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Biodegradation of Petroleum in Marine Seep Sediments

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Biodegradation of Petroleum in Marine Seep Sediments Biodegradation of petroleum in marine seep sediments Sonakshi Mishra Biodegradation of petroleum in marine seep sediments Dissertation Submitted for the degree of Doctorate in Natural Sciences - Dr. rer. nat. - Zur Erlangung des Grades eines Doktors der Naturwissenschaften - Dr. rer. nat. - Faculty of Mathematics and Nature Science, Christian-Albrechts-University of Kiel Mathematisch-Naturwissenschaftliche Fakultät der Christian-Albrechts-Universität zu Kiel Submitted by Vorgelegt von Sonakshi Mishra, M.Sc. Kiel, 2016 Declaration I, Sonakshi Mishra, hereby declare that apart from the guidance of my supervisors, I have independently and entirely conducted this doctoral work and written the dissertation without any kind of unauthorized aid. Neither this nor a similar work has been published, submitted for publication, or submitted for an examination procedure to another department or institution. I assure that the presented research project has been conducted in full compliance with the rules of good scientific practice laid by the German Research Foundation (DFG). Kiel, .................................. .....................………………………………………… Sonakshi Mishra, M.Sc. Erklärung Hiermit erkläre ich, Sonakshi Mishra, dass ich, abgesehen von der Unterstützung meiner Betreuer, diese Doktorarbeit eigenständig und ohne unerlaubte Hilfe durchgeführt habe. Weder diese noch eine ähnliche Arbeit wurde an einer anderen Abteilung oder Hochschule im Rahmen eines Prüfungsverfahrens vorgelegt, veröffentlicht oder zur Veröffentlichung vorgelegt. Ich versichere, dass die Arbeit unter Einhaltung der guten wissenschaftlichen Praxis der Deutschen Forschungsgemeinschaft entstanden ist. Kiel, .................................. .....................………………………………………… Sonakshi Mishra, M.Sc. 1. Reviewer: Prof. Dr. Klaus Wallmann 2. Reviewer: Prof. Dr. Tina Treude Date of PhD defense: 23.03.2016 Place of PhD defense: Kiel, Germany I dedicate my entire doctoral work to both my beloved grandfathers, Shri Bamadev Mishra (1904 - 2007) and Shri Raghunath Mahapatra (1929 - 2015). This is for you both Bapa and Aja, the first teacher I ever had and the first scientist I ever saw. Thank you for that and a lot more………. I missed the final goodbye. But this is how I will keep both of you with me, forever. Contents Abstract ......................................................................................................................................... 2 Zusammenfassung ...................................................................................................................... 3 1. Introduction .......................................................................................................................... 5 1.1 Petroleum: Formation and Composition.............................................................................5 1.2 Sources of petroleum in the ocean ......................................................................................6 1.3 Natural seepage of petroleum.............................................................................................7 1.4 Fate of petroleum in the marine environment .................................................................. 10 1.5 Biodegradation of petroleum in marine sediments........................................................... 12 2. Objectives ............................................................................................................................ 24 3. Outline of manuscripts ..................................................................................................... 26 4. Manuscript I ........................................................................................................................ 28 5. Manuscript II. ...................................................................................................................... 70 6. Manuscript III. ..................................................................................................................110 7. Final Summary and Conclusion.....................................................................................165 1 Abstract This study presented for the first time the use of intact sediment cores in a continuous sediment-oil-flow-through (SOFT) system for investigating the degradation of petroleum under a simulated petroleum seepage. It suggests that the use of the SOFT system, which is designed to maintain the natural fabric and heterogeneity of the marine sediments, provides a more comprehensive understanding of the in situ processes involved in petroleum degradation at marine seeps compared to the traditional use of sediment slurries. The SOFT system enabled quasi in situ monitoring of ongoing biogeochemical changes taking place in sediments during petroleum seepage and to the best of our knowledge, showed microbial methanogenic degradation of hydrocarbons in an almost natural setting. The biogeochemical response of sediments from hydrocarbon adapted sites like the Caspian Sea, North Alex Mud Volcano in the Eastern Mediterranean, the Santa Barbara Channel and non-adapted site like the Eckernfoerde Bay in the Baltic Sea to petroleum seepage was investigated and compared using the SOFT system. Distinct redox zonation was established in the sediment cores that evolved temporally and spatially during the upward migration of petroleum. Sulfate reduction and methanogenesis were identified as two major processes involved in the degradation of petroleum at seeps. The concentrations of n-alkanes decreased successively towards the sediment surface. Methanogenesis was identified to be involved in degradation of mid- to long-chain alkanes whereas sulfate reduction was identified to be the more dominant process involved in both short and mid- to long chain alkane degradation. The microbial diversity decreased in sediments after the onset of petroleum seepage indicating that only few specialized microbes are involved in the degradation of petroleum under in situ conditions. Short-chain volatile alkanes like ethane, propane, isobutane, n-butane, pentane and hexane were almost completely depleted in the sulfate reducing zone. Clade SCA1 and clade LCA2 were identified as two key sulfate reducing bacteria in the Caspian Sea sediments responsible for short-chain alkane degradation and for mid- to long-chain alkane degradation, respectively, whereas 2 syntrophic archaea of the genus Methanosarcina was identified to be involved in the methanogenic degradation of long- chain alkanes. Among all sites, the fastest response to petroleum addition was seen in the North Alex Mud Volcano sediments followed by sediments from the Caspian Sea, the Santa Barbara Channel and the Eckernfoerde Bay suggesting that microbial communities in sediments with prior adaptation to hydrocarbon seepage are more efficient in degrading hydrocarbons compared to microbial communities from non-adapted sediments. Zusammenfassung Diese Studie zeigt die erstmalige Anwendung intakter Sedimentkerne in einem kontinuierlichen Sediment-Öl-Durchflusssystem (SOFT-System), welches den Abbau von Erdöl unter einem simulierten Erdölaustritt untersuchte. Das SOFT-System, welches entwickelt wurde um die natürliche Struktur und Heterogenität des marinen Sediments aufrechtzuerhalten, ermöglichte ein umfassenderes Verständnis der in situ Prozesse während des Erdölabbaus an den marinen Quellen, als die traditionell genutzten Sediment- Slurries (Sedimentgemische). Das SOFT System ermöglichte quasi in situ Untersuchungen der biogeochemischen Veränderungen, welche im Sediment während des Ölabbaus stattfanden. Des Weiteren wurde, nach bestem Wissen, der mikrobielle methanogene Abbau des Erdöls in einer beinahe natürlichen Umgebung gezeigt. Die biogeochemische Reaktion der Sedimente in an Kohlenwasserstoffe angepasste Gebieten wie dem Kaspischen Meer, dem North Alex Schlammvulkan im östlichen Mittelmeer und dem Santa Barbara Kanal, wurden mit einem Gebiet das nicht an einen Erdölausritt angepasst war, der Eckernfoerder Bucht in der Ostsee, unter Verwendung des SOFT Systems untersucht und verglichen. Es wurde eine ausgeprägte Redox-Zonierung in den Sedimentkernen festgestellt, welche sich mit dem aufsteigenden Erdöl zeitlich und räumlich bildete. Als die zwei, am Erdölabbau beteiligen Hauptprozesse, wurden Sulfatreduktion und Methanogenese identifiziert. Die Konzentration der n-Alkane verringerte sich sukzessiv in Richtung der Sedimentoberfläche. Die Methanogenese wurde 3 als beteiligter Prozess beim Abbau der mittel- und langkettigen Alkene erkannt, während Sulfatreduktion als dominanter Prozess in beides involviert war, den Abbau der kur z-, sowie der mittel- und langkettigen Alkane. Die mikrobielle Diversität verringerte sich nach Beginn des Erdölaustritts im Sediment, was darauf hinweist, dass nur einige wenige spezialisierte Bakterien in den Erdölabbau unter in situ Bedingungen involviert waren. Kurzkettige, flüchtige Alkane wie Ethan, Propan, Isobutan, n-Butan, Pentan und Hexan wurden beinahe vollständig in der Sulfatreduktionszone aufgebraucht. Die monophyletische Gruppe SCA1 wurde als eine der zwei Hauptsulfatreduzierer im Sediment des Kaspischen Meers identifiziert und war für den Abbau der kurzkettigen Alkane verantwortlich, während die monophyletische Gruppe LCA2 als zweiter Hauptsulfatreduzierer für den Abbau der mittel- und langkettigen Alkane identifiziert wurde. Wohingegen syntrophische Archaea der Gattung Methanosarcina für den methanogenen Abbau der langkettigen Alkane identifiziert wurden. Alle Beprobungsstandorte
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