Location: Mycotoxin Prevention and Applied Microbiology Research
2023 Annual Report
Objectives
The major goals of this project are to maintain and enhance the quality, diversity, and utility of the ARS Culture Collection holdings, including strains held in the ARS Patent Culture Collection, and to conduct and support microbiological research that advances agricultural production, food safety, public health, and economic development. Objective 1 provides for the curation and management of the ARS Culture Collection, including the acquisition and distribution of microbial strains and associated information. This objective provides scientists worldwide with access to high quality microbial germplasm through culture deposit and distribution services that facilitate research, publication, and technology transfer. Objective 2 is designed to improve understanding and utilization of microbial diversity through genetic and phenotypic characterization of strains in the ARS Culture Collection, and through the development of improved tools for microbial identification and characterization. Successful completion of goals under Objective 1 will provide scientists working on Objective 2 with access to microbial cultures, associated metadata, and tools to transfer research findings to the scientific community. Research conducted under Objective 2 will provide novel germplasm, microbiological expertise, and strain characterization data that enhances the value of the ARS Culture Collection and improves its curation.
Objective 1: Efficiently and effectively acquire, distribute, back-up, and maintain the safety, genetic integrity, health, and viability of priority microbial genetic resources and associated information in the ARS Culture Collection.
Objective 2: Enhance the value of priority microbial genetic resources in the ARS Culture Collection by conducting comparative phenotypic, phylogenetic and genomic analyses. Record and disseminate characterization data via the ARS Culture Collection database and other data sources.
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, 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, and phenotypic approaches and analyses to elucidate their phylogenetic relationships, ensure accurate species identification, and enhance their utility for research and development.
Progress Report
This is the final report for this project which terminated in March 2023. See the report for the replacement project, 5010-22410-025-000D, “Management and Characterization of Microbial Genetic Resources and Associated Descriptive Information” for additional information.
Research under Objective 1 was designed to maintain and preserve the microbial germplasm in the ARS Culture Collection as well as distribute this germplasm to the scientific community and to accession new microbial germplasm to enhance the value and diversity of the ARS Culture Collection. Over the course of this project, we distributed 21,441 microbial strains to over 1,000 scientists from across the United States and 55 other countries. The strain distributions conservatively represent an in-kind contribution of $4 million in support of microbiological research and biotechnological innovation over the course of this project. We also expanded the ARS Culture Collection through accessioning 1,145 new strains of fungi and bacteria during this project. This included many types of specimens from genera of important crop-associated fungi including Colletotrichum, Parastagonospora, Sarocladium and Fusarium. These strains fill important taxonomic gaps in the ARS Culture Collection and represent economically and ecologically important microbes that are important to the ARS mission. Furthermore, the utility and security of the collection was improved by adding or updating 23,867 strain history and inventory records. We also digitized the entire U.S. Army Quartermaster collection making these strains available to researchers for the first time. The ARS Culture Collection received approximately 6,000 isolates from the U.S. Army Quartermaster collection in the mid-1970s. These strains, which represent a global collection of various fungi associated with the biodegradation of military supplies and other cellulose materials, as well as various plant pathogens, have been stored at NCAUR for the last 45 years. The data on the strains were stored on index cards, and only approximately 350 strains of specific research interest were previously accessioned.
This year, in response to ARS research program needs and customer requests, we accessioned 376 new microbial strains (211 strains in the open collection and 165 strains in the Patent Culture Collection). In addition, 5,780 strains were sent to 533 scientists from across the United States and 45 other countries during FY2023. We also acquired and accessioned 202 Oomycetes strains in the genera Phytophthora, Phytopythium, Pythium, Halophytophthora and Nothophytophthora from around the world. This included 94 type strains, which are the representative strain for the species. Most of these strains are important plant pathogens of crops as well as horticultural and native plant species. Many of these strains came from retiring USDA-APHIS scientist Dr. Gloria Abad. The Oomycetes are morphologically very similar to fungi but are more closely related to the brown algae. This required the development of a new procedure for maintenance and preservation techniques to ensure the long-term viability of these strains. This year, we lyophilized over 1,000 microbial strains, which includes 10 ampoules per strain for a total of 10,000 ampoules. These lyophilized cultures can be shipped directly to customers, significantly increasing the number of strains that can be distributed each year. This includes the 376 new microbial deposits, of which one ampoule per strain is sent to the backup collection at the National Laboratory for Genetic Resources Preservation (NLGRP) in Fort Collins, Colorado. The remaining lyophilized strains represent the backlog of depleted strains that were shipped during the Covid max-telework period and when the lyophilization apparatus underwent repairs. We have now fully replenished these depleted stocks.
Research under Objective 2 is focused on generating and utilizing DNA-sequence based analyses of genetic variation and phenotypic data to characterize agronomically important microbes in the ARS Culture Collection and to make these strains and associated metadata publicly available to promote agricultural production, biotechnological development and food safety. Over the course of this project, we provided DNA-based identification to over 7,000 strains of fungi and bacteria in the ARS Culture Collection. We completed a large-scale DNA study clarifying the naming system within the fungal genus Fusarium. Members of Fusarium are the most economically destructive group of toxin-producing plant pathogens and emergent human pathogens. We found that three new Fusarium species are fungal pathogens farmed by beetles as a source of food. Native to Asia, fungus- farming ambrosia beetles have recently emerged as a global threat to several economically important woody hosts, including avocado, citrus, cacao, Chinese tea and rubber. These invasive pests and the pathogenic fungi they farm also pose a significant threat to urban landscapes and native forests here in the U.S. and abroad. We also completed a study to characterize the genetic diversity of a global collection of 171 Fusarium strains either known or predicted to produce toxins in wheat and barley and identified 33 new toxin-producing, plant pathogenic Fusarium species.
This year we completed the DNA-based identification and updated the taxonomy of 2,500 strains of Fusarium in the collection. We also completed a DNA-based identification of all 94 Trichoderma strains in the collection, resulting in the identification of 11 novel species and updating the taxonomy of 61 strains. This year we worked with various collaborators to generate metabolome data on 500 strains of Streptomyces and whole genome data on 1,157 strains of Bacillus.
Accomplishments
1. Native and weedy grasses are a source of ergot disease epidemics in barley. The fungal pathogen, Claviceps purpurea causes ergot disease. This pathogen poses a significant threat to agriculture and food safety as the dark ergot bodies, which contain various toxic compounds, get harvested with the grain and can cause severe poisoning in humans and livestock. C. purpurea is known to infect a wide range of grass species including barley, rye and wheat as well as many native, invasive and weedy grasses that grow in ditches along crop fields. An ARS researcher in Peoria, Illinois, worked with a researcher at Colorado State University to understand the role of non-crop grasses in the survival, reproduction and spread of the ergot fungus C. purpurea. Data from field surveys found that brome grasses, including smooth brome, were the most susceptible to infection by C. purpurea, were found in the greatest abundance near barley fields with a history of ergot, and had the greatest number of ergot bodies in the seed heads. Our findings indicate that smooth brome represents a significant source of pathogen inoculum, and the amount of inoculum is capable of causing disease in nearby barley fields when weather conditions are optimal.
2. Discovered four species of fungi new to science found colonizing crop roots. The semiarid steppe ecosystem in the Republic of Kazakhstan is excellent for cultivating wheat, barley, oats and other agronomically important crops. Improving the knowledge of fungi associated with these crops has the potential to promote agricultural production through identification of beneficial and pathogenic fungi that colonize crop roots, especially given a wide range of fungi colonize post-harvest residues of wheat and wild cereals. An ARS researcher in Peoria, Illinois, worked with researchers in Hungary and Kazakhstan to identify the fungi colonizing roots of wheat, barley, oat, wild cereals, lentil and flax. We discovered that members of the filamentous fungal genus Fusarium were the most dominant group comprising two-thirds of the 435 isolates recovered. Based on genetic analyses of DNA sequence data of the 290 Fusarium isolates, there were seven species of Fusarium recovered and four of these were new to science. These were formally described as novel Fusarium species using detailed morphological data. This study will be of interest to a wide range of biologists who are interested in cataloging the diversity of Fusarium species associated with crops and their potential role as either beneficial or pathogenic species and how they may promote or reduce crop yields.
Review Publications
Akhmetova, G.K., Knapp, D.G., Ozer, G., O'Donnell, K., Laraba, I., Kiyas, A., Zabolotskich, V., Kovacs, G.M., Molnar, O. 2022. Multilocus molecular phylogenetic-led discovery and formal recognition of four novel root-colonizing Fusarium species from northern Kazakhstan and the phylogenetically divergent Fusarium steppicola lineage. Mycologia. 115(1):16-31. https://doi.org/10.1080/00275514.2022.2119761.
Wyka, S., Broders, K. 2022. Brome grasses represent the primary source of Claviceps purpurea inoculum associated with barley fields in the San Luis Valley of Colorado. Canadian Journal of Plant Pathology. 45(1):15-29. https://doi.org/10.1080/07060661.2022.2091041.
Nottingham, A.T., Scott, J.J., Saltonstall, K., Broders, K., Montero-Sanchez, M., Puspok, J., Baath, E., Meir, P. 2022. Microbial diversity declines in warmed tropical soil and respiration rise exceed predictions as communities adapt. Nature Microbiology. 7:650–1660. https://doi.org/10.1038/s41564-022-01200-1.
Jerushalmi, S., Maymon, M., O'Donnell, K., Freeman, S. 2022. Members of the Fusarium oxysporum complex causing wilt symptoms in medical cannabis in Israel, Italy, and North America comprise a polyphyletic assemblage. Plant Disease. 106(10):2656-2662. https://doi.org/10.1094/PDIS-01-22-0155-RE.
Harmon, C., Castlebury, L.A., Boundy-Mills, K., Broders, K.D., Hyten, A.M., Jacobs, J., Knight-Connoni, V., Mollov, D.S., Riojas, M.A., Sharma, P. 2023. Standards of diagnostic validation: recommendations for reference collections. PhytoFrontiers. 3(1):43-50. https://doi.org/10.1094/PHYTOFR-05-22-0050-FI.
Queiroz, C.A., Caniato, F.F., Siqueira, V.K.S., de Moraes Catarino, A., Hanada, R.E., O'Donnell, K., Laraba, I., Rehner, S.A., Sousa, N.R., Silva, G.F. 2023. Population genetic analysis of Fusarium decemcellulare, a guaraná pathogen, reveals high genetic diversity in the Amazonas state, Brazil. Plant Disease. 107(5):1343-1354. https://doi.org/10.1094/PDIS-01-22-0083-RE.
