Description
Subsurface microbial communities play critical roles in the attenuation of anthropogenic contaminants, as well as global biogeochemical cycling. It has been established that bacterial partitioning (i.e., whether the organism is sediment attached or planktonic) may drastically affect the levels of metabolic activity and rates of bio-degradation. At the highly contaminated Field Research Center, sediment-attached cells account for upwards of 90% of total biomass but exhibit considerably lower metabolic activity (on a per cell basis). Due to inherent sampling challenges, accurate prediction of the distribution and partitioning of microbial communities within the subsurface remains largely unresolved. This, combined with the shift in partitioning driven by environmental perturbation, underscores the need for tools capable of measuring field relevant attachment/detachment kinetics.
Microfluidics allow for the direct observation of attachment kinetics, which at larger scales are obscured by microbial growth, the destructive nature of sediment sampling, and the inability to capture data over relevant timescales. However, to date, microfluidic devices have largely lacked field relevance, limiting their applicability to larger scales. To directly observe attachment kinetics while minimizing microbial growth effects and preserving field relevance, we developed silicon microfluidic devices derived from field‑based, micro-computed tomography. Multiple device geometries have been produced, iteratively incorporating relevant surface charge, roughness, tortuosity, and pore‑throat distributions, all of which could substantially impact partitioning. Developed microfluidic platforms also offer the advantage of allowing direct comparison with more traditional mesoscale transport approaches, such as packed bed reactors (PBRs). Fabricated devices have been used to investigate the transport of the gram-negative, GFP expressing, field isolate Stenotrophomonas GW821-FHT01H02 (H02), a highly ubiquitous bacterium in both groundwater and sediments. Here, we compare bacterial transport behavior at field‑relevant velocities across these scales and demonstrate that incorporating attachment and detachment rates measured at the microscale improves the prediction of transport times in mesoscale models.
Analysis of other environmental variables (e.g., pH, DO, and heavy metals) have previously failed to explain in-situ partitioning of H02. Our results indicate that small changes in seepage velocity substantially change H02 attachment kinetics. An increase in velocity from 7 to 14 mm/hr resulted in an approximate 3x reduction in bacterial attachment, mirroring results from the PBR studies. Under the high flow condition, an equilibrium detachment rate of 8%/hr was observed, while no appreciable detachment was observed under the low flow condition. Additionally, we combined image‑processing techniques with computational fluid dynamics modeling to examine how localized fluid shear influences bacterial attachment. Results indicate a greater tendency for cells to attach to the shadowed side of columns, with this preference becoming more pronounced with increased velocity.
Finally, to examine how community context may reshape these dynamics, we introduced an additional RFP‑expressing bacterial field isolate into the devices (Pseudomonas N2E2). N2E2, an efficient biofilm former, altered the relationship between velocity and H02 partitioning, allowing H02 to form biofilms at velocities exceeding its typical tolerance. Together, these findings establish a cross‑scale framework in which microscale measurements and hydrodynamic mapping inform mesoscale transport predictions, advancing mechanistic understanding of microbial attachment and partitioning in porous media.