USDA Initiative Explores Fungal Strategies in the Battle Against Food Contaminants

USDA Initiative Explores Fungal Strategies in the Battle Against Food Contaminants

Seraiah Alexander
Seraiah Alexander
January 08, 2024
5 min

Foodborne pathogens and mycotoxins are a looming threat to public health, food safety, and agricultural economies. These contaminants can infect crops, causing harm to the quality and security of our food supply. To tackle this issue, the U.S. Department of Agriculture’s Agricultural Research Service (USDA ARS) has undertaken an initiative aimed at revolutionizing food safety practices. The project is dedicated to developing sustainable methods to protect crops and ensure the security of the food supply chain. 

A major part of the initiative is exploring the potential of antimicrobial mushrooms in agriculture and how they can enhance the safety of food by protecting crops against aflatoxin-producing fungi and bacteria. Aflatoxins are found in crops like corn, tree nuts, and peanuts and can lead to severe health implications such as liver cancer and developmental issues.

Contaminated crops do not need to be directly consumed to cause these effects, as the toxins remain in products that are derived from animals that have consumed the contaminant. These developments offer a promising solution for preventing dangerous pathogens from entering the food supply. 

Tackling pathogens and mycotoxins for crop protection and food safety

The “Novel Methods for the Mitigation of Human Pathogens and Mycotoxin Contamination of High-Value California Specialty Crops” is a research project focused on enhancing the food safety standards in California’s sector.

Managed by the Foodborne Toxin Detection and Prevention Research Unit, this comprehensive effort aims to address aspects of safety with a specific focus on improving standards for California’s specialty crops. From 2021 to 2026, this initiative will tackle a range of challenges caused by pathogens.

The seven primary objectives include:

  1. Identifying and characterizing agricultural soils that are capable of suppressing pathogenic bacteria like Salmonella enterica, Escherichia coli, and Listeria monocytogenes. This research will lead to a greater understanding of soil properties and how to naturally enhance crop safety and resist bacteria infections. 
  2. Studying the microbiomes found on lettuce that grows in indoor verticle hydroponic systems. Since little is known about the effects of this growth style on plant microbiomes, researchers will compare the microbes of indoor-grown leafy greens with conventional outdoor cropping systems. This comparison will help researchers understand the effects of different growing systems on microorganisms that could either be beneficial or detrimental to crop and human health.
  3. Addressing the impact of black Aspergillus species on grapes and raisins. The common mold species can produce a mycotoxin called ochratoxin A, which poses significant health risks to consumers, such as kidney damage and potential carcinogenic effects. 
  4. Investigating different beneficial bacteria strains as biocontrol agents that can prevent the growth and spread of the fungal species. By isolating these antifungal compounds, researchers can determine ways to manage fungal diseases in vineyards and pistachio orchards, reducing reliance on chemical fungicides and enhancing the overall success of these crops.
  5. Formulating resistant management strategies and eliminating mycotoxins, primarily for azole-resistant Aspergillus strains in tree nut orchards. Azole-resistant aspergilli are known for their substantial mycotoxin production. Researchers will assess the prevalence of these resistant fungal strains and develop natural control methods to address the growing threat of fungicide resistance in agricultural settings.
  6. Exploring new ways to control mycotoxin contamination through final and insect management. This would include evaluating the effectiveness of X-ray-based irridation as a sustainable alternative to traditional gamma irridation methods as a means to sterilize and control the populations of specific insect species. Many insects are carriers and facilitators of fungal infections, so determining a different means to manage their populations would lead to healthier crops and, therefore, lower levels of mycotoxins.
  7. Investigating the use of previously approved natural products as chemical interventions to inhibit food-associated mycotoxins, fungal pathogens, and their insect pest transmitters. This research will determine which natural products can effectively inhibit mycotoxins and fungal pathogens commonly found in food contaminations for safer and more sustainable alternatives to conventional pesticides and fungicides.

By addressing each of these objectives, the project not only significantly contributes to the advancement of agricultural science but also ensures the well-being and safety of consumers. This initiative will make California’s agricultural sector a leading example for managing pathogens and mycotoxins for a safer and more secure food supply system.

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Mushroom-based solutions for pathogen mitigation strategies

A recent study from the USDA ARS has determined that a mushroom called Taiwanofungus camphoratus has antimicrobial potential. A component of the mushroom has demonstrated success in inhibiting fungi and bacteria growth in foods because of specific bioactive compounds that directly kill or inhibit the growth of bacteria by disrupting vital cellular processes. This breakthrough suggests that the mushroom derivative can reduce contamination from toxin-producing or heat-tolerant fungi that survive traditional food sanitation processes (1). 

“Edible mushrooms [are] a source of bioactive compounds, and certain medicinal mushrooms have emerged as beneficial ingredients of dietary supplements,” said ARS molecular biologist and primary author of the study Jong H. Kim. “[We] found that a component of the mushroom Taiwanofungus camphoratus (TC) could be developed as a food ingredient having antimicrobial potential, thus inhibiting the growth of fungi and bacteria in foods.”

Although the antimicrobial agents from edible mushrooms haven’t been entirely explored for their application in food production, mushrooms like T. camphoratus are a promising avenue for natural food preservation.

Additionally, the research looked more into the development of antimicrobial agents, such as the natural fungicide strobilurin, which is obtained from the pinecone cap mushroom (Strobilurus tenacellus). Strobilurin and its derivatives are a class of fungicides that disrupt the respiratory process in fungi, preventing their growth and spread.

“Many antimicrobial agents have been developed from mushroom ingredients for crop protection, [including] the natural fungicide strobilurin,” Kim adds. “Strobilurins [are] one of the most important classes of agricultural fungicide.”  

The exploration into these mushroom-based solutions is an innovative approach to food safety as it enhances the protection of crops with minimal environmental impact. 

These mushrooms aren’t the first instances of fungi being used as a natural means of protecting crops. For example, the well-known and commonly consumed oyster mushroom (Pleurotus ostreatus) has shown promise as a means to kill nematodes that infest many kinds of root vegetables. The mushroom uses its hyphae to kill and catch the parasitic worms, offering a potential way to deal with the pest without the use of toxic pesticides.

Other fungi, such as Metarhizium anisopliae and Beauveria bassiana, produce spores that attach to insects and grow inside their bodies, eventually killing them. Trichoderma harzianum, a species known for its antifungal properties, fights off crop pathogens by colonizing the roots of the plants. By doing so, the fungus outcompetes the pathogens for space and nutrients, which helps prevent diseases like root rot and wilt.

 Although conventional pesticides are the most common means of dealing with crop diseases and pathogens, they often have detrimental effects on human and environmental health, and their efficiency only goes so far. The exploration of natural alternatives like fungi is a major step towards more effectively addressing pest and disease issues while contributing to the long-term sustainability of agricultural systems. 

The findings from the initiative may pave the way for more environmentally responsible agricultural methodologies that revolutionize how we manage our crops. As the research initiative continues over the next few years, it has the potential to offer groundbreaking contributions to agricultural science and food safety. 


  1. Kim, Jong H., Christina C. Tam, Kathleen L. Chan, Noreen Mahoney, Luisa W. Cheng, Mendel Friedman, and Kirkwood M. Land. 2022. “Antimicrobial Efficacy of Edible Mushroom Extracts: Assessment of Fungal Resistance.” Applied Sciences 12 (9): 4591. https://doi.org/10.3390/app12094591.

Fact Checked: Shannon Ratliff


Seraiah Alexander

Seraiah Alexander

Content Editor

Table Of Contents

Tackling pathogens and mycotoxins for crop protection and food safety
Mushroom-based solutions for pathogen mitigation strategies

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