DOCSLIB.ORG

Physiology of Pseudovibrio Sp. FO-BEG1 – a Facultatively Oligotrophic and Metabolically Versatile Bacterium

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Physiology of Pseudovibrio Sp. FO-BEG1 – a Facultatively Oligotrophic and Metabolically Versatile Bacterium Physiology of Pseudovibrio sp. FO-BEG1 – a facultatively oligotrophic and metabolically versatile bacterium Dissertation zur Erlangung des Doktorgrades der Naturwissenschaften - Dr. rer. nat. - dem Fachbereich Biologie/Chemie der Universität Bremen vorgelegt von Vladimir Bondarev Bremen, Februar 2012 Die vorliegende Arbeit wurde in der Zeit von Januar 2008 bis Februar 2012 am Max-Planck- Institut für Marine Mikrobiologie in Bremen angefertigt. 1. Gutachterin: Prof. Dr. Heide Schulz-Vogt 2. Gutachter: Prof. Dr. Ulrich Fischer 3. Prüfer: Prof. Dr. Rudolf Amann 4. Prüfer: PD Dr. Jens Harder Table of contents Summary 4 Zusammenfassung 6 Chapter I General introduction 8 The genus Pseudovibrio 9 Sponges and sponge-bacteria associations 13 Bacterial secretion systems and their role in symbiosis 16 Type III secretion system 16 Type VI secretion system 18 Oligotrophy in the oceans and bacterial adaptations 19 Phosphorus in oceanic environments 20 Phosphate limitation and the Pho regulon 23 Aim of the thesis 25 Chapter II The genus Pseudovibrio contains metabolically versatile and symbiotically interacting bacteria 34 Chapter III Isolation of facultatively oligotrophic bacteria 107 Chapter IV Pseudovibrio denitrificansT versus Pseudovibrio sp. FO-BEG1 – a comparison 121 Chapter V Response to phosphate limitation in Pseudovibrio sp. strain FO-BEG1 138 Chapter VI General conclusions 185 New aspects of the physiology of Pseudovibrio spp.-related strains 186 Pseudovibrio sp. FO-BEG1: a facultative symbiont of marine invertebrates 190 Phosphate starvation of Pseudovibrio sp. FO-BEG1 and implications for the environment 193 Pseudovibrio sp. strains FO-BEG1 and JE062 belong to the Pseudovibrio denitrificans species 200 Perspectives 201 Acknowledgments 210 Summary Bacteria belonging to the genus Pseudovibrio are frequently found in marine habitats, mainly in association with sponges, corals and tunicates. Particularly sponges harbor populations of Pseudovibrio spp.-related bacteria, which led to the proposal that this genus contains sponge symbionts. However, the physiology of the genus Pseudovibrio is insufficiently studied and hardly anything is known about its relevance in the environment. In the course of this thesis, the Pseudovibrio strain FO-BEG1 was investigated. It had previously been enriched together with the sulfide oxidizing Beggiatoa sp. 35Flor from a black band diseased coral and was eventually cultured axenically, permitting sequencing of the genome as well as metabolic studies and investigations of physiological changes under different growth conditions. The results of the genomic and physiological analyses of Pseudovibrio strain FO- BEG1 are described in Chapter II. Strain FO-BEG1 was shown to be a generalistic bacterium with a versatile metabolism, capable of importing and oxidizing a wide range of organic and inorganic compounds to meet its carbon, nitrogen, phosphorous and energy requirements under oxic and anoxic conditions. Furthermore, the genomic analysis of strain FO-BEG1 revealed adaptations to a eukaryote-associated life style. Genes that could promote bacteria-host interactions and facilitate attachment or invasion of host cells were identified in the genome of Pseudovibrio sp. FO-BEG1. Interestingly, comparative genomics with Pseudovibrio strain JE062, a strain that has been isolated from a sponge, demonstrated the presence of almost identical physiological and symbiosis-related features in the genome of the sponge-associated isolate, indicating a close relationship of both strains. Additionally, strain FO-BEG1 was shown to grow under extreme nutrient limitation, which has been studied along with the isolation of other bacteria capable to grow in nutrient-rich and -depleted environments, as shown in Chapter III. In Chapter IV, the phylogenetic affiliation of Pseudovibrio sp. FO-BEG1 is discussed. This question is resolved by using a polyphasic approach and comparing the genotypic and phenotypic data with the Pseudovibrio denitrificans type strain. It is suggested that Pseudovibrio sp. FO-BEG1 represents a new strain within the P. denitrificans species and not a new species within the genus Pseudovibrio, because the two strains are physiologically very - 4 - similar and the genotypic analysis revealed values which are only at the border of justifying the description of a new species. Growth under phosphate limited conditions, as described in Chapter V, induces an adaptive response in Pseudovibrio sp. FO-BEG1, characterized by the secretion of a yellow component into the medium. Detailed chemical, physiological and proteomic analysis were performed to characterize changes in the metabolism of Pseudovibrio sp. FO-BEG1 cells grown under phosphate limitation and phosphate surplus. Along with secretion of yet unidentified metabolites, FO-BEG1 cells regulate the expression of proteins involved in many different cellular processes like cell envelope modification and oxidative stress response and induce the expression of enzymes required for degradation of phosphorus-containing molecules as well as high-affinity transporters for phosphates and phosphonates. Furthermore, initial analysis of secreted metabolites was performed using a Fourier transform ion cyclotron resonance mass spectrometer, which will help to chemically and structurally characterize the extracellular compounds. - 5 - Zusammenfassung Bakterien, die zur Gattung Pseudovibrio gehören, findet man in marinen Habitaten, hauptsächlich assoziiert mit Schwämmen, Korallen und Tunikaten. Insbesondere werden Schwämme von Pseudovibrio spp.-verwandten Bakterien besiedelt, was zu der Vermutung führte, dass die Gattung Pseudovibrio auch Symbionten von Schwämmen einschließt. Allerdings ist die Physiologie dieser Bakterien noch unzureichend untersucht. Auch die Auswirkungen des Metabolismus und die daraus resultierende Relevanz für den marinen Lebensraum sind ungeklärt. In der vorliegenden Dissertation wurde der Stamm Pseudovibrio sp. FO-BEG1 untersucht. Wurde der Stamm FO-BEG1 anfänglich zusammen mit dem sulfidoxidierenden Bakterium Beggiatoa sp. 35Flor aus einer von der Schwarzband- Krankheiten befallenen Koralle angereichert, so wird er derzeit axenisch kultiviert. Das Vorhandensein dieser Reinkultur ermöglichte die Sequenzierung des Genoms von Pseudovibrio sp. FO-BEG1, sowie Untersuchungen über den Metabolismus und den physiologischen Veränderungen bei unterschiedlichen Wachstumsbedingungen. Die Ergebnisse der genomischen und physiologischen Analyse von Pseudovibrio sp. FO-BEG1 sind in Kapitel II dargestellt. Es wurde gezeigt, dass Stamm FO-BEG1 ein generalistisches Bakterium mit einem vielfältigen Metabolismus ist. Es hat die Fähigkeit, viele unterschiedliche organische und anorganische Substanzen aufzunehmen und zu oxidieren, um seine Kohlenstoff-, Stickstoff-, Phosphor- und Energieversorgung unter oxischen und anoxischen Bedingungen zu gewährleisten. Weiterhin wurde bei der genomischen Untersuchung festgestellt, dass Stamm FO-BEG1 Anpassungen an eine Eukaryoten-assozierte Lebensweise aufweist. Es wurden Gene identifiziert, die für Interaktionen zwischen Bakterien und dem Wirt sowie die Anhaftung oder das Eindringen in die Wirtszellen notwendig sein können. Zusätzlich wurde das Genom eines zweiten Stammes, Pseudovibrio sp. JE062, der direkt aus einem Schwamm isoliert wurde, für vergleichende Genomik verwendet. Es wurde festgestellt, dass die untersuchten physiologischen und symbiotischen Eigenschaften, die bei Pseudovibrio sp. FO-BEG1 identifiziert wurden, auf genetischer Ebene fast identisch im Stamm JE062 vorliegen, was darauf hinweist, dass die Stämme FO-BEG1 und JE062 miteinander nah verwandt sind. Zusätzlich konnte gezeigt werden, dass Pseudovibrio sp. FO-BEG1 unter extremer Nährstofflimitierung wachsen kann. Dieser Aspekt wurde, im Vergleich mit anderen Bakterien, die unter Nährstoffmangel sowie Nährstoffüberfluss leben können, genauer in Kapitel III untersucht. - 6 - In Kapitel IV wird auf genotypischer und phänotypscher Ebene die phylogenetische Zugehörigkeit von Pseudovibrio sp. FO-BEG1 in einer vergleichenden, polyphasischen Untersuchung mit dem Pseudovibrio denitrificans Typstamm diskutiert. Die Resultate deuten darauf hin, dass Pseudovibrio sp. FO-BEG1 einen neuen Stamm innerhalb der P. denitrificans Spezies darstellt. Für die Beschreibung einer neuen Pseudovibrio Spezies konnten nicht genügend physiologische und genotypische Unterschiede zwischen P. denitrificansT und dem Stamm FO-BEG1 festgestellt werden. In Kapitel V wird die adaptive Antwort von Pseudovibrio sp. FO-BEG1 auf Phosphatlimitierung, die durch die Ausscheidung einer gelben Substanz ins Medium charakterisiert ist, diskutiert. Chemische, physiologische und proteomische Untersuchungen wurden durchgeführt, um die Unterschiede zwischen Pseudovibrio sp. FO-BEG1 Zellen, die unter Phosphatlimitierung bzw. -überfluss gewachsen sind, zu charakterisieren. Neben der Sekretion von bisher unidentifizierten Metaboliten verändern FO-BEG1 Zellen unter Phosphatlimitierung die Expression von Proteinen, die an verschiedenen zellulären Prozessen beteiligt sind. Zum Beispiel führt Phosphatlimitierung zur Modifikation der Zellmembran, zur Induktion von Proteinen zum Schutz vor oxidativem Stress und auch zur Induktion von Enzymen für den Abbau phosphorhaltiger Verbindungen. Außerdem ist die Expression hochaffiner Transporter für Phosphate und Phosphonate hochreguliert. Darüber hinaus wurden erste Analysen der ausgeschiedenen Metabolite mittels Fouriertransformations- Ionenzyklotronresonanz-Massenspektrometrie
Load more

Recommended publications
  • Bismis-2016 Abstract Book
    BISMiS-2016 Abstract Book Third Meeting of Bergey's International Society for Microbial Systematics on Microbial Systematics and Metagenomics September 12-15, 2016 | Pune, INDIA PUNE UNIT Abstracts - Opening Address - Keynotes Abstract Book | BISMiS-2016 | Pune, India Opening Address TAXONOMY OF PROKARYOTES - NEW CHALLENGES IN A GLOBAL WORLD Peter Kämpfer* Justus-Liebig-University Giessen, HESSEN, Germany Email: [email protected] Systematics can be considered as a comprehensive science, because in science it is an essential aspect in comparing any two or more elements, whether they are genes or genomes, proteins or proteomes, biochemical pathways or metabolomes (just to list a few examples), or whole organisms. The development of high throughput sequencing techniques has led to an enormous amount of data (genomic and other “omic” data) and has also revealed an extensive diversity behind these data. These data are more and more used also in systematics and there is a strong trend to classify and name the taxonomic units in prokaryotic systematics preferably on the basis of sequence data. Unfortunately, the knowledge of the meaning behind the sequence data does not keep up with the tremendous increase of generated sequences. The extent of the accessory genome in any given cell, and perhaps the infinite extent of the pan-genome (as an aggregate of all the accessory genomes) is fascinating but it is an open question if and how these data should be used in systematics. Traditionally the polyphasic approach in bacterial systematics considers methods including both phenotype and genotype. And it is the phenotype that is (also) playing an essential role in driving the evolution.
    [Show full text]
  • A Genomic Journey Through a Genus of Large DNA Viruses
    University of Nebraska - Lincoln DigitalCommons@University of Nebraska - Lincoln Virology Papers Virology, Nebraska Center for 2013 Towards defining the chloroviruses: a genomic journey through a genus of large DNA viruses Adrien Jeanniard Aix-Marseille Université David D. Dunigan University of Nebraska-Lincoln, [email protected] James Gurnon University of Nebraska-Lincoln, [email protected] Irina V. Agarkova University of Nebraska-Lincoln, [email protected] Ming Kang University of Nebraska-Lincoln, [email protected] See next page for additional authors Follow this and additional works at: https://digitalcommons.unl.edu/virologypub Part of the Biological Phenomena, Cell Phenomena, and Immunity Commons, Cell and Developmental Biology Commons, Genetics and Genomics Commons, Infectious Disease Commons, Medical Immunology Commons, Medical Pathology Commons, and the Virology Commons Jeanniard, Adrien; Dunigan, David D.; Gurnon, James; Agarkova, Irina V.; Kang, Ming; Vitek, Jason; Duncan, Garry; McClung, O William; Larsen, Megan; Claverie, Jean-Michel; Van Etten, James L.; and Blanc, Guillaume, "Towards defining the chloroviruses: a genomic journey through a genus of large DNA viruses" (2013). Virology Papers. 245. https://digitalcommons.unl.edu/virologypub/245 This Article is brought to you for free and open access by the Virology, Nebraska Center for at DigitalCommons@University of Nebraska - Lincoln. It has been accepted for inclusion in Virology Papers by an authorized administrator of DigitalCommons@University of Nebraska - Lincoln. Authors Adrien Jeanniard, David D. Dunigan, James Gurnon, Irina V. Agarkova, Ming Kang, Jason Vitek, Garry Duncan, O William McClung, Megan Larsen, Jean-Michel Claverie, James L. Van Etten, and Guillaume Blanc This article is available at DigitalCommons@University of Nebraska - Lincoln: https://digitalcommons.unl.edu/ virologypub/245 Jeanniard, Dunigan, Gurnon, Agarkova, Kang, Vitek, Duncan, McClung, Larsen, Claverie, Van Etten & Blanc in BMC Genomics (2013) 14.
    [Show full text]
  • Genus-Wide Comparison of Pseudovibrio Bacterial Genomes Reveal Diverse Adaptations to Different Marine Invertebrate Hosts
    RESEARCH ARTICLE Genus-wide comparison of Pseudovibrio bacterial genomes reveal diverse adaptations to different marine invertebrate hosts Anoop Alex1,2*, Agostinho Antunes1,2* 1 CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Porto, Portugal, 2 Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal * [email protected] (AA); [email protected] (AA) a1111111111 a1111111111 a1111111111 a1111111111 Abstract a1111111111 Bacteria belonging to the genus Pseudovibrio have been frequently found in association with a wide variety of marine eukaryotic invertebrate hosts, indicative of their versatile and symbiotic lifestyle. A recent comparison of the sponge-associated Pseudovibrio genomes has shed light on the mechanisms influencing a successful symbiotic association with OPEN ACCESS sponges. In contrast, the genomic architecture of Pseudovibrio bacteria associated with Citation: Alex A, Antunes A (2018) Genus-wide other marine hosts has received less attention. Here, we performed genus-wide compara- comparison of Pseudovibrio bacterial genomes reveal diverse adaptations to different marine tive analyses of 18 Pseudovibrio isolated from sponges, coral, tunicates, flatworm, and sea- invertebrate hosts. PLoS ONE 13(5): e0194368. water. The analyses revealed a certain degree of commonality among the majority of https://doi.org/10.1371/journal.pone.0194368 sponge- and coral-associated bacteria. Isolates from other marine invertebrate host, tuni- Editor: Zhi Ruan, Zhejiang University, CHINA cates, exhibited a genetic repertoire for cold adaptation and specific metabolic abilities Received: November 12, 2017 including mucin degradation in the Antarctic tunicate-associated bacterium Pseudovibrio sp. Tun.PHSC04_5.I4. Reductive genome evolution was simultaneously detected in the flat- Accepted: March 1, 2018 worm-associated bacteria and the sponge-associated bacterium P.
    [Show full text]
  • Isolation of an Antimicrobial Compound Produced by Bacteria Associated with Reef-Building Corals
    A peer-reviewed version of this preprint was published in PeerJ on 18 August 2016. View the peer-reviewed version (peerj.com/articles/2275), which is the preferred citable publication unless you specifically need to cite this preprint. Raina J, Tapiolas D, Motti CA, Foret S, Seemann T, Tebben J, Willis BL, Bourne DG. 2016. Isolation of an antimicrobial compound produced by bacteria associated with reef-building corals. PeerJ 4:e2275 https://doi.org/10.7717/peerj.2275 Isolation of an antimicrobial compound produced by bacteria associated with reef-building corals Jean-Baptiste Raina Corresp., 1, 2, 3, 4, 5 , Dianne Tapiolas 2 , Cherie A Motti 2 , Sylvain Foret 3, 6 , Torsten Seemann 7 , Jan Tebben 8, 9 , Bette L Willis 3, 4 , David G Bourne 2, 4 1 Climate Change Cluster (C3), University of Technology Sydney, Sydney, NSW, Australia 2 Australian Institute of Marine Science, Townsville, QLD, Australia 3 James Cook University, Australian Research Council Centre of Excellence for Coral Reef Studies, Townsville, QLD, Australia 4 Marine Biology and Aquaculture, College of Science and Engineering, James Cook University of North Queensland, Townsville, QLD, Australia 5 James Cook University, AIMS@JCU, Townsville, QLD, Australia 6 Research School of Biology, Australian National University, Canberra, ACT, Australia 7 Victorian Life Sciences Computation Initiative, University of Melbourne, Melbourne, Victoria, Australia 8 Section Chemical Ecology, Alfred Wegener Institute, Bremerhaven, Germany 9 University of New South Wales, Sydney, NSW, Australia Corresponding Author: Jean-Baptiste Raina Email address: [email protected] Bacterial communities associated with healthy corals produce antimicrobial compounds that inhibit the colonization and growth of invasive microbes and potential pathogens.
    [Show full text]
  • Lindane Bioremediation Capability of Bacteria Associated with the Demosponge Hymeniacidon Perlevis
    marine drugs Article Lindane Bioremediation Capability of Bacteria Associated with the Demosponge Hymeniacidon perlevis Stabili Loredana 1,2,*, Pizzolante Graziano 2, Morgante Antonio 2, Nonnis Marzano Carlotta 3,4, Longo Caterina 3,4, Aresta Antonella Maria 5, Zambonin Carlo 5, Corriero Giuseppe 3,4 and Alifano Pietro 2 1 Istituto per l’Ambiente Marino Costiero, Unità Operativa di Supporto di Taranto, CNR, Via Roma 3, 74123 Taranto, Italy 2 Dipartimento di Scienze e Tecnologie Biologiche ed Ambientali, Università del Salento, Via Prov.le Lecce Monteroni, 73100 Lecce, Italy; [email protected] (P.G.); [email protected] (M.A.); [email protected] (A.P.) 3 Dipartimento di Biologia, Università di Bari Aldo Moro, 70125 Bari, Italy; [email protected] (N.M.C.); [email protected] (L.C.); [email protected] (C.G.) 4 CoNISMa, Piazzale Flaminio 9, 00196 Roma, Italy 5 Dipartimento di Chimica, Università di Bari Aldo Moro, 70125 Bari, Italy; [email protected] (A.A.M.); [email protected] (Z.C.) * Correspondence: [email protected]; Tel.: +39-0832-298971 Academic Editors: Vassilios Roussis, Efstathia Ioannou and Keith B. Glaser Received: 23 January 2017; Accepted: 27 March 2017; Published: 6 April 2017 Abstract: Lindane is an organochlorine pesticide belonging to persistent organic pollutants (POPs) that has been widely used to treat agricultural pests. It is of particular concern because of its toxicity, persistence and tendency to bioaccumulate in terrestrial and aquatic ecosystems. In this context, we assessed the role of bacteria associated with the sponge Hymeniacidon perlevis in lindane degradation.
    [Show full text]
  • Appendix 1. Validly Published Names, Conserved and Rejected Names, And
    Appendix 1. Validly published names, conserved and rejected names, and taxonomic opinions cited in the International Journal of Systematic and Evolutionary Microbiology since publication of Volume 2 of the Second Edition of the Systematics* JEAN P. EUZÉBY New phyla Alteromonadales Bowman and McMeekin 2005, 2235VP – Valid publication: Validation List no. 106 – Effective publication: Names above the rank of class are not covered by the Rules of Bowman and McMeekin (2005) the Bacteriological Code (1990 Revision), and the names of phyla are not to be regarded as having been validly published. These Anaerolineales Yamada et al. 2006, 1338VP names are listed for completeness. Bdellovibrionales Garrity et al. 2006, 1VP – Valid publication: Lentisphaerae Cho et al. 2004 – Valid publication: Validation List Validation List no. 107 – Effective publication: Garrity et al. no. 98 – Effective publication: J.C. Cho et al. (2004) (2005xxxvi) Proteobacteria Garrity et al. 2005 – Valid publication: Validation Burkholderiales Garrity et al. 2006, 1VP – Valid publication: Vali- List no. 106 – Effective publication: Garrity et al. (2005i) dation List no. 107 – Effective publication: Garrity et al. (2005xxiii) New classes Caldilineales Yamada et al. 2006, 1339VP VP Alphaproteobacteria Garrity et al. 2006, 1 – Valid publication: Campylobacterales Garrity et al. 2006, 1VP – Valid publication: Validation List no. 107 – Effective publication: Garrity et al. Validation List no. 107 – Effective publication: Garrity et al. (2005xv) (2005xxxixi) VP Anaerolineae Yamada et al. 2006, 1336 Cardiobacteriales Garrity et al. 2005, 2235VP – Valid publica- Betaproteobacteria Garrity et al. 2006, 1VP – Valid publication: tion: Validation List no. 106 – Effective publication: Garrity Validation List no. 107 – Effective publication: Garrity et al.
    [Show full text]
  • Pyani Documentation Release 0.2.9
    pyani Documentation Release 0.2.9 Leighton Pritchard Sep 08, 2021 Contents: 1 Build information 1 2 PyPI version and Licensing 3 3 conda version 5 4 Description 7 5 Reporting problems and requesting improvements9 5.1 Citing pyani ..............................................9 5.2 About pyani .............................................. 29 5.3 QuickStart Guide............................................. 29 5.4 Requirements............................................... 33 5.5 Installation Guide............................................ 37 5.6 Basic Use................................................. 42 5.7 Examples................................................. 51 5.8 pyani subcommands.......................................... 51 5.9 Use With a Scheduler.......................................... 55 5.10 Testing.................................................. 57 5.11 Contributing to pyani .......................................... 58 5.12 Licensing................................................. 59 5.13 pyani package.............................................. 60 5.14 Indices and tables............................................ 114 Python Module Index 115 Index 117 i ii CHAPTER 1 Build information 1 pyani Documentation, Release 0.2.9 2 Chapter 1. Build information CHAPTER 2 PyPI version and Licensing 3 pyani Documentation, Release 0.2.9 4 Chapter 2. PyPI version and Licensing CHAPTER 3 conda version If you’re feeling impatient, please head over to the QuickStart Guide 5 pyani Documentation, Release 0.2.9 6 Chapter 3. conda
    [Show full text]
  • Biologically Active Peptides from Marine Proteobacteria: Discussion Article
    vv ISSN: 2640-8007 DOI: https://dx.doi.org/10.17352/ojb LIFE SCIENCES GROUP Received: 12 January, 2021 Mini Review Accepted: 04 February, 2021 Published: 05 February, 2021 *Corresponding author: Komal Anjum, Post Doctorate, Biologically active peptides Department of Medicine and Pharmacy, College of Medicine and Pharmacy, Ocean University of China, China, Email: from marine proteobacteria: Keywords: Marine proteobacteria; Marine peptides; Antimicrobial; Antitumor; Antiviral Discussion article https://www.peertechz.com Komal Anjum* Post Doctorate, Department of Medicine and Pharmacy, College of Medicine and Pharmacy, Ocean University of China, China Abstract Marine bioactive peptides are deliberated as an abundant source of natural products that may give long-hual fi tness, in comparison to other resources. Numerous literature concerning bioactive peptides from marine proteobacteria has been summarized, which shows the possibleness of therapeutic effi cacy comprehensive wide spectra of bioactivities against many infectious agents. Their antimicrobial, antitumor, antiviral, and other bioactivities have gained an attention for the medicine development toward a new fl ow of drug explicate, for therapy and control of several diseases. Nonetheless, the execution of the action of several peptides has been still unexplored. So in this glance, this mini-review is focused on some peptides by which they intervene with microbial infection. This compilation is one of the main extract to be implicit particularly for the conversion of biomolecules into desired medicines. Introduction Antimicrobial peptides from bacteria are classifi ed depending on their route of arrangements (tissue pathway) for The marine microorganisms are considered an unexplored instance the ribosomal (bacteriocin) route or non-ribosomal living creature. It has been noticed that these marine bacteria route.
    [Show full text]
  • Microbial Communities Associated with the Invasive Hawaiian Sponge Mycale Armata
    The ISME Journal (2009) 3, 374–377 & 2009 International Society for Microbial Ecology All rights reserved 1751-7362/09 $32.00 www.nature.com/ismej SHORT COMMUNICATION Microbial communities associated with the invasive Hawaiian sponge Mycale armata Guangyi Wang, Sang-Hwal Yoon and Emilie Lefait Department of Oceanography, University of Hawaii at Manoa, Honolulu, HI, USA Microbial symbionts are fundamentally important to their host ecology, but microbial communities of invasive marine species remain largely unexplored. Clone libraries and Denaturing gradient gel electrophoresis analyses revealed diverse microbial phylotypes in the invasive marine sponge Mycale armata. Phylotypes were related to eight phyla: Proteobacteria, Actinobacteria, Bacter- oidetes, Cyanobacteria, Acidobacteria, Chloroflexi, Crenarchaeota and Firmicutes, with predomi- nant alphaproteobacterial sequences (458%). Three Bacterial Phylotype Groups (BPG1–– associated only with sequence from marine sponges; BPG2––associated with sponges and other marine organisms and BPG3––potential new phylotypes) were identified in M. armata. The operational taxonomic units (OTU) of cluster BPG2-B, belonging to Rhodobacteraceae, are dominant sequences of two clone libraries of M. armata, but constitute only a small fraction of sequences from the non-invasive sponge Dysidea sp. Six OTUs from M. armata were potential new phylotypes because of their low sequence identity with their reference sequences. Our results suggest that M. armata harbors both sponge-specific phylotypes and bacterial phylotypes from other marine organisms. The ISME Journal (2009) 3, 374–377; doi:10.1038/ismej.2008.107; published online 6 November 2008 Subject Category: microbial ecology and functional diversity of natural habitats Keywords: sponge–microbe symbiosis; invasive marine sponges; microbial diversity; Mycale armata Marine invasive species pose a serious threat to the library construction and denaturing gradient gel world’s oceans.
    [Show full text]
  • Culturable Microorganisms Associated with Sea Cucumbers and Microbial Natural Products
    marine drugs Review Culturable Microorganisms Associated with Sea Cucumbers and Microbial Natural Products Lei Chen * , Xiao-Yu Wang, Run-Ze Liu and Guang-Yu Wang * Department of Bioengineering, School of Marine Science and Technology, Harbin Institute of Technology at Weihai, Weihai 264209, China; [email protected] (X.-Y.W.); [email protected] (R.-Z.L.) * Correspondence: [email protected] or [email protected] (L.C.); [email protected] or [email protected] (G.-Y.W.); Tel.: +86-631-5687076 (L.C.); +86-631-5682925 (G.-Y.W.) Abstract: Sea cucumbers are a class of marine invertebrates and a source of food and drug. Numerous microorganisms are associated with sea cucumbers. Seventy-eight genera of bacteria belonging to 47 families in four phyla, and 29 genera of fungi belonging to 24 families in the phylum Ascomycota have been cultured from sea cucumbers. Sea-cucumber-associated microorganisms produce diverse secondary metabolites with various biological activities, including cytotoxic, antimicrobial, enzyme- inhibiting, and antiangiogenic activities. In this review, we present the current list of the 145 natural products from microorganisms associated with sea cucumbers, which include primarily polyketides, as well as alkaloids and terpenoids. These results indicate the potential of the microorganisms associated with sea cucumbers as sources of bioactive natural products. Keywords: sea cucumber; bioactivity; diversity; microorganism; polyketides; alkaloids Citation: Chen, L.; Wang, X.-Y.; Liu, 1. Introduction R.-Z.; Wang, G.-Y. Culturable Sea cucumbers are marine invertebrates that belong to the class Holothuroidea of the Microorganisms Associated with Sea phylum Echinodermata. Globally, there are about 1500 species of sea cucumbers [1], which Cucumbers and Microbial Natural are divided into three subclasses: Aspidochirotacea, Apodacea, and Dendrochirotacea, and Products.
    [Show full text]
  • Macrocyclic Colibactin Induces DNA Double-Strand Breaks Via Copper-Mediated Oxidative Cleavage
    HHS Public Access Author manuscript Author ManuscriptAuthor Manuscript Author Nat Chem Manuscript Author . Author manuscript; Manuscript Author available in PMC 2020 March 16. Published in final edited form as: Nat Chem. 2019 October ; 11(10): 880–889. doi:10.1038/s41557-019-0317-7. Macrocyclic colibactin induces DNA double-strand breaks via copper-mediated oxidative cleavage Zhong-Rui Li1,2, Jie Li4,6, Wenlong Cai2, Jennifer Y. H. Lai1, Shaun M. K. McKinnie4, Wei- Peng Zhang1, Bradley S. Moore4,5, Wenjun Zhang2,3,*, Pei-Yuan Qian1,* 1Department of Ocean Science and Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China. 2Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, USA. 3Chan Zuckerberg Biohub, San Francisco, California 94158, USA. 4Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California 92093, USA. 5Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California 92093, USA. 6Present address: Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina, USA Abstract Colibactin is an assumed human gut bacterial genotoxin, whose biosynthesis is linked to clb genomic island that distributes widespread in pathogenic and commensal human enterobacteria. Colibactin-producing gut microbes promote colon tumor formation and enhance progression of colorectal cancer via DNA double-strand breaks-induced cellular senescence and death; however, the chemical basis contributing to the pathogenesis at the molecular level has not been fully characterized. Here we report the discovery of colibactin-645 a macrocyclic colibactin metabolite that recapitulates the previously assumed genotoxicity and cytotoxicity.
    [Show full text]
  • Anthropogenic Impacts Following Extreme Storms Affect Sponge Health and Bacterial Communities
    On a reef far, far away: Anthropogenic Impacts Following Extreme Storms Affect Sponge Health and Bacterial Communities Supplemental Information Tables -Supplemental Table S1. Metadata for all samples collected -Supplemental Table S2. ANOSIM comparisons of the weighted UniFRAC distance matrix values for sponge bacterial communities by health state -Supplemental Table S3. ANOSIM comparisons of the weighted UniFRAC distance matrix values for healthy sponge bacterial communities by site -Supplemental Table S4. ANOSIM comparisons of the weighted UniFRAC distance matrix values for healthy sponge communities by collection date -Supplemental Table S5. Differentially abundant bacterial Families in healthy sponges and in seawater samples determined by DESeq2 -Supplemental Table S6. Bacterial taxa significantly associated with recent flooding events according to Indicator Species Analysis -Supplemental Table S7. Bacterial strains, primers, and annealing conditions used for qPCR analysis Figures -Supplemental Figure S1. Percent abundance of bacterial Families in a) healthy Xestospongia muta b) healthy Agelas clathrodes, c) Seawater, and d) diseased sponge samples . Supplemental Table S1. Sample Metadata Sample ID Species Collection Date Site* Depth (m) Sample Type AAEa61 Agelas clathrodes 6 August 2016 East Bank - Buoy 4 19.8 - 22.9 Diseased sponge AAEa62 Agelas clathrodes 6 August 2016 East Bank - Buoy 4 19.8 - 22.9 Diseased sponge AAEa63 Agelas clathrodes 6 August 2016 East Bank - Buoy 4 19.8 - 22.9 Diseased sponge AAEa64 Agelas clathrodes 6 August
    [Show full text]