Browsing by Author "Hirsch, Penny"

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    Exploiting mycorrhizal selection of beneficial rhizosphere bacteria from the soil microbiome.
    (Cranfield University, 2021-09) Masters-Clark, Emily; Mauchline, Tim; Otten, Wilfred; Hirsch, Penny; Brennan, Fiona; Clark, Ian; Harris, Jim A.
    Soil health is dependent on its diverse communities of microbes. Many of these microorganisms enhance plant growth and enrich the soil. However, the interactions between communities of beneficial microbes remain unclear. Arbuscular mycorrhizal fungi (AMF) are responsible for the most prolific beneficial plant-fungal interaction. However, their influence on the diverse range of plant growth promoting rhizobacteria (PGPR) that also associate with plant roots is yet to be fully elucidated. This research investigates the tripartite interactions between host plant-AMF-PGPR using next-generation sequencing and culture- dependent methodology to define the effect of AMF inoculation on the taxonomic and functional characteristics of the bacterial assemblage of the root microbiome of white clover (Trifolium repens). Soil from two land use types (grassland and bare fallow) amended with fertiliser and/or AMF inoculants are used to describe the effect of these management components on the function of beneficial microbes in cropping systems. The AMF Funneliformis geosporum affected the taxonomic composition of bacteria in the rhizosphere but not the rhizoplane. However, soil type and fertiliser were more influential determinants of bacterial taxa and function. Using split-root microcosm experiments with root exclusion meshes, the dispersal of bacteria was observed in the absence of AMF hyphae. The approaches were combined to show that root microbiome establishment is independent of AMF hyphal facilitation or selection of beneficial bacterial traits or taxa. In vitro predictive measures were used to design a putative Phosphorus solubilising consortium comprised of synergistic P-solubilising rhizobacteria and AMF. Plant health parameters were influenced by the addition of Ca₃PO₄ but were unaffected by any microbial combination. The performance of a putative bioinoculant is dependent on many external factors which can negatively impact the intended function. This work is an important indicator of the complexity of the soil microbiome and demonstrates the profound influence of agronomic inputs on microbial function.
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    Microbial diversity in contaminated soil
    (2002-09) O'Flaherty, S. M.; Magan, Naresh; Hirsch, Penny
    Little is known about soil population dynamics: how microbial communities are affected by environmental stress; whether they respond adversely, or adjust to it; what the extent and duration of these adjustments might be; which genera of bacteria are the most reliable indicators of soil quality. Inevitably, it is beyond the scope of this thesis to resolve all these issues, but it nonetheless sets out to address specific objectives which should cumulatively enhance our total understanding of the soil microbial environment. A three year study of abiotic environmental stress, using a distinctive multi-disciplinary methodology, examined how pseudomonad communities react to chronic metal pollution from sewage sludge. It deployed three profiling methods: population size, catabolic and genetic diversity, across three sequential sampling times, and processed large numbers of bacterial isolates to facilitate meaningful data analysis. This process required innovative methodologies. Efficient analysis of numerous pseudomonad isolates necessitated semi-automation, by adapting ERIC profiling to run on Genescan, a specialist application for analysing sequence data, hitherto unused to fingerprint soil isolates. Specialist computer programmes were designed to compare multiple isolates. A database system was built to gather ERIC profiles and convert them to generate standardised data for subsequent analysis. The main body of this thesis focuses on the interpretation of genetic relationships, largely derived from ERIC profiles, for which a series of programs was built. Alongside them, the BIOLOG™ technique is deployed to profile catabolic diversity and thus compare the function of environmental samples at different sampling times. Population composition, a third dimension, was examined using conventional plate counts. Initial findings that population diversity might be affected by metal stress were not, in the end, corroborated by the extended study. Both catabolic and population studies proved inconclusive, highlighting only subtle differences between metal-contaminated plots. Soil pseudomonads, in contrast to rhizobia, failed to prove sensitive indicators of low level metal contaminants.