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Enzyme Production and Activities of Lignocellulolytic Fungi Cultivated on Agricultural Residues

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Enzyme Production and Activities of Lignocellulolytic Fungi Cultivated on Agricultural Residues ENZYME PRODUCTION AND ACTIVITIES OF LIGNOCELLULOLYTIC FUNGI CULTIVATED ON AGRICULTURAL RESIDUES by GRACE NKECHINYERE IJOMA Submitted in accordance with the requirements for the degree of Doctor of Philosophy in the subject Environmental Science at the UNIVERSITY OF SOUTH AFRICA SUPERVISOR: PROF M. TEKERE November 2016 i Declaration Name: Grace Nkechinyere Ijoma Student number: 51787717 Degree: Doctor of Philosophy: Environmental Science Enzyme Production and Activities of Ligninolytic Fungi cultivated on Agricultural Residues I declare that the above dissertation/thesis is my own work and that all the sources that I have used or quoted have been indicated and acknowledged by means of complete references. SIGNATURE DATE 08 November 2016 ii Abstract A total of 30 fungal fruiting bodies were collected from decaying plant materials (barks and litter) from the wild based on morphological variations. Nine of these fungi purified to monoaxenic cultures were included in the present study and also a type strain Ganoderma lucidum ATCC- 32471. These fungi were screened for lignocellulolytic activities, five of these organisms produced ligninolytic enzymes when exposed to two different concentrations of guaiacol (0.02% and 0.2%) on two different media (MEA and PDA). All ten fungal isolates screened for cellulolytic activity were positive for the production of the cellulase enzyme. The fungal isolates were characterised using morphological and molecular methods. Molecular characterization using ITS1 and ITS4 primers was able to identify these fungal isolates to degrees of accuracy ranging from 98% to 100%. The phylogenetic and lineage analysis showed that the species varied amongst phylum Basidiomycota, Ascomycota and early diverging fungal lineages Mucormycotina. Both monocultures and dual cultures of these 10 fungal species were cultivated for the purpose of spectrophotometrically quantifying and evaluating enzyme production on agricultural waste residues; corn cob, sugar cane bagasse and wheat straw. A pattern of antagonistic invasion interaction was identified to demonstrate increased enzyme production on dual cultures. Four of these fungal species, Trichoderma sp. KN10, Rhizopus microsporus KN2, Fomitopsis sp. KN1 and Coriolopsis sp. KN6 demonstrated tendencies of invasion and replacement in co-cultures. The fungi and their dual cultures showed varying levels of enzyme production. Analysis of mean showed dual culture interactions involving KN10 with values for MnP production approximately at 1.46U/ml compared to monoculture of 0.06U/ml. Further, dual laccase values approximately at 0.09U/ml compared to monocultures of 0.05U/ml. Overall the highest enzyme activity was observed using wheat straw. This study demonstrated and proved that agricultural waste residues can be used for lignocellulytic enzyme production and that antagonistic invasion by some fungi (in particular Trichoderma sp. KN10) in co-cultures can increase production of one or more of the three enzyme laccase, lignin peroxidase and manganese peroxidase. Keywords: fungi, dual cultures, competition, antagonism, ligninolytic enzymes, agricultural residues iii Acknowledgements Although the popular African adage says that “It takes a village to raise a child”. I would like the artistic license to rephrase by saying that “It took a village to research and write this thesis”. I have been blessed by the people that I met during the course of this study and with whom I hope I have cultivated life-long friendships. I am grateful for the support of my supervisor, Prof. M. Tekere, in her professional capacity as a mentor. I am grateful for the support shown to me by the Faculty of Applied Science in the Pearson Institute of Higher Education during the course of this study and I appreciate the laboratory facilities privileges accorded me during the course of this study. I would especially like to thank Dr Piet Bothma the Dean of Applied Sciences for his support throughout the period of my research. I appreciate the support given by my friend and colleague Terence Mashangwa. Thank you for making yourself available and taking my endless calls when I needed a sound-board. I would also like to thank Eunice Elloms, although fate brought us together during the course of this study, our common goal of educational pursuit has guaranteed our lasting friendship. Thank you, for humbly becoming my laboratory partner and cooking for me during the grueling one year of laboratory research and being the mother to my kids when I travelled for presentations. To my most faithful laboratory partner and student Oliver Kabui Wanjau, words are rather empty to describe the depth of my gratitude. I can only say wherever and whenever you are ready to embark on this journey of research I shall be by your side. To Annie Monanga, my pride and joy, you showed me why I became a teacher that it is possible to teach and be taught. Thank you for the time you have invested in my work. I would be like to thank my guru Dr Ramganesh Selvaranjan and friend, Dr Timothy Sibanda. Both of you showed me that there is divine intervention. You were my miracle, your assistance at the crucial time of my studies made a difference. The drive I saw in both of you as Post-PhD fellows has shown me that this is only the beginning for me. My sincere gratitude goes to Mr iv Taboga Mathiba who contributed immensely into making my data coherent and providing statistical knowledge for the running of the software used for the data in this study. I was a novice when I met you and truly appreciate you patience. I am also indebted to my undergraduate Lecturer, mentor and friend Mr Sunday Joseph, your contributions towards my studies could not have come at a better time. I am sincerely grateful. Finally to my children, my life’s work, my blessings, my reason, my purpose, my heart beat. Offordile, Ekenedilichukwu, Ollanma and Uchechi. The sacrifices you have had to make, I cannot thank you enough. I desperately hope I can repay the lost time. I thank you. v Dedication To the memory of my father, Isaac Chijioke Ijoma 1943 – 2003 I did as you persuasively asked………. Ditto… Felicia Ngozi Odinnma Ijoma (neé Amolo) 1953 – 2017 You were here…. vi Table of Contents Pages Declaration ii Abstract iii Acknowledgements iv Dedication vi Table of Contents vii List of Figures xii List of Table xvi List of Abbreviations xvii List of Conference and Research Article Manuscript Submitted xix Chapter 1 Overview 1 References 4 Chapter 2 Literature Review 7 2.1 Lignocellulose: Nature’s tightly wrapped gift 7 2.2 Composition of Lignocellulose 7 2.2.1 Cellulose 8 2.2.2 Hemicellulose 9 2.2.3 Lignin 11 2.3 Lignocellulosic Agricultural residues used in this study 13 2.3.1 Corn Cob 13 2.3.2 Sugar cane bagasse 14 2.3.3 Wheat straw 16 2.4 Pre-treatment of Lignocellulosic Biomass 17 2.4.1 Physical Pre-treatment methods 18 2.4.1.1 Mechanical Comminution 18 2.4.1.2 Pyrolysis and Torrefaction 19 2.4.1.3 Microwave irradiation 20 2.4.2 Physico-chemical Pre-treatment methods 20 2.4.2.1 Steam explosion 20 2.4.2.2 Liquid Hot Water Pre-treatment 21 2.4.2.3 Ammonia fibre explosion 22 2.4.2.4 Carbon dioxide explosion 23 2.4.3 Chemical Pre-treatment 23 vii 2.4.3.1 Acid Pre-treatment 23 2.4.3.2 Organosolv Pre-treatment 24 2.4.3.3 Alkaline Pre-treatment 25 2.4.3.4 Oxidizing Pre-treatment – Hydrogen Peroxide 26 2.4.3.5 Wet Oxidation 27 2.4.3.6 Ozonolysis 27 2.4.4 Biological Pre-treatment 28 2.4.4.1 Bacteria 28 2.4.4.2 Brown rot fungi 29 2.4.4.3 Soft-rot fungi 30 2.4.4.4 White-rot fungi 30 2.5 Ligninolytic Enzymes 31 2.5.1 Laccases 32 2.5.2 Peroxidases 35 2.5.2.1 Lignin Peroxidase 35 2.5.2.2 Manganese Peroxidases 37 2.5.2.3 Versatile Peroxidases 39 2.5.2.4 Accessory Lignin degrading enzymes 40 2.6 Other enzymes involved in lignocellulose degradation – Cellulolytic enzymes 41 2.6.1 Cellulases 41 2.6.2 Hemicellulases 42 2.7 Factors that influence enzyme production by ligninolytic fungi 43 2.7.1 Substrate concentration 43 2.7.2 Nutrient composition 44 2.7.3 Inducers and Mediators 45 2.7.4 Organic Acids 47 2.8 Fungal Interspecific Interactions in Mixed Cultures 48 2.8.1 Competition 49 2.8.1.1 Outcomes of competitive interspecific interactions 50 2.8.2 Mechanisms employed in antagonistic interspecific interactions 52 2.8.2.1 Morphological response to antagonistic interspecific interactions 53 2.8.2.1.1 Gross mycelial contact 53 2.8.2.1.2 Hyphal Interference 54 2.8.2.2 Physiological response to interspecific interactions 56 viii 2.8.2.2.1 Accelerated secondary metabolism 56 2.8.2.3 Biochemical response to interspecific interactions 57 2.8.2.3.1 Antibiosis 57 2.8.2.3.2 Mycoparasitism 57 2.8.2.3.3 Pigmentation 60 2.8.2.3.4 Enzymatic activities 62 2.9 Application of antagonistic interspecific interactions 65 2.9.1 Biological Control 65 2.9.2 Biopulping in Paper Production 65 2.9.3 Improved Enzyme Production 66 2.10 Aims and Objectives of Study 67 References 68 Chapter 3 Isolation, Screening and Molecular Characterization of Ligninolytic 113 Fungi 3.0 Abstract 113 3.1 Introduction 113 3.2 Literature Review 115 3.2.1 Isolation of Ligninolytic Fungi 115 3.2.2 Molecular Characterisation of Fungi 117 3.2.3 Screening of Ligninolytic Fungi 120 3.3 Materials and Method 122 3.3.1 Sample Area 122 3.3.2 Isolation of Fungal Species and Cultivation Conditions 123 3.3.3 Screening 124 3.3.3.1 Cellulolytic Activity 124 3.3.3.2 Ligninolytic Activity 124 3.3.3.3 Morphological Characterisation – Microscopy 124 3.2.3.4 Molecular Characterisation 124 3.2.3.4.1 Genomic DNA Extraction 124 3.3.3.4.2 DNA Amplification
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