PREVALENCE, RISK ASSESSMENT AND SURVIVAL KINETICS OF INDICATOR AND PATHOGENIC BACTERIA IN WATER, SEDIMENT AND BIVALVE SHELLFISH FROM COCHIN ESTUARY Thesis submitted to Cochin University of Science and Technology in Partial Fulfilment of the Requirements for the Award of the Degree of Doctor of Philosophy in Microbiology Under the Faculty of Marine Sciences By ALLY C. ANTONY Reg. No: 3947 DEPARTMENT OF MARINE BIOLOGY, MICROBIOLOGY AND BIOCHEMISTRY SCHOOL OF MARINE SCIENCES COCHIN UNIVERSITY OF SCIENCE AND TECHNOLOGY KOCHI –682 016, INDIA May 2017 Prevalence, Risk Assessment and Survival Kinetics of Indicator and Pathogenic Bacteria in Water, Sediment and Bivalve Shellfish from Cochin Estuary Ph.D. Thesis under the Faculty of Marine Sciences Author Ally C. Antony Research Scholar Department of Marine Biology, Microbiology and Biochemistry School of Marine Sciences Cochin University of Science and Technology Kochi – 682 016 Supervising Guide Dr. A. A. Mohamed Hatha Professor Department of Marine Biology, Microbiology and Biochemistry School of Marine Sciences Cochin University of Science and Technology Kochi – 682 016 Department of Marine Biology, Microbiology and Biochemistry School of Marine Sciences Cochin University of Science and Technology Kochi – 682 016 May 2017 Department of Marine Biology, Microbiology and Biochemistry School of Marine Sciences Cochin University of Science and Technology Kochi – 682 016 Dr. A. A Mohamed Hatha Professor This is to certify that the thesis entitled “Prevalence, Risk Assessment and Survival Kinetics of Indicator and Pathogenic Bacteria in Water, Sediment and Bivalve Shellfish from Cochin Estuary” is an authentic record of research work carried out by Ms. Ally C. Antony under my supervision and guidance in the Department of the Marine Biology, Microbiology and Biochemistry, School of Marine Sciences, Cochin University of Science and Technology, in partial fulfilment of the requirements for the award of the degree of Doctor of Philosophy in Microbiology of Cochin University of Science and Technology, and no part thereof has been presented for the award of any other degree, diploma or associateship in any other University or Institution. All the relevant corrections and modifications suggested by the audience during the pre-submission seminar and recommended by the Doctoral Committee have been incorporated in the thesis. Kochi - 682 016 Prof. (Dr.) A. A. Mohamed Hatha May 2017 (Supervising Guide) I hereby declare that the thesis entitled “Prevalence, Risk Assessment and Survival Kinetics of Indicator and Pathogenic Bacteria in Water, Sediment and Bivalve Shellfish from Cochin Estuary” is a genuine record of research work done by me under the supervision and guidance of Dr. A. A. Mohamed Hatha, Professor, Department of Marine Biology, Microbiology and Biochemistry, Cochin University of Science and Technology and no part thereof has been presented for the award of any other degree, diploma or associateship in any other University or Institution earlier. Kochi - 682 016 Ally C. Antony May 2017 It gives me immense pleasure to gratefully acknowledge all those who have helped me in making of this thesis possible. First and foremost let me acknowledge my Lord Jesus Christ for the tremendous support and blessing showered upon me throughout this journey. “I can do all things through him who strengthens me”. Throughout my venture I enjoyed the powerful guidance of the holy spirit without whom this thesis would not have been accomplished. I would like to express my sincere gratitude to my supervising guide Dr. A. A. Mohamed Hatha, Professor, Department of Marine Biology, Microbiology and Biochemistry, for his immense support, guidance and encouragement throughout the course of my Ph.D. programme. His valuable advice, vision and the kind of passion he himself kept for research, has inspired me to undertake my research work more seriously. The freedom and flexibility that I was granted during my work needs special mention, as it has helped a lot to improve my individual research skills, making me more independent and confident. I would like to thank him for being so kind to me in correcting the thesis in very short span of time, in spite of his busy schedule. The valuable suggestions rendered have contributed significantly in improving the thesis. I gratefully acknowledge all the past and present HODs of the Department of Marine Biology, Microbiology and Biochemistry and the present and past Directors of the School of Marine Sciences for allowing me to use the facilities of the institution. I am deeply grateful to the faculty members Dr. Rosamma Philip, Dr. A. V. Saramma, Dr. Bijoy Nandan, Dr. Aneykutty Joseph, and Dr. Babu Philip for their expert advice and valuable suggestions which helped me to improve my work. I am highly indebted to Dr. A. V. Saramma, for kindly introducing and recommending me as research student to my supervisor Dr. A. A. Mohamed Hatha, which has enabled me to get enrolled in this prestigious institution. I sincerely acknowledge the University Grants Commission for providing me FIP teacher fellowship to pursue Ph.D programme. I also place on record my sincere gratitude to the Management and the Principal, M.E.S College, Marampally for permitting me to avail the teacher fellowship giving all the support which enabled me to undertake this Ph.D programme. I would like to thank the administrative office staff of the Department of Marine Biology, Microbiology and Biochemistry, the Librarian and other staff of the School of Marine Sciences Library for the support rendered to me during the research. I gratefully acknowledge Dr. M. Mini, Professor, College of Veterinary and Animal Sciences, Mannuthy for sharing her knowledge which was helpful for me in the initial phase in designing my research work. I’m thankful for my lab mates for their co-operation and accepting me as one among them, which made the journey much comfortable and happier. It will be ungrateful from my part if I do not acknowledge their contributions. My special thanks are due to Reshma Silvester, for sparing her valuable time in teaching me the basics of molecular biology and for proof reading of my manuscripts and thesis. I place on record my sincere thanks to Dr. Vipindas for kindly sharing his valuable knowledge and helping me in meeting some of my objectives. I am highly indebted to Ajith Joseph, for his sincere help in formatting my reference in a very perfect manner. I would like to express my sincere gratitude to Ms. Debora for her valuable suggestions, sharing her knowledge as well as proof reading my whole thesis carefully in very short span of time. My sincere thanks are due to Dr. Mujeeb Rahiman, who very kindly shared his knowledge, taught us many things and offered all help wherever possible. I express my gratitude to Divya P. S. for helping me a lot, especially in the initial part of my work. My special thanks are due to my companion Aneesa. Our train journeys were platforms for active discussions, sharing and with nostalgia I cherish those memories. My special thanks are due to my friends Soumya Krishnankutty, Bini Francis, Jesmi Yousuf, Jabir T, Ajin Madhav, Nifty, Neethu, Soumya M, ThasneemT.R, Nashad, Vishnu P.S, Satheesh T.B, Suresh, Gigi, Vincent, Dr. Jaseetha, Jemi and Vishnupriya for their kind cooperation and help offered whenever required. I fondly acknowledge Sajna and my friends from other labs Manomi, Bhavya, Sruthy, Rosmine, Solly, Neema Job, and Abhijith for the timely help rendered. I express my sincere gratitude to the HOD, Dr. Manzurali P.P and all other faculty members of the Department of Biosciences, M.E.S College, Marampally for their tremendous support. I express my heartfelt thanks to Dr. Mini K. Paul for her moral support and encouragement and Dr. Umesh B. T. for helping me to get all the office correspondence done on time, throughout my FIP period. I also thank Mr. Vivas Salim for his wonderful expertise in photo editing which was very much useful in my thesis preparation. I am happy to acknowledge Ms. Annu Mariya for handling my classes during the period of my absence in the college. I gratefully acknowledge Rev. Fr. Kuriakose Cheruvallil for strengthening me spiritually through his kind visits, sincere prayers and blessings. With deep sense of gratitude I acknowledge the prayers of Rev. Fr. George Koilparambil, Rev. Fr Robin Kuzhinjalil and Rev. Fr. Stenny Kunnekkadan. I also thank Sr. Flowry, Sr. Nitha and Sr. Joycy for their constant prayers and blessings throughout my venture. I bow before the memories of my beloved parents, late Mr. C.J. Antony and late Mrs. Flower Antony and deeply acknowledge their love, sacrifice, blessings and prayers which helped in bringing me this far. I also fondly remember and acknowledge the advice and support rendered by my beloved father in law, late Mr. K.O.George. I thank my sisters Mrs. Latha Jose, Mrs. Jancy Biju, Mrs. Joycy Seby and brothers in law Mr. Biju Jose and Mr. Seby Manavalan for their sincere love, care and prayers. I gratefully acknowledge Mr. Jose K.F, who has whole heartedly supported and motivated me as my guardian throughout my academic life, without which I could not have gone this far. I fondly remember my brother Mr. John C.A and sister in law Mrs. Simmy John for their love and prayers. I also acknowledge the moral support and encouragement received from my husbands’ brothers Mr. Joshy George and Dr. Varghese Jaison, co-sisters Mrs. Asha Joshi, Mrs. Liza Joy and Dr. Laly Jaison. I gratefully acknowledge Dr. Joy George for the goodwill, advice and affection shown towards me and for procuring me some of the essential requirements necessary to carry out my research work. Last but not the least let me acknowledge my family who has stood as a pillar of support as I pursued my passion for research.