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  • 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
    Stopnišek, Nejc
    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 undetectable in neutral or high pH soils, Burkholderia are able to grow at pH values as high as 9, suggesting that beside abiotic factors such as pH, biological interactions such as the presence of interacting partners might contribute to Burkholderia abundance and diversity. In a second part of the thesis, we investigated the interactions of Burkholderia with fungi. Interactions between fungi and selected Burkholderia strains are described, but less is known about their relevance in explaining Burkholderia’s biogeography and preference for low pH soils, or the mechanisms underlying such interactions. We used a proteomic approach to gain first insight into the physiological changes occurring in Burkholderia glathei, a common soil bacterium, while interacting with two fungi, Alternaria alternata or Fusarium solani. Interestingly, the proteome of B. glathei underwent similar changes with both fungi, and these changes revealed a highly beneficial effect for the bacterium, which apparently derived much of its carbon, nitrogen and phosphate from the fungi. Additionally, co-occurrence network analysis and growth experiments revealed that these associations between Burkholderia and fungi are very common in soils and occur with a broad range of fungal partners. In the third part of the thesis, we investigated the interaction of Burkholderia with plants, with the focus on the role of oxalate degradation in root colonization. Oxalotrophy (the use of oxalate as a carbon source) was a feature restricted to plantbeneficial Burkholderia strains and absent from the pathogenic strains. To evaluate whether oxalotrophy was involved in rhizosphere competence, we compared the colonization of lupin and maize by a mutant strain of B. phytofirmans, which was impaired in oxalate degradation, with that of its wild type. The results showed that the wild type strain had a significant advantage in root colonization compared to the mutant strain, suggesting that oxalate degradation plays an important role in biological interactions of Burkholderia with plants. All three studies have extended our knowledge of the different lifestyles of Burkholderia in soils and have unveiled some part of their immense ecological potential.
    Type of material - dissertation ; adult, serious
    Publication and manufacture - Zürich : [N. Stopnišek], 2014
    Language - english
    COBISS.SI-ID - 108484867
    DOI

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