Colloidal Mobility in Contaminated Subsurface Systems: Linking Biological and Chemical Processes

This dissertation investigates how colloids mediate contaminant mobility and microbial community structure in the chemically extreme groundwater of the ENIGMA Field Research Center (eFRC) at the Y-12 National Security Complex. Integrating directional hydrology, conservative tracer tests, ion and metal chemistry, colloid statistics, transmission electron microscopy (TEM), and genome-resolved multi-omics, the work links pore-scale interactions to ecosystem-scale trends and advances colloid transport from idealized theory to field conditions. Electron microscopy revealed ultra-small cells attached to sediment, providing the first direct evidence of such microbial interactions at the eFRC site. A synthesis of colloid transport models (colloid filtration theory, DLVO, and pore-to-continuum-scale approaches) shows why dissolved-phase frameworks fail under nitrate-rich, metal-loaded conditions and motivates empirical tests in this setting. Field analyses demonstrate that hydrologic variability and steep geochemical gradients jointly structure colloid dynamics: shallow intervals exhibit diffuse orientations, whereas deeper zones show stable, aligned transport vectors (Watson-Williams: 26 and 28 vertical and 35 and 36 lateral contrasts significant, p< 0.05). Bromide behaved conservatively in lab and field, confirming clear picture of advective pathways. Ion data revealed strong nitrate enrichment in upper wells and covariation among sulfate, chloride, and nitrate, consistent with redox stratification and mixed sources. The deep zones paired chemical extremes with intermittently connected flow. Colloid distributions were highly structured (pairwise Kolmogorov-Smirnov D≈0.27-0.46 at L8, all p< 0.001), with L8 well emerging as a chemically forced, high-mobility, uranium-maximum spot. L7 well was intermediate, and upper and medium wells formed a more stable cluster. Transmission Electron Microscopy images were grouped as abiotic, biotic, and mixed colloids (mineral fragments, EPS-rich aggregates, ultra-small cells, viruses, vesicles) and documented well-specific viral attachment states (χ²=14.26, df=3, p=0.0026). Microbial communities differed strongly among wells (PERMANOVA pseudo-F=9.74, p=0.001) and tracked geochemistry (Mantel r=0.628, p=0.001). At the same time, colloids contributed an independent, geochemistry-controlled signal (partial Mantel r≈0.143, p=0.005). Genome-resolved results demonstrate abundant mobile genetic elements and Caudoviricetes-dominated viromes, recurrent functional groupings (transporter-CRISPR, energy-nucleotide), and a predictive metals panel (W, Zr, B, Cd, Mg, Mn, U). The dominance of Rhodanobacter denitrificans spp. under high nitrate, low pH conditions suggest niche-specific adaptations that reduce microbial diversity. Overall, the findings support a unified framework: geochemical filtering sets community and metabolic structure; hydrologic coupling and colloids redistribute cells, viruses, plasmids, and metals; genomic plasticity consolidates successful adaptations. The work establishes the first metagenomic and viromic baseline for Subsurface Observatory (SSO) wells Saturated Zone 2 (SZ2) and offers a transferable framework for forecasting contaminant mobility and microbial resilience at nuclear legacy sites.