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Polyphasische Taxonomie, Kerngenom Und Lebenszyklus Von Rhodopirellula-Stämmen

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Polyphasische Taxonomie, Kerngenom Und Lebenszyklus Von Rhodopirellula-Stämmen Polyphasische Taxonomie, Kerngenom und Lebenszyklus von Rhodopirellula-Stämmen Dissertation zur Erlangung des Grades eines Doktors der Naturwissenschaften -Dr. rer. nat.- Dem Fachbereich Biologie/Chemie der Universität Bremen vorgelegt von Carsten S. Frank aus Rödermark Bremen, Mai 2011 Die Untersuchungen zu der vorliegenden Doktorarbeit wurden von November 2007 bis Mai 2011 am Max-Planck-Institut für Marine Mikrobiologie in Bremen durchgeführt. 1. Gutachter: Prof. Dr. Rudolf Amann 2. Gutachter: PD Dr. Jens Harder 3. Prüfer: Prof. Dr. Ulrich Fischer 4. Prüfer: Dr. Marcus Elvert Tag der Promotion: 04. Juli 2011 2 _____________________________________________________Inhaltsverzeichnis Inhaltsverzeichnis Inhaltsverzeichnis.........................................................................................................I Abkürzungsverzeichnis ..............................................................................................III Zusammenfassung.................................................................................................... IV Teil I: Darstellung der Ergebnisse im Gesamtzusammenhang....................................1 A. Einleitung .............................................................................................................1 1. Taxonomie........................................................................................................1 1.1. Definition von Arten .................................................................................1 1.2. Polyphasische Taxonomie.......................................................................3 2. Das Phylum der Planctomyceten......................................................................5 3. Rhodopirellula baltica .......................................................................................8 3.1. Lebenszyklus von Rhodopirellula baltica ...............................................11 4. Bakterien und ihre Umwelt..............................................................................12 4.1. Einfluss der Nährstoffe auf mikrobielles Leben......................................12 4.2. Sessile Lebensweise als Anpassung an Umweltbedingungen ..............13 5. Kultivierung von Bakterien ..............................................................................15 5.1. Chemostate ...........................................................................................15 6. Microarrays.....................................................................................................16 6.1. Klassische Anwendung von Microarrays ...............................................16 6.2. Definition des Kerngenoms....................................................................17 6.3. Anwendung von Microarrays zur Genomanalyse ..................................17 7. Zielsetzung der Arbeit.....................................................................................19 B. Ergebnisse und Diskussion................................................................................20 1. Physiologische Eigenschaften von Rhodopirellula- Stämmen........................20 2. Morphologische Eigenschaften von Rhodopirellula- Stämmen.......................22 3. Chemotaxonomie von Rhodopirellula-Stämmen ............................................23 3.1. Clusteranalyse der Lipidprofile ..............................................................25 3.2. Clusteranalyse der physiologischen Daten............................................27 4. Pigmentierung von Rhodopirellula-Stämmen .................................................27 5. Einfluss von Ammonium auf Rhodopirellula-Stämme.....................................28 5.1. Modell für einen Ammoniumsensor .......................................................29 5.2. Die ökologische Dimension ...................................................................30 I Inhaltsverzeichnis_____________________________________________________ 6. Wachstum von R. baltica SH1T bei verschiedenen Phosphatkonzentrationen... ....................................................................................................................... 32 7. Wachstum von R. baltica SH1T unter mikroaerophilen und anaeroben.............. Bedingungen .................................................................................................. 33 8. Definition des Kerngenoms von R. baltica ..................................................... 33 8.1. Microarraystudien.................................................................................. 34 8.2. Genomsequenzierung........................................................................... 36 8.3. Vergleich der Ergebnisse aus Microarray- und Genomanalyse ............ 37 9. G+C-Gehalt.................................................................................................... 42 10. Stammdifferenzierung und Benennung neuer Arten ...................................... 43 11. Ausblick.......................................................................................................... 44 C. Literatur.......................................................................................................... 45 Teil II: Publikationen ................................................................................................. 60 A. Publikationsliste mit Erläuterungen.................................................................... 60 B. Publikationen ..................................................................................................... 61 1. Ammonium and attachment of Rhodopirellula baltica ........................................62 2. Polyphasic taxonomy of Rhodopirellula-related strains: Emended description of the genus Rhodopirellula and the species Rhodopirellula baltica, and the description of Rhodopirellula europaea sp. nov., Rhodopirellula sallentina sp. nov., Rhodopirellula maiorica sp. nov., Rhodopirellula flandrensis sp. nov., Rhodopirellula gimesia sp. nov., Rhodopirellula syltensis sp. nov., Rhodopirellula philippinensis sp. nov., Rhodopirellula clava sp. nov., Rhodopirellula magna sp. nov. and Rhodopirellula bahusiensis sp. nov. and the description of the Rhodopilula gen. nov. with Rhodopilula apulia sp. nov. .......................................... 71 3. The core genome of Rhodopirellula baltica........................................................113 C. Danksagung................................................................................................. 141 Error! Bookmark not defined. II ________________________________________________Abkürzungsverzeichnis Abkürzungsverzeichnis ANI Durchschnittliche Nukleotididentität (average nucleotide identity) ASW Artifizielles Seewasser BLAST Basic local alignment search tool bp Basenpaar(e) CDS Protein coding sequences CGH Comparative genomic hybridization DDH DNA-DNA-Hybridisierung FAME Fettsäuremethylester GC Gaschromatographie GC-MS Gaschromatographie-Massenspektroskopie gDNA Genomische Desoxyribonukleinsäure HPLC High performance liquid chromatography ICM Intracytoplasmatische Membran KEGG Kyoto Encyclopedia of Genes and Genomes LC-MS Flüssigkeitschromatographie-Massenspektroskopie Mb Megabasen MLSA Multilocus Sequenz Analyse MS Massenspektroskopie OD600 Optische Dichte gemessen bei 600 nm ORF Offener Leserahmen (open reading frame) OTU Operational taxonomic unit PC Phosphatidylcholin PE Phosphatidylethanolamin PG Phosphatidylglycerin RB Rhodopirellula baltica R. baltica Rhodopirellula baltica PCR Polymerasekettenreaktion RP-HPLC Reverse phase high performance liquid chromatography rRNA Ribosomale Ribonukleinsäure SH Schlesner Heinz TLC Dünnschichtchromatographie (thin layer chromatography) UPGMA Unweighted pair group method with averages III Zusammenfassung____________________________________________________ Zusammenfassung Planctomyceten der Art Rhodopirellula baltica waren in den letzten Jahren Gegenstand einer ganzen Reihe von Untersuchungen. Diese beinhalteten die komplette Sequenzierung und Annotation des Genoms, Transkriptomstudien sowie die Isolation neuer Stämme. Neben der intrazellulären Kompartimentierung gehört der dimorphe Lebenszyklus mit juvenilen, freischwimmenden und adulten, angehaftet lebenden Zellen und die damit verbundene Bildung von Rosetten zu den herausstechensten Merkmalen von R. baltica. Die Schwerpunkte der Arbeit lagen auf drei Projekten. In einer polyphasischen Taxonomiestudie wurden 17 neu isolierte Stämme auf ihre morphologischen, physiologischen und chemotaxonomischen Charakteristika hin untersucht. Auf Grundlage dieser sowie phylogenetischer Daten erfolgte die Benennung der neuen Gattung Rhodopilula gen. nov. mit der Art Rhodopilula apulia sp. nov. und der zehn neuen Rhodopirellula Arten Rhodopirellula europaea sp. nov., Rhodopirellula sallentina sp. nov., Rhodopirellula maiorica sp. nov., Rhodopirellula flandrensis sp. nov., Rhodopirellula gimesia sp. nov., Rhodopirellula syltensis sp. nov., Rhodopirellula philippinensis sp. nov., Rhodopirellula clava sp. nov., Rhodopirellula magna sp. nov. und Rhodopirellula bahusiensis sp. nov.. Die Physiologie der Stämme wurde insbesondere hinsichtlich der Reaktion auf Ammonium untersucht. In vorherigen Studien erfolgte die Kultivierung von R. baltica meist unter stickstoffgesättigten Bedingungen, während der immer Zellhaufen von sich aneinander anhaftenden Zellen beobachtet wurden. Diese Zellaggregate wurden in ammonium-limitierten Kulturen nur in kleinen Mengen gefunden. Es dominierten freischwimmende Zellen. Mittels Durchflusszytometrie wurde ein Anstieg
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