DOCSLIB.ORG

Actinoalloteichus Fjordicus Sp. Nov. Isolated from Marine Sponges: Phenotypic, Chemotaxonomic and Genomic Characterisation

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Actinoalloteichus Fjordicus Sp. Nov. Isolated from Marine Sponges: Phenotypic, Chemotaxonomic and Genomic Characterisation Nouioui I, Ruckert C, Willemse J, van Wezel GP, Klenk H-P, Busche T, Kalinowski J, Bredholt H, Zotchev SB. Actinoalloteichus fjordicus sp. nov. isolated from marine sponges: phenotypic, chemotaxonomic and genomic characterisation. Antonie van Leeuwenhoek, International Journal of General and Molecular Microbiology 2017 DOI: https://doi.org/10.1007/s10482-017-0920-9 Copyright: ©The Authors 2017. This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original authors and the source, provide a link to the Creative Commons license, and indicate if changes were made DOI link to article: https://doi.org/10.1007/s10482-017-0920-9 Date deposited: 21/08/2017 This work is licensed under a Creative Commons Attribution 4.0 International License Newcastle University ePrints - eprint.ncl.ac.uk Antonie van Leeuwenhoek DOI 10.1007/s10482-017-0920-9 ORIGINAL PAPER Actinoalloteichus fjordicus sp. nov. isolated from marine sponges: phenotypic, chemotaxonomic and genomic characterisation Imen Nouioui . Christian Ru¨ckert . Joost Willemse . Gilles P. van Wezel . Hans-Peter Klenk . Tobias Busche . Jo¨rn Kalinowski . Harald Bredholt . Sergey B. Zotchev Received: 25 April 2017 / Accepted: 25 July 2017 Ó The Author(s) 2017. This article is an open access publication Abstract Two actinobacterial strains, ADI 127-17T neighbours. Digital DNA: DNA hybridization and and GBA 129-24, isolated from marine sponges Antho ANI values between strains ADI 127-17T and GBA dichotoma and Geodia barretti, respectively, collected 129-24 were 97.6 and 99.7%, respectively, whereas at the Trondheim fjord in Norway, were the subjects of the corresponding values between both tested strains a polyphasic study. According to their 16S rRNA gene and type strains of their closely related phylogenetic sequences, the new isolates were preliminarily clas- neighbours, A. hoggarensis and A. hymeniacidonis, sified as belonging to the genus Actinoalloteichus. were well below the threshold for delineation of Both strains formed a distinct branch, closely related prokaryotic species. Therefore, strains ADI 127-17T to the type strains of Actinoalloteichus hoggarensis (= DSM 46855T) and GBA 129-24 (= DSM 46856) and Actinoalloteichus hymeniacidonis, within the are concluded to represent a novel species of the genus evolutionary radiation of the genus Actinoalloteichus Actinoalloteichus for which the name of Actinoallote- in the 16S rRNA gene-based phylogenetic tree. ichus fjordicus sp. nov. (type strain ADI Isolates ADI 127-17T and GBA 129-24 exhibited 127-17T = DSM 46855T = CECT 9355T) is pro- morphological, chemotaxonomic and genotypic fea- posed. The complete genome sequences of the new tures distinguishable from their close phylogenetic strains were obtained and compared to that of A. hymeniacidonis DSM 45092T and A. hoggarensis DSM 45943T to unravel unique genome features and Electronic supplementary material The online version of biosynthetic potential of the new isolates. this article (doi:10.1007/s10482-017-0920-9) contains supple- mentary material, which is available to authorized users. I. Nouioui Á H.-P. Klenk J. Willemse Á G. P. van Wezel School of Biology, Newcastle University, Molecular Biotechnology, Sylvius Laboratories, Leiden Newcastle upon Tyne NE1 7RU, UK University, 2333BE Leiden, The Netherlands C. Ru¨ckert Á T. Busche Á J. Kalinowski H. Bredholt Microbial Genomics and Biotechnology, Center for Xellia Pharmaceuticals, Silurveien 2, 0380 Oslo, Norway Biotechnology (CeBiTec), Bielefeld University, 33594 Bielefeld, Germany S. B. Zotchev (&) Department of Pharmacognosy, University of Vienna, C. Ru¨ckert Althanstraße 14, 1090 Vienna, Austria Sinskey Laboratory, Department of Biology, e-mail: [email protected] Massachusetts Institute of Technology, Cambridge, MA 02142, USA 123 Antonie van Leeuwenhoek Keywords Marine sponges Á Actinobacteria Á 9(H2) in small amounts. The diagnostic phospho- Actinoalloteichus Á Chemotaxonomy Á Comparative lipids are phosphatidylethanolamine and phos- genomics Á New species Á Secondary metabolite phatidylmonomethylethanolamine. The G?C content biosynthesis gene clusters of their DNA is 72–73 mol% (Tamura et al. 2000). Actinoalloteichus strains have been isolated from different habitats: A. cyanogriseus, the type species of the genus from a soil sample collected in the Yunnan Introduction province of China (Tamura et al. 2000), the halophilic Actinoalloteichus hoggarensis from Saharan soil Mycelial actinobacteria are the major sources of a (Boudjelal et al. 2015), Actinoalloteichus nanshanen- variety of bioactive and potentially pharmaceutically sis from the rhizosphere of a fig tree (Xiang et al. useful compounds, some of which are being developed 2011), Actinoalloteichus spitiensis from a soil in the into anticancer agents (Feling et al. 2003; Prudhomme cold desert of the Indian Himalayas (Singla et al. et al. 2008; Bhatnagar and Kim 2010) and antibiotics 2005) and Actinoalloteichus hymeniacidonis from the (Subramani and Aalbersberg 2012; Manivasagan et al. sponge Hymeniacidon perleve collected at the inter- 2014). Recently, marine actinobacteria have become a tidal beach of Dalian on the Chinese Yellow Sea focus of intensive research since they have been (Zhang et al. 2006). shown to have a remarkable potential for producing So far, several secondary metabolites have been unique secondary metabolites not previously isolated isolated from Actinoalloteichus spp., including the from terrestrial actinobacteria (Zotchev 2012). Many cytotoxic macrolactam BE-14106 from soil-derived A. such metabolites have antimicrobial activities, sug- cyanogriseus (Fujita et al. 2016), cytotoxic cyclopen- gesting that they may be used as ‘‘chemical weapons’’ tenones from A. nanshanensis sp. nov. NEAU 119 to inhibit the growth of organisms competing for (Wang et al. 2013), antifungal neomaclafungins from nutritional sources (Davies and Ryan 2012). A role for marine Actinoalloteichus sp. NPS702 (Sato et al. secondary metabolites as signaling molecules has also 2012), and cytotoxic bipyridine and cyanogramide been proposed after discovering their effect on gene alkaloids from marine-derived A. cyanogriseus WH1- expression of other bacteria exposed to sub-inhibitory 2216-6 (Fu et al. 2011, 2014). concentrations of the compounds (Yim et al. 2007). The fact that just a few Actinoalloteichus isolates Whatever their role is, it must be very important for studied so far already yielded several novel com- actinobacteria, since genome sequencing typically pounds suggests a substantial potential of this genus reveals the presence of 20–40 gene clusters (most of for drug discovery. Here, we describe the isolation, them ‘‘silent’’) dedicated to the biosynthesis of morphological, chemotaxonomic and genome-based secondary metabolites in each species (Horinouchi characterisation of two new representatives of this 2007). relatively rare genus from marine sponges collected in The genus Actinoalloteichus (Tamura et al. 2000), the Trondheim fjord (Norway). The comparison of the belonging to the family Pseudonocardiaceae (Emb- complete genome sequences of members of the genus ley et al. 1988; Stackebrandt et al. 1997) and Actinoalloteichus might unravel unknown gene clus- suborder Pseudonocardineae (Labeda et al. 2011), ters dedicated to the biosynthesis of bioactive sec- currently encompasses five species with valid names ondary metabolites. according to LPSN classification (Euze´by 1997), with Actinoalloteichus cyanogriseus as the type species (Tamura et al. 2000). Members of the genus Materials and methods Actinoalloteichus form substrate and aerial mycelium with an aggregation of straight spore chains. Their Sampling of marine sponges cell walls contain meso-diaminopimelic acid and are rich in glutamate, glucosamine and alanine. Major Samples of marine sponges Geodia barretti and Antho cellular fatty acids are iso-C15:0, anteiso-C15:0, iso- dichotoma were collected at the Tautra ridge (Trond- C16:0 and C17:0. The predominant menaquinone is heim fjord, Norway, 6303600N and 1003100E) using the MK-9(H4) with the presence of MK-8(H4) and MK- MINERVA underwater remote-operated vehicle 123 Antonie van Leeuwenhoek equipped with a net and a robotic manipulator. The Lechevalier 1970), diaminopimelic acid (Staneck and collected sponges did not represent endangered or Roberts 1974), menaquinone (Collins 1985) and polar protected species and the samples were collected by a lipid (Minnikin et al. 1984) profiles were detected national Norwegian university (Norwegian University using chromatographic methods. Fatty acid extracts of Science and Technology) for research purposes. (Miller 1982; Kuykendall et al. 1988) were analysed Sponge samples of approximately 300 g (G. barretti, and identified by gas chromatography (Agilent 6890N depth 62. 7 m) and 175 g (A. dichotoma, depth 60 m) instrument) using the Standard Microbial Identifica- were retrieved and transferred to 1–l sterile plastic tion (MIDI) system and the ACTIN6 database (Sasser containers with screw caps filled with sterile artificial 1990). Cryo-scanning electron microscopy was per- seawater. Samples were kept at 10 °C during transport formed according to Celler et al. (2016) for description (about 3 h) and stored at 4 °C until processing. of the morphological features of both isolates after growth on ISP2 agar
Load more

Recommended publications
  • Actinoalloteichus Fjordicus Sp. Nov. Isolated from Marine Sponges: Phenotypic, Chemotaxonomic and Genomic Characterisation
    Antonie van Leeuwenhoek DOI 10.1007/s10482-017-0920-9 ORIGINAL PAPER Actinoalloteichus fjordicus sp. nov. isolated from marine sponges: phenotypic, chemotaxonomic and genomic characterisation Imen Nouioui . Christian Ru¨ckert . Joost Willemse . Gilles P. van Wezel . Hans-Peter Klenk . Tobias Busche . Jo¨rn Kalinowski . Harald Bredholt . Sergey B. Zotchev Received: 25 April 2017 / Accepted: 25 July 2017 Ó The Author(s) 2017. This article is an open access publication Abstract Two actinobacterial strains, ADI 127-17T neighbours. Digital DNA: DNA hybridization and and GBA 129-24, isolated from marine sponges Antho ANI values between strains ADI 127-17T and GBA dichotoma and Geodia barretti, respectively, collected 129-24 were 97.6 and 99.7%, respectively, whereas at the Trondheim fjord in Norway, were the subjects of the corresponding values between both tested strains a polyphasic study. According to their 16S rRNA gene and type strains of their closely related phylogenetic sequences, the new isolates were preliminarily clas- neighbours, A. hoggarensis and A. hymeniacidonis, sified as belonging to the genus Actinoalloteichus. were well below the threshold for delineation of Both strains formed a distinct branch, closely related prokaryotic species. Therefore, strains ADI 127-17T to the type strains of Actinoalloteichus hoggarensis (= DSM 46855T) and GBA 129-24 (= DSM 46856) and Actinoalloteichus hymeniacidonis, within the are concluded to represent a novel species of the genus evolutionary radiation of the genus Actinoalloteichus Actinoalloteichus for which the name of Actinoallote- in the 16S rRNA gene-based phylogenetic tree. ichus fjordicus sp. nov. (type strain ADI Isolates ADI 127-17T and GBA 129-24 exhibited 127-17T = DSM 46855T = CECT 9355T) is pro- morphological, chemotaxonomic and genotypic fea- posed.
    [Show full text]
  • Systematic Research on Actinomycetes Selected According
    Systematic Research on Actinomycetes Selected according to Biological Activities Dissertation Submitted in fulfillment of the requirements for the award of the Doctor (Ph.D.) degree of the Math.-Nat. Fakultät of the Christian-Albrechts-Universität in Kiel By MSci. - Biol. Yi Jiang Leibniz-Institut für Meereswissenschaften, IFM-GEOMAR, Marine Mikrobiologie, Düsternbrooker Weg 20, D-24105 Kiel, Germany Supervised by Prof. Dr. Johannes F. Imhoff Kiel 2009 Referent: Prof. Dr. Johannes F. Imhoff Korreferent: ______________________ Tag der mündlichen Prüfung: Kiel, ____________ Zum Druck genehmigt: Kiel, _____________ Summary Content Chapter 1 Introduction 1 Chapter 2 Habitats, Isolation and Identification 24 Chapter 3 Streptomyces hainanensis sp. nov., a new member of the genus Streptomyces 38 Chapter 4 Actinomycetospora chiangmaiensis gen. nov., sp. nov., a new member of the family Pseudonocardiaceae 52 Chapter 5 A new member of the family Micromonosporaceae, Planosporangium flavogriseum gen nov., sp. nov. 67 Chapter 6 Promicromonospora flava sp. nov., isolated from sediment of the Baltic Sea 87 Chapter 7 Discussion 99 Appendix a Resume, Publication list and Patent 115 Appendix b Medium list 122 Appendix c Abbreviations 126 Appendix d Poster (2007 VAAM, Germany) 127 Appendix e List of research strains 128 Acknowledgements 134 Erklärung 136 Summary Actinomycetes (Actinobacteria) are the group of bacteria producing most of the bioactive metabolites. Approx. 100 out of 150 antibiotics used in human therapy and agriculture are produced by actinomycetes. Finding novel leader compounds from actinomycetes is still one of the promising approaches to develop new pharmaceuticals. The aim of this study was to find new species and genera of actinomycetes as the basis for the discovery of new leader compounds for pharmaceuticals.
    [Show full text]
  • Of Bergey's Manual
    BERGEY’S MANUAL® OF Systematic Bacteriology Second Edition Volume Five The Actinobacteria, Part A and B BERGEY’S MANUAL® OF Systematic Bacteriology Second Edition Volume Five The Actinobacteria, Part A and B Michael Goodfellow, Peter Kämpfer, Hans-Jürgen Busse, Martha E. Trujillo, Ken-ichiro Suzuki, Wolfgang Ludwig and William B. Whitman EDITORS, VOLUME FIVE William B. Whitman DIRECTOR OF THE EDITORIAL OFFICE Aidan C. Parte MANAGING EDITOR EDITORIAL BOARD Fred A. Rainey, Chairman, Peter Kämpfer, Vice Chairman, Paul De Vos, Jongsik Chun, Martha E. Trujillo and William B. Whitman WITH CONTRIBUTIONS FROM 116 COLLEAGUES William B. Whitman Bergey’s Manual Trust Department of Microbiology 527 Biological Sciences Building University of Georgia Athens, GA 30602-2605 USA ISBN 978-0-387-95043-3 ISBN 978-0-387-68233-4 (eBook) DOI 10.1007/978-0-387-68233-4 Springer New York Dordrecht Heidelberg London Library of Congress Control Number: 2012930836 © 2012, 1984–1989 Bergey’s Manual Trust Bergey’s Manual is a registered trademark of Bergey’s Manual Trust. All rights reserved. This work may not be translated or copied in whole or in part without the written permission of the publisher (Springer Science+Business Media, LLC, 233 Spring Street, New York, NY 10013, USA), except for brief excerpts in connection with reviews or scholarly analysis. Use in connection with any form of information storage and retrieval, electronic adaptation, computer software, or by similar or dissimilar methodology now known or hereafter developed is forbidden. The use in this publication of trade names, trademarks, service marks, and similar terms, even if they are not identified as such, is not to be taken as an expression of opinion as to whether or not they are subject to proprietary rights.
    [Show full text]
  • Complete Genome Sequence of the Actinomycete Actinoalloteichus
    Schaffert et al. Standards in Genomic Sciences (2016) 11:91 DOI 10.1186/s40793-016-0213-3 SHORT GENOME REPORT Open Access Complete genome sequence of the actinomycete Actinoalloteichus hymeniacidonis type strain HPA 177T isolated from a marine sponge Lena Schaffert1, Andreas Albersmeier1, Anika Winkler1, Jörn Kalinowski1, Sergey B. Zotchev2 and Christian Rückert1,3* Abstract Actinoalloteichus hymeniacidonis HPA 177T is a Gram-positive, strictly aerobic, black pigment producing and spore- forming actinomycete, which forms branching vegetative hyphae and was isolated from the marine sponge Hymeniacidon perlevis. Actinomycete bacteria are prolific producers of secondary metabolites, some of which have been developed into anti-microbial, anti-tumor and immunosuppressive drugs currently used in human therapy. Considering this and the growing interest in natural products as sources of new drugs, actinomycete bacteria from the hitherto poorly explored marine environments may represent promising sources for drug discovery. As A. hymeniacidonis, isolated from the marine sponge, is a type strain of the recently described and rare genus Actinoalloteichus, knowledge of the complete genome sequence enables genome analyses to identify genetic loci for novel bioactive compounds. This project, describing the 6.31 Mbp long chromosome, with its 5346 protein- coding and 73 RNA genes, will aid the Genomic Encyclopedia of Bacteria and Archaea project. Keywords: Actinoalloteichus, Strictly aerobic, Non-motile, Gram-positive, Non-acid-fast, Branching vegetative hyphae, Spore forming, Secondary metabolite biosynthesis gene clusters Introduction actinomycetes became a focus of research since they Strain HPA 177T is the type strain of the species Acti- have evolved the greatest genomic and metabolic diver- noalloteichus hymeniacidonis, it was isolated from the sity and are auspicious sources of novel secondary me- marine sponge Hymeniacidon perlevis at the intertidal tabolites and enzymes [5, 7–9].
    [Show full text]
  • Contents Topic 1. Introduction to Microbiology. the Subject and Tasks
    Contents Topic 1. Introduction to microbiology. The subject and tasks of microbiology. A short historical essay………………………………………………………………5 Topic 2. Systematics and nomenclature of microorganisms……………………. 10 Topic 3. General characteristics of prokaryotic cells. Gram’s method ………...45 Topic 4. Principles of health protection and safety rules in the microbiological laboratory. Design, equipment, and working regimen of a microbiological laboratory………………………………………………………………………….162 Topic 5. Physiology of bacteria, fungi, viruses, mycoplasmas, rickettsia……...185 TOPIC 1. INTRODUCTION TO MICROBIOLOGY. THE SUBJECT AND TASKS OF MICROBIOLOGY. A SHORT HISTORICAL ESSAY. Contents 1. Subject, tasks and achievements of modern microbiology. 2. The role of microorganisms in human life. 3. Differentiation of microbiology in the industry. 4. Communication of microbiology with other sciences. 5. Periods in the development of microbiology. 6. The contribution of domestic scientists in the development of microbiology. 7. The value of microbiology in the system of training veterinarians. 8. Methods of studying microorganisms. Microbiology is a science, which study most shallow living creatures - microorganisms. Before inventing of microscope humanity was in dark about their existence. But during the centuries people could make use of processes vital activity of microbes for its needs. They could prepare a koumiss, alcohol, wine, vinegar, bread, and other products. During many centuries the nature of fermentations remained incomprehensible. Microbiology learns morphology, physiology, genetics and microorganisms systematization, their ecology and the other life forms. Specific Classes of Microorganisms Algae Protozoa Fungi (yeasts and molds) Bacteria Rickettsiae Viruses Prions The Microorganisms are extraordinarily widely spread in nature. They literally ubiquitous forward us from birth to our death. Daily, hourly we eat up thousands and thousands of microbes together with air, water, food.
    [Show full text]
  • Phylogenetic Appraisal of Antagonistic, Slow Growing Actinomycetes Isolated from Hypersaline Inland Solar Salterns at Sambhar Salt Lake, India
    View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Frontiers - Publisher Connector ORIGINAL RESEARCH ARTICLE published: 10 July 2013 doi: 10.3389/fmicb.2013.00190 Phylogenetic appraisal of antagonistic, slow growing actinomycetes isolated from hypersaline inland solar salterns at Sambhar salt Lake, India Polpass Arul Jose and Solomon Robinson David Jebakumar* Department of Molecular Microbiology, School of Biotechnology, Madurai Kamaraj University, Madurai, India Edited by: Inland solar salterns established in the vicinity of Sambhar Lake are extreme saline Axel Schippers, Federal Institute for environments with high salinity and alkalinity. In view of the fact that microbes inhabiting Geosciences and Natural Resources such extreme saline environments flourish the contemporary bioprospecting, it was (BGR), Germany aimed to selectively isolate slow growing and rare actinomycetes from the unexplored Reviewed by: Mohammad Ali Amoozegar, solar salterns. A total of 14 slow growing actinomycetes were selectively isolated from University of Tehran, Iran three composite soil samples of inland solar salterns. Among the isolates, four groups Sabrina Hedrich, Federal Institute for were formed according to similarity of the banding patterns obtained by amplified Geosciences and Natural ribosomal DNA restriction analysis (ARDRA). A subset of representative isolates for each Resources, Germany ARDRA group was identified using 16S rDNA sequence based phylogenetic analysis *Correspondence: Solomon Robinson David and subsequently the entire isolates were assigned under three different genera; Jebakumar, Department of Streptomyces, Pseudonocardia, and Actinoalloteichus. The genus Streptomyces was Molecular Microbiology, School of found to be the dominant among the isolates. Furthermore, rare actinomycete genus Biotechnology, Madurai Kamaraj Actinoalloteichus was isolated for the first time from solar saltern.
    [Show full text]
  • Genome-Based Taxonomic Classification of the Phylum
    ORIGINAL RESEARCH published: 22 August 2018 doi: 10.3389/fmicb.2018.02007 Genome-Based Taxonomic Classification of the Phylum Actinobacteria Imen Nouioui 1†, Lorena Carro 1†, Marina García-López 2†, Jan P. Meier-Kolthoff 2, Tanja Woyke 3, Nikos C. Kyrpides 3, Rüdiger Pukall 2, Hans-Peter Klenk 1, Michael Goodfellow 1 and Markus Göker 2* 1 School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom, 2 Department Edited by: of Microorganisms, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Martin G. Klotz, Germany, 3 Department of Energy, Joint Genome Institute, Walnut Creek, CA, United States Washington State University Tri-Cities, United States The application of phylogenetic taxonomic procedures led to improvements in the Reviewed by: Nicola Segata, classification of bacteria assigned to the phylum Actinobacteria but even so there remains University of Trento, Italy a need to further clarify relationships within a taxon that encompasses organisms of Antonio Ventosa, agricultural, biotechnological, clinical, and ecological importance. Classification of the Universidad de Sevilla, Spain David Moreira, morphologically diverse bacteria belonging to this large phylum based on a limited Centre National de la Recherche number of features has proved to be difficult, not least when taxonomic decisions Scientifique (CNRS), France rested heavily on interpretation of poorly resolved 16S rRNA gene trees. Here, draft *Correspondence: Markus Göker genome sequences
    [Show full text]
  • Resource for Scientific Discovery
    RESOU R CE OPEN 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life Supratim Mukherjee1,10, Rekha Seshadri1,10, Neha J Varghese1, Emiley A Eloe-Fadrosh1, Jan P Meier-Kolthoff2 , Markus Göker2 , R Cameron Coates1,9, Michalis Hadjithomas1, Georgios A Pavlopoulos1 , David Paez-Espino1 , Yasuo Yoshikuni1, Axel Visel1 , William B Whitman3, George M Garrity4,5, Jonathan A Eisen6, Philip Hugenholtz7 , Amrita Pati1,9, Natalia N Ivanova1, Tanja Woyke1, Hans-Peter Klenk8 & Nikos C Kyrpides1 We present 1,003 reference genomes that were sequenced as part of the Genomic Encyclopedia of Bacteria and Archaea (GEBA) initiative, selected to maximize sequence coverage of phylogenetic space. These genomes double the number of existing type strains and expand their overall phylogenetic diversity by 25%. Comparative analyses with previously available finished and draft genomes reveal a 10.5% increase in novel protein families as a function of phylogenetic diversity. The GEBA genomes recruit 25 million previously unassigned metagenomic proteins from 4,650 samples, improving their phylogenetic and functional interpretation. We identify numerous biosynthetic clusters and experimentally validate a divergent phenazine cluster with potential new chemical structure and antimicrobial activity. This Resource is the largest single release of reference genomes to date. Bacterial and archaeal isolate sequence space is still far from saturated, and future endeavors in this direction will continue to be a valuable resource for scientific discovery. Systematic surveys of the diversity of cultivated microorganisms have subsequent experiments. Typically, a type strain has well-character- lagged behind improvements in sequencing technologies. Traditionally, ized taxonomic and phenotypic data, isolation source metadata, and most isolate sequencing projects are chosen based on the clinical or other criteria, as defined by the International Code of Nomenclature biotechnological relevance of the target organisms or their physiology1.
    [Show full text]
  • Identifying Untapped Microbial Resources in the Marine Sponge Microbiome
    Identifying untapped microbial resources in the marine sponge microbiome A thesis submitted for the award of Doctor of Philosophy at School of Medicine, Faculty of Medicine, Nursing and Health Sciences, Flinders University Qi Yang December 2016 i TABLE OF CONTENTS LIST OF TABLES .......................................................................................................... vi LIST OF FIGURES....................................................................................................... viii LIST OF ABBREVIATIONS ............................................................................................ x SUMMARY .................................................................................................................... xii DECLARATION ........................................................................................................... xiv ACKNOWLEDGEMENTS ............................................................................................. xv Chapter 1: Introduction ................................................................................................. 1 1.1 Sponge molecular taxonomy ......................................................................................... 1 1.1.1 Sponge taxonomy: from morphology to molecular ...................................................... 3 1.1.2 Various DNA markers for sponge molecular taxonomy .............................................. 5 1.1.3 Phylogenetic classification: update of Demospongiae (class) sponge ........................ 9 1.2
    [Show full text]
  • Dissertation
    DISSERTATION Titel der Dissertation Community structure and distribution of functional microbial groups within two complex environments: microorganisms associated with marine sponges and potential sulfur-compounds-reducing microorganisms in peatlands. angestrebter akademischer Grad Doktorin der Naturwissenschaften (Dr. rer.nat.) Verfasserin / Verfasser: Doris Steger Matrikel-Nummer: 9803561 Dissertationsgebiet (lt. Stu- 444 Ökologie dienblatt): Betreuerin / Betreuer: Univ.-Prof. Dr. Michael Wagner Wien, am 18 März 2010 Formular Nr.: A.04 Contents Outline ......1 Part I Sulfate reducers in peatlands Introduction 5 Microorganisms with Novel Dissimilatory (Bi)Sulfite Reductase Genes are Widespread in Geographically Distant, Low-Sulfate Peatlands .21 Part II Hybridization regimes in DNA microarray experiments Introduction .....79 Spatial Gradients of Target Nucleic Acids Govern DNA Microarray Hybridization Assays ..87 Part III Microorganisms in marine Sponges Introduction 113 Sponge-Associated Microorganisms: Evolution, Ecology, and Biotechnological Potential .125 Diversity and Mode of Transmission of Ammoniaoxidizing Archaea in Marine Sponges .195 Part IV Summary ....205 Appendix ..211 Outline Part I of this thesis describes the analysis of dsrAB-carrying microorganisms in terrestrial wetlands. Newly developed tools such as a functional gene microarray, quantitative PCR assays and dsrB based denaturing gradient gel electrophoresis as well as clone libraries were applied to unravel the widespread occurrence of deep-branching dsrAB lineages, which outnumbered characterized dsrAB lineages in the Schlöppnerbrunnen fen system. Part II validates the signal variability in DNA microarray hybridizations. A simplified microarray format and numerical simulation tests were applied to investigate systematic variations in detected signal intensities and to explore underlying mechanisms of observed spatial gradients. Part III gives a comprehensive overview on the community structure of sponge associated microorganisms.
    [Show full text]
  • Greek–Russian–English Alphabets
    Greek–Russian–English Alphabets Greek letter Greek name English equivalent Russian letter English equivalent Α a Alpha (a¨) Аа(a¨) Β b Beta (b) Бб(b) Вв(v) GgGamma (g) Гг(g) DdDelta (d) Дд(d) Ε e Epsilon (e) Ее(ye) Ζ z Zeta (z) Жж(zh) Зз(z) Η Z Eta (a¯) Ии(i, e¯) YyTheta (th) Йй(e¯) Ι i Iota (e¯) Кк(k) Лл(l) Κ k Kappa (k) Мм(m) LlLambda (l) Нн(n) Оо(oˆ,o) Μ m Mu (m) Оо(oˆ,o) Пп(p) Ν n Nu (n) Рр(r) XxXi (ks) Сс(s) Тт(t) ΟοOmicron a Ууo¯o¯ PpPi (P) Фф(f) Хх(kh) Ρ r Rho (r) Хх(kh) Цц(ts) SsSigma (s) Чч(ch) Τ t Tau (t) Шш(sh) Υ v Upsilon (u¨,o¯o¯) Щщ(shch) Ъъ8 F ø Phi (f) Ыы(e¨) Χ w Chi (H) Ьь(e¨) CcPsi (ps) Ээ(e) Юю(u¯) OoOmega (o¯) Яя(ya¨) 1088 Greek–Russian–English Alphabets English–Greek–Latin numbers English Greek Latin 1 mono uni 2 bis di 3 tris Tri 4 tetrakis tetra 5 pentakis penta 6 hexakis hexa 7 heptakis hepta 8 octakis octa 9 nonakis nona 10 decakis deca International Union of Pure and Applied Chemistry: Rules Concerning Numerical Terms Used in Organic Chemical Nomenclature (specifically as prefixes for hydrocarbons) 1 mono‐ or hen‐ 10 deca‐ 100 hecta‐ 1000 kilia‐ 2di‐ or do‐ 20 icosa‐ 200 Dicta‐ 2000 dilia‐ 3 tri‐ 0 triaconta‐ 300 tricta‐ 3000 trilia‐ 4 tetra‐ 40 tetraconta‐ 400 tetracta 4000 tetralia‐ 5 penta‐ 50 pentaconta‐ 500 pentactra 5000 pentalia‐ 6 hexa‐ 60 hexaconta‐ 600 Hexacta 6000 hexalia‐ 7 hepta‐ 70 hepaconta‐ 700 heptacta‐ 7000 hepalia‐ 8 octa‐ 80 octaconta‐ 800 ocacta‐ 8000 ocatlia‐ 9 nona‐ 90 nonaconta‐ 900 nonactta‐ 9000 nonalia‐ Source: IUPAC, Commission on Nomenclature of Organic Chemistry (N.
    [Show full text]