BIOSURFACTANT PRODUCTION AND APPLICATIONS IN OIL CONTAMINATE CONTROL by ©Qinhong Cai A thesis submitted to the School of Graduate Studies in partial fulfillment of the requirements for the Degree of Doctor of Philosophy Faculty of Engineering and Applied Science Memorial University of Newfoundland May 2019 St. John’s Newfoundland and Labrador Canada ABSTRACT Surfactants are a versatile group of chemicals. They are amphiphilic compounds that exert impacts at interfaces among air, water, oil, and solid phases. Currently, the prevalent players in the market are chemically synthesized surfactants, which have concerns of considerable toxicity and low biodegradability. Because they are mainly derived from fossil fuels, they are not sustainable in the long run and the production costs are subjected to the price variance of raw materials. In view of these limitations, biosurfactants have been proposed as promising alternatives. They are surfactant molecules produced by microorganisms during their growth. Biosurfactants exist naturally in the environment and play some roles in the ecosystem even without human interferences. In this dissertation we define this virtue as “environmental friendly”. They are also renewable and non/less toxic. They have also been found with the intriguing advantages such as enormous structural diversity, lower critical micellar concentrations (CMCs), and the feasibility to use renewable and/or waste streams as the source of production. Biosurfactants are considered as multifunctional biomolecules of the 21st century with a thriving global market share. Their applications in environmental and oil industries are among the top market sectors thanks to their environmental friendly nature. In order to harness the power of biosurfactants, the economic effectiveness of production of these molecules needs improvements. The inocula/microorganisms are the engine of a production process, which determine the maximum yield potential and the functionality of biosurfactants, yet limited inocula have been reported. The functional I diversity of biosurfactants includes emulsification, dissolution, dispersion, emulsion breaking, reduction in viscosity, and surface activity, which result in a broad spectrum of potential applications in oil contaminate control including soil washing, enhanced bioremediation, oily wastewater treatment, and spilled oil dispersion. However, limited research efforts have been placed into evaluating the application potential of biosurfactants in oil contaminate control. The objectives of this thesis are to 1) identify novel and robust biosurfactant producing microorganisms and develop hyper-production mutants; 2) examine the functionality of the produced biosurfactants; and 3) investigate the potential of using these produced biosurfactants in diverse applications of oil contaminate control. The outputs of the thesis include: (1) the successful isolation, identification, characterization and functionality analysis of one-hundred-and-fourteen biosurfactant producing and oil degrading marine bacteria; (2) the discovery of a novel bacterial species, Alcanivorax atlaticus for the first time and its proposed type strain with comprehensive genotype and phenotype characterizations; (3) an in-depth characterization, functionality analysis and application demonstration of a novel bioemulsifier (exmulsins) and its bacterium (Exiguobacterium sp. N4-1P); (4) reporting of thirty-seven novel oil-in-water emulsion breaking marine bacteria for oily wastewater treatment, and a recommended screening strategy for their identification; (5) the first attempt to genetically modify Rhodococcus strains for hyper production of biosurfactant and to investigate the dispersing abilities of the the produced biosurfactants; and (6) a comprehensive investigation of 4 II types of biosurfactants produced from selected isolates and mutants as marine oil spill dispersants. III ACKNOWLEDGEMENTS Foremost, I would like to express my sincere gratitude to my supervisors, Dr. Baiyu Zhang and Dr. Bing Chen. They patiently provided the vision, encouragement, advice and support necessary for me to proceed through the program. Most importantly, they recognized my potential and inspired me to be a researcher. They have been caring, nuturing and supportive throughout my program. In the meantime, they have always encouraged innovation and trained me in critical thinking and independent research. Special thanks to my supervisory committee member, Dr. Timothy Nedwed and my co- author Dr. Yumin Zhao for their support, guidance and helpful suggestions. I gratefully acknowledge the Natural Sciences and Engineering Research Council of Canada (NSERC), Research and Development Corporation Newfoundland and Labrador (NL-RDC) and School of Graduate Studies at the Memorial University of Newfoundland (MUN) for providing financial support. My further appreciation goes to Zhiwen Zhu, Weiyun Lin, Pu Li, Liang Jing, Xudong Ye, Xing Song, Yongrui Pi, Fuqiang Fan, Ze Lv, Samira Narimannejad and Tong Cao for their assistance in sampling, sample and data analysis and their invaluable friendship. Other than them, I would also thank Hongjing Wu, Jisi Zheng, Bo Liu, Masood Ahmad, He Zhang, Zelin Li, Yunwen Tao, Xixi Li, Min Yang at The Northern Region Persistent Organic Pollution Control (NRPOP) Laboratory for their friendship and support during my PhD program. I wish to thank my Mom, Hong Peng for her unconditional love which supports me pursuing my dreams. My gratitude also goes to all my family members and friends. IV TABLE OF CONTENT ABSTRACT…. .................................................................................................................... I ACKNOWLEDGEMENTS .............................................................................................. IV TABLE OF CONTENT ..................................................................................................... V LIST OF TABLES ............................................................................................................ XI LIST OF FIGURES ....................................................................................................... XIII LIST OF ABBREVIATIONS AND SYMBOLS .......................................................... XVI CHAPTER 1 INTRODUCTION AND OVERVIEW ........................................................ 1 1.1 Background .......................................................................................................... 2 1.2 Structural Properties of Biosurfactants and their Classification .......................... 4 1.3 Production of Biosurfactants ................................................................................ 9 1.4 Biosurfactant Functionality and Applications in the Oil Contaminate Control . 11 1.5 Objectives and Structure of the Thesis ............................................................... 14 CHAPTER 2 SCREENING OF BIOSURFACTANT-PRODUCING BACTERIA FROM OFFSHORE OIL AND GAS PLATFORMS IN NORTH ATLANTIC CANADA ........ 19 2.1 Introduction ........................................................................................................ 20 2.2 Materials and Methods ....................................................................................... 22 2.2.1 Samples for the isolation ............................................................................. 22 2.2.2 Screening and isolation ............................................................................... 24 2.2.3 Identification and phylogenetic analysis of isolates ................................... 25 2.2.4 Performance of the isolated biosurfactant producers .................................. 26 2.2.5 Diversity analysis ........................................................................................ 27 2.3 Results and Discussion ....................................................................................... 27 2.3.1 Phylogenetic analysis of isolates ................................................................ 27 2.3.2 Distribution and diversity of the isolates .................................................... 40 V 2.3.3 Performance evaluation of all isolated biosurfactant producers ................. 43 2.4 Summary ............................................................................................................ 48 CHAPTER 3 ALCANIVORAX ATLATICUS SP. NOV., A BIOSURFACTANT PRODUCING AND ALKANE DEGRADING BACTERIUM ISOLATED FROM PETROLEUM HYDROCARBON CONTAMINATED COASTAL SEDIMENT ......... 50 3.1 Introduction ........................................................................................................ 51 3.2 Methodology ...................................................................................................... 52 3.2.1 Isolation of the bacterial strain .................................................................... 52 3.2.2 16S rDNA sequencing and phylogenetic analysis ...................................... 53 3.2.3 Cell morphology analysis ........................................................................... 53 3.2.4 Bacterial growth conditions and bacterial motility ..................................... 54 3.2.5 Biochemical tests ........................................................................................ 55 3.2.6 Membrane-based phospholipid-derived fatty acid (PLFA) analysis .......... 55 3.2.7 Complete genome sequencing .................................................................... 56 3.2.8 Biosurfactant production ............................................................................