ORT: a workflow linking genome-scale metabolic models with reactive transport codes.

MOTIVATION: Nutrient and contaminant behavior in the subsurface are governed by multiple coupled hydrobiogeochemical processes which occur across different temporal and spatial scales. Accurate description of macroscopic system behavior requires accounting for the effects of microscopic and especially microbial processes. Microbial processes mediate precipitation and dissolution and change aqueous geochemistry, all of which impacts macroscopic system behavior. As 'omics data describing microbial processes is increasingly affordable and available, novel methods for using this data quickly and effectively for improved ecosystem models are needed. RESULTS: We propose a workflow ('Omics to Reactive Transport-ORT) for utilizing metagenomic and environmental data to describe the effect of microbiological processes in macroscopic reactive transport models. This workflow utilizes and couples two open-source software packages: KBase (a software platform for systems biology) and PFLOTRAN (a reactive transport modeling code). We describe the architecture of ORT and demonstrate an implementation using metagenomic and geochemical data from a river system. Our demonstration uses microbiological drivers of nitrification and denitrification to predict nitrogen cycling patterns which agree with those provided with generalized stoichiometries. While our example uses data from a single measurement, our workflow can be applied to spatiotemporal metagenomic datasets to allow for iterative coupling between KBase and PFLOTRAN. AVAILABILITY AND IMPLEMENTATION: Interactive models available at https://pflotranmodeling.paf.subsurfaceinsights.com/pflotran-simple-model/. Microbiological data available at NCBI via BioProject ID PRJNA576070. ORT Python code available at https://github.com/subsurfaceinsights/ort-kbase-to-pflotran. KBase narrative available at https://narrative.kbase.us/narrative/71260 or static narrative (no login required) at https://kbase.us/n/71260/258. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Water Table Dynamics and Biogeochemical Cycling in a Shallow, Variably-Saturated Floodplain.

Three-dimensional variably saturated flow and multicomponent biogeochemical reactive transport modeling, based on published and newly generated data, is used to better understand the interplay of hydrology, geochemistry, and biology controlling the cycling of carbon, nitrogen, oxygen, iron, sulfur, and uranium in a shallow floodplain. In this system, aerobic respiration generally maintains anoxic groundwater below an oxic vadose zone until seasonal snowmelt-driven water table peaking transports dissolved oxygen (DO) and nitrate from the vadose zone into the alluvial aquifer. The response to this perturbation is localized due to distinct physico-biogeochemical environments and relatively long time scales for transport through the floodplain aquifer and vadose zone. Naturally reduced zones (NRZs) containing sediments higher in organic matter, iron sulfides, and non-crystalline U(IV) rapidly consume DO and nitrate to maintain anoxic conditions, yielding Fe(II) from FeS oxidative dissolution, nitrite from denitrification, and U(VI) from nitrite-promoted U(IV) oxidation. Redox cycling is a key factor for sustaining the observed aquifer behaviors despite continuous oxygen influx and the annual hydrologically induced oxidation event. Depth-dependent activity of fermenters, aerobes, nitrate reducers, sulfate reducers, and chemolithoautotrophs (e.g., oxidizing Fe(II), S compounds, and ammonium) is linked to the presence of DO, which has higher concentrations near the water table.

Time-Lapse Electrical Geophysical Monitoring of Amendment-Based Biostimulation.

Biostimulation is increasingly used to accelerate microbial remediation of recalcitrant groundwater contaminants. Effective application of biostimulation requires successful emplacement of amendment in the contaminant target zone. Verification of remediation performance requires postemplacement assessment and contaminant monitoring. Sampling-based approaches are expensive and provide low-density spatial and temporal information. Time-lapse electrical resistivity tomography (ERT) is an effective geophysical method for determining temporal changes in subsurface electrical conductivity. Because remedial amendments and biostimulation-related biogeochemical processes often change subsurface electrical conductivity, ERT can complement and enhance sampling-based approaches for assessing emplacement and monitoring biostimulation-based remediation. Field studies demonstrating the ability of time-lapse ERT to monitor amendment emplacement and behavior were performed during a biostimulation remediation effort conducted at the Department of Defense Reutilization and Marketing Office (DRMO) Yard, in Brandywine, Maryland, United States. Geochemical fluid sampling was used to calibrate a petrophysical relation in order to predict groundwater indicators of amendment distribution. The petrophysical relations were field validated by comparing predictions to sequestered fluid sample results, thus demonstrating the potential of electrical geophysics for quantitative assessment of amendment-related geochemical properties. Crosshole radar zero-offset profile and borehole geophysical logging were also performed to augment the data set and validate interpretation. In addition to delineating amendment transport in the first 10 months after emplacement, the time-lapse ERT results show later changes in bulk electrical properties interpreted as mineral precipitation. Results support the use of more cost-effective surface-based ERT in conjunction with limited field sampling to improve spatial and temporal monitoring of amendment emplacement and remediation performance.

Calcite precipitation dominates the electrical signatures of zero valent iron columns under simulated field conditions.

Calcium carbonate is a secondary mineral precipitate influencing zero valent iron (ZVI) barrier reactivity and hydraulic performance. We conducted column experiments to investigate electrical signatures resulting from concurrent CaCO(3) and iron oxides precipitation under simulated field geochemical conditions. We identified CaCO(3) as a major mineral phase throughout the columns, with magnetite present primarily close to the influent based on XRD analysis. Electrical measurements revealed decreases in conductivity and polarization of both columns, suggesting that electrically insulating CaCO(3) dominates the electrical response despite the presence of electrically conductive iron oxides. SEM/EDX imaging suggests that the electrical signal reflects the geometrical arrangement of the mineral phases. CaCO(3) forms insulating films on ZVI/magnetite surfaces, restricting charge transfer between the pore electrolyte and ZVI particles, as well as across interconnected ZVI particles. As surface reactivity also depends on the ability of the surface to engage in redox reactions via charge transfer, electrical measurements may provide a minimally invasive technology for monitoring reactivity loss due to CaCO(3) precipitation. Comparison between laboratory and field data shows consistent changes in electrical signatures due to iron corrosion and secondary mineral precipitation.

A comparison of the low frequency electrical signatures of iron oxide versus calcite precipitation in granular zero valent iron columns.

Geophysical methods have been proposed as technologies for non-invasively monitoring geochemical alteration in permeable reactive barriers (PRBs). We conducted column experiments to investigate the effect of mineralogy on the electrical signatures resulting from iron corrosion and mineral precipitation in Fe0 columns using (a) Na2SO4, and (b) NaHCO3 plus CaCl2 mixture, solutions. At the influent interface where the reactions were most severe, a contrasting time-lapse electrical response was observed between the two columns. Solid phase analysis confirmed the formation of corrosion halos and increased mineralogical complexity in the corroded sections of the columns compared to the minimal/non-corroded sections. We attribute the contrasting time-lapse signatures to the differences in the electrical properties of the mineral phases formed within the two columns. While newly precipitated/transformed polarizable and semi-conductive iron oxides (mostly magnetite and green rust) increase the polarization and conductivity of the sulfate column, the decrease of both parameters in the bicarbonate column is attributed to the precipitation of non-polarizable and non-conductive calcite. Our results show that precipitate mineralogy is an important factor influencing the electrical properties of the corroded iron cores and must be considered if electrical geophysical methods are to be developed to monitor PRB barrier corrosion processes in situ.

Web-accessible scientific workflow system for performance monitoring.

We describe the design and implementation of a web-accessible scientific workflow system for environmental performance monitoring. This workflow environment integrates distributed automated data acquisition with server side data management and information visualization through flexible browser-based data access tools. Component technologies include a rich browser-based client, a back-end server for methodical data processing, user management, and result delivery, and third party applications which are invoked by the back-end using web services. This environment allows for reproducible, transparent result generation by a diverse user base, and provides a seamless integration between data selection, analysis applications, and result delivery. This workflow system has been implemented for several sites and monitoring systems with different degrees of complexity.