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Michael Dieter Klein Lehrstuhl für Mikrobiologie der Technischen Universität München Dissimilatory (bi-) sulfite reductase as a marker for phylogenetic and ecological studies of sulfate-reducing prokaryotes Michael Dieter Klein 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 (Dr. rer. nat.) genehmigten Dissertation. Vorsitzender: Univ.- Prof. Dr. Erwin Grill Prüfer der Dissertation: 1. Univ.- Prof. Dr. Michael Wagner Universität Wien / Österreich 2. Univ.- Prof. Dr. Karl-Heinz Schleifer Die Dissertation wurde am 21.10.2004 bei der Technischen Universität München eingereicht und durch die Fakultät Wissenschaftszentrum Weihenstephan für Ernährung, Landnutzung und Umwelt am 17.12.2004 angenommen. Parts of this work have been published in advance: Dubilier, N., C. Mulders, T. Ferdelman, D. de Beer, A. Pernthaler, M. Klein, M. Wagner, C. Erseus, F. Thiermann, J. Krieger, O. Giere and R. Amann (2001). “Endosymbiotic sulphate-reducing and sulphide-oxidizing bacteria in an oligochaete worm.” Nature 411(6835): 298-302. Klein, M., M. Friedrich, A. J. Roger, P. Hugenholtz, S. Fishbain, H. Abicht, L. L. Blackall, D. A. Stahl and M. Wagner (2001). “Multiple lateral transfer events of dissimilatory sulfite reductase genes between major lineages of sulfate-reducing prokaryotes.” Journal of Bacteriology 183(20): 6028-6035. Schmid, M., U. Twachtmann, M. Klein, M. Strous, S. Juretschko, M. Jetten, J. W. Metzger, K. H. Schleifer and M. Wagner (2000). “Molecular evidence for genus level diversity of bacteria capable of catalyzing anaerobic ammonium oxidation.” Syst Appl Microbiol 23(1): 93-106. In preparation: Zverlov, V., Klein, M., Lücker, S., Friedrich, M.W., Kellermann, J., Stahl, D.A., Loy, A., and M. Wagner (2004). „Lateral Gene Transfer of Dissimilatory (Bi)Sulfite Reductase Revisited“, submitted to J. Bacteriol. Abbreviations: AMP Adenosine-mono-phosphate APS Adenosine – 5´phosphosulfate ATP Adenosinetriphosphate bp base pairs DNA Deoxyribonucleic acid dsr Gene coding for the dissimilatory sulfite reductase Dsr Dissimilatory sulfite reductase, the protein dsrA/ DsrA Partial sequence of dsr / Dsr alpha subunit as sequenced by the primers presented dsrAB approximately 1.9 kb long fragment of the dsr operon, encompassing most of the alpha and beta subunit of the dsr DsrAB Amino acid sequence inferred form dsrAB dsrB /DsrB Partial sequence of dsr / Dsr beta subunit as sequenced by the primers presented et al. et alteri und andere g Gravity GC or GC% Mol % Guanine + Cytosine h Hour H+ Proton H2 Hydrogen Indel Insertion / deletion events of certain sequences IS Insertion sequences kb Kilo base, 1000 nucleotide bases kDa Kilo Dalton min Minute ml milliliter mM milli molar nm Nanometer PAGE Polyacrylamidegelelectrophoresis PAPS Phospho-adenosine – 5´phosphosulfate PCR polymerase chain reaction rRNA Ribosomal ribonucleic acid S Svedberg (s-1) s Second 2- S or H2S Sulfide or hydrogen sulfide SDS Sodium- dodecyl- sulfate 2- SO3 Sulfite 2- SO4 Sulfate SRB Sulfate reducing bacteria/bacterium SRP Sulfate reducing prokaryotes/prokaryote UTP Uraciltriphosphate A INTRODUCTION.........................................................................................................1 A.1 The global sulfur cycle .............................................................................................................................................1 A.2 Physiological traits of sulfate reducing prokaryotes........................................................................................2 A.3 Habitats of sulfate reducing prokaryotes............................................................................................................4 A.4 Phylogeny of sulfate reducing prokaryotes ........................................................................................................5 A.5 Detection of SRP using 16S rRNA as marker ...................................................................................................7 A.6 The dissimilatory sulfite reductase – an alternative marker molecule for sulfate reducing prokaryotes .........................................................................................................................................................................9 A.7 Extension of the DsrAB data base ......................................................................................................................11 A.8 The aims of this Ph.D. thesis.................................................................................................................................12 B MATERIAL AND METHODS..................................................................................13 B.1 Reference strains, and clone maintenance ........................................................................................................13 B.2 DNA extraction from pure cultures and environmental samples ..............................................................15 B.3 Polymerase chain reaction amplification of dsrAB genes .............................................................................16 B.4 Molecular cloning of dsrAB genes into pCRTM2.1 or pCR-XL-TOPO vectors and identification of dsrAB carrying clones....................................................................................................................................................16 B.5 Sequencing of cloned dsrAB gene fragments....................................................................................................17 B.6 Gelretardation ..........................................................................................................................................................17 B.7 Phylogenetic Analysis .............................................................................................................................................17 B.7.1 Pure culture databank....................................................................................................................................... 17 B.7.2 Environmental databank.................................................................................................................................. 18 B.7.3 Alignment and phylogenetic analysis of 16rRNA gene data..................................................................... 18 B.7.4 Alignment and phylogenetic analysis of DsrAB data (amino acid based analysis).............................. 19 B.7.5 Calculation of Distance matrices.................................................................................................................... 19 B.7.6 Analysis of short environmental DsrAB sequence fragments................................................................... 19 B.7.7 Alignment of DsrA to DsrB and phylogenetic analysis of this databank................................................ 20 B.7.8 Phylogenetic analysis of dsrAB gene sequences (nucleic acid based analysis)..................................... 21 B.8 Preparation of tissue of the oligochaet Olavius algarvensis for fluorescence in situ hybridization (FISH) .................................................................................................................................................................................21 B.9 Fluorescence in situ hybridization ......................................................................................................................21 C RESULTS AND DISCUSSION...............................................................................23 C.1 Establishment of reference strain DsrAB databank ......................................................................................23 C.1.1 Reevaluation of PCR primers for amplification of dsrAB gene fragments............................................. 23 C.1.2 Inconsistencies between Edman degradation/ inference from nucleotide sequencing.......................... 26 C.1.3 DsrAB sequence alignment and characteristic motives ............................................................................. 27 C.1.4 Conservation profile of DsrAB....................................................................................................................... 28 C.2 Comparison of 16S rRNA and DsrAB-based phylogeny for SRP reference strains.............................29 C.2.1 Comparative analysis of 16S rRNA gene and DsrAB sequence based phylogeny............................... 29 C.2.2 Further analysis on dsrAB originating from Desulfobacula toluolica ..................................................... 35 C.2.3 Comparison of 16S rRNA gene sequence similarity and DsrAB identity values between SRP ......... 41 C.2.4 Further reflections on lateral gene transfer................................................................................................... 45 C.2.4.1 Comparison of G+C% content of dsrA and dsrB ............................................................................... 45 C.2.4.2 Comparative analysis of genomic G+C% content and dsrAB G+C% content.............................. 46 C.2.4.3 Consequences of lateral gene transfer................................................................................................... 47 C.3 Analysis of environmental DsrAB sequences...................................................................................................49 C.3.1 Global traits in DsrAB based environmental surveys................................................................................
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