Biofumigation cover crops: Enhancing soil health and combating pests

Introduction

Soil fumigants are pesticides that, when applied to the soil, form a gas to control pests that disrupt plant growth and crop production. Fumigation suppresses weeds and soilborne plant pathogens in crops such as potatoes, onions, sugar beets, tomatoes, mint, carrots and strawberries in the Pacific Northwest.

Chemical fumigation is widely practiced. Globally, agricultural producers applied 2.17 million tons of pesticides (active ingredients) to crops in 2020. U.S. producers applied 0.37 million tons. Common chemical fumigants used in the United States are chloropicrin, 1,3-dichloropropene, metam sodium and dazomet. While chemical fumigation has been shown to be effective, it is expensive. Recent research also shows that it impacts soil health.

There is another way for producers to use fumigants that does not involve synthetic chemicals. A practice known as biofumigation is an eco-friendly alternative that employs cover crops such as mustard, canola and oilseed radish. In this publication, producers will learn how these crops, when incorporated into the soil at the right time and in the correct manner, preserve and enhance soil health while combating pests, diseases and weeds.

Pros and cons of chemical fumigants

Studies have found that chemical fumigation works. It was shown to be the most effective approach to controlling weeds, pathogens and soilborne diseases in the Treasure Valley of Eastern Oregon and southwestern Idaho. Fumigation controls weeds such as yellow nutsedge (Cyperus esculentus) and the pathogens responsible for pink root and potato early dying.

While it has proven successful, chemical fumigation is expensive. At a cost of approximately $741 per hectare, a 2024 study found the cost of fumigating potato acreage would add up to about $13.5 million in Oregon alone.

Besides economic costs, a 2010 study found that repeated application of these chemical fumigants damaged soil health by reducing microbial biomass and enzyme activities; altering the structure of microbial communities; and affecting carbon/nitrogen cycling and mineralization.

A 2021 study found that chemical fumigation alters soil carbon transformation. When comparing soils treated with fresh barley plant residues to those treated with metam sodium, researchers observed lower respiration rates (428 mg CO₂ C kg^-1 dry soil) and a higher percentage (22%) of leftover plant residues in the metam sodium-fumigated soil.

In addition to the carbon cycle, studies have reported that chemical fumigation with metam sodium or chloropicrin affects the soil nitrogen cycle by significantly inhibiting nitrification. Chemical fumigants can kill soil microorganisms through direct contact, albeit in a nonselective manner, particularly when used at high concentrations.

Fumigation and soil health

Agricultural practices can positively or negatively impact soil health by modifying the physical, chemical and biological processes that control nutrient mineralization, soil aggregate formation, soil mineral sorption, microbial processing of residue and carbon transport into the subsoil.

Soil health is a crucial aspect of sustainable agriculture, as it directly influences crop productivity and environmental sustainability. Soil health depends on the maintenance of four major functions: carbon transformations, nutrient cycles, soil structure maintenance, and the regulation of pests and diseases.

Soil health is essential to maintaining fertility, structure and nutrient cycling. Potential alternatives to chemical fumigation, such as biofumigation cover crops and green manure, are needed to manage soilborne diseases, enhance soil health, increase microbial biodiversity and improve productivity.

There are many types of cover crops, from legumes to grasses and brassicas. Each benefits soil health in unique ways.

What is biofumigation?

Biofumigation is the process of incorporating glucosinolate-containing crops such as Brassicas to suppress soilborne pests. Glucosinolates are diverse secondary metabolites found in various Brassica species, such as mustard, oilseed radish, arugula (Figure 1) and related plants, playing a crucial role in plant defense mechanisms.

The types and concentrations of glucosinolate can vary significantly among different species and even among cultivars within the same species. These complex sulfur-containing compounds are stored in the vacuoles of plant cells, separate from the enzyme myrosinase, which catalyzes glucosinolate breakdown. This compartmentalization prevents the premature release of bioactive products.

When tissue of these plants is damaged by chopping, tilling or other mechanical disruption, glucosinolate and myrosinase come into contact. This initiates a chemical reaction in the presence of moisture that releases isothiocyanates, potent biofumigants that are toxic to pathogens and pests. ITCs are chemically similar to the active ingredient in the commonly used chemical fumigantVapam® (Natriun N-methyl-dithiocarbamate). The enzymatic activity of myrosinase is not limited to plant tissues; it can also be found in certain soil fungi and microbial communities, further contributing to glucosinolate hydrolysis when cover crop residues are incorporated into the soil.

Biofumigation cover crops and agronomic management

The plant families Brassicaceae, Caricaceae and Capparaceae contain more glucosinolate than other plants. Brassicaceae produce high levels of glucosinolate (Table 2) that are similar to the compounds released from the commercial chemical fumigant metam sodium (methyl isothiocyanate). Brassicas have shown potential for managing soilborne pests, including Verticillium dahliae and plant-parasitic nematodes.

Biofumigation cover crops not only suppress soilborne pathogens and pests but also attract pollinators with their abundant, nectar-rich, vibrantly colored flowers (Figure 2). These blooms provide a critical source of nectar and pollen, especially when other floral resources are scarce, supporting the health and diversity of bees, butterflies and other pollinators. Additionally, the habitat enhancement created by these crops fosters biodiversity and ecosystem stability, offering shelter for beneficial insects while potentially boosting yields of nearby pollinator-dependent crops.

Follow crop recommendation guidelines from seed suppliers for seeding rates, planting time, fertilization and irrigation to maximize the effectiveness of biofumigation cover crops. Proper seeding rates ensure adequate biomass production. Plant at the right time to optimize growth and glucosinolate levels. Apply fertilizers according to recommended guidelines to enhance biomass and biofumigation potential. Maintain adequate soil moisture through recommended irrigation practices to support crop establishment and growth.

Cover-crop termination

The timing and method of cover crop termination are critical to biofumigation’s success. Manage these factors to release natural compounds into the soil, target pests and pathogens, and improve soil conditions for subsequent crops.

Termination timing

Effective pest control strategies depend heavily on the termination timing of crop growth stage and method. Terminating biofumigation crops like mustard or radish at the flowering stage (Figures 2 and 3) or just before seed set is crucial because it maximizes the concentration of glucosinolates within the plant. These are the key compounds responsible for producing the volatile, pest-suppressing ITCs when the plant tissue is chopped and incorporated into the soil, thus achieving the most effective biofumigation action against soilborne pathogens and pests.

Research shows that terminating mustard at early flowering can result in up to 40%–60% higher pest suppression compared to termination at later stages. One study also highlighted that glucosinolate concentrations vary across plant developmental stages, with levels peaking at flowering, and noted that root glucosinolate concentrations are highest at early growth stages and diminish as the plant matures. To harness the maximum biofumigant potential, carefully time termination — preferably at the flowering stage — to ensure optimal glucosinolate availability.

Techniques for terminating and incorporating biofumigants

Mechanical maceration techniques such as flail-mowing, roller-crimping or rotary tilling are highly effective at maximizing glucosinolate hydrolysis (Figure 4). Biofumigant cover crops should be finely chopped into smaller fragments to increase the surface area for enzyme-substrate interactions. The more thoroughly the plant tissues are macerated, the more complete the enzymatic conversion of glucosinolate to ITCs. This process accelerates the biofumigant action and enhances the overall effectiveness of pest and pathogen suppression.

The residues should be incorporated into the soil immediately using equipment like a rototiller. Research in 2022 demonstrated that plant biomass should be incorporated into the soil immediately to preserve ITC concentrations. A delay of just four days can significantly reduce its effectiveness.

Field trials on oilseed radish and brown mustard in 2020 examined the effects of different termination methods. The study found that combining mechanical tissue maceration, soil incorporation with a handheld rototiller and the use of plastic covers significantly enhanced the glucosinolate-to-ITC conversion process. Covering the soil with black plastic sheeting after incorporation helps to trap volatile ITCs, extending their fumigation effect and improving pest and pathogen control. Covering soil with plastic mulch also creates a microenvironment that retains moisture and raises soil temperatures, further boosting the biofumigation process, especially under high tunnels.

In large-scale operations, cultipacking or other sealing methods, such as irrigation and plastic tarps, are recommended to trap the biofumigation gases in the soil. Overall, for biofumigant crops to reach their full potential, growers must carefully manage termination timing and incorporate strategies like irrigation and soil coverage to optimize ITC release and efficacy.

Optimal condition for release of biofumigant compounds

The hydrolysis process of glucosinolate into ITCs depends on environmental conditions, including soil moisture and temperature. Rapid soil incorporation of biofumigant crops immediately after termination is essential to minimize the volatilization and loss of ITCs to the atmosphere. A 2009 study emphasized the importance of soil moisture, noting that irrigating the soil before or right after incorporation enhances ITC concentrations. Moisture promotes myrosinase activity and improves the conversion efficiency of glucosinolate to ITCs, making the biofumigant effect more pronounced. This highlights the necessity for integrated management practices that consider soil conditions alongside crop termination.

Impact of biofumigant cover crops

Plant diseases

Soilborne diseases are a significant challenge to crop production, leading to reduced crop performance, decreased yields and increased production costs worldwide. This section covers the control of soilborne pathogens using biofumigant cover crops.

Research in France highlighted that planting Brassica juncea reduced the incidence of root rot (caused by Rhizoctonia solani) in sugar beets. The severity of the disease and R. solani incidence level reduced in subsequent years after incorporating mustard cover crops in soil from nearly 30% in 2005 to 15% in 2007, which is significantly lower than the control bare soil.

In-vitro investigations on the impact of Brassica species on Phytophthora spp. demonstrated that B. juncea inhibited the mycelial growth of Phytophthora spp.

Rotating crops with canola and rapeseed (B. napus) helps reduce Rhizoctonia disease in potatoes.

Biofumigation cover crops can also help manage soilborne diseases in nursery soils. In 2020 greenhouse trials, yellow mustard (White Gold), arugula (Astro), mighty mustard (Pacific Gold), rape (Dwarf Essex), turnip (Purple Top Forage), brown mustard (Kodiak) and mustard green (Amara) effectively reduced disease severity from R. solani and P. nicotiane in viburnum and hydrangea, except for radish, when incorporated two weeks before planting.

Brassica crops like B. nigra, B. juncea and B. carinata release high amounts of propenyl isothiocyanate, which helps suppress Fusarium oxysporum in nursery soils.

Using brassica cover crops can be an effective strategy for disease management through biofumigation.

Nematode control

Nematodes are microscopic worms present in almost all environments, from aquatic to terrestrial (soil). The majority of nematode species play crucial roles in nutrient cycling and organic matter decomposition. But some are plant-parasitic and pose significant threats to agricultural production. Species such as root-knot nematodes (Meloidogyne spp.), cyst nematodes (Heterodera spp.) and root-lesion nematodes (Pratylenchus spp.) feed on plant roots, causing damage that leads to reduced water and nutrient uptake, stunted growth and yield losses.

Chemical fumigation and synthetic nematicides are commonly used to control nematodes, which can be expensive and environmentally harmful. As a result, alternative strategies, such as the use of biofumigant cover crops, are gaining popularity as eco-friendly and cost-effective solutions for nematode management.

A greenhouse study in New Mexico showed that broccoli (Arcadia) had the least root-knot nematode damage, while mustard (Caliente 61, Caliente 199 and Pacific Gold) increased nematode numbers. In 2012, yellow mustard was found to decrease population densities of the plant-parasitic nematode Globodera rostochiensis in potatoes. A greenhouse study in Australia found that mixing broccoli tissue into nematode-infested soil reduced root-knot nematode (M. incognita) levels, with the highest rate (20 g per pot) lowering infestation to 5%, compared to 100% in untreated soil.

Brassica cover crops can suppress root-knot nematodes, but effectiveness varies by species, location and biomass produced. In Australia, fodder radish significantly reduced root-knot nematodes in vegetables, showing resistance due to genetic traits rather than just glucosinolates. Another study found that cultivating radish as a cover crop effectively reduced the egg population of M. japonica, supporting their use in nematode management.

Soil health

Soil is a viable living ecosystem that helps sustain the lives of plants, humans and animals. Soil has many functions. Some of its key roles include maintaining the soil microbiome, filtering heavy metals and pollutants, infiltrating water and cycling nutrients.

Soil health can be maintained by maximizing soil cover, biodiversity and living roots while reducing physical disturbance and agrochemical use. Besides controlling diseases and applying nematode pressure, biofumigant cover crops maintain soil health by:

• Increasing nutrient cycling.
• Retaining water.
• Stabilizing aggregate.
• Contributing organic matter.
• Reducing groundwater pollution by preventing nitrate leaching.

Studies have demonstrated the potential of cover crops to enhance soil health and nutrient dynamics across different cropping systems. A 2022 study evaluated the performance of brassica cover crops — brown mustard, fodder radish and turnip rape — alongside the legume purple vetch in a sunflower rotation. Findings indicated that fodder radish produced the highest biomass, while brassicas exhibited a significantly higher carbon-to-nitrogen (C:N) ratio than legumes. Preceding sunflower planting, brown mustard plots had the greatest nitrogen availability (200 lb ha^-1), and both fodder radish and purple vetch contributed to increased soil mineral nitrogen.

In a chile pepper rotation in southern New Mexico, researchers investigated the biofumigant potential of mustard (Caliente 61, Caliente 199 and Pacific Gold) and broccoli (Arcadia). In the first year, Pacific Gold produced substantial biomass (1,241 kg ha^-1), leading to increased soil organic matter (1.12%), reduced soil pH (7.44), and improved water infiltration compared to fallow plots. However, in the second year, poor biomass production resulted in no significant increase in soil organic matter. Similarly, another study assessed the benefits of white mustard as a cover crop in potato-wheat rotations and found that its inclusion reduced the incidence of Verticillium dahliae while enhancing soil water infiltration.

Research in the Pacific Northwest investigated the effects of white mustard incorporation on microbial biomass carbon across various soil types, including Quincy sand, Quincy loamy fine sand, Timmerman sandy loam, Warden silt loam and Shano silt loam. Results indicated that white mustard significantly increased microbial biomass carbon in all soil types except Warden silt loam. The highest microbial biomass carbon was observed in Shano silt loam, with approximately 260 mg C/kg of soil after mustard incorporation, outperforming chemical fumigation (220 mg C/kg).

A 2009 study found that incorporating B. juncea residues increased porosity in the topsoil (0–10 cm) compared to bare soil. Similarly, a study in Tasmania comparing ryegrass, brassicas and fallow treatments found that cover crops significantly enhanced soil microbial communities. Both brassicas and ryegrass increased bacterial, fungal and eukaryotic populations, with B. juncea showing particularly strong effects two and four weeks post-incorporation compared to fallow plots.

Weeds

In agricultural, forestry and rangeland systems, as well as in natural landscapes, it is often essential to reduce the presence of weeds to meet land-use objectives. Weeds compete with crops for nutrients, water, space and light. They also serve as alternative hosts for disease-causing microorganisms and pests. Weeds are widely controlled with herbicides. Herbicides initially worked well, but more recently, researchers identified weeds resistant to almost 21 herbicide modes of action. Currently, 530 weeds are known to be resistant to herbicides, according to the International Herbicide-resistant Weed Database. Nearly 50% of them are found in the U.S. and Australia.

In addition to resistance problems, herbicides could harm the environment through drift and hazardous leaching into groundwater.

As a countermeasure to herbicide resistance, focus has shifted to controlling weeds with biological measures — the most common being cover crops. Biofumigant cover crops have started to attract researchers due to the release of allelochemical ITC, which has the potential to inhibit weed seed germination (Figure 5).

A study in Canada examined the impact of Indian mustard and oat cover crops on weed suppression. The treatments included different mustard-oat combinations planted in spring and fall. Initially, Indian mustard exhibited limited weed-suppression capabilities. But by 2015 and 2016, its effectiveness increased, likely due to higher glucosinolate production from potassium sulfate application. In spring 2015, mustard-based treatments significantly reduced weed density from about 2,200 to more than 600 plants per square meter. Similar reductions were observed in fall 2015 and 2016 compared to the control (no cover crops).

A 2009 study found that brown and yellow mustard cover crops reduced hairy galinsoga (Galinsoga quadriradiata) biomass by 90%–99% over two years. However, other studies suggest that brassicas may suppress weeds by immobilizing nitrogen, which can negatively impact certain crops like brome grass and barley. Additionally, brassica biofumigation has been reported to reduce oilseed crop yield.

These variations in weed suppression and crop impact likely depend on soil conditions, glucosinolate levels, and the timing and method of incorporation.

Summary and future interest

Biofumigation is a growing alternative to chemical fumigation. It is effective in controlling nematodes, diseases and weeds. Additionally, biofumigation cover crops help improve soil health.

The effectiveness of biofumigant crops in agricultural systems depends on a holistic approach that integrates proper crop selection, strategic timing and optimized termination methods. Managing environmental factors such as soil moisture and temperature, in combination with mechanical practices, ensures maximum ITC production and persistence.

Ultimately, a well-planned biofumigation strategy can significantly contribute to sustainable integrated pest and disease management, reduce the reliance on chemical fumigants, and improve soil health in the long term.

Resources

• Mustards | Sustainable Agriculture Research & Education Program, University of California, Davis
• Canola/Rape | Sustainable Agriculture Research & Education Program, University of California, Davis
• Cover Crop Fact Sheet Forage Turnip and Rape, Cornell University
• Radish as a cover crop | Integrated Crop Management, Iowa State University
• Torabian, S., E. Kim, R. Qin, V. Sathuvalli, H.T. Gollany, M. Kleber. 2025. Soil microbial biomass influenced by cover crop after fumigation of potato fields. Science of the Total Environment. 958, 177910.

Acknowledgment

Financial support for this project was provided by the Oregon Department of Agriculture — Speciality Crop Block Grant.

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