Location: Crop Bioprotection Research
2025 Annual Report
Objectives
Objective 1: Develop effective entomopathogenic fungi for implementation as augmentative biological controls to support integrated pest management systems.
Objective 2: Expand fundamental knowledge of biological interactions between the beneficial pathogens(s), target host pest and crop environment to enhance the production, formulation, and application of beneficial microbial products for sustainable pest management.
Approach
The commercial use of microbial pathogens as biopesticides to manage crop pests continues to be constrained not only by expensive production methods, limited shelf-life, and variable pest control efficacy, but also by a lack of understanding of how basic fungal metabolism affects liquid-culture production in the factory and pest control efficacy in the field. This research project focuses on developing beneficial microbes (predominantly entomopathogenic fungi) as biopesticides and follows a vertical research path from understanding microbe metabolism during liquid culture production through practical formulation processing and integrative application into pest management systems. Although we have empirical data supporting efficient production of beneficial fungi, we still lack a basic understanding of the interaction between physical and nutritional conditions of liquid culture and the basic metabolisms of these organisms. To fill this void, effective microbial biopesticides will be developed by uncovering at the molecular level how entomopathogenic microbes interact with nutritional and environmental conditions present during the production, formulation, and application processes. Gaining this understanding is critical given that these processes likely affect fungal differentiation, biopesticide yield, product stability, and pest control efficacy. Post-production, research will evaluate specific processing and formulation technologies to create a usable product that retains physical characteristics suited for application against targeted pests and is expected to focus on product storage and handling characteristics for sprayable (yeast-like blastospores) and granular (microsclerotia-based) fungal biopesticides. Following application, the host plant environment will be studied to identify interactions among a variety of pest control practices (e.g. crop genetics providing host plant resistance to fungal pathogens) within specific cropping systems. Microbial biopesticides represent an additional tool for the management of crop pests. Non-chemical pest control tools such as these are particularly important for organic, chemically sensitive, and natural environments where few pest control measures are available, and to avoid the development of pesticide resistance to current chemical insecticides and transgenic crops used for pest control. The strategic development of microbial biocontrol agents will enhance the nation’s ability to effectively control pests and support increasingly sustainable crop production.
Progress Report
The project focused on developing beneficial microbes, especially insect-killing fungi as biopesticides for crop protection in corn, cotton, potatoes and vegetables. The goal was to expand pest control tools and support the nation’s ability to meet the growing agricultural demands.
Under Objective 1, Sub-objective 1.1, ARS researchers in Peoria, Illinois, completed studies to improve fungal production and formulation for biopesticide development. The use of fungal biopesticides is constrained by high production costs, limited shelf-life, and variable pest control efficacy. To address this, a formulation of insect-killing fungi was developed and tested against whiteflies in cotton and vegetable crops. Large quantities of infective fungal spores called blastospores were produced in liquid culture and processed into wettable powder by spray drying. This formulation had identical spore viability and insecticidal efficacy as a commercial strain of insect-killing fungi. When applied to field grown plants in collaboration with ARS researchers in Byron, Georgia, this treatment caused significant mortality in whiteflies, outperforming the commercial strains under hot field conditions.
In cooperation with industry, ARS researchers helped advance the development of a new biological pesticide designed to control the Colorado potato beetle, one of the most destructive pests of potatoes and related crops. This product works by delivering double-stranded RNA (dsRNA), a natural molecule that turns off a critical beetle gene. When the insect eats the biopesticide product, the gene is shut down, ultimately killing the beetle without the use of traditional chemical insecticides. ARS researchers improved the spray-drying process to make dsRNA into a stable dry powder that can be stored and easily applied in the field. The new powder formulations kept their activity and are now being evaluated by our industry partners. This collaboration combines ARS’s formulation expertise with industry production technologies to develop a new biological pesticide for crop protection.
Under Sub-objective 1.2, to support commercial scale production of fungal biopesticides, ARS researchers in Peoria, Illinois, evaluated the genetic stability of insect-killing fungi that have been repeatedly grown in a commercial setting. This research addresses an industry concern about the stability of these strains under production conditions. The fungi underwent 60 continuous growth cycles, which caused changes in their ability to grow, consume glucose, and mediate the pH of their cultures. The research shows some strains are genetically very stable, while some change relatively rapidly and lose traits important to their activity. This research benefits commercial manufacturers of these fungi by letting them know which species are more prone to genetic instability. This ensures these fungal biopesticides have consistent crop protection performance on the farm.
Under Objective 2, Sub-objective 1, ARS researchers in Peoria, Illinois, developed new genomic resources for insect-killing fungi used in crop protection. We have successfully completed draft genome sequencing for approximately 800 insect-killing fungal strains collected globally by ARS researchers in Montpellier, France and are publicly available on GenBank. These genomic resources are useful for understanding traits important for biocontrol and are actively being used by industry and university partners.
ARS researchers in Peoria, Illinois, identified genes associated with the development of a specific fungal structure known as a blastospore. Blastospores are a special type of cell that grows rapidly and are the desired product of these fungal cultures for many biopesticide products. Understanding how different growing (“culturing”) conditions affect blastospores production allows us to optimize the production methods. The study also provided new insight into the structure of the cell wall of the fungus, which improves our understanding of how these cells survive stress. These findings will be used to develop new processes for producing these beneficial fungi as crop protection products.
We collaborated with researchers from Auburn, Alabama to characterize the effects of duplicating a virulence- related gene naturally found in an insect-killing fungi. The results showed it was more potent and significantly faster in killing wax moths. Understanding how genes in these insect-killing fungi function, will allow research to improve the efficacy of these biopesticides.
Under Sub-objective 2.2, ARS researchers in Peoria, Illinois, developed improved methods to study insect-killing fungi and viruses that can be used as natural pest controls (“biocontrol agents”), and partnered with university and industry researchers to sequence the genome of the banded cricket, an insect farmed for food and feed, creating an important new tool for disease management and selective breeding. These studies led to the first catalog of viruses found in farmed crickets across North America, including both known and newly discovered viruses. Researchers also found that the condition of the insect at the time of infection can influence how deadly a fungus is, and that certain immune proteins help pests such as cabbage loopers resist fungal infection. These discoveries provide fundamental knowledge of how insects respond to beneficial fungi, making it easier to select the most effective fungal strains for pest control. For the next phase of research, ARS researchers will partner with other USDA scientists across Midwestern states to survey a naturally occurring biocontrol agent of the Japanese beetle in different populations. The goal is to use this natural enemy to help slow or prevent the spread of Japanese beetles into western states.
Under Sub-objective 2.3, ARS researchers in Peoria, Illinois, identified dual-purpose corn resistance genes that protect corn from both insect and mold damage. Insect and mold damage to corn costs millions of U.S. dollars because of lower yields and added expense for pesticide applications. Ear molds often take advantage of insect damage to begin their infection and then contaminate the grain with toxins that are harmful to people and animals. Host plant resistance can reduce mold damage but often focuses on controlling either the insect or the fungus, but not both. We identified several corn genes that create natural compounds that protect the plant from both insects and mold. Corn cells that expressed these genes simultaneously reduced the growth of pest insects and toxin-producing fungal diseases. These new dual-purpose resistance genes differ from traditional host plant resistance genes which only target one pest. By breeding the new genes into food and feed varieties of corn, we will add to our integrated pest control arsenal.
Honeybees are crucial pollinators, responsible for pollination of 70% of the top 100 food crops with a global estimated economic value from $235 to $285 billion. However, honeybee health is severely threatened by parasites and pathogens. New tools for controlling honeybee parasites and pathogens are urgently needed. In collaboration with ARS’s microbial culture collection in Peoria, Illinois, we sequenced the genomes of more than 100 microbes associated with bees and bee environments and made them publicly available. These genomes will facilitate further research to better understand how these microbes impact the life cycle of these important pollinators. This research has also identified possible pesticidal proteins in microbial species not previously known to possess
pesticidal properties. Efforts have started to confirm and characterize the pesticidal properties of these proteins.
In a separate study, we collected approximately 300 bees, including native bees and honeybees from the local prairie space, to evaluate the bacterial and fungal communities they harbored. We have isolated a variety of microbes from these samples and this microbial collection will be used to further understand the dynamic interaction between native bees and honeybees. Additionally, this will offer insight into the microbiome of various native bee species, which have, to date, been understudied and underappreciated pollinators.
Bumblebees have also faced declines in recent years due to a combination of factors such as habitat loss, spillovers of parasites and viruses, and exposure to pesticides. We are currently collaborating with university researchers in Bloomington, Illinois, to evaluate parasite prevalence in bumblebees collected from Conservation Reserve Program habitats of varying ages and sizes. This research includes evaluating how the local environment shapes the gut microbiome of different bumblebee species. Like honeybees, some species of bumblebees have been domesticated for use as pollinators and outperform honeybees in pollination of specialty crops such as tomatoes and blueberries, so understanding their health is of key importance to those agricultural sectors.
Accomplishments
1. Generated critical field data to guide biological control strategies against the invasive Japanese beetles. Japanese beetles are among the most destructive invasive insect pests in the United States, causing hundreds of millions of dollars in crop and landscape losses each year. In partnership with Animal and Plant Health Inspection Service (APHIS), ARS researchers in Peoria, Illinois, conducted a multi-site study to track a naturally occurring microsporidian parasite that infects Japanese beetles. Researchers measured how widespread the parasite was in the beetle populations and how severely individual beetles were infected. By showing where the parasite is already helping to suppress beetle numbers, and where it is not, this research identifies areas where natural control is working and where targeted releases may be needed. These findings provide valuable guidance for regulatory agencies, turf and nursery growers, and state inspection programs working to reduce beetle damage and slow its spread. These findings directly support the Farmers First agenda and contribute to restoring America-First rural prosperity by generating critical data for APHIS and state agencies to evaluate and guide the potential deployment of a self-sustaining, low-cost biocontrol strategy for this invasive pest.
2. Plant defenses against insects enhance effectiveness of fungal biocontrol agents. New tools for pest management are urgently needed as many pests have become resistant to chemical insecticides. Biological control is a promising alternative to chemical insecticides, but faces adoption hurdles due to inconsistent effectiveness. Understanding how insects, plants, and biological control agents interact is crucial for effective pest management and wider adoption of biological control. ARS researchers in Peoria, Illinois, discovered that plant damage by insects stimulates the plant defense genes that can enhance or reduce the effectiveness of beneficial fungi at killing insect pests. This discovery explains why beneficial fungi show inconsistent effectiveness at killing insects in the field and will guide the development of new strategies that harness insect-plant-fungi interactions to improve efficacy and adoption of beneficial fungi in pest control. This research will contribute to national food security and rural economic development by facilitating commercial production of biological control agents that provide consistent effectiveness in pest management and are widely accepted by farmers.
Review Publications
Sauers, L.A., Bassingthwaite, T., Sierra-Rivera, B., Hampton, K.J., Duffield, K.R., Gore, H., Ramirez, J.L., Sadd, B.M. 2024. Membership robustness but structural change of the native gut microbiota of bumble bees upon systemic immune induction. Microbiology Spectrum. https://doi.org/10.1128/spectrum.00861-24.
Mascarin, G.M., Shrestha, S., Cortes, M.V., Ramirez, J.L., Dunlap, C.A., Coleman, J.J. 2024. CRISPR-Cas9-mediated enhancement of Beauveria bassiana virulence with overproduction of oosporein. Fungal Biology and Biotechnology. https://doi.org/10.1186/s40694-024-00190-5.
Dunlap, C.A., Johnson, E.T., Burkett-Cadena, M., Cadena, J., Muturi, E.J. 2024. Lysinibacillus pinottii sp. nov., a novel species with anti-mosquito and anti-mollusk activity. Antonie Van Leeuwenhoek. https://doi.org/10.1007/s10482-024-01993-7.
Muturi, E.J., Dunlap, C.A., Perry, W.L., Rhykerd, R.L. 2024. Cover crop species influences soil fungal species richness and community structure. PLOS ONE. 19(9). Article e0308668. https://doi.org/10.1371/journal.pone.0308668.
Robinson, K., Duffield, K.R., Ramirez, J.L., Cohnstaedt, L.W., Ashworth, A.J., Jesudhasan, P., Arsi, K., Morales Ramos, J.A., Rojas, M.G., Crippen, T.L., Shanmugasundaram, R., Vaughan, M.M., Webster, C.D., Sealey, W.M., Purswell, J.L., Oppert, B.S., Neven, L.G., Cook, K.L., Donoghue, A.M. 2024. MINIstock: Model for INsect Inclusion in sustainable agriculture: USDA-ARS's research approach to advancing insect meal development and inclusion in animal diets. Journal of Economic Entomology. 117(4):1199-1209. https://doi.org/10.1093/jee/toae130.
Zhang, S., Duffield, K.R., Foquet, B., Ramirez, J.L., Sadd, B.M., Sakaluk, S.K., Hunt, J., Bailey, N.W. 2025. A high-quality reference genome and comparative genomics of the widely-farmed banded cricket (Gryllodes sigillatus) identifies selective breeding targets. Ecology and Evolution. 15:1-12. https://doi.org/10.1002/ece3.71134.