Contributions of biofilm-induced flow heterogeneities to solute retention and anomalous transport features in porous media.

Microbial biofilms are ubiquitous within porous media and the dynamics of their growth influence surface and subsurface flow patterns which impacts the physical properties of porous media and large-scale transport of solutes. A two-dimensional pore-scale numerical model was used to evaluate the impact of biofilm-induced flow heterogeneities on conservative transport. Our study integrates experimental biofilm images of Paenibacillus 300A strain in a microfluidic device packed with cylindrical grains in a hexagonal distribution, with mathematical modeling.

Machine Learning Analysis of Hydrologic Exchange Flows and Transit Time Distributions in a Large Regulated River.

Hydrologic exchange between river channels and adjacent subsurface environments is a key process that influences water quality and ecosystem function in river corridors. High-resolution numerical models were often used to resolve the spatial and temporal variations of exchange flows, which are computationally expensive. In this study, we adopt Random Forest (RF) and Extreme Gradient Boosting (XGB) approaches for deriving reduced order models of hydrologic exchange flows and associated transit time distributions, with integrated field observations (e.

Representing Organic Matter Thermodynamics in Biogeochemical Reactions via Substrate-Explicit Modeling.

Predictive biogeochemical modeling requires data-model integration that enables explicit representation of the sophisticated roles of microbial processes that transform substrates. Data from high-resolution organic matter (OM) characterization are increasingly available and can serve as a critical resource for this purpose, but their incorporation into biogeochemical models is often prohibited due to an over-simplified description of reaction networks. To fill this gap, we proposed a new concept of biogeochemical modeling-termed -that enables parameterizing OM-specific oxidative degradation pathways and reaction rates based on the thermodynamic properties of OM pools.

WHONDRS-GUI: a web application for global survey of surface water metabolites.

Background: The Worldwide Hydrobiogeochemistry Observation Network for Dynamic River Systems (WHONDRS) is a consortium that aims to understand complex hydrologic, biogeochemical, and microbial connections within river corridors experiencing perturbations such as dam operations, floods, and droughts. For one ongoing WHONDRS sampling campaign, surface water metabolite and microbiome samples are collected through a global survey to generate knowledge across diverse river corridors. Metabolomics analysis and a suite of geochemical analyses have been performed for collected samples through the Environmental Molecular Sciences Laboratory (EMSL).

On Modeling Ensemble Transport of Metal Reducing Motile Bacteria.

Many metal reducing bacteria are motile with their run-and-tumble behavior exhibiting series of flights and waiting-time spanning multiple orders of magnitude. While several models of bacterial processes do not consider their ensemble motion, some models treat motility using an advection diffusion equation (ADE). In this study, Geobacter and Pelosinus, two metal reducing species, are used in micromodel experiments for study of their motility characteristics.

Subsurface biogeochemistry is a missing link between ecology and hydrology in dam-impacted river corridors.

Global investment in hydropower is rapidly increasing, fueled by a need to manage water availability and by incentives promoting renewable energy sources. This expansion poses unrecognized risks to the world's vulnerable freshwater ecosystems. While many hydropower impacts have been investigated, dam-induced alterations to subsurface processes influence river corridor ecosystem health in ways that remain poorly understood.

Regulation-Structured Dynamic Metabolic Model Provides a Potential Mechanism for Delayed Enzyme Response in Denitrification Process.

In a recent study of denitrification dynamics in hyporheic zone sediments, we observed a significant time lag (up to several days) in enzymatic response to the changes in substrate concentration. To explore an underlying mechanism and understand the interactive dynamics between enzymes and nutrients, we developed a trait-based model that associates a community's traits with functional enzymes, instead of typically used species guilds (or functional guilds). This enzyme-based formulation allows to collectively describe biogeochemical functions of microbial communities without directly parameterizing the dynamics of species guilds, therefore being scalable to complex communities.

An analysis platform for multiscale hydrogeologic modeling with emphasis on hybrid multiscale methods.

One of the most significant challenges faced by hydrogeologic modelers is the disparity between the spatial and temporal scales at which fundamental flow, transport, and reaction processes can best be understood and quantified (e.g., microscopic to pore scales and seconds to days) and at which practical model predictions are needed (e.

Dissipative-particle-dynamics model of biofilm growth.

A dissipative-particle-dynamics model for the quantitative simulation of biofilm growth controlled by substrate (nutrient) consumption, advective and diffusive substrate transport, and hydrodynamic interactions with fluid flow (including fragmentation and reattachment) is described. The model was used to simulate biomass growth, decay, and spreading. It predicts how the biofilm morphology depends on flow conditions, biofilm growth kinetics, the rheomechanical properties of the biofilm, and adhesion to solid surfaces.

Lessons learned from bacterial transport research at the South Oyster Site.

This paper provides a review of bacterial transport experiments conducted by a multiinvestigator, multiinstitution, multidisciplinary team of researchers under the auspices of the U.S. Department of Energy (DOE).

Model-based analysis of the role of biological, hydrological and geochemical factors affecting uranium bioremediation.

Uranium contamination is a serious concern at several sites motivating the development of novel treatment strategies such as the Geobacter-mediated reductive immobilization of uranium. However, this bioremediation strategy has not yet been optimized for the sustained uranium removal. While several reactive-transport models have been developed to represent Geobacter-mediated bioremediation of uranium, these models often lack the detailed quantitative description of the microbial process (e.

Direct coupling of a genome-scale microbial in silico model and a groundwater reactive transport model.

The activity of microorganisms often plays an important role in dynamic natural attenuation or engineered bioremediation of subsurface contaminants, such as chlorinated solvents, metals, and radionuclides. To evaluate and/or design bioremediated systems, quantitative reactive transport models are needed. State-of-the-art reactive transport models often ignore the microbial effects or simulate the microbial effects with static growth yield and constant reaction rate parameters over simulated conditions, while in reality microorganisms can dynamically modify their functionality (such as utilization of alternative respiratory pathways) in response to spatial and temporal variations in environmental conditions.

Modeling and sensitivity analysis of electron capacitance for Geobacter in sedimentary environments.

In situ stimulation of the metabolic activity of Geobacter species through acetate amendment has been shown to be a promising bioremediation strategy to reduce and immobilize hexavalent uranium [U(VI)] as insoluble U(IV). Although Geobacter species are reducing U(VI), they primarily grow via Fe(III) reduction. Unfortunately, the biogeochemistry and the physiology of simultaneous reduction of multiple metals are still poorly understood.

Coupling a genome-scale metabolic model with a reactive transport model to describe in situ uranium bioremediation.

The increasing availability of the genome sequences of microorganisms involved in important bioremediation processes makes it feasible to consider developing genome-scale models that can aid in predicting the likely outcome of potential subsurface bioremediation strategies. Previous studies of the in situ bioremediation of uranium-contaminated groundwater have demonstrated that Geobacter species are often the dominant members of the groundwater community during active bioremediation and the primary organisms catalysing U(VI) reduction. Therefore, a genome-scale, constraint-based model of the metabolism of Geobacter sulfurreducens was coupled with the reactive transport model HYDROGEOCHEM in an attempt to model in situ uranium bioremediation.

Change of collision efficiency with distance in bacterial transport experiments.

Understanding the mechanisms of bacterial transport in aquifers is important in developing bioremediation strategies. Collision efficiency (alpha) is one important parameter used in modeling bacterial transport. This study was undertaken to measure change in alpha with distance by performing a bacterial transport experiment in Oyster, Virginia.

Conceptual and numerical model of uranium(VI) reductive immobilization in fractured subsurface sediments.

A conceptual model and numerical simulations of bacterial U(VI) reduction in fractured subsurface sediments were developed to assess the potential feasibility of biomineralization at the fracture/matrix interface as a mechanism for immobilization of uranium in structured subsurface media. The model envisions flow of anaerobic groundwater, with or without acetate as an electron donor for stimulation of U(VI) reduction by dissimilatory metal-reducing bacteria (DMRB), within mobile macropores along a one-dimensional flow path. As the groundwater moves along the flow path, U(VI) trapped in the immobile mesopore and micropore domains (the sediment matrix) becomes desorbed and transferred to the mobile macropores (fractures) via a first-order exchange mechanism.

Apparent decreases in colloid deposition rate coefficients with distance of transport under unfavorable deposition conditions: a general phenomenon.

The transport of polystyrene microspheres was examined in packed glass beads under a variety of environmentally relevant ionic strength and flow conditions. The observed profiles of numbers of retained microspheres versus distance from the column entrance were much steeper than expected based on a constant rate coefficient of deposition acrossthe length of the column, indicating apparent decreases in deposition rate coefficients with transport distance. Deviation in the profile from log-linear decreases with distance was greatest under highly unfavorable conditions (low ionic strength), relatively reduced under mildly unfavorable conditions (high ionic strength), and was eliminated under favorable conditions.

An evaluation of conditioning data for solute transport prediction.

The large and diverse body of subsurface characterization data generated at a field research site near Oyster, Virginia, provides a unique opportunity to test the impact of conditioning data of various types on predictions of flow and transport. Bromide breakthrough curves (BTCs) were measured during a forced-gradient local-scale injection experiment conducted in 1999. Observed BTCs are available at 140 sampling points in a three-dimensional array within the transport domain.

Relative dominance of physical versus chemical effects on the transport of adhesion-deficient bacteria in intact cores from South Oyster, Virginia.

Bacterial transport experiments were conducted using intact sediment cores collected from sites on the Delmarva Peninsula near South Oyster, VA, to delineate the relative importance of physical and chemical heterogeneity in controlling transport of an adhesion-deficient bacterial strain. Electron microscopy revealed that the sediments consisted of quartz and feldspar with a variable amount of clay and iron and aluminum hydroxide coatings on the grains. A nonmotile, gram-negative indigenous groundwater strain, designated as Comamonas sp.