Investigating Soil Health Changes After Irrigation Sanitizer Application in Desert Southwest Production Systems: A Guide to Soil Health

Soil is an integral part of all ecosystems, including agricultural ecosystems. This is due to the fact that soil is the point where the atmosphere (the planet’s air), the biosphere (the planet’s living things), the hydrosphere (the planet’s water), and the lithosphere (the planet’s rock) meet. These connections, pictured in Figure 1, work together to make life possible.

Measuring soil health is complex and considers many different but interrelated parameters. These parameters determine the soil’s abilities (e.g., filtering water, storing carbon, and helping with plant growth; NRCS, accessed December 10, 2025). These functions often require a diverse and abundant microbiome, which are the collection of bacteria, viruses, and fungi within the soil (Rieke & Cappellazzi, 2021). The microbiota, perform actions like forming plant-available nutrients in exchange for easy-to-digest carbon sources that they use as food (Ahammed et al., 2025).

Image

Soil health indicators (SHIs) are selected soil properties that can be monitored to assess the overall health of soil. Currently, the US Department of Agriculture (USDA) Natural Resources Conservation Service (NRCS), lists a range of indicators including forms of soil carbon and nitrogen as well as soil physical and chemical properties that are especially useful when assessing the health of soil.

These parameters can be utilized not only to determine the health status of the soil, but also to determine steps that can be taken to improve soil function (e.g., increasing crop yield through supplemental nitrogen additions). Soil sampling throughout the year can be an important tool used to understand the current soil health profile for a field. Utilizing soil monitoring allows the grower to have a more complete picture of the status of the soil and can inform the best treatment for their crop or soil.

Soil carbon can be incredibly beneficial to soil health. The soil carbon fractions (the different types of carbon within the soil) listed in Table 1 are used as indicators of soil health, and include organic and inorganic carbon fractions, as well as indicators of carbon cycling. While it can be helpful to know the total amount of carbon in the soil, knowing the various forms of carbon can help assess different functions in the soil as well.

Organic carbon fractions in the soil include the carbon derived from once-living things. Those which are considered indicative of soil health are soil organic carbon (SOC; the total amount of organic carbon in the soil), active carbon (measured as permanganate-oxidizable carbon; the ideal food source for microbiota in the soil), soil organic matter (SOM; indicative of how much decomposing plant and microbial tissue is in the soil), and ß-glucosidase (beta-glucosidase; an enzyme that is produced that helps break down hard-to-digest molecules into easy-to-digest molecules for soil microbiota). These carbon indicators all serve functions in the soil, typically to do with providing a food source for microbes, who can in turn provide nutrients for plants. As these carbon fractions tend to be low in Arizona’s soils, it is most often beneficial to add organic carbon into your soil. Treatment recommendations include cover cropping various species like grasses, which can add in organic carbon fractions to the soil while acting as an armor against wind and water erosion (Arp et al., 2024; Sanyal & Arp, 2025) and the application of organic amendments like compost or biochar.

Inorganic carbon fractions include soil inorganic carbon (SIC; calcium carbonate) and soil respiration (the amount of carbon dioxide microbes “breathe out” when they perform their activities). Soil respiration will naturally increase with the addition of more organic carbon, which will spike microbial activity. Soils in the US Southwest tend to have a high amount of SIC, leading to a buildup of caliche. Caliche is a cement-like crust or chunks of lime in or on the soil (University of Arizona Cooperative Extension, 2025). This crusting can prevent water infiltration during irrigation events, creating more runoff and evaporation, decreasing irrigation efficiency. Because SIC occurs naturally in the soils in the region, it is important to increase SOC fractions through amendments to adjust the ratio of SOC to SIC, as SIC cannot be removed from the soil. Additionally, for growers looking to manage caliche in their soils, the University of Arizona Cooperative Extension released a quick guide in 2025 with management tips and tricks.

Even though the planet’s atmosphere is almost 80 percent nitrogen, this gaseous nitrogen (the nitrogen in gas form) is not accessible to crops. Therefore, plants team up with soil microbes that can take the nitrogen from the air and turn it into the plant-available mineral form. Soil nitrogen is one of the most important parameters that can limit plant growth in agroecosystems (Zak & Whitford, 1988; Cui et al., 2019). The NRCS-recognized nitrogen parameters are included in Table 2 below. and much like soil carbon, this includes both organic and inorganic forms of nitrogen.

Organic forms of nitrogen include soil proteins (which are proteins from plants and microbes, which serve as nitrogen stores in the soil that are harder to break down) and potentially mineralizable nitrogen (the nitrogen in organic matter that microbes can more easily transform into ammonium and nitrates). Inorganic forms of nitrogen are mainly soil nitrates, which some microbes can create when given organic nitrogen (Grzyb et al., 2021). By increasing organic matter in the soil using the same recommendations to increase soil organic carbon, you can reduce the required amount of nitrogen amendments throughout the growing season. Additionally, cover cropping leguminous plants is especially helpful, as these are species that can host nitrogen fixing bacteria in their root systems that will naturally add more nitrogen into the soil.

Soil physical and chemical properties include soil pH, which is the measurement of how acidic or alkaline the soil is, soil electrical conductivity (EC), which is a measurement of the salts in the soil, as well as aggregate stability (how resistant the soil is to erosion) and nutrient composition (mostly plant macro- and micronutrients like calcium, iron, manganese, among others). A list and summary of these parameters is included in Table 3. Together, these various properties can paint a picture of how much food and water is available to the plants and microbes in the soil. With fewer stable aggregates (a lower wet aggregate stability value), the soil is more susceptible to erosion, which can lead to nutrient loss and pollution of the local ecosystem. With more alkalinity (high pH), plants may not be able to take up as many nutrients. With more salts (higher soil EC), plants may be unable to take up essential nutrients and water. These are all qualities the soils in the Southwest tend to share.

Because these fields in the US Southwest tend to have these qualities, treatment may be required to maximize yield. If a particular field has low aggregate stability, a gradual approach of cover cropping to increase organic carbon fractions in the soil could help. Increasing aggregate stability by improving soil organic matter can have effects like helping salts leach from the soil as well. If the soils have a high measured pH (e.g., the pH exceeds 8), additional sulfur-based amendments such as sulfur burner can also be useful to bring the pH to a more neutral range (Mullen et al., 2016). The addition of gypsum followed by leaching the soil with plenty of water can help mitigate sodium and salt concentrations as well (Bello et al., 2021).

Production systems that use pre-harvest agricultural water treatments apply the water/antimicrobial mixture to the crops and soils. As so much of soil health is dependent on the soil microbiota, measuring soil health in treated operations provides insights into what changes may (or may not) be happening. In such assessments, noting the interplay between the SHIs is of key importance. This type of complex assessment can provide insight into measures that can be taken to improve the ability of the soil to perform ecosystem functions, including increasing crop yield.

Assessing soil health and soil properties can be done through commercial soil health labs. While cost varies between each lab, ranges of costs that can be expected are provided in Table 4. These ranges are compiled from three prominent commercial laboratories, including the Cornell Soil Health Laboratory (Cornell Soil Health Laboratory, accessed December 27, 2025), WARD Laboratories (WARD Laboratories, Inc., accessed December 27, 2025), and Oregon State University’s Soil Labs (Oregon State University Crop & Soil Science, 2025) . While each soil test can be relatively inexpensive, performing all tests can be fairly costly. These costs can be mitigated by:

Once such assessments are completed, it is possible to make informed decisions about treatments, many of which involve increasing soil cover and biodiversity by the use of cover crops, which can increase some key soil parameters that are important to microbial and plant growth and function. Additionally, the unique characteristics of the US Desert Southwest tend to suggest the soils may benefit from additional sulfur amendments to reduce the pH to a more neutral range. Ultimately, the management of the soil and any additional steps taken depend on the desires of the growers.

This work was supported by the Arizona Department of Agriculture through the Specialty Crop Block Grant number SCBGP 22-19 and SCBGP 23-21.

Ahammed, I., Mondal, R., Nesa, J., Mandal, A. K., & Sadat, A. (2025). Understanding the role of soil microbiota and its’ interplay with environment to ensure sustainable development for the future generations. Applied Soil Ecology : A Section of Agriculture, Ecosystems & Environment, 212, Article 106217. https://doi.org/10.1016/j.apsoil.2025.106217

Arp, T., Stackpole, C., & Sanyal, D. (2024). Cover Crops and Carbon Sequestration: A Perspective for Desert Soils. University of Arizona Cooperative Extension Publication number: az2084-2024. http://hdl.handle.net/10150/672951

Bello, S. K., Alayafi, A. H., AL-Solaimani, S. G., & Abo- Elyousr, K. A. M. (2021). Mitigating Soil Salinity Stress with Gypsum and Bio-Organic Amendments: A Review. Agronomy (Basel), 11(9), 1735. https://doi.org/10.3390/agronomy11091735

Cornell Soil Health Laboratory. (n.d.). Soil health analysis packages. Cornell University. Accessed December 27, 2025, from https://soilhealthlab.cals.cornell.edu/testing-services/soil-health-analysis-packages/

Grzyb, A., Wolna-Maruwka, A., & Niewiadomska, A. (2021). The Significance of Microbial Transformation of Nitrogen Compounds in the Light of Integrated Crop Management. Agronomy (Basel), 11(7), Article 1415. https://doi.org/10.3390/agronomy11071415

Mullen, R., Lentz, E., & Watson, M. (2016, 3 November). Soil Acidification: How to Lower Soil pH. Ohio State University Extension. Ohioline. https://ohioline.osu.edu/factsheet/agf-507#:~:text=Many%20plant%20 species%20require%20acid,soil%20pH%20will%20 not%20occur)

NRCS. (n.d.). Soil Health Assessment. Accessed 10 December, 2025 from https://www.nrcs.usda.gov/conservation-basics/natural-resource-concerns…

Oregon State University Crop & Soil Science. (2025). FY25 fee book. Oregon State University. Accessed December 27, 2025, from https://cropandsoil.oregonstate.edu/sites/agscid7/files/crop-soil/asset…

Rieke, E., & Cappellazzi, S. (2021). Assessing Soil Health: Measuring the Soil Microbiome. Crops and Soils Magazine, 54(2), 32–35. https://doi.org/10.1002/crso.20099

Sanyal, D., & Arp, T. (2025). The Basics to Winter Cover Crop Considerations for Arizona Growers. University of Arizona Cooperative Extension Publication number: az2111-202. https://extension.arizona.edu/publicationbasics-winter-cover-crop-considerations-arizona-growers

University of Arizona Cooperative Extension. (2025). Caliche Quick Guide. https://extension.arizona.edu/publication/caliche-quick-guide

WARD Laboratories, Inc. (n.d.). Pricing. Accessed December 27, 2025, from https://www.wardlab.com/pricing/

Zak, J., & Whitford, W. (1988). Interactions among soil biota in desert ecosystems. Agriculture, Ecosystems & Environment, 24(1), 87–100. https://doi.org/10.1016/0167-8809(88)90058-8