Research Project: Improving Soil and Water Productivity and Quality in Irrigated Cropping Systems

Location: Water Management Research

2025 Annual Report

Objectives
The San Joaquin Valley of California is one of the richest agricultural regions in the world. Crop production in this region relies on irrigation water, which is increasingly jeopardized by a substantial water crisis. This multidisciplinary project includes three main goals. Our first goal is to develop agricultural management strategies that enhance soil quality and water productivity. Secondly, our work will help optimize the efficiency of irrigation practices. Finally, this work helps maximize the potential for using low-quality water. Specifically, we will evaluate the impacts of soil conservation practices, cover crops, and whole orchard recycling in cropping systems dominant in the San Joaquin Valley. These strategies impact soil’s capacity to store and filter water. Next, through on-farm experimentation and remote-sensing modeling, we will identify ways to enhance irrigation efficiency. To achieve this, we will determine seasonal crop water demands, optimize irrigation timing and amounts, and evaluate if lower irrigation inputs impact nectarine, pomegranate, and citrus yield and quality. Further, salt, selenium (Se), and boron (B) laden drainage and groundwater sources will be considered for irrigation of many cropping systems. Salt and B tolerant crops utilize such poor-quality waters, manage trace elements residing in the soil from the use of these waters, and can serve as Se-enriched products of economic and nutritional value. Altogether, this systems-level approach thoroughly evaluates many tools that California growers and producers can use to manage their farms under increasing water limitations. This research is urgent and addresses the critical needs of growers and commodity boards. Moreover, these data can be used to address the goals of government and non-profit organizations to enhance agricultural sustainability within the decade. Objective 1: Identify benefits of conservation practices (cover crop, crop diversification, whole orchard recycling, organic soil amendment) for irrigated agriculture. • Sub-objective 1.A: Evaluate the capacity of conservation practices to enhance irrigation water productivity. • Sub-objective 1.B: Determine greenhouse gas emissions, understand N dynamics, and develop N management strategies in almonds orchards after WOR. • Sub-objective 1.C: Investigate interactive effects of organic and inorganic N fertilization and soil building conservation practices for improving soil and water quality in California almond orchards. Objective 2: Develop deficit irrigation strategies for perennial fruiting crops. • Sub-objective 2.A: Determine water requirement and deficit irrigation strategies in early-season nectarine. • Sub-objective 2.B: Develop deficit irrigation strategies for optimized water productivity in pomegranate. • Sub-objective 2.C: Determine watershed-scale crop water use and water savings using simulated deficit irrigation in commercially grown citrus. Objective 3: Develop sustainable agricultural water reuse systems with alternative crops to protect soil/environmental health of drainage impacted soils when using poor-quality water.

Approach
Sub-objective 1A: We aim to reveal impacts of cover crops on soil water holding capacity, soil biological diversity, berry yield and quality, and weed pressure in a table grape vineyard. Soil and vines will be analyzed to quantify soil microbial biomass and community compositions, soil carbon (C) and nutrients, and crop yield, quality, and water productivity. If cover crops fail to re-establish, we will re-seed. Sub-objective 1B: We aim to quantify GHG emissions, woodchip mineralization, and nutrient availability in orchard soils after whole orchard recycling (WOR). Using field plots, soil GHG emissions, nitrate leaching potential, and nitrogen (N) transformation and movement will be quantified. Lab experiments will evaluate impacts of woodchip sizes and soil moisture on similar soil properties. If field operations interfere with sampling, we will sample the field, once accessible. Sub-objective 1C: We aim to reveal impacts of compost with conservation practices on soil biological properties. Soil microcosms developed from WOR and cover crop almond orchards will be amended with compost or inorganic N fertilizer and evaluated for soil microbial properties, C, N, and nitrate. Grower selection of cover crop species will not impact the project. Sub-objective 2A: We hypothesize that postharvest deficit irrigation (DI) reduces consumptive water use in early-season nectarine without affecting fruit yield and quality. DI strategies will be applied to nectarine research plots and tree health and fruit yield and quality metrics will be determined. If the pre-selected DI rates are too high or too low, they will be adjusted. Sub-objective 2B: We hypothesize that regulated DI increases water use efficiency, water productivity, and economic returns in pomegranate. Field and laboratory measurements will evaluate effects of DI on soil water availability, pomegranate tree growth characteristics, fruit yield and quality, and water productivity. If lysimeters, used to guide irrigation scheduling fail, then water content and weather data will be used. Sub-objective 2C: We aim to determine consumptive water use in evapotranspiration (ET) of citrus crops under grower practice and simulated DI. At two citrus orchards, eddy-covariance towers with sensors will be used to calculate standardized reference ET, which will be compared to corresponding satellite pixel estimates and to local ground-based estimates. If data is not available from growers, we will use the field, remote sensing, and published data. Objective 3: We aim to develop agronomic systems tolerant to poor-quality water that can manage soil selenium; determine drainage water impacts on salt-tolerant crops in crop rotation; and reveal the effects of long-term saline irrigation in pistachio. Guayule, agretti, and pistachio crop yield, quality, and salt accumulation will be evaluated in field trials with poor-quality irrigation water. If cooperator field plots are no longer available, alternative sites will be used.

Progress Report
This report documents FY 2025 progress for project 2034-13000-013-000D, “Improving Soil and Water Productivity and Quality in Irrigated Cropping Systems”, which began in January 2022. In support of Sub-bjective 1A, research continued on a table grape vineyard to evaluate impacts of cool season cover crops on soil properties, water dynamics, and yield. There were not significant treatment effects on soil aggregate stability, moisture retention, or saturated hydraulic conductivity in vine rows or alleys, but soil sorptivity was significantly lower in the vine rows of rye treatment plots. Soil microbial biomass was significantly higher in the alleys of cover crop treatments relative to the control in June and September, signifying that residues from mown cover crops are stimulating the proliferation of soil biota. Soil extracellular polysaccharides were extracted and weed surveys were conducted. Analyses of these datasets are ongoing. In fall 2024, cover crops plots had similar table grape yield and cluster counts relative to an unplanted control, but some quality metrics were significantly improved in both cover crop treatments (fewer rotten or yellow berries), or only in the rye treatment (less shatter and higher visual quality score). Under Sub-objective 1B, soil nutrients and water dynamics were affected by whole orchard recycling (WOR) in both field and laboratory experiments. WOR refers to on-site grinding or chipping of whole trees after orchard removal, and incorporation of that biomass into the topsoil. WOR implementation has increased dramatically in recent years in response to bans on agricultural residue burning in the Central Valley of California. In an almond orchard established in 2019, data have been collected to profile how WOR affects soil nutrients by monitoring their gas losses [mainly carbon dioxide (CO2) from woodchip decomposition, and nitrous oxide, which reflects fertilizer losses], nitrate leaching, and changes in soil carbon (C) and nitrogen (N) concentration. Woodchip decomposition rates were initially high and decreased substantially with time. By year six, there were no significant differences in CO2 emission rates between WOR treated plots and control plots without woodchips, and soil organic carbon increased significantly over time, 57% higher in WOR treated plots in top 15-cm soil. A modeling approach showed that woodchips improved soil water retention, with a potential irrigation reduction up to 20% without reducing root water uptake. Research collaborators reported consistently, and significantly higher kernel yields from WOR field plots comparing to no-WOR treatment. ARS data supported that the increased yield was attributed to the increased soil C, water and nutrient retention, improved soil properties, and an overall positive effect of WOR on soil ecosystem services. A lab incubation experiment was conducted for eight months by incorporating woodchips of different sizes into soil, with varying soil water content, temperature, and N application rates to profile influence on N availability with data being processed. The field data were summarized in two publications and one under review during the reporting year. For Sub-objective 1C, research continued on two trials examining the outcomes of WOR or cover crops on almond orchard productivity and soil properties, important for water use efficiency. WOR significantly enhanced soil microbial biomass (SMB), populations of arbuscular mycorrhizal fungi (AMF), C, and N in tree row soils consistently across the growing season (April, June, and August) relative to conventional management without WOR. Similar benefits were revealed for alleys, wherein soil N and C were enhanced in WOR treatment in June (t-test, p less than 0.05). Cool-season, interrow, cover cropping in almonds with mustard, oats, and pea resulted in alley soils with significantly higher abundances of AMF and marginally higher SMB in April relative to herbicide-maintained control plots. In tree row soils, SMB, AMF, C and N were not significantly different based on cover cropping treatment in April, June, or August. Together these results reveal that WOR and cover crops have potential to boost soil properties important for aggregation and water use efficiency in almond production. For Sub-objective 2A, a nectarine orchard was maintained by collecting cuttings, planting new rootstock, and grafting trees to replace diseased trees. Nectarine bloom and fruit set counts were measured in March and April, respectively. Fruits were thinned in April according to commercial production practice. Leaf stomatal conductance readings were taken manually each month for the growing season. Soil moisture content was automatically recorded using electronic sensors installed in each irrigation treatment plot. Fruits were manually harvested in June, separated into marketable and non-marketable groups, counted and weighed on a per tree basis for a total of 432 trees. Three fruits were taken from each tree and will be analyzed for pH, soluble solids, skin color, and flesh firmness after designed elapsed days in the laboratory or in cold storage. In support of Sub-objective 2B, infrared sensors were installed above the canopy of a pomegranate orchard to measure the tree temperature during the growing season. Trees under deficit irrigation will experience mild to severe water stress and should show higher canopy temperature than trees not under stress. Similar to the previous crop cycle, pomegranate trees are being irrigated according to evapotranspiration needs estimated using weather station data and crop coefficient values. Four irrigation treatments are used to replace 100%, 75%, 75%+125%, and 50% irrigation demand daily during the entire growing season. Soil moisture content is automatically recorded continuously using electronic sensors installed in each irrigation treatment plot. Fruit yield and quality will be determined during and after harvest in October. During harvest, fruits will be separated into marketable and non-marketable groups, with weight and total number of each group determined. Fruit quality determined were external fruit surface color and juice Brix and pH values determined after room-temperature storage for 3, 7, or 14 days or in cold storage for 2, 4, and 8 weeks. Under Sub-objective 2C, electronic sensors on the three eddy-covariance tower systems were calibrated quarterly and maintained daily or as needed during the growing season. With citrus being an evergreen plant, field measurements are continuously made in all four seasons. To determine citrus tree leaf water status and tree size, leaf stomatal conductance and leaf area index readings were taken at approximately 14-day intervals. High frequency data from the flux towers were downloaded and analyzed regularly for quality analysis and estimation of crop water use as daily evapotranspiration. In support of Objective 3, research continued successfully growing and evaluating salt and boron tolerant varieties of broccoli, lettuce, citrus, cactus, guayule, perennial grass species, hybrid poplars, and young and mature pistachio trees, for physiological and yield responses to irrigation with high saline water. ARS researchers used soil sensors in these studies to measure real -time changes in soil moisture and salinity with saline irrigation, and soluble boron (B) in field-installed growing tiles, as well as in saline soils supporting mature pistachio trees under field irrigation with saline waters. Researchers are studying uptake and speciation of Selenium (Se), and accumulation of B, sodium (Na) and chloride (Cl) in all edible parts and leaves, and measuring the effects of salinity and B on yields, nutritional quality, total phenolics in edible parts, including pistachio nut and prickly pear fruit, and measuring latex and rubber production in guayule with cooperation of ARS in Albany, California. The tested plant species have accumulated Se ranging from 2 to 12 mg Se/kg DW in plant tissues, including the predominate selenoamnio acid- selenomethionine-, and have produced bio-based products, e.g., guayule rubber and resin, edible Se enriched plant tissues, nuts and fruit. Additionally, ARS is irrigating guayule with saline waters and measurements are made to determine the amount of Se removed from soil via plant uptake and Se volatilization (volatilization rates were as high as 75 ug/m2/24 hr during the year). In saline irrigated field-grown pistachios, the highest leaf Na, Cl, and B concentrations were measured at: 20,000, 14,000, and 2,000 mg/kg DM, respectively, while the saline -irrigated soils had an average soil salinity EC values ranging from 8-10 dS/m, and concentrations of ions ranging as follows: Na (2,000-2500 mg/L), Cl (1,600-2,000 mg/L) and B (7-9 mg/L). Edible nut yields for mature pistachio trees irrigated with saline water ranged from 250 to 2500 lbs/acre, while younger 6-year-old pistachio trees on two different rootstocks grown in tiles produced nut yields between 180 lbs/acre (PG-1 rootstock) and 220 lbs (UCB-1 rootstock). Importantly, researchers only observed a slight nut yield decrease after 6 years of saline irrigation in the younger pistachio trees. Moreover, in all saline-irrigated studies, a resulting increased soil salinity reduced the uptake of soluble B and Se by all plants. Regarding soil Se losses, they observed net losses (10-18%/year) of soluble soil Se primarily at 0-45 cm for in saline microplots planted to grasses, guayule, and poplar trees. Most of the removed Se (up to 20%) was by plant uptake, with approximately 10% losses from volatilization and excessive precipitation. Researchers also are studying the growth, health, biochemical responses, and rubber and resin production in five guayule ecotypes grown under varying salinity levels and in two distinct soil types using lysimeter tiles.

Accomplishments
1. Precision agriculture research optimizes predictions of citrus orchard water use. Precision agriculture methods, including satellite models, are widely used in arid regions of the United States by regulatory agencies to estimate water used to grow specialty crops. However, water use models for specialty crops like citrus are inaccurate because direct field measurements to calibrate and validate simulations are lacking. ARS scientists in Parlier, California, Riverside, California, and Maricopa, Arizona, along with researchers from the University of California, collaborated to evaluate the water use dynamics of major citrus varieties using field measurements from eddy covariance systems against the widely-used OpenET satellite models. Compared to direct field measurements, up to 30% over prediction was found for the simulated evapotranspiration using the OpenET models and large discrepancies occurred in the spring season. These findings can be used by regulatory agencies and stakeholders to make appropriate compensatory adjustments when using satellite simulation models for water use determinations of citrus and other specialty crops.

2. Irrigation with waters of reduced quality produced selenium-enriched bioproducts. Selenium is a natural component found in soils and groundwater used for irrigated agriculture on the west side of Central California. ARS researchers in Parlier, California, investigated whether this might impact the crops grown. They demonstrated that in many crops, including mushrooms, irrigation with waters of reduced quality during times of drought, can produce biobased products that are selenium enriched. This change enhances the nutritional quality of the food product and can increase the antioxidant capacity and/or stress resistance of the irrigated crop. This provides new markets for growers in regions with low quality irrigation water supplies.

3. Nutritional value enhancement of onions and tomatoes through novel foliar selenium biofortification using biochar and deficit irrigation. Selenium (Se) deficiency in humans can be mitigated through Se biofortification of food crops. However, this can be challenging in areas with suboptimal soils that are Se-deficient and where water is scarce. ARS researchers in Parlier, California, demonstrated that, in a light-textured soil under water limiting conditions, the use of deficit irrigation and biochar enhanced water retention on the irrigated production of onions and tomatoes grown for Se biofortification. Incorporating biochar and utilizing deficit irrigation as a water management strategy combined with foliar application of inorganic Se resulted in effective biofortification strategies under drought conditions. This research provides nutrient dense products for consumers grown with reduced irrigation water inputs.

4. Cover cropping enhances soil microbial characteristics that can reduce vineyard fertilizer and irrigation demands. Microbes in soil like bacteria and fungi are sensitive to management, can enhance soil structure through production of sticky compounds and hyphae, and arbuscular mycorrhizal fungi (AMF) can directly uptake water for their host plants. ARS scientists in Parlier, California, revealed that cover cropping enhanced soil microbial biomass and AMF in vineyard soils. These benefits increased with cover cropping duration and extended beyond the termination of the cover crop. Further, a multi-location project across 15 ARS stations revealed this trend to be consistent across most cover crop trials and determined that cover cropping exerted a stronger influence on AMF than other conservation management practices. These findings can help growers reduce fertilizer use and irrigation demands by promoting native beneficial microorganisms in their soils.

5. Whole orchard recycling improves soil properties and tree growth. Whole orchard recycling (WOR) involves chipping of wood biomass from old orchards and returning to soil prior to replant and has become popular practice in recent years in California. Knowledge of nutrient cycling and dynamics is needed for effective management decisions. Researchers in Parlier, California, conducted field and lab research showing that although the decomposition rate of woodchips (in the form of carbon dioxide release) after being incorporated into soil is initially high, it decreased substantially with time, resulting in increased organic carbon in soil and improved soil properties, such as increased water retention and reduced nitrate leaching. A modeling effort based on field data suggests that WOR could lead to an irrigation reduction by up to 20% with minimal effect on root water uptake. The findings confirm that WOR is an effective management strategy for growers, having an overall positive effect on soil ecosystem functions, and contributing to increased crop yield.

Review Publications
Gao, S., Hendratna, A., Pflaum, T. 2024. Assessment of biochar adsorption capacity for ammonium and nitrate and implications on soil nitrogen management. Journal of Advanced Agricultural Technologies. 11(2):17–27. http://doi.org/10.18178/joaat.11.2.17-27.
Fernando, M.R., Hale, L.E., Shrestha, A. 2024. Does a native and introduced cover crop species differ in their ability to suppress? A study in a table grape vineyard. International Journal of Pest Management. p. 1-9. https://doi.org/10.1080/09670874.2024.2419902.
Culumber, C.M., Gao, S., Thao, T., Poret-Peterson, A.T., Zuber, C., Camarena-Onofre, D., Perez-Sandoval, J.C., Hendratna, A., Holtz, B. 2025. Impact of whole orchard recycling on greenhouse gas emissions, soil carbon storage, and almond productivity in a replanted orchard. Agriculture, Ecosystems & Environment. 389. Article 109664. https://doi.org/10.1016/j.agee.2025.109664.
de Morais, E., Silva, C., Gao, S., Melo, L., Benevenute, P., Lago, B., Teodoro, J., Guilherme, L. 2025. Rapid adsorption of ammonium on coffee husk and chicken manure-derived biochars: Mechanisms unveiled by chemical speciation, physical, and spectroscopic approaches. Sustainability. 17. Article 1616. https://doi.org/10.3390/su17041616.
Bali, K., Putnam, D., Wang, D., Begna, S.H., Holder, B., Mohamed, A., Paloutzian, L., Dahlke, H.E., Eltarabily, M.G. 2024. Midsummer deficit irrigation of alfalfa for water conservation in the San Joaquin Valley of California. Journal of Irrigation and Drainage Engineering. 150(6). Article 04024029. https://doi.org/10.1061/JIDEDH.IRENG-10213.
Dhungel, R., Anderson, R.G., French, A.N., Skaggs, T.H., Ajami, H., Wang, D. 2024. Intercomparison of citrus evapotranspiration among eddy covariance, OpenET ensemble models, and the water and energy balance model (BAITSSS). Agricultural Water Management. 304. Article 109066. https://doi.org/10.1016/j.agwat.2024.109066.
Eltarabily, M., Mohamed, A.Z., Begna, S.H., Wang, D., Putnam, D.H., Scudiero, E., Bali, K.M. 2024. Simulated soil water distribution patterns and water use of alfalfa under different subsurface drip irrigation depths. Agricultural Water Management. 293. Article 108693. https://doi.org/10.1016/j.agwat.2024.108693.
Inge Rocha, F., Roriguez Ramos, J., Fernando, M., Hale, L.E. 2025. Interrow cover crops in a semi-arid vineyard increase plant beneficial functional potential of the soil microbiome, both in vine rows and interrows, a benefit that increases with cover crop duration. Environmental Microbiome. 20. Article 66. https://doi.org/10.1186/s40793-025-00726-1.
Roper III, W.R., Acosta Martinez, V., Veum, K.S., Burgess, C.J., Moore, J.M., Manter, D.K., Stewart, C.E., Emmett, B.D., Liebig, M.A., Fischel, M.H., Lehman, R.M., Franco Jr, J.G., Johnson, J.M., Weyers, S.L., Mikha, M.M., Trippe, K.M., Maul, J.E., Dungan, R.S., Gollany, H.T., Ducey, T.F., Hale, L.E., Jin, V.L., Cavadini, J., Reardon, C.L. 2025. Unraveling edaphic, environmental, and management drivers of soil microbial communities via ester-linked fatty acid methyl esters using a multilocation agroecosystem study. Geoderma. 453. Article 117158. https://doi.org/10.1016/j.geoderma.2024.117158.
Thao, T., Culumber, C.M., Poret-Peterson, A.T., Zuber, C.A., Holtz, B.A., Gao, S. 2024. Evaluating the seasonal effects of whole orchard recycling on water movement and nitrogen retention for a newly established almond orchard: Simulation using HYDRUS-1D. Agricultural Water Management. 299. Article 108882. https://doi.org/10.1016/j.agwat.2024.108882.
Thao, T., Begna, S.H., Hale, L.E., Bali, K.M., Wang, D., Gao, S. 2025. Intercropping alfalfa during almond orchard establishment reduces winter soil nitrogen and water losses, provides on-farm revenue. Agrosystems, Geosciences & Environment. 8(1). Article e70024. https://doi.org/10.1002/agg2.70024.
Reed, D., Chu, H., Peter, B., Chen, J., Abraha, M., Amiro, B., Anderson, R.G., Arain, M., Arruda, P., Barron-Gafford, G., Bernacchi, C.J., Beverly, D., Biraud, S., Black, A., Blanken, P., Bohrer, G., Bowler, R., Bowling, D., Bret-Harte, M., Bretfeld, M., Brunsell, N., Bullock, S., Celis, G., Chen, X., Classen, A., Cook, D., Cueva, A., Dalmagro, H., Davis, K., Desai, A., Duff, A., Dunn, A., Durden, D., Edgar, C., Euskirchen, E., Bracho, R., Ewers, B., Flanagan, L., Florian, C., Foord, V., Forbrich, I., Forsythe, B., Frank, J., Garatuza-Payan, J., Goslee, S.C., Gough, C., Green, M., Griffis, T., Helbig, M., Hill, A., Hinkle, C., Horne, J., Humphreys, E., Ikawa, H., Iwahana, G., Jassal, R., Johnson, B., Johnson, M., Kannenberg, S., Kelsey, E., King, J., Knowles, J., Knox, S., Kobayashi, H., Kolb, T., Kolka, R., Krauss, K., Kutzbach, L., Lamb, B., Law, B., Lee, S., Lee, X., Liu, H., Loescher, H., Malone, S., Matamala, R., Mauritz, M., Metzger, S., Meyer, G., Mitra, B., Munger, J., Nesic, Z., Noormets, A., O'Halloran, T., O'Keeffe, P., Oberbauer, S., Oechel, W., Oikawa, P., Olivas, P., Ouimette, A., Pastorello, G., Perez-Quezada, J., Phillips, C.L., Posse, G., Qu, B., Scott, R.L., Reba, M.L., Wang, D., Schreiner-Mcgraw, A.P. 2025. Network of networks: Time-series clustering of Ameriflux sites. Agricultural and Forest Meteorology. https://doi.org/10.1016/j.agrformet.2025.110686.
Banuelos, G.S., Centofanti, T., Zambrano, M.C., Arroyo, I.S., Wang, D. 2025. Selenium biofortification and growth of onions as affected by Se application, biochar and irrigation. Journal of Food Composition and Analysis. 140. Article 107217. https://doi.org/10.1016/j.jfca.2025.107217.
Banuelos, G.S., Centofanti, T., Zambrano, M.C., Arroyo, I.S., Wang, D. 2025. Selenium biofortification in field-grown tomatoes as affected by Stanleya pinnata-derived organic Se application, biochar and irrigation. Journal of Agriculture and Food Research. 23. Article 102162. https://doi.org/10.1016/j.jafr.2025.102162.
Zhou, F., Qi, M., Ren, R., Shi, J., Zhao, W., Wu, H., Banuelos, G.S., Liang, D. 2025. Systematic comparison of the effects of exogenous inorganic selenium and organic selenium on the quality and antioxidant capacity of Pleurotus eryngii. Journal of the Science of Food and Agriculture. Article 10970010. https://doi.org/10.1002/jsfa.14346.