Location: Mycotoxin Prevention and Applied Microbiology Research
2025 Annual Report
Objectives
The major goals of this project will be most effectively achieved through strengthening the relationship between the ARS Culture Collection and the user community and fostering a synergistic relationship. To this end, we will implement a “virtuous cycle” of collection management (Graphical Project Summary) to achieve the project goals and enhance our connection to the user community.
Objective 1: Acquire, distribute, back-up, and maintain the safety, genetic integrity, health, and viability of priority microbial genetic resources and associated descriptive information in the ARS Culture Collection.
Sub-objective 1.A: Maintain the safety, genetic integrity, viability and accessibility of priority microbial genetic resources and associated information in the ARS Culture Collection.
Sub-objective 1.B: Enhance the diversity and utility of the ARS Culture Collection by acquiring germplasm representing type material or novel strains important to ARS and other microbial research programs.
Objective 2: Increase the value of priority microbial resources in the ARS Culture Collection for research and development by conducting integrated phylogenetic, physiological, phenotypic, and metabolomic analyses. Connect these multiple data types to accession records in the ARS Culture Collection, and deposit in appropriate public databases.
Sub-objective 2.A: Characterize 2,500 priority strains of bacteria and fungi.
Sub-objective 2.B: Update the metadata on strains in the ARS Culture Collection using the Ag Data Commons website to facilitate research by ARS and other scientists worldwide.
Approach
More than 98,000 accessions consisting of microbial cultures of agriculturally, industrially, and medically important bacteria and fungi will be maintained in a secure centralized limited-access facility. These microbial genetic resources will be effectively preserved and secured, characterized to improve their utility, taxonomic accuracy, and made available to support agricultural and other research projects worldwide. In addition to maintaining and distributing currently held strains, high priority microbial genetic resources will be acquired and safeguarded so that these critical resources are widely available for microbial research and development. Microbial cultures will be characterized with a combination of genetic, genomic, metabolomic, and phenotypic approaches and analyses to elucidate their phylogenetic relationships, secondary metabolite profiles, ensure accurate species identification, and enhance their utility for research and development.
Progress Report
The ARS Culture Collection, originally known as the Northern Regional Research Laboratory (NRRL) in Peoria, Illinois, is one of the largest public collections of microorganisms in the world. It holds over 98,000 strains of fungi and bacteria that are available to the public, along with more than 7,500 strains used in patent applications. This collection is one of only two places officially recognized by the World Intellectual Property Organization to store microbes for patents, helping scientists meet legal requirements when they invent new products that use microbes. The main goals of the ARS Culture Collection are to support research and innovation that improves food safety, public health, farming, and economic growth. Scientists study how microbes work and how their natural traits can be used to solve real-world problems, while also making microbial germplasm resources easier to use. Microbes from this collection have played a big role in discoveries in medicine, agriculture, and technology, and have been mentioned in around 70,000 patents and scientific papers.
The ARS Culture Collection plays a major role in helping scientists make new discoveries by collecting, protecting, and sharing important microorganisms. Last year, they added over 260 new strains to their collection and shared more than 5,000 strains with researchers across the U.S., which helped support science and innovation worth about $1 million. They also worked hard to keep the collection accurate and useful by adding important strains that help scientists better understand different types of bacteria and fungi. One example is the addition of 56 strains of Phytophthora infestans, a harmful plant disease that affects potatoes and tomatoes. These samples help farmers and scientists develop new resistant potato and tomato varieties to fight crop loss caused by this disease.
To make things easier for users, the ARS team improved their website based on feedback from scientists and companies. The new site lets users search and download information about the microbes, making it faster to find what they need. This helps businesses in agriculture, biotechnology, and food production get the right microbes used in the production of antibiotics, enzymes, and biofuels.
Another big focus is using DNA to better understand and identify microbes.
Scientists at ARS worked on several projects to study plant diseases and harmful bacteria. They created new tools to identify and detect microscopic bacteria like Enterobacter, which can affect humans, animals, and plants. These tools help doctors and farmers quickly figure out what bacteria is causing the problem and allowing them to quickly treat the plant or animal to prevent further illness or crop loss.
They also studied corn diseases and updated the names of certain microbes using DNA data. This helps corn breeders develop improved varieties. In Peoria, Illinois, ARS scientists sequenced the DNA of over 850 strains of Bacillus, a microbe useful in fighting pests. They made this data public so others can use it to create better pest control products.
Finally, the ARS Culture Collection shared even more data online through a partnership with the National Agricultural Library. Their page was the most visited on the site, showing how valuable this information is to companies developing new products in farming and medicine. By making this data easy to access, ARS helps drive innovation across the country.
Accomplishments
1. ARS creates new, low-cost tool for identifying potentially harmful bacteria species. Bacteria in the genus Enterobacter are common harmful bacteria found both indoors and outdoors, that infect both plants and immuno-compromised patients and have developed antibiotic resistance. Although they are a common, medically-significant group of bacteria, accurately identifying which species belong in the group has proved difficult and costly. An ARS scientist contributed to the design and validation of a low-cost method for accurate identification of Enterobacter strains. The method was able to detect all strains belonging to Enterobacter but did not recognize closely related species of bacteria. This tool was also used to assess the accuracy of strains in the ARS Culture Collection previously deposited as Enterobacter and found that 42 of the 120 strains were not Enterobacter. These strains were later identified by DNA sequence and found to be several closely related bacterial species.
These findings and the identification tool developed will be of value to clinicians and plant diagnosticians enabling them to quickly and accurately identify pathogenic strains. This will benefit patients by getting an accurate diagnosis and treatment plan; and growers by identifying the pathogen species that allows them to develop a management plan to reduce crop losses.
2. ARS identifies 30 new fungal species including pathogens of corn, wheat and barley. Fungal plant pathogens in the genus Fusarium cause some of the most important diseases of major U.S. crops. Understanding the genetic variability and geographic distribution of this group is fundamental to developing improved disease management strategies. An ARS scientist in Peoria, Illinois, contributed to the characterization of 75 Fusarium species, including 30 new species, with descriptions that contained information on geographic distribution. These species included many pathogens of wheat, barley, corn, oat, potato, and hops. The information generated by this study will be used by plant pathologists and plant breeders to improve disease resistance and disease management which in turn will directly benefit U.S. farmers and the $200 billion agricultural economy. This information will also be valuable to diagnostic labs and regulatory agencies as they establish guidelines for detecting and monitoring Fusarium pathogens on agricultural commodities.
Review Publications
Broders, K.D., Capador-Barreto, H.D., Iriarte, G., Wright, S.J., Espinosa, H., Bauer, M., Lemus-Peralta, M.A., Rojas, E., Spear, E.R. 2024. Oomycete communities in lowland tropical forest soils vary in species abundance and comprise saprophytes and pathogens of seeds and seedlings of multiple plant species. American Journal of Botany. https://doi.org/10.1002/ajb2.16425.
Sandoval-Denis, M., Costa, M.M., Broders, K.D., Becker, Y., Maier, W., Yurkov, A., Kermode, A., Buddie, A.G., Ryan, M.J., Schumacher, R.K., Groenewald, J.Z., Crous, P.W. 2025. An integrative re-evaluation of the Fusarium sambucinum species complex. Studies in Mycology. 110(1). https://doi.org/10.3114/sim.2025.110.01.
Jordan, S., Plother, J.F., de Maayer, P., Broders, K., Kvitko, B.H., Coutinho, T.A., Smits, T.H.M. 2025. Design of genus-specific semi-nested primers for simple and accurate identification of Enterobacter strains. BMC Microbiology. https://doi.org/10.1186/s12866-025-04175-1.