Environmental Organic Geochemistry of Sediments from Wadi Gaza and Investigation of Bioremediation of Petroleum Derivatives and Herbicides by Cyanobacterial Mats under Different Experimental Conditions Von der Fakultät für Mathematik und Naturwissenschaften der Carl von Ossietzky Universität Oldenburg zur Erlangung des Grades und Titels eines Doktors der Naturwissenschaften -Dr. rer. nat.- angenommene Dissertation von Herrn Nimer Mohamed Deeb Safi geboren am 13. Februar 1967 in Jabalia, Gazastreifen, Palästina Erster Gutachter: Prof. Dr. Jürgen Rullkötter Zweiter Gutachter: Prof. Dr. Gerd Liebezeit Tag der Disputation: 05.03.2004 For my parents and my wife, my children, my brothers and my sister Publications and Presentations Safi, N. M. D., Lee, N., Köster, J., Safi, J., El-Nahhal, Y., Wagner, M., Rullkötter, J., 2003. Biodegradation of petroleum model compounds by cyanobacterial mats in mesocosm experiments in Gaza (Palestine) (Oral). In: Book of abstracts I, 21st International Meeting on Organic Geochemistry, September 8-12th, pp.138-139, Krakow, Poland. Safi, N. M. D., Köster, J., Safi, J., El-Nahhal, Y., Rullkötter, J., 2002. Biodegradation of polycyclic aromatic petroleum compounds by cyanobacterial mats in mesocosm experiments in Gaza (Palestine) (Oral). In: Book of Abstracts, 3rd European Meeting on Environmental Chemistry, December 11-14, p. 4, Geneva, Switzerland. Köster, J., Groetzschel, S., Safi, N., de Beer, D., Rullkötter, J., 2002. Laboratory experiments with microbial mats: Biodegradation of petroleum model compounds and physiological response to pollution (Poster). In: Book of Abstracts, 3rd European Meeting on Environmental Chemistry, December 11-14, p. 110, Geneva, Switzerland. Safi, N. M. D., Köster, J., Rullkötter, J., 2001. Fossil fuel pollution in Wadi Gaza and biodegradation of petroleum model compounds by cyanobacterial mats (Oral). In: J. Mascle, A., Lascaratos, S., Fowler, D., Gutnick, C., Papaconstantinou, F. Boero (eds.), Rapport du 36eme Congrès de la Commission Internationale pour l’Exploration Scientifique de la Mer Méditerranée (CIESM), 36. CIESM, 24 –28 September, p. 209, Monte Carlo, Monaco, France. Köster, J., Safi, N., Abed, R., Groetzschel, S., de Beer, D., Rullkötter, J., 2001. Biodegradation of petroleum model compounds by microbial mats and isolated micro- organisms (Oral). In: Book of abstracts I, 20th International Meeting on Organic Geochemistry, 10 – 14 September, pp. 75-76, Nancy, France Acknowledgments I would like to express my deep gratitude and many thanks to my supervisor Prof. Dr. Jürgen Rullkötter for giving me the opportunity to carry out this Ph.D. work and for his advice, innovative ideas, interesting discussions, continuous encouragement through all my research and the excellent working environment at the Institute of Chemistry and Biology of the Marine Environment (ICBM). Special thanks are also due to Prof. Dr. Gerd Liebezeit for being a referee of this thesis. I am indebted to Dr. Jürgen Köster for his continuous support, encouragement, critical reading, comments and suggestions. Dr. Köster was always available for advice and motivating discussions. My sincerest thanks go to Prof. Dr. Jamal Safi and Dr. Yasser El-Nahhal at the Environmental Protection and Research Institute (EPRI), Gaza, Palestine for their advice, continuous encouragement and supplying the samples through all my study. Many thanks are due to the members of the Organic Geochemistry group at (ICBM) for their general help, comfortable atmosphere in our labs, and for constructive comments, stimulating discussions and ideas. I thank Dr. Dirk de Beer for giving me the opportunity to carry out experiments at the Max Planck Institute for Marine Microbiology (MPI), Bremen. This research was funded by the Deutsche Forschungsgemeinschaft (DFG), grant no. Ru 458/18, and by ICBM. Table of contents 1 Introduction ........................................................................................................................ 1 1.1 Objectives ....................................................................................................................... 1 1.2 Organic pollutants in sediments ..................................................................................... 2 1.3 Microbial mats................................................................................................................ 4 1.4 The environmental situation of Wadi Gaza.................................................................... 7 1.5 Composition of crude oil.............................................................................................. 10 1.6 Oil spills: Impact on the environment .......................................................................... 11 1.7 Biodegradation and bioremediation.............................................................................. 13 1.8 Organo-clay complexes ................................................................................................ 15 1.9 Degradation of crude oil ............................................................................................... 17 1.10 Degradation of petroleum model compounds............................................................... 19 1.11 Degradation of the herbicides 2,4-dichlorophenoxyacetic acid (2,4-D) and terbutryn 21 1.11.1 Degradation of 2,4-dichlorophenoxyacetic acid (2,4-D).................................. 22 1.11.2 Degradation of terbutryn................................................................................... 24 2 Materials and Methods .............................................................................................. 26 2.1 Microbial mat and sediment samples ........................................................................... 26 2.1.1 Environmental setting of the microbial mats.................................................... 26 2.1.2 Collection and preservation of mat samples..................................................... 26 2.1.3 Sediment samples ............................................................................................. 27 2.2 Laboratory experiments................................................................................................ 27 2.2.1 Preparation of organo-clay complexes for the slurry experiments................... 27 2.2.2 Slurry experiment with petroleum model compounds...................................... 28 2.2.3 Slurry experiment with oil-loaded organo-clay complexes.............................. 30 2.2.3.1 Stabilization of the crude oil................................................................. 30 2.2.3.2 Preparation of oil-loaded organo-clay complexes ................................ 30 2.2.4 Slurry experiment with 2,4-D and terbutryn herbicides ................................... 31 2.2.4.1 Chemicals.............................................................................................. 31 2.2.4.2 Terbutryn experiment............................................................................ 31 2.2.4.3 2,4-D Experiment.................................................................................. 32 2.2.5 Microscopy and cultivation .............................................................................. 32 i 2.3 Mesocosm experiments ................................................................................................ 33 2.3.1 Experimental ponds at Gaza ............................................................................. 33 2.3.2 Collection and pre-inoculation of microbial mats for pond experiments......... 33 2.3.3 Pond operation and monitoring ........................................................................ 33 2.3.4 Microbiological monitoring of microbial mats................................................. 34 2.3.5 Contamination experiment with intact mats in the sectioned pond (petroleum model compounds)......................................................................... 36 2.3.5.1 Inoculation of the sectioned pond......................................................... 36 2.3.5.2 Preparation and application of the organoclay-model compounds for the mesocosm experiments.............................................................. 36 2.3.6 Summer experiment.......................................................................................... 36 2.3.7 Recontamination experiment with intact mats in the sectioned pond (Winter experiment).......................................................................................... 37 2.4 Analytical procedure..................................................................................................... 38 2.4.1 Sample preparation ........................................................................................... 38 2.4.2 Ultrasonic extraction......................................................................................... 38 2.4.3 Precipitation of asphaltenes .............................................................................. 38 2.4.4 Internal standards.............................................................................................. 39 2.4.5 Separation of the bitumen by column chromatography.................................... 39 2.4.6 Derivatisation.................................................................................................... 40 2.4.7 Gas chromatographic analysis .......................................................................... 40 2.4.8 Combined gas chromatographic/mass spectrometric analysis (GC/MS) ........