Ruminant livestock are important sources of human food and global greenhouse gas emissions. Feed degradation and methane formation by ruminants rely on metabolic interactions between rumen microbes and affect ruminant productivity. Rumen and camelid foregut microbial community composition was determined in 742 samples from 32 animal species and 35 countries, to estimate if this was influenced by diet, host species, or geography. Similar bacteria and archaea dominated in nearly all samples, while protozoal communities were more variable. The dominant bacteria are poorly characterised, but the methanogenic archaea are better known and highly conserved across the world. This universality and limited diversity could make it possible to mitigate methane emissions by developing strategies that target the few dominant methanogens. Differences in microbial community compositions were predominantly attributable to diet, with the host being less influential. There were few strong co-occurrence patterns between microbes, suggesting that major metabolic interactions are non-selective rather than specific.

A general description of the mathematical and numerical formulations used in modern numerical reactive transport codes relevant for subsurface environmental simulations is presented. The formulations are followed by short descriptions of commonly used and available subsurface simulators that consider continuum representations of flow, transport, and reactions in porous media. These formulations are applicable to most of the subsurface environmental benchmark problems included in this special issue. The list of codes described briefly here includes PHREEQC, HPx, PHT3D, OpenGeoSys (OGS), HYTEC, ORCHESTRA, TOUGHREACT, eSTOMP, HYDROGEOCHEM, CrunchFlow, MIN3P, and PFLOTRAN. The descriptions include a C. I. Steefel ( ) · B. Arora · S. Molins · N. Spycher

Sinvolving fl ow, transport, and biogeochemical processes in the subsurface environment requires appropriate modeling tools consistent with the application. While certain problems may be solved using relatively simple analytical or semianalytical models, other problems may require more sophisticated numerical models, either one-or multidimensional, that simulate water fl ow, solute transport, and a range of biogeochemical reactions. To have the fl exibility in optimally addressing general as well as site-specifi c environmental problems, one may thus need a toolbox containing a variety of computer programs of varying complexities. A large number of such computer tools have been developed jointly by the U.S. Salinity Laboratory (USSL) and the University of California, Riverside (UCR) during a time span of about 30 yr and released to the public. It is our objective to describe the most pertinent of these computer programs and discuss several applications.We describe here the history of development, the main processes involved, and selected applications of HYDRUS and related models and software packages (Table 1). Our main focus is initially on the numerical HYDRUS models, their predecessors, and various modifi cations and extensions thereof [e.g., SWMS_2D, HYDRUS-1D, HYDRUS-2D, HYDRUS (2D/3D), and HP1] that resulted from the work of several groups of developers in the United States, the Czech Republic, Israel, the Netherlands, and Belgium. We also summarize several other modeling tools, however, that were developed in close collaboration between the USSL and UCR, such as the CXTFIT and STANMOD codes for analytical transport modeling, as well as additional software and databases (e.g., RETC, Rosetta, and UNSODA) for analyzing unsaturated soil hydraulic properties. All of the tools and databases, with the exception of HYDRUS-2D and HYDRUS (2D/3D), are in the public domain. A CD containing the various codes and manuals is freely available from USSL. Most codes can also be downloaded freely from both the HYDRUS website (www.hydrus2d.com or www. Mathema cal models have become indispensable tools for studying vadose zone fl ow and transport processes. We reviewed the history of development, the main processes involved, and selected applica ons of HYDRUS and related models and so ware packages developed collabora vely by several groups in the United States, the Czech Republic, Israel, Belgium, and the Netherlands. Our main focus was on modeling tools developed jointly by the U.S. Salinity Laboratory of the USDA, Agricultural Research Service, and the University of California, Riverside. This collaboraon during the past three decades has resulted in the development of a large number of numerical [e.g., SWMS_2D, HYDRUS-1D, HYDRUS-2D, HYDRUS (2D/3D), and HP1] as well as analy cal (e.g., CXTFIT and STANMOD) computer tools for analyzing water fl ow and solute transport processes in soils and groundwater. The research also produced addi onal programs and databases (e.g., RETC, Rose a, and UNSODA) for quan fying unsaturated so...

Vapor movement is often an important part in the total water flux in the vadose zone of arid or semiarid regions because the soil moisture is relatively low. The two major objectives of this study were to develop a numerical model in the HYDRUS‐1D code that (i) solves the coupled equations governing liquid water, water vapor, and heat transport, together with the surface water and energy balance, and (ii) provides flexibility in accommodating various types of meteorological information to solve the surface energy balance. The code considers the movement of liquid water and water vapor in the subsurface to be driven by both pressure head and temperature gradients. The heat transport module considers movement of soil heat by conduction, convection of sensible heat by liquid water flow, transfer of latent heat by diffusion of water vapor, and transfer of sensible heat by diffusion of water vapor. The modifications allow a very flexible way of using various types of meteorological information at the soil–atmosphere interface for evaluating the surface water and energy balance. The coupled model was evaluated using field soil temperature and water content data collected at a field site. We demonstrate the use of standard daily meteorological variables in generating diurnal changes in these variables and their subsequent use for calculating continuous changes in water contents and temperatures in the soil profile. Simulated temperatures and water contents were in good agreement with measured values. Analyses of the distributions of the liquid and vapor fluxes vs. depth showed that soil water dynamics are strongly associated with the soil temperature regime.

The remarkable complexity of soil and its importance to a wide range of ecosystem services presents major challenges to the modeling of soil processes. Although major progress in soil models has occurred in the last decades, models of soil processes remain disjointed between disciplines or ecosystem services, with considerable uncertainty remaining in the quality of predictions and several challenges that remain yet to be addressed. First, there is a need to improve exchange of knowledge and experience among the different disciplines in soil science and to reach out to other Earth science communities. Second, the community needs to develop a new generation of soil models based on a systemic approach comprising relevant physical, chemical, and biological processes to address critical knowledge gaps in our understanding of soil processes and their interactions. Overcoming these challenges will facilitate exchanges between soil modeling and climate, plant, and social science modeling communities. It will allow us to contribute to preserve and improve our assessment of ecosystem services and advance our understanding of climate-change feedback mechanisms, among others, thereby facilitating and strengthening communication among scientific disciplines and society. We review the role of modeling soil processes in quantifying key soil processes that shape ecosystem services, with a focus on provisioning and regulating services. We then identify key challenges in modeling soil processes, including the systematic incorporation of heterogeneity and uncertainty, the integration of data and models, and strategies for effective integration of knowledge on physical, chemical, and biological soil processes. We discuss how the soil modeling community could best interface with modern modeling activities in other disciplines, such as climate, ecology, and plant research, and how to weave novel observation and measurement techniques into soil models. We propose the establishment of an international soil modeling consortium to coherently advance soil modeling activities and foster communication with other Earth science disciplines. Such a consortium should promote soil modeling platforms and data repository for model development, calibration and intercomparison essential for addressing contemporary challenges.

The HYDRUS-1D and HYDRUS (2D/3D) computer software packages are widely used finite-element models for simulating the one-and two-or three-dimensional movement of water, heat, and multiple solutes in variably saturated media, respectively. In 2008, Šimůnek et al. (2008b) described the entire history of the development of the various HYDRUS programs and related models and tools such as STANMOD, RETC, ROSETTA, UNSODA, UNSATCHEM, HP1, and others. The objective of this manuscript is to review selected capabilities of HYDRUS that have been implemented since 2008. Our review is not limited to listing additional processes that were implemented in the standard computational modules, but also describes many new standard and nonstandard specialized add-on modules that significantly expanded the capabilities of the two software packages. We also review additional capabilities that have been incorporated into the graphical user interface (GUI) that supports the use of HYDRUS (2D/3D). Another objective of this manuscript is to review selected applications of the HYDRUS models such as evaluation of various irrigation schemes, evaluation of the effects of plant water uptake on groundwater recharge, assessing the transport of particle-like substances in the subsurface, and using the models in conjunction with various geophysical methods.Abbreviations: CRS, cosmic-ray sensing; EC, electrical conductivity; ERT, electrical resistivity tomography; FEM, finite element mesh; GPR, ground-penetrating radar; GUI, graphical user interface; TDT, time-domain transmissometry.The HYDRUS-1D and HYDRUS (2D/3D) software packages (Šimůnek et al., 2008b) are finite-element models for simulating the one-and two-or three-dimensional movement of water, heat, and multiple solutes in variably saturated media, respectively. The standard versions, as well as various specialized add-on modules, of the HYDRUS programs numerically solve the Richards equation for saturated-unsaturated water flow and convection-dispersion type equations for heat and solute transport. The flow equation incorporates a sink term to account for water uptake by plant roots as a function of water and salinity stress. Both compensated and uncompensated water uptake by roots can be considered. The heat transport equation considers movement by both conduction and convection with flowing water. The governing convection-dispersion solute transport equations are written in a relatively general form by including provisions for nonlinear, nonequilibrium reactions between the solid and liquid phases and linear equilibrium reactions between the liquid and gaseous phases. The transport models also account for convection and dispersion in the liquid phase as well as diffusion in the gas phase, thus permitting the models to simulate solute transport simultaneously in both the liquid and gaseous phases. Hence, both adsorbed and volatile solutes, such as pesticides and fumigants, can be considered.The solute transport equations further incorporate the effects of zero-order production, first-o...

No abstract

[1] Considerable research suggests that colloid deposition in porous media is frequently not consistent with filtration theory predictions under unfavorable attachment conditions. Filtration theory was developed from an analysis of colloid attachment to the solid-water interface of a single spherical grain collector and therefore does not include the potential influence of pore structure, grain-grain junctions, and surface roughness on straining deposition. This work highlights recent experimental evidence that indicates that straining can play an important role in colloid deposition under unfavorable attachment conditions and may explain many of the reported limitations of filtration theory. This conclusion is based upon pore size distribution information, size exclusion, time-and concentration-dependent deposition behavior, colloid size distribution information, hyperexponential deposition profiles, the dependence of deposition on colloid and porous medium size, batch release rates, micromodel observations, and deposition at textural interfaces. The implications of straining in unsaturated and heterogeneous systems are also discussed, as well as the potential influence of system solution chemistry and hydrodynamics. The inability of attachment theory predictions to describe experimental colloid transport data under unfavorable conditions is demonstrated. Specific tests to identify the occurrence and/or absence of straining and attachment are proposed.