DOCSLIB.ORG

Isolation and Characterisation of Uncommon Myxobacteria and Other Marine Bacteria and Their Multilocus Sequences Analyses from Indonesia’S Biodiversity

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Isolation and Characterisation of Uncommon Myxobacteria and Other Marine Bacteria and Their Multilocus Sequences Analyses from Indonesia’S Biodiversity Isolation and characterisation of uncommon myxobacteria and other marine bacteria and their multilocus sequences analyses from Indonesia’s biodiversity Von der Fakultät für Lebenswissenschaften der Technischen Universität Carolo-Wilhelmina zu Braunschweig zur Erlangung des Grades einer Doktorin der Naturwissenschaften (Dr. rer. nat.) genehmigte D i s s e r t a t i o n von Rina Andriyani aus Bandung / Indonesia 1. Referentin oder Referent: Professor Dr. Michael Steinert 2. Referentin oder Referent: Privatdozent Dr. Joachim Wink eingereicht am: 01.03.2021 mündliche Prüfung (Disputation) am: 20.05.2021 Druckjahr 2021 The Entirely Merciful, the Especially Merciful This dissertation is dedicated to my beloved parents and our big family Vorveröffentlichungen der Dissertation Teilergebnisse aus dieser Arbeit wurden mit Genehmigung der Fakultät für Lebenswissenschaften, vertreten durch den Mentor der Arbeit, in folgenden Beiträgen vorab veröffentlicht: Posterbeiträge 1. R. Andriyani, K. I. Mohr, T. Mozef, M. Steinert, J. Wink, “Screening of Indonesian myxobacteria for new antibacterials and antifungals”, The 7th HIPS Symposium, Saarbrücken, 2017. 2. R. Andriyani, E. Sudarman, K. I. Mohr, T. Mozef, M. Steinert, J. Wink, “Compounds from Myxococcus sp. (MxGP53TM) a strain isolated from Indonesian soil”, The 10th International PhD Symposium, HZI, Braunschweig, 2017. 3. R. Andriyani, K. I. Mohr, T. Mozef, M. Steinert, J. Wink, et al., “A novel gliding bacterium of the family Flammeovirgaceae isolated from Bali Beach Indonesia”, The 11th International PhD Symposium, HZI Braunschweig, 2018. 4. R. Andriyani, K. I. Mohr, C. Risdian, T. Mozef, M. Steinert, J. Wink, “Drug discovery pipeline from a gliding bacterium to the isolation of antibacterial compounds by utilizing Indonesian biodiversity”, The 12th International PhD Symposium, HZI Braunschweig, 2019. 1 Preface and acknowledgements First of all, I would like to thank all of German-Indonesian Antiinfective Cooperation’s stakeholders in Germany and Indonesia. Thanks to the Federal Ministry of Education and Research, the Helmholtz Centre for Infection Research, the Graduate School of Helmholtz Centre for Infection Research and the Technische Universität Braunschweig in Germany. Thanks to the Ministry of Research and Technology of Indonesia, the Research Center of Chemistry and the Research Unit for Cleaning Technology in Indonesia. To Dr. Tjandrawati Mozef as the German-Indonesian Antiinfective Cooperation project’s lead collaborator from Indonesia who provided this opportunity and supported me. To the Head of Indonesian Institute of Sciences (LIPI), Dr. L.T. Handoko, the Head of Research Center of Chemistry at that time, Dr. Agus Haryono, the Head of Research Unit for Cleaning Technology (previous and present) Dr. Rike Yudianti and Dr. Ajeng Arum Sari, who gave me the eligibility for receiving this duty. Thanks to the staff as well. To the Director of Helmholtz Centre for Infection Research, the Director of the Graduate School of Helmholtz Centre for Infection Research, the Dean of The Faculty of Life Sciences of Technische Universität Braunschweig, the Head of Microbiology Department of Technische Universität Braunschweig and the staff as well who have assisted me for administration business during this study. Special thanks to my supervisors and thesis committee members, PD Dr. Joachim Wink and Prof. Dr. Michael Steinert. Without the Letter of Acceptance from you, it would have been impossible to receive the Riset-Pro scholarship from the Indonesian government to enrol in the PhD programme in the Technische Universität Braunschweig and the Graduate School of Helmholtz Centre for Infection Research. Also, to Dr. Kathrin I. Mohr and Dr. Raimo Franke as two of the thesis committee members. Thank you for your advice, support, keywords and guidance for my research. 2 To Prof. Marc Stadler as the Department of Microbial Drugs (MWIS) group leader and the staff for allowing me to work in the chemistry laboratory. To the team of Microbial Strain Collection (MISG): Stephanie Schulz, Klaus P. Conrad, Wera Collisi, Jolla Lulla, Birte Trunkwalter and Aileen Gollasch. To all the PhD students, the internship students and the postdoctoral researchers in the Helmholtz Centre for Infection Research, especially in the MISG and MWIS groups, also the PhD students from the Indonesian Institute of Sciences during this period. Thank you for the discussion moments and the togetherness on special occasions. To all teachers and lecturers who have shared their knowledge and broadened my perspective. It is not only about the science; thank you very much for your dedication and professionalism. To all friends everywhere, especially Christina Pape, Rani, Fitri, Okky, Yani, Rossy Chaerun Nisa, Rahma, Amelia, Mba Rere, Ulrike Tarajona, Mango, Uthay, Florian, Perda, Kikin, Astri, Khadija, Kwame, Tanya, Indonesian Moeslem Union of Braunschweig, and Indonesian Students Union of Braunschweig. Thank you for your support and friendship. Thanks to all authors in my references and Google, which made everything easier to find. I would like to thank Enago (www.enago.com) for the English language review. Last but not least, thanks to the Greatest who makes everything possible, has been guiding my soul to think clearly when I felt lost and doubtful. You always send answers, even in an unpredictable way. I have known You deeply in every chapter of my life. 3 CONTENTS Vorveröffentlichungen der Dissertation .............................................................................. 1 Posterbeiträge ...................................................................................................................... 1 Preface and Acknowledgements ......................................................................................... 2 Contents .............................................................................................................................. 4 Abbreviations ...................................................................................................................... 8 Chapter 1. Introduction ..................................................................................................... 11 1.1 Background ................................................................................................................. 11 1.2 Aims ............................................................................................................................ 12 1.3 Objectives ................................................................................................................... 12 1.4 Research location ........................................................................................................ 12 1.5 Research funding ........................................................................................................ 12 Chapter 2. Screening of culturable gliding bacteria isolated from some regions in Indonesia as sources for antiinfective substances .............................................................................. 13 2.1 Background ................................................................................................................ 13 2.2 Hypothesis................................................................................................................... 23 2.3 State of the art ............................................................................................................. 23 2.4 Materials and methods ................................................................................................ 24 2.4.1 Materials ................................................................................................................ 24 2.4.2 Methods.................................................................................................................. 24 2.4.2.1 Isolation of the bacteria .................................................................................... 24 2.4.2.2 Extraction, polymer chain reaction, and sequencing of DNA ......................... 26 2.4.2.2.a Extraction of Genomic DNA ...................................................................... 26 2.4.2.2.b Gel electrophoresis .................................................................................... 27 4 2.4.2.2.c Polymerase chain reaction .......................................................................... 27 2.4.2.2.d Strain identification .................................................................................... 27 2.4.2.3 Antiinfectives bioassay .................................................................................... 28 2.4.2.3.a Sample preparation ..................................................................................... 28 2.4.2.3.b Test strains preparation .............................................................................. 29 2.4.2.3.c Serial dilution test ....................................................................................... 29 2.4.3 Identification of the active compounds ................................................................. 29 2.5 Result and Discussion ................................................................................................. 30 2.5.1 Isolation of myxobacteria ...................................................................................... 30 2.5.2 Bioactivity screening and secondary metabolite analysis on gliding bacteria samples from Indonesia ................................................................................................
Load more

Recommended publications
  • The 2014 Golden Gate National Parks Bioblitz - Data Management and the Event Species List Achieving a Quality Dataset from a Large Scale Event
    National Park Service U.S. Department of the Interior Natural Resource Stewardship and Science The 2014 Golden Gate National Parks BioBlitz - Data Management and the Event Species List Achieving a Quality Dataset from a Large Scale Event Natural Resource Report NPS/GOGA/NRR—2016/1147 ON THIS PAGE Photograph of BioBlitz participants conducting data entry into iNaturalist. Photograph courtesy of the National Park Service. ON THE COVER Photograph of BioBlitz participants collecting aquatic species data in the Presidio of San Francisco. Photograph courtesy of National Park Service. The 2014 Golden Gate National Parks BioBlitz - Data Management and the Event Species List Achieving a Quality Dataset from a Large Scale Event Natural Resource Report NPS/GOGA/NRR—2016/1147 Elizabeth Edson1, Michelle O’Herron1, Alison Forrestel2, Daniel George3 1Golden Gate Parks Conservancy Building 201 Fort Mason San Francisco, CA 94129 2National Park Service. Golden Gate National Recreation Area Fort Cronkhite, Bldg. 1061 Sausalito, CA 94965 3National Park Service. San Francisco Bay Area Network Inventory & Monitoring Program Manager Fort Cronkhite, Bldg. 1063 Sausalito, CA 94965 March 2016 U.S. Department of the Interior National Park Service Natural Resource Stewardship and Science Fort Collins, Colorado The National Park Service, Natural Resource Stewardship and Science office in Fort Collins, Colorado, publishes a range of reports that address natural resource topics. These reports are of interest and applicability to a broad audience in the National Park Service and others in natural resource management, including scientists, conservation and environmental constituencies, and the public. The Natural Resource Report Series is used to disseminate comprehensive information and analysis about natural resources and related topics concerning lands managed by the National Park Service.
    [Show full text]
  • A Polysaccharide-Degrading Marine Bacterium Flammeovirga Sp. MY04 and Its Extracellular Agarase System
    中国科技论文在线 http://www.paper.edu.cn J. Ocean Univ. China (Oceanic and Coastal Sea Research) DOI 10.1007/s11802-012-1929-3 ISSN 1672-5182, 2012 11 (3): 375-382 http://www.ouc.edu.cn/xbywb/ E-mail:[email protected] A Polysaccharide-Degrading Marine Bacterium Flammeovirga sp. MY04 and Its Extracellular Agarase System HAN Wenjun1), 2), 3), GU Jingyan1), 3), YAN Qiujie2), LI Jungang2), WU Zhihong3), *, GU Qianqun1), *, and LI Yuezhong3) 1) Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, P. R . C hi n a 2) School of Life Science and Biotechnology, Mianyang Normal University, Mianyang 621000, P. R. China 3) State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Jinan 250100, P. R. China (Received February 2, 2012; revised April 8, 2012; accepted May 29, 2012) © Ocean University of China, Science Press and Springer-Verlag Berlin Heidelberg 2012 Abstract Bacteria of the genus Flammeovirga can digest complex polysaccharides (CPs), but no details have been reported re- garding the CP depolymerases of these bacteria. MY04, an agarolytic marine bacterium isolated from coastal sediments, has been identified as a new member of the genus Flammeovirga. The MY04 strain is able to utilize multiple CPs as a sole carbon source and -1 -1 grows well on agarose, mannan, or xylan. This strain produces high concentrations of extracellular proteins (490 mg L ± 18.2 mg L liquid culture) that exhibit efficient and extensive degradation activities on various polysaccharides, especially agarose. These pro- -1 -1 teins have an activity of 310 U mg ± 9.6 U mg proteins.
    [Show full text]
  • Two Independent Retrons with Highly Diverse Reverse Transcriptases In
    Proc. Natl. Acad. Sci. USA Vol. 87, pp. 942-945, February 1990 Biochemistry Two independent retrons with highly diverse reverse transcriptases in Myxococcus xanthus (multicopy single-stranded DNA/2',5'-phosphodiester/codon usage/myxobacteria) SUMIKO INOUYE, PETER J. HERZER, AND MASAYORI INOUYE Department of Biochemistry, University of Medicine and Dentistry of New Jersey, Robert Wood Johnson Medical School, Piscataway, NJ 08854 Communicated by Russell F. Doolittle, November 27, 1989 (received for review September 29, 1989) ABSTRACT A reverse transcriptase (RT) was recently found that the Mx65 retron is highly diverse and independent found in Myxococcus xanthus, a Gram-negative soil bacterium. from the Mx162 retron and that RT associated with the Mx65 This RT has been shown to be associated with a chromosomal retron has only 47% identity with RT for the Mx162 retron. region designated a retron responsible for the synthesis of a peculiar extrachromosomal DNA called msDNA (multicopy single-stranded DNA). We demonstrate that M. xanthus con- MATERIALS AND METHODS tains two independent, unlinked retrons, one for the synthesis Materials. The clone of the 9.0-kilobase (kb) Pst I fragment of msDNA-Mxl62 and the other for msDNA-Mx65. The struc- containing the Mx65 retron was obtained (8). Restriction tural analysis of the retron for msDNA-Mx65 revealed that the enzymes were purchased from New England Biolabs and coding regions for msdRNA (msr) and msDNA (msd), and an Boehringer Mannheim. open reading frame (ORF) downstream of msr are arranged in A deletion mutant strain ofthe Mx162 retron, AmsSX, was the same manner as found for the Mx162 retron.
    [Show full text]
  • CUED Phd and Mphil Thesis Classes
    High-throughput Experimental and Computational Studies of Bacterial Evolution Lars Barquist Queens' College University of Cambridge A thesis submitted for the degree of Doctor of Philosophy 23 August 2013 Arrakis teaches the attitude of the knife { chopping off what's incomplete and saying: \Now it's complete because it's ended here." Collected Sayings of Muad'dib Declaration High-throughput Experimental and Computational Studies of Bacterial Evolution The work presented in this dissertation was carried out at the Wellcome Trust Sanger Institute between October 2009 and August 2013. This dissertation is the result of my own work and includes nothing which is the outcome of work done in collaboration except where specifically indicated in the text. This dissertation does not exceed the limit of 60,000 words as specified by the Faculty of Biology Degree Committee. This dissertation has been typeset in 12pt Computer Modern font using LATEX according to the specifications set by the Board of Graduate Studies and the Faculty of Biology Degree Committee. No part of this dissertation or anything substantially similar has been or is being submitted for any other qualification at any other university. Acknowledgements I have been tremendously fortunate to spend the past four years on the Wellcome Trust Genome Campus at the Sanger Institute and the European Bioinformatics Institute. I would like to thank foremost my main collaborators on the studies described in this thesis: Paul Gardner and Gemma Langridge. Their contributions and support have been invaluable. I would also like to thank my supervisor, Alex Bateman, for giving me the freedom to pursue a wide range of projects during my time in his group and for advice.
    [Show full text]
  • {Replace with the Title of Your Dissertation}
    The Mechanism of Foaming in Deep-Pit Swine Manure Storage A Dissertation SUBMITTED TO THE FACULTY OF UNIVERSITY OF MINNESOTA BY Mi Yan IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF DOCTOR OF PHILOSOPHY Adviser: Bo Hu October, 2016 © Mi Yan 2016 i Acknowledgements There are many people that contribute to this PhD thesis with their work, advice or encouragement. First of all, I would like to thank my advisor Dr. Bo Hu, who gave me the opportunity and long term support to write this dissertation. He gave me the freedom to work on my idea and plans, and gave great suggestions when I need support. There are many difficult time during this research, but there is always great support provided from him, from technical discussion to mental encouragement. I am also grateful to my committee members Dr. Larry Jacobson, Dr. Steve Severtson and Dr. Gerald Shurson. They took time from their tight schedule to make critical remarks and helpful suggestions, as well as their confidence on me and my work. Thanks are also dedicated to several experts, particularly to Dr. Chuck Clanton and David Schmidt for their valuable inputs and inspiring discussions. Besides valuable discussions, Dr. Brian Hetchler and Dr. Neslihan Akdeniz provide a great amount of valuable samples for experiments. I am also grateful to Dr. Michael Sadowsky that provided great help in microbial sequencing analysis, to Dr. LeeAnn Higgins and Dr. Susan Viper that provided great help in proteomic analysis. My colleagues at Bioproducts and Biosystems Engineering played an important role towards the successful completion of this dissertation.
    [Show full text]
  • Eelgrass Sediment Microbiome As a Nitrous Oxide Sink in Brackish Lake Akkeshi, Japan
    Microbes Environ. Vol. 34, No. 1, 13-22, 2019 https://www.jstage.jst.go.jp/browse/jsme2 doi:10.1264/jsme2.ME18103 Eelgrass Sediment Microbiome as a Nitrous Oxide Sink in Brackish Lake Akkeshi, Japan TATSUNORI NAKAGAWA1*, YUKI TSUCHIYA1, SHINGO UEDA1, MANABU FUKUI2, and REIJI TAKAHASHI1 1College of Bioresource Sciences, Nihon University, 1866 Kameino, Fujisawa, 252–0880, Japan; and 2Institute of Low Temperature Science, Hokkaido University, Kita-19, Nishi-8, Kita-ku, Sapporo, 060–0819, Japan (Received July 16, 2018—Accepted October 22, 2018—Published online December 1, 2018) Nitrous oxide (N2O) is a powerful greenhouse gas; however, limited information is currently available on the microbiomes involved in its sink and source in seagrass meadow sediments. Using laboratory incubations, a quantitative PCR (qPCR) analysis of N2O reductase (nosZ) and ammonia monooxygenase subunit A (amoA) genes, and a metagenome analysis based on the nosZ gene, we investigated the abundance of N2O-reducing microorganisms and ammonia-oxidizing prokaryotes as well as the community compositions of N2O-reducing microorganisms in in situ and cultivated sediments in the non-eelgrass and eelgrass zones of Lake Akkeshi, Japan. Laboratory incubations showed that N2O was reduced by eelgrass sediments and emitted by non-eelgrass sediments. qPCR analyses revealed that the abundance of nosZ gene clade II in both sediments before and after the incubation as higher in the eelgrass zone than in the non-eelgrass zone. In contrast, the abundance of ammonia-oxidizing archaeal amoA genes increased after incubations in the non-eelgrass zone only. Metagenome analyses of nosZ genes revealed that the lineages Dechloromonas-Magnetospirillum-Thiocapsa and Bacteroidetes (Flavobacteriia) within nosZ gene clade II were the main populations in the N2O-reducing microbiome in the in situ sediments of eelgrass zones.
    [Show full text]
  • The Sunlit Microoxic Niche of the Archaeal Eukaryotic Ancestor Comes 2 to Light
    bioRxiv preprint doi: https://doi.org/10.1101/385732; this version posted August 20, 2018. 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. 1 The sunlit microoxic niche of the archaeal eukaryotic ancestor comes 2 to light 3 4 Paul-Adrian Bulzu1#, Adrian-Ştefan Andrei2#, Michaela M. Salcher3, Maliheh Mehrshad2, 5 Keiichi Inoue5, Hideki Kandori6, Oded Beja4, Rohit Ghai2*, Horia L. Banciu1,7 6 1Department of Molecular Biology and Biotechnology, Faculty of Biology and Geology, Babeş-Bolyai 7 University, Cluj-Napoca, Romania 8 2Institute of Hydrobiology, Department of Aquatic Microbial Ecology, Biology Centre of the Academy 9 of Sciences of the Czech Republic, České Budějovice, Czech Republic. 10 3Limnological Station, Institute of Plant and Microbial Biology, University of Zurich, Seestrasse 187, 11 CH-8802 Kilchberg, Switzerland. 12 4Faculty of Biology, Technion Israel Institute of Technology, Haifa, Israel. 13 5The Institute for Solid State Physics, The University of Tokyo, Kashiwa, Japan 14 6Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Nagoya, Japan. 15 7Molecular Biology Center, Institute for Interdisciplinary Research in Bio-Nano-Sciences, Babeş- 16 Bolyai University, Cluj-Napoca, Romania 17 18 19 20 21 # These authors contributed equally to this work 22 *Corresponding author: Rohit Ghai 23 Institute of Hydrobiology, Department of Aquatic Microbial Ecology, Biology Centre of the Academy 24 of Sciences of the Czech Republic, Na Sádkách 7, 370 05, České Budějovice, Czech Republic.
    [Show full text]
  • Isolation, Antimicrobial Activity of Myxobacterial Crude Extracts and Identification of the Most Potent Strains
    Arch Biol Sci. 2017;69(3):561-568 https://doi.org/10.2298/ABS161011132C Isolation, antimicrobial activity of myxobacterial crude extracts and identification of the most potent strains Ivana Charousová*, Juraj Medo and Soňa Javoreková Department of Microbiology, Faculty of Biotechnology and Food Sciences, Slovak University of Agriculture in Nitra, Tr. A. Hlinku 2, 949 76 Nitra, Slovakia *Corresponding author: [email protected] Received: October 11, 2016; Revised: November 14, 2016; Accepted: November 18, 2016; Published online: December 14, 2016 Abstract: Broad spectrum antimicrobial agents are urgently needed to fight frequently occurring multidrug-resistant pathogens. Myxobacteria have been regarded as “microbe factories” for active secondary metabolites, and therefore, this study was performed to isolate two bacteriolytic genera of myxobacteria, Myxococcus sp. and Corallococcus sp., from 10 soil/sand samples using two conventional methods followed by purification with the aim of determining the antimicrobial activity of methanol extracts against 11 test microorganisms (four Gram-positive, four Gram-negative, two yeasts and one fungus). Out of thirty-nine directly observed strains, 23 were purified and analyzed for antimicrobial activities. Based on the broth microdilution method, a total of 19 crude extracts showed antimicrobial activity. The range of inhibited wells was more important in the case of anti-Gram-positive-bacterial activity in comparison with the anti-Gram-negative-bacterial and antifungal activity. In light of the established degree and range of antimicrobial activity, two of the most active isolates (BNEM1 and SFEC2) were selected for further characterization. Morphological parameters and a sequence similarity search by BLAST revealed that they showed 99% sequence similarity to Myxococcus xanthus − BNEM1 (accession no.
    [Show full text]
  • Microbiome Exploration of Deep-Sea Carnivorous Cladorhizidae Sponges
    Microbiome exploration of deep-sea carnivorous Cladorhizidae sponges by Joost Theo Petra Verhoeven A Thesis submitted to the School of Graduate Studies in partial fulfillment of the requirements for the degree of Doctor of Philosophy Department of Biology Memorial University of Newfoundland March 2019 St. John’s, Newfoundland and Labrador ABSTRACT Members of the sponge family Cladorhizidae are unique in having replaced the typical filter-feeding strategy of sponges by a predatory lifestyle, capturing and digesting small prey. These carnivorous sponges are found in many different environments, but are particularly abundant in deep waters, where they constitute a substantial component of the benthos. Sponges are known to host a wide range of microbial associates (microbiome) important for host health, but the extent of the microbiome in carnivorous sponges has never been extensively investigated and their importance is poorly understood. In this thesis, the microbiome of two deep-sea carnivorous sponge species (Chondrocladia grandis and Cladorhiza oxeata) is investigated for the first time, leveraging recent advances in high-throughput sequencing and through custom developed bioinformatic and molecular methods. Microbiome analyses showed that the carnivorous sponges co-occur with microorganisms and large differences in the composition and type of associations were observed between sponge species. Tissues of C. grandis hosted diverse bacterial communities, similar in composition between individuals, in stark contrast to C. oxeata where low microbial diversity was found with a high host-to-host variability. In C. grandis the microbiome was not homogeneous throughout the host tissue, and significant shifts occured within community members across anatomical regions, with the enrichment of specific bacterial taxa in particular anatomical niches, indicating a potential symbiotic role of such taxa within processes like prey digestion and chemolithoautotrophy.
    [Show full text]
  • The Gut Microbiome of the Sea Urchin, Lytechinus Variegatus, from Its Natural Habitat Demonstrates Selective Attributes of Micro
    FEMS Microbiology Ecology, 92, 2016, fiw146 doi: 10.1093/femsec/fiw146 Advance Access Publication Date: 1 July 2016 Research Article RESEARCH ARTICLE The gut microbiome of the sea urchin, Lytechinus variegatus, from its natural habitat demonstrates selective attributes of microbial taxa and predictive metabolic profiles Joseph A. Hakim1,†, Hyunmin Koo1,†, Ranjit Kumar2, Elliot J. Lefkowitz2,3, Casey D. Morrow4, Mickie L. Powell1, Stephen A. Watts1,∗ and Asim K. Bej1,∗ 1Department of Biology, University of Alabama at Birmingham, 1300 University Blvd, Birmingham, AL 35294, USA, 2Center for Clinical and Translational Sciences, University of Alabama at Birmingham, Birmingham, AL 35294, USA, 3Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA and 4Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, 1918 University Blvd., Birmingham, AL 35294, USA ∗Corresponding authors: Department of Biology, University of Alabama at Birmingham, 1300 University Blvd, CH464, Birmingham, AL 35294-1170, USA. Tel: +1-(205)-934-8308; Fax: +1-(205)-975-6097; E-mail: [email protected]; [email protected] †These authors contributed equally to this work. One sentence summary: This study describes the distribution of microbiota, and their predicted functional attributes, in the gut ecosystem of sea urchin, Lytechinus variegatus, from its natural habitat of Gulf of Mexico. Editor: Julian Marchesi ABSTRACT In this paper, we describe the microbial composition and their predictive metabolic profile in the sea urchin Lytechinus variegatus gut ecosystem along with samples from its habitat by using NextGen amplicon sequencing and downstream bioinformatics analyses. The microbial communities of the gut tissue revealed a near-exclusive abundance of Campylobacteraceae, whereas the pharynx tissue consisted of Tenericutes, followed by Gamma-, Alpha- and Epsilonproteobacteria at approximately equal capacities.
    [Show full text]
  • Emended Descriptions of the Genera Myxococcus and Corallococcus, Typification of the Species Myxococcus Stipitatus and Myxococcu
    International Journal of Systematic and Evolutionary Microbiology (2009), 59, 2122–2128 DOI 10.1099/ijs.0.003566-0 Emended descriptions of the genera Myxococcus and Corallococcus, typification of the species Myxococcus stipitatus and Myxococcus macrosporus and a proposal that they be represented by neotype strains. Request for an Opinion Elke Lang and Erko Stackebrandt Correspondence DSMZ – Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Inhoffenstr. Elke Lang 7B, 38124 Braunschweig Germany [email protected] The genus Corallococcus was separated from the genus Myxococcus mainly on the basis of differences in morphology and consistency of swarms and fruiting bodies of the respective members. Phylogenetic, chemotaxonomic and physiological evidence is presented here that underpins the separate status of these phylogenetically neighbouring genera. Emended descriptions of the two genera are presented. The data also suggest that the species Corallococcus macrosporus belongs to the genus Myxococcus. To the best of our knowledge, the type strains of the species Myxococcus macrosporus and Myxococcus stipitatus are not available from any established culture collection or any other source. A Request for an Opinion is made regarding the proposal that strain Cc m8 (5DSM 14697 5CIP 109128) be formally recognized as the neotype strain for the species Myxococcus macrosporus, replacing the designated type strain Windsor M271T, and that strain Mx s8 (5DSM 14675 5JCM 12634) be formally recognized as the neotype strain for the species Myxococcus stipitatus, replacing the designated type strain Windsor M78T. Introduction The genus Myxococcus was described by Thaxter (1892), Within the family Myxococcaceae, delineation of genera, who first recognized that the myxobacteria, formerly descriptions of species and affiliations of strains to species assigned to the fungi, were in fact bacteria.
    [Show full text]
  • Biodiversity of the Hypersaline Urmia Lake National Park (NW Iran)
    Diversity 2014, 6, 102-132; doi:10.3390/d6010102 OPEN ACCESS diversity ISSN 1424-2818 www.mdpi.com/journal/diversity Review Biodiversity of the Hypersaline Urmia Lake National Park (NW Iran) Alireza Asem 1,†,*, Amin Eimanifar 2,†,*, Morteza Djamali 3, Patricio De los Rios 4 and Michael Wink 2 1 Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China 2 Institute of Pharmacy and Molecular Biotechnology (IPMB), Heidelberg University, Im Neuenheimer Feld 364, Heidelberg D-69120, Germany; E-Mail: [email protected] 3 Institut Méditerranéen d’Ecologie et de Paléoécologie UMR 6116 du CNRS-Europôle Méditerranéen de l’Arbois-Pavillon Villemin-BP 80, Aix-en-Provence Cedex 04 13545, France; E-Mail: [email protected] 4 Environmental Sciences School, Natural Resources Faculty, Catholic University of Temuco, Casilla 15-D, Temuco 4780000, Chile; E-Mail: [email protected] † These authors contributed equally to this work. * Authors to whom correspondence should be addressed; E-Mails: [email protected] (A.A.); [email protected] (A.E.); Tel.: +86-150-6624-4312 (A.A.); Fax: +86-532-8203-2216 (A.A.); Tel.: +49-6221-544-880 (A.E.); Fax: +49-6221-544-884 (A.E.). Received: 3 December 2013; in revised form: 13 January 2014 / Accepted: 27 January 2014 / Published: 10 February 2014 Abstract: Urmia Lake, with a surface area between 4000 to 6000 km2, is a hypersaline lake located in northwest Iran. It is the saltiest large lake in the world that supports life. Urmia Lake National Park is the home of an almost endemic crustacean species known as the brine shrimp, Artemia urmiana.
    [Show full text]