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Determination of Genes Involved in Bacterial Phosphate Solubilisation

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Determination of Genes Involved in Bacterial Phosphate Solubilisation Lincoln University Digital Thesis Copyright Statement The digital copy of this thesis is protected by the Copyright Act 1994 (New Zealand). This thesis may be consulted by you, provided you comply with the provisions of the Act and the following conditions of use: you will use the copy only for the purposes of research or private study you will recognise the author's right to be identified as the author of the thesis and due acknowledgement will be made to the author where appropriate you will obtain the author's permission before publishing any material from the thesis. DETERMINATION OF GENES INVOLVED IN BACTERIAL PHOSPHATE SOLUBILISATION A thesis submitted in fulfilment of the requirements for the Degree of Doctor of Philosophy at Lincoln University by Pei-Chun (Lisa) Hsu Lincoln University New Zealand 2014 Abstract of a thesis submitted in fulfilment of the requirements for the Degree of Doctor of Philosophy in Molecular Microbiology Determination of Genes Involved in Bacterial Phosphate Solubilisation Pei-Chun (Lisa) Hsu Agricultural systems depend on continued inputs of phosphate fertiliser to maintain productivity. However, due to ever increasing global demand, the finite reserves of phosphate rock are being rapidly depleted. This is compounded by the fact that half of the soluble phosphate in fertiliser applied to soil is converted to sparingly-soluble minerals such as calcium phosphate which are unavailable for plant uptake. It is therefore important to investigate strategies that will improve the utilisation of phosphate in soil-plant systems. While it has been demonstrated that phosphate- solubilising bacteria can utilise sparingly-soluble phosphate minerals in soil, the mechanisms by which this occur remain unclear. In this project, 105 rhizobacteria were assessed for a number of plant growth-promoting traits, such as production of 1-aminocyclopropane-1-carboxylate deaminase, phytase, and inorganic phosphate solubilisation using plate screening assays. Ten of the most effective phosphate-solubilising isolates were further assessed using an in vitro hydroxyapatite liquid culture assay. Analysis of culture filtrates revealed that the effective phosphate-solubilising isolates, Pseudomonas spp. and Burkholderia sp., were predominantly secreting 2-keto-gluconic acid rather than the expected gluconic acid. In addition, a yet to be characterised organic acid was secreted by several Pseudomonas spp. strains which may also be involved in phosphate solubilisation. In an attempt to identify novel genes involved in phosphate solubilisation, three isolates of different bacterial genera, Enterobacter sp. Wi28, Pseudomonas sp. Ha200 and Burkholderia sp. Ha185, derived from diverse geographic locations were subjected to random transposon mutagenesis. This enabled the identification of two unique uncharacterised genes from Burkholderia sp. Ha185. One mutant, hemX::Tn5(F18), with a mutation in hemX gene involved in haem biosynthesis, exhibited an almost complete abolition in hydroxyapatite solubilisation. The second mutant bxpC::Tn5(F13) i exhibited partial and delayed solubilisation. The translated product of the bxpC gene encodes a novel hypothetical protein with unknown function. However, based on a combination of organic acid, qRT- PCR and bioinformatics analysis, it is hypothesised that BxpC is a potential cargo protein involved in protection and transport of the calcium bound 2-ketogluconic acid compound. Through the use of a Burkholderia sp. Ha185 GFP-tagged strain in conjunction with a gnotobiotic in vivo plant assay developed in this study, the colonisation pattern of Burkholderia sp. Ha185 and its derivatives on ryegrass roots over three week duration was defined. The preliminary characterisation of the bxpC and hemX identified in the study and defining the interaction of Burkholderia sp. Ha185 on the plant root provides a greater understanding of phosphate cycling by bacteria and its relationship to the plant. The novel pathways and findings of this study have provided further insights into the underlying mechanisms of inorganic phosphate solubilisation in soil-plant systems. Keywords: Burkholderia, Pseudomonas, phosphate solubilisation, perennial ryegrass, plant-growth promotion, hydroxyapatite, gene regulation, rhizosphere, rhizoplane. ii Acknowledgements First and foremost, I would like to express my sincere appreciation to Dr. Mark Hurst, for the inspiration he has been to me and who has shown the elements of a genius. His valuable and constructive suggestions have guided me through many difficulties and challenges faced during this research. His willingness to give precious time and effort in this project highlighted his generosity and benevolent personality, which has been very much appreciated. Without Dr. Mark Hurst’s daily supervision and constant help, this PhD research would not have been possible. I would like to extend my heartfelt gratitude to Dr. Maureen O'Callaghan and Dr. Carolyn Mander for giving me the opportunity to undertake this challenging project and fulfil the Degree of Doctor of Philosophy. I am extremely grateful to both of them for constant support and advice throughout this project, for professional guidance and for patiently reading and proofreading my thesis even during the stressful periods and afterhours. I would also like to express my sincere gratitude to my supervisor Professor Leo Condron for the enormous support throughout the study and research. I am particularly grateful for his motivation, enthusiasm, optimism, and positive spirit! His guidance and endless encouragement helped me all the way through. The success and final outcome of this research project would simply not have been possible without Professor Leo Condron, and I could not have imagined having a better supervisor for my PhD study. Advice and supervision given by Professor Tim Clough and Dr. Steven Wakelin has been a great help, especially by sharing the most current journal articles related to this field of research from time to time and by providing useful critiques of this research work. In addition, I wish to thank my office mates Daria Rybakova, and Molly and Polly who constantly supported me throughout these years. Thanks for putting up with me unconditionally through the ups and downs and for understanding the stresses encountered during the PhD study. I could not possibly to go through the PhD without all of your company and support. I wish to acknowledge the help provided by the following colleagues from AgResearch; thanks to Emily Gerard for technical support and assistance in the lab, Sandra Young for thoughtful discussion and sharing her professional knowledge in microbiology, Lincoln Harper for his help and patient explanations of molecular techniques, Amy Beattie for her company in the lab and whose presence created a comfortable workspace, thanks to Sandra Jones who taught me and guided me through protein purification, and shared valuable personal experiences, Dr. Jana Monk for sharing her methodology in various microbiology experiments, Dr. Sean Marshall for insightful guidance and iii encouragement, Dr. Chikako van Koten for mathematical calculation and statistical assessments, Paul Maclean and Aurelie Laugraud for their bioinformatics support, Pauline Hunt for preparing posters for conferences and amazing artistic drawing in this thesis, Brent Conlan and Russel McAuliffe for IT support. I would also like to extend my many thanks to the Lincoln University analytical group, especially Joy Jiao for developing and optimising the HPLC method, and Lynne Clucas for the ICP assessment and analysis. Special thanks to Manfred Ingerfeld from Canterbury University at the Confocal Microscope Facility for assisting with plant sample preparation and taking images using the confocal microscope. I would also like to thank Dr. Sam Yu from Izon Science Ltd. who offered the quantitative size measurement of particles by qNano. Furthermore, I wish to thanks Dr. Courtney Giles, Dr. Alan Richardson and Dr. Jane Hill for their support and kind collaborations. Special thanks to Dr. Courtney Giles for hosting me while I visited her at the University of Vermont and her new research group, Research on Adaptation to Climate Change, USA in 2012. I also thank the Ministry of Business, Innovation and Employment (MBIE) for funding this project and granting my scholarship over three years. Many thanks to both MBIE and AgResearch for granting my attendance and travel to the New Zealand Microbiological Society conference, Rhizosphere 3 conference, and to the International Society for Microbial Ecology 14 conference. Last but not least, I would like to express my deepest gratitude and appreciation to my beloved parents Tony Hsu and Mei Wang, my brother David Hsu, and my partner Mark Mai for their tremendous support both morally and financially. Thank you all for always being there for me, believing in me, understanding me, and for your unconditional love throughout these years. Without all of your constant encouragement and support I would have never made it this far. The Pseudomonas sp. Ha200 strain characterised from this study has been published in: Giles, C. D., Hsu, P.-C., Richardson, A. E., Hurst, M. R. H., & Hill, J. E. (2014). Plant assimilation of phosphorus from an insoluble organic form is improved by addition of an organic anion producing Pseudomonas sp. Soil Biology and Biochemistry, 68(0), 263-269. doi: http://dx.doi.org/10.1016/ j.soilbio.2013.09.026 iv Table of Contents Abstract………………………………………………………………………………………………………………………………………………………
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