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Anaerobic Microbial Transformation of Chlorinated Alkanes in Cultures Derived from Besòs River Estuary Sediments Siti Hatijah

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Anaerobic Microbial Transformation of Chlorinated Alkanes in Cultures Derived from Besòs River Estuary Sediments Siti Hatijah ADVERTIMENT. Lʼaccés als continguts dʼaquesta tesi queda condicionat a lʼacceptació de les condicions dʼús establertes per la següent llicència Creative Commons: http://cat.creativecommons.org/?page_id=184 ADVERTENCIA. El acceso a los contenidos de esta tesis queda condicionado a la aceptación de las condiciones de uso establecidas por la siguiente licencia Creative Commons: http://es.creativecommons.org/blog/licencias/ WARNING. The access to the contents of this doctoral thesis it is limited to the acceptance of the use conditions set by the following Creative Commons license: https://creativecommons.org/licenses/?lang=en Escola d’Enginyeria Departament d'Enginyeria Química, Biològica i Ambiental “Anaerobic microbial transformation of chlorinated alkanes in cultures derived from Besòs River estuary sediments” PhD Thesis Siti Hatijah Mortan Doctorat en Ciència i Tecnologia Ambientals Supervised by Dr Ernest Marco Urrea Dra Gloria Caminal Saperas Bellaterra, Cerdanyola del Vallès, Barcelona March 2017 Title: Anaerobic microbial transformation of chlorinated alkanes in cultures derived from Besòs River estuary sediments Presented by: Siti Hatijah Mortan Supervised by: Ernest Marco Urrea and Gloria Caminal Saperas PhD program in Environmental Science and Technology Departament d'Enginyeria Química, Biològica i Ambiental Escola d’Enginyeria Universitat Autònoma de Barcelona, Bellatera, 2017 This work was supported by the Xarxa de Referència en Biotecnologia de la Generalitat de Catalunya (Premi Pot d’Idees 2016), the Spanish Ministry of Economy and Competitiveness and FEDER(project CTM2013-48545-C2-1-R) and supported by the Generalitat de Catalunya (Consolidated Research Group 2014-SGR-476). The author acknowledges the predoctoral fellowship from Ministry of Higher Education Malaysia and Universiti Malaysia Pahang. Part of this work has been done in collaboration with the Department Isotope Biogeochemistry, Helmholtz Centre for Environmental Research-UFZ, Germany (Dr. L. Adrian); Departament de Genètica i Microbiologia, Universitat Autònoma de Barcelona (Dra. N. Gaju, Dra. M. Martínez, E. Parladé); Departament de Cristal-lografia, Mineralogia i Dipòsits Minerals, Facultat de Geologia, Universitat de Barcelona (Dra. M. Rosell, Dr. J. Palau); Department of Earth and Environmental Sciences, University of Waterloo, Canada (Dr. O. Shouakar-Stash). ERNEST MARCO URREA, Professor Agregat Interí del Departament d'Enginyeria Química, Biològica i Ambiental de la Universitat Autònoma de Barcelona, GLORIA CAMINAL SAPERAS, Investigador Científic del Institut de Química Avançada de Catalunya (IQAC) del CSIC, CERTIFIQUEM: Que el titulat en Enginyeria Bioquímica Siti Hatijah Mortan ha realitzat sota la nostra direcció, en els laboratoris del Departament d'Enginyeria Química, Biològica i Ambiental el treball que amb el títol “Anaerobic microbial transformation of chlorinated alkanes in cultures derived from Besòs River estuary sediments”, es presenta en aquesta memòria, la qual constitueix la seva Tesi per optar al Grau de Doctor per la Universitat Autònoma de Barcelona. I perquè en prengueu coneixement i consti als efectes oportuns, presentem a l’Escola d’Enginyeria de la Universitat Autònoma de Barcelona l’esmentada Tesi, signant el present certificat a Bellaterra, Marc 2017. Dr. Ernest Marco Urrea Dra. Gloria Caminal Saperas ACKNOWLEDGEMENT First and foremost, a very special gratitude to Dr Ernest Marco and Dr Gloria Caminal Saperas for being such a wonderful and helpful supervisors to me. Thank you very much for your guidance and I am highly indebted to both of you for all the encouragement, the patience for my shortcomings and open up the opportunity for me to work in such an interesting research. A special thank you to Dr Lucia Martin-Gonzalez for took a great care of me in the lab and Alba Trueba-Santiso whom I’ve shared so many fun and memorable times working with the ‘anaerobic babies’. I would like to take this moment also to express my appreciation to Dr Teresa Vicent and everyone in “Toxics” Research Group, UAB for your continuous support and I am very grateful being a member of this extremely supportive research group. Special mention to Dr Lorenz Adrian and his research group in the Department Isotope Biogeochemistry (UFZ), Leipzig, Germany for the opportunity to do my research stay in your lab. Working in UFZ was a great joy and experience, thanks to this wonderful group of people. Thank you very much also to Dr Monica Rosell from Departament de Mineralogia (UB), Dr Ivonne Nijenhuis (UFZ), Dr Nuria Gaju, Dr Maira Martinez-Alonso and Eloi Parlade from Departament de Genètica i Microbiologia (UAB) for our research collaboration. I also want to thanks the members of the Departament d'Enginyeria Química, Biològica i Ambiental and Institut de Ciència i Tecnologia Ambiental (ICTA) for their helpful assistance. I would like to acknowledge Manuel Plaza and Lucia Delgado for their technical assistance. Sincere thanks are extended to the examination committee for reviewing this thesis. Last but not least, special thanks to my family and good friends who have provided me their support and understanding throughout this whole PhD journey. ‘Gracias a todos! Gracies a tothom!’ Abstract ABSTRACT Halogenated compounds (organohalides) are recalcitrant organic compounds, exhibiting toxic effects on human health and the ecosystem. Among the organohalides, chlorinated alkanes such as chloroethanes and chloropropanes received less attention despite their large use in the industry and have caused serious environmental problems. Physicochemical processes are the most commonly used technology to treat groundwaters contaminated with these compounds, however these techniques imply high operational costs and require a post-treatment step to completely destroy these compounds. Biodegradation has become a more suitable, cost-efficient and environmental friendly technology to address contamination of these compounds. In this study, we aimed to obtain an enrichment culture containing organohalide-respiring bacteria able to transform halogenated alkanes. A stable nonmethanogenic enriched anaerobic culture that exclusively dehalogenates vicinally chlorinated and brominated alkanes via dihaloelimination was established from Besòs River estuary sediments (Barcelona, Spain). Application of genus specific primers targeting 16S rRNA gene sequences together with the observation of physiological characteristics of the dechlorinating culture indicated that a Dehalogenimonas strain was the responsible for chlorinated alkane degradation in the microcosms. The increase of Dehalogenimonas 16S rRNA gene copies using quantitative PCR (qPCR) revealed that 1,2-dichloropropane (1,2-DCP) dechlorination was coupled to Dehalogenimonas growth in this culture. Carbon and dual carbon-chlorine (C-Cl) isotope fractionation during anaerobic biodegradation of 1,2-DCP and 1,2-dichloroethane (1,2-DCA), respectively, by Dehalogenimonas-containing enrichment culture were determined in this study. Compound specific isotope analysis revealed that the Dehalogenimonas-catalyzed carbon isotopic i Abstract fractionation (ε) of the 1,2-DCP-to-propene reaction was −15.0 ± 0.7‰ and differs significantly from other Dehalococcoides strains eventhough they harbored the same functional reductive dehalogenase (DcpA) for 1,2-DCP-to-propene dechlorination. The dual element C-Cl isotope correlation obtained (Ʌ = 1.89 ± 0.02) during 1,2-DCA-to-ethene dichloroelimination by Dehalogenimonas was significantly discernible from those reported for Dehalococcoides catalyzing a similar dihaloelimination reaction and aerobic oxidation. This illustrates the potential use of dual C-Cl isotope approach to distinguish between different degradation pathways (oxidation, hydrolytic dehalogenation and dihaloelimination). After overcoming the challenges in developing a stable culture, isolation of Dehalogenimonas became the next objective. To date, only three species belonging to Dehalogenimonas genus have been isolated and this study constituted the first evidence of a Dehalogenimonas culture enriched in Europe. The isolation approach consisted of the dilution to extinction method and the addition of selected antibiotics. After thirteen sequential transfer of this culture fed with 1,2-DCP-to-propene and two consecutive 10-7 dilutions followed by the addition of streptomycin for five transfers, a clone library of bacterial amplicons revealed that Dehalogenimonas sp. constituted 87 % of the predominant bacteria, followed by Desulfovibrio sp. (12 %) and unclassified Veillonellaceae (1 %). Further work is currently underway in our lab to isolate the Dehalogenimonas sp. In this study, a preliminary list of reductive dehalogenase (RDase) candidates involved in the transformation of 1,1,2-trichloroethane (1,1,2-TCA) and 1,2-dibromoethane (EDB) by this Dehalogenimonas culture was attempted using shotgun proteomics analysis (LTQ-Orbitrap). In addition, blue native polyacrylamide gel electrophoresis (BN-PAGE) approach combined with dechlorination activity assays were performed to identify the RDase responsible for 1,1,2-TCA ii Abstract dichloroelimination. Eventhough dechlorination activity was detected in a gel slice of the BN- PAGE of the culture growing with 1,1,2-TCA, no RDase was identified by neither liquid chromatography tandem mass spectrometry (LC-MS/MS) analysis nor sodium dodecyl sulfate- polyacrylamide gel electrophoresis (SDS-PAGE). The absence of RDase can be due to several reasons including low protein content and the
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