Organic materials include crop residues, manures, and other organic amendments that are commonly added to the soil in a crop production system. It is the breakdown and microbial digestion process of organic materials that can contribute to stable soil organic matter (SOM). Thus, organic materials are not the same as SOM.
The decomposition of organic materials is a process that is carried out by naturally occurring soil microbes. Organic material decomposition is an important aspect of nutrient cycling, soil fertility, and soil health.
The naturally occurring soil microorganisms, that include bacteria, fungi, actinomycetes, protozoa, and soil fauna (organisms such as nematodes, mites, springtails, and earthworms) drive the biochemical transformations converting complex organic compounds in organic materials into smaller, simpler, plant-available forms (Paul 2015; Sylvia et al. 2005).
In the initial steps of decomposition, these organisms exude extracellular enzymes that break down the large complex polymers (i.e., cellulose, hemicellulose, lignin, proteins, and lipids) in organic materials. The rate of decomposition is strongly influenced by substrate chemistry decay (Jenkinson 1981; Brady and Weil 2017).
The residues that decompose most rapidly have low carbon-to-nitrogen (C:N) ratios (higher N concentration), such as legumes or many manures. The low C:N ratio materials decompose most rapidly because microorganisms have sufficient nitrogen (N) to support biomass growth and enzyme production (Palm et al. 2001; Magdoff and van Es 2021). The microbes work hard to break down the complex organic materials, and they provide a great service in the process, but what they are seeking is N.
Organic materials with high C:N rations, such as cereal grain straw and most harvested crop residues are usually slower to decompose due to slower microbial activity. This is the result of microbes scavenging for mineral N, ammonium NH4+ or nitrate NO3− to meet their metabolic demands (McGill and Cole 1981; Janzen and Kucey 1988).
When sufficient mineral N is lacking in the soil, the microbes will consume most of the available N and incorporate into their own bodies. This can cause short-term nitrogen immobilization (McGill and Cole 1981; Janzen and Kucey 1988). We often see that in the field with early crop growth immediately following a previous crop.
Mineralization refers to the conversion of organically bound nutrients into inorganic, plant-available forms. Nitrogen mineralization involves microbial depolymerization of organic N compounds (e.g., the breakdown into amino acids and proteins) followed by the release of ammonium (NH₄⁺) (Figure 1; Stevenson and Cole 1999).
Figure 1. The nitrogen cycle. Source: Stevenson, 1982.
Mineralization becomes dominant as the decomposition process continues. The NH₄⁺-N (N in the form of ammonium) that is produced in the first steps of mineralization is rapidly converted to NO₃⁻-N by specialized autotrophic bacteria (Nitrosomonas and Nitrobacter). These bacterial organisms are abundant in healthy soil and we commonly see clear evidence of that in our agricultural soils. This is critically important because NO₃⁻-N is the primary form of N taken up by most crop plants. (Chapman et al. 2013).
The balance between immobilization and mineralization is central to predicting nutrient availability during crop growth. Environmental factors such as temperature, moisture, aeration, and pH regulate the rate of all of these transformations (Brady and Weil 2017; Paul 2015).
Other essential plant nutrients follow similar mineralization pathways. For example, organic phosphorus (P) must be enzymatically cleaved by phosphatases to release inorganic orthophosphate (McGill and Cole 1981). Organic sulfur (S) compounds are transformed into sulfate (SO₄²⁻), commonly much slower than N due to their chemical composition and the activity of specific microbes (Stevenson and Cole 1999).
Micronutrients such as zinc (Zn), copper (Cu), and iron (Fe), are released and mineralized during ligand degradation or humus (a diverse group of large, complex organic compounds) transformation, ultimately mineralizing into plant-available ions that are soluble or exchangeable in the soil (Brady and Weil 2017).
Nutrient mineralization plays a critical role in maintaining soil health and productivity. The breakdown and conversion of organic materials is important in providing essential nutrients to crops and it also contributes to SOM formation, improved soil particle aggregation and better soil structure, improved internal water movement and drainage, and overall carbon sequestration (Follett et al. 2001).
Effective management of residues incorporated into the soil is an important feature in managing soil health. The decomposition of organic materials, as well as mineralization and immobilization processes, are indicative of healthy soil (Kaspar et al. 1990; White 1994).
References:
Brady, N.C., and R.R. Weil. 2017. The nature and properties of soils. 15th ed. Pearson, Upper Saddle River, NJ.
Chapman, S.J., J.A. Campbell, Q. Fraser, G.C. Puri, and R. Lilly. 2013. Nitrogen mineralization and nitrification in Scottish soils: Effects of organic matter, texture, and land use. Soil Use Manag. 29: 612–621.
Drinkwater, L.E., D.K. Letourneau, F. Workneh, A. Himes, and R.A. Shennan. 1998. Fundamental differences between conventional and organic tomato agroecosystems in California. Ecol. Appl. 8: 1098–1112.
Follett, R.F., J.M. Kimble, and R. Lal (eds.). 2001. The potential of U.S. grazing lands to sequester carbon and mitigate the greenhouse effect. CRC Press, Boca Raton, FL.
Gruhn, P., F. Goletti, and M.Y. Azam. 2000. Integrated nutrient management, soil fertility, and sustainable agriculture: Current issues and future challenges. International Food Policy Research Institute, Washington, DC.
Janzen, H.H., and R.M. Kucey. 1988. C, N, and S mineralization of crop residues as influenced by crop species and nutrient regime. Plant Soil 106: 35–41.
Jenkinson, D.S. 1981. The fate of plant and animal residues in soil. In: E.A. Paul and J.N. Ladd, editors, Soil biochemistry. Vol. 5. Marcel Dekker, New York. p. 505–561.
Kaspar, T.C., D.C. Erbach, and R.M. Cruse. 1990. Corn response to seed-row residue removal. Soil Sci. Soc. Am. J. 54: 1112–1117.
Magdoff, F., and H. van Es. 2021. Building soils for better crops: Ecological management for healthy soils. 4th ed. SARE, College Park, MD.
McGill, W.B., and C.V. Cole. 1981. Comparative aspects of organic C, N, S, and P cycling through soil organic matter. Geoderma 26: 267–286.
Palm, C.A., C.N. Gachengo, R.J. Delve, G. Cadisch, and K.E. Giller. 2001. Organic inputs for soil fertility management in tropical agroecosystems: Application of an organic resource database. Agric. Ecosyst. Environ. 83: 27–42.
Paul, E.A. (ed.). 2015. Soil microbiology, ecology, and biochemistry. 4th ed. Academic Press, San Diego, CA.
Stevenson, F.J., and M.A. Cole. 1999. Cycles of soil: Carbon, nitrogen, phosphorus, sulfur, micronutrients. 2nd ed. John Wiley & Sons, New York.
Sylvia, D.M., J.J. Fuhrmann, P.G. Hartel, and D.A. Zuberer (eds.). 2005. Principles and applications of soil microbiology. 2nd ed. Pearson Prentice Hall, Upper Saddle River, NJ.
White, C.S. 1994. Monoterpenes: Their effects on ecosystem nutrient cycling. J. Chem. Ecol. 20: 1381–1406.
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First, I want to thank everyone who participated in last week's Vegetable Pest Losses Survey.
This year's survey included the return of the lettuce disease losses section. While several diseases were present and managed last season, downy mildew accounted for the majority of disease management costs by a wide margin. This really underscores the
impact that last spring's unusually rainy weather had on disease development across the Yuma lettuce production region.
No one can predict exactly what this upcoming spring will bring, but there has been discussion about the possibility of a strong El Niño leading to an extended monsoon season. If that proves true, the conditions would once again support spring
downy mildew development. The pathogen only needs about 3 to 4 hours of continuous leaf wetness to infect lettuce, so periods of overnight moisture, prolonged morning dew, or frequent rainfall when inoculum (spores) are present increase disease risk.
With that in mind, this seems like a good opportunity to review what is known about downy mildew and discuss strategies for its management.
Resistance in lettuce to Bremia lactucae, the causal oomycete pathogen behind downy mildew, is inherited in a gene-for-gene fashion, meaning one major gene product in the plant host interacts with one major gene product in the pathogen. When
resistance is present, this leads to an incompatible interaction between plant and pathogen and results in complete immunity to infection. Resistance genes in these types of interactions most often encode a protein molecule that acts like a burglar
alarm. These molecular sensors in the host bind to proteins secreted specifically by the pathogen, and when that happens a storm of defense responses is activated in the plant that excludes further infection. This is not the only mode of genetic resistance
found in plants, but it is often the most drastic and effective against obligate parasites like downy mildew.
But this simple gene-for-gene interaction often puts incredible selection pressure on the pathogen populations to change such that they can get around the resistance. By losing the molecule that the plant detects in order to initiate a defense response,
the pathogen becomes unrecognizable to the resistance genes a plant variety may have. Just like spraying the same mode of action over and over again leads to a pest population developing resistance to a pesticide, the same selection applies to genetic
resistance. The longer a resistance gene is deployed in a region, the more likely the pathogen population is to change in response until that resistance gene is no longer effective at managing the disease.
One of the biggest challenges with lettuce downy mildew is that B. lactucae is constantly changing over time. It exists as many different races, where each race has a different reaction to the resistance genes bred into lettuce varieties. You
can think of these races as different versions of the same pathogen. A lettuce variety that resists one race may still be susceptible to another.
These races are identified by testing them against a panel of lettuce varieties with known resistance genes. In the western United States, races are named by the International Bremia Evaluation Board-U.S. (IBEB-US) and are given names with a number followed by the country’s abbreviation, such as 8US, 9US, or 10US. The populations found in the western U.S. are different from those found in Europe, so each region uses its own independent naming system.
The downy mildew population has changed considerably over time. Earlier races (1US through 4US) are now rarely found in commercial lettuce production. During the 2000s and 2010s, races 5US through 8US became the most common. Race 9US was recognized after being detected repeatedly between 2015 and 2017, and the newest officially recognized race, 10US, was designated in 2025. Below is a pie chart showing the relative frequency of the races identified from 114 Yuma County downy mildew samples between 2023-2024:
Figure 1: Pathotyping results of 114 lettuce samples from Yuma County collected between 2023 and 2024. Data source: https://bremia.ucdavis.edu/bremia_database_main.php
The results show that much of the downy mildew population found in Yuma County is made up of novel strains of Bremia lactucae that have not yet been officially classified as a race. An official race is only recognized after it has been shown to be stable and widespread over multiple locations and growing seasons. These newer strains may disappear over time, or they may eventually become established and earn an official race designation. In the meantime, this means growers and lettuce breeders in Yuma County are often dealing with strains that can dodge the resistance in some lettuce varieties before those strains are common enough to be officially recognized. It also highlights why relying on resistance alone is not enough to manage the disease.
Table 1: Pathotyping and fungicide sensitivity results of samples from Yuma County collected in 2025.
This trend appears to be continuing. All of the downy mildew samples sent for race testing last season were identified as novel strains rather than known, officially designated races.
It's impossible to predict exactly how these new strains will respond to the resistance genes found in today's commercial lettuce varieties. However, because they have not been previously characterized, they are more likely to overcome existing genetic
resistance than the races we already know about.
New strains develop naturally over time. They can arise when different strains exchange genetics (i.e. intermate) or through random mutations. When growers plant varieties with similar resistance packages over large areas, the pathogen population
is placed under strong selection pressure. Any strain that happens to acquire the ability to infect those resistant varieties gains a major advantage and gets to reproduce without competition where other strains cannot. Over just a few disease
cycles, those successful strains can become much more common in the population until they are the predominant strain overall.
An important point to remember is that the resistance bred into commercial lettuce varieties is not wearing out or becoming weaker over time. The genetics in the lettuce remain just as effective as when the variety was released. What changes is the
pathogen. As the downy mildew population evolves new strains emerge that can bypass resistance genes that previously worked very well.
That means that varieties carrying resistance to races 5US through 10US are still doing exactly what they were designed to do. They continue to suppress those known races and help prevent them from becoming widespread in commercial fields. So, if
you experience significant downy mildew in a field planted with a variety that has a strong resistance package, the culprit is most likely one of these newer, uncharacterized strains rather than a failure of the variety itself.
Unfortunately, Bremia lactucae can evolve much faster than scientists can identify new races and breeders can develop and release resistant varieties. That's why no resistance package should be viewed as a stand-alone solution.
This is also why extension, researchers, and the seed and crop protection industries place so much emphasis on the integrated pest management (IPM) concept. Genetic resistance is an essential tool, but it works best and remains the most sustainable when combined with other management practices. For novel strains that can slip past host resistance, timely fungicide applications and other disease management strategies become especially important for maintaining control.
Figure 2: Mean disease severity by treatment. Disease severity was determined by rating 10 plants within each of the five replicate plots per treatment using the following rating system: 0 = no downy mildew present; 1 = downy mildew present on bottom leaves of plant; 2 = downy mildew present on bottom leaves and lower wrapper leaves; 3 = downy mildew present on bottom leaves and all wrapper leaves; 4 = downy mildew present on bottom leaves, wrapper leaves, and cap leaf; 5 = downy mildew present on entire plant. Disease severity is displayed as the mean of five replicates across all three lettuce varieties and bars show a 95% confidence interval around the mean calculated from individual treatment data. Compact letter display (CLD) above boxes show significantly different treatments (Kruskal-Wallis ANOVA and Dunn’s test). Boxes sharing the same letter(s) are not significantly different from one another. Fb = “followed by” in the rotation. Not all products are registered yet for use in lettuce. The inclusion of specific fungicide products or formulations in these trials does not constitute an endorsement or recommendation over other labeled products.
The most effective way to manage lettuce downy mildew is to use an integrated approach. Plant varieties with a strong resistance package against races 5US through 10US, and pair that resistance with timely, full-label-rate fungicide applications when environmental conditions favor disease. This combination provides the broadest and most reliable protection against both known races and the novel strains that continue to emerge in Yuma County.
If you have any concerns regarding the health of your plants/crops please consider submitting samples to the Yuma Plant Health Clinic for diagnostic service or booking a field visit with me:
Christopher Detranaltes, Ph.D.
Cooperative Extension – Yuma County
Email: cdetranaltes@arizona.edu
Cell: 602-689-7328
6425 W 8th St Yuma, Arizona 85364 – Room 109Despite mechanical challenges with seed placement early in the trial season, our robotic lettuce thinning and weeding equipment demonstrated exceptional precision in plant spacing and weed management operations. The University of Arizona Cooperative Extension's ongoing evaluation, funded by the Arizona Iceberg Lettuce Council, continues to generate valuable data that will help Yuma-region growers make informed adoption decisions.
Preliminary results from this trial will be presented at the Southwest Agricultural Summit on February 18–20. Join us in the Precision Weeding Technology session to learn key performance metrics, operational insights, and recommendations for integrating robotic weed and thinning technology into your operation. Growers, pest control advisors, and industry stakeholders are welcome to attend.Western flower thrips (Frankliniella occidentalis) is one of the most economically important insect pests affecting vegetable production in Arizona’s vegetable-growing regions. This species is particularly problematic in head, leaf, romaine, and baby-leaf lettuces, as well as cabbage and spinach. Feeding injury results in cosmetic leaf scarring and contamination of harvested plant parts, reducing marketability and crop value. Western flower thrips are present throughout the growing season in leafy vegetable crops, but typically reach their highest population levels during the spring as temperatures increase.
Bean thrips (Caliothrips fasciatus) emerged as a significant pest in Arizona vegetable production in the fall of 2017, especially in fall lettuce. Populations often migrate into vegetable fields from nearby cotton and alfalfa. Bean thrips have a broad host range that includes many vegetable crops such as asparagus, beans, beets, cabbage, cantaloupes, carrots, cauliflower, fennel, kale, leeks, lettuce, melons, peas, peppers, radishes, Swiss chard, tomatoes, and turnips. Several common weeds also serve as hosts, including field bindweed, milkweed, mallows, mulleins, redroot pigweed, sowthistle, and prickly lettuce. Similar to western flower thrips, bean thrips cause cosmetic leaf scarring and contamination of harvested plant parts, leading to quality losses and reduced market acceptance.
Fall 2025 Insecticide Efficacy Results
Results from the fall 2025 trial demonstrate that a mixture of Entrust at 2 fl oz/ac and M-Pede provided the most effective control (>70%) of western flower thrips, outperforming Entrust applied alone. Entrust at 2 fl oz/ac, when mixed with Des X, provided approximately 50% thrips suppression, similar to that of Entrust applied alone at 4 fl oz/ac. This indicates that insecticidal soap can improve Entrust efficacy against citrus thrips. Entrapment and M-Pede alone provided only limited suppression (~35%) of western flower thrips (Fig. 3).
Similarly, insecticidal soaps significantly improved Entrust performance against bean thrips. Tank mixes of Entrust at 2 fl oz/ac with either M-Pede or Des X resulted in the greatest reductions (≈80%), exceeding control achieved with Entrust applied alone at 4 fl oz/ac (63%). In contrast, Entrust at 2 fl oz/ac mixed with Captiva Prime provided moderate suppression (56%), and the remaining products evaluated were ineffective (Fig 4). Overall, these findings highlight the value of integrating insecticidal soaps with Entrust to enhance thrips control and improve management efficiency in organic production systems.
Figure 3. Seasonal western flower thrips numbers per 5 Romaine lettuce plants as
affected by selected organic insecticide applications. Insecticides were applied once a
week for 3 weeks. Kenetic (0.25% v/v) was used in all insecticide treatments except
Entrapment, where Ampersand (0.25% v/v) was used.
Figure 4. Seasonal bean thrips numbers per 5 Romaine lettuce plants as affected by
selected organic insecticide applications. Insecticides were applied once a week for 3
weeks. Kenetic (0.25% v/v) was used in all insecticide treatments except Entrapment,
where Ampersand (0.25% v/v) was used.
In Yuma Valley, precipitation is not the primary driver of crop water supply; irrigation is. Yet rainfall still matters because it can act like a biological “switch,” briefly reshaping field conditions in ways that influence weeds and plant disease. A single storm can alter soil surface moisture, stimulate germination, increase canopy humidity, and adjust access and irrigation timing. For Integrated Pest Management (IPM), these short windows often have outsized consequences compared with the annual total. Using annual precipitation totals from AZMET (Yuma Valley station), 1987–2025, the long-term trend is slightly upward, but the signal is extremely weak relative to the natural variability.
Figure 1 summarizes annual precipitation over time and includes a fitted linear trendline (the red line). The long-term mean annual precipitation is 2.63 inches (the yellow line), emphasizing how arid this production system is. The most recent year provides useful context: 2025 annual precipitation was 5.91 inches, which is substantially above the long-term mean (by 3.28 inches). That single year does not redefine the long-term trajectory by itself, but it illustrates the central message of the dataset: large departures from the mean can occur even when the multi-decadal trend is weak.
Figure 1. Annual total precipitation at the AZMET Yuma Valley station (1987–2025). Points/line represent annual totals; the horizontal reference indicates the long-term mean (2.63 in). The fitted linear regression trendline indicates a slight increasing tendency over the period.
The trendline equation shown on the figure is:
The slope (0.0111 inches per year) corresponds to roughly 0.11 inches per decade, which is small in magnitude. Meanwhile, R² = 0.0074 indicates the linear trend explains less than 1% of the year-to-year variability, meaning annual precipitation is dominated by irregular storm years and interannual fluctuations, not a strong flat wetting or drying signal.
Why this matters for IPM
For pest management, the most relevant feature of Yuma Valley precipitation is not the weak long-term slope but the timing and periodicity of rainfall and the biological responses it triggers:
The key message from Figure 1 is straightforward: annual rainfall in Yuma Valley does not exhibit a strong long-term linear trend from 1987 to 2025, and any increase suggested by the trendline is minor relative to variability. Years like 2025 (5.91 inches) sit far above the long-term mean (2.63 inches), highlighting that single-year abnormalities can be operationally meaningful even when the multi-decadal trend is weak.
VegIPM Update Vol. 17, Num. 15
July 22, 2026
Results of trap catches below!!
Whitefly: Adult activity remains steady across locations; above average for this time of the year, especially high numbers seen in North Gila Valley. Historically, whitefly numbers peak in July.
Thrips: Adult thrips activity remained low over the last two weeks. About average for this time of the year. Historically, thrips numbers remain low until Sept-Oct.
