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Dactylosporangium and Some Other Filamentous Actinomycetes

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Dactylosporangium and Some Other Filamentous Actinomycetes Biosystematics of the Genus Dactylosporangium and Some Other Filamentous Actinomycetes Byung-Yong Kim (BSc., MSc. Agricultural Chemistry, Korea University, Korea) Thesis submitted in accordance with the requirements of the Newcastle University for the Degree of Doctor of Philosophy November 2010 School of Biology, Faculty of Science, Agriculture and Engineering, Newcastle University, Newcastle upon Tyne, United Kingdom Dedicated to my mother who devoted her life to our family, and to my brother who led me into science "Whenever I found out anything remarkable, I have thought it my duty to put down my discovery on paper, so that all ingenious people might be informed thereof." - Antonie van Leeuwenhoek, Letter of June 12, 1716 “Freedom of thought is best promoted by the gradual illumination of men’s minds, which follows from the advance of science.”- Charles Darwin, Letter of October 13, 1880 ii Abstract This study tested the hypothesis that a relationship exists between taxonomic diversity and antibiotic resistance patterns of filamentous actinomycetes. To this end, 200 filamentous actinomycetes were selectively isolated from a hay meadow soil and assigned to groups based on pigments formed on oatmeal and peptone-yeast extract-iron agars. Forty-four representatives of the colour-groups were assigned to the genera Dactylosporangium, Micromonospora and Streptomyces based on complete 16S rRNA gene sequence analyses. In general, the position of these isolates in the phylogenetic trees correlated with corresponding antibiotic resistance patterns. A significant correlation was found between phylogenetic trees based on 16S rRNA gene and vanHAX gene cluster sequences of nine vancomycin-resistant Streptomyces isolates. These findings provide tangible evidence that antibiotic resistance patterns of filamentous actinomycetes contain information which can be used to design novel media for the selective isolation of rare and uncommon, commercially significant actinomycetes, such as those belonging to the genus Dactylosporangium, a member of the family Micromonosporaceae. A culture-independent, nested PCR procedure based on genus-specific oligonucleotide primers detected the presence of Dactylosporangium strains in 14 out of 21 environmental samples. Clones generated from the 14 positive samples formed novel phyletic lines in the Dactylosporangium 16S rRNA gene tree. Presumptive dactylosporangiae were isolated from 7 of these samples using a medium designed to be selective for members of the genus Dactylosporangium. One hundred and two out of 219 representative presumptive dactylosporangiae were considered to be bona fide members of the genus Dactylosporangium as they gave PCR amplification products with primers specific for this taxon. Representatives of the Dactylsporangium isolates formed distinct phyletic lines in the Dactylosporangium 16S rRNA gene tree were designated as new species, namely Dactylosporangium luridum sp. nov. and Dactylosporangium luteum sp. nov., based on a polyphasic study. Similarly, “Dactylosporangium salmoneum” NRRL B-16294 was validly described as a new species, Dactylosporangium salmoneum sp. nov., nom. rev. In addition, “Dactylosporangium variesporum” NRRL B-16296 was transferred to the genus Saccharothrix as Saccharothrix variisporea corrig. (ex. Tomita et al. 1977) sp. nov., nom. rev. Some of the representative Dactylosporangium isolates inhibited the growth of Bacillus subtilis, Kocuria rhyzophila and Staphylococcus aureus strains, suggesting that novel Dactylosporangium strains might be a rich source of novel antibiotics. Verrucosispora maris AB-18-032, another member of the family Micromonosporaceae, produces atrop-abyssomicin C, the first natural inhibitor of the para-aminobenzoic acid pathway. The self-protective mechanism of this strain was sought by conjugating an atrop-abyssomicin C sensitive Streptomyces griseus strain against a genomic DNA library prepared from V. maris AB-18-032. Seven resultant resistant exconjugants were screened for atrop-abyssomicin C resistance genes using four designed PCR primers. The failure to detect PCR amplification products suggests that the resistance shown by the exconjugants is conferred by mutation within the S. griseus strain or by cloning of unidentified resistance genes from the V. maris strain. iii Acknowledgements I would like to express my deepest gratitude to my supervisor Prof. Michael Goodfellow MBE who has supported me with respect to both academic and private issues during my stay at Newcastle. This project would never have been accomplished without his consideration, encouragement and guidance. I am also grateful to Dr. Jem Stach and Dr. Gabriel Uguru for their valuable discussions and many helpful suggestions. I am very indebted to Prof. Hans-Peter Fiedler (University of Tübingen), Prof. David Labeda (USDA-ARS), Prof. David Hopwood (John Innes Centre) and Dr. Hee-Jeon Hong (University of Cambridge) for their advice and support. I would also like to thank all of the staff in the school of Biology, notably Dr. Heather Finlayson, Dr. Ian Singleton, Ms. Jan Fife, Mr. David Moir, Mr. Roger Furness, Ms. Nikki Morton and Ms. Deborah Bond for their many kindnesses and help. I am especially grateful to my former supervisors, Prof. Won-Gi Bang, Prof. In-Geol Choi and Dr. Heesang Song (Korea University), and to Prof. Jongsik Chun (Seoul National University) for their encouragement. My sincere gratitude goes to my colleagues in KACC (Korean Agricultural Culture Collection), Dr. Soon-Wo Kwon, Dr. Hang-Yeon Weon and Dr. Jaekyeong Song for their assistance and support. My Laboratory Managers, Mrs. Roselyn Brown and Mrs. Miriam Earnshaw shared their extensive experience of laboratory work and their wisdom of life with me. Indeed, my Newcastle life would have failed without them. I am grateful to laboratory members: Amanda, Ankur, Annie, Ashley, Cathy, Jeni, Liz, Madhav, Porntipa, Rakesh, Sanjay, Tiago, Yash and Yashodhara for helpful discussions and assistances, and to my colleagues in China: Dr. Hong Jiang, Dr. Kui Hong, Dr. Wen-Jun Li, Qingyi and Dylan. I also owe lots of thanks to my best friends, Daeik and Jonghun who have always stood by me as pillars of strength. I gratefully acknowledge financial support from the Newcastle University for an Overseas Research Student (ORS) Award, an International Postgraduate Scholarship (NUIPS) and for childcare funding. I am also indebted to the National Institute for International Education of the Korean Government (NIIED) for a National Scholarship. Attendance at several academic conferences was supported by the Society of General Microbiology. I take deep pleasure in thanking my dear wife, Munja and our two lovely sons, Soo- Young and Junyoung for their love and patience during this tough journey. Finally, this study and all my achievements are dedicated to my mother, brother and four sisters who have always been my source of energy. It is through their selfless sacrifices that I have made it this far. iv Author’s Declaration Except where acknowledgement has been given, this dissertation is the original work of the author. The material presented has never been submitted to the Newcastle University or to any other educational establishment for purposes of obtaining a higher degree. November 2010 Byung-Yong Kim v Publications Related to the Thesis Publications: Byung-Yong Kim, James E. M. Stach, Hang-Yeon Weon, Soon-Wo Kwon and Michael Goodfellow (2010). Dactylosporangium luridum sp. nov., Dactylosporangium luteum sp. nov. and Dactylosporangium salmoneum sp. nov., nom. rev., isolated from soil. International Journal of Systematic and Evolutionary Microbiology 60, 1813-1823. Byung-Yong Kim, Roselyn Brown, David P. Labeda and Michael Goodfellow (2010). Reclassification of ‘Dactylosporangium variesporum’ as Saccharothrix variisporea corrig. (ex Tomita et al. 1977) sp. nov., nom. rev. International Journal of Systematic and Evolutionary Microbiology (In press). Byung-Yong Kim, Jenileima Devi Kshetrimayum and Michael Goodfellow (2010) Detection, selective isolation and characterisation of Dactylosporangium strains from diverse environmental samples. Environmental Microbiology (submitted). Oral presentation: Byung-Yong Kim (2009). Detection, Selective Isolation and Characterisation of Dactylosporangium Strains. 15th International Symposium on Biology of Actinomycetes, Shanghai, China. Poster presentations: Byung-Yong Kim, Roselyn Brown, James E. M. Stach and Michael Goodfellow (2009). Taxonomic Approach to the Soil Resistome. Society of General Microbiology, Harrogate, UK. Byung-Yong Kim, Roselyn Brown, James E. M. Stach, Anthony G. O’Donnell and Michael Goodfellow (2007). Systematic Approach to Antibiotic Resistance of Actinomycetes isolated from Soil. 11th International Conference on Culture Collection, Goslar, Germany. Byung-Yong Kim, James E. M. Stach, Anthony G. O’Donnell and Michael Goodfellow (2007). Diversity of Antibiotic-Resistant Actinomycetes in Soil. 14th International Symposium on Biology of Actinomycetes, Newcastle upon Tyne, UK. vi Abbreviation bp Base pair ng Nanogram μl Microliter 10× Tenfold concentration no. Number M Molar nt Nucleotide v/v Volume/volume w/v Weight/volume rpm Revolutions per minute dNTP Deoxynucleoside triphosphate DMSO Dimethylsulfoxide EDTA Ethylenediamine tetraacetic acid FAME Fatty acid methyl ester %G+C Percentage of guanine and cytosine RNase Ribonuclease rRNA Ribosomal RNA PCR Polymerase Chain Reaction Taq DNA Polymerase Thermus aquaticus DNA polymerase SSM Simple matching coefficient
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