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ARS Home » Pacific West Area » Riverside, California » Agricultural Water Efficiency and Salinity Research Unit » Research » Research Project #432385

Research Project: Sustaining Irrigated Agriculture in an Era of Increasing Water Scarcity and Reduced Water Quality

Location: Agricultural Water Efficiency and Salinity Research Unit

2017 Annual Report

Objective 1: Evaluate the effects of degraded irrigation waters on crop water use and yield at commercial production scales. Subobjective 1A: Evaluate the impact of salinity on crop water use and productivity by observing evapotranspiration and carbon fluxes in commercial almond and pistachio orchards exhibiting a range of salinities. Subobjective 1B: Develop quantitative relationships between remotely-sensed plant canopy observations and measured crop water use and productivity. Objective 2: Develop an innovative, open informatics platform for disseminating information, tools, and recommendations for the management of marginal quality irrigation and artificial recharge waters. Subobjective 2A: Develop a web-based platform for disseminating information, tools, and recommendations for evaluating and managing saline irrigation waters. Subobjective 2B: Develop improved models to support managed aquifer recharge (MAR) treatment of alternative water resources for irrigation.

Drought, climate change, and competition for resources are reducing the availability of irrigation water and farmland in arid and semi-arid regions. One strategy for maintaining or enhancing productivity in the face of diminished resource availability is to make greater use of marginal lands and alternative water sources, both for irrigation and for recharging depleted aquifers. Sustainable use of low quality waters requires soil, water, and crop management practices that optimize crop production and aquifer recharge while minimizing the degradation of natural resources by salts and other contaminants. Advanced models and decision-support tools are needed to evaluate alternative management practices and to assist growers and water managers in satisfying increasingly stringent regulations. In this project, we use micro-meteorological methods to evaluate field-scale crop productivity and water-use across a network of research sites in commercial orchards exhibiting a range of soil salinities and irrigation water qualities. Additionally, we develop an open, web-based informatics platform for disseminating information, models, and decision-support for the use of saline irrigation waters. Lastly, we develop modeling tools focusing on two problems associated with alternative waters and managed aquifer recharge operations: (i.) decreasing infiltration due to soil clogging by colloids; and (ii.) infiltration depths and setback distances required to ensure microbial safety at groundwater extraction points. The project should lead to improved recommendations for managing alternative water resources for irrigation and recharge, and produce new capabilities for predicting the effects of management decisions on crop yields and on soil and water quality.

Progress Report
This is the first report for this new project which began in February of 2017. Please see the report for the previous project, 2036-61000-015-00D, “Effects of Agricultural Water Management and Land Use Practices on Regional Water Quality”, for additional information. Objective 1 of this project involves monitoring and modeling water use and crop productivity in five commercial almond and pistachio orchards using irrigation waters of varying quality. During Fiscal Year 2017, monitoring sites were established in the cooperators’ fields (Objective 1a). The monitoring sites consist of eddy covariance (ECV) towers and instrumentation, plus soil monitoring instrumentation. The five systems have been operational since shortly after the start of the project with minimal data gaps. Data workflows for processing the ECV data have been established and preliminary data analysis has begun. A cooperating graduate student from University of California Riverside (project 2036-61000-018-02S) has begun incorporating the soil water content and electrical conductivity observations in her modeling research. Field surveys of soil electrical conductivity were performed to characterize within-field spatial variability (Objective 1b). However, there was a problem with the instrumentation, and the data may have to be discarded and recollected. Satellite data needed to evaluate spatial variability in terms of the Canopy Response Salinity Index (CRSI) has been identified. The focus of Objective 2 is the development of informatics and modeling tools for salt-affected irrigated agricultural systems and for managed aquifer recharge operations. Under Objective 2a, we established a public source code repository ( that will hold all computer code to be developed under Objective 2a. Thus far, the repository holds code for the first software application, Fluxpart (, a computer program that processes high frequency eddy covariance data so that measured water vapor and carbon dioxide fluxes can be separated into their constitutive components: the water vapor flux into transpiration and direct evaporation components, and the carbon dioxide flux into photosynthesis and respiration components. Among other applications, Fluxpart will be used to process data being collected under Objective 1a. In addition to the source code, the Fluxpart repository has links to full documentation and installation instructions. Design work and some preliminary coding for the next software applications (web-based implementations of UNSODA, RETC, Handbook 60) has been initiated and will continue during the remainder of this year (Objective 2a). Under Objective 2b, considerable research was directed towards developing improved models to support managed aquifer recharge (MAR). In particular, several models were developed and used to study the influence of high velocity regions on microbial transport from infiltration basins. Experimental studies of virus transport and fate under MAR conditions were also analyzed with a model, and the relative importance of various removal mechanisms was quantified. A novel model was constructed and used to simulate the transport and retention of stable and aggregating polydispersed colloidal suspensions. An interagency agreement (2036-61000-018-03I) was established between the U.S. Environmental Protection Agency and USDA ARS to assess the performance of drywells for storm water capture and enhanced aquifer recharge. Experimental and mathematical modeling studies of drywell behavior at the Fort Irwin U.S. Army Base were initiated on this topic.

1. Critical role of high velocity regions on pathogen transport and retention. Contamination of drinking water and fresh produce by disease causing microorganisms poses a risk to human health, and surveys of groundwater frequently detect low concentrations of pathogens. An ARS researcher at Riverside, California and collaborators, modified a mathematical model to simulate the influence of field-scale variations in water velocity on pathogen transport and fate. Results demonstrate that pathogen migration in soil is very sensitive to velocity variations, and that high velocity regions (e.g., preferential flow pathways) will control the ultimate transport potential of pathogens in soils and groundwater. However, the results also depended on the amount of pathogen retention and water exchanged with lower velocity regions. The developed model provides a valuable tool to better assess risks of groundwater microbial contamination, and the simulation results identify the critical role of high velocity regions on pathogen transport and fate in the field and at managed aquifer recharge sites.

2. Transport and fate of viruses under managed aquifer recharge conditions. Treated wastewater and storm water runoff that contains disease causing viruses have been employed at managed aquifer recharge (MAR) sites to store and recover scarce water supplies. The transport and fate of three viruses during MAR conditions was examined in experimental and modeling studies by an ARS researcher at Riverside, California, and collaborators from the University of California, Riverside, Flinders University, Australia, and the Commonwealth Scientific and Industrial Research Organization in Australia. Viruses were always very effectively and irreversibly removed by the soil. Current MAR guidelines only give credit for virus removal by death or inactivation in the water. Our results demonstrate that virus removal in the soil occurs at a much higher rate, and this suggests that current MAR guidelines may be overly conservative.

Review Publications
Bradford, S.A., Feike, L.J., Schijven, J., Torkzaban, S. 2017. Critical role of preferential flow in field-scale pathogen transport and retention. Vadose Zone Journal. 16(4):1-13. doi: 10.2136/vzj2016.12.0127.
Scudiero, E., Skaggs, T.H., Corwin, D.L. 2017. Simplifying field-scale assessment of spatiotemporal changes of soil salinity. Science of the Total Environment. 587:273-281. doi: 10.1016/j.scitotenv.2017.02.136.
Liang, J., Bradford, S.A., Simunek, J., Hartmann, A. 2017. Adapting HYDRUS-1D to simulate overland flow and reactive transport during sheet flow deviations. Vadose Zone Journal. 16(6):1-18. doi: 10.2136/vzj2016.11.0113.
Scudiero, E., Corwin, D.L., Anderson, R.G., Yemoto, K.K., Clary, W.A., Wang, Z., Skaggs, T.H. 2017. Remote sensing is a viable tool for mapping soil salinity in agricultural lands. California Agriculture. 1-8. doi: 10.3733/ca.2017a0009.