11 M060072591U NORTH-WEST UNIVERSITY tilt• YUNIBESITI YA BOKONE•BOPHIRIMA NOOROVVE S-UNIVERSITEIT PHYLOGENETIC SCREENING FOR POSSIBLE NOVEL ANTIBIOTIC PRODUCING ACTINOMYCETES FROM RHIZOSPHERIC SOIL SAMPLES COLLECTED FROM NGAKA MODIRI MOLEMA DISTRICT IN NORTH WEST PROVINCE, SOUTH AFRICA I BY MOBOLAJI FELICIA ADEGBOYE A thesis submitted in fulfilment of the requirements for the degree of DOCTOR OF PHILOSOPHY (BIOLOGY) DEPARTMENT OF BIOLOGICAL SCIENCES FACULTY OF SCIENCE, AGRICULTURE AND TECHNOLOGY NORTH-WEST UNIVERSITY, MAFIKENG CAMPUS SOUTH AFRICA Supervisor: Professor Olubukola 0. Babalola 2014 LIBRARY o MAFIKENG CAMPUS CALL NO.: 2021 -02- 0 4 DECLARATION I, the undersigned, declare that this thesis submitted to the North-West University for the degree of Doctor of Philosophy in Biology in the Faculty of Science, Agriculture and Technology, School of Environmental and Health Sciences, and the work contained herein is my original work with exemption to the citations and that this work has not been submitted at any other University in partial or entirely for the award of any degree. Name: Mobolaji Felicia Adegboye Signature: .....~ •·· ··· ····· ·· .. ··············· ..... Date: .... ~S.. .. ....a~ ·1·· ·'.}Q~i; ... ............ .... DEDICATION This work is dedicated to Almighty God for His faithfulness over my life and for making my helpers to be many. ii ACKNOWLEDGEMENTS I would like to express my deepest thanks, gratitude and appreciation to my supervisor and mentor, Prof. Olubukola 0. Babalola for giving me the opportunity to pursue my doctoral degree under her supervision and for her encouragement, help and kind support. Her invaluable advice, suggestions, discussions and guidance were a real support to me. I acknowledge with honour and gratitude the International Foundation for Science (IFS) for research grant (F/5330-1 ), Connect Africa Scholarship Award, H3ABioNet/SANBio Scholarship and North-West University for offering me bursary/scholarship award to pursue the PhD degree. A special thanks to those who helped me with my techniques or/and part of my research at one stage or another, Dr T.O. Aiyelabola, Dr J. Jordaan, Dr R.Y. Olobatoke, Dr C.N. Wose Kinge, Prof. C.N. Ateba, Dr H. Tak, and Ms R. Huyser I can never thank you enough for all your troubles. I appreciate my colleagues in Microbial Biotechnology Research Group for contributing to such an inspiring and pleasant atmosphere especially Ms K. Sebogodi for serving as a translator during the sample col lection. Thank you all. I also thank all members of staff of the Department of Biological Sciences, North-West University for their support during the period of this study, especially the HOD, Prof. 0 . Ruzvidzo. I am deeply grateful for all the academicians who have been so nice, helpful and supportive, Prof. E.E. Ebenso, Prof. D.A. Akinpelu, Prof. E. Useh, Prof. 0. Olowu, Prof. S.H. Taole and Prof. N.P. Sithebe. I am indebted and thankful to the Alaos and Babarindes for paying for my fli ght ticket and for making my coming to South Africa a reality, thanks for believing in my dream. I am iii also indebted to Dr 0.0. Aiyegoro, Mr 0 .0. Awolusi, Akinbolas, Owolabis and Aromolarans for being true friends who have stood the test of time. A special appreciation to my Pastors and the household of God for upholding me with prayers, especially Pastor T. Ajorin, Pastor M. Owolabi, Pastor and Pastor (Mrs) A. Oduaran. During my study I was fortunate to find several friends who have provided not only friendship but also encouragement, support and understanding. I would specifically like to acknowledge Mrs A. Akindolire, Dr A. Adebayo, Mr E.W. Bumunang, Ms K. Masenya, Dr L. Ngoma, Mrs C.O. Ajilogba, Ms M. Khantsi, Mrs B.R. Aremu, Mr S.O Aremu, Mr E. Megbowon, Mr A. Robinson, Mrs L. Modise, Mrs M. Egbuta, Mrs 0. Akande and Mrs M.O. Fashola for making my stay in South Africa a memorable one. I would like to thank my family members especially Opeyemi Oladepo and my wonderful son, Adetomiwa Ayomide. I am honored to be a product of such a loving and supportive family who have always encouraged me to explore all my educational endeavours throughout my academic career. Lastly, I give all glory to Almighty God, the Alpha and Omega for making it possible to accomplish this research work and its completion a reality. iv TABLE OF CONTENTS DECLARATION ... .. ...... .... ..... ..... .................. .... ..... ...... .......... ...... ..... .... .... ... .... ...... ..... ..... .......... i DEDICATION .. .................. .......... ... ... ..... ..... ..... ... ... ...... ....... ... ..... ..... ...... ... ... .... ... .. ...... ...... ....... ii ACKNOWLEDGEMENTS ..... .. .. ...... ...... .... .... .... .... .... ... ... ................... .. ... .. ........ ... .. .......... .... .. iii TABLE OF CONTENTS .......... ...... ............ .. ..... ............ ..... ..... ..... .. .... ..... .......... .... .............. ...... V LIST OF TABLES ...... ... ..... ..... ..... ....... ............ .. ... ... ...... ..... ...... ..... .. .. .. .. .. ... .... .. .. ..... .... .. ..... ...... xi LIST OF FIGURES ......... ..... ....... ..... ............... .. ... ... .. ...... ..... ..... ... .. .... ...... .. .... .. .. .. ...... .......... ... xii GENERAL ABSTRACT .......... .... ..... ...... ..... .... ... ...... .. .. ..... ......... ......... ... ........... .. ..... ... ...... ..... xv CHAPTER I .. ........ ..... ..... ..... ... .. .. .. ............. ... ... ... ............. .... ..... ... .. ...... ....... .... .... ............... .. ..... 1 I . I General Introduction ..... ................................... ........... ... .. .... ... ....... .. ..... .... .. .... .... .... .. ... .... .... 1 LIST OF PUBLICATIONS ... .... .... ..... ........... ... .......... ....... ...... ........ ............... ......... ....... ...... .. ... 8 CHAPTER 2 .. ... ......... .. .... .. .. .. ...... ................... ...... ..... ...... .......... .. .......... ... ....... ....... ................ I 0 Taxonomy and Ecology of Antibiotic Producing Actinomycetes .... ... .... ....... ... ... ... ................ I 0 Abstract ... ... ... ... .. ....... ......... ....... .... ............. .... .... ........ ... ....... .. ... .... ..... ...... .......... .... .................. I 0 2.1 Introduction .... ..... ... .. ... ..... .. .......... ............ ..... ...... ..... .... .. ..... ..... ..... ...... ...... ... ... .... ....... .. .. .... I 0 2.2 Taxonomy of antibiotic producing actinomycetes ... .. ............ ...... .. ..... ...... ..... .... ... ... ...... .... 12 2.2.1 Suborder Actinomycineae ............ ... ..................... ............ ... .. .. .. ..... ................ ........... .. 14 2.2.2 Suborder Streptomycineae .................... ............. .. .... ... ... ...... .. ....... ............. .... ... ....... .. 14 2.2.3 Suborder Corynebacterineae ... ...... ..... ..... ..... .. .... ...... ............... ........ .. .... ... ... ..... ........... 15 2.2.4 Suborder Micrococcineae ......... ..... ... .. ...... ..... ...... ..... .... .. .. .. ........... .............................. 16 2.2.5 Suborder Micromonosporineae ................... ....... ............... ..... ............. .......... .... .......... 17 2.2.6 Suborder Propionibacteriaceae .. ......... ... ..... ....... ........... .. ..... ... ... .. ....... .... .. .. .. .. ........... .. 17 2.2. 7 Suborder Streptosporangineae ... .... ..... ..... .... ........ .... .. .... ........ .... ..... .... .... .. ........ ..... ...... 18 2.2.8 Suborder Frankineae .... ..... ..... .... .. .. ... ....... ....... .. .......... ........ .. .. .. ... ..... ..... .. .. ....... .. ... ..... 19 2.3 Ecology of antibiotic producing actinomycetes ..... ............... .. ...... ... .. ...... ... .. .... ... .............. 19 2.3 .1 Actinomycetes as soil inhabitant... ... ... ..... .... ............. ....... ..... ... ........... ......... .. .. ..... ...... 20 2.3 .2 Actinomycetes as rhizobacteria ..... ....... .. .. .. ... ......... ... ... ....... .. ...... .. ........... .. ..... .. .......... 21 2.4 Conclusion ............ ... ...... ... .... ...... ......... .... .... ......................... .. ........... ... .. .................... .. ..... 23 CHAPTER 3 ............... .. ... ........ ....... .. .............. .. ........ ..... .. .. ...... .. .. .. .... ... .. ... ... .......... ... ..... .... .. ... 24 Actinomycetes: A Yet Inexhaustive Source of Bioactive Secondary Metabolites ..... ...... .. ... .. 24 Abstract .. .. .... ............... ......... .. .. ..... ........ ..... ... ...... .... .. .... .. .. ... ......... ..... ................. .. ... ................ 24 3.1 lntroduction ....... .. ..... ... ... ..... ..... ........ ... ..... ..... ...... ..... .... .. .... ...... ..... ............ ......... .. .. .. .......... 25 3.2. Actinomycetes as producers of secondary metabolites .... ..... ... .. ............. .... ... ................. 26 3.3. Antimicrobial activities of actinomycete secondary metabolites .... ... ............ .... .. ........... 28 3.4. Important classes of antibiotics produced by actinomycetes .. .. .... .... ....................... ......... 34 V 3.4.1 ~-Lactams ............... .... ... ..... ................................................. .. ... .. ................................. 34 3.4.2 Aminoglycosides ......................... ......................................... .. ................... .. ..... .......... 36 3.4.3 Glycopepti des .... ............... ........ ...........................