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Publication Date
2025-02-11
Type
doctoral thesis
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Citation
Abstract
The soil microbiome plays a crucial role in an array of important ecological processes, such as biogeochemical cycling, drought resilience, and the formation of soil structure. Metagenomics has revolutionised our understanding of diverse and predominantly unculturable microbial communities in soil, shedding light on their essential ecosystem functions. However, metagenomic techniques for soil microbiomes remain relatively new, and broader applications require considerable optimisation of pipelines.
This thesis examines the Irish soil microbiome through metagenomic analysis of 131 soil samples. Taxonomy classification for soil metagenomics was first optimised by developing an in-silico mock community comprising all known soil-specific bacteria, archaea, and fungi. In-silico metagenomic datasets created using this mock community facilitated the identification of optimal taxonomy classification parameters, including tools, thresholds, and a custom database, which were then applied to map the Irish microbiomes comprehensively. Comparing these taxonomic profiles from shotgun and corresponding amplicon sequencing data, we found that both methods provide moderately similar results, including consistent identification of major phyla, similar patterns of community differentiation, and a similar relationship between nitrogen functions and phyla. Differences between the two methods mainly stemmed from differences in reference taxonomy, underscoring the need for a unified taxonomic framework to ensure reliability and comparability of metagenomic analyses. Next, 107 Metagenome-Assembled Genomes (MAGs) were recovered from 32 deeply sequenced subsamples, revealing antimicrobial resistance in unculturable yet abundant microbial fractions. Alongside elongation factor Tu, K+ transport activator, and arsenic resistance transporter, abundant genes conferring resistance to antibiotics like isoniazid, spectinomycin, and rifamycin, common antibiotics used in cattle, were identified, indicating potential bidirectional transfer of genes between soil and its surrounding environment. This study also recovered a novel Thaumarchaeota MAG that encodes an ammonia-oxidising gene, enhancing our understanding of ammonia-oxidising archaea in agricultural soils.
Overall, this thesis, advances knowledge in soil metagenomics as well as microbial diversity and potential functions in Irish soils and identifies novel genomic assemblies, crucial for updating soil-specific databases and managing microbial activity amid global environmental changes.
Publisher
University of Galway
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Rights
Attribution-NonCommercial-NoDerivatives 4.0 International