The Delaware Microbiome Project: taxonomic and functional marker gene exploration of diverse environments
Date
2025
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Publisher
University of Delaware
Abstract
Microbial communities are integral to global biogeochemical cycles, governing nutrient transformations, ecosystem stability, and environmental health. Understanding their diversity and functional potential across ecosystems is essential for addressing critical environmental challenges, including water security, nutrient pollution, and climate change. This dissertation examines microbial community structure and functional gene diversity across freshwater, sediment, soil, and submarine groundwater discharge (SGD) environments, emphasizing the influence of land use and land cover (LULC), chemical gradients, and seasonal variability. ☐ To achieve this, a standardized sequencing and computational workflow was developed by integrating established methodologies to assess microbial diversity and functional gene composition across various sample types. This approach enabled the characterization of microbial communities using phylogenetic (16S and 18S rRNA) and functional marker genes associated with carbon, nitrogen, phosphorus, sulfur, and arsenic cycling. The workflow produced robust results, demonstrating its applicability across diverse environments and varying DNA concentrations. ☐ The research findings reveal patterns in microbial diversity and ecosystem function. LULC were found to have a stronger influence on microbial diversity than seasonal variations, with wetlands and forested environments supporting greater taxonomic and functional gene diversity compared to anthropogenically impacted areas such as man-made impoundments and recreational lands. Among chemical variables, calcium concentrations emerged as a significant driver of microbial community composition, influencing nitrogen and carbon cycling genes. Principal component analysis (PCA) highlighted distinct clustering patterns in soil samples, whereas freshwater and sediment samples exhibited greater overlap. Network analysis further demonstrated that human disturbances reshape microbial interactions by reducing cooperative relationships and increasing competitive dynamics. ☐ The study also identified significant microbial populations of Candidate Phyla Radiation (CPR) Bacteria and DPANN Archaea, along with contributions to nitrogen cycling in SGD. Dissimilatory nitrate reduction to ammonium (DNRA) was found to be a dominant nitrogen transformation pathway in SGD, reducing nitrogen species before export to the marine environment. Additionally, SGD samples exhibited high abundances of CPR Bacteria and DPANN Archaea, with deep SGD samples reaching up to 53% relative abundance. These poorly characterized microbial groups appear to be strongly influenced by depth and salinity, suggesting that SGD environments function as reservoirs of microbial diversity with largely unexplored ecological roles. ☐ These findings underscore the pivotal role of microbial communities in regulating nutrient cycles and maintaining ecosystem health across diverse environments. By integrating taxonomic and functional gene profiling, this study provides an insight into regional microbial diversity, particularly in ecosystems affected by anthropogenic activity. The standardized sequencing workflow established in this dissertation offers a valuable framework for future microbial research, facilitating long-term environmental monitoring and the discovery of novel microbial members.
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Keywords
Principal component analysis, Candidate Phyla Radiation, Anthropogenic activity