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Microbial Ecology of Phytoplankton Blooms of the Arabian Sea and Their Implications

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Microbial Ecology of Phytoplankton Blooms of the Arabian Sea and Their Implications Microbial Ecology of Phytoplankton Blooms of the Arabian Sea and their Implications A Thesis submitted to Goa University for the Award of the Degree of DOCTOR OF PHILOSOPHY IN MICROBIOLOGY 579' / 7__ 'e m / ehc. By Subhajit Basu (M.Sc.) Research Guide Prof Irene Furtado Goa University Taleigao, Goa AUGUST 2013 T - 6-3.1 ... With Dedication to Memories... O f Guruji and Baba, Who always inspired to pursue research. Declaration As required by .the Goa University ordinance OB-9.9, I state that the present thesis entitled “MICROBIAL ECOLOGY OF PHYTOPLANKTON BLOOMS OF THE A r a bia n Se a a n d t h e ir implications ” is my original contribution, and the same has not been submitted on any previous occasion. To the best of my knowledge the present study is the first comprehensive work of its kind from the study area. The literature related to the problem investigated has been cited. Due acknowledgements have been made wherever facilities and suggestions have been availed of. Subhajit Basu Department of Microbiology Goa University August 2013 Certificate This is to certify, that this thesis entitled “Microbial Ecology of Phytoplankton Blooms of the Arabian Sea and their implications”, submitted by Subhajit Basu for the award of the degree of Doctor of Philosophy in Microbiology is based on his original studies carried out under my guidance and supervision. The thesis or any part thereof has not been previously submitted for any other degree or diploma in any Universities or Institutions. Prof. Irene Furtado Research Guide and Supervisor Department of Microbiology Goa University Taleigao Plateau Goa-403206 August 2013 A cknowledgements I remain indebted to my mentor and guide Prof Irene Furtado for supervising me throughout the course of this PhD work. Training under my guide shaped orientation of thoughts to pursue research. My sincere acknowledgements of the unfailing patient supervision which helped to finally sail through in presenting this thesis, a journey which began during the ‘Advanced post-graduate diploma in Marine Microbiology and Technology’ (An UGC sponsored 1 year course in innovative teaching and research), conducted for a year during 2006-2007 at the Goa University, Department of Microbiology. I also sincerely acknowledge Dr M Sudhakar (Advisor; Ministry of Earth Sciences) in facilitating shipboard experience during this course; and to Dr SG Prabhu Matondkar (Former Senior Principal Scientist; National Institute of Oceanography-CSIR, Goa) for extending the rare opportunity to participate in FORV Sagar Sampada 253 cruise of March-2007 in the Northern Arabian Sea. Preliminary observations of bloom during this cruise led to the further proposal of this research work. I express my profound gratitude to my internal-guide Dr SG Prabhu Matondkar, and my sincere acknowledgments of his immense contribution in this thesis for all the assistance, discussions, and invaluable advice from his rich oceanographic experience, opportunities to participate in several cruises, extending laboratory facilities with prompt help and support whenever required throughout the course of this work. I acknowledge the critical assessment of this work provided by VC’s nominee Dr Savita Kerkar and by Prof GN Nayak, former Dean of Life Sciences and Environment. I am grateful to Prof. Satish R Shetye, Vice-Chancellor, Goa University and former Director, National Institute of Oceanography (CSIR), for allowing laboratory facilities and opportunity to carry out this research work. I convey my gratitude to Prof SK Dubey (Head of the Department), Dr S Nazareth, Dr S Garg of the department of Microbiology, Goa University and to Prof S Bhosle, Dean of Life Sciences and Environment, for all the support and help whenever required. I gratefully acknowledge the Space Application Centre (ISRO), Ahmedabad fellowships received during the period 2007-2010. Special thanks to Prof. Joaquim I Goes (Lamont Doherthy Earth Observatory, New York) for all the discussions. I was lucky enough to be working with him onboard three cruises and leamt oceanographic techniques hands-on, immensely benefiting from his expertise. I am also thankful to Dr AK Shukla and Dr KN Babu for training to process OCM-II images at the Space Application centre (ISRO) Ahmedabad, Goa and also the help provided by Dr. RM Dwivedi in providing some of the OCM images. My sincere acknowledgments to Dr S Shivaji (Director, LaCONES- CCMB) and Dr. Pavan Kumar Pindi of CCMB (CSIR) laboratories, Hyderabad for extending facilities and the brief hands-on experience received to carry out 16SrDNA sequencing and PCR techniques which helped later during this work. I also sincerely thank Prof Deepti D Deobagkar (Director, Bioinformatics centre, Pune-University) for all the discussions on phylogenetic analysis. • My sincere thanks also to S Sreepada and Dr NC Thakur at the National Institute of Oceanography, Goa for extending laboratory facilities at critical junctures; to Dr Helga-doR Gomes (Lamont Doherthy Earth Observatory, New York) for all your help and discussion during the cruises; and to Prof Colin R Roesler, Bowdein, USA for the brief discussion on analysis of C-DOM absorbtion spectra. I am also thankful to Dr RM Dwivedi, Mini Raman (Space Application Centre, ISRO, Ahmedabad), and Dr KB Padmakumar (CMLRE, Kochi) for help and co-operation during the cruises. Thanks also to all the cruise participants, to M/s Norinco staff, officers and crews of FORV Sagar Sampada, ORV Sagar Kanya and CRV Sagar Manjusha who have been always helpful and cooperative. To my colleagues Suraksha and Dr Sushma at NIO, Goa, thanks for the unstinted help, support and encouragements you have provided me and to my lab-mates Sherryanne, Sanika and Sushma in AF-36, Department of Microbiology, I thank you all for being there and providing help whenever it mattered most. It was my pleasure to be working with you all. To my family and friends, thanks for all your support, love and help as always to move ahead............ Subfiajit Basu Contents Chapter I Marine Phytoplankton blooms and associated Bacteria 1 1.1 Introduction 2 1.2 Factors regulating bloom formation 4 1.3 Marine Bacteria associated with Phytoplankton 12 1.4 Phytoplankton blooms of the Arabian Sea 29 Chapter II Microbial Ecology of Noctiluca miliaris bloom 33 2.1 Materials and Methods 2.1.1 Study Site and Cruise Tracks 35 2.1.2 Collection of bloom 3 8 2.1.3 Bloom and Non-bloom sampling stations 39 2.1.3.1 Chlorophyll a as indicator of bloom 39 2.1.3.2 Concentration of Noctiluca miliaris 40 2.1.4 Physical Charactersitics 42 2.1.4.1 Wind-speed 42 2.1.4.2 Photosynthetic available radiation 42 2.1.4.3 Hydrographic characteristics 42 2.1.4.4 Mesoscale-features 43 2.1.5 Chemical charactersitics 43 2.1.5.1 Dissolved Oxygen 43 2.1.5.2 Dissolved Inorganic nutrients 45 2.1.6 Organic matter production 49 2.1.6.1 Photosynthetic Carbon fixation 49 2.1.6.2 C-DOM 50 2.1.7 Microbial analysis 52 2.1.7.1 Evaluation of bacterial distribution 50 2.1.7.2 Heterotrophic Nanoflagellate counts 53 2.1.7.3 Bacterial Production rates 54 2.1.8 Data analysis 55 2.2 Results 2.2.1 Detection and tracking of bloom 56 2.2.2 Bloom and non-bloom sampling stations 58 2.2.3 Physical charactersitics 63 2.2.3.1 Wind-speed 63 2.2.3.2 Photosynthetic available radiation 63 2.2.3.3 Hydrographic charactersitics 65 2.2.3.4 Mesoscale-features 67 2.2.4 Chemical charactersitics 69 2.2.4.1 Dissolved oxygen 69 2.2.4.2 Dissolved inorganic nutrients 71 2.2.5 Organic carbon turnover 81 2.2.6 Chromophoric dissolved organic matter 82 2.2.7 Microbial distribution of N miliaris bloom 85 2.2.7.1 Heterotrophic bacteria 85 22.1.2 Bacterial Biomass Production rates 93 2.2.13 Autotrophic picocyanobacteria 96 2.2.7.4 Heterotrophic Nanoflagellates 100 2.2.7.5 Bacterial relationship with ecosystem components 102 2.3 Discussion 108 2.4 Salient results 113 Chapter III Microbial Ecology of Trichodesmium erythaeum bloom 118 3.1 Materials and Methods 3.1.1 Study Site and Cruise track 120 2.1.2 Collection of bloom 120 2.1.3 Bloom and Non-bloom sampling stations 120 2.1.3.1 HPLC analysis of bloom pigments 120 2.1.3.2 Concentration of Trichodesmium 121 3.1.4 Physical Characteristics 121 3.1.4.1 Wind-speed 121 3.1.4.2 Sea-surface temperature 121 3.1.5 Chemical charactersitics 121 3.1.5.1 Dissolved Oxygen 121 3.1.5.2 Dissolved Inorganic nutrients 121 3.1.6 Chromophoric dissolved organic matter (C-DOM) 122 3.1.7 Evaluation of Bacterial distribution 122 3.1.8 Data analysis 122 3.2 Results 3.2.1 Distribution of bloom 123 3.2.2 Chemotaxonomic analysis of bloom community 127 3.2.3 Physico-chemical environment of the bloom 128 3.2.3.1 Wind-speed 128 3.2.3.2 Sea-surface temperature 129 3.2.3.3 Dissolved Oxygen 130 3.2.3.4 Dissolved inorganic nutrients 131 3.2.4 Distribution of bacteria 135 3.2.5 C-DOM charactersitics 137 3.2.6 Bloom C-DOM-bacterial relationships 138 3.3 Discussion 142 3.4 Salient results 146 Chapter IV Phylogenetic characterization of the retrieved bacterial flora from the Arabian Sea Phytoplankton blooms 149 4.1 Materials and Methods 4.1.1 Collection of bloom samples 151 4.1.2 Enumeration and retrieval of bacteria 152 4.1.3 Phenotypic and biochemical characterization 153 4.1.4 Chemotaxonomic characterization 158 4.1.5 Molecular characterization 159 4.1.6 16SrDNA sequence analysis 160 4.1.7 Bacterial identification 161 4.1.8 Phylogenetic and community analysis 162 4.2 Results 4.2A Bacterial flora of N miliaris bloom phases 163 4.2A.1 Culturable bacterial load 164 4.2A.2 Description of flora: active and declining phase 164 4.2A.3 Phenotypic
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