DOCSLIB.ORG

TECHNISCHE UNIVERSITÄT MÜNCHEN Lehrstuhl Für Mikrobielle Ökologie Biodiversität Und Enzymatisches Verderbspotential Von

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
TECHNISCHE UNIVERSITÄT MÜNCHEN Lehrstuhl Für Mikrobielle Ökologie Biodiversität Und Enzymatisches Verderbspotential Von TECHNISCHE UNIVERSITÄT MÜNCHEN Lehrstuhl für Mikrobielle Ökologie Biodiversität und enzymatisches Verderbspotential von Rohmilch-Mikrobiota Mario George Freiherr von Neubeck Vollständiger Abdruck der von der Fakultät „Wissenschaftszentrum Weihenstephan für Ernährung, Landnutzung und Umwelt“ der Technischen Universität München zur Erlangung des akademischen Grades eines Doktors der Naturwissenschaften genehmigten Dissertation. Vorsitzender: Prof. Dr. Ulrich Kulozik Prüfer der Dissertation: 1. Prof. Dr. Siegfried Scherer 2. Prof. Dr. Rudi F. Vogel Die Dissertation wurde am 29.04.2019 bei der Technischen Universität München eingereicht und durch die Fakultät „Wissenschaftszentrum Weihenstephan für Ernährung, Landnutzung und Umwelt“ am 19.09.2019 angenommen. INHALTSVERZEICHNIS INHALTSVERZEICHNIS INHALTSVERZEICHNIS ....................................................................................................... I LISTE DER VORVERÖFFENTLICHUNGEN .................................................................. IV ZUSAMMENFASSUNG ........................................................................................................ V SUMMARY ........................................................................................................................... VII ABBILDUNGSVERZEICHNIS ........................................................................................ VIII TABELLENVERZEICHNIS ................................................................................................ XI ABKÜRZUNGSVERZEICHNIS ....................................................................................... XIV 1 EINLEITUNG........................................................................................................... - 1 - 1.1 Mikrobielle Flora in Rohmilch und Milchhalbfabrikaten und ihre Enzyme ............. - 1 - 1.2 Aufbau und Regulation des apr-Operons der Gattung Pseudomonas....................... - 4 - 1.2.1 Aufbau des apr-Operons........................................................................................ - 4 - 1.2.2 Regulation des apr-Operons .................................................................................. - 6 - 1.3 Taxonomische Einordnung neuer Bakterienarten ..................................................... - 8 - Die Gattung Pseudomonas .............................................................................................. - 10 - 1.4 Zielsetzung der Arbeit ............................................................................................. - 12 - 2 MATERIAL UND METHODEN .......................................................................... - 13 - 2.1 Nährmedien und Lösungen ...................................................................................... - 13 - 2.2 Rohmilchproben, Milchhalbfabrikate, isolierte Mikroorganismen und Referenzstämme ................................................................................................................................. - 17 - 2.2.1 Isolierung von Mikroorganismen aus Rohmilchen und Milchhalbfabrikaten ..... - 19 - 2.2.2 Zur Beschreibung neuer Pseudomonas-Arten verwendete Referenzstämme ...... - 19 - 2.2.3 Zur Genomsequenzierung und Analyse des apr-Operons verwendete Pseudomonas- Stämme ................................................................................................................ - 20 - 2.3 Identifizierung von Mikroorganismen durch FTIR-Spektroskopie ......................... - 21 - 2.4 Charakterisierung von Mikroorganismen zur Auswahl geeigneter FTIR- Referenzdatenbanken .............................................................................................. - 23 - 2.5 Identifizierung repräsentativer Mikroorganismen mittels Gensequenzanalyse ...... - 25 - 2.6 Molekulargenetische Methoden .............................................................................. - 26 - 2.6.1 Isolierung RNA-freier, genomischer DNA.......................................................... - 26 - 2.6.2 Isolierung von Nukleinsäuren durch mechanische Zell-Lyse ............................. - 26 - 2.6.3 In-vitro-Amplifikation von DNA durch Polymerase-Kettenreaktion (PCR) ...... - 27 - 2.6.4 Agarose-Gelelektrophorese ................................................................................. - 29 - I INHALTSVERZEICHNIS 2.6.5 Aufreinigung der PCR-Produkte ......................................................................... - 29 - 2.6.6 DNA-Sequenzierung von PCR-Produkten .......................................................... - 30 - 2.6.7 Genomsequenzierung .......................................................................................... - 30 - 2.7 Bioinformatische Methoden .................................................................................... - 34 - 2.7.1 Einzelgen-Sequenzanalyse .................................................................................. - 34 - 2.7.2 Phylogenetische Sequenzanalyse und Identifizierung potentiell unbekannter Gattungen und Arten............................................................................................ - 35 - 2.7.3 Bestimmung der durchschnittlichen Nukleotid-Übereinstimmung von Genomen untereinander (average nucleotide identity =ANI) .............................................. - 36 - 2.7.4 Vorhersage und Identifizierung von Genen in Genomen .................................... - 37 - 2.8 Charakterisierung neuer Pseudomonas-Arten ......................................................... - 39 - 2.8.1 Phänotypische Charakterisierungen .................................................................... - 39 - 2.8.2 Chemotaxonomische Charakterisierung .............................................................. - 41 - 2.8.3 Hinterlegung in öffentlichen Stammsammlungen ............................................... - 42 - 2.9 Konservierung der isolierten Mikroorganismen ...................................................... - 42 - 2.10 Agardiffusions-Tests zur Visualisierung lipolytischer und proteolytischer Enzyme . - 43 - 2.11 Statistik .................................................................................................................... - 44 - 3 ERGEBNISSE......................................................................................................... - 45 - 3.1 Mikrobielle Biodiversität in Rohmilchen und Milchhalbfabrikaten ....................... - 45 - 3.1.1 Gesamtkeimzahlen der Rohmilchen und Milchhalbfabrikate ............................. - 45 - 3.1.2 Biodiversitäts-Analyse der Rohmilchen und Milchhalbfabrikate ....................... - 49 - 3.2 Lipolytische und proteolytische Aktivität der repräsentativen Mikrobiota ............. - 69 - 3.3 Genetische Variabilität und Phylogenie des apr-Operons der Gattung Pseudomonas ... - 78 - 3.3.1 Untersuchung der genetischen Variabilität des apr-Operons .............................. - 81 - 3.3.2 Untersuchung der Phylogenie des apr-Operons .................................................. - 85 - 3.4 Beschreibung neuer Pseudomonas-Arten ................................................................ - 89 - 3.4.1 Genetische und phylogenetische Analysen ......................................................... - 90 - 3.4.2 Morphologische und physiologische Charakterisierung ................................... - 101 - 3.4.3 Chemotaxonomische Charakterisierung ............................................................ - 106 - 4 DISKUSSION ....................................................................................................... - 111 - 4.1 Biodiversität der Rohmilch- und Milchhalbfabrikat-Mikrobiota .......................... - 111 - 4.2 Lipolytische und proteolytische Aktivität der repräsentativen Mikrobiota ........... - 121 - II INHALTSVERZEICHNIS 4.3 Genetische Variabilität und Phylogenie des apr-Operons der Gattung Pseudomonas ... - 128 - 4.4 Beschreibung neuer Pseudomonas-Arten .............................................................. - 132 - 4.4.1 Neubeschreibung der Arten Pseudomonas helleri sp. nov. und Pseudomonas weihenstephanensis sp. nov. .............................................................................. - 132 - 4.4.2 Neubeschreibung der Arten Pseudomonas lactis sp. nov. und Pseudomonas paralactis sp. nov. ............................................................................................. - 136 - 5 SCHLUSSFOLGERUNG UND AUSBLICK ..................................................... - 142 - 6 ANHANG .............................................................................................................. - 144 - LITERATURVERZEICHNIS ........................................................................................ - 177 - DANKSAGUNG ............................................................................................................... - 202 - III LISTE DER VORVERÖFFENTLICHUNGEN LISTE DER VORVERÖFFENTLICHUNGEN Publikationen Teile der vorliegenden Dissertation wurden bereits vorab veröffentlicht: Schlussbericht zum AiF Projekt 16588 N – „Hitzestabile mikrobielle Enzyme in Rohstoffen zur Milchverarbeitung – Qualitätssicherung, Entwicklung eines Testsystems und technologische Optionen“ vom 15.10.2014. von Neubeck, M., Baur, C., Krewinkel, M., Stoeckel, M., Kranz, B., Stressler, T., Fischer, L., Hinrichs, J., Scherer, S. und Wenning, M. (2015). Biodiversity of refrigerated raw milk microbiota and their enzymatic spoilage potential. International Journal of Food Microbiology 211, 57-65. von Neubeck, M., Huptas, C., Gluck, C., Krewinkel, M., Stoeckel, M., Stressler,
Load more

Recommended publications
  • Metaproteogenomic Insights Beyond Bacterial Response to Naphthalene
    ORIGINAL ARTICLE ISME Journal – Original article Metaproteogenomic insights beyond bacterial response to 5 naphthalene exposure and bio-stimulation María-Eugenia Guazzaroni, Florian-Alexander Herbst, Iván Lores, Javier Tamames, Ana Isabel Peláez, Nieves López-Cortés, María Alcaide, Mercedes V. del Pozo, José María Vieites, Martin von Bergen, José Luis R. Gallego, Rafael Bargiela, Arantxa López-López, Dietmar H. Pieper, Ramón Rosselló-Móra, Jesús Sánchez, Jana Seifert and Manuel Ferrer 10 Supporting Online Material includes Text (Supporting Materials and Methods) Tables S1 to S9 Figures S1 to S7 1 SUPPORTING TEXT Supporting Materials and Methods Soil characterisation Soil pH was measured in a suspension of soil and water (1:2.5) with a glass electrode, and 5 electrical conductivity was measured in the same extract (diluted 1:5). Primary soil characteristics were determined using standard techniques, such as dichromate oxidation (organic matter content), the Kjeldahl method (nitrogen content), the Olsen method (phosphorus content) and a Bernard calcimeter (carbonate content). The Bouyoucos Densimetry method was used to establish textural data. Exchangeable cations (Ca, Mg, K and 10 Na) extracted with 1 M NH 4Cl and exchangeable aluminium extracted with 1 M KCl were determined using atomic absorption/emission spectrophotometry with an AA200 PerkinElmer analyser. The effective cation exchange capacity (ECEC) was calculated as the sum of the values of the last two measurements (sum of the exchangeable cations and the exchangeable Al). Analyses were performed immediately after sampling. 15 Hydrocarbon analysis Extraction (5 g of sample N and Nbs) was performed with dichloromethane:acetone (1:1) using a Soxtherm extraction apparatus (Gerhardt GmbH & Co.
    [Show full text]
  • Arthrobacter Paludis Sp. Nov., Isolated from a Marsh
    TAXONOMIC DESCRIPTION Zhang et al., Int J Syst Evol Microbiol 2018;68:47–51 DOI 10.1099/ijsem.0.002426 Arthrobacter paludis sp. nov., isolated from a marsh Qi Zhang,1 Mihee Oh,1 Jong-Hwa Kim,1 Rungravee Kanjanasuntree,1 Maytiya Konkit,1 Ampaitip Sukhoom,2 Duangporn Kantachote2 and Wonyong Kim1,* Abstract A novel Gram-stain-positive, strictly aerobic, non-endospore-forming bacterium, designated CAU 9143T, was isolated from a hydric soil sample collected from Seogmo Island in the Republic of Korea. Strain CAU 9143T grew optimally at 30 C, at pH 7.0 and in the presence of 1 % (w/v) NaCl. The phylogenetic trees based on 16S rRNA gene sequences revealed that strain CAU 9143T belonged to the genus Arthrobacter and was closely related to Arthrobacter ginkgonis SYP-A7299T (97.1 % T similarity). Strain CAU 9143 contained menaquinone MK-9 (H2) as the major respiratory quinone and diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, two glycolipids and two unidentified phospholipids as the major polar lipids. The whole-cell sugars were glucose and galactose. The peptidoglycan type was A4a (L-Lys–D-Glu2) and the major cellular fatty T acid was anteiso-C15 : 0. The DNA G+C content was 64.4 mol% and the level of DNA–DNA relatedness between CAU 9143 and the most closely related strain, A. ginkgonis SYP-A7299T, was 22.3 %. Based on phenotypic, chemotaxonomic and genetic data, strain CAU 9143T represents a novel species of the genus Arthrobacter, for which the name Arthrobacter paludis sp. nov. is proposed. The type strain is CAU 9143T (=KCTC 13958T,=CECT 8917T).
    [Show full text]
  • S41598-018-29442-2 1
    www.nature.com/scientificreports OPEN Actinobacteria associated with Chinaberry tree are diverse and show antimicrobial activity Received: 28 February 2018 Ke Zhao1, Jing Li1, Meiling Shen1, Qiang Chen1, Maoke Liu2, Xiaolin Ao1, Decong Liao1, Accepted: 10 July 2018 Yunfu Gu1, Kaiwei Xu1, Menggen Ma1, Xiumei Yu1, Quanju Xiang1, Ji Chen1, Xiaoping Zhang1 & Published: xx xx xxxx Petri Penttinen 3,4 Many actinobacteria produce secondary metabolites that include antimicrobial compounds. Since most of the actinobacteria cannot be cultivated, their antimicrobial potential awaits to be revealed. We hypothesized that the actinobacterial endophyte communities inside Melia toosendan (Chinaberry) tree are diverse, include strains with antimicrobial activity, and that antimicrobial activity can be detected using a cultivation independent approach and co-occurrence analysis. We isolated and identifed actinobacteria from Chinaberry, tested their antimicrobial activities, and characterized the communities using amplicon sequencing and denaturing gradient gel electrophoresis as cultivation independent methods. Most of the isolates were identifed as Streptomyces spp., whereas based on amplicon sequencing the most abundant OTU was assigned to Rhodococcus, and Tomitella was the most diverse genus. Out of the 135 isolates, 113 inhibited the growth of at least one indicator organism. Six out of the 7577 operational taxonomic units (OTUs) matched 46 cultivated isolates. Only three OTUs, Streptomyces OTU4, OTU11, and OTU26, and their corresponding isolate groups were available for comparing co-occurrences and antimicrobial activity. Streptomyces OTU4 correlated negatively with a high number of OTUs, and the isolates corresponding to Streptomyces OTU4 had high antimicrobial activity. However, for the other two OTUs and their corresponding isolate groups there was no clear relation between the numbers of negative correlations and antimicrobial activity.
    [Show full text]
  • Diversitat De Comunitats Heteròtrofes Associades a Les Aigües De Consum
    Diversitat de comunitats heteròtrofes associades a les aigües de consum Laura Sala Comorera ADVERTIMENT. La consulta d’aquesta tesi queda condicionada a l’acceptació de les següents condicions d'ús: La difusió d’aquesta tesi per mitjà del servei TDX (www.tdx.cat) i a través del Dipòsit Digital de la UB (diposit.ub.edu) ha estat autoritzada pels titulars dels drets de propietat intel·lectual únicament per a usos privats emmarcats en activitats d’investigació i docència. No s’autoritza la seva reproducció amb finalitats de lucre ni la seva difusió i posada a disposició des d’un lloc aliè al servei TDX ni al Dipòsit Digital de la UB. No s’autoritza la presentació del seu contingut en una finestra o marc aliè a TDX o al Dipòsit Digital de la UB (framing). Aquesta reserva de drets afecta tant al resum de presentació de la tesi com als seus continguts. En la utilització o cita de parts de la tesi és obligat indicar el nom de la persona autora. ADVERTENCIA. La consulta de esta tesis queda condicionada a la aceptación de las siguientes condiciones de uso: La difusión de esta tesis por medio del servicio TDR (www.tdx.cat) y a través del Repositorio Digital de la UB (diposit.ub.edu) ha sido autorizada por los titulares de los derechos de propiedad intelectual únicamente para usos privados enmarcados en actividades de investigación y docencia. No se autoriza su reproducción con finalidades de lucro ni su difusión y puesta a disposición desde un sitio ajeno al servicio TDR o al Repositorio Digital de la UB.
    [Show full text]
  • Evolutionary Genomics of Conjugative Elements and Integrons
    Université Paris Descartes École doctorale Interdisciplinaire Européenne 474 Frontières du Vivant Microbial Evolutionary Genomic, Pasteur Institute Evolutionary genomics of conjugative elements and integrons Thèse de doctorat en Biologie Interdisciplinaire Présentée par Jean Cury Pour obtenir le grade de Docteur de l’Université Paris Descartes Sous la direction de Eduardo Rocha Soutenue publiquement le 17 Novembre 2017, devant un jury composé de: Claudine MÉDIGUE Rapporteure CNRS, Genoscope, Évry Marie-Cécile PLOY Rapporteure Université de Limoges Érick DENAMUR Examinateur Université Paris Diderot, Paris Philippe LOPEZ Examinateur Université Pierre et Marie Curie, Paris Alan GROSSMAN Examinateur MIT, Cambdridge, USA Eduardo ROCHA Directeur de thèse CNRS, Institut Pasteur, Paris ِ عمحمود ُبدرويش َالنرد َم ْن انا ِٔ َقول ُلك ْم ما ا ُقول ُلك ْم ؟ وانا لم أ ُك ْن َ َج ًرا َص َق َل ْت ُه ُالمياه َفأ ْص َب َح ِوهاً و َق َصباً َثق َب ْت ُه ُالرياح َفأ ْص َب َح ًنايا ... انا ِع ُب َالن ْرد ، ا َرب ُح يناً وا َس ُر يناً انا ِم ُثل ُك ْم ا وا قل قليً ... The dice player Mahmoud Darwish Who am I to say to you what I am saying to you? I was not a stone polished by water and became a face nor was I a cane punctured by the wind and became a lute… I am a dice player, Sometimes I win and sometimes I lose I am like you or slightly less… Contents Acknowledgments 7 Preamble 9 I Introduction 11 1 Background for friends and family . 13 2 Horizontal Gene Transfer (HGT) . 16 2.1 Mechanisms of horizontal gene transfer .
    [Show full text]
  • Epidemiological and Molecular Analysis of Virulence and Antibiotic Resistance in Acinetobacter Baumannii
    UNIVERSIDAD COMPLUTENSE DE MADRID FACULTAD DE VETERINARIA DEPARTAMENTO DE BIOQUÍMICA Y BIOLOGÍA MOLECULAR IV TESIS DOCTORAL Epidemiological and Molecular Analysis of Virulence and Antibiotic Resistance in Acinetobacter baumannii Análisis Epidemiológico y Molecular de la Virulencia y la Antibiorresistencia en Acinetobacter baumannii MEMORIA PARA OPTAR AL GRADO DE DOCTOR PRESENTADA POR Elias Dahdouh DIRECTORA Mónica Suárez Rodríguez Madrid, 2017 © Elias Dahdouh, 2016 UNIVERSIDAD COMPLUTENSE DE MADRID FACULTAD DE VETERINARIA DEPARTAMENTO DE BIOQUIMICA Y BIOLOGIA MOLECULAR IV TESIS DOCTORAL Análisis Epidemiológico y Molecular de la Virulencia y la Antibiorresistencia en Acinetobacter baumannii Epidemiological and Molecular Analysis of Virulence and Antibiotic Resistance in Acinetobacter baumannii MEMORIA PARA OPTAR AL GRADO DE DOCTOR PRESENTADA POR Elias Dahdouh Directora Mónica Suárez Rodríguez Madrid, 2016 UNIVERSIDAD COMPLUTENSE DE MADRID FACULTAD DE VETERINARIA Departamento de Bioquímica y Biología Molecular IV ANALYSIS EPIDEMIOLOGICO Y MOLECULAR DE LA VIRULENCIA Y LA ANTIBIORRESISTENCIA EN Acinetobacter baumannii EPIDEMIOLOGICAL AND MOLECULAR ANALYSIS OF VIRULENCE AND ANTIBIOTIC RESISTANCE IN Acinetobacter baumannii MEMORIA PARA OPTAR AL GRADO DE DOCTOR PRESENTADA POR Elias Dahdouh Bajo la dirección de la doctora Mónica Suárez Rodríguez Madrid, Diciembre de 2016 First and foremost, I would like to thank God for the continued strength and determination that He has given me. I would also like to thank my father Abdo, my brother Charbel, my fiancée, Marisa, and all my friends for their endless support and for standing by me at all times. Moreover, I would like to thank Dra. Monica Suarez Rodriguez and Dr. Ziad Daoud for giving me the opportunity to complete this doctoral study and for their guidance, encouragement, and friendship.
    [Show full text]
  • Within-Arctic Horizontal Gene Transfer As a Driver of Convergent Evolution in Distantly Related 2 Microalgae
    bioRxiv preprint doi: https://doi.org/10.1101/2021.07.31.454568; this version posted August 2, 2021. 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 Within-Arctic horizontal gene transfer as a driver of convergent evolution in distantly related 2 microalgae 3 Richard G. Dorrell*+1,2, Alan Kuo3*, Zoltan Füssy4, Elisabeth Richardson5,6, Asaf Salamov3, Nikola 4 Zarevski,1,2,7 Nastasia J. Freyria8, Federico M. Ibarbalz1,2,9, Jerry Jenkins3,10, Juan Jose Pierella 5 Karlusich1,2, Andrei Stecca Steindorff3, Robyn E. Edgar8, Lori Handley10, Kathleen Lail3, Anna Lipzen3, 6 Vincent Lombard11, John McFarlane5, Charlotte Nef1,2, Anna M.G. Novák Vanclová1,2, Yi Peng3, Chris 7 Plott10, Marianne Potvin8, Fabio Rocha Jimenez Vieira1,2, Kerrie Barry3, Joel B. Dacks5, Colomban de 8 Vargas2,12, Bernard Henrissat11,13, Eric Pelletier2,14, Jeremy Schmutz3,10, Patrick Wincker2,14, Chris 9 Bowler1,2, Igor V. Grigoriev3,15, and Connie Lovejoy+8 10 11 1 Institut de Biologie de l'ENS (IBENS), Département de Biologie, École Normale Supérieure, CNRS, 12 INSERM, Université PSL, 75005 Paris, France 13 2CNRS Research Federation for the study of Global Ocean Systems Ecology and Evolution, 14 FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, 75016 Paris, France 15 3 US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 16 Cyclotron Road, Berkeley,
    [Show full text]
  • Which Organisms Are Used for Anti-Biofouling Studies
    Table S1. Semi-systematic review raw data answering: Which organisms are used for anti-biofouling studies? Antifoulant Method Organism(s) Model Bacteria Type of Biofilm Source (Y if mentioned) Detection Method composite membranes E. coli ATCC25922 Y LIVE/DEAD baclight [1] stain S. aureus ATCC255923 composite membranes E. coli ATCC25922 Y colony counting [2] S. aureus RSKK 1009 graphene oxide Saccharomycetes colony counting [3] methyl p-hydroxybenzoate L. monocytogenes [4] potassium sorbate P. putida Y. enterocolitica A. hydrophila composite membranes E. coli Y FESEM [5] (unspecified/unique sample type) S. aureus (unspecified/unique sample type) K. pneumonia ATCC13883 P. aeruginosa BAA-1744 composite membranes E. coli Y SEM [6] (unspecified/unique sample type) S. aureus (unspecified/unique sample type) graphene oxide E. coli ATCC25922 Y colony counting [7] S. aureus ATCC9144 P. aeruginosa ATCCPAO1 composite membranes E. coli Y measuring flux [8] (unspecified/unique sample type) graphene oxide E. coli Y colony counting [9] (unspecified/unique SEM sample type) LIVE/DEAD baclight S. aureus stain (unspecified/unique sample type) modified membrane P. aeruginosa P60 Y DAPI [10] Bacillus sp. G-84 LIVE/DEAD baclight stain bacteriophages E. coli (K12) Y measuring flux [11] ATCC11303-B4 quorum quenching P. aeruginosa KCTC LIVE/DEAD baclight [12] 2513 stain modified membrane E. coli colony counting [13] (unspecified/unique colony counting sample type) measuring flux S. aureus (unspecified/unique sample type) modified membrane E. coli BW26437 Y measuring flux [14] graphene oxide Klebsiella colony counting [15] (unspecified/unique sample type) P. aeruginosa (unspecified/unique sample type) graphene oxide P. aeruginosa measuring flux [16] (unspecified/unique sample type) composite membranes E.
    [Show full text]
  • Within-Arctic Horizontal Gene Transfer As a Driver of Convergent Evolution in Distantly Related 1 Microalgae 2 Richard G. Do
    bioRxiv preprint doi: https://doi.org/10.1101/2021.07.31.454568; this version posted August 2, 2021. 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 Within-Arctic horizontal gene transfer as a driver of convergent evolution in distantly related 2 microalgae 3 Richard G. Dorrell*+1,2, Alan Kuo3*, Zoltan Füssy4, Elisabeth Richardson5,6, Asaf Salamov3, Nikola 4 Zarevski,1,2,7 Nastasia J. Freyria8, Federico M. Ibarbalz1,2,9, Jerry Jenkins3,10, Juan Jose Pierella 5 Karlusich1,2, Andrei Stecca Steindorff3, Robyn E. Edgar8, Lori Handley10, Kathleen Lail3, Anna Lipzen3, 6 Vincent Lombard11, John McFarlane5, Charlotte Nef1,2, Anna M.G. Novák Vanclová1,2, Yi Peng3, Chris 7 Plott10, Marianne Potvin8, Fabio Rocha Jimenez Vieira1,2, Kerrie Barry3, Joel B. Dacks5, Colomban de 8 Vargas2,12, Bernard Henrissat11,13, Eric Pelletier2,14, Jeremy Schmutz3,10, Patrick Wincker2,14, Chris 9 Bowler1,2, Igor V. Grigoriev3,15, and Connie Lovejoy+8 10 11 1 Institut de Biologie de l'ENS (IBENS), Département de Biologie, École Normale Supérieure, CNRS, 12 INSERM, Université PSL, 75005 Paris, France 13 2CNRS Research Federation for the study of Global Ocean Systems Ecology and Evolution, 14 FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, 75016 Paris, France 15 3 US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 16 Cyclotron Road, Berkeley,
    [Show full text]
  • Tales of Diversity: Genomic and Morphological Characteristics of Forty-Six Arthrobacter Phages
    RESEARCH ARTICLE Tales of diversity: Genomic and morphological characteristics of forty-six Arthrobacter phages Karen K. Klyczek1☯, J. Alfred Bonilla1☯, Deborah Jacobs-Sera2☯, Tamarah L. Adair3, Patricia Afram4, Katherine G. Allen5, Megan L. Archambault1, Rahat M. Aziz6, Filippa G. Bagnasco3, Sarah L. Ball7, Natalie A. Barrett8, Robert C. Benjamin6, Christopher J. Blasi9, Katherine Borst10, Mary A. Braun10, Haley Broomell4, Conner B. Brown5, Zachary S. Brynell3, Ashley B. Bue1, Sydney O. Burke3, William Casazza10, Julia A. Cautela8, Kevin Chen10, Nitish S. Chimalakonda3, Dylan Chudoff4, Jade A. Connor3, Trevor S. Cross4, Kyra N. Curtis3, Jessica A. Dahlke1, Bethany M. Deaton3, Sarah J. Degroote1, Danielle M. DeNigris8, Katherine C. DeRuff9, Milan Dolan5, David Dunbar4, Marisa a1111111111 S. Egan8, Daniel R. Evans10, Abby K. Fahnestock3, Amal Farooq6, Garrett Finn1, a1111111111 Christopher R. Fratus3, Bobby L. Gaffney5, Rebecca A. Garlena2, Kelly E. Garrigan8, Bryan 3 5 2 4 a1111111111 C. Gibbon , Michael A. Goedde , Carlos A. Guerrero Bustamante , Melinda Harrison , 8 11 10 6 a1111111111 Megan C. Hartwell , Emily L. Heckman , Jennifer Huang , Lee E. Hughes , Kathryn 8 8 10 3 a1111111111 M. Hyduchak , Aswathi E. Jacob , Machika Kaku , Allen W. Karstens , Margaret A. Kenna11, Susheel Khetarpal10, Rodney A. King5, Amanda L. Kobokovich9, Hannah Kolev10, Sai A. Konde3, Elizabeth Kriese1, Morgan E. Lamey8, Carter N. Lantz3, Jonathan S. Lapin2, Temiloluwa O. Lawson1, In Young Lee2, Scott M. Lee3, Julia Y. Lee- Soety8, Emily M. Lehmann1, Shawn C. London8, A. Javier Lopez10, Kelly C. Lynch5, Catherine M. Mageeney11, Tetyana Martynyuk8, Kevin J. Mathew6, Travis N. Mavrich2, OPEN ACCESS Christopher M. McDaniel5, Hannah McDonald10, C. Joel McManus10, Jessica E.
    [Show full text]
  • Elucidation of Spatiotemporal Variations in Functional Genes Involved in the Nitrogen Cycle Along the West Coast of India
    Elucidation of spatiotemporal variations in functional genes involved in the nitrogen cycle along the west coast of India A thesis submitted to Goa University for the award of degree of Doctor of Philosophy In MICROBIOLOGY By JASMINE GOMES Under the guidance of Dr. RAKHEE KHANDEPARKER Senior Scientist Biological Oceanography Division CSIR-National Institute of Oceanography Dona Paula-Goa 403004 April 2018 CERTIFICATE Certified that the research work embodied in this thesis entitled ―Elucidation of spatiotemporal variations in functional genes involved in the nitrogen cycle along the west coast of India‖ submitted by Ms. Jasmine Gomes for the award of Doctor of Philosophy degree in Microbiology at Goa University, Goa, is the original work carried out by the candidate himself under my supervision and guidance. Dr. Rakhee Khandeparker Senior Scientist Biological Oceanography Division CSIR-National Institute of Oceanography, Dona Paula – Goa 403004 DECLARATION As required under the University ordinance, I hereby state that the present thesis for Ph.D. degree entitled ―Elucidation of spatiotemporal variations in functional genes involved in the nitrogen cycle along the west coast of India" is my original contribution and that the thesis and any part of it has not been previously submitted for the award of any degree/diploma of any University or Institute. To the best of my knowledge, the present study is the first comprehensive work of its kind from this area. The literature related to the problem investigated has been cited. Due acknowledgement have been made whenever facilities and suggestions have been availed of. JASMINE GOMES Acknowledgment I take this privilege to express my heartfelt thanks to everyone involved to complete my Ph.D successfully.
    [Show full text]
  • Phage-Induced Lysis Enhances Biofilm Formation in Shewanella Oneidensis MR-1
    The ISME Journal (2011) 5, 613–626 & 2011 International Society for Microbial Ecology All rights reserved 1751-7362/11 www.nature.com/ismej ORIGINAL ARTICLE Phage-induced lysis enhances biofilm formation in Shewanella oneidensis MR-1 Julia Go¨deke, Kristina Paul, Ju¨ rgen Lassak and Kai M Thormann Department of Ecophysiology, Max-Planck-Institut fu¨r Terrestrische Mikrobiologie, Marburg, Germany Shewanella oneidensis MR-1 is capable of forming highly structured surface-attached communities. By DNase I treatment, we demonstrated that extracellular DNA (eDNA) serves as a structural component in all stages of biofilm formation under static and hydrodynamic conditions. We determined whether eDNA is released through cell lysis mediated by the three prophages LambdaSo, MuSo1 and MuSo2 that are harbored in the genome of S. oneidensis MR-1. Mutant analyses and infection studies revealed that all three prophages may individually lead to cell lysis. However, only LambdaSo and MuSo2 form infectious phage particles. Phage release and cell lysis already occur during early stages of static incubation. A mutant devoid of the prophages was significantly less prone to lysis in pure culture. In addition, the phage-less mutant was severely impaired in biofilm formation through all stages of development, and three-dimensional growth occurred independently of eDNA as a structural component. Thus, we suggest that in S. oneidensis MR-1 prophage-mediated lysis results in the release of crucial biofilm-promoting factors, in particular eDNA. The ISME Journal (2011) 5, 613–626; doi:10.1038/ismej.2010.153; published online 21 October 2010 Subject Category: microbe–microbe and microbe–host interactions Keywords: Shewanella; biofilm; eDNA; lysis; phage Introduction been demonstrated to adhere to various surfaces and form biofilms (Bagge et al., 2001; Thormann et al., Shewanella oneidensis MR-1 belongs to the Gram- 2004, 2005, 2006; Teal et al., 2006; McLean et al., negative g-proteobacteria and is characterized by an 2008a; Zhang et al., 2010).
    [Show full text]