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The microbiology of lean and obese soil

Jones, F. P. (2017) The microbiology of lean and obese soil. PhD thesis, University of Reading

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The bacterial genus Bradyrhizobium is biologically important within soils, with different representatives found to perform a range of functions including nitrogen fixation through symbioses, photosynthesis and denitrification. The Highfield experiment at Rothamsted provides an opportunity to study the impact of plants on microbial communities as it has three long-term contrasting regimes; permanent grassland, arable and bare fallow (devoid of plants). The bare fallow plots have a significant reduction in soil carbon and microbial biomass. Bradyrhizobium has been shown by metagenomic studies on soil to be one of the most abundant and active groups including in bare fallow soil indicating that some phenotypes are adapted to survive in the absence of plants. A culture collection was created with isolates obtained from contrasting soil types from Highfield in addition to woodland soil, gorse (Ulex europeaus) and broom (Cytisus scoparius) root nodules. The collection’s phylogeny has been explored by sequencing housekeeping genes to determine whether soil treatment affects the core genome. One grassland and one bare fallow isolate had their genome sequenced and differences have been assessed to establish their potential for a range of functions and to direct future experiments. The functional diversity of the collection has been investigated using carbon metabolism assays to identify key substrates and determine whether the isolates group according to soil treatment. Symbiosis capacity and role in nitrogen cycling has been examined using nodulation tests, anaerobic growth on nitrate and nitrous oxide production and reduction through denitrification. A high level of diversity can be seen throughout the collection with differences being linked to niche adaptation. Understanding more about Bradyrhizobium could give clues on how above ground management impacts a key group within the soil community. Furthermore, the first assembled genomes of two non-symbiotic Bradyrhizobium strains isolated from soil provide an important resource for microbiology and soil ecology.

Item Type:Thesis (PhD)
Thesis Supervisor:Hirsch, P., Clark, I., Shaw, L. and Woodward, M.
Thesis/Report Department:School of Archaeology, Geography & Environmental Science
Identification Number/DOI:
Divisions:Science > School of Archaeology, Geography and Environmental Science > Department of Geography and Environmental Science
ID Code:69408
Date on Title Page:2016


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