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Etiology of Maize Root Rot in Oman: Causal Agents and Effects of a Compost Based Organic Growing System

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Etiology of Maize Root Rot in Oman: Causal Agents and Effects of a Compost Based Organic Growing System Etiology of Maize Root rot in Oman: Causal agents and effects of a compost based organic growing system Dissertation for the acquisition of the academic degree Doktor der Agrarwissenschaften (Dr. Agr.) Submitted to the Faculty of Organic Agricultural Sciences, Of the University of Kassel By Mahmood Saleh Ali Al-Ansari Kassel, April 2018 This work has accepted by the faculty the faculty of organic Agricultural sciences of the University of Kassel as a thesis for acquiring the academic degree Doctor of Agricultural sciences The Thesis was reviewed and approved by the following: 1st Supervisor: Prof. Dr. Maria Finckh (University of Kassel) 2nd Supervisor: Prof. Dr. Abdullah Al-Sadi (Sultan Qaboos University) Examiner: Prof. Dr. Rainer Joergenson Examiner: Dr. Christian Bruns Defense Date: 23 July 2018 Place: Witzenhausen, Germany Table of Contents Table of Contents ........................................................................................................................................... i List of Abbreviations ..................................................................................................................................... v Table of Figures ............................................................................................................................................ vi Table of Tables ............................................................................................................................................. ix Dedication ..................................................................................................................................................... x 1. General introduction ........................................................................................................................ 1 1.1 Introduction .......................................................................................................................... 1 1.2 Objectives .............................................................................................................................. 3 1.3 Structure of the Thesis .......................................................................................................... 4 1.4 References ................................................................................................................................. 6 2. Etiology of maize root rot in Oman.................................................................................................. 8 Abstract ............................................................................................................................................ 8 2.1 Introduction .......................................................................................................................... 9 2.2 Materials and Methods ....................................................................................................... 10 2.2.1 Survey and assessment of incidence .................................................................................. 10 2.2.2 Seed sampling ..................................................................................................................... 12 2.2.3 Identification of fungal species ........................................................................................... 13 2.2.4 Pathogenicity tests .............................................................................................................. 14 2.2.5 Data Analysis ....................................................................................................................... 16 2.3 Results ................................................................................................................................. 17 2.3.1 Incidence and distribution of maize root rot disease ......................................................... 17 2.3.2 Seed infections in the field and in commercial seed batches ............................................. 19 2.3.3 Pathogenicity tests .............................................................................................................. 20 2.4 Discussion ............................................................................................................................ 22 2.5 References ............................................................................................................................... 24 2.6 Supplementary Figures ............................................................................................................ 27 i 3. Organic compost based management increases microbial diversity and reduces maize root rot in Oman 29 Abstract .......................................................................................................................................... 29 3.1 Introduction ........................................................................................................................ 30 3.2 Materials and Methods ....................................................................................................... 32 3.2.1 Soil and rhizosphere sampling ............................................................................................ 32 3.2.2 Soil chemical properties ...................................................................................................... 33 3.2.3 Soil DNA extraction and next generation sequencing analyses .......................................... 33 3.2.4 Isolation of fungi from soil using culture-dependent methods .......................................... 34 3.2.5 Identification of fungal species ........................................................................................... 34 3.2.6 Data Analysis ....................................................................................................................... 35 3.3 Results ................................................................................................................................. 35 3.3.1 Soil chemical properties ...................................................................................................... 35 3.3.2 Extraction of genomic DNA from Soil ................................................................................. 36 3.3.3 Isolation of fungi from soil using different methods .......................................................... 37 3.4 Discussion ............................................................................................................................ 43 3.5 Concluding remarks ................................................................................................................. 46 3.6 References ............................................................................................................................... 48 4. Transitions in microbial communities during the composting process in an arid environment ... 53 Abstract .......................................................................................................................................... 53 4.1 Introduction ........................................................................................................................ 54 4.2 Material and methods......................................................................................................... 57 4.2.1 Microbial community structure analysis ............................................................................. 58 4.2.2 Statistical analysis ............................................................................................................... 58 4.3 Results ................................................................................................................................. 59 4.3.1 Changes of Physico-Chemical Properties ............................................................................ 59 4.3.2 Microbial Community Structures ........................................................................................ 62 4.4 Discussion ............................................................................................................................ 69 4.5 Concluding remarks ............................................................................................................. 72 ii 4.6 References ............................................................................................................................... 74 4.7 Supplementary Data ................................................................................................................ 77 5. Differential effects of organic amendments on compost physico-chemical properties, phytotoxicity and microbial communities in an arid environment ............................................................ 79 Abstract .......................................................................................................................................... 79 5.1 Introduction ........................................................................................................................ 80 5.2 Materials and Methods ....................................................................................................... 82 5.2.1 Compost Samples ................................................................................................................ 82 5.2.2 Physico-Chemical Properties ............................................................................................... 82 5.2.3 Phytotoxicity Test (Germination index) .............................................................................
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