DOCSLIB.ORG

ERDC/EL TR-12-33 "Identification of Microbial Gene Biomarkers for In

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
ERDC/EL TR-12-33 ERDC/EL TR-12-33 Strategic Environmental Research and Development Program Identification of Microbial Gene Biomarkers for in situ RDX Biodegradation Project ER-1609 Fiona. H. Crocker, Karl J. Indest, Carina M. Jung, December 2012 Dawn E. Hancock, Megan E. Merritt, Christine Florizone, Hao-Ping Chen, Gordon R. Stewart, Songhua Zhu, Nicole Sukdeo, Marie-Claude Fortin, Steven J. Hallam, William W. Mohn, Lindsay D. Eltis, Nancy N. Perreault, Jian-Shen Zhao, Louise Paquet, Annamaria Halasz, and Jalal Hawari Environmental Laboratory Environmental Approved for public release; distribution is unlimited. Strategic Environmental Research and ERDC/EL TR-12-33 Development Program December 2012 Identification of Microbial Gene Biomarkers for in situ RDX Biodegradation Project ER-1609 Fiona. H. Crocker, Karl J. Indest, Carina M. Jung, Dawn E. Hancock, and Megan E. Merritt Environmental Laboratory U.S. Army Engineer Research and Development Center 3909 Halls Ferry Road Vicksburg, MS 39180-6199 Christine Florizone, Hao-Ping Chen, Gordon R. Stewart, Songhua Zhu, Nicole Sukdeo, Marie-Claude Fortin, Steven J. Hallam, William W. Mohn, and Lindsay D. Eltis Department of Microbiology and Immunology University of British Columbia 2350 Health Sciences Mall Vancouver, British Columbia Canada V6T 1Z3 Nancy N. Perreault, Jian-Shen Zhao, Louise Paquet, Annamaria Halasz and Jalal Hawari Biotechnology Research Institute, NRC 6100 Royalmount Avenue Montreal, Quebec Canada H4P 2R2 Final report Approved for public release; distribution is unlimited. Prepared for U.S. Army Corps of Engineers Washington, DC 20314-1000 ERDC/EL TR-12-33 ii Abstract Objectives of this project were to: (a) elucidate RDX degradation pathways in model RDX-degrading bacteria, (b) design and develop molecular tools to identify genes responsible for RDX biodegradation, and (c) correlate the response of biomarker(s) to concentrations of RDX and/or rates of RDX degradation. Gordonia sp. KTR9 and Shewanella oneidensis MR-1 served as model bacterial systems for the aerobic and anaerobic degradation of RDX, respectively. Genome annotation and functional characterization of the plasmid pGKT2 in KTR9 revealed that xplA gene is both necessary and sufficient for RDX degradation. Shewanella oneidensis MR-1 was shown to efficiently degrade RDX anaerobically via two initial routes: (a) sequential N-NO2 reduction to the corresponding nitroso (N-NO) derivatives; and (b) mono- denitration followed by ring cleavage. The qPCR molecular tools described in this report have the potential to be used by remediation specialists for site characterization, treatment recommendations, and for evaluation and optimization of the treatment process. The fundamental information gained in this study suggests that XplA- mediated aerobic denitration of RDX may be subjected to inhibitory effects in response to nitrogen availability. Additional research is required to determine reliable guidelines to inform site managers of specific field concentrations of ammonium and nitrate that will increase RDX treatment times. Also, techniques to effectively lower the inorganic nitrogen concentrations to non-inhibitory levels for the aerobic RDX biodegradation pathway will need to be determined. DISCLAIMER: The contents of this report are not to be used for advertising, publication, or promotional purposes. Citation of trade names does not constitute an official endorsement or approval of the use of such commercial products. All product names and trademarks cited are the property of their respective owners. The findings of this report are not to be construed as an official Department of the Army position unless so designated by other authorized documents. DESTROY THIS REPORT WHEN NO LONGER NEEDED. DO NOT RETURN IT TO THE ORIGINATOR. ERDC/EL TR-12-33 iii Contents Figures and Tables .................................................................................................................................. v Acronyms ................................................................................................................................................ix Preface ................................................................................................................................................. xiii 1 Project Objectives .......................................................................................................................... 1 2 Project Background ....................................................................................................................... 6 3 Gordonia sp. KTR9 Genome Annotation and Regulation of RDX Biodegradation ............... 13 Introduction ............................................................................................................................ 13 Gordonia sp. KTR9 genome assembly, annotation, and functional characterization of pGKT2 ..................................................................................................... 13 Methods ...................................................................................................................................... 14 Results and discussion .............................................................................................................. 19 Conclusions ................................................................................................................................ 31 Proteomic analysis of KTR9 RDX Biodegradation ................................................................ 31 Introduction ................................................................................................................................ 31 Methods ...................................................................................................................................... 32 Results and discussion .............................................................................................................. 35 Conclusions ................................................................................................................................ 38 Regulation of RDX biotransformation and gene expression in Gordonia sp. KTR9 ........... 39 Introduction ................................................................................................................................ 39 Methods ...................................................................................................................................... 40 Results and discussion .............................................................................................................. 44 Conclusion .................................................................................................................................. 58 Role of nitrogen limitation and GlnR on RDX degradation ................................................... 59 Introduction ................................................................................................................................ 59 Methods ...................................................................................................................................... 59 Results and discussion .............................................................................................................. 62 Conclusions ................................................................................................................................ 75 4 Determination of RDX Biodegradation Pathways in Shewanella oneidensis MR-1 ............. 76 Introduction ............................................................................................................................ 76 Growth physiology of Shewanella oneidensis MR-1 on RDX as a carbon or nitrogen source or electron acceptor .................................................................................... 77 Introduction ................................................................................................................................ 77 Methods ...................................................................................................................................... 77 Results and discussion .............................................................................................................. 81 Conclusions ................................................................................................................................ 84 Gene disruption and characterization of RDX pathways in mutant strains ........................ 86 Introduction ................................................................................................................................ 86 Methods ...................................................................................................................................... 86 ERDC/EL TR-12-33 iv Results and discussion .............................................................................................................. 89 Conclusions ................................................................................................................................ 94 Transcriptomic analysis of MR-1 RDX biodegradation ......................................................... 95 Introduction ................................................................................................................................ 95 Methods ...................................................................................................................................... 95 Results and discussion .............................................................................................................
Load more

Recommended publications
  • Here to from Here?
    ORAL PRESENTATIONS INDEX 1.1 Revisiting genotypic and phenotypic properties as an aid to circumscribe species of the genus Salinispora .......................... 1 1.2 The use of whole genome sequencing to confirm the recognition of M. noduli and M. saelicesensis ........................... 2 1.3 Genome-scale data call for a taxonomic rearrangement of Geodermatophilaceae ................................................................... 3 1.4 Diversity and distribution of sphingomonads ................... 4 1.5 Genome-informed Bradyrhizobium taxonomy: where to from here? .................................................................................... 5 1.6 Divergence and gene flow in Xanthomonas plant pathogens 6 2.1 A core-genome sequence based taxonomy of the family Leptotrichiaceae calculated using EDGAR 2.0 ......................... 7 2.2 A global catalogue of microbial genome: type strain sequencing project of WDCM .................................................... 8 2.3 Genome sequence-based criteria for species demarcation: insights from the genus Rickettsia .............................................. 9 2.4 What exactly are bacterial subspecies? ............................. 10 3.1 Actinobacterial biodiversity: a potential driver for the South African Bio-economy ..................................................... 11 3.2 Identification and recovery of “missing microbes” from the gut microbiota of human populations living non-industrial lifestyles .....................................................................................
    [Show full text]
  • Gordonia Alkanivorans Sp. Nov., Isolated F Rorn Tar-Contaminated Soil
    International Journal of Systematic Bacteriology (1999), 49, 1513-1 522 Printed in Great Britain Gordonia alkanivorans sp. nov., isolated f rorn tar-contaminated soil Christei Kummer,’ Peter Schumann’ and Erko Stackebrandt2 Author for correspondence : Christel Kummer. Tel : + 49 36 4 1 65 66 66. Fax : + 49 36 4 1 65 66 52. e-mail : chkummer @ pmail. hki-jena.de ~ Hans-Knoll-lnstitut fur Twelve bacterial strains isolated from tar-contaminated soil were subjected to Naturstoff-Forschunge.V., a polyphasic taxonomic study. The strains possessed meso-diaminopimelicacid D-07745 Jena, Germany as the diagnostic diamino acid of the peptidoglycan, MK-9(H2) as the * DSMZ - Deutsche predominant menaquinone, long-chain mycolic acids of the Gordonia-type, Sammlung von Mikroorganismen und straight-chain saturated and monounsaturated fatty acids, and considerable Zellkulturen GmbH, amounts of tuberculostearic acid. The G+C content of the DNA was 68 molo/o. D-38124 Braunschweig, Chemotaxonomic and physiologicalproperties and 165 rDNA sequence Germany comparison results indicated that these strains represent a new species of the genus Gordonia. Because of the ability of these strains to use alkanes as a carbon source, the name Gordonia alkanivorans is proposed. The type strain of Gordonia alkanivorans sp. nov. is strain HKI 0136T(= DSM 4436gT). Keywords: Actinomycetales, Gordonia alkanivorans sp. nov., tar-contaminated soil, degradation, alkanes INTRODUCTION al., 1988). The genus was emended (Stackebrandt et al., 1988) to accommodate Rhodococcus species con- The genus Gordonia belongs to the family taining mycolic acids with 48-66 carbon atoms and Gordoniaceae of the suborder Corynebacterineae MK-9(H2) as the predominant menaquinone. Rhodo- within the order Actinomycetales (Stackebrandt et al., coccus aichiensis and Nocardia amarae were reclassified 1997).
    [Show full text]
  • Gordonia Amicalis Sp. Nov., a Novel Dibenzothiophene-Desulphurizing Actinomycete
    International Journal of Systematic and Evolutionary Microbiology (2000), 50, 2031–2036 Printed in Great Britain Gordonia amicalis sp. nov., a novel dibenzothiophene-desulphurizing actinomycete Seung Bum Kim,1 Roselyn Brown,1 Christopher Oldfield,2 Steven C. Gilbert,2 Sergei Iliarionov3 and Michael Goodfellow1 Author for correspondence: Michael Goodfellow. Tel: j44 191 222 7706. Fax: j44 191 222 5228. e-mail: m.goodfellow!ncl.ac.uk 1 Department of The taxonomic position of a dibenzothiophene-desulphurizing soil Agricultural and actinomycete was established using a polyphasic taxonomic approach. The Environmental Science, T University of Newcastle, organism, strain IEGM , was shown to have chemical and morphological Newcastle upon Tyne properties typical of members of the genus Gordonia. The tested strain formed NE1 7RU, UK a distinct phyletic line within the evolutionary radiation occupied by the genus 2 Department of Biological Gordonia, with Gordonia alkanivorans DSM 44369T, Gordonia desulfuricans Sciences, Napier University, NCIMB 40816T and Gordonia rubropertincta DSM 43197T as the most closely Edinburgh EH10 5DT, UK related organisms. Strain IEGMT has a range of phenotypic properties that 3 Institute of Ecology and distinguish it from representatives of all of the validly described species of Genetics of Microorganisms, 13 Golev Gordonia. It was also sharply distinguished from the type strains of Gordonia Street, Perm 614081, Russia desulfuricans and Gordonia rubropertincta on the basis of DNA–DNA relatedness data. The combined genotypic and phenotypic data show that strain IEGMT merits recognition as a new species of Gordonia. The name proposed for the new species is Gordonia amicalis; the type strain is IEGMT (l DSM 44461T l KCTC 9899T).
    [Show full text]
  • Gordonia Bronchialis Type Strain (3410)
    Lawrence Berkeley National Laboratory Recent Work Title Complete genome sequence of Gordonia bronchialis type strain (3410). Permalink https://escholarship.org/uc/item/4c00p3q7 Journal Standards in genomic sciences, 2(1) ISSN 1944-3277 Authors Ivanova, Natalia Sikorski, Johannes Jando, Marlen et al. Publication Date 2010-01-28 DOI 10.4056/sigs.611106 Peer reviewed eScholarship.org Powered by the California Digital Library University of California Standards in Genomic Sciences (2010) 2:19-28 DOI:10.4056/sigs.611106 Complete genome sequence of Gordonia bronchialis type strain (3410T) Natalia Ivanova1, Johannes Sikorski2, Marlen Jando2, Alla Lapidus1, Matt Nolan1, Susan Lu- cas1, Tijana Glavina Del Rio1, Hope Tice1, Alex Copeland1, Jan-Fang Cheng1, Feng Chen1, David Bruce1,3, Lynne Goodwin1,3, Sam Pitluck1, Konstantinos Mavromatis1, Galina Ovchin- nikova1, Amrita Pati1, Amy Chen4, Krishna Palaniappan4, Miriam Land1,5, Loren Hauser1,5, Yun-Juan Chang1,5, Cynthia D. Jeffries1,5, Patrick Chain1,3, Elizabeth Saunders1,3, Cliff Han1,3, John C. Detter1,3, Thomas Brettin1,3, Manfred Rohde6, Markus Göker2, Jim Bristow1, Jona- than A. Eisen1,7, Victor Markowitz4, Philip Hugenholtz1, Hans-Peter Klenk2, and Nikos C. Kyrpides1* 1 DOE Joint Genome Institute, Walnut Creek, California, USA 2 DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany 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 HZI – Helmholtz Centre for Infection Research, Braunschweig, Germany 7 University of California Davis Genome Center, Davis, California, USA *Corresponding author: Nikos C.
    [Show full text]
  • A Genome Compendium Reveals Diverse Metabolic Adaptations of Antarctic Soil Microorganisms
    bioRxiv preprint doi: https://doi.org/10.1101/2020.08.06.239558; this version posted August 6, 2020. 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-NC-ND 4.0 International license. August 3, 2020 A genome compendium reveals diverse metabolic adaptations of Antarctic soil microorganisms Maximiliano Ortiz1 #, Pok Man Leung2 # *, Guy Shelley3, Marc W. Van Goethem1,4, Sean K. Bay2, Karen Jordaan1,5, Surendra Vikram1, Ian D. Hogg1,7,8, Thulani P. Makhalanyane1, Steven L. Chown6, Rhys Grinter2, Don A. Cowan1 *, Chris Greening2,3 * 1 Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Hatfield, Pretoria 0002, South Africa 2 Department of Microbiology, Monash Biomedicine Discovery Institute, Clayton, VIC 3800, Australia 3 School of Biological Sciences, Monash University, Clayton, VIC 3800, Australia 4 Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA 5 Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Alameda 340, Santiago 6 Securing Antarctica’s Environmental Future, School of Biological Sciences, Monash University, Clayton, VIC 3800, Australia 7 School of Science, University of Waikato, Hamilton 3240, New Zealand 8 Polar Knowledge Canada, Canadian High Arctic Research Station, Cambridge Bay, NU X0B 0C0, Canada # These authors contributed equally to this work. * Correspondence may be addressed to: A/Prof Chris Greening ([email protected]) Prof Don A. Cowan ([email protected]) Pok Man Leung ([email protected]) bioRxiv preprint doi: https://doi.org/10.1101/2020.08.06.239558; this version posted August 6, 2020.
    [Show full text]
  • Gordonia Polyisoprenivorans from Groundwater
    Brazilian Journal of Microbiology (2006) 37:168-174 ISSN 1517-8382 GORDONIA POLYISOPRENIVORANS FROM GROUNDWATER CONTAMINATED WITH LANDFILL LEACHATE IN A SUBTROPICAL AREA: CHARACTERIZATION OF THE ISOLATE AND EXOPOLYSACCHARIDE PRODUCTION Roberta Fusconi1*; Mirna Januária Leal Godinho1; Isara Lourdes Cruz Hernández1; Nelma Regina Segnini Bossolan2 1Departamento de Ecologia e Biologia Evolutiva, Universidade Federal de São Carlos, São Carlos, SP, Brasil; 2Instituto de Física, Universidade de São Paulo, São Carlos, SP, Brasil Submitted: April 30, 2004; Returned to authors for corrections: June 01, 2005; Approved: February 26, 2006 ABSTRACT A strain of Gordonia sp. (strain Lc), from landfill leachate-contaminated groundwater was characterized by polyphasic taxonomy and studied for exopolysaccharide (EPS) production. The cells were Gram-positive, catalase-positive, oxidase-negative and non-motile. The organism grew both aerobically and, in anoxic environment, in the presence of NaNO3. Rods occured singly, in pairs or in a typical coryneform V-shaped. The organism had morphological, physiological and chemical properties consistent with its assignment to the genus Gordonia and mycolic and fatty acid pattern that corresponded to those of G. polyisoprenivorans DSM 44302T. The comparison of the sequence of the first 500 bases of the 16S rDNA of strain Lc gave 100% similarity with the type strain of Gordonia polyisoprenivorans DSM 44302T. Experiments conducted in anaerobic conditions in liquid E medium with either glucose or sucrose as the main carbon source showed that sucrose did not support the growth of Lc strain and that on glucose the maximum specific growth rate was 0.17h-1, representing a generation time of approximately 4 hours. On glucose, a maximum of total EPS was produced during the exponential phase (126.17 ± 15.63 g l-1).
    [Show full text]
  • Investigation of New Actinobacteria for the Biodesulphurisation of Diesel Fuel
    Investigation of new actinobacteria for the biodesulphurisation of diesel fuel Selva Manikandan Athi Narayanan A thesis submitted in partial fulfilment of the requirements of Edinburgh Napier University, for the award of Doctor of Philosophy May 2020 Abstract Biodesulphurisation (BDS) is an emerging technology that utilises microorganisms for the removal of sulphur from fossil fuels. Commercial-scale BDS needs the development of highly active bacterial strains which allow easier downstream processing. In this research, a collection of actinobacteria that originated from oil-contaminated soils in Russia were investigated to establish their phylogenetic positions and biodesulphurisation capabilities. The eleven test strains were confirmed as members of the genus Rhodococcus based on 16S rRNA and gyrB gene sequence analysis. Two organisms namely strain F and IEGM 248, confirmed as members of the species R. qingshengii and R. opacus, respectively based on the whole- genome sequence based OrthoANIu values, exhibited robust biodesulphurisation of dibenzothiophene (DBT) and benzothiophene (BT), respectively. R. qingshengii strain F was found to convert DBT to hydroxybiphenyl (2-HBP) with DBTO and DBTO2 as intermediates. The DBT desulphurisation genes of strain F occur as a cluster and share high sequence similarity with the dsz operon of R. erythropolis IGTS8. Rhodococcus opacus IEGM 248 could convert BT into benzofuran. The BDS reaction of both strains follows the well-known 4S pathway of desulphurisation of DBT and BT. When cultured directly in a biphasic growth medium containing 10% (v/v) oil (n-hexadecane or diesel) containing 300 ppm sulphur, strain F formed a stable oil-liquid emulsion, making it unsuitable for direct industrial application despite the strong desulphurisation activity.
    [Show full text]
  • Characterization of Actinobacteria Degrading and Tolerating Organic Pollutants and Tolerating Organic Pollutants
    Characterization of Actinobacteria Degrading Characterization of Actinobacteria Degrading and Tolerating Organic Pollutants and Tolerating Organic Pollutants Irina Tsitko Irina Tsitko Division of Microbiology Division of Microbiology Department of Applied Chemistry and Microbiology Department of Applied Chemistry and Microbiology Faculty of Agriculture and Forestry Faculty of Agriculture and Forestry University of Helsinki University of Helsinki Academic Dissertation in Microbiology Academic Dissertation in Microbiology To be presented, with the permission of the Faculty of Agriculture and Forestry of the To be presented, with the permission of the Faculty of Agriculture and Forestry of the University of Helsinki, for public criticism in Auditorium 1015 at Viikki Biocentre, University of Helsinki, for public criticism in Auditorium 1015 at Viikki Biocentre, Viikinkaari 5, on January 12th, 2007, at 12 o’clock noon. Viikinkaari 5, on January 12th, 2007, at 12 o’clock noon. Helsinki 2007 Helsinki 2007 Supervisor: Professor Mirja Salkinoja-Salonen Supervisor: Professor Mirja Salkinoja-Salonen Department of Applied Chemistry and Microbiology Department of Applied Chemistry and Microbiology University of Helsinki University of Helsinki Helsinki, Finland Helsinki, Finland Reviewers Doctor Anja Veijanen Reviewers Doctor Anja Veijanen Department of Biological and Environmental Science Department of Biological and Environmental Science University of Jyväskylä University of Jyväskylä Jyväskylä, Finland Jyväskylä, Finland Docent Merja Kontro Docent Merja Kontro University of Helsinki University of Helsinki Department of Ecological and Environmental Sciences Department of Ecological and Environmental Sciences Lahti, Finland Lahti, Finland Opponent: Professor Edward R.B. Moore, Opponent: Professor Edward R.B. Moore, Department of Clinical Bacteriology Department of Clinical Bacteriology Sahlgrenska University Hospital, Sahlgrenska University Hospital, Göteborg University Göteborg University Göteborg, Sweden.
    [Show full text]
  • Gordonia Polyisoprenivorans Sp. Nov., a Rubber-Degrading Actinomycete Isolated from an Automobile Tyre
    International Journal of Systematic Bacteriology (1 999): 49, 1785-1 791 Printed in Great Britain Gordonia polyisoprenivorans sp. nov., a rubber-degrading actinomycete isolated from an automobile tyre Alexandros Linos,’ Alexander Steinbuchel,’ Cathrin Sproer2 and Reiner M. Kroppenstedt’ Author for correspondence: Reiner M. Kroppenstedt. Tel: +49 531 2616 227. Fax: +49 531 2616 418. e-mail : [email protected] lnstitut fur Mikrobiologie, A rubber-degrading bacterium (strain KdZT)was isolated from fouling tyre Universitat Munster, water inside a deteriorated automobile tyre. The strain was aerobic, Gram- CorrensstraBe 3, 48149 Munster, Germany positive, produced elementary branching hyphae which fragmented into rodkoccus-li ke elements and showed chemotaxonomic markers which were 2 DSMZ - Deutsche Sammlung von consistent with the classification of Gordonia, i.e. meso-diaminopimelicacid, Mikroorganismen und N-glycolyl muramic acid, arabinose and galactose as diagnostic sugars, a fatty Zellkulturen, Mascheroder acid pattern composed of unbranched saturated and monounsaturated fatty Weg 1b, 381 24 B raunsc hweig, Germany acids with a considerable amount of tuberculostearic acid, and mycolic acids comprising 58-66 carbon atoms with two principal mycolic acids C,, and C,, counting for over 60%. Results of 16s rDNA analyses as well as chemotaxonomic results, led to the conclusion that Gordonia sp. strain KdZT (= DSM 443023 represents a new species within the genus Gordonia for which the name Gordonia polyisoprenivorans is proposed. Keywords: Gordonia
    [Show full text]
  • Gordonia Bronchialis Type Strain (3410T)
    Standards in Genomic Sciences (2010) 2:19-28 DOI:10.4056/sigs.611106 Complete genome sequence of Gordonia bronchialis type strain (3410T) Natalia Ivanova1, Johannes Sikorski2, Marlen Jando2, Alla Lapidus1, Matt Nolan1, Susan Lu- cas1, Tijana Glavina Del Rio1, Hope Tice1, Alex Copeland1, Jan-Fang Cheng1, Feng Chen1, David Bruce1,3, Lynne Goodwin1,3, Sam Pitluck1, Konstantinos Mavromatis1, Galina Ovchin- nikova1, Amrita Pati1, Amy Chen4, Krishna Palaniappan4, Miriam Land1,5, Loren Hauser1,5, Yun-Juan Chang1,5, Cynthia D. Jeffries1,5, Patrick Chain1,3, Elizabeth Saunders1,3, Cliff Han1,3, John C. Detter1,3, Thomas Brettin1,3, Manfred Rohde6, Markus Göker2, Jim Bristow1, Jona- than A. Eisen1,7, Victor Markowitz4, Philip Hugenholtz1, Hans-Peter Klenk2, and Nikos C. Kyrpides1* 1 DOE Joint Genome Institute, Walnut Creek, California, USA 2 DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany 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 HZI – Helmholtz Centre for Infection Research, Braunschweig, Germany 7 University of California Davis Genome Center, Davis, California, USA *Corresponding author: Nikos C. Kyrpides Keywords: obligate aerobic, human-pathogenic, endocarditis, Gram-positive, non-motile, Gordoniaceae, GEBA Gordonia bronchialis Tsukamura 1971 is the type species of the genus. G. bronchialis is a human-pathogenic organism that has been isolated from a large variety of human tissues. Here we describe the features of this organism, together with the complete genome sequence and annotation. This is the first completed genome sequence of the family Gordoniaceae.
    [Show full text]
  • 1 a Cytoplasmic Peptidoglycan Amidase Homologue Controls Mycobacterial Cell Wall
    1 A cytoplasmic peptidoglycan amidase homologue controls mycobacterial cell wall 2 synthesis 3 4 Cara C. Boutte1, Christina E. Baer2, Kadamba Papavinasasundaram2, Weiru 5 Liu1, Michael R Chase1, Xavier Meniche2, Sarah M. Fortune1, Christopher M. 6 Sassetti2, Thomas R. Ioerger3, Eric J. Rubin1,4,* 7 8 1Department of Immunology and Infectious Disease, Harvard T.H. Chan School 9 of Public Health, Boston, MA 02115, USA 10 2Department of Microbiology and Physiological Systems, University of 11 Massachusetts Medical School, Worcester, MA 01655, USA 12 3Department of Computer Science, Texas A&M University, College Station, TX 13 77842, USA 14 4Department of Microbiology and Immunobiology, Harvard Medical School, 15 Boston, MA 02115, USA 16 *correspondence: [email protected] 17 18 Author contributions: Conceptualization, C.C.B. and E.J.R.; Methodology, C.C.B., 19 C.E.B., M.R.C. and E.J.R.; Investigation, C.C.B., T.R.I., W.L., X.M., K.P.; 20 Resources, C.C.B., C.E.B., K.P., C.M.S., E.J.R.; Writing-Original Draft, C.C.B.; 21 Writing-Review & Editing, C.C.B., T.R.I., C.M.S., C.E.B., E.J.R.; Visualization, 22 C.C.B.; Supervision, S.R.M., C.M.S., E.J.R.; Funding acquisition, E.J.R., C.C.B. 23 1 24 Abbreviations: Mtb = Mycobacterium tuberculosis. Msmeg = Mycobacterium 25 smegmatis. PG = peptidoglycan. Protein and gene names refer to the M. 26 smegmatis homologs. When the Mtb proteins and genes are discussed, they are 27 indicated, e.g.: CwlMTB.
    [Show full text]
  • Universidad Politécnica De Valencia
    UNIVERSIDAD POLITÉCNICA DE VALENCIA ESCUELA TÉCNICA SUPERIOR DE INGENIEROS AGRÓNOMOS DIVERSIDAD DE ACTINOMICETOS NOCARDIOFORMES PRODUCTORES DE ESPUMAS BIOLÓGICAS AISLADOS DE PLANTAS DEPURADORAS DE AGUAS RESIDUALES DE LA COMUNIDAD VALENCIANA TRABAJO FINAL DE CARRERA INGENIERO AGRÓNOMO PRESENTADO POR: ALBERT SOLER HERNÁNDEZ DIRIGIDO POR: GONZALO CUESTA AMAT JOSE LUIS ALONSO MOLINA VALENCIA, JULIO DE 2008 ESCUELA TÉCNICA Anexo 4 SUPERIOR DE INGENIEROS Autorización del director/a, AGRÓNOMOS codirector/a o tutor/a Datos del trabajo de fin de carrera Autor: Albert Soler Hernández DNI: 22584259-F Título: DIVERSIDAD DE ACTINOMICETOS NOCARDIOFORMES PRODUCTORES DE ESPUMAS BIOLÓGICAS AISLADOS DE PLANTAS DEPURADORAS DE AGUAS RESIDUALES DE LA COMUNIDAD VALENCIANA Área o áreas de conocimiento a las que corresponde el trabajo: Microbiología y Medio Ambiente Titulación: Ingeniero Agrónomo A cumplimentar por el director/a, codirector/a o tutor/a del trabajo Nombre y apellidos: Gonzalo Cuesta Amat Departamento: Biotecnología En calidad de: X director/a codirector/a tutor/a Autorizo la presentación del trabajo de fin de carrera cuyos datos figuran en el apartado anterior y certifico que se adecua plenamente a los requisitos formales, metodológicos y de contenido exigidos a un trabajo de fin de carrera, de acuerdo con la normativa aplicable en la ETSIA. (Firma)* Gonzalo Cuesta Amat Jose Luis Alonso Molina Valencia, 21 de Julio de 2008 En el caso de codirección, han de firmar necesariamente los que sean profesores de esta Escuela; si existe tutor o tutora,
    [Show full text]