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Ecology of the Genus Burkholderia in the Soil

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Ecology of the Genus Burkholderia in the Soil Zurich Open Repository and Archive University of Zurich Main Library Strickhofstrasse 39 CH-8057 Zurich www.zora.uzh.ch Year: 2014 Ecology of the Genus Burkholderia in the Soil Stopnisek, Nejc Posted at the Zurich Open Repository and Archive, University of Zurich ZORA URL: https://doi.org/10.5167/uzh-101419 Dissertation Originally published at: Stopnisek, Nejc. Ecology of the Genus Burkholderia in the Soil. 2014, University of Zurich, Faculty of Science. Ecology of the Genus Burkholderia in the Soil Dissertation zur Erlangung der naturwissenschaftlichen Doktorwürde (Dr. sc. nat.) vorgelegt der Mathematisch-naturwissenschaftlichen Fakultät der Universität Zürich von Nejc Stopnisek aus Slowenien Promotionskomitee Prof. Dr. Leo Eberl (Vorsitz) Prof. Dr. Jakob Pernthaler Dr. Laure Weisskopf Zürich, 2014 Ago Table of Contents Summary ........................................................................................................................ I Zusammenfassung ........................................................................................................ III Abbreviations ................................................................................................................ V General introduction ...................................................................................................... 1 The genus Burkholderia ........................................................................................................... 1 Soil as habitat for Burkholderia the genus ......................................................................... 5 Burkholderia in the soil ............................................................................................................ 7 Burkholderia tolerance mechanisms relevant in acidic soils...................................... 8 Ecological functions Burkholderia of in the soil ............................................................... 9 Interactions of Burkholderia species with soil microbes ............................................. 9 Aims of the thesis ........................................................................................................ 12 Part I: Biogeography of Burkholderia sp. in soil ......................................................... 13 Aims of the project.................................................................................................................. 13 Unpublished results ............................................................................................................... 14 Design of a quantitative PCR (qPCR) protocol targeting the Burkholderia 16S rRNA gene ............................................................................................................................................................ 14 Primer selection and specificity assessment ....................................................................................... 14 Optimization of the qPCR method and Burkholderia measurement of sp. relative abundance in soils ........................................................................................................................................... 16 Effect of pH change on the abundance of the genus Burkholderia ................................ 18 Material and methods .................................................................................................................................... 18 Results and discussion ................................................................................................................................... 20 Published Results .................................................................................................................... 24 Part II: Burkholderia-fungi interactions ....................................................................... 41 Aims of the project.................................................................................................................. 41 Unpublished results ............................................................................................................... 42 Effect of fungal presence and absence on e Burkholderia relativ abundance in the soil ............................................................................................................................................................... 42 Methods and material .................................................................................................................................... 42 Results and discussion ................................................................................................................................... 43 Genome of B. glathei LMG14190 .................................................................................................... 46 Materials and methods .................................................................................................................................. 46 Results and discussion ................................................................................................................................... 46 Published results ..................................................................................................................... 50 Molecular mechanisms underlying the close between association soil Burkholderia and fungi ................................................................................................................................................... 50 Abstract ................................................................................................................................................................ 51 Introduction ....................................................................................................................................................... 52 Methods ................................................................................................................................................................ 54 Results and discussion ................................................................................................................................... 59 Conclusion ........................................................................................................................................................... 70 Acknowledgements ......................................................................................................................................... 71 Literature ............................................................................................................................................................. 72 Tables, figures and legends.......................................................................................................................... 81 Supplementary legends and figures......................................................................................................... 88 Part III: Role of oxalotrophy in Burkholderia – plant interactions .............................. 89 Aims of the project.................................................................................................................. 89 Published results ..................................................................................................................... 91 General Conclusions .................................................................................................. 106 Outlook ...................................................................................................................... 110 Literature .................................................................................................................... 111 Acknowledgments ...................................................................................................... 121 Appendix .................................................................................................................... 123 List of transporters predicted from online tool TransAPP ..................................... 123 Curriculum vitae ........................................................................................................ 152 Summary The genus Burkholderia consists of 86 phylogenetically closely related species that are metabolically highly versatile. This enables them to be ubiquitously present in the environment as free-living bacteria as well as in antagonistic, mutualistic or symbiotic associations with plants, fungi and animals. Soil is the environment that contains the largest pool of Burkholderia diversity. Soil Burkholderia are involved in a large number of processes, such as decomposition of organic matter, detoxification/removal of pollutants or nitrogen fixation. Even though these processes are well understood, there is still a lack of knowledge regarding the ecology of Burkholderia in the soil. To better understand the environmental parameters affecting Burkholderia distribution and abundance in the soil we investigated the relative abundance of the genus Burkholderia in the soil at a trans-continental and at a local scale and correlate the obtained abundances with environmental parameters. The results showed that Burkholderia relative abundance was significantly influenced by soil pH. In contrast to most bacteria, Burkholderia favored low pH environments and were undetectable in neutral and alkaline soils. However, while their relative abundance was influenced by the soil pH, their diversity was not. Moreover, in vitro growth experiments revealed that although they are
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