152 research outputs found
Does It Pay Off to Explicitly Link Functional Gene Expression to Denitrification Rates in Reaction Models?
Environmental omics and molecular-biological data have been proposed to yield improved quantitative predictions of biogeochemical processes. The abundances of functional genes and transcripts relate to the number of cells and activity of microorganisms. However, whether molecular-biological data can be quantitatively linked to reaction rates remains an open question. We present an enzyme-based denitrification model that simulates concentrations of transcription factors, functional-gene transcripts, enzymes, and solutes. We calibrated the model using experimental data from a well-controlled batch experiment with the denitrifier Paracoccous denitrificans. The model accurately predicts denitrification rates and measured transcript dynamics. The relationship between simulated transcript concentrations and reaction rates exhibits strong non-linearity and hysteresis related to the faster dynamics of gene transcription and substrate consumption, relative to enzyme production and decay. Hence, assuming a unique relationship between transcript-to-gene ratios and reaction rates, as frequently suggested, may be an erroneous simplification. Comparing model results of our enzyme-based model to those of a classical Monod-type model reveals that both formulations perform equally well with respect to nitrogen species, indicating only a low benefit of integrating molecular-biological data for estimating denitrification rates. Nonetheless, the enzyme-based model is a valuable tool to improve our mechanistic understanding of the relationship between biomolecular quantities and reaction rates. Furthermore, our results highlight that both enzyme kinetics (i.e., substrate limitation and inhibition) and gene expression or enzyme dynamics are important controls on denitrification rates
Estimating Groundwater Recharge in Fully Integrated pde-Based Hydrological Models
Groundwater recharge is the main forcing of regional groundwater flow. In traditional partial-differential-equation (pde)-based models that treat aquifers as separate compartments, groundwater recharge needs to be defined as a boundary condition or it is a coupling condition to other compartments. Integrated models that treat the vadose and phreatic zones as a continuum allow for a more sophisticated calculation of subsurface fluxes, as feedbacks between both zones are captured. However, they do not contain an explicit groundwater-recharge term so it needs to be estimated by post-processing. Groundwater recharge consists of changes in groundwater storage and of the flux crossing the water table, which can be calculated based on hydraulic gradients. We introduce a method to evaluate the change of groundwater storage by a time-cumulative water balance over the depth section of water table fluctuations, avoiding the use of a specific yield. We demonstrate the approach first by a simple 1-D vertical model that does not allow for lateral outflow and illustrates the ambiguity of computing groundwater recharge by different methods. We then apply the approach to a 3-D model with a complex topography and subsurface structure. The latter example shows that groundwater recharge is highly variable in space and time with notable differences between regional and local estimates. Local heterogeneity of topography or subsurface properties results in complex redistribution patterns of groundwater. In fully integrated models, river-groundwater exchange flow may severely bias the estimate of groundwater recharge. We, therefore, advise masking out groundwater recharge at river locations
Comparison of Instantaneous and Constant-Rate Stream Tracer Experiments Through Parametric Analysis of Residence Time Distributions
Artificial tracers are frequently employed to characterize solute residence times in stream systems and infer the nature of water retention. When the duration of tracer application is different between experiments, tracer breakthrough curves at downstream locations are difficult to compare directly. We explore methods for deriving stream solute residence time distributions (RTD) from tracer test data, allowing direct, non-parametric comparison of results from experiments of different durations. Paired short- and long-duration field experiments were performed using instantaneous and constant-rate tracer releases, respectively. The experiments were conducted in two study reaches that were morphologically distinct in channel structure and substrate size. Frequency- and time domain deconvolution techniques were used to derive RTDs from the resulting tracer concentrations. Comparisons of results between experiments of different duration demonstrated few differences in hydrologic retention characteristics inferred from short- and long-term tracer tests. Because non-parametric RTD analysis does not presume any shape of the distribution, it is useful for comparisons across tracer experiments with variable inputs and for validations of fundamental transport model assumptions
Recommended from our members
A field comparison of multiple techniques to quantify groundwater–surface-water interactions
Groundwater–surface-water (GW-SW) interactions in streams are difficult to quantify because of heterogeneity in hydraulic and reactive processes across a range of spatial and temporal scales. The challenge of quantifying these interactions has led to the development of several techniques, from centimeter-scale probes to whole-system tracers, including chemical, thermal, and electrical methods. We co-applied conservative and smart reactive solute-tracer tests, measurement of hydraulic heads, distributed temperature sensing, vertical profiles of solute tracer and temperature in the stream bed, and electrical resistivity imaging in a 450-m reach of a 3rd-order stream. GW-SW interactions were not spatially expansive, but were high in flux through a shallow hyporheic zone surrounding the reach. NaCl and resazurin tracers suggested different surface–subsurface exchange patterns in the upper ⅔ and lower ⅓ of the reach. Subsurface sampling of tracers and vertical thermal profiles quantified relatively high fluxes through a 10- to 20-cm deep hyporheic zone with chemical reactivity of the resazurin tracer indicated at 3-, 6-, and 9-cm sampling depths. Monitoring of hydraulic gradients along transects with MINIPOINT streambed samplers starting ∼40 m from the stream indicated that groundwater discharge prevented development of a larger hyporheic zone, which progressively decreased from the stream thalweg toward the banks. Distributed temperature sensing did not detect extensive inflow of ground water to the stream, and electrical resistivity imaging showed limited large-scale hyporheic exchange. We recommend choosing technique(s) based on: 1) clear definition of the questions to be addressed (physical, biological, or chemical processes), 2) explicit identification of the spatial and temporal scales to be covered and those required to provide an appropriate context for interpretation, and 3) maximizing generation of mechanistic understanding and reducing costs of implementing multiple techniques through collaborative research.This is the publisher’s final pdf. The article is copyrighted by the Society for Freshwater Science and published by the University of Chicago Press. It can be found at: http://www.jstor.org/action/showPublication?journalCode=fresscie
- …