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GM Maize Crops and Plant Growth-Promoting Characterization of the Isolated Strains Analysis of Bacterial Diversity in the Rhizosphere of GM and Non- GM Maize Crops and Plant Growth-Promoting Characterization of the Isolated Strains By NASEER AHMAD Department of Plant Sciences Faculty of Biological Sciences Quaid-i-Azam University Islamabad-Pakistan 2013 Analysis of Bacterial Diversity in the Rhizosphere of GM and Non-GM Maize Crops and Plant Growth-Promoting Characterization of the Isolated Strains A thesis submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy By NASEER AHMAD Department of Plant Sciences Faculty of Biological Sciences Quaid-i-Azam University Islamabad-Pakistan 2013 i DECLARATION OF ORIGINALITY I hereby declare that the work accomplished in this thesis is the result of my own research carried out in the Molecular Systematics and Applied Ethnobotany Lab, Department of Biotechnology, Quaid-i-Azam University Islamabad. This thesis has not been published previously nor does it contain any material from the published resources that can be considered as the violation of international copyright law. Furthermore I also declare that I am aware of the terms ‘copyright’ and ‘plagiarism’ and if any copyright violation was found out in this work I will be responsible of the consequences of any such violation. Signature: _________ Name: Naseer Ahmad Date: / /2013 ii CERTIFICATE This thesis submitted by Mr. Naseer Ahmad, is accepted in its present form by the Department of Plant Sciences, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad as satisfying the thesis requirements for the degree of Doctor of Philosophy (Plant Sciences). Supervisor Prof. Dr. Zabta Khan Shinwari Chairman Department of Biotechnology External examiner External examiner Chairperson Prof. Dr. Asghari Bano Chairperson Department of Plant Sciences Date: / / iii This thesis is dedicated with love and gratitude To My Parents Who taught me the first word to speak, the first alphabet to write, the first step to take and have raised me to be the person I am today. iv v AUTHOR DECLARATION I hereby declare that I am the sole author of this thesis. This is a true copy of the thesis, including any required final revisions, as accepted by my examiners and supervisor. Any errors in the thesis are only mine. Naseer Ahmad vi LIST OF CONTENTS DECLARATION OF ORIGINALITY ........................................................................... ii CERTIFICATE ................................................................................................................ iii LIST OF TABLES ......................................................................................................... xvi LIST OF FIGURES ..................................................................................................... xviii LIST OF ABBREVIATIONS ........................................................................................ xx ACKNOWLEDGEMENTS ........................................................................................ xxiii ABSTRACT ................................................................................................................. xxvi 1. INTRODUCTION .............................................................................................. 1 1.1. Brief summary of the genetically modified (GM) plants ..................................... 1 1.1.1. Biosafety concerns of GM plants ................................................................. 2 1.1.2. The impact of GM crops on soil microorganisms ....................................... 2 1.1.3. Impacts of GM plants on environment ........................................................ 4 1.1.4. Impact of GM maize on animals .................................................................. 6 1.1.5. Effects of GM crops on fungi ...................................................................... 6 1.1.6. Effects GM crops on non-target insects ....................................................... 7 1.1.7. Cross pollination and gene flow in GM maize crops ................................... 8 1.2. Rhizospheric bacterial community ....................................................................... 9 1.2.1. Soil as a reservoir for microbial diversity .................................................... 9 1.2.2. Why soil serves as a habitat for such enormous microbial diversity ........... 9 1.2.3. Rhizosphere bacterial diversity analysis based on cultured based approaches ..................................................................................................... 10 1.2.4. Rhizosphrere bacterial diversity on direct metagenomic based approaches 11 vii 1.2.5. Next-generation sequencing (NGS) ........................................................... 11 1.2.6. Pyrosequencing based approaches for rhizosphere microbial community analysis .......................................................................................................... 11 1.3. Plant microbe interactions .................................................................................. 15 1.3.1. The way plant and microbe interacts with each other ............................... 16 1.3.2. Culturing uncultured microbes as a source of secondary metabolites ....... 17 1.3.3. Plant growth promotion characterization ................................................... 22 1.3.4. Plant growth promoting rhizobacteria ....................................................... 22 1.3.5. Mechanisms of plant growth promotion .................................................... 22 1.3.6. PGPR as biofertilizers ................................................................................ 23 1.3.7. Phosphate solubilization ............................................................................ 23 1.3.8. Nitrogen fixation ........................................................................................ 23 1.3.9. PGPR as phytostimulators ......................................................................... 24 1.3.10. Indole acetic acid (IAA) ............................................................................ 24 1.4. Functional characterization ................................................................................ 25 1.4.1. PGPR as biocontrol agents ........................................................................ 25 1.4.2. Biocontrol mechanisms of PGPR .............................................................. 25 1.4.3. Competition for nutrients ........................................................................... 25 1.4.4. Antibiotics production ............................................................................... 25 1.4.5. Production of lytic enzymes ...................................................................... 26 1.4.6. Niche exclusion .......................................................................................... 26 1.5. Hypothesis .......................................................................................................... 27 1.6. Research objectives ............................................................................................ 27 2. REVIEW OF LITERATURE ......................................................................... 28 2.1. Biosafety issues related to transgenic crops ....................................................... 28 2.2. Transgenics plants and their impacts on soil microbes ...................................... 30 2.3. Rhizospheric bacterial diversity ......................................................................... 31 viii 2.4. Culture based approaches .................................................................................. 33 2.5. Culture independent approaches ......................................................................... 33 2.6. Plant microbes interaction .................................................................................. 36 2.7. Functional characterization ................................................................................ 38 3. MATERIALS AND METHODS ..................................................................... 42 3.1. Field experimental design ................................................................................... 42 3.2. Rhizospheric soil sampling and processing ........................................................ 42 3.3. Isolation and characterization of rhizospheric bacterial community .................. 43 3.3.1. Isolation and identification of culturable bacterial strains. ........................ 43 3.4. Culture based approach to evaluate bacterial diversity ...................................... 43 3.4.1. Bacterial culturing medias ......................................................................... 43 3.4.2. Tryptic soy broth agar (TSB+A) ................................................................ 44 3.4.3. Low-nutrient R2A medium ........................................................................ 44 3.4.4. Mixed media .............................................................................................. 44 3.4.5. Cultured analysis ........................................................................................ 45 3.4.6. Colony forming unit (CFU) calculation ..................................................... 45 3.4.7. Sub-culturing and isolation of pure strains ................................................ 45 3.4.8. Bacterial glycerol stock ............................................................................. 46 3.4.9. Bacterial colony counting and identification ............................................
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