The effect of soil samples on growth, phenotype, and the root microbiome of tubtim chum phae rice (oryza sativa)

THAI NGUYEN UNIVERSITY UNIVERSITY OF AGRICULTURE AND FORESTRY NGUYEN THI MY DUYEN TOPIC TITLE: THE EFFECT OF SOIL SAMPLES ON GROWTH, PHENOTYPE, AND THE ROOT MICROBIOME OF TUBTIM CHUM PHAE RICE (ORYZA SATIVA) BACHELOR THESIS Study Mode : Full – time Major : Biotechnology Faculty : Biotechnology and Food Technology Batch : 2014 – 2018 Thai Nguyen, 05/06/2018 THAI NGUYEN UNIVERSITY UNIVERSITY OF AGRICULTURE AND FORESTRY NGUYEN THI MY DUYEN TOPIC TITLE: THE EFFECT OF SOIL SAMPLES ON GROWTH, PHENOTYPE, AND THE ROOT MICROBIOME OF TUBTIM CHUM PHAE RICE (ORYZA SATIVA) BACHELOR THESIS Study Mode : Full - time Major : Biotechnology Faculty : Biotechnology and Food Technology Batch : 2014 – 2018 Supervisors : Dr Songsak Wattanachaisaereekul Dr Nguyen Xuan Vu MSc Phimrak Khaokhajorn Thai Nguyen, 05/06/2018 i DOCUMENTATION PAGE WITH ABSTRACT Thai Nguyen University of Agriculture and Forestry Major Biotechnology Student name Nguyen Thi My Duyen Student ID DTN1451150003 The effect of soil samples on growth, phenotype and the root microbiome of Tubtim Chum Phae rice Thesis Title (Oryza Sativa) Dr Songsak Wattanachaisaereekul Supervisors Dr Nguyen Xuan Vu MSc Phimrak Khaokhajorn Abstract: Tubtim Chum Phae rice is rice from hybridization between Hom Mali rice and Sung Yod rice It can be grown all year round and in all regions of Thailand It is known that rice contain a number of nutrients and bioactive compounds, including dietary fiber and phytochemicals with potent antioxidant activities Hypertension appears to have a complex association with endothelial dysfunction and oxidative stress When people regularly eat Tubtim Chum Phae rice, it will reduce myocardial infarction risk, as for dyslipidemic subjects, it has been reported that can improve low-density lipoprotein (LDL)- and high-density lipoprotein (HDL)-cholesterol concentrations and enhance cellular cholesterol efflux to serum and anti-oxidant effects, anti-inflammatory effects, cancer risk The purpose of this study is to study and point out the difference of soil sample groups to growth, phenotype and microbiome system of root in the revolution of Tubtim Chum Phae rice Keywords: Tubtim Chum Phae, growth and phenotype of rice plant, microbiome system Number of pages: Date of Submission: ii ACKNOWLEDGMENTS First and foremost, I would like to express my sincere and deepest gratitude to my supervisor, Dr Songsak Wattanachaisaereekul from the School of Bioresources and Technology, King Mongkut’s University of Technology Thonburi (KMUTT), Thailand, who providing me the opportunity to conduct research in his lab and giving me endless support during the internship since December 15th, 2017 to May 30th, 2018 and then special thank and highly thankful goes to my advisors Msc Phimrak Khaokhajorn from the School of Bioresources and Technology, King Mongkut’s University of Technology Thonburi (KMUTT), Thailand, who cared so much about my work, and who responded to my questions and queries so promptly, for their patience, motivation, enthusiasm, and immense knowledge I have been extremely lucky to have a supervisor and one advisor like them I would also like to thank P’Phan, one staff from Fungal Biotechnology, the School of Bioresources and Technology, King Mongkut’s University of Technology Thonburi (KMUTT), Thailand and Dr Nguyen Xuan Vu from the Biotechnology and Food Department of Thai Nguyen University of Agriculture and Forestry (TUAF), Thai Nguyen City, Vietnam, who used to help, support and give me encouragements during this thesis implementation Last but not the least; I would like to thank my family: my Mother, for giving birth to me at the first place and supporting me spiritually throughout my life Many thank you and best regards Student Nguyen Thi My Duyen iii CONTENT DOCUMENTATION PAGE WITH ABSTRACT ACKNOWLEDGMENTS iii CONTENT iv LIST OF ABBREVIATIONS vi LIST OF TABLE vii LIST OF FIGURE viii PART INTRODUCTION 1.1 Tubtim Chum Phae rice 1.1.1 Important of Tubtim Chum Phae rice 1.1.2 Life cycle of Tubtim Chum Phae rice 1.2 Microbiota 1.2.1 Plant microbiota 1.2.2 Rice microbiota 1.2.3 Microbiome engineering 1.2.4 Microbiota application for plant growth promote 1.3 Types of soil sample 1.3.1 Chemical soil 1.3.2 Intensive Chemical soil 1.3.3 Transition soil 10 1.4 Objectives 10 PART METHODOLOGY 11 2.1 Equipment and materials 11 2.1.1 Equipment 11 2.1.2 Materials 11 2.2 Methods 13 2.2.1 Soil sample preparation 13 2.2.2 Rice germination 14 2.2.3 Rice growing 14 iv 2.2.4 Rice phenotype observation 15 2.2.5 Measure pH of soil sample 15 2.3 Inspection of quantity microbiome in Chemical, Intensive Chemical, Transition soil by DNA extraction 16 2.4 Measure Nanodrop 17 PART RESULTS AND DISCUSSIONS 19 3.1 The effect of the soil on the revolution of a rice plant with each Chemical, Intensive Chemical and Transition soil group 19 3.1.1 Comparison the different of rice plant about the color of rice leaves and the tiller number of rice plant in Chemical soil group 20 3.1.2 Comparison the different of rice plant about the color of rice leaves and the tiller number of rice plant in Intensive Chemical soil group 22 3.1.3 Comparison the different of rice plant about the color of rice leaves and tiller number of rice plant in Transition soil group 23 3.1.4 Comparison the different of rice plant between Chemical soil, Intensive Chemical soil, Transition soil groups 26 3.1.5 Observation of the change of pH in three types of soil sample 28 3.2 The result of Nanodrop 29 3.3 The result of DNA extraction for check microbiome from soil samples 30 PART CONCLUSIONS AND SUGESTIONS 32 REFERENCES 33 v LIST OF ABBREVIATIONS G Gram Mg Milligram Kg Kilogram µl Microliter Min Minute Hrs Hour mL Milliliter C Chemical soil I Intensive Chemical soil T Transition soil Rpm Revolution per DNA Deoxyribonucleic acid EDTA Ethylenediaminetetraacetic acid TAE Tris- acetate-EDTA Ng Nano gram Kb Kilo base °C Degree Celsius DI Deionized NaCl Sodium Chloride NaOH Sodium hydroxide SDS Sodium dodecyl sulfate PEG Polyethylene glycol vi LIST OF TABLE Table 2.1 Equipment used for studies 11 Table 2.2 DNA extraction buffer 12 Table 2.3 Data of soil sample collected from somewhere in Thailand 13 Table 2.4 Weight amount of the soil sample in growth rice plant 14 Table 3.1 Variation in the phenotype of rice plant in Chemical soil group after every week from week until week 20 Table 3.2 Variation in the phenotype of rice plant in Intensive Chemical soil after every week from week until week 22 Table 3.3 Variation in the phenotype of rice plant in Intensive Chemical soil after every week from week until week 24 Table 3.4 Variation in the phenotype of rice plant between three soil groups after every week from week until week 26 Table 3.5 Calculation the average of pH all of soil sample to observe the different of soil to rice plant 28 Table 3.6 The result of Nanodrop after DNA extraction 29 vii LIST OF FIGURE Figure 1.1 Growth stages of the rice plant Part of the image collection of the International Rice Research Institute (IRRI) Figure 1.2 Plant-growth promoting microbes are capable of conferring benefits to multiple species of plant hosts, and of offering improved tolerance to multiple stresses simultaneously (Image from Coleman-Derr at al Front Microbiol., 06 June 2014) Figure 3.1 Comparison the average of the tiller number of rice plant in Chemical soil group from week until week 21 Figure 3.2 Comparison the average of the tiller number of rice plant in Intensive Chemical soil group from week until week 23 Figure 3.3 Compared average of the tiller number of rice plant in Transition soil group from week until week 25 Figure 3.4 Comparison the average of the tiller number of rice plant in Chemical soil, Intensive Chemical soil, Transition soil group from week until week 27 Figure 3.5 The average of pH of soil sample during growth rice progress and compare the differences between each sample 28 Figure 3.6 The result of electrophoresis of DNA from soil samples of the best rice plant Land M: Kb DNA ladder, land 2: C2/1, land 2: C2/2, land 3: C2/3, land 4: I2/1, land 5: I2/2, land 6: I2/3, land 7: O3/1, land 8: O3/2, land 9: O3/3 30 viii ... UNIVERSITY OF AGRICULTURE AND FORESTRY NGUYEN THI MY DUYEN TOPIC TITLE: THE EFFECT OF SOIL SAMPLES ON GROWTH, PHENOTYPE, AND THE ROOT MICROBIOME OF TUBTIM CHUM PHAE RICE (ORYZA SATIVA) BACHELOR THESIS... study and point out the difference of soil sample groups to growth, phenotype and microbiome system of root in the revolution of Tubtim Chum Phae rice Keywords: Tubtim Chum Phae, growth and phenotype... Weight soil samples and 500g of soil standard and 48g rice bran was mixed with cow dung in the bag and mix well together Then, pour into pot and added more kg of soil standard and mixed continue