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Entwicklung Eines Datenbank-Gestützten Computerprogramms Zur Taxonomischen Identifizierung Von Mikrobiellen Populationen Auf Molekularbiologischer Basis

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Entwicklung Eines Datenbank-Gestützten Computerprogramms Zur Taxonomischen Identifizierung Von Mikrobiellen Populationen Auf Molekularbiologischer Basis Entwicklung eines Datenbank-gestützten Computerprogramms zur taxonomischen Identifizierung von mikrobiellen Populationen auf molekularbiologischer Basis Anwendung dieses Programms auf die Charakterisierung der Diversität stickstofffixierender und denitrifzierender Mikroorganismen in Abhängigkeit einer Stickstoffdüngung Inaugural-Dissertation zur Erlangung des Doktorgrades der Mathematisch-Naturwissenschaftlichen Fakultät der Universität zu Köln vorgelegt von Christopher Rösch aus München Hundt Druck Köln, 2005 Berichterstatter: Prof. Dr. H. Bothe Prof. Dr. D. Schomburg Tag der mündlichen Prüfung: 11. Juli 2005 Meinen Eltern Abstract The present work aimed at developing a novel method which allows to characterize microbial communities from environmental samples in a comprehensive and rapid way. Approaches tried so far either supplied information about the identity of a small fraction of organisms within the total community (e. g. by sequencing of clone libraries), or demonstrated the diversity of organisms without identifying them (e. g. community profiling). In the approach presented here, a method for determining such profiles (by tRFLP analysis) was combined with an automatic analysis by a computer program (TReFID) newly developed for the current study. For the characterization of microorganisms, three different data bases have been constructed: (1) for denitrifying bacteria: a nosZ data base with 607 entries (2) for dinitrogen fixing bacteria: a nifH data base with 1,318 entries (3) for bacteria in general: a 16S rDNA data base with 22,145 entries Thus a comprehensive data set has been developed particularly for the 16S rRNA gene. The use of the TReFID program now allows investigators to characterize bacterial communities from any environmental sample in a rather comprehensive way. Several control analyses showed that the TReFID program is suited for the analysis of environmental samples. TReFID was also used to assess the effect of nitrogen fertilizations on the composition of the microbial community is a N- limited forest soil in the vicinity of Cologne (Dünnwald). One plot was fertilized several times with ammonium nitrate, whereas the other plot was left undisturbed as a control. Soil samples were taken at different time intervals and analyzed for the bacterial composition with respect to total bacteria (16S rRNA gene), denitrifying and N2-fixing bacteria (nifH and nosZ, respectively). The following results emerged from this study a) the diversity of N2-fixing bacteria (assessed by the nifH gene) was about the same in both plots at the beginning of the study, but – surprisingly – decreased in the control plot while the fertilized plot remained unaffected. b) The total bacterial community (16S rRNA gene) was more diverse in the fertilized plot than in control prior to the start of the fertilization. Fertilization decreased diversity. c) The data set for denitrification (nosZ) was too small to draw definitive conclusions due to the limited number of entries for this gene in TReFID. Despite the fact that the present study is seemingly the first attempt to comprehensively characterize the bacterial community in a forest soil, the obtained data set is not yet sufficient for general conclusions, since the data obtained cannot be referred to results by others due to the lack of comparable studies in the literature. In the meantime, the TReFID program has successfully been applied to characterize the microbial community along a salt gradient at an inland salt habitat (S. Eilmus, diploma thesis, 2005). Abstract Im Vordergrund dieser Arbeit stand die Entwicklung einer neuartigen Methode, um mikrobielle Ge- meinschaften aus Umweltproben schnell und umfassend charakterisieren zu können. Die bisherigen methodischen Ansätze lieferten entweder Informationen über die Identität der Organismen in einer kleinen Stichprobe (z. B. Sequenzieren von Klonbibliotheken), oder sie demonstrieren die Diversität, ohne dass die Organismen identifiziert werden können (z. B. Erstellen von Profilen). In dem hier vor- gestellten Ansatz wurde eine Methode zur Erstellung solcher Profile (tRFLP) mit einer automatisierten Auswertung über das hierfür entwickelte Computerprogramm (TReFID) verbunden. In der Aus- wertung werden die experimentell erhaltenen Profile mit eigens erstellten Datenbanken abgeglichen, um Organismenlisten von untersuchten Proben zu erstellen. Es wurden drei Datenbanken erstellt: (1) zur Charakterisierung denitrifizierender Mikroorganismen: nosZ-Datenbank (607 Einträge) (2) zur Charakterisierung stickstofffixierender Mikroorganismen: nifH-Datenbank (1318 Einträge) (3) zur Charakterisierung der bakteriellen Gemeinschaft: 16S rDNA-Datenbank (22145 Einträge) Speziell für das 16S rRNA-Gen wurde somit einumfangreicher Datensatz erarbeitet. Damit ist es jetzt unter Verwendung der TReFID-Programms möglich geworden, mikrobielle Lebensgemeinschaften von beliebigen Standorten umfassend zu charakterisieren. Eine Evaluierung der TReFID-Methode an- hand verschiedener Kontrollen zeigte, dass die Methode zur Analyse von (Umwelt-)Gemeinschaften geeignet ist. Die TReFID-Methode wurde exemplarisch auf einen Waldboden angewandt, um dort den Effekt von Stickstoffdüngung auf die mikrobielle Gemeinschaft zu untersuchen. Hierfür wurden zwei Versuchsflächen im Dünnwald (Köln) ausgewählt, dessen Boden Stickstoff-limitiert war. Eine der bei- den Versuchflächen wurde mehrfach gedüngt. Zu verschiedenen Zeitpunkten wurde Bodenproben ent- nommen und analysiert. Mit der TReFID-Methode wurde der Effekt der Düngung auf die bakterielle Gesamtgemeinschaft und auf die Teilgemeinschaften stickstofffixierender und denitrifizierender Mikroorganismen untersucht. Die Anwendung auf den Dünnwaldboden ergab unerwartete Befunde: Die nifH-Diversität war in beiden Versuchsflächen anfangs gleich; doch nach der Düngung war die Diversität in der Kontrollfläche herabgesetzt und in der gedüngten Fläche unverändert. Im Falle der 16S rDNA wies die später gedüngte Fläche anfangs eine wesentlich höhere Diversität auf, aber infolge der Düngung sank diese auf das Niveau der Kontrollfläche. Zur Charakterisierung der Diversität von Denitrifikanten war die TReFID-Methode nur eingeschränkt geeignet, da zu wenige Sequenzen dieses Gens bekannt sind und die Datengrundlage für TReFID entsprechend klein war. Da jedoch bisher keine vergleichbaren Untersuchungen durchgeführt wurden, ist eine objektive Bewertung dieser Befunde nicht möglich. Die vorliegende Arbeit ist ein erster Versuch, aus der Kom- bination von tRFLP-Profilen mit Datenbanken die Gemeinschaft denitrifizierender oder N2-fixierender Mikroorganismen eines Umweltstandortes zu beschreiben. Das TReFID-Verfahren wurde inzwischen mit Erfolg zur Charakterisierung der mikrobiellen Gemeinschaft im Salzgradienten einer Binnensalz- stelle angewandt (Diplomarbeit S. Eilmus, 2005). Inhaltsverzeichnis 1 Einleitung....................................................................................................................................... 1 1.1 Diversität und Ökologische Bedeutung von Bakterien ............................................................. 1 1.1.1 Diversität von Bodenbakterien......................................................................................................................... 1 1.1.2 Systematik und Artbegriff bei Bakterien.......................................................................................................... 2 1.1.3 „Unkultivierbarkeit“ bei Umweltbakterien ...................................................................................................... 2 1.2 Der Stickstoffkreislauf und daran beteiligte Prokaryoten........................................................ 3 1.2.1 Stickstofffixierung............................................................................................................................................ 4 1.2.2 Nitrifikation...................................................................................................................................................... 6 1.2.3 Denitrifikation.................................................................................................................................................. 6 1.3 Anlass und Zielsetzung der vorliegenden Arbeit...................................................................... 7 1.4 Zusammenfassung des experimentellen Ansatzes .................................................................... 9 2 Material und Methoden ............................................................................................................... 10 2.1 Laborkulturen von Bakterien für Kontrollversuche .............................................................. 10 2.1.1 Verwendete Bakterienstämme und ihre Herkunft .......................................................................................... 10 2.1.2 Kultivierungsbedingungen für Laborstämme von Bakterien..........................................................................11 2.1.3 Anlegen von Dauerkulturen zur Aufbewahrung von Bakterienstämmen ....................................................... 12 2.2 Standort für die Untersuchung der Bakteriengemeinschaft ................................................... 12 2.2.1 Der Standort Dünnwald und Beschreibung der Versuchsflächen................................................................... 12 2.2.2 Entnahme, Aufarbeitung und Lagerung der Bodenproben.............................................................................15 2.3 Bodenanalysen von Dünnwaldproben...................................................................................
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