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Isolation and Identification of Potential Bioinoculants Based on Phosphate Solubilizing and Plant Growth Promoting Benefits Rachel Raths South Dakota State University

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Isolation and Identification of Potential Bioinoculants Based on Phosphate Solubilizing and Plant Growth Promoting Benefits Rachel Raths South Dakota State University South Dakota State University Open PRAIRIE: Open Public Research Access Institutional Repository and Information Exchange Electronic Theses and Dissertations 2019 Isolation and Identification of Potential Bioinoculants based on Phosphate Solubilizing and Plant Growth Promoting Benefits Rachel Raths South Dakota State University Follow this and additional works at: https://openprairie.sdstate.edu/etd Part of the Agronomy and Crop Sciences Commons, Microbiology Commons, Plant Biology Commons, and the Soil Science Commons Recommended Citation Raths, Rachel, "Isolation and Identification of Potential Bioinoculants based on Phosphate Solubilizing and Plant Growth Promoting Benefits" (2019). Electronic Theses and Dissertations. 3359. https://openprairie.sdstate.edu/etd/3359 This Thesis - Open Access is brought to you for free and open access by Open PRAIRIE: Open Public Research Access Institutional Repository and Information Exchange. It has been accepted for inclusion in Electronic Theses and Dissertations by an authorized administrator of Open PRAIRIE: Open Public Research Access Institutional Repository and Information Exchange. For more information, please contact [email protected]. ISOLATION AND IDENTIFICATION OF POTENTIAL BIOINOCULANTS BASED ON PHOSPHATE SOLUBILIZING AND PLANT GROWTH PROMOTING BENEFITS BY RACHEL RATHS A thesis submitted in partial fulfillment of the requirements for the Master of Science Major in Biological Sciences Specialization in Microbiology South Dakota State University 2019 iii I would like to dedicate this to my husband who encouraged me and made me laugh every day of the last two years and helping keep Elam alive during this crazy time of life. iv ACKNOWLEDGMENTS I would like to thank Heike Bücking for all her help and guidance in my research as my PI, as well as my committee members. I would also like to acknowledge the help and guidance of Dr. Bücking’s lab members, and more specifically I would like to thank Vincent Peta and Alex Soupir for mentoring me and for their technical guidance and support in my research. I would like to acknowledge Novozymes North America, specifically Timothy Lilburn and Deborah Springer, for funding and providing the isolates for the genome announcements and species description papers. I am grateful to Kevin Garcia, Arjun Kafle, Kevin Cope, Jaya Krishna Yakha, Senthil Subramanian, and Heike Bücking for considering me as a contributor for the following review paper. I would also like to thank Ralco Nutrition Inc. for financially supporting me and allowing me to split my time between school and work. And finally, I would like to thank my family and parents for helping me get through grad school while maintaining a career and a family. v CONTENTS LIST OF FIGURES .......................................................................................................................ix LIST OF TABLES ......................................................................................................................... x ABSTRACT .................................................................................................................................xi CHAPTER 1 ............................................................................................................................... 1 INTRODUCTION ............................................................................................................ 1 WORLD FOOD DEMAND ............................................................................................... 2 Issues with Increasing Production ........................................................................... 4 PLANT GROWTH PROMOTING BACTERIA .................................................................... 7 Biological Nitrogen Fixation ..................................................................................... 9 Indole-3-acetic acid ................................................................................................ 11 Suppression of fungal pathogens ........................................................................... 13 Culturing, Characterizing, and Commercializing PGPB .......................................... 16 PHOSPHATE SOLUBILIZING BACTERIA ........................................................................ 18 Soil Phosphorus Forms ........................................................................................... 18 Inorganic P Compounds ......................................................................................... 21 Organic P Compounds ............................................................................................ 23 Phosphate Solubilizing Microorganisms ................................................................ 24 Inorganic Phosphate Solubilizing ........................................................................... 26 Genetics of Inorganic Phosphate Solubilization .................................................... 30 Organic Phosphate Solubilization .......................................................................... 32 Genetics of Organic Phosphate Solubilization ....................................................... 35 Analytical measurement of phosphorus ................................................................ 38 The use of PSB as biofertilizers .............................................................................. 40 CHAPTER 2 ............................................................................................................................. 44 Draft genome sequence of Pseudoherbaspirillum gen. nov., sp. nov. OM1, a novel bacterium isolated from farm soil ............................................................................. 44 Abstract .................................................................................................................. 44 Announcement ...................................................................................................... 44 Pseudoherbaspirillum sperare gen. nov. sp. nov., a novel species and genus of the Oxalobacteraceae ...................................................................................................... 48 Abstract .................................................................................................................. 48 vi Introduction ........................................................................................................... 49 Isolation and ecology ............................................................................................. 50 Phenotypic characterization .................................................................................. 50 MALDI-TOF MS ....................................................................................................... 53 DNA isolation, sequencing and genome annotation ............................................. 54 16S rRNA phylogeny ............................................................................................... 55 Genome features ................................................................................................... 56 Proposal Pseudoherbaspirillum sperare gen. nov. sp. nov, strain OM1 ............... 58 Description of Pseudoherbaspirillum sperare gen. nov. sp. nov ........................... 59 CHAPTER 3 ............................................................................................................................. 61 Draft genome sequence of Massilia sp. MC02 isolated from a sandy-loam maize soil .............................................................................................................................. 61 Abstract .................................................................................................................. 61 Announcement ...................................................................................................... 61 Massilia arenosa sp. nov., a novel addition to the Massilia genus, isolated from the soil of a cultivated maize field ................................................................................... 65 Abstract .................................................................................................................. 65 Introduction ........................................................................................................... 66 Isolation.................................................................................................................. 68 Morphology ............................................................................................................ 69 16S RNA phylogeny ................................................................................................ 70 Physiology and Chemotaxonomy ........................................................................... 72 MALDI-TOF ............................................................................................................. 75 Genome Features ................................................................................................... 76 Proposal of Massilia arenosa sp. nov. MC02 ......................................................... 79 Description of M. arenosa sp. nov. ........................................................................ 80 CHAPTER 4 ............................................................................................................................. 84 Draft Genome of Massilia sp. nov., a Novel Bacterial Species of the Oxalobacteraceae family ..........................................................................................
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