DOCSLIB.ORG

(12) Patent Application Publication (10) Pub

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
(12) Patent Application Publication (10) Pub US 2003O228616A1 (19) United States (12) Patent Application Publication (10) Pub. No.: US 2003/022861.6 A1 Arezi et al. (43) Pub. Date: Dec. 11, 2003 (54) DNA POLYMERASE MUTANTS WITH part of application No. 09/896,923, filed on Jun. 29, REVERSE TRANSCRIPTASE ACTIVITY 2001, which is a continuation-in-part of application No. 09/698,341, filed on Oct. 27, 2000. (75) Inventors: Bahram Arezi, Carlsbad, CA (US); Holly Hogrefe, San Diego, CA (US); (60) Provisional application No. 60/162,600, filed on Oct. Joseph A. Sorge, Wilson, WY (US); 29, 1999. Connie Jo Hansen, San Diego, CA (US) (30) Foreign Application Priority Data Correspondence Address: Oct. 27, 2000 (WO)........................... PCT/USOO/29706 PALMER & DODGE, LLP KATHLEEN M. WILLIAMS / STR Publication Classification 111 HUNTINGTONAVENUE BOSTON, MA 02199 (US) (51) Int. Cl." ............................ C12O 1/68; CO7H 21/04; C12P 19/34; C12N 9/22; C12N 1/20; (73) Assignee: Stratagene C12N 15/74 (52) U.S. Cl. ............................. 435/6; 435/69.1; 435/199; (21) Appl. No.: 10/435,766 435/252.3; 435/320.1; 435/912; 536/23.2 (22) Filed: May 12, 2003 (57) ABSTRACT Related U.S. Application Data The present invention relates to compositions and kits comprising a mutant DNA polymerase with increased (63) Continuation-in-part of application No. 10/223,650, reverse transcriptase activity. The invention also relates to filed on Aug. 19, 2002, which is a continuation-in methods for using the Subject compositions and kits. Patent Application Publication Dec. 11, 2003. Sheet 1 of 26 US 2003/0228616 A1 Figure 1. Oligonucleotide primers for Quikchange mutagenesis and GAPDH target amplification F-Pfu408F 5’-CTAgATTTTAgAgCCTTCTATCCCTCgATT-3 R-Pf408F 5'-AATCgAgggATAgAAggCTCTAAAATCTAg-3 F-Pfu408Y 5'-CTAgATTTTAgAgCCTACTATCCCTCgATT-3’ R-Pful408Y 5'-AATCgAgggATAgTAggCTCTAAAATCTAg-3 F-JDFL408F 5’-CTAgACTTTCgTAgTTTCTACCCTTCAATCATAATC-3' R-JDFL408F 5'-gATTATgATTgAAgggTAgAAACTACgAAAgTCTAg-3 F-JDFL408Y 5'-CTAgACTTTCgTAgTTACTACCCTTCAATCATAATC-3' R-JDFL408Y 5’-gATTATgATTgAAggg.TAgTAACTACgAAAgTCTAg-3 F-JDFL408W 5'-CTAgACTTTCgTAgTTggTACCCTTCAATCATAATC-3' R-JDFL408W 5-gATTATgATTgAAggg.TACCAACTACgAAAgTCTAg-3 GAPDH-F 5'-CgAgCCACATCgCTCAg-3 GAPDH-R 5’-CATgTAgTTgAggTCAATgAA-3' Patent Application Publication Dec. 11, 2003 Sheet 2 of 26 US 2003/0228616 A1 Figure 2. DNA dependent DNA polymerization activity (3H-TTP inc.) of the WTs and mutants Lysate volume (pl) RNA dependent DNA polymerization activity (3H-TTP inc.) of the WTs and mutants Lysate volume (l) S og 0.8 Clis 0.7 s 0.6 EC up 0.5 9 0.4 i 5 0.3 ac9 E 0.2 2. s 0. O 5 SS -0.1 OF3 JD LF LY LW Patent Application Publication Dec. 11, 2003 Sheet 3 of 26 US 2003/0228616 A1 Figure 3 DNA dependent DNA polymerization activity (3H-TTP inc.) of the Exo plus WT and the mutants Lysate volume (ul) RNA dependent DNA polymerization activity (3H-TTP inc.) of the Exo plus WT and mutants Lysate volume (ul) Patent Application Publication Dec. 11, 2003. Sheet 4 of 26 US 2003/0228616A1 Figure 4. RNA dependent DNA polymerization activity (33P-GTP Inc.) of purified enzymes 2 of each enzyme/Rxn Patent Application Publication Dec. 11, 2003. Sheet 5 of 26 US 2003/0228616A1 Figure 5. 150 bp 2 3 4 5 1: Negative control (no StrataScript) StrataScript (2 units) exo-JDF3 (2 units) exo-JDF3 LH (2 units) exo-JDF3 LF (2 units) Patent Application Publication Dec. 11, 2003. Sheet 7 of 26 US 2003/0228616A1 Pful 571 KLPGLLELEYEGF. YKRGFFWTKKRYAWIDEEG. KVITRGLEIWRRDWSE 68 JDF 570 KPGETELEYEGE . YVRGEFWTKKKYAVIDEEG. KITRGLEIWRRDWSE 617 Tgo 570 KLPGLLELEYEGF. YKRGFFWTKKKYAVTDEED. KITTRGLEIWRROWSE 617 Tli 573 KLPGLL ELEYEGF. YLRGEFWTKKRYAVIDEEG. RITTRGLEVWRRDWSE 62O Tsp. 571 KLPGLLELEYEGF. YVRGFFWTKKKYALIDEEG. KTRGLEWRRDWSE 68 Mvo 630 ELPEGMELEFEGH. EKRGIFWTKKKYALIEDDG. HIWWKGLEWWRRDWSN 677 RB69 676 NKQHLMFMDREAIAGPPLGSKGIGGFWTGKKRYALNVWDMEGTRYAEPKLKIMGLETQKSSTPK 739 T4 672 NREHMHMDREAISCPFLGSKGVGGFWKAKKRYALNVYDMEDKRFAEPHLKIMGMETOOSSTPK 735 Eco 585 RLTSALELEYETHFCRFLMPTIRGADTGSKKRYAGLIQEG. DKQRMVFKGLETVRTDWTP 643 Patent Application Publication Dec. 11, 2003 Sheet 13 of 26 US 2003/0228616 A1 TTTTCTTGCCAGGTCTCTTGAGTTTCGCAAGGGTCTTCTCGACCAGCTCAA F S C Q V S K V S O G. S S R P A Q TGGTCTTGTCGTCATTGTTTNNNNNNNNNNNNNNNNNNNNNCCCGGGGACT W S C R H C X X X X X X X X P G T DNA : TCATACTGGCGGTAATAGACAGGGATTCCTTCCTCAAGGACTTCCCGGGAG --1 : S Y W R is k T G T P S S R T S R E DNA: GCATTGGAGTTTTTTGGTGGGGCTTTCACAGGATTTGCTCATCTTGTGGAT +1 : A. L. E. F. F. G G A F T G F A H L V D DNA: TTCTCGTTCGATTGAATCGTCCACTTGAGGGTGTAGGTCGAGACGGTGGA F S F D I C P L E G W G R D G - G DNA GCGCGTATTCCGGGAGCGGGTCTTGAGGCTCCAT"TTTTCAGTCCTCCTCCG + 1 : A R T P G A G L E A P F F S P P P DNA : GCGAAGAAGTGGAACTCAAGCCGGGTGTTAGCTTAGTTATGTTCCCAACT +1 : A K K W N S S R W L A Y V M F P T DNA: CCTCCAGCACCTCCAGGATCCCCTCAATCCCGGAACCTCGAAGCCCCTCTC P P A P P G S P Q S R N L E A P L. DNA: GTGGATCTTTCTAACTTCCTCTGCCTCCGGGTTTATCCAGACCGCCCACAT +l : W D L S N F L C L R V Y P D R P H. DNA: GCCGGCTCTCAGCGCACCCTCGAAATCCTCCGCGTAGGTGTCGCCGATGTG +1 : A G S O R T L E I L R W G V A D V DNA: GATTGCCTCGTCCGGCTCGACCCCGAAGCATCGAGCGGTTTTCTGAACATC +1 : D C L W R L D P E A S S G F L N I. DNA TCGGGCATCGGCTTATACGCCAGAACCTCGTCGGCGAAGAAGGTTCCCTCA +1 : S G T G Y A R T S S A K K V P S DNA : ATGTAGTCCATCAGGCCGAACCTCTCGAGGGGGGGCCCGGTACCCAATTCG +1 : M. le S I R P N L S R G G P W P N S DNA : CCCTATAGTGAGTCGATTACAATTCACTGGCCGTCGTTTTACAACGTCGTG +1 : P Y S E S T T H. W P S F Y N V V ACTGGGAAAACCCTGGCGTTACCCAACTTAAGTCGCTTTGCAGCACATCCC T G. K. T. L. A. L. P N L S R F A A. H. P CC Patent Application Publication Dec. 11, 2003 Sheet 14 of 26 US 2003/0228616 A1 Pfu wild type SEQ ID NO: 3 Amino acid sequence mildvdyiteegkpvirlfkkengkfkiehdirtfrpyiyallrddskieevkkitgerhgkiv rivdvek vekkf ligkpitvwklylehpqdvptirekvrehpavvdifeydipfakrylidkglipmegeeelkilafdietlyhege efgkgpiimisyadeneakvitwknidlpyvev vs seremikrflriirekdpdiivityngdsfalfpylakiraek lgikltigrdgsepkmqrigdmtavevkgrihfallyhvitrtinlptytleavyeaifgkpkekvyadeiakawe sgenlervakys medakatyeligkeflpmeiqlsrlvggplwdvsrsstgnlvewfillrkayernevapnkpsee eygrrlresy togfvkepekglwenivyldfralypsiiithnvispatlinlegcknydiapavghkfckdipgfi psllghl leerqkiktkmketcdpiekilldyrokaikllansfygyygyakarwyckecaesvtawgrkyielv wkeleekfgfkvliyidtdglyatipggeseeikkkalefvkyinsklpglleleyegfykrgffvtkkryavide egkvitrogleivrrdwsei aketcarvletilkhgdiveeavriivkevicklanyeippeklaiyeqi triplheyk aligphvavakklaakgvkikpgmvigyivlrgdgpisnraillaeeydpkkhkydaey yiendvlpavlrilegfg yrkedlryqktrovgltswlnikks SEQ ID NO: 4 Polynucleotide sequence atgattittagatgtggatta Catalactogalagaaggaaaacctgttattaggctattoaaaaaagagaacggaaaa tittaagatagagcatgatagaacttittagaccatacatttacgctcittctoaggogatgattcaaagattgaagaa gttaagaaaataacgggggaaaggcatggaaagattgttgaga attgttgatgtagagaaggttgagaaaaagttt citcggcaa.gcct attaccgtgtggaaactittatttggaacatc.cccaagatgttcc.cactattagagaaaaagtt agagaacatCcagcagttgtc.gaCat Ctt C9aatacga tatt ccatttgcaaagagatacct catcgacaaaggc ctaataccalatggagggggaagaagagctaaagattcttgcct tcgatatagaaaccctctatoacgaaggagaa gagtttggaaaagg.ccca attataatgattagttatgcagatgaaaatgaagcaaaggtgattacttggaaaaac atagatct tccatacgttgaggttgtat Caagcgagagagagatgataaagagatttctgaggattatcagggag aaggatcCtgaCattatagittacttataatggag act cattcgcatt.cccatatt tag.cgaaaagggcagaaaaa Cttgggattaaattalaccattggaa.gagatggaag.cgagccCaagatgcagagaataggcqatatgacggctgta daagtcaagggaagaatacatttcgacttgtaticatgtaataacaagga caataaatctoccaa.catacacacta gaggctgtatatgaa.gcaatttittggaaagcCaaaggagalagg tatacgc.cgacgagatagcaaaagcctgggaa agtggagaga a CCttgagagagttgcCaaatact.cgatggaagatgcaaaggcaact tatgaact.cgggaaagaa tt CCttCCaatggalaatticagctttcaagattagttggacaac Ctt tatgggatgtttcaaggtoaag cacaggg aaccttgtagagtggttct tact taggaaag.cctacgaaagaaacgaagtagctCcaaacaa.gc.caagtgaagag gagtatcaaagaaggct Cagggagagctacacagg toggatt.cgttaaagagcCagaaaaggggttgttgggaaaac at agtatacctagattittagagcc.ctatatcCCtcgattata attacccacaatgtttct cocq atactictaaat Cttgagggatgcaagaactatgatatcgct.cct Caagtaggccacaagttctgcaagga catcc cteggttittata cCaagttct cttgggacatttgttagaggaaagacaaaagattalaga caaaaatgaaggaalactCaagatcctata gaaaaaatact cottgactatagacaaaaag.cgataaaactct tag caaattctttctacggatattatggctat gcaaaag Caagatgg tactgtaaggag tetgctgaga.gcgttact.gc.ctggggaagaaagta Catcgagttagta tggaaggagct cqaagaaaagtttggatttaaagtcc totacattgacactgateggtotctatgcaactatocca ggaggagaaagtgaggaaataaagaaaaaggctictagaatttgtaaaatacataa attcaaagct coctgg actg citagagcttgaatatgaagggittittatalagaggggattctitcqttacgaagaagagg tatgcagtaatagatgaa gaaggaaaagttcattact.cgtggtttagagatagittaggagagattggagtgaaattgcaaaagaaact caagct agagttittggaga caatactaaaacacggagatgttgaagaagctgtgagaatag taaaagaagtaatacaaaag cittgccaattatcaaatticcaccagagaagctc.gcaatatatgag cagataacaag accattacatgagtataag gcgatagg to ct cacgtagctgttgcaaagaalactagctogctaaaggagttaaaataaag.ccaggaatgg taatt ggatacatag tact tagaggcgatggit CCaattagcaataggg CalattctagotgaggaatacgatCccaaaaag cacaagtatgacgcagaatattacatggagaacCaggttctitcCag Cogg tact taggatattggagggatttgga tacagaaaggaag acct cagataccaaaagacaaga caagttcggcctaact tcc togcttaa.cattaaaaaatcc tag Patent Application Publication Dec. 11, 2003. Sheet 26 of 26 US 2003/0228616 A1 Figure 8 M 0 5 10 15 20 25 % DMSO 9 kb 3 kb 2 kb kb 0.5 kb US 2003/022861.6 A1 Dec. 11, 2003 DNA POLYMERASE MUTANTS WITH REVERSE 0009 Reverse transcription is commonly performed with TRANSCRIPTASE ACTIVITY Viral reverse transcriptases isolated from Avian mycloblas tosis virus (AMV-RT) or Moloney murine leukemia virus RELATED APPLICATIONS (MMLV-RT), which are active in the presence of magnesium OS. 0001. This application is a Continuation-in-Part of U.S. application Ser. No. 10/223,650, filed Aug. 19, 2002,
Load more

Recommended publications
  • 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).
    [Show full text]
  • Natural and Lignocellulose-Enriched Microbial Communities in Great Boiling Spring, NV
    UNLV Theses, Dissertations, Professional Papers, and Capstones 12-2012 Natural and Lignocellulose-Enriched Microbial Communities in Great Boiling Spring, NV Jessica Cole University of Nevada, Las Vegas Follow this and additional works at: https://digitalscholarship.unlv.edu/thesesdissertations Part of the Bacteriology Commons, Biology Commons, and the Environmental Microbiology and Microbial Ecology Commons Repository Citation Cole, Jessica, "Natural and Lignocellulose-Enriched Microbial Communities in Great Boiling Spring, NV" (2012). UNLV Theses, Dissertations, Professional Papers, and Capstones. 1518. http://dx.doi.org/10.34917/4301608 This Thesis is protected by copyright and/or related rights. It has been brought to you by Digital Scholarship@UNLV with permission from the rights-holder(s). You are free to use this Thesis in any way that is permitted by the copyright and related rights legislation that applies to your use. For other uses you need to obtain permission from the rights-holder(s) directly, unless additional rights are indicated by a Creative Commons license in the record and/ or on the work itself. This Thesis has been accepted for inclusion in UNLV Theses, Dissertations, Professional Papers, and Capstones by an authorized administrator of Digital Scholarship@UNLV. For more information, please contact [email protected]. NATURAL AND LIGNOCELLULOSE-ENRICHED MICROBIAL COMMUNITIES IN GREAT BOILING SPRING, NV by Jessica K. Cole Bachelor of Science in Biology University of Nevada - Las Vegas 2010 A thesis submitted in partial fulfillment of the requirements for the Master of Science in Biological Sciences School of Life Sciences College of Sciences The Graduate College University of Nevada, Las Vegas December 2012 Copyright by Jessica K.
    [Show full text]
  • FOUNDATIONS for a GEOBIOCHEMICAL CHARACTERIZATION of MUDPOTS in YELLOWSTONE NATIONAL PARK Georgia Dahlquist Montana Tech
    Montana Tech Library Digital Commons @ Montana Tech Graduate Theses & Non-Theses Student Scholarship Summer 2017 FOUNDATIONS FOR A GEOBIOCHEMICAL CHARACTERIZATION OF MUDPOTS IN YELLOWSTONE NATIONAL PARK Georgia Dahlquist Montana Tech Follow this and additional works at: http://digitalcommons.mtech.edu/grad_rsch Part of the Geochemistry Commons Recommended Citation Dahlquist, Georgia, "FOUNDATIONS FOR A GEOBIOCHEMICAL CHARACTERIZATION OF MUDPOTS IN YELLOWSTONE NATIONAL PARK" (2017). Graduate Theses & Non-Theses. 132. http://digitalcommons.mtech.edu/grad_rsch/132 This Thesis is brought to you for free and open access by the Student Scholarship at Digital Commons @ Montana Tech. It has been accepted for inclusion in Graduate Theses & Non-Theses by an authorized administrator of Digital Commons @ Montana Tech. For more information, please contact [email protected]. FOUNDATIONS FOR A GEOBIOCHEMICAL CHARACTERIZATION OF MUDPOTS IN YELLOWSTONE NATIONAL PARK by Georgia Dahlquist A thesis submitted in partial fulfillment of the requirements for the degree of Master of Science in Geoscience: Geochemistry Option Montana Tech 2017 ii Abstract Mudpots are acidic, turbid thermal features formed by the argillic or sericitic alteration of rock with enough fluid to create a viscous feature. Prior to this research, the combination of interdisciplinary sampling for geochemistry, mineralogy, and microbiology of rhyolite hosted mudpots, particularly in chemically distinct subregions of an area, remained largely unavailable. This work discusses mudpots and nearby hot springs sampled in Yellowstone National Park (YNP) in July 2016 and the measured in situ pH, temperature, and conductivity values, and dissolved oxygen concentrations. Water, filtered via gravity pre-filtration and 1.2 µm and 0.8/0.2µm syringe filtration, yielded δD and δ18O values and major anions, cations, and trace element concentrations.
    [Show full text]
  • Archaeal Viruses from Yellowstone's High Temperature Environments
    Ón ÀV >i>Ê6ÀÕÃiÃÊvÀÊ9iÜÃÌi½ÃÊ} Ê/i«iÀ>ÌÕÀiÊ ÛÀiÌà -ARK9OUNG \"LAKE7IEDENHEFT\*AMIE3NYDER\*OSH3PUHLER\&RANCISCO2OBERTO\4REVOR$OUGLAS 4HERMAL"IOLOGY)NSTITUTE -ONTANA3TATE5NIVERSITY "OZEMAN )DAHO.ATIONAL,ABORATORY )DAHO&ALLS #ORRESPONDING!UTHOR $EPARTMENTOF0LANT3CIENCES !G"IO3CIENCE -ONTANA3TATE5NIVERSITY "OZEMAN -4 0HONE&AX% MAILMYOUNG MONTANAEDU Óä "/ ,Ê ""9Ê Ê " -/,9Ê Ê9 "7-/" Ê /" Ê*, -/, / )N GENERAL OUR UNDERSTANDING OF !RCHAEA LAGS FAR BEHIND OUR KNOWLEDGE OF THE OTHER TWO DOMAINS OF LIFE"ACTERIA AND %UKARYA5NLIKETHEOTHERDOMAINSOFLIFE VERYFEWVIRUSESOF!RCHAEAHAVEBEENCHARACTERIZED/FTHEAPPROXIMATELY VIRUSESDESCRIBEDTODATE ONLYAREASSOCIATEDWITHARCHAEALHOSTSMANYOFTHESEFROMTHERMOPHILIC#RENARCHAEOTA)NTHIS WORKWEDESCRIBETHEDISCOVERY ISOLATION ANDPRELIMINARYCHARACTERIZATIONOFVIRUSESANDNOVELVIRUS LIKEPARTICLESISOLATED DIRECTLYFROMDIVERSETHERMALENVIRONMENTSIN9ELLOWSTONE.ATIONAL0ARK)NADDITION TOTALENVIRONMENTAL$.!EXTRACTED FROMTHREEDISTINCTLOCATIONSISUSEDTOASSESSTHEDIVERSITYOFTHERESIDENTARCHAEALCOMMUNITYANDTOEVALUATETHEDIVERSITYOF THERMOPHILICVIRUSES4HEUNPRECEDENTEDDIVERSITYOFTHERMALFEATURES^ IN9ELLOWSTONE.ATIONAL0ARKHASPROVIDED USTHEOPPORTUNITYTOASSESSHOSTANDVIRUSDIVERSITYWITHINASINGLESITEANDAMONGGEOGRAPHICALLYSEPARATEDSITESWITHDISTINCT GEOCHEMICALSIGNATURES iÞÊ7À`à ÀV >i> >ÀV >i>ÊÛÀÕÃià --6]Ê-/6]Ê-,6]Ê >`Ê-6Ê-ÕvLÕÃ Ì iÀ>ÊÛÀÕÃià ÛÀ>Ê`ÛiÀÃÌÞ Archaeal Viruses from Yellowstone’s High Temperature Environments 291 1.0 INTRODUCTION temperature spectrum (Hohn et al. 2002). Most cultured Historically, the isolation and characterization of viruses
    [Show full text]
  • Microbial Community Structure and Sulfur Biogeochemistry in Mildly Acidic Sulfidic Geothermal Springs in Yellowstone National Park
    Microbial community structure and sulfur biogeochemistry in mildly acidic sulfidic geothermal springs in Yellowstone National Park Authors: Richard E. Macur, Zackary J. Jay, W.P. Taylor, M.A. Kozubal, B.D. Kocar, W.P. Inskeep NOTICE: This is the peer reviewed version of the following article: Macur RE, Jay Z, Taylor WP, Kozubal MA, Kocar BD, Inskeep WP , "Microbial community structure and sulfur biogeochemistry in mildly acidic sulfidic geothermal springs in Yellowstone National Park," Geobiology, January 2013 11(1):86-99, which has been published in final form at http://dx.doi.org/10.1111/gbi.12015. This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Self-Archiving." Macur RE, Jay Z, Taylor WP, Kozubal MA, Kocar BD, Inskeep WP , "Microbial community structure and sulfur biogeochemistry in mildly acidic sulfidic geothermal springs in Yellowstone National Park," Geobiology, January 2013 11(1):86-99. Made available through Montana State University’s ScholarWorks scholarworks.montana.edu Microbial community structure and sulfur biogeochemistry in mildly-acidic sulfidic geothermal springs in Yellowstone National Park R.E. MACUR,1,2 Z.J. JAY,1 W.P. TAYLOR,1 M.A. KOZUBAL,1 B.D. KOCAR3 AND W.P. INSKEEP1 1Thermal Biology Institute and Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, MT, USA 2Center for Biofilm Engineering, Montana State University, Bozeman, MT, USA 3Stanford Synchrotron Radiation Lightsource, Menlo Park, CA, USA ABSTRACT Geothermal and hydrothermal waters often contain high concentrations of dissolved sulfide, which reacts with oxygen (abiotically or biotically) to yield elemental sulfur and other sulfur species that may support microbial metabolism.
    [Show full text]
  • Archaeal and Bacterial Communities in Geochemically Diverse Hot Springs of Yellowstone National Park
    Geobiology (2005), 3, 211–227 ArchaealBlackwellGeomicrobiologyORIGINAL Publishing ARTICLE in YellowstoneLtd and bacterial communities in geochemically diverse hot springs of Yellowstone National Park, USA D. R. MEYER-DOMBARD1,*, E. L. SHOCK2 AND J. P. AMEND1,3 1Department of Earth and Planetary Sciences, Washington University, St. Louis, MO 63130, USA 2Departments of Geological Sciences and Chemistry, Arizona State University, Tempe, AZ 85287, USA 3Division of Biology and Biomedical Sciences, Washington University, St. Louis, MO 63130, USA *Present address: Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA 02142, USA ABSTRACT Microbiological and geochemical surveys were conducted at three hot springs (Obsidian Pool, Sylvan Spring, and ‘Bison Pool’) in Yellowstone National Park (Wyoming, USA). Microbial community structure was investi- gated by polymerase chain reaction (PCR) amplification of 16S rRNA gene sequences from DNA extracted from sediments of each hot spring, followed by molecular cloning. Both bacterial and archaeal DNA was retrieved from all samples. No Euryarchaea were found, but diverse Crenarchaea exist in all three pools, particularly affiliating with deep-branching, but uncultivated organisms. In addition, cloned DNA affiliating with the Desulphurococcales and Thermoproteales was identified, but the distribution of taxa differs in each hot spring. The bacterial community at all three locations is dominated by members of the Aquificales and Thermodesul- fobacteriales, indicating that the ‘knallgas’ reaction (aerobic hydrogen oxidation) may be a central metabolism in these ecosystems. To provide geochemical context for the microbial community structures, energy-yields for a number of chemolithoautotrophic reactions are provided for >80 sampling sites in Yellowstone, including Obsidian Pool, Sylvan Spring, and ‘Bison Pool’.
    [Show full text]