Source: NORTHERN REGIONAL RES CENTER submitted to
MANAGEMENT AND GENETIC CHARACTERIZATION OF AGRICULTURAL AND BIOTECHNOLOGICAL MICROBIAL RESOURCES
Sponsoring Institution
Agricultural Research Service/USDA
Project Status
TERMINATED
Funding Source
Reporting Frequency
Annual
Accession No.
0413230
Grant No.
(N/A)
Project No.
3620-22410-012-00D
Proposal No.
(N/A)
Multistate No.
(N/A)
Program Code
(N/A)
Project Start Date
May 14, 2008
Project End Date
Apr 23, 2013
Grant Year
(N/A)
Project Director
LABEDA D P
Recipient Organization
NORTHERN REGIONAL RES CENTER
(N/A)
PEORIA,IL 61604
Performing Department
(N/A)
Non Technical Summary
(N/A)
Animal Health Component
(N/A)
Research Effort Categories
Basic
50%
Applied
25%
Developmental
25%
Classification

Knowledge Area (KA)Subject of Investigation (SOI)Field of Science (FOS)Percent
2014020110280%
2014010110220%
Knowledge Area
201 - Plant Genome, Genetics, and Genetic Mechanisms;

Subject Of Investigation
4020 - Fungi; 4010 - Bacteria;

Field Of Science
1102 - Mycology;
Goals / Objectives
Objective 1: Strategically expand the genetic diversity in the ARS Culture Collection and improve associated information for priority microbial genetic resources. Sub-objective 1.A. Acquire from diverse sources samples of food-borne pathogenic bacteria, actinobacteria from equine sources, basidiomycetous yeasts, plant pathogenic fungi, and grain storage molds to fill current gaps in the ARS Culture Collection for these priority microbial strains. Sub-objective 1.B. In consultation with the microbial research community, identify microbial genetic resources associated with discontinued research programs, or held by researchers who are nearing retirement, and attempt to acquire those of strategic importance to current or future agricultural research programs. Objective 2: Conserve priority microbial genetic resources efficiently and effectively, and distribute them and associated information worldwide. Sub-objective 2.A. Conserve more than 90,000 accessions of priority microbial genetic resources and associated information, emphasizing food-borne pathogenic bacteria, actinobacteria from equine sources, basidiomycetous yeasts, plant pathogenic fungi, and grain storage molds, as well as microbes of biomedical and biotechnological importance. Sub-objective 2.B. Back-up at the National Center for Genetic Resources Preservation (NCGRP) approximately 15,000 strains (emphasizing Fusarium) that are currently preserved under liquid nitrogen vapor only at the National Center for Agricultural Utilization Research (NCAUR). Sub-objective 2.C. Continue to improve data management and technology transfer procedures, emphasizing improvements in user interface for the public access catalog system. Sub-Objective 2.D. Distribute on request microbial accessions and information that meet the specific needs of agricultural, biomedical, and biotechnological researchers. Objective 3: Strategically characterize (¿genotype¿) and evaluate (¿phenotype¿) priority microbial genetic resources through multigene analyses, and with key morphological, physiological, and biochemical descriptors. Sub-objective 3.A. Develop and apply multigene markers for phylogenetic and genetic diversity analyses of priority microbial genetic resources. Incorporate characterization data into GRIN and/or other databases, and apply the data to providing accurate taxonomic identifications, as well as to predicting the agricultural and biotechnological utility of newly discovered taxa. Sub-objective 3.B. Determine the phenotypic diversity and elucidate the population genetic structure for the Fusarium Head Blight (FHB) species Fusarium graminearum and F. asiacticum. Map their worldwide distribution, as a first step of establishing a molecular surveillance system for the early detection of Fusarium populations introduced to North America.
Project Methods
New species and novel strains of known species of plant pathogens and mycotoxigenic fungi, food-borne pathogens, actinobacteria important to animal health and biotechnology, and yeasts will be isolated from nature or acquired from reports in the literature and from cooperators worldwide. New strain accessions will be cataloged in the collection database, preserved by lyophilization and/or freezing in liquid nitrogen vapor where appropriate, and information related to well characterized strains will be made publicly available on the Collection website. Information provided by ARS Program leadership, national and international microbiology societies and culture collection organizations will identify microbial collections in danger of being lost and important collections will be acquired and accessioned where existing resources permit. The entire collection is secured in a limited access room and records for strain inventory and distribution are maintained on the collection database system. High priority microbial strains held only as frozen preparations under liquid nitrogen vapor phase will be duplicated and shipped to NCGRP for backup in a liquid nitrogen freezer dedicated for microbial germplasm. Strains will be freely distributed to the scientific community worldwide but requestors must provide required documentation or permits before animal or plant pathogenic strains or those requiring Biosafety Level II confinement are distributed. Through phylogenetic analysis of sequences from multiple gene loci, evaluate the diversity and systematics of actinomycetes, Bacillus, Aspergillus, and yeasts of importance to agriculture, food safety, and biotechnology. A multilocus genotyping assay previously developed for identification of FHB species and trichothecene chemotypes will be applied to a global collection of FHB isolates to determine the current distribution and trichothecene chemotype diversity of Fusarium graminearum and F. asiacticum populations. Population diversity and relatedness will then be assessed using a published panel of variable number tandem repeat markers. Differences in pathogen fitness and aggressiveness in individual populations will be evaluated by determining a range of phenotypic characteristics, such as growth, reproduction, and toxin production.

Progress 05/14/08 to 04/23/13

Outputs
Progress Report Objectives (from AD-416): Objective 1: Strategically expand the genetic diversity in the ARS Culture Collection and improve associated information for priority microbial genetic resources. Sub-objective 1.A. Acquire from diverse sources samples of food-borne pathogenic bacteria, actinobacteria from equine sources, basidiomycetous yeasts, plant pathogenic fungi, and grain storage molds to fill current gaps in the ARS Culture Collection for these priority microbial strains. Sub-objective 1.B. In consultation with the microbial research community, identify microbial genetic resources associated with discontinued research programs, or held by researchers who are nearing retirement, and attempt to acquire those of strategic importance to current or future agricultural research programs. Objective 2: Conserve priority microbial genetic resources efficiently and effectively, and distribute them and associated information worldwide. Sub-objective 2.A. Conserve more than 90,000 accessions of priority microbial genetic resources and associated information, emphasizing food- borne pathogenic bacteria, actinobacteria from equine sources, basidiomycetous yeasts, plant pathogenic fungi, and grain storage molds, as well as microbes of biomedical and biotechnological importance. Sub- objective 2.B. Back-up at the National Center for Genetic Resources Preservation (NCGRP) approximately 15,000 strains (emphasizing Fusarium) that are currently preserved under liquid nitrogen vapor only at the National Center for Agricultural Utilization Research (NCAUR). Sub- objective 2.C. Continue to improve data management and technology transfer procedures, emphasizing improvements in user interface for the public access catalog system. Sub-Objective 2.D. Distribute on request microbial accessions and information that meet the specific needs of agricultural, biomedical, and biotechnological researchers. Objective 3: Strategically characterize (�genotype�) and evaluate (�phenotype�) priority microbial genetic resources through multigene analyses, and with key morphological, physiological, and biochemical descriptors. Sub- objective 3.A. Develop and apply multigene markers for phylogenetic and genetic diversity analyses of priority microbial genetic resources. Incorporate characterization data into GRIN and/or other databases, and apply the data to providing accurate taxonomic identifications, as well as to predicting the agricultural and biotechnological utility of newly discovered taxa. Sub-objective 3.B. Determine the phenotypic diversity and elucidate the population genetic structure for the Fusarium Head Blight (FHB) species Fusarium graminearum and F. asiacticum. Map their worldwide distribution, as a first step of establishing a molecular surveillance system for the early detection of Fusarium populations introduced to North America. Approach (from AD-416): New species and novel strains of known species of plant pathogens and mycotoxigenic fungi, food-borne pathogens, actinobacteria important to animal health and biotechnology, and yeasts will be isolated from nature or acquired from reports in the literature and from cooperators worldwide. New strain accessions will be cataloged in the collection database, preserved by lyophilization and/or freezing in liquid nitrogen vapor where appropriate, and information related to well characterized strains will be made publicly available on the Collection website. Information provided by ARS Program leadership, national and international microbiology societies and culture collection organizations will identify microbial collections in danger of being lost and important collections will be acquired and accessioned where existing resources permit. The entire collection is secured in a limited access room and records for strain inventory and distribution are maintained on the collection database system. High priority microbial strains held only as frozen preparations under liquid nitrogen vapor phase will be duplicated and shipped to NCGRP for backup in a liquid nitrogen freezer dedicated for microbial germplasm. Strains will be freely distributed to the scientific community worldwide but requestors must provide required documentation or permits before animal or plant pathogenic strains or those requiring Biosafety Level II confinement are distributed. Through phylogenetic analysis of sequences from multiple gene loci, evaluate the diversity and systematics of actinomycetes, Bacillus, Aspergillus, and yeasts of importance to agriculture, food safety, and biotechnology. A multilocus genotyping assay previously developed for identification of FHB species and trichothecene chemotypes will be applied to a global collection of FHB isolates to determine the current distribution and trichothecene chemotype diversity of Fusarium graminearum and F. asiacticum populations. Population diversity and relatedness will then be assessed using a published panel of variable number tandem repeat markers. Differences in pathogen fitness and aggressiveness in individual populations will be evaluated by determining a range of phenotypic characteristics, such as growth, reproduction, and toxin production. The objectives of this project were designed to enhance the quality, diversity, and utility of the ARS Culture Collection holdings, and to produce and support microbiological research that advances agricultural production, food safety, public health, and economic development. Over the course of the project, we accessioned 10,118 isolates into the general collection and 667 isolates into the ARS Patent Culture Collection. The ARS Patent Culture Collection distributed 1,945 isolates, including 1,140 domestically and 845 to foreign scientists. More than 39, 700 isolates were distributed from the general collection, including 6, 422 isolates sent to ARS scientists, 22,965 isolates sent to other scientists within the United States, and 10,313 isolates sent to scientists in 76 different countries. Using a conservative estimate of monetary value based on fees charged by other major culture collections, strain distributions from the general collection during this project cycle represent an $8 million in-kind contribution in support of microbiological research and biotechnological innovation. The impact of this contribution is evidenced through the citation of strains from the ARS Culture Collection in 3,515 publications and 2,350 patent applications during this period. The addition of an online strain request module for the ARS Culture Collection database greatly facilitated public access to strains and request processing. A full time collection staff was developed, improving operations and significantly advancing efforts to generate a comprehensive electronic inventory. Approximately 48,230 inventory records have been added or updated and 3,544 previously uncataloged strains have been added to the permanent collection. These activities provide for continued preservation of agriculturally and biotechnologically significant microbial germplasm and distribution to researchers in ARS and throughout the world. Accurate identification of microbial isolates is a critical requirement for agricultural, medical, and industrial science. Development and testing of novel DNA sequence databases for rapid, accurate identification of microbial groups represented in the ARS Culture Collection provided tools to make accurate identification of microbes accessible to a wider variety of scientists, including non-specialists. Gene sequence databases were compiled and evaluated for identification of several microbial groups and provide an invaluable resource for strain identification and pathogen surveillance by researchers worldwide. Original research detailing microbial diversity is represented in 61 peer- reviewed papers and 42 authoritative book chapters including the discovery and description of more than 14 new species of filamentous fungi important in food safety, plant pathology, environmental, veterinary, or human health, as well as numerous new yeast species and new or revised species of Streptomyces important in biotechnology or animal health. These research activities and accomplishments underscore the importance of microbial germplasm collections as an invaluable resource and driving force for innovative research. Accomplishments 01 Maintenance and distribution of strains in the ARS Culture Collection. Access to accurately identified microbial isolates is critical to microbiological research that advances agricultural production, food safety, public health, and economic development. ARS scientists in the Bacterial Foodborne Pathogens and Mycology Research Unit, National Center for Agricultural Utilization Research, Peoria, Illinois, have supported microbiological research by operating and improving the ARS Culture Collection. In the previous 12 months, nearly 400 microbial isolates were accessioned into the collection and nearly 6,000 microbial isolates were distributed to scientists in the United States and 51 other countries. The utility and availability of this collection was improved by updating 48,000 inventory records and adding 3,500 previously uncataloged microbial isolates to an electronic database of available cultures. Using a conservative estimate of monetary value, strain distributions from the ARS Culture Collection during the last 12 months represent an $1.2 million in-kind contribution in support of microbiological research and biotechnological innovation. The broad impact of the ARS Culture Collection in advancing agricultural science and biotechnology is evidenced by the fact that microbial strains from the ARS Culture Collection have been cited in more than 1,200 scientific publications and 100 patents during the last year. 02 Molecular characterization of priority actinobacterial genetic resources. The range of biodiversity represented by the microbial strains held in the ARS Culture Collection in Peoria, Illinois, is not known because of the limited or incorrect characterization of many strains, making it difficult to assess its real or potential value by customers involved in agricultural and biotechnology research. The diversity within the ARS Culture Collection of strains of the genus Streptomyces, whose species produce many commercially important antibiotics, was estimated by ARS scientists in the Bacterial Foodborne Pathogens and Mycology Research Unit, National Center for Agricultural Utilization Research, Peoria, Illinois, based on the sequences of five protein-coding genes. A prototype database containing sequences of the five genes includes 87% of described species and analysis of the dataset confirmed the taxonomic diversity of this genus and also identified a number of described species that are equivalent as well as several strains that have published genome sequences that are misidentified. These studies demonstrated the value of the ARS Culture Collection as a source of reference germplasm for gene sequencing studies to address practical problems of strain identification. 03 Yeast species could provide a tool for control of codling moths. Codling moths are important pests in apple production that reduce the marketable yield of orchards. ARS scientists in the Bacterial Foodborne Pathogens and Mycology Research Unit, National Center for Agricultural Utilization Research, Peoria, Illinois, in collaboration with scientists in Sweden and Brazil, discovered that species of the yeast genus Metschnikowia appear essential for development of codling moth larvae in apple fruits. This knowledge will be useful in developing new strategies for the control of this important apple pathogen. 04 Protecting future commercial harvests of true morels. Commercial harvesting of true morels has grown into highly lucrative cottage industries in several morel-rich countries, including China, Turkey, and the United States. To protect this renewable resource, ARS scientists in the Bacterial Foodborne Pathogens and Mycology Research Unit, National Center for Agricultural Utilization Research, Peoria, Illinois, in collaboration with scientists in China, Europe, and North America, determined the utility of the fungal barcode gene for identifying morels so that previously unknown species can be detected and identified for further genetic evaluation. Towards this end, we developed a dedicated, web-accessible informational database called Morchella MLST (http://www.cbs.knaw.nl/morchella/) that facilitates DNA sequence-based identifications of true morels via the web. Moreover, pure cultures of diverse morel species were made and are stored in the ARS Culture Collection to benefit biotechnologists interested in cultivating morels commercially. Finally, the results of this study provide invaluable information needed to develop appropriate practices for the conservation and sustainable harvest of morels. 05 Novel azuki bean pathogen discovered in Hokkaido, Japan. Production of azuki beans in Japan, which are used in numerous traditional foods in Asia, is threatened by a novel root rot disease. The present study was initiated to characterize the azuki bean pathogen in Japan, as part of a broad research program to establish a global picture of bean pathogen diversity, host range, and geographic distribution. ARS scientists in the Bacterial Foodborne Pathogens and Mycology Research Unit, National Center for Agricultural Utilization Research, Peoria, Illinois, in collaboration with scientists in Japan and Argentina, discovered that the novel pathogen of azuki bean was also pathogenic to mung bean, kidney bean, and soybean, and theorize that the azuki bean pathogen was introduced into Japan from South America. These research findings promote agricultural biosecurity by providing plant pathologists and quarantine officials with tools for pathogen detection and identification and they should assist bean breeders in their efforts to develop cultivars with broad-based resistance to the diverse bean root rot pathogens. 06 Protecting avocado production worldwide from invasive beetles and pathogenic fungi. ARS scientists in the Bacterial Foodborne Pathogens and Mycology Research Unit, National Center for Agricultural Utilization Research, Peoria, Illinois, discovered at least eight closely related pathogenic fungi that are being cultivated for food by invasive wood boring beetles in the genus Euwallacea, an exotic beetle native to Asia. These beetles and the Fusarium fungi that they farm currently pose a significant threat to avocado production worldwide. In addition, these wood infesting beetles are economically destructive pests of cacao, rubber trees, and tea in Asia, and literally hundreds of urban landscape trees in Los Angeles and surrounding counties in southern California. Research reported in this study promotes agricultural biosecurity by providing plant pathologists, insect biologists, and quarantine officers with robust tools for the early detection and identification of these economically destructive plant pathogens.

Impacts
(N/A)

Publications

  • Sugui, J.A., Peterson, S.W., Clark, L.P., Nardone, G., Folio, L., Riedlinger, G., Zelazny, A.M., Holland, S.M., Kwon-Chung, K.J. 2012. Aspergillus tanneri sp. nov., a new pathogen that causes invasive disease refractory to antifungal therapy. Journal of Clinical Microbiology. 50(10) :3309-3317.
  • Du, X., Zhao, Q., Yang, Z.L., Hansen, K., Taskin, H., Buyukalaca, S., Dewsbury, D., Moncalvo, J., Douhan, G.Q., Robert, V.A., Crous, P.W., Rehner, S.A., Rooney, A.P., Sink, S.L., O'Donnell, K. 2012. How well do ITS rDNA sequences differentiate species of true morels (Morchella)? Mycologia. 104(6):1351-1368.
  • Salter, C.E., O'Donnell, K., Sutton, D.A., Marancik, D.P., Knowles, S., Clauss, T.M., Berliner, A.L., Camus, A.C. 2012. Dermatitis and systemic mycosis in lined seahorses Hippocampus erectus associated with a marine- adapted Fusarium solani species complex pathogen. Diseases of Aquatic Organisms. 101(1):23-31.
  • Peter, G., Dlauchy, D., Price, N.P., Kurtzman, C.P. 2012. Diddensiella caesifluorescens gen. nov., sp. nov., a riboflavin-producing yeast species of the family Trichomonascaceae. International Journal of Systematic and Evolutionary Microbiology. 62(12):3081-3087.
  • Kurtzman, C.P., Robnett, C.J. 2013. Relationships among genera of the Saccharomycotina (Ascomycota) from multigene phylogenetic analysis of type species. Federation Of European Microbiological Societies Yeast Research. 13(1):23-33.
  • Labeda, D.P., Goodfellow, M., Brown, R., Ward, A.C., Lanoot, B., Vanncanneyt, M., Swings, J., Kim, S.B., Liu, Z., Chun, J., Tamura, T., Oguchi, A., Kikuchi, T., Kikuchi, H., Nishii, T., Tsuji, K., Yamaguchi, Y., Tase, A., Takahashi, M., Sakane, T., Suzuki, K.I., Hatano, K. 2012. Phylogenetic study of the species within the family Streptomycetaceae. Antonie Van Leeuwenhoek. 101(1):73-104.
  • Aoki, T., Tanaka, F., Suga, H., Hyakumachi, M., Scandiani, M.M., O'Donnell, K. 2012. Fusarium azukicola sp. nov., an exotic azuki bean root-rot pathogen in Hokkaido, Japan. Mycologia. 104(5):1068-1084.
  • Chen, Y., Ntai, I., Ju, K., Unger, M., Zamdborg, L., Robinson, S.J., Doroghazi, J.R., Labeda, D.P., Metcalf, W.W., Kelleher, N.L. 2012. A proteomic survey of nonribosomal peptide and polyketide biosynthesis in actinobacteria. Journal of Proteome Research. 11(1):85�94.
  • Xess, I., Mohapatra, S., Shivaprakash, M.R., Chakrabarti, A., Benny, G.L., O'Donnell, K., Padhye, A.A. 2012. Evidence implicating Thamnostylum lucknowense as an etiological agent of Rhino-orbital Mucormycosis. Journal of Clinical Microbiology. 50(4):1491-1494.
  • Mendel, Z., Protasov, A., Sharon, M., Ben-Yehuda, S., O'Donnell, K., Rabaglia, R., Wysoki, M., Freeman, S. 2012. An Asian ambrosia beetle Euwallacea fornicatus and its novel symbiotic fungus Fusarium sp. pose a serious threat to the Israeli avocado industry. Phytoparasitica. 40(3):235- 238.
  • Kurtzman, C.P. 2012. Candida kuoi sp. nov., a new anamorphic species of the Starmerella yeast clade that synthesizes sophorolipids. International Journal of Systematic and Evolutionary Microbiology. 62(9):2307-2311.
  • Kuo, M., Dewsbury, D.R., O'Donnell, K., Carter, M., Rehner, S.A., Moore, J. , Moncalvo, J., Canfield, S.A., Stephenson, S.L., Methven, A.S., Volk, T.J. 2012. Taxonomic revision of true morels (Morchella) in Canada and the United States. Mycologia. 104(5):1159-1177.
  • Jurjevic, Z., Peterson, S.W., Horn, B.W. 2012. Aspergillus section Versicolores, nine new species and multilocus DNA sequence based phylogeny. IMA Fungus. 3(1):59-79.
  • Peterson, S.W. 2012. Aspergillus and Penicillium identification using DNA sequences: Barcode or MLST? Applied Microbiology and Biotechnology. 95(2) :339-344.
  • Witzgall, P., Proffit, M., Rozpedowska, E., Becher, P., Andreadis, S., Coracini, M., Lindblom, T., Bengtsson, M., Ream, L.J., Kurtzman, C.P., Piskur, J., Knight, A.L. 2012. �This is not an apple��yeast mutualism in codling moth. Journal of Chemical Ecology. 38(8):949-957.
  • Horn, B.W., Olarte, R.A., Peterson, S.W., Carbone, I. 2013. Sexual reproduction in Aspergillus tubingensis from section Nigri. Mycologia 105(5): 1153-1163.


Progress 10/01/11 to 09/30/12

Outputs
Progress Report Objectives (from AD-416): Objective 1: Strategically expand the genetic diversity in the ARS Culture Collection and improve associated information for priority microbial genetic resources. Sub-objective 1.A. Acquire from diverse sources samples of food-borne pathogenic bacteria, actinobacteria from equine sources, basidiomycetous yeasts, plant pathogenic fungi, and grain storage molds to fill current gaps in the ARS Culture Collection for these priority microbial strains. Sub-objective 1.B. In consultation with the microbial research community, identify microbial genetic resources associated with discontinued research programs, or held by researchers who are nearing retirement, and attempt to acquire those of strategic importance to current or future agricultural research programs. Objective 2: Conserve priority microbial genetic resources efficiently and effectively, and distribute them and associated information worldwide. Sub-objective 2.A. Conserve more than 90,000 accessions of priority microbial genetic resources and associated information, emphasizing food- borne pathogenic bacteria, actinobacteria from equine sources, basidiomycetous yeasts, plant pathogenic fungi, and grain storage molds, as well as microbes of biomedical and biotechnological importance. Sub- objective 2.B. Back-up at the National Center for Genetic Resources Preservation (NCGRP) approximately 15,000 strains (emphasizing Fusarium) that are currently preserved under liquid nitrogen vapor only at the National Center for Agricultural Utilization Research (NCAUR). Sub- objective 2.C. Continue to improve data management and technology transfer procedures, emphasizing improvements in user interface for the public access catalog system. Sub-Objective 2.D. Distribute on request microbial accessions and information that meet the specific needs of agricultural, biomedical, and biotechnological researchers. Objective 3: Strategically characterize (�genotype�) and evaluate (�phenotype�) priority microbial genetic resources through multigene analyses, and with key morphological, physiological, and biochemical descriptors. Sub- objective 3.A. Develop and apply multigene markers for phylogenetic and genetic diversity analyses of priority microbial genetic resources. Incorporate characterization data into GRIN and/or other databases, and apply the data to providing accurate taxonomic identifications, as well as to predicting the agricultural and biotechnological utility of newly discovered taxa. Sub-objective 3.B. Determine the phenotypic diversity and elucidate the population genetic structure for the Fusarium Head Blight (FHB) species Fusarium graminearum and F. asiacticum. Map their worldwide distribution, as a first step of establishing a molecular surveillance system for the early detection of Fusarium populations introduced to North America. Approach (from AD-416): New species and novel strains of known species of plant pathogens and mycotoxigenic fungi, food-borne pathogens, actinobacteria important to animal health and biotechnology, and yeasts will be isolated from nature or acquired from reports in the literature and from cooperators worldwide. New strain accessions will be cataloged in the collection database, preserved by lyophilization and/or freezing in liquid nitrogen vapor where appropriate, and information related to well characterized strains will be made publicly available on the Collection website. Information provided by ARS Program leadership, national and international microbiology societies and culture collection organizations will identify microbial collections in danger of being lost and important collections will be acquired and accessioned where existing resources permit. The entire collection is secured in a limited access room and records for strain inventory and distribution are maintained on the collection database system. High priority microbial strains held only as frozen preparations under liquid nitrogen vapor phase will be duplicated and shipped to NCGRP for backup in a liquid nitrogen freezer dedicated for microbial germplasm. Strains will be freely distributed to the scientific community worldwide but requestors must provide required documentation or permits before animal or plant pathogenic strains or those requiring Biosafety Level II confinement are distributed. Through phylogenetic analysis of sequences from multiple gene loci, evaluate the diversity and systematics of actinomycetes, Bacillus, Aspergillus, and yeasts of importance to agriculture, food safety, and biotechnology. A multilocus genotyping assay previously developed for identification of FHB species and trichothecene chemotypes will be applied to a global collection of FHB isolates to determine the current distribution and trichothecene chemotype diversity of Fusarium graminearum and F. asiacticum populations. Population diversity and relatedness will then be assessed using a published panel of variable number tandem repeat markers. Differences in pathogen fitness and aggressiveness in individual populations will be evaluated by determining a range of phenotypic characteristics, such as growth, reproduction, and toxin production. The goals of this project include enhancing the Agricultural Research Service (ARS) Culture Collection by acquiring novel microbial germplasm and genetic characterization of this germplasm through gene sequence analysis. In the past 12 months, the total number of strains accessioned into the general and patent collections has been 839 and 218, respectively. The ARS Patent Culture Collection has distributed 562 strains including 327 to scientists in the U.S. and 235 to foreign scientists. Strain distributions from the general collection totaled 6, 100, with 1,092 to ARS scientists, 2,839 to other scientists in the U.S., and 2,169 to foreign scientists. The ARS Culture Collection website has 12,916 strain records available in the public catalog, had over 30,241 visitors from over 124 different countries and has been indexed by at least 68 different search engines. The online strain request module for the ARS Culture Collection database system/website has simplified the client request process and facilitated request processing. Approximately 15,000 digital inventory records have been updated for the collection. These activities provided for the preservation of agriculturally significant microbial strains and their distribution to ARS researchers and others throughout the world. The ARS Culture Collection has a tremendous impact on microbiological research and innovation as evidenced by the citation of strains from this collection in 2,681 publications and 1,925 patent applications during the current 5 year project cycle. Accurate identification of microbial isolates is a critical element of agricultural, medical and industrial research. Novel DNA sequence databases were developed and tested for rapid and accurate identification of microbial groups represented in the ARS Culture Collection to facilitate precise identification of microbes by other scientists, including non-specialists. While testing gene sequence databases for identification of corn isolates of the mold Aspergillus versicolor, a cause of sick building syndrome and animal toxicosis, 9 new Aspergillus species were discovered and an identification guide developed to aid scientists studying similar problems. A recent equine abortion outbreak provided an opportunity to test multi-gene sequence databases for two actinomycete genera and it was determined that one species, Streptomyces atriruber, has been present on infected equine placentas for over 10 breeding seasons. The sequence databases will assist veterinary microbiologists in discovering if similar microorganisms are responsible for abortions in other livestock. A yeast multigene sequence database was used to evaluate strains in the collection and several new species of yeasts were discovered. Web-based databases of gene sequence and various observable traits were developed for the fungal genus Fusarium, which produces toxins in grains and head blight disease on many grain crops such as wheat and barley. The expanded web databases for this group will simplify the accurate identification of toxin producing strains as well as improving surveillance of the migration of this pathogen in North America. Accomplishments 01 Support of agricultural science and biotechnological innovation through operation of the ARS Culture Collection. During the last 12 months, scientists in the Bacterial Foodborne Pathogens and Mycology Research Un (BFP), USDA, ARS, National Center for Agricultural Utilization Research (NCAUR), Peoria, IL, provided approximately 6,700 strains of agriculturally and biotechnologically significant bacteria and fungi in response to requests from scientists in the United States and around the world. The maintenance and distribution of these important microbial strains has a significant impact on scientific investigation and biotechnological innovation. A search of the current literature and U.S. patent databases indicated that microbial strains provided by the ARS Culture Collection were used in at least 2681 scientific publications an enabled 1925 patent applications during the last five years. 02 Identification of novel biotechnological potential among actinobacteria the ARS Culture Collection. The potential utility of the biodiversity represented by the microbial strains held in the ARS Culture Collection Peoria, IL, is not fully known because of the limited characterization o many strains in this collection. Scientists in the Bacterial Foodborne Pathogens and Mycology Research Unit (BFP), USDA, ARS, National Center f Agricultural Utilization Research (NCAUR), Peoria, IL, characterized the diversity and potential utility of a large set of strains from the actinomycete genus Streptomyces, whose species produce many medically important antibiotics. The species identities of previously uncharacterized strains were determined, and several new species were identified for the first time. Through collaborations with scientists at University of Illinois and Northwestern University it was determined tha a large number of these actinobacteria have the genetic potential to produce new compounds of value to human or animal health. These studies demonstrated that the biological and biosynthetic diversity represented the holdings of the ARS Culture Collection may be greater than originall thought, increasing its value as a resource for new product discovery.

Impacts
(N/A)

Publications

  • Labeda, D.P. 2012. Genus XIII. Umezawaea Labeda and Kroppenstedt 2007, 2761vp. In: Goodfellow, M., Kampfer, P., Busse, H., Trujillo, M.E., Suzuki, K., Ludwig, W., Whitman, W.B., editors. Bergey�s Manual of Systematic Bacteriology. 2nd edition, volume 5. New York, NY: Springer. p. 1427-1430.
  • Labeda, D.P. 2012. Genus VI. Crossiella Labeda 2001, 1578vp. In: Goodfellow, M., Kampfer, P., Busse, H., Trujillo, M.E., Suzuki, K., Ludwig, W., Whitman, W.B., editors. Bergey�s Manual of Systematic Bacteriology. 2nd edition, volume 5. New York, NY: Springer. p. 1359-1363.
  • Labeda, D.P. 2012. Genus IX. Kutzneria Stackebrandt, Kroppenstedt, Jahnke, Kemmerling and Gurtler 1994, 267vp. In: Goodfellow, M., Kampfer, P., Busse, H., Trujillo, M.E., Suzuki, K., Ludwig, W., Whitman, W.B., editors. Bergey�s Manual of Systematic Bacteriology. 2nd edition, volume 5. New York, NY: Springer. p. 1371-1375.
  • Erol, E., Sells, S.F., Williams, N., Kennedy, L., Locke, S.J., Labeda, D.P. , Donahue, J.M., Carter, C.N. 2012. An investigation of a recent outbreak of nocardioform placentitis caused abortions in horses. Veterinary Microbiology. 158(2012):425-430.
  • Hughes, S.R., Bischoff, K.M., Gibbons, W.R., Bang, S.S., Pinkelman, R., Slininger, P.J., Qureshi, N., Liu, S., Saha, B.C., Jackson, J.S., Cotta, M. A., Rich, J.O., Javers, J. 2012. Random UV-C mutagenesis of Scheffersomyces (formerly Pichia) stipitis NRRL Y-7124 to improve anaerobic growth on lignocellulosic sugars. Journal of Industrial Microbiology and Biotechnology. 39(1):163�173.
  • Price, N.P., Ray, K.J., Vermillion, K., Dunlap, C.A., Kurtzman, C.P. 2011. Structural characterization of novel sophorolipid biosurfactants from a newly-identified species of Candida yeast. Carbohydrate Research. 348:33- 41. DOI: 10.1016/j.carres.2011.07.016.
  • Schoch, C.L., Seifert, K.A., Huhndorf, S., Robert, V., Spouge, J.L., Bolchacova, E., Voigt, K., Chen, W., Miller, A.N., Wingfield, M.J., Aime, M., An, K., Bai, F., Barreto, R.W., Begerow, D., Bergeron, M., Blackwell, M., Boekhout, T., Bogale, M., Boonyuen, N., Burgaz, A.R., Olariaga, I., Cai, L., Cardinali, G., Chaverri, P., Coppins, B.J., Crespo, A., Crous, P. W., Cubas, P., Damm, U., De Beer, Z., De Hoog, G., Del-Prado, R., Dentinger, B., Duong, T.S., Divakar, P.K., Maharachchikumbura, S.S., Okane, I., Otte, J., Eberhardt, U., Elshahed, M.S., Fliegerova, K., Raja, H.A., Ge, Z., Schmitt, I., Redecker, D., Groenewald, J.Z., Groenewald, M., Grube, M., Gryzenhout, M., Guo, L., Hagen, F., Hambleton, S., Hamelin, R.C., Hansen, K., Harrold, P., Heller, G., Hirayama, K., Shearer, C., Hoffman, K. , Hofstetter, V., Hognabba, F., Schubler, A., Sotome, K., Suh, S., Houbraken, J., Hughes, K., Huhtinen, S., Hyde, K.D., James, T., Park, D., Johnston, P.R., Jones, E., Kelly, L.J., Kirk, P.M., Knapp, D.G., Koljalg, U., Kovacs, G.M., Kurtzman, C.P., Landvik, S., Leavitt, S.D., Levesque, C., Liggenstoffer, A.S., Liimatainen, K., Lombard, L., Luangsa-Ard, J., Lumbsch, H., Maganti, H., Schindel, D., Tretter, E., Weib, M., Mctaggart, A.R., Methven, A.S., Meyer, W., Moncalvo, J., Mongkolsamrit, S., Nagy, L.G. , et al. 2012. Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi. Proceedings of the National Academy of Sciences. 109(16):6241-6246.
  • Labeda, D.P. 2011. Multilocus sequence analysis of phytopathogenic species of the genus Streptomyces. International Journal of Systematic and Evolutionary Microbiology. 61(10):2525-2531.
  • Kurtzman, C.P. 2011. A new methanol assimilating yeast, Ogataea parapolymorpha, the ascosporic state of Candida parapolymorpha. Antonie Van Leeuwenhoek. 100(3):455-462.
  • Peter, G., Dlauchy, D., Tornai-Lehoezki, J., Kurtzman, C.P. 2011. Ogataea saltuana sp. nov., a novel methanol-assimilating yeast species. Antonie Van Leeuwenhoek. 100(3):375-383.
  • Hawksworth, D.L., Crous, P.W., Redhead, S.A., Reynolds, D.R., Samson, R.A., Seifort, K.A., Taylor, J.W., Samson, R.A., Abaci, O., Asan, A., Bai, F., De Beer, W.Z., Begerow, D., Boekhout, T., Buzina, W., Cai, L., Cannon, P.F. , Damm, U., Daniel, H., Demirel, R., Van Diepeningen, A.D., Eberhardt, U., Fell, J.W., Frisvad, J.C., Geml, J., Glienke, C., Groenwald, M., Gueho- Kellermanne, E., Hong, S., Houbraken, J., Huhndorf, S.M., Hyde, K.D., Johnston, P.R., Koljalg, U., Kurtzman, C.P., Lagneau, P., Levesque, C., Liu, X., Lombard, L., Meyer, W., Miller, A., Minter, D.W., Najafzadeh, M.J. , Ozerskaya, S.M., Pennycook, S.R., Peterson, S.W., Pettersson, O.V., Quaedvlieg, W., Robert, V.A., Ruibal, C., Schnurer, J., Schoers, H., Slippers, B., Spierenburg, H., Taskin, E., Thrane, U., Uztan, A., Varga, J. , Vasco, A., Videira, S.I., De Vries, R.P., Weir, B.S., Yilmaz, N., Yurkov, A. 2011. The Amsterdam declaration on fungal nomenclature. IMA Fungus. 2(1):105-112.
  • Labeda, D.P., Goodfellow, M. 2012. Family I. Pseudonocardiaceae Embley, Smida, and Stackebrandt 1989, 205VP emend. Labeda, Goodfellow, Chun, Zhi and Li 2010a. In: Goodfellow, M., Kampfer, P., Busse, H., Trujillo, M.E., Suzuki, K., Ludwig, W., Whitman, W.B., editors. Bergey�s Manual of Systematic Bacteriology. 2nd edition, volume 5. New York, NY: Springer. p. 1302-1305.
  • Labeda, D.P. 2012. Genus III. Actinokineospora Hasegawa 1988a, 449VP. In: Goodfellow, M., Kampfer, P., Busse, H., Trujillo, M.E., Suzuki, K., Ludwig, W., Whitman, W.B., editors. Bergey�s Manual of Systematic Bacteriology. 2nd edition, volume 5. New York, NY: Springer. p. 1325-1330.
  • Von Jan, M., Riegger, N., Potter, G., Schumann, P., Verbarg, S., Sproer, C. , Rohde, M., Lauer, B., Labeda, D.P., Klenk, H. 2011. Kroppenstedtia eburnea gen. nov., sp. nov., a novel thermoactinomycete isolated by environmental screening, and emended description of the family Thermoactinomycetaceae Matsuo et al. 2006 emend. Yassin et al. 2009. International Journal of Systematic and Evolutionary Microbiology. 61(9) :2304-2310.
  • Peterson, S.W., Orchard, S.S., Menon, S. 2011. Penicillium menonorum, a new species related to P. pimiteouiense. IMA Fungus. 2(2):121-125.
  • Labeda, D.P. 2012. The suborder Glycomycineae, family Glycomycetaceae and genus Glycomyces. In: Goodfellow, M., Kampfer, P., Busse, H., Trujillo, M. E., Suzuki, K., Ludwig, W., Whitman, W.B., editors. Bergey�s Manual of Systematic Bacteriology. 2nd edition, volume 5. New York, NY: Springer. p. 546-553.
  • Labeda, D.P. 2012. Genus II: Stackebrandtia Labeda and Kroppenstedt 2005, 1690vp. In: Goodfellow, M., Kampfer, P., Busse, H., Trujillo, M.E., Suzuki, K., Ludwig, W., Whitman, W.B., editors. Bergey�s Manual of Systematic Bacteriology. 2nd edition, volume 5. New York, NY: Springer. p. 553-554.
  • Labeda, D.P., Goodfellow, M. 2012. Order XIII. Pseudonocardineae ord.nov. In: Goodfellow, M., Kampfer, P., Busse, H., Trujillo, M.E., Suzuki, K., Ludwig, W., Whitman, W.B., editors. Bergey�s Manual of Systematic Bacteriology. 2nd edition, volume 5. New York, NY: Springer. p. 1301.
  • Labeda, D.P. 2012. Genus IV. Actinosynnema Hasegawa, Lechevalier and Lechevalier 1978, 304al. In: Goodfellow, M., Kampfer, P., Busse, H., Trujillo, M.E., Suzuki, K., Ludwig, W., Whitman, W.B., editors. Bergey�s Manual of Systematic Bacteriology. 2nd edition, volume 5. New York, NY: Springer. p.1331-1334.
  • Labeda, D.P. 2012. Genus Goodfellowiella (Labeda and Kroppenstedt 2006) Labeda, Kroppenstedt, Euzeby and Tindall 2008, 1048vp. In: Goodfellow, M., Kampfer, P., Busse, H., Trujillo, M.E., Suzuki, K., Ludwig, W., Whitman, W. B., editors. Bergey�s Manual of Systematic Bacteriology. 2nd edition, volume 5. New York, NY: Springer. p. 1363-1366.
  • Labeda, D.P. 2012. Genus X. Lechevalieria Labeda, Hatano, Kroppenstedt and Tamura 2001, 1049vp. In: Goodfellow, M., Kampfer, P., Busse, H., Trujillo, M.E., Suzuki, K., Ludwig, W., Whitman, W.B., editors. Bergey�s Manual of Systematic Bacteriology. 2nd edition, volume 5. New York, NY: Springer. p. 1379-1379.
  • Labeda, D.P. 2012. Genus XI. Lentzea Yassin, Rainey, Brzezinka, Jahnke, Weissbrodt, Budzikiewicz, Stackebrandt, and Schaal 1995, 362vp emend. Labeda, Hatano, Kroppenstedt and Tamura 2001, 1049. In: Goodfellow, M., Kampfer, P., Busse, H., Trujillo, M.E., Suzuki, K., Ludwig, W., Whitman, W. B., editors. Bergey�s Manual of Systematic Bacteriology. 2nd edition, volume 5. New York, NY: Springer. p. 1379-1383.
  • Labeda, D.P. 2012. Genus XV. Saccharothrix Labeda, Testa, Lechevalier and Lechevalier 1984, 429vp emend. Labeda and Lechevalier 1989, 422. In: Goodfellow, M., Kampfer, P., Busse, H., Trujillo, M.E., Suzuki, K., Ludwig, W., Whitman, W.B., editors. Bergey�s Manual of Systematic Bacteriology. 2nd edition, volume 5. New York, NY: Springer. p. 1415-1419.
  • Labeda, D.P. 2012. Genus VIII. Kibdelosporangium Shearer, Colman, Ferrin, Nisbet and Nash 1986, 48. In: Goodfellow, M., Kampfer, P., Busse, H., Trujillo, M.E., Suzuki, K., Ludwig, W., Whitman, W.B., editors. Bergey�s Manual of Systematic Bacteriology. 2nd edition, volume 5. New York, NY: Springer. p. 1366-1371.
  • Kurtzman, C.P. 2012. Komagataella populi sp. nov. and Komagataella ulmi sp. nov., two new methanol assimilating yeasts from exudates of deciduous trees. Antonie Van Leeuwenhoek. 101(4):859-868.
  • Kurtzman, C.P., Robnett, C.J. 2012. Saitoella coloradoensis sp. nov., a new species of the Ascomycota, subphylum Taphrinomycotina. Antonie Van Leeuwenhoek. 101(4):795-802.
  • Aoki, T., Scandiani, M.M., O Donnell, K. 2011. Phenotypic, molecular phylogenetic, and pathogenetic characterization of Fusarium crassistipitatum sp. nov., a novel soybean sudden death syndrome pathogen from Argentina and Brazil. Mycoscience. 53(3):167-186.
  • Du, X., Zhao, Q., O'Donnell, K., Rooney, A.P., Yang, Z.L. 2012. Multigene molecular phylogenetics reveals true morels (Morchella) are especially species-rich in China. Fungal Genetics and Biology. 49(6):455-469.


Progress 10/01/10 to 09/30/11

Outputs
Progress Report Objectives (from AD-416) Objective 1: Strategically expand the genetic diversity in the ARS Culture Collection and improve associated information for priority microbial genetic resources. Sub-objective 1.A. Acquire from diverse sources samples of food-borne pathogenic bacteria, actinobacteria from equine sources, basidiomycetous yeasts, plant pathogenic fungi, and grain storage molds to fill current gaps in the ARS Culture Collection for these priority microbial strains. Sub-objective 1.B. In consultation with the microbial research community, identify microbial genetic resources associated with discontinued research programs, or held by researchers who are nearing retirement, and attempt to acquire those of strategic importance to current or future agricultural research programs. Objective 2: Conserve priority microbial genetic resources efficiently and effectively, and distribute them and associated information worldwide. Sub-objective 2.A. Conserve more than 90,000 accessions of priority microbial genetic resources and associated information, emphasizing food- borne pathogenic bacteria, actinobacteria from equine sources, basidiomycetous yeasts, plant pathogenic fungi, and grain storage molds, as well as microbes of biomedical and biotechnological importance. Sub- objective 2.B. Back-up at the National Center for Genetic Resources Preservation (NCGRP) approximately 15,000 strains (emphasizing Fusarium) that are currently preserved under liquid nitrogen vapor only at the National Center for Agricultural Utilization Research (NCAUR). Sub- objective 2.C. Continue to improve data management and technology transfer procedures, emphasizing improvements in user interface for the public access catalog system. Sub-Objective 2.D. Distribute on request microbial accessions and information that meet the specific needs of agricultural, biomedical, and biotechnological researchers. Objective 3: Strategically characterize (�genotype�) and evaluate (�phenotype�) priority microbial genetic resources through multigene analyses, and with key morphological, physiological, and biochemical descriptors. Sub- objective 3.A. Develop and apply multigene markers for phylogenetic and genetic diversity analyses of priority microbial genetic resources. Incorporate characterization data into GRIN and/or other databases, and apply the data to providing accurate taxonomic identifications, as well as to predicting the agricultural and biotechnological utility of newly discovered taxa. Sub-objective 3.B. Determine the phenotypic diversity and elucidate the population genetic structure for the Fusarium Head Blight (FHB) species Fusarium graminearum and F. asiacticum. Map their worldwide distribution, as a first step of establishing a molecular surveillance system for the early detection of Fusarium populations introduced to North America. Approach (from AD-416) New species and novel strains of known species of plant pathogens and mycotoxigenic fungi, food-borne pathogens, actinobacteria important to animal health and biotechnology, and yeasts will be isolated from nature or acquired from reports in the literature and from cooperators worldwide. New strain accessions will be cataloged in the collection database, preserved by lyophilization and/or freezing in liquid nitrogen vapor where appropriate, and information related to well characterized strains will be made publicly available on the Collection website. Information provided by ARS Program Leadership, national and international microbiology societies and Culture Collection organizations will identify microbial collections in danger of being lost and important collections will be acquired and accessioned where existing resources permit. The entire collection is secured in a limited access room and records for strain inventory and distribution are maintained on the collection database system. High priority microbial strains held only as frozen preparations under liquid nitrogen vapor phase will be duplicated and shipped to the National Center for Genetic Resources Preservation. NCGRP for backup in a liquid nitrogen freezer dedicated for microbial germplasm. Strains will be freely distributed to the scientific community worldwide but requestors must provide required documentation or permits before animal or plant pathogenic strains or those requiring Biosafety Level II confinement are distributed. Through phylogenetic analysis of sequences from multiple gene loci, evaluate the diversity and systematics of actinomycetes, Bacillus, Aspergillus, and yeasts of importance to agriculture, food safety, and biotechnology. A multilocus genotyping assay previously developed for identification of FHB species and trichothecene chemotypes will be applied to a global collection of FHB isolates to determine the current distribution and trichothecene chemotype diversity of Fusarium graminearum and F. asiacticum populations. Population diversity and relatedness will then be assessed using a published panel of variable number tandem repeat markers. Differences in pathogen fitness and aggressiveness in individual populations will be evaluated by determining a range of phenotypic characteristics, such as growth, reproduction, and toxin production. The overall goals of this project are to enhance the Agricultural Research Service (ARS) Culture Collection through acquisition of novel microbial germplasm and to characterize this germplasm genetically through gene sequence analysis. A total of 811 strains have been accessioned into the general collection and 149 deposits made into the Patent Collection. The Patent Culture Collection has distributed 337 strains including 179 to scientists in the United States, and 158 to foreign scientists. Strain distributions from the general collection totaled approximately 7,828, including 836 strains to the Institute of Genomic Biology, University of Illinois, to complete the ARS contribution to a collaborative research project, 1,501 to ARS scientists, 3,648 to other non-ARS scientists in the United States, and 1,843 to foreign scientists. The ARS Culture Collection website now has 12,425 strain records available in the public access catalog, had over 24,252 visitors from over 120 different countries and has been indexed by at least 79 different search engines. The online strain request module for the Culture Collection database system/website has facilitated the processing and tracking of strain requests using the collection staff. These activities provide for continued preservation of agriculturally and biotechnologically significant microbial germplasm and distribution to researchers in ARS as well as throughout the world. Continued collaboration with scientists at the Institute of Genomic Biology, University of Illinois, through a Material Transfer Agreement and cooperative agreement has been leveraged to provide raw sequence data for the house-keeping genes atpD, rpoB, and trpB for approximately 1,400 strains of actinomycetes of the genus Streptomyces, including both type of strains as well as uncharacterized strains in support of project objectives. The data are being assembled and organized into a web-based online identification database which will be made available to the scientific community worldwide. The identification database is being tested continually as the data are processed and entered and several new species have been detected within the strain collection. Two new methanol- utilizing yeast species, Ogataea saltuana and Ogatae parapolymorpha, were discovered within the holdings of the Yeast Culture Collection. Methanol- utilizing yeasts have been genetically modified in the past to produce large quantities of recombinant proteins and this discovery provides molecular biologists with novel microorganisms for biotechnological exploitation. In regard to the Fusarium Head Blight (FHB) research component of the project, a population of nivalenol-producing Fusarium cereal pathogens was discovered to be present in the U.S. for the first time. Nivalenol is of greater public health concern than deoxynivalenol, which is produced by most FHB populations in the U.S. The identification of a nivalenol-producing population in the U.S. indicates the need for additional monitoring, and for the development and use of rapid mycotoxin test kits capable of detecting nivalenol and differentiating it from the more common deoxynivalenol. Accomplishments 01 Molecular characterization of priority microbial genetic resources. The biodiversity of much of the microbial germplasm held in the Agricultural Research Service (ARS) Culture Collection in Peoria, IL, is not known because of limited characterization for many strains, making it difficul to assess its real or potential value by customers involved in agricultural and biotechnology research. The diversity of various groups of microbes within the Collection was estimated, particularly for poorly characterized isolates, based on the sequences of various genes. The identification system being developed for the actinomycete genus Streptomyces, whose species produce many of the medically important antibiotics, has already demonstrated the presence of unrecognized new species. In collaboration with scientists at the Institute of Genomic Biology, University of Illinois, scientists in the ARS Bacterial Foodbor Pathogens and Mycology Research Unit, National Center for Agricultural Utilization Research (NCAUR), Peoria, IL, discovered over 400 bacterial strains with the genes necessary to produce novel natural products, such as antibiotics. These research accomplishments contribute to the characterization of germplasm held in the Collection and provide knowled regarding potential uses in biotechnology, crop production, and food safety. As a result of the efforts to preserve and characterize the strains within the Collection, during the past year, 8,165 strains from the ARS Culture Collection were sent out in response to requests from industry, academic, and government scientists in 57 countries, which included requests from 464 different scientists in the U.S. 02 Identification of a new cereal pathogen population in the United States. Fusarium head blight [FHB] is a disease of cereal crops, caused by a fungal pathogen, which results in significant economic and health proble throughout the world. In collaboration with scientists at the Agricultur Research Service (ARS) Cereal Disease Laboratory in St. Paul, MN, scientists in the Agricultural Research Service (ARS) Bacterial Foodborn Pathogens and Mycology Research Unit, National Center for Agricultural Utilization Research, Peoria, IL, identified the first significant U.S. population of FHB pathogens that can contaminate grain with the mycotoxi nivalenol (NIV). This is significant because NIV can be more toxic to humans and livestock than the toxin deoxynivalenol, or DON, which is produced by previously recognized FHB populations in the U.S. These results alert grain producers and processors to the possible presence of NIV in grain, and indicate the need to utilize, as appropriate, mycotoxi detection kits that are capable of detecting NIV. In addition, by providing plant breeders with accurate information about the spectrum of FHB pathogens present in U.S. fields, these data will be of use to cerea breeding programs aimed at developing broad-based resistance to fungal pathogens.

Impacts
(N/A)

Publications

  • Kurtzman, C.P. 2011. Babjeviella Kurtzman & M. Suzuki (2010). In: Kurtzman, C.P., Fell, J.W., Boekhout, T., editors. The Yeasts, a Taxonomic Study. Volume 2, 5th edition. New York, NY: Elsevier. p. 329-331.
  • Kurtzman, C.P., de Hoog, G.S. 2011. Cephaloascus Hanawa (1920). In: Kurtzman, C.P., Fell, J.W., Boekhout, T., editors. The Yeasts, a Taxnomic Study. Volume 2, 5th edition. New York, NY: Elsevier. p. 341-344.
  • Kurtzman, C.P. 2011. Lodderomyces van der Walt (1971). In: Kurtzman, C.P., Fell, J.W., Boekhout, T., editors. The Yeasts, a Taxonomic Study. Volume 2, 5th edition. New York, NY: Elsevier. p. 561-563.
  • Kurtzman, C.P. 2011. Hyphopichia von Arx & van der Walt (1976). In: Kurtzman, C.P., Fell, J.W., Boekhout, T., editors. The Yeasts, a Taxonomic Study. Volume 2, 5th edition. New York, NY: Elsevier. p. 435-438.
  • Kurtzman, C.P. 2011. Phaffomyces Y. Yamada, Higashi, S. Ando & Mikata (1997). In: Kurtzman, C.P., Fell, J.W., Boekhout, T., editors. The Yeasts, a Taxonomic Study. Volume 2, 5th edition. New York, NY: Elsevier. p. 681- 684.
  • Kurtzman, C.P. 2011. Starmera Y. Yamada, Higashi, Ando & Mikata (1997). In: Kurtzman, C.P., Fell, J.W., Boekhout, T., editors. The Yeasts, a Taxonomic Study. Volume 2, 5th edition. New York, NY: Elsevier. p. 805-810.
  • Kurtzman, C.P. 2011. Millerozyma Kurtzman & M. Suzuki (2010). In: Kurtzman, C.P., Fell, J.W., Boekhout, T., editors. The Yeasts, a Taxonomic Study. Volume 2, 5th edition. New York, NY: Elsevier. p. 625-628.
  • Kurtzman, C.P. 2011. Scheffersomyces Kurtzman & M. Suzuki (2010). In: Kurtzman, C.P., Fell, J.W., Boekhout, T., editors. The Yeasts, a Taxonomic Study. Volume 2, 5th edition. New York, NY: Elsevier. p. 773-777.
  • Kurtzman, C.P. 2011. Priceomyces M. Suzuki & Kurtzman (2010). In: Kurtzman, C.P., Fell, J.W., Boekhout, T., editors. The Yeasts, a Taxonomic Study. Volume 2, 5th edition. New York, NY: Elsevier. p. 719-724.
  • Kurtzman, C.P. 2011. Yamadazyma Billon-Grand (1989). In: Kurtzman, C.P., Fell, J.W., Boekhout, T., editors. The Yeasts, a Taxonomic Study. Volume 2, 5th edition. New York, NY: Elsevier. p. 919-925.
  • Kurtzman, C.P. 2011. Peterozyma Kurtzman & Robnett (2010). In: Kurtzman, C. P., Fell, J.W., Boekhout, T., editors. The Yeasts, a Taxonomic Study. Volume 2, 5th edition. New York, NY: Elsevier. p. 677-680.
  • Kurtzman, C.P. 2011. Zygotorulaspora Kurtzman (2003). In: Kurtzman, C.P., Fell, J.W., Boekhout, T., editors. The Yeasts, a Taxonomic Study. Volume 2, 5th edition. New York, NY: Elsevier. p. 949-951.
  • Kurtzman, C.P. 2011. Trigonopsis Schachner emend. Kurtzman & Robnett (2007) . In: Kurtzman, C.P., Fell, J.W., Boekhout, T., editors. The Yeasts, a Taxonomic Study. Volume 2, 5th edition. New York, NY: Elsevier. p. 1331- 1335.
  • Smith, M.Th., Kurtzman, C.P. 2011. Lipomyces Lodder & Kreger-van Rij (1952) . In: Kurtzman, C.P., Fell, J.W., Boekhout, T., editors. The Yeasts, a Taxonomic Study. Volume 2, 5th edition. New York, NY: Elsevier. p. 545-560.
  • Smith, M.Th., de Hoog, G.S., Malloch, D., Kurtzman, C.P. 2011. Trichomonascus H.S. Jackson emend. Kurtzman & Robnett (2007). In: Kurtzman, C.P., Fell, J.W., Boekhout. T., editors. Volume 2, 5th edition. New York, NY: Elsevier. p. 875-881.
  • Lachance, M., Kurtzman, C.P. 2011. Kodamaea Y. Yamada, T. Suzuki, Matsuda & Mikata emend. Rosa, Lachance, Starmer, Barker, Bowles & Schlag-Edler (1999). In: Kurtzman, C.P., Fell, J.W., Boekhout, T., editors. The Yeasts, a Taxonomic Study. Volume 2, 5th edition. New York, NY: Elsevier. p. 483- 490.
  • Smith, M.Th., de Hoog, G., Statzell-Tallman, A., Kurtzman, C.P. 2011. Blastobotrys von Klopotek (1967). In: Kurtzman, C.P., Fell, J.W., Boekhout, T., editors. The Yeasts, a Taxonomic Study. Volume 2, 5th edition. New York, NY: Elsevier. p. 959-977.
  • Kurtzman, C.P., Smith, M.Th. 2011. Myxozyma van der Walt, Weijman & von Arx (1981). In: Kurtzman, C.P., Fell, J.W., Boekhout, T., editors. The Yeasts, a Taxonomic Study. Volume 2, 5th edition. New York, NY: Elsevier. p. 1303-1312.
  • Kurtzman, C.P. 2011. Wickerhamia Soneda (1960). In: Kurtzman, C.P., Fell, J.W., Boekhout, T., editors. The Yeasts, a Taxonomic Study. Volume 2, 5th edition. New York, NY: Elsevier. p. 887-889.
  • Suzuki, M., Kurtzman, C.P. 2011. Schwanniomyces Klocker emend. M. Suzuki & Kurtzman (2010). In: Kurtzman, C.P., Fell, J.W., Boekhout, T., editors. The Yeasts, a Taxonomic Study. Volume 2, 5th edition. New York, NY: Elsevier. p. 785-794.
  • Suzuki, M., Prasad, G.S., Kurtzman, C.P. 2011. Debaryomyces Lodder & Kreger-van Rij (1952). In: Kurtzman, C.P., Fell, J.W., Boekhout, T., editors. The Yeasts, a Taxonomic Study. Volume 2, 5th edition. New York, NY: Elsevier. p. 361-372.
  • Kurtzman, C.P., Fell, J.W., Boekhout, T. 2011. Definition, classification and nomenclature of the yeasts. In: Kurtzman, C.P., Fell, J.W., Boekhout, T., editors. The Yeasts, a Taxonomic Study. Volume 1, 5th edition. New York, NY: Elsevier. p. 3-5.
  • Bandoni, R.J., Weiss, M., Boekhout, T., Fell, J.W., Kurtzman, C.P. 2011. Glossary of terms used in this book. In: Kurtzman, C.P., Fell, J.W., Boekhout, T., editors. The Yeasts, a Taxonomic Study. Volume 1, 5th edition. New York, NY: Elsevier. p. 279-289.
  • Payne, R.W., Kurtzman, C.P., Fell, J.W., Boekhout, T. 2011. Key to species and summary of species characteristics. In: Kurtzman, C.P., Fell, J.W., Boekhout, T., editors. The Yeasts, a Taxonomic Study. Volume 1, 5th edition. New York, NY: Elsevier. p. 175-277.
  • Lachance, M.-A., Boekhout, T., Scorzetti, G., Fell, J.W., Kurtzman, C.P. 2011. Candida Berkhout (1923). In: Kurtzman, C.P., Fell, J.W., Boekhout, T. , editors. The Yeasts, a Taxonomic Study. Volume 2, 5th edition. New York, NY: Elsevier. p. 987-1278.
  • Park, B., Park, J., Cheong, K., Choi, J., Jung, K., Lee, Y., Ward, T.J., O Donnell, K., Geiser, D.M., Kang, S. 2010. Cyber-infrastructure for Fusarium (CiF): Three integrated platforms supporting strain identification, phylogenetics, comparative genomics, and knowledge sharing. Nucleic Acids Research. DOI: 10.1093/nar/gkq1166.
  • Koganti, S., Kuo, T., Kurtzman, C.P., Smith, N., Ju, L. 2011. Production of arabitol from glycerol: Strain screening and study of factors affecting production yield. Applied Microbiology and Biotechnology. 90(1):257-267.
  • Kurtzman, C.P. 2010. Description of new yeast species � is one strain enough? Bergey's International Society for Microbial Systematics Bulletin. 1(pt 1):17-24.
  • Manitchotpisit, P., Skory, C.D., Peterson, S.W., Price, N.P., Vermillion, K., Leathers, T.D. 2012. Poly (beta-L-malic acid) production by diverse phylogenetic clades of Aureobasidium pullulans. Journal of Industrial Microbiology and Biotechnology. 39(1):125-132. DOI: 10.1007/s10295-011- 1007-7
  • Labeda, D.P., Goodfellow, M., Chun, J., Zhi, X.Y., Li, W.J. 2011. Reassessment of the systematics of the suborder Pseudonocardineae: transfer of the genera within the family Actinosynnemataceae Labeda and Kroppenstedt 2000 emend. Zhi et al. 2009 into an emended family Pseudonocardiaceae.... International Journal of Systematic and Evolutionary Microbiology. 61(6)1259-1264.
  • Kim, B., Brown, R., Labeda, D.P., Goodfellow, M. 2011. Reclassification of "Dactylosporangium variesporum" as Saccharothrix variisporea corrig. (ex Tomita et al. 1977) sp. nov., nom. rev. International Journal of Systematic and Evolutionary Microbiology. 61(2):310-314.
  • Kurtzman, C.P. 2011. Saturnispora Liu & Kurtzman (1991). In: Kurtzman, C.P. , Fell, J.W., Boekhout, T., editors. The Yeasts, a Taxonomic Study. Volume 2, 5th edition. New York, NY: Elsevier. p. 765-772.
  • Graham, J.R., Ellis, J.D., Benda, N.D., Kurtzman, C.P., Boucias, D.G. 2011. Kodamaea ohmeri (Ascomycota: Saccharomycotina) presence in commercial Bombus impatiens Cresson and feral Bombus pensylvanicus DeGeer (Hymenoptera: Apidae) colonies. Journal of Apicultural Research. 50(3):218- 226.
  • Kurtzman, C.P. 2011. Sugiyamaella Kurtzman & Robnett (2007). In: Kurtzman, C.P., Fell, J.W., Boekhout, T., editors. The Yeasts, a Taxonomic Study. Volume 2, 5th edition. New York, NY: Elsevier. p. 817-822.
  • Kurtzman, C.P., Price, N.P., Ray, K.J., Kuo, T. 2010. Production of sophorolipids biosurfactants by multiple species of the Starmerella (Candida) bombicola yeast clade. FEMS Microbiology Letters. 311(2):140-146.
  • Peter, G., Dlauchy, D., Tornai-Lehoczki, J., Suzuki, M., Kurtzman, C.P. 2011. Spencermartinsiella europaea gen. nov., sp. nov., a new member of the family Trichomonascaceae. International Journal of Systematic and Evolutionary Microbiology. 61(4):993-1000.
  • Gilbert, J., Clear, R.M., Ward, T.J., Gaba, D., Tekauz, A., Turkington, T. K., Woods, S.M., Nowicki, T., O Donnell, K. 2010. Relative aggressiveness and production of 3- or 15-acetyl deoxynivalenol and deoxynivalenol by Fusarium graminearum in spring wheat. Canadian Journal of Plant Pathology. 32(2):146.152.
  • Gale, L.R., Harrison, S.A., Ward, T.J., O Donnell, K., Milus, E.A., Gale, S.W., Kistler, H.C. 2011. Nivalenol-type populations of Fusarium graminearum and F. asiaticum are prevalent on wheat in Southern Louisiana. Phytopathology. 101(1):124-134.


Progress 10/01/09 to 09/30/10

Outputs
Progress Report Objectives (from AD-416) Objective 1: Strategically expand the genetic diversity in the ARS Culture Collection and improve associated information for priority microbial genetic resources. Sub-objective 1.A. Acquire from diverse sources samples of food-borne pathogenic bacteria, actinobacteria from equine sources, basidiomycetous yeasts, plant pathogenic fungi, and grain storage molds to fill current gaps in the ARS Culture Collection for these priority microbial strains. Sub-objective 1.B. In consultation with the microbial research community, identify microbial genetic resources associated with discontinued research programs, or held by researchers who are nearing retirement, and attempt to acquire those of strategic importance to current or future agricultural research programs. Objective 2: Conserve priority microbial genetic resources efficiently and effectively, and distribute them and associated information worldwide. Sub-objective 2.A. Conserve more than 90,000 accessions of priority microbial genetic resources and associated information, emphasizing food- borne pathogenic bacteria, actinobacteria from equine sources, basidiomycetous yeasts, plant pathogenic fungi, and grain storage molds, as well as microbes of biomedical and biotechnological importance. Sub- objective 2.B. Back-up at the National Center for Genetic Resources Preservation (NCGRP) approximately 15,000 strains (emphasizing Fusarium) that are currently preserved under liquid nitrogen vapor only at the National Center for Agricultural Utilization Research (NCAUR). Sub- objective 2.C. Continue to improve data management and technology transfer procedures, emphasizing improvements in user interface for the public access catalog system. Sub-Objective 2.D. Distribute on request microbial accessions and information that meet the specific needs of agricultural, biomedical, and biotechnological researchers. Objective 3: Strategically characterize (�genotype�) and evaluate (�phenotype�) priority microbial genetic resources through multigene analyses, and with key morphological, physiological, and biochemical descriptors. Sub- objective 3.A. Develop and apply multigene markers for phylogenetic and genetic diversity analyses of priority microbial genetic resources. Incorporate characterization data into GRIN and/or other databases, and apply the data to providing accurate taxonomic identifications, as well as to predicting the agricultural and biotechnological utility of newly discovered taxa. Sub-objective 3.B. Determine the phenotypic diversity and elucidate the population genetic structure for the Fusarium Head Blight (FHB) species Fusarium graminearum and F. asiacticum. Map their worldwide distribution, as a first step of establishing a molecular surveillance system for the early detection of Fusarium populations introduced to North America. Approach (from AD-416) New species and novel strains of known species of plant pathogens and mycotoxigenic fungi, food-borne pathogens, actinobacteria important to animal health and biotechnology, and yeasts will be isolated from nature or acquired from reports in the literature and from cooperators worldwide. New strain accessions will be cataloged in the collection database, preserved by lyophilization and/or freezing in liquid nitrogen vapor where appropriate, and information related to well characterized strains will be made publicly available on the Collection website. Information provided by ARS Program leadership, national and international microbiology societies and culture collection organizations will identify microbial collections in danger of being lost and important collections will be acquired and accessioned where existing resources permit. The entire collection is secured in a limited access room and records for strain inventory and distribution are maintained on the collection database system. High priority microbial strains held only as frozen preparations under liquid nitrogen vapor phase will be duplicated and shipped to NCGRP for backup in a liquid nitrogen freezer dedicated for microbial germplasm. Strains will be freely distributed to the scientific community worldwide but requestors must provide required documentation or permits before animal or plant pathogenic strains or those requiring Biosafety Level II confinement are distributed. Through phylogenetic analysis of sequences from multiple gene loci, evaluate the diversity and systematics of actinomycetes, Bacillus, Aspergillus, and yeasts of importance to agriculture, food safety, and biotechnology. A multilocus genotyping assay previously developed for identification of FHB species and trichothecene chemotypes will be applied to a global collection of FHB isolates to determine the current distribution and trichothecene chemotype diversity of Fusarium graminearum and F. asiacticum populations. Population diversity and relatedness will then be assessed using a published panel of variable number tandem repeat markers. Differences in pathogen fitness and aggressiveness in individual populations will be evaluated by determining a range of phenotypic characteristics, such as growth, reproduction, and toxin production. The overall goals of this project are to enhance the Agricultural Research Service (ARS) Culture Collection through acquisition of novel microbial germplasm and to characterize this germplasm genetically through gene sequence analysis. A total of 3,518 strains have been accessioned into the general collection and 89 deposits made into the Patent Collection. The Patent Culture Collection has distributed 415 strains (since June 1, 2009), including 272 to scientists in the United States, and 183 to foreign scientists. Strain distributions from the general collection totaled approximately 15,368 (since June 1, 2009), including 6,507 strains to the Institute of Genomic Biology (IGB), University of Illinois as the ARS contribution to a collaborative research project, 2,547 to ARS scientists, 3,747 to non-ARS scientists in the United States, and 2,567 to foreign scientists. The ARS Culture Collection website now has 11,843 strain records available in the public access catalog, had over 21,600 visitors from 124 different countries and has been indexed by 82 different search engines. The online strain request module for the Culture Collection database system/website went live on January 1, 2010, greatly facilitating strain requests by customers and simplifying request fulfillment and tracking by the collection staff. These activities provide for continued preservation of agriculturally and biotechnologically significant microbial germplasm and distribution to researchers in ARS as well as throughout the world. Collaboration with scientists at the IGB, University of Illinois, has been leveraged to identify 190 uncharacterized strains from the ARS Actinobacterial Culture Collection through the 16S ribosomal DNA (rRNA) gene sequences provided by the IGB high-throughput sequencing facility. This collaboration is also facilitating the development and testing of a multi-gene sequence database by providing sequence for more than 900 known and unidentified Streptomyces strains. In addition, phylogenetic analyses to study the genetic relatedness of the genus Bacillus has resulted in the description of a new subspecies. Lastly, it has been determined that ochratoxigenic Aspergillus niger strains can be disinguished from non-toxigenic A. niger strains on the basis of calmodulin gene sequences, providing a basis for the development of gene probes for rapid detection of toxin producers. Accomplishments 01 MOLECULAR CHARACTERIZATION OF PRIORITY MICROBIAL GENETIC RESOURCES. The biodiversity of much of the microbial germplasm held in the Agricultural Research Service (ARS) Culture Collection located at the National Center for Agricultural Utilization Research Center in Peoria, Illinois, is not known because of limited characterization for many strains, making it difficult to assess its real or potential value by customers involved in agricultural and biotechnology research. Molecular diversity was estimat particularly for poorly characterized isolates, based on the sequences various genes. The partial sequences of four different protein-coding genes for plant pathogenic Streptomyces species and several thought to b closely related to them demonstrated that the 10 different pathogenic species can be discriminated and identified based on these gene sequence Additionally, similar sequences are being collected for all streptomycet in the ARS Actinobacterial Culture Collection by leveraging a National Institutes of Health (NIH)-funded collaboration with the Institute of Genomic Biology (IGB), University of Illinois. A similar study of the fungal genus Hamigera and the genera of all ascomycete yeasts was also completed, providing an overview of genetic relationships that are usefu for prediction of utility of species agricultural, biotechnological and medical applications. The knowledge obtained from these research accomplishments provides improved characterization of the germplasm held in the Collection and discernment of potential uses in biotechnology as well as insights for disease control, toxin reduction, and prevention of food spoilage. 02 CHARACTERIZATION OF AN INTRODUCED CEREAL PATHOGEN POPULATION. Fusarium head blight [FHB] is a disease of cereal crops, caused by a fungal pathogen, which results in significant economic and health problems throughout the world. A novel population of FHB pathogen was found in Louisiana, including a fungal species previously reported only from Asia and South America. In addition, FHB pathogens producing the mycotoxin nivalenol, considered to be rare in the United States, were found at hig frequencies. These results are critical to promoting food safety and cereal production through improved detection of mycotoxin-contaminated grain and through variety improvement efforts that account for the entir spectrum of pathogen and toxin types. Field tests for differences in tox production and aggressiveness on wheat in Germany and Canada using strai representing the previously dominant (15-acetyldeoxynivalenol (15ADON) population) and novel (3-acetyldeoxynivalenol (3ADON)) populations indicated that 3ADON isolates produced more toxin and could pose a great risk to food safety, but aggressiveness and deoxynivalenol (DON) production of 3ADON and 15ADON chemotypes was quite similar on highly resistant lines of wheat, indicating that breeding and use of highly resistant lines should be an effective means of minimizing the threat to food safety posed by the novel 3ADON population. Infection of a susceptible wheat variety by members of the novel 3ADON population resul in grain that is more heavily contaminated with trichothecene toxins, while the 3ADON and 15ADON isolates produced essentially the same amount of toxin when infecting moderately resistant wheat varieties, suggesting that as the percentage of 3ADON strains increases, DON levels in cereals are likely to increase in epidemic years. The wider use of moderately resistant cultivars, however could help to mitigate the food safety impa of changes in the pathogen population.

Impacts
(N/A)

Publications

  • Labeda, D.P., Price, N.P., Donahue, J.M., Williams, N.M., Sells, S.F. 2009. Streptomyces atriruber sp. nov. and Streptomyces silaceus sp. nov.: New Species of Equine Origin. International Journal of Systematic and Evolutionary Microbiology. 59(11):2899-2903.
  • Nelson, D.M., Glawe, A.J., Labeda, D.P., Cann, I.K., Mackie, R.I. 2009. Paenibacillus tundrae sp. nov. and Paenibacillus xylanexedens sp. nov., Psychrotolerant, Xylan-Degrading, Bacteria from Alaskan Tundra. International Journal of Systematic and Evolutionary Microbiology. 59(pt. 7):1708-1714.
  • Balajee, S., Kano, R., Baddley, J.W., Moser, S.A., Marr, K.A., Alexander, B.D., Andes, D., Kontoyiannis, D.P., Perrone, G., Peterson, S.W., Brandt, M.E., Pappas, P.G., Chiller, T. 2009. Molecular Identification of Aspergillus Species: Transplant Associated Infection Surveillance Network (TRANSNET). Journal of Clinical Microbiology. 47(10):3138-3141.
  • Kato, A., Rooney, A.P., Furutani, Y., Hirose, S. 2010. Evolution of Trappin Genes in Mammals. BMC Evolutionary Biology. 10(31). Available: http://www.biomedcentral.com/1471-2148/10/31.
  • Connor, N., Sikorski, J., Rooney, A.P., Kopac, S., Koeppel, A.F., Burger, A., Cole, S.G., Perry, E.B., Krizanc, D., Field, N.C., Slaton, M., Cohan, F.M. 2010. Ecology of Speciation in the Genus Bacillus. Applied and Environmental Microbiology. 76(5):1349-1358.
  • Tamura, T., Ishida, Y., Otoguro, M., Hatano, K., Labeda, D.P., Price, N.P., Suzuki, K. 2008. Reclassification of Streptomyces caeruleus as a Synonym of Actinoalloteichus cyanogriseus and Reclassification of Streptomyces spheroides and Streptomyces laceyi as Later Synonyms of Streptomyces niveus. International Journal of Systematic and Evolutionary Microbiology. 58(12):2812-2814.
  • Von Der Ohe, C., Gauthier, V., Tamburic-Ilincic, L., Brule-Babel, A., Fernando, D.W., Clear, R., Ward, T.J., Miedaner, T. 2010. A Comparison of Aggressiveness and Deoxynivalenol Production Between Canadian Fusarium graminearum Isolates with 3-Acetyl and 15-Acetyldeoxynivalenol Chemotypes in Field-Grown Spring Wheat. European Journal of Plant Pathology. 127(3) :407-417.
  • Labeda, D.P., Price, N.P., Tan, G.A., Goodfellow, M., Klenk, H. 2010. Emendation of the Genus Actinokineospora Hasegawa 1988 and Transfer of Amycolatopsis fastidiosa Henssen et al. 1987 as Actinokineospora fastidiosa comb. nov. International Journal of Systematic and Evolutionary Microbiology. 60(6):1444-1449.
  • Rooney, A.P. 2009. Evolution of Moth Sex Pheromone Desaturases. Annals of the New York Academy of Sciences. 1170:506-510.


Progress 10/01/08 to 09/30/09

Outputs
Progress Report Objectives (from AD-416) Objective 1: Strategically expand the genetic diversity in the ARS Culture Collection and improve associated information for priority microbial genetic resources. Sub-objective 1.A. Acquire from diverse sources samples of food-borne pathogenic bacteria, actinobacteria from equine sources, basidiomycetous yeasts, plant pathogenic fungi, and grain storage molds to fill current gaps in the ARS Culture Collection for these priority microbial strains. Sub-objective 1.B. In consultation with the microbial research community, identify microbial genetic resources associated with discontinued research programs, or held by researchers who are nearing retirement, and attempt to acquire those of strategic importance to current or future agricultural research programs. Objective 2: Conserve priority microbial genetic resources efficiently and effectively, and distribute them and associated information worldwide. Sub-objective 2.A. Conserve more than 90,000 accessions of priority microbial genetic resources and associated information, emphasizing food- borne pathogenic bacteria, actinobacteria from equine sources, basidiomycetous yeasts, plant pathogenic fungi, and grain storage molds, as well as microbes of biomedical and biotechnological importance. Sub- objective 2.B. Back-up at the National Center for Genetic Resources Preservation (NCGRP) approximately 15,000 strains (emphasizing Fusarium) that are currently preserved under liquid nitrogen vapor only at the National Center for Agricultural Utilization Research (NCAUR). Sub- objective 2.C. Continue to improve data management and technology transfer procedures, emphasizing improvements in user interface for the public access catalog system. Sub-Objective 2.D. Distribute on request microbial accessions and information that meet the specific needs of agricultural, biomedical, and biotechnological researchers. Objective 3: Strategically characterize (�genotype�) and evaluate (�phenotype�) priority microbial genetic resources through multigene analyses, and with key morphological, physiological, and biochemical descriptors. Sub- objective 3.A. Develop and apply multigene markers for phylogenetic and genetic diversity analyses of priority microbial genetic resources. Incorporate characterization data into GRIN and/or other databases, and apply the data to providing accurate taxonomic identifications, as well as to predicting the agricultural and biotechnological utility of newly discovered taxa. Sub-objective 3.B. Determine the phenotypic diversity and elucidate the population genetic structure for the Fusarium Head Blight (FHB) species Fusarium graminearum and F. asiacticum. Map their worldwide distribution, as a first step of establishing a molecular surveillance system for the early detection of Fusarium populations introduced to North America. Approach (from AD-416) New species and novel strains of known species of plant pathogens and mycotoxigenic fungi, food-borne pathogens, actinobacteria important to animal health and biotechnology, and yeasts will be isolated from nature or acquired from reports in the literature and from cooperators worldwide. New strain accessions will be cataloged in the collection database, preserved by lyophilization and/or freezing in liquid nitrogen vapor where appropriate, and information related to well characterized strains will be made publicly available on the Collection website. Information provided by ARS Program leadership, national and international microbiology societies and culture collection organizations will identify microbial collections in danger of being lost and important collections will be acquired and accessioned where existing resources permit. The entire collection is secured in a limited access room and records for strain inventory and distribution are maintained on the collection database system. High priority microbial strains held only as frozen preparations under liquid nitrogen vapor phase will be duplicated and shipped to NCGRP for backup in a liquid nitrogen freezer dedicated for microbial germplasm. Strains will be freely distributed to the scientific community worldwide but requestors must provide required documentation or permits before animal or plant pathogenic strains or those requiring Biosafety Level II confinement are distributed. Through phylogenetic analysis of sequences from multiple gene loci, evaluate the diversity and systematics of actinomycetes, Bacillus, Aspergillus, and yeasts of importance to agriculture, food safety, and biotechnology. A multilocus genotyping assay previously developed for identification of FHB species and trichothecene chemotypes will be applied to a global collection of FHB isolates to determine the current distribution and trichothecene chemotype diversity of Fusarium graminearum and F. asiacticum populations. Population diversity and relatedness will then be assessed using a published panel of variable number tandem repeat markers. Differences in pathogen fitness and aggressiveness in individual populations will be evaluated by determining a range of phenotypic characteristics, such as growth, reproduction, and toxin production. Significant Activities that Support Special Target Populations Collections of well characterized microbial germplasm are an invaluable resource for agricultural and biotechnology research. The overall goals of this project are to enhance the Agricultural Research Service (ARS) Culture Collection through acquisition of novel microbial germplasm and to characterize this germplasm genetically through gene sequence analysis. In FY 2008, a total of 3,133 strains have been accessioned into the general collection, including large collections of Listeria and Salmonella strains and 137 deposits made into the Patent Collection. The Patent Culture Collection has distributed 468 strains (since July 1, 2008) , including 41 to ARS scientists, 239 to non-ARS scientists in the United States, and 188 to foreign scientists. Strain distributions from the general collection totaled 4,124 (since July 1, 2007), including 719 to ARS scientists, 1,838 to non-ARS scientists in the United States, and 2, 039 to foreign scientists. The ARS Culture Collection website now has 11, 217 strain records available in the public access catalog, had over 21, 000 visitors from 129 different countries and has been indexed by 69 different search engines. The development of an online, automated system for client requests for microbial germplasm from the collection is in progress. These activities provide for continued preservation of agriculturally and biotechnologically significant microbial germplasm and distribution to researchers in ARS as well as throughout the world. Phylogenetic analyses of the genus Bacillus has resulted in the description of a new subspecies. A phylogenetic study of plant pathogenic Streptomyces based on the sequences of 4 house-keeping genes is almost completed and will be expanded to encompass species representing the entire genus. It has been determined that ochratoxigenic Aspergillus niger strains can be disinguished from non-toxigenic A. niger strains on the basis of calmodulin gene sequences, providing a basis for the development of gene probes for rapid detection of toxin producers. Multigene sequence analysis resolved genus assignments of the biotechnologically important yeast species that can grow on methanol as a sole source of carbon. The majority of the species were placed in the genus Ogataea, but three of the species were recognized as separate from Ogataea and their earlier placement in the genus Komagataella was confirmed. Progress achieved in FY2008 has potential scientific impact for academic, government,and industrial researchers by providing new and better characterized microbial germplasm that can be exploited in many areas of research such as those related to energy production disease control in plants and animals and food safety. Technology Transfer Number of New/Active MTAs(providing only): 1 Number of Web Sites managed: 1

Impacts
(N/A)

Publications

  • Blackwell, M., Kurtzman, C.P., Lachance, M., Suh, S. 2009. Saccharomycotina, Saccharomycetales. Available: http://www.tolweb. org/Saccharomycotina/29043/2009.01.22.
  • Koeppel, A., Perry, E., Sikorski, J., Krizanc, D., Warner, A., Ward, D.M., Rooney, A.P., Brambilla, E., Connor, N., Ratcliff, R.M., Nevo, E., Cohan, F.M. 2008. Identifying the Fundamental Units of Bacterial Diversity: A Paradigm Shift to Incorporate Ecology into Bacterial Systematics. Proceedings of the National Academy of Sciences. 105(7):2504-2509.
  • Mertens, J.A., Burdick, R.C., Rooney, A.P. 2008. Identification, Biochemical Characterization, and Evolution of the Rhizopus oryzae 99-880 Polygalacturonase Gene Family. Fungal Genetics and Biology. 45(12):1616- 1624.
  • Balajee, A., Baddley, J.W., Peterson, S.W., Nickle, D., Varga, J., Boey, A. , Lass-Florl, C., Samson, R.A. 2009. Aspergillus alabamensis, a New Clinically Relevant Species in the Section Terrei. Eukaryotic Cell. 8(5) :713-722.
  • Labeda, D.P., Kroppenstedt, R.M. 2008. Proposal for the new genus Allokutzneria gen. nov. within the suborder Pseudonocardineae and transfer of Kibdelosporangium albatum Tomita et al. 1993 as Allokutzneria albata comb. nov. International Journal of Systematic and Evolutionary Microbiology. 58:1472-1475.
  • Vaishampayan, P., Miyashita, M., Ohnishi, A., Satomi, M., Rooney, A.P., Duc, M.T., Venkateswaran, K. 2009. Description of Rummeliibacillus stabekisii gen. nov., sp. nov. and Reclassification of Bacillus pycnus Nakamura et al. 2002 as Rummeliibacillus pycnus comb. nov. International Journal of Systematic and Evolutionary Microbiology. 59(Pt 5):1094-1099.
  • Kurtzman, C.P., Labeda, D.P. 2009. Type Culture Collections and Their Databases. In: Schaechter, M. editor. Encyclopedia of Microbiology. Volume 6, 3rd edition. Oxford, United Kingdom: Elsevier. p. 306-312.
  • Suga, H., Karugia, G.W., Ward, T.J., Gale, L.R., Tomimura, K., Nakajima, T. , Miyasaka, A., Koizumi, S., Kageyama, K., Hyakumachi, M. 2008. Molecular Characterization of the Fusarium graminearum Species Complex in Japan. Phytopathology. 98(2):159-166.
  • Frank, D.N., Wysocki, A., Specht-Glick, D., Rooney, A.P., Feldman, R.A., St Amand, A.L., Pace, N.R., Trent, J.D. 2009. Microbial Diversity in Chronic Open Wounds. Journal of Wound Repair and Regeneration. 17(2):163- 172.
  • Bishop, J.A., Chase, N., Kurtzman, C.P., Merz, W.G. 2008. Production of White Colonies on CHROMagar Candida(TM) by Members of the Candida glabrata Clade and Other Species with Overlapping Phenotypic Traits. Journal of Clinical Microbiology. 46(10):3498-3500.
  • Bishop, J.A., Chase, N., Magill, S.S., Kurtzman, C.P., Fiandaca, M.J., Merz, W.G. 2008. Candida bracarensis Detected Among Isolates of Candida glabrata by Petide Nucleic Acid Fluorescence in Situ Hybirdization: Susceptibility Data and Documentation of Presumed Infection. Journal of Clinical Microbiology. 46(2):443-446.
  • Balajee, S.A., Borman, A.M., Brandt, M.E., Cano, J., Cuenca-Estrella, M., Dannaoui, E., Guarro, J., Haase, G., Kibbler, C.C., Meyer, W., O Donnell, K., Petti, C.A., Rodriguez-Tudela, J.L., Sutton, D., Velegraki, A., Wickes, B.L. 2009. Sequence-Based Identification of Aspergillus, Fusarium, and Mucorales in the Clinical Laboratory: Where Are We and Where Should We Go From Here? Journal of Clinical Microbiology. 47(4):877-884.