 20850; Departments of ¶Molecular Biophysics and Biochemistry and §§Chemistry, Yale University, New Haven, CT 06520-8114; and ʈDepartment of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061 Communicated by Carl R. Woese, University of Illinois at Urbana–Champaign, Urbana, IL, August 21, 2003 (received for review July 22, 2003) The hyperthermophile Nanoarchaeum equitans is an obligate sym- (6–8). Genomic DNA was either digested with restriction en- biont growing in coculture with the crenarchaeon Ignicoccus. zymes or sheared to provide clonable fragments. Two plasmid Ribosomal protein and rRNA-based phylogenies place its branching libraries were made by subcloning randomly sheared fragments point early in the archaeal lineage, representing the new archaeal of this DNA into a high-copy number vector (Ϸ2.8 kbp library) kingdom Nanoarchaeota. The N. equitans genome (490,885 base or low-copy number vector (Ϸ6.3 kbp library). DNA sequence pairs) encodes the machinery for information processing and was obtained from both ends of plasmid inserts to create repair, but lacks genes for lipid, cofactor, amino acid, or nucleotide ‘‘mate-pairs,’’ pairs of reads from single clones that should be biosyntheses. -
Phylogenetics of Archaeal Lipids Amy Kelly 9/27/2006 Outline
Phylogenetics of Archaeal Lipids Amy Kelly 9/27/2006 Outline • Phlogenetics of Archaea • Phlogenetics of archaeal lipids • Papers Phyla • Two? main phyla – Euryarchaeota • Methanogens • Extreme halophiles • Extreme thermophiles • Sulfate-reducing – Crenarchaeota • Extreme thermophiles – Korarchaeota? • Hyperthermophiles • indicated only by environmental DNA sequences – Nanoarchaeum? • N. equitans a fast evolving euryarchaeal lineage, not novel, early diverging archaeal phylum – Ancient archael group? • In deepest brances of Crenarchaea? Euryarchaea? Archaeal Lipids • Methanogens – Di- and tetra-ethers of glycerol and isoprenoid alcohols – Core mostly archaeol or caldarchaeol – Core sometimes sn-2- or Images removed due to sn-3-hydroxyarchaeol or copyright considerations. macrocyclic archaeol –PMI • Halophiles – Similar to methanogens – Exclusively synthesize bacterioruberin • Marine Crenarchaea Depositional Archaeal Lipids Biological Origin Environment Crocetane methanotrophs? methane seeps? methanogens, PMI (2,6,10,15,19-pentamethylicosane) methanotrophs hypersaline, anoxic Squalane hypersaline? C31-C40 head-to-head isoprenoids Smit & Mushegian • “Lost” enzymes of MVA pathway must exist – Phosphomevalonate kinase (PMK) – Diphosphomevalonate decarboxylase – Isopentenyl diphosphate isomerase (IPPI) Kaneda et al. 2001 Rohdich et al. 2001 Boucher et al. • Isoprenoid biosynthesis of archaea evolved through a combination of processes – Co-option of ancestral enzymes – Modification of enzymatic specificity – Orthologous and non-orthologous gene -
Archaeoglobus Profundus Type Strain (AV18T)
Standards in Genomic Sciences (2010) 2:327-346 DOI:10.4056/sigs.942153 Complete genome sequence of Archaeoglobus profundus type strain (AV18T) Mathias von Jan1, Alla Lapidus2, Tijana Glavina Del Rio2, Alex Copeland2, Hope Tice2, Jan-Fang Cheng2, Susan Lucas2, Feng Chen2, Matt Nolan2, Lynne Goodwin2,3, Cliff Han2,3, Sam Pitluck2, Konstantinos Liolios2, Natalia Ivanova2, Konstantinos Mavromatis2, Galina Ovchinnikova2, Olga Chertkov2, Amrita Pati2, Amy Chen4, Krishna Palaniappan4, Miriam Land2,5, Loren Hauser2,5, Yun-Juan Chang2,5, Cynthia D. Jeffries2,5, Elizabeth Saunders2, Thomas Brettin2,3, John C. Detter2,3, Patrick Chain2,4, Konrad Eichinger6, Harald Huber6, Ste- fan Spring1, Manfred Rohde7, Markus Göker1, Reinhard Wirth6, Tanja Woyke2, Jim Bristow2, Jonathan A. Eisen2,8, Victor Markowitz4, Philip Hugenholtz2, Nikos C Kyrpides2, and Hans-Peter Klenk1* 1 DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany 2 DOE Joint Genome Institute, Walnut Creek, California, USA 3 Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA 4 Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, California, USA 5 Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA 6 University of Regensburg, Microbiology – Archaeenzentrum, Regensburg, Germany 7 HZI – Helmholtz Centre for Infection Research, Braunschweig, Germany 8 University of California Davis Genome Center, Davis, California, USA *Corresponding author: Hans-Peter Klenk Keywords: hyperthermophilic, marine, strictly anaerobic, sulfate respiration, hydrogen utili- zation, hydrothermal systems, Archaeoglobaceae, GEBA Archaeoglobus profundus (Burggraf et al. 1990) is a hyperthermophilic archaeon in the eu- ryarchaeal class Archaeoglobi, which is currently represented by the single family Archaeog- lobaceae, containing six validly named species and two strains ascribed to the genus 'Geoglobus' which is taxonomically challenged as the corresponding type species has no va- lidly published name. -
Assessment of the Carbon Monoxide Metabolism of the Hyperthermophilic Sulfate-Reducing Archaeon Archaeoglobus Fulgidus VC-16 by Comparative Transcriptome Analyses
Hindawi Publishing Corporation Archaea Volume 2015, Article ID 235384, 12 pages http://dx.doi.org/10.1155/2015/235384 Research Article Assessment of the Carbon Monoxide Metabolism of the Hyperthermophilic Sulfate-Reducing Archaeon Archaeoglobus fulgidus VC-16 by Comparative Transcriptome Analyses William P. Hocking, Irene Roalkvam, Carina Magnussen, Runar Stokke, and Ida H. Steen Department of Biology, Centre for Geobiology, University of Bergen, 5020 Bergen, Norway Correspondence should be addressed to Ida H. Steen; [email protected] Received 10 April 2015; Revised 9 June 2015; Accepted 14 June 2015 Academic Editor: Uwe Deppenmeier Copyright © 2015 William P. Hocking et al. 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. The hyperthermophilic, sulfate-reducing archaeon, Archaeoglobus fulgidus, utilizes CO as an energy source and it is resistant to the toxic effects of high CO concentrations. Herein, transcription profiles were obtained from A. fulgidus during growth with CO and sulfate or thiosulfate, or without an electron acceptor. This provided a basis for a model of the CO metabolism of A. fulgidus. The model suggests proton translocation by “Mitchell-type” loops facilitated by Fqo catalyzingred aFd :menaquinone oxidoreductase reaction, as the major mode of energy conservation, rather than formate or H2 cycling during respiratory growth. The bifunctional CODH (cdhAB-2) is predicted to play an ubiquitous role in the metabolism of CO, and a novel nitrate reductase- associated respiratory complex was induced specifically in the presence of sulfate. A potential role of this complex in relation to Fdred and APS reduction is discussed. -
Differences in Lateral Gene Transfer in Hypersaline Versus Thermal Environments Matthew E Rhodes1*, John R Spear2, Aharon Oren3 and Christopher H House1
Rhodes et al. BMC Evolutionary Biology 2011, 11:199 http://www.biomedcentral.com/1471-2148/11/199 RESEARCH ARTICLE Open Access Differences in lateral gene transfer in hypersaline versus thermal environments Matthew E Rhodes1*, John R Spear2, Aharon Oren3 and Christopher H House1 Abstract Background: The role of lateral gene transfer (LGT) in the evolution of microorganisms is only beginning to be understood. While most LGT events occur between closely related individuals, inter-phylum and inter-domain LGT events are not uncommon. These distant transfer events offer potentially greater fitness advantages and it is for this reason that these “long distance” LGT events may have significantly impacted the evolution of microbes. One mechanism driving distant LGT events is microbial transformation. Theoretically, transformative events can occur between any two species provided that the DNA of one enters the habitat of the other. Two categories of microorganisms that are well-known for LGT are the thermophiles and halophiles. Results: We identified potential inter-class LGT events into both a thermophilic class of Archaea (Thermoprotei) and a halophilic class of Archaea (Halobacteria). We then categorized these LGT genes as originating in thermophiles and halophiles respectively. While more than 68% of transfer events into Thermoprotei taxa originated in other thermophiles, less than 11% of transfer events into Halobacteria taxa originated in other halophiles. Conclusions: Our results suggest that there is a fundamental difference between LGT in thermophiles and halophiles. We theorize that the difference lies in the different natures of the environments. While DNA degrades rapidly in thermal environments due to temperature-driven denaturization, hypersaline environments are adept at preserving DNA. -
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. -
Title Genomic Analysis of the Marine Hyperthermophilic Archaeon
Genomic analysis of the marine hyperthermophilic archaeon Title Aeropyrum( Dissertation_全文 ) Author(s) Daifuku, Takashi Citation 京都大学 Issue Date 2015-03-23 URL https://doi.org/10.14989/doctor.k19034 学位規則第9条第2項により要約公開; 許諾条件により本文 Right は2019-08-01に公開 Type Thesis or Dissertation Textversion ETD Kyoto University 1. General introduction Chapter 1 General introduction Gene repertoires and genome organizations differ between closely related microbial organisms depending on the ecological characteristics of each habitat (Cohan and Koeppel 2008). The cyanobacterial Prochlorococcus spp. account for a significant fraction of primary production in the ocean (Goericke and Welschmeyer 1993) and show physiological features relevant to the different ecological niches within a stratified oceanic water column (Moore et al. 1998; West et al. 2001). The whole-genomic comparisons of the Prochlorococcus spp. strains show gross signatures according to this niche differentiation (Rocap et al. 2003). Alpha-proteobacterium Pelagibacter ubique which belongs to the SAR11 clade in the phylogenetic tree based on the 16S rRNA gene is the most abundant microorganism in the ocean (Morris et al. 2002). The genomes of the SAR11 isolates are highly conserved in the core genes that are common to all strains (Medini et al. 2005) and show synteny (the conservation of DNA sequence and gene order) (Bentley and Parkhill 2004). However, variations exist among genes for phosphorus metabolism, glycolysis, and C1 metabolism, suggesting that adaptive specialization in nutrient resource utilization is important for niche partitioning (Grote et al. 2012). This adaptation at the genomic level was also observed in archaea. The members of the genus Pyrococcus are anaerobic and hyperthermophilic archaea (Fiala and Stetter 1 1. -
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.