Model-data interaction in groundwater studies: Review of methods, applications and future directions

This manuscript version is made available under the CC-BY-NC-ND 4.0 license: http://creativecommons.org/licenses/by-nc-nd/4.0/ which permits use, distribution and reproduction in any medium, provided the original work is properly cited. This author accepted manuscript is made available following 24 month embargo from date of publication (Sept 2018) in accordance with the publisher’s archiving policyWe define model-data interaction (MDI) as a two way process between models and data, in which on one hand data can serve the modeling purpose by supporting model discrimination, parameter refinement, uncertainty analysis, etc., and on the other hand models provide a tool for data fusion, interpretation, interpolation, etc. MDI has many applications in the realm of groundwater and has been the topic of extensive research in the groundwater community for the past several decades. This has led to the development of a multitude of increasingly sophisticated methods. The progress of data acquisition technologies and the evolution of models are continuously changing the landscape of groundwater MDI, creating new challenges and opportunities that must be properly understood and addressed. This paper aims to review, analyze and classify research on MDI in groundwater applications, and discusses several related aspects including: (1) basic theoretical concepts and classification of methods, (2) sources of uncertainty and how they are commonly addressed, (3) specific characteristics of groundwater models and data that affect the choice of methods, (4) how models and data can interact to provide added value in groundwater applications, (5) software and codes for MDI, and (6) key issues that will likely form future research directions. The review shows that there are many tools and techniques for groundwater MDI, and this diversity is needed to support different MDI objectives, assumptions, model and data types and computational constraints. The study identifies eight categories of applications for MDI in the groundwater literature, and highlights the growing gap between MDI practices in the research community and those in consulting, industry and government.Behzad Ataie-Ashtiani and Craig T. Simmons acknowledge support from the National Centre for Groundwater Research and Training, Australia. Behzad Ataie-Ashtiani also appreciates the support of the Research Office of the Sharif University of Technology, Iran

Spring Hydrograph Simulation of Karstic Aquifers: Impacts of Variable Re-charge Area, Intermediate Storage and Memory Effects

© 2017 Elsevier. This manuscript version is made available under the CC-BY-NC-ND 4.0 license http://creativecommons.org/licenses/by-nc-nd/4.0/ This author accepted manuscript is made available following 24 month embargo from date of publication (June 2017) in accordance with the publisher’s archiving policyA simple conceptual rainfall–runoff model is proposed for the estimation of groundwater balance components in complex karst aquifers. In the proposed model the effects of memory length of different karst flow systems of base-flow, intermediate-flow, and quick-flow and also time variation of recharge area (RA) during a hydrological year were investigated. The model consists of three sub-models: soil moisture balance (SMB), epikarst balance (EPB), and groundwater balance (GWB) to simulate the daily spring discharge. The SMB and EPB sub-models utilize the mass conservation equation to compute the variation of moisture storages in the soil cover and epikarst, respectively. The GWB sub-model computes the spring discharge hydrograph through three parallel linear reservoirs for base-flow, intermediate-flow, and quick-flow. Three antecedent recharge indices are defined and embedded in the model structure to deal with the memory effect of three karst flow systems to antecedent recharge flow. The Sasan Karst aquifer located in the semi-arid region of south-west Iran with a continuous long-term (21-years) daily meteorological and discharge data are considered to describe model calibration and validation procedures. The effects of temporal variations of RA of karst formations during the hydrological year namely invariant RA, two RA (winter and summer), four RA (seasonal), and twelve RA (monthly) are assessed to determine their impact on the model efficiency. Results indicated that the proposed model with monthly-variant RA is able to reproduce acceptable simulation results based on modified Kling-Gupta efficiency (KGE = −0.83). The results of density-based global sensitivity analysis for dry (June to September) and a wet (October to May) period reveal the dominant influence of RA (with sensitivity indices equal to 0.89 and 0.93, respectively) in spring discharge simulation. The sensitivity of simulated spring discharge to memory effect of different karst formations during the dry period is greater than the wet period. In addition, the results reveal the important role of intermediate-flow system in the hydrological modeling of karst systems during the wet period. Precise estimation of groundwater budgets for a better decision making regarding water supplies from complex karst systems with long memory effect can considerably be improved by use of the proposed model

Response of leaf stable carbon isotope composition to temporal and spatial variabilities of aridity index on two opposite hillslopes in a native vegetated catchment

© 2017 Elsevier. This manuscript version is made available under the CC-BY-NC-ND 4.0 license http://creativecommons.org/licenses/by-nc-nd/4.0/ This author accepted manuscript is made available following 24 month embargo from date of publication (July 2017) in accordance with the publisher’s archiving policyThe stable carbon isotope composition (δ13C) has been demonstrated to be a useful indicator of environmental conditions occurring during plant growth. Previous studies suggest that tree leaf δ13C is correlated with mean annual precipitation (MAP) over a broad range of climates with precipitation between 100 and 2000 mm/year. However, this relationship confirmed at the large scale may not be present at the local scale with complex terrain where factors other than precipitation may lead to additional variability in plant water stress. In this study, we investigated δ13C of tree leaves in a native vegetation catchment over a local gradient of hydro-climatic conditions induced by two hillslopes with opposite aspects. Significant seasonal variations, calculated as a difference between the maximum and minimum δ13C values for each tree, were observed for two species, up to 1.9‰ for Eucalyptus (E.) paniculata, and up to 2.7‰ for Acacia (A.) pycnantha on the north-facing slope (NFS). Also the mean δ13C values calculated from all investigated trees of each hillslope were significantly different and leaf δ13C on the NFS was higher by 1.4 ± 0.5‰ than that on the south-facing slope (SFS). These results cannot be explained by the negligible difference in precipitation between the two hillslopes located just 200 m apart. The correlation coefficients between the δ13C of E. tree leaves and the integrated aridity index (AI) were statistically significant for temporal observations on the NFS (R2 0.18–0.44, p-value 0.00–0.06), and spatial observations (R2 = 0.35, p-value 0.05) at the end of the dry season. These results suggest that AI as a measure of plant water stress is better associated with leaf δ13C than precipitation. Therefore, leaf δ13C value can be used as a valuable proxy for plant water stress across the landscape in both time and space

Density-based global sensitivity analysis of sheet-flow travel time: Kinematic wave-based formulations

© 2017 Elsevier. This manuscript version is made available under the CC-BY-NC-ND 4.0 license: http://creativecommons.org/licenses/by-nc-nd/4.0/ This author accepted manuscript is made available following 12 month embargo from date of publication (February 2018) in accordance with the publisher’s archiving policyDespite advancements in developing physics-based formulations to estimate the sheet-flow travel time (), the quantification of the relative impacts of influential parameters on has not previously been considered. In this study, a brief review of the physics-based formulations to estimate including kinematic wave (K-W) theory in combination with Manning’s roughness (K-M) and with Darcy-Weisbach friction formula (K-D) over single and multiple planes is provided. Then, the relative significance of input parameters to the developed approaches is quantified by a density-based global sensitivity analysis (GSA). The performance of K-M considering zero-upstream and uniform flow depth (so-called K-M1 and K-M2), and K-D formulae to estimate the over single plane surface were assessed using several sets of experimental data collected from the previous studies. The compatibility of the developed models to estimate over multiple planes considering temporal rainfall distributions of Natural Resources Conservation Service, NRCS (I, Ia, II, and III) are scrutinized by several real-world examples. The results obtained demonstrated that the main controlling parameters of through K-D and K-M formulae are the length of surface plane (mean sensitivity index  = 0.72) and flow resistance (mean  = 0.52), respectively. Conversely, the flow temperature and initial abstraction ratio of rainfall have the lowest influence on (mean is 0.11 and 0.12, respectively). The significant role of the flow regime on the estimation of over a single and a cascade of planes are also demonstrated. Results reveal that the K-D formulation provides more precise over the single plane surface with an average percentage of error, APE equal to 9.23% (the APE for K-M1 and K-M2 formulae were 13.8%, and 36.33%, respectively). The superiority of Manning-jointed formulae in estimation of is due to the incorporation of effects from different flow regimes as flow moves downgradient that is affected by one or more factors including high excess rainfall intensities, low flow resistance, high degrees of imperviousness, long surfaces, steep slope, and domination of rainfall distribution as NRCS Type I, II, or III

Vulnerability mapping of coastal aquifers to seawater intrusion: Review, development and application

© 2018 Published by Elsevier Ltd. This manuscript version is made available under the CC-BY-NC-ND 4.0 license: http://creativecommons.org/licenses/by-nc-nd/4.0/ This author accepted manuscript is made available following 24 month embargo from date of publication (December 2018) in accordance with the publisher’s archiving policyIn this study, a review of the overlay/index methods served for delineation of vulnerable zones in coastal aquifers affected by SWI is provided. Then, a more realistic presentation of the vulnerability mapping of coastal aquifers to SWI through modified GALDIT index method by incorporating the influential factors on SWI is established. The modifications on GALDIT method including incorporating the seaward hydraulic gradient (i) instead of the height of groundwater level above sea level (L) (so-called GAiDIT), and considering hydraulic gradient (i) as an additional parameter to the GALDIT (so-called GALDIT-i). Three GALDIT, GAiDIT, and GALDIT-i methods were evaluated with data from three coastal confined and phreatic/confined aquifers located in the south of the Caspian Sea, northern Iran. While no highly vulnerable zone was recognized by GALDIT method across three studied aquifers, averagely 43.4% and 50.5% of aquifers area were defined as highly vulnerable zones by GAiDIT and GALDIT-i, respectively. Furthermore, the final vulnerability maps obtained by GALDIT-i and then GAiDIT indicates higher correlation by three groundwater quality indices specific to SWI including ( = 0.72 and 0.63) and ( = 0.69 and 0.62) and also the distribution of TDS in groundwater ( = 0.71 and 0.61) compared with GALDIT ( = 0.33, 0.42, and 0.36, respectively). The values of vulnerability index obtained by GALDIT-i and GAiDIT are more strongly correlated with the length of SWI into the aquifer () based on Strack's analytical approach than GALDIT ( = 0.52, 0.36, and 0.32, respectively). The results of sensitivity analysis indicated that the hydraulic gradient, height of groundwater level above sea level, aquifer type, and existing status of seawater intrusion has the greatest impact on the groundwater vulnerability across the studied aquifers by GALDIT-i and GAiDIT methods. Results also indicated that serving the influential parameters in GALDIT methods regarding the hydrological and anthropogenic characteristics across the aquifer provide a more realistic characterization of the SWI. This modification leads to an accurate aquifer vulnerability mapping to SWI in aquifers characterized by transient anthropogenic drivers (e.g. pumping) which can be served as a promising tool for decision-making to properly assess and manage risk

Non-pumping reactive wells filled with mixing nano and micro zero-valent iron for nitrate removal from groundwater: Vertical, horizontal, and slanted wells

Crown Copyright © 2018 Published by Elsevier B.V. This manuscript version is made available under the CC-BY-NCND 4.0 license: http://creativecommons.org/licenses/by-nc-nd/4.0/ This author accepted manuscript is made available following 24 month embargo from date of publication (Feb 2018) in accordance with the publisher’s archiving policyNon-pumping reactive wells (NPRWs) filled by zero-valent iron (ZVI) can be utilized for the remediation of groundwater contamination of deep aquifers. The efficiency of NPRWs mainly depends on the hydraulic contact time (HCT) of the pollutant with the reactive materials, the extent of the well capture zone (Wcz), and the relative hydraulic conductivity of aquifer and reactive material (Kr). We investigated nitrate removal from groundwater using NPRWs filled by ZVI (in nano and micro scales) and examined the effect of NPRWs orientations (i.e. vertical, slanted, and horizontal) on HCT and Wcz. The dependence of HCT on Wcz for different Kr values was derived theoretically for a homogeneous and isotropic aquifer, and verified using particle tracking simulations performed using the semi-analytical particle tracking and pathlines model (PMPATH). Nine batch experiments were then performed to investigate the impact of mixed nano-ZVI, NZVI (0 to 2 g l−1) and micro-ZVI, MZVI (0 to 4 g l−1) on the nitrate removal rate (with initial =132 mg l−1). The NPRWs system was tested in a bench-scale sand medium (60 cm length × 40 cm width × 25 cm height) for three orientations of NPRWs (vertical, horizontal, and slanted with inclination angle of 45°). A mixture of nano/micro ZVI, was used, applying constant conditions of pore water velocity (0.024 mm s−1) and initial nitrate concentration (128 mg l−1) for five pore volumes. The results of the batch tests showed that mixing nano and micro Fe0 outperforms these individual materials in nitrate removal rates. The final products of nitrate degradation in both batch and bench-scale experiments were , , and N2(gas). The results of sand-box experiments indicated that the slanted NPRWs have a higher nitrate reduction rate (57%) in comparison with vertical (38%) and horizontal (41%) configurations. The results also demonstrated that three factors have pivotal roles in expected HCT and Wcz, namely the contrast between the hydraulic conductivity of aquifer and reactive materials within the wells, the mass of Fe0 in the NPRWs, and the orientation of NPRWs adopted. A trade-off between these factors should be considered to increase the efficiency of remediation using the NPRWs system

Impacts of groundwater depth on regional scale soil gleyization under changing climate in the Poyang Lake Basin, China

This manuscript version is made available under the CC-BY-NC-ND 4.0 license: http://creativecommons.org/licenses/by-nc-nd/4.0/ which permits use, distribution and reproduction in any medium, provided the original work is properly cited. This author accepted manuscript is made available following 24 month embargo from date of publication (November 2018) in accordance with the publisher’s archiving policyVarious natural and anthropogenic factors affect the formation of gleyed soil. It is a major challenge to identify the key hazard factors and evaluate the dynamic evolutionary process of soil gleyization at a regional scale under future climate change. This study addressed this complex challenge based on regional groundwater modelling for a typical agriculture region located in the Ganjiang River Delta (GRD) of Poyang Lake Basin, China. We first implemented in-situ soil sampling analysis and column experiments under different water depths to examine the statistical relationship between groundwater depth (GD) and gleyization indexes including active reducing substance, ferrous iron content, and redox potential. Subsequently, a three-dimensional groundwater flow numerical model for the GRD was established to evaluate the impacts of the historical average level and future climate change on vadose saturation and soil gleyization (averaged over 2016–2050) in the irrigated farmland. Three climate change scenarios associated with carbon dioxide emission (A1B, A2, and B1) were predicted by the ECHAM5 global circulation model published in IPCC Assessment Report (2007). The ECHAM5 outputs were applied to quantify the variation of groundwater level and to identify the potential maximum gleyed zones affected by the changes of meteorological and hydrological conditions. The results of this study indicate that GD is an indirect indicator for predicting the gradation of soil gleyization at the regional scale, and that the GRD will suffer considerable soil gleyization by 2050 due to fluctuations of the water table induced by future climate changes. Compared with the annually average condition, the climate scenario B1 will probably exacerbate soil gleyization with an 8.8% increase in total gleyed area in GRD. On average, the highly gleyed areas will increase in area by 29.7 km2, mainly on the riverside area, and the medium-slightly gleyed area will increase by 19.2 km2 in the middle region.This work was partially supported by the National Key R&D Program of China (No. 2016YFC0402800), the National Natural Science Foundation of China (Nos. 41772254, 41502226, and 41402198), and the Fundamental Research Funds for the Central Universities (No. 2018B18714). We are grateful to Jiangxi Institute of Survey and Design, who provides the detailed hydrogeological data of PLB for establishing three-dimensional groundwater flow model. Yun Yang gratefully acknowledges financial support from China Scholarship Council (CSC No. 201706715023) during the visit to National Centre for Groundwater Research and Training (NCGRT), Australia. Behzad Ataie-Ashtiani and Craig T. Simmons acknowledge support from the National Centre for Groundwater Research and Training, Australia

Expanding the diversity of mycobacteriophages: insights into genome architecture and evolution.

Mycobacteriophages are viruses that infect mycobacterial hosts such as Mycobacterium smegmatis and Mycobacterium tuberculosis. All mycobacteriophages characterized to date are dsDNA tailed phages, and have either siphoviral or myoviral morphotypes. However, their genetic diversity is considerable, and although sixty-two genomes have been sequenced and comparatively analyzed, these likely represent only a small portion of the diversity of the mycobacteriophage population at large. Here we report the isolation, sequencing and comparative genomic analysis of 18 new mycobacteriophages isolated from geographically distinct locations within the United States. Although no clear correlation between location and genome type can be discerned, these genomes expand our knowledge of mycobacteriophage diversity and enhance our understanding of the roles of mobile elements in viral evolution. Expansion of the number of mycobacteriophages grouped within Cluster A provides insights into the basis of immune specificity in these temperate phages, and we also describe a novel example of apparent immunity theft. The isolation and genomic analysis of bacteriophages by freshman college students provides an example of an authentic research experience for novice scientists

A communal catalogue reveals Earth’s multiscale microbial diversity

Our growing awareness of the microbial world’s importance and diversity contrasts starkly with our limited understanding of its fundamental structure. Despite recent advances in DNA sequencing, a lack of standardized protocols and common analytical frameworks impedes comparisons among studies, hindering the development of global inferences about microbial life on Earth. Here we present a meta-analysis of microbial community samples collected by hundreds of researchers for the Earth Microbiome Project. Coordinated protocols and new analytical methods, particularly the use of exact sequences instead of clustered operational taxonomic units, enable bacterial and archaeal ribosomal RNA gene sequences to be followed across multiple studies and allow us to explore patterns of diversity at an unprecedented scale. The result is both a reference database giving global context to DNA sequence data and a framework for incorporating data from future studies, fostering increasingly complete characterization of Earth’s microbial diversity

Search for dark matter produced in association with bottom or top quarks in √s = 13 TeV pp collisions with the ATLAS detector

A search for weakly interacting massive particle dark matter produced in association with bottom or top quarks is presented. Final states containing third-generation quarks and miss- ing transverse momentum are considered. The analysis uses 36.1 fb−1 of proton–proton collision data recorded by the ATLAS experiment at √s = 13 TeV in 2015 and 2016. No significant excess of events above the estimated backgrounds is observed. The results are in- terpreted in the framework of simplified models of spin-0 dark-matter mediators. For colour- neutral spin-0 mediators produced in association with top quarks and decaying into a pair of dark-matter particles, mediator masses below 50 GeV are excluded assuming a dark-matter candidate mass of 1 GeV and unitary couplings. For scalar and pseudoscalar mediators produced in association with bottom quarks, the search sets limits on the production cross- section of 300 times the predicted rate for mediators with masses between 10 and 50 GeV and assuming a dark-matter mass of 1 GeV and unitary coupling. Constraints on colour- charged scalar simplified models are also presented. Assuming a dark-matter particle mass of 35 GeV, mediator particles with mass below 1.1 TeV are excluded for couplings yielding a dark-matter relic density consistent with measurements