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Investigation on the Production of Secondary Metabolites from Anoxygenic Phototrophic Bacteria

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Investigation on the Production of Secondary Metabolites from Anoxygenic Phototrophic Bacteria Investigation on the production of secondary metabolites from anoxygenic phototrophic bacteria. Dissertation Zur Erlangung des Doktorgrades der Mathematisch-Naturwissenschaftlichen Fakultät der Christian-Albrechts-Universität zu Kiel Vorgelegt von Min Sun Kiel 2015 Referent: Prof. Dr. Johannes F. Imhoff Korreferentin: Prof. Dr. Ute Hentschel-Humeida Tag der mündlichen Prüfung: 19.02.2016 Zum Druck genehmigt: Ja gez. Prof. Dr. Johannes F. Imhoff This present work was carried out at the GEOMAR Helmholtz Centre for Ocean Research Kiel Christian-Albrechts-University of Kiel from August 2011 to August 2015 under the supervision of Prof. Dr. Johannes F. Imhoff. Scientific contribution All the strains used in this studied were offered by Prof. Dr. Johannes F. Imhoff. Allochromatium vinosum strain MT86 was isolated and identified by Dr. Marcus Tank. All bioassays of crude extracts, fractions and pure compounds were done by Arlette Wenzel-Storjohann (Marine Natural Products, GEOMAR). NMR measurement was performed at the Otto-Diels Institute of Organic Chemistry (Christian-Albrechts University of Kiel) and NMR data analysis was analysis by the assistance of Dr. Bin Wu (Zhejiang University, China) and Prof. Dr. Alex Zeeck (BioViotica Naturstoffe GmbH, Götingen). Prof. Dr. Alex Zeeck did the TLC and IR, CD, and polarimetry measurements. All other experiments were done by Min Sun under supervision of Prof. Dr. Johannes F. Imhoff at GEOMAR Marine Microbiology Department. Erklärung Hiermit erkläre ich, dass ich die vorliegende Arbeit unter Einhaltung der Regeln guter wissenschaftlicher Praxis der Deutschen Forschungsgesellschaft verfasst habe, und dass sie nach Form und Inhalt meine eigene Arbeit ist. Außer den angegebenen Quellen und Hilfsmitteln wurden keine weiteren verwendet. Sie wurde keiner anderen Stelle im Rahmen eines Prüfungsverfahrens vorgelegt. Dies ist mein erstes und bisher einziges Promotionsverfahren. Min Sun Kiel, den 15. 12. 2015 Table of contents 1 INTRODUCTION ...................................................................................................... 1 1.1 Natural products ................................................................................................................. 1 1.1.1 Definition ............................................................................................................................. 1 1.1.2 Category ............................................................................................................................... 1 1.2 Marine natural products ................................................................................................... 5 1.3 Methods of natural products screening ....................................................................... 11 1.3.1 Polyketides ......................................................................................................................... 11 1.3.2 Nonribosomal peptides ...................................................................................................... 14 1.3.3 Phenanzines ....................................................................................................................... 16 1.3.4 Terpenes ............................................................................................................................. 17 1.3.5 Updating tools for exploration of diversities of natural compounds .................................. 18 1.4 Anoxygenic phototrophic bacteria ................................................................................ 19 1.4.1 Purple bacteria ................................................................................................................... 19 1.4.2 Green bacteria .................................................................................................................... 20 1.4.3 Heliobacteriaceae ............................................................................................................... 21 1.4.4 Aerobic anoxygenic phototrophic bacteria (AAPBs) ........................................................ 21 1.5 Aims of this study.............................................................................................................. 21 2 MATERIALS AND METHODS ........................................................................ 24 2.1 Preparation of the medium ............................................................................................. 24 2.2 Bacterial strains ................................................................................................................ 28 2.3 Cultivation experiments .................................................................................................. 30 2.3.1 Optimization of the growth condition for the cultivation of A. vinosum MT86 ................ 30 2.3.2 Media for screening of optimal cultivation condition ........................................................ 31 2.3.3 Scale up to a 36 L culture volume of A. vinosum strain MT86 .......................................... 31 2.3.4 Salt tolerance of A. vinosum strain MT86 .......................................................................... 32 2.4 Chemical screening and structure identification ....................................................... 33 2.4.1 Extraction procedures ........................................................................................................ 33 2.4.2 Analytical HPLC-DAD/MS ............................................................................................... 35 2.4.3 Fractionation of crude supernatant extract by semi-preparative HPLC ............................. 36 2.4.4 Screening of crude cell extract (TLC)................................................................................ 38 2.4.5 Antimicrobial activities screening ..................................................................................... 38 2.4.6 NMR analysis .................................................................................................................... 40 i 2.4.7 TOF-MS ............................................................................................................................. 40 2.5 Other strains of phototrophic bacteria ........................................................................ 41 2.5.1 First screening of selected strains ...................................................................................... 41 2.5.2 Scale up of cultivation of Rubrivivax gelatinosus strain 151 and fractionation the crude extract by semi-preparative HPLC ..................................................................................... 41 2.6 Genetic screening .............................................................................................................. 42 2.6.1 DNA extraction .................................................................................................................. 42 2.6.2 PCR and sequencing .......................................................................................................... 42 2.6.3 Gel electrophoresis............................................................................................................. 45 2.6.4 Purification ......................................................................................................................... 45 2.6.5 BLASTn analyses .............................................................................................................. 45 2.7 Genome evaluation of phototrophic bacteria from databases ............................... 45 3 RESULTS ..................................................................................................................... 52 3.1 First screening of A. vinosum strain MT86 ................................................................. 52 3.1.1 Metabolite profiles of A. vinosum MT86 ........................................................................... 52 3.1.2 Fractionation of supernatant extracts by semi-preparative HPLC ..................................... 54 3.1.3 NMR analysis of the fractions from the 20 L supernatant extract ..................................... 54 3.1.4 Bioactivity of crude supernatant and cell extracts from the 20 L culture .......................... 55 3.2 Optimization of the growth conditions and culture of 36 L of A. vinosum strain MT86. ..................................................................................................................... 56 3.2.1 Media for screening of optimal cultivation conditions ...................................................... 56 3.2.2 Scale up to a 36 L volume culture of A. vinosum MT86.................................................... 61 3.3 Salt tolerance of A. vinosum MT86 ............................................................................... 64 3.3.1 Comparison of culture broths with 0%, 0.33%, 0.67%, 1%, and 1.67% salts ................... 64 3.3.2 Comparison of culture broths with 2.33%, 2.5%, 2.67%, and 3.33 % salts....................... 68 3.3.3 Bioactivity tests of crude extracts from controls Pf media and from cultures grown at different salt concentrations. .............................................................................................. 72 3.3.4 Scale up of cultures to a 50 L volume at two salt concentrations ...................................... 73 3.3.5 NMR analysis of compound F13 from 0.67% salts concentration .................................... 80 3.3.6 Bioactivity tests of fractions from cultures grown at 0.67% salts.....................................
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