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General Discusion IDENTIFICATION OF NITROGEN FIXING MICROSYMBIONTS FROM Mucuna bracteata NODULES SALWANI BINTI SHAFFIE UNIVERSITI SAINS MALAYSIA APRIL 2011 IDENTIFICATION OF NITROGEN FIXING MICROSYMBIONTS FROM Mucuna bracteata NODULES by SALWANI BINTI SHAFFIE Thesis submitted in fulfillment of the requirement for the degree of Master of Science APRIL 2011 ACKNOWLEDGEMENTS First and foremost to my supervisor, Dr. Amir Hamzah b. Ahmad Ghazali, I have only my sincerest gratitude for your endless supervision, counsel and encouragement. Thank you for your spent time and such patience with me over the years. My special thanks to Prof Nazalan Najimudin for your help, support and great idea especially for helping me in molecular part. To Kak Mun, Kak Ai, Kak Lin, Kak Wan, Ika, Poi Leng and Fatin, thank you for all those time you spent for supporting, teaching and helping me to finish my lab works and also complete the thesis. I enjoy being with you guys especially when we managed to catch the sneaky rats! My special dedication to Dr Sam Allen, for giving me a hand in finishing my thesis writing. Also not forgotten, to Kak Nurul Huda for cleaning my lab and your kind heart for lending me the chemicals and lab apparatus. From the bottom of my heart, thanks to all my friends throughout my life in USM for supporting me directly and indirectly. Last but not least, my deepest gratitude to my family especially my husband, Afdzal b. Nazri and wonderful baby, Syafinaz bt Afdzal. My deepest thanks also to my parents, Shaffie b. Isa and Sharifah Haryati bt. Sharif Jaafar and parents in law, Nazri b. Said and Raudzah bt. Abdullah for your understanding, sacrifices and never ending supports….. Above all, praise to ALLAH, for without HIS consent, none of this is possible. ii TABLE OF CONTENTS Page ACKNOWLEDGEMENTS ii TABLE OF CONTENTS iii LIST OF TABLES ix LIST OF FIGURES x LIST OF PLATES xi LIST OF ABBREVIATIONS xii ABSTRAK xiii ABSTRACT xv CHAPTER 1: INTRODUCTION 1 1.1 Objectives 4 CHAPTER 2: LITERATURE REVIEW 5 2.1 The Superiority of Mucuna bracteata As a Cover Crop 5 2.2 Nodulation of Leguminous Plant 5 2.3 The Importance of the N2 Fixation Process 7 2.4 Nitrogenase Enzyme 9 2.4.1 nifH gene 10 2.5 Evolution of Hydrogen During N2 Fixation 11 2.6 Uptake Hydrogenase Enzyme 12 2.7 Qubit System (N2 fixation laboratory package) 13 2.8 N2-Fixing Bacterial Symbiosis in Legume 14 2.9 Rhizobium sp. 15 2.10 Bradyrhizobium sp. 17 2.11 Isolation of Rhizobia 18 iii CHAPTER 3: ISOLATION AND CHARACTERIZATION OF N2-FIXING MICROSYMBIONTS FROM M. bracteata NODULES AND SCREENING FOR SYMBIOTIC ASSOCIATION 3.1 Introduction 19 3.2 Materials and Methods 21 3.2.1 Isolation 21 3.2.1.1 Collecting Nodules from the field 21 3.2.1.2 Isolation of microsymbionts from nodules 21 3.2.1.2.1 Yeast Extract Mannitol Broth (YEMB) and Yeast 22 Extract Mannitol Agar (YEMA) 3.2.1.2.2 Bromothymol blue (BTB) 22 3.2.1.3 Alkalinity and acidity production on YEMA 22 3.2.1.4 Growth characteristics on different media 23 3.2.1.4.1 Congo red dye 23 3.2.1.4.2 Peptone Glucose Agar (PGA) 23 3.2.1.5 Maintenance of bacterial culture 24 3.2.2 Bacterial Identification 24 3.2.2.1 Gram staining 24 3.2.2.1.1 Endospore staining for Gram positive strain 25 3.2.2.2 Bright field and Phase contrast microscopy test 25 3.2.2.3 Biochemical tests 25 3.2.2.3.1 Growth at various temperatures 26 3.2.2.3.2 Tolerance to various pH levels 26 3.2.2.3.3 Motility test 26 3.2.2.3.4 Oxidase test 26 3.2.2.3.5 Growth in 2% Sodium chloride (NaCl) 27 3.2.2.3.6 Growth in 0.1% Brilliant blue indicator 27 3.2.2.3.7 Utilization of different carbon sources 27 3.2.2.3.8 Utilization of different amino acid sources 28 3.2.2.3.9 Lysine decarboxylase test 28 3.2.2.3.10 Arginine dihydrolase 28 iv 3.2.2.3.11 Phenylalanine deaminase test 28 3.2.3 Plant Growth and Nodulation Screening 31 3.2.3.1 Surface sterilization and germination of M. bracteata seeds 31 3.2.3.2 Growth pot preparation 31 3.2.3.3 Bacterial inoculum preparation 31 3.2.3.3.1 Viable cell count using drop plate technique 32 3.2.3.4 Observation of inoculated M. bracteata under greenhouse 32 conditions. 3.2.3.5 Measurement of N2 fixation activity via H2 evolution test 33 3.2.3.6 Observation of plant growth at day of harvest 37 3.2.3.7 Leaf chlorophyll content 37 3.2.3.7.1 SPAD reading 37 3.2.3.7.2 Standard curve of leaf chlorophyll content 37 3.2.3.8 Leaf protein assay 38 3.2.3.9 Statistical analysis 39 3.3 Results 41 3.3.1 Bacterial Isolation 41 3.3.1.1 Growth rate of isolates 41 3.3.1.2 Colony characteristics 41 3.3.1.3 Growth characteristics on different media 47 3.3.2 Bacterial Identification 48 3.3.2.1 Microscopic characteristics 48 3.3.2.2 Biochemical tests 49 3.3.3 Plant Growth and Nodulation Screening 51 3.3.3.1 N2 fixation activity via H2 evolution test 51 3.3.3.2 Nodule observation and dry weight 53 3.3.3.3 Leaf chlorophyll content 55 3.3.3.4 Leaf protein content 56 3.3.3.5 Plant dry weight 57 3.3.3.6 Plant length 58 3.3.3.7 Number of leaves 61 v 3.4 Discussion 62 CHAPTER 4: MOLECULAR IDENTIFICATION OF N2-FIXING MICROSYMBIONT FROM NODULES OF Mucuna bracteata 4.1 Introduction 72 4.2 Materials and Methods 75 4.2.1 Luria Bertani (LB) Medium 75 4.2.2 Genomic DNA extraction 75 4.2.2.1Gel electrophoresis 76 4.2.2.2 Tris-Acetate-EDTA (TAE) buffer 77 4.2.3 Genomic DNA quantification 77 4.2.4 Molecular identification of microsymbionts through partial 16S rDNA 78 sequence analysis 4.2.4.1 PCR amplification of partial 16S rRNA gene 78 4.2.4.2 Partial 16S rRNA gene PCR product purification 79 4.2.4.3 Ligation with pGEM-T Cloning Vector 79 4.2.4.4 Escherichia coli JM109 (Competent cell) Preparation 80 4.2.4.5 Transformation 80 4.2.4.6 Plasmid Extraction 81 4.2.4.7 Confirmation of inserted partial 16S rRNA gene with enzyme 82 digestion 4.2.4.8 Sequencing of Recombinant pGEM-T with partial 16S rRNA 82 gene 4.2.5 Detection of nifH gene 84 4.2.5.1 Amplification of nifH gene 84 4.2.5.2 Purification of nifH gene 86 4.2.5.3 Sequencing of nifH gene 86 4.3 Results 87 4.3.1 Genomic DNA extraction 87 4.3.1.2 Genomic DNA quantification 88 vi 4.3.2 Molecular identification of microsymbionts using partial 16S rDNA 89 sequence analysis 4.3.2.1 PCR amplification of partial 16S rRNA gene 89 4.3.2.2 Cloning of partial 16S r rRNA gene 89 4.3.2.3 Plasmid Extraction 90 4.3.2.4 Confirmation of insert with enzyme digestion 90 4.3.2.5 Sequencing of recombinant pGEM-T with partial 16S rRNA 91 gene 4.3.3 Detection of nifH gene 92 4.3.3.1 Amplification of nifH gene 92 4.3.3.2 Sequencing of nifH gene 94 4.5 Discussion 95 100 CHAPTER 6: GENERAL DISCUSSION AND CONCLUSION REFERENCES 113 APPENDIX A: Standard curve of leaf chlorophyll content for M. bracteata. 129 APPENDIX B: Standard curve of protein content for M. bracteata. 129 APPENDIX C: Statistical analysis for plant growth of M. bracteata using SPSS 130 V.15.0. APPENDIX D: DNA extraction kit 132 APPENDIX E: Degenerate nucleotides/ bases. 132 APPENDIX F: PCR product purification kit 133 APPENDIX G: Plasmid (pGEM-T) 133 APPENDIX H: Preparation for 100 ml of 1X TSS solution 133 APPENDIX I: Preparation for 100 ml of 50 μg/ml X-Gal solution 134 APPENDIX J: Preparation for 100 μl of 0.1M IPTG solution 134 APPENDIX K: Plasmid purification kit 135 APPENDIX L: Enzyme digestion (Not1 and EcoR1) 135 vii APPENDIX M:. DNA marker 136 APPENDIX N: The detailed descriptions of 16S rDNA sequence of the strains obtained from the Blastn in NCBI 137 APPENDIX O: The detailed descriptions of nifH sequence of the strains obtained 150 from the Blastn in NCBI LIST OF PUBLICATIONS 154 viii LIST OF TABLES Tables Page 3.1 Ingredients (g/L) for Yeast Mannitol Broth (YEMB) and Yeast Mannitol 22 Agar (YEMA) preparation 3.2 Ingredients (g/L) for Peptone Glucose Agar (PGA) medium preparation 23 3.3 Treatments for planting M. bracteata in greenhouse 33 3.4 Morphology and biochemical characteristics of isolated microsymbionts from 41 M.bracteata root nodules 4.1 Ingredient (g/L) for Luria Bertani (LB) medium preparation 75 4.2 List of primer set used for nifH gene PCR amplification. 84 4.3 nifH gene PCR profile for primer nifH1 and nifH2 85 4.4 nifH gene PCR profile for primer nifH3 and nifH4 85 4.5 Genomic DNA quantification via UV spectrophotometer 88 4.6 BLASTn analysis of partial 16S rDNA sequences of 13 microsymbionts 91 isolated from the root nodules of M.
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