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United States Department of Agriculture

Agricultural Research Service

Research Project: MANAGEMENT AND GENETIC CHARACTERIZATION OF AGRICULTURAL AND BIOTECHNOLOGICAL MICROBIAL RESOURCES
2012 Annual Report


1a.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.


1b.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.


3.Progress Report:
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.


4.Accomplishments
1. 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 Unit (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 and enabled 1925 patent applications during the last five years.

2. Identification of novel biotechnological potential among actinobacteria in the ARS Culture Collection. The potential utility of the biodiversity represented by the microbial strains held in the ARS Culture Collection in Peoria, IL, is not fully known because of the limited characterization of many strains in this collection. Scientists in the Bacterial Foodborne Pathogens and Mycology Research Unit (BFP), USDA, ARS, National Center for 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 that 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 in the holdings of the ARS Culture Collection may be greater than originally thought, increasing its value as a resource for new product discovery.


Review Publications
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.

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., 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.

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.

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.

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.

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.

Last Modified: 11/25/2014
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