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United States Department of Agriculture

Agricultural Research Service

Research Project: Systematics and Diagnostics of Emerging and Quarantine-Significant Plant Pathogenic Fungi

Location: Systematic Mycology and Microbiology

2013 Annual Report


1a.Objectives (from AD-416):
1. Identify and describe invasive and emerging plant pathogens, including rust and smut pathogens of quarantine significance; canker and anthracnose pathogens of tree, forage, and oil crops; and fungi associated with potential biofuel crops. 2. Develop robust phylogenetic classification systems for plant-associated fungi to better predict pathogen behavior and to enable development of accurate diagnostic methods for closely related or morphologically similar species.


1b.Approach (from AD-416):
Fungi in these groups will be collected, cultured and characterized microscopically to screen for taxa of interest and provide provisional identifications. For smut and bunt fungi, initial focus will be on species of Tilletia closely related to dwarf bunt, T. controversa. Species of Ustilago including segregate genera and Urocystis (flag smut) will also be collected and characterized as encountered. Species of Phomopsis and related canker pathogens in the Gnomoniaceae will be the major focus among the canker fungi as well as Neonectria and related nectriaceous fungi. Rust and anthracnose fungi (primarily Colletotrichum) associated with sugarcane, switchgrass, and turf grasses will also be collected and characterized. PCR will be performed to amplify ribosomal and protein-coding genes, including ITS, LSU, EF1-alpha, and RNA polymerase gene regions. For determining initial identities and superficial relationships of newly obtained taxa, the ITS regions of the nuclear ribosomal repeat unit will be sequenced, compared with existing data in GenBank, and correlated with morphological data. For determining species relationships across these genera and relationships of genera, the ITS, LSU, tef1-a, ß-tub, and rpb gene regions will be analyzed along with other genes to be determined including the single copy DNA lyase Apn2, Mat1M72F/R for the combined Mat1, intergenic region and 5’ Apn2 and the single copy SOD2 gene. Whole genome DNA sequencing from Colletotrichum isolates will be performed using short read next generation sequencing technology from genomic DNA. Population-level and phylogenomic relationships of anthracnose pathogens of grasses will be determined. For population scale analyses, genotypic data will be combined into multilocus haplotypes for each isolate and used to perform population genetic analyses. Coalescent-based analyses may be applied in an interactive manner based on observed population considerations to provide estimates of parameters such as migration, historical population sizes, and test for evolutionary scenarios that reflect various demographic outcomes. As new pathogens in these groups emerge, species previously unknown to science yet related to known pathogens in these groups will be described, illustrated and characterized. Taxonomic monographs will be published and made available as online resources as well as PCR-based diagnostic assays for pathogens of agronomic significance.


3.Progress Report:
Progress was made on both objectives, which fall under Problem Statement 1, Diagnostics, Etiology and Systematics of Plant Disease and use molecular and morphological approaches to classify and characterize taxonomically difficult groups of disease-causing fungi. This enables accurate identifications, which are essential for controlling the diseases these fungi cause, to breed for resistance, and to alleviate potential plant quarantine and import/export issues.

Under Objective 1, significant progress was made in identifying and describing invasive and emerging plant pathogens. Several monographic accounts of plant pathogenc fungi related to chestnut blight were published including Ophiognomonia and Melanconiella, both groups that cause anthracnose and canker diseases of hardwood trees. A major worldwide account of the fungi in the genus Diaporthe on Citrus was completed.

Under Objective 2, significant progress was made towards resolving the phylogeny of a group of fungi including several tree pathogens to determine and predict the environmental conditions correlated with host associations and speciation events. Progress was made in developing a diagnostic test to determine the presence of the cause of boxwood blight.


4.Accomplishments
1. Intercontinental fungi killing beech trees. Beech bark disease caused by fungi causes significant damage to beech trees both in Europe and North America. Exactly which fungus is killing the beech trees has been unclear because more than one kind of fungus is involved. This research confirmed that the fungus killing beech trees in North America is different from the one in Europe. Yet, another fungus was confirmed on beech trees and many hardwood trees in both Europe and North America. Surprisingly a fourth fungus occurs only in Asia on beech and other hardwood trees. This paper clearly defines the fungi associated with beech bark disease. Quarantine officials will use this research to prevent the movement of fungi the kill beech trees across continents.

2. A disease of oranges and other citrus crops called melanose or stem end rot is caused by a fungus that has been confused with fungi on other hosts. In this research three different species were found to occur on citrus in the United States. One of these is a species new to science known only from California and Spain. This new species is named, described and illustrated. Another species occurs only on citrus throughout the world. A third species that occurs on citrus is also found on other woody plants. This research will be used by plant breeders who are working to develop oranges and other citrus crops that are resistant to this disease. In addition plant quarantine officials will use this research to prevent the spread of these diseases on citrus.

3. Fungi can destroy invasive weeds without the use of harmful chemicals. In working to control Japanese stiltgrass, an invasive weed from Asia, a fungus was found that kills this weed. This fungus had never been seen before, so it was given a name after the host and described in detail in order to tell it from similar fungi. Portions of the DNA were sequenced and compared with other fungi. Plant pathologists and conservation biologists will determine if this new fungus can be safely and effectively used to control Japanese stiltgrass.


Review Publications
Minnis, A.M., Kennedy, A.H., Grenier, D.B., Palm, M.E., Rossman, A.Y. 2012. Phylogeny and taxonomic revision of the Planistromellaceae including its coelomycetous anamorphs: contributions towards a monograph of the genus Kellermania. Studies in Mycology. 29:11-28.

Crouch, J., Tomaso-Peterson, M. 2012. Anthracnose disease of centipedegrass turf caused by Colletotrichum eremochloae, a new fungal species closely related to Colletotrichum sublineola. Mycologia. 104(5):1085-1096.

O'Connell, R.J., Thon, M.R., Hacquard, S., Van Themaat, E.V., Amyotte, S., Kleemann, J., Torres-Quintero, M., Damm, U., Buiate, E., Epstein, L., Alkan, N., Altmuller, J., Alvarado, B.L., Bauser, C., Becker, C., Birren, B.W., Chen, Z., Crouch, J., Duvick, J., Farman, M., Gan, P., Heiman, D., Henrissat, B., Howard, R.J., Kabbage, M., Koch, C., Kubo, Y., Law, A., Lebrun, M.H., Lee, Y.H., Miyara, L., Moore, N., Neumann, U., Panaccione, D.G., Panstruga, R., Place, M., Proctor, R., Prusky, D., Rech, G., Reinhardt, R., Rollins, J.A., Rounsley, S., Schardl, C., Schwartz, D.C., Shenoy, N., Shirasu, K., Stuber, K., Sukno, S.A., Sweigard, J.A., Takano, Y., Takahara, H., Vanderdoes, H.C., Voll, L., Will, I., Young, S., Zeng, Q., Zhang, J., Zhou, S., Dickman, M.B., Schulze-Lefert, P., Ma, L.J., Vaillancourt, L.J. 2012. Life-style transitions in plant pathogenic Colletotrichum fungi deciphered by genome and transcriptome analyses. Nature Genetics. 44:1060-1065.

Molnar, T., Walsh, E., Capik, J., Sathuvalli, V., Mehlenbacher, S., Rossman, A.Y., Zhang, N. 2013. A real-time PCR assay for early detection of eastern filbert blight. Plant Disease. 97:813-818.

Voglmayr, H., Rossman, A.Y., Castlebury, L.A., Walter, J.M. 2012. Multigene phylogeny and taxonomy of the genus Melanconiella (Diaporthales). Fungal Diversity. 57:1-44.

Minnis, A.M., McTaggart, A.R., Rossman, A.Y., Aime, C.M. 2012. Taxonomy of mayapple rust: the genus Allodus resurrected. Mycologia. 104(4):942-950.

Salgado-Salazar, C., Rossman, A.Y., Samuels, G.J., Capdet, M., Chaverri, P. 2012. Multigene phylogenetic analyses of the Thelonectria coronata and T. veuillotiana species complexes. Mycologia. 104(6):1325-1350.

Baynes, M.A., Russell, D.M., Newcombe, G., Carta, L.K., Rossman, A.Y., Ismaiel, A.A. 2012. A mutualistic interaction between a fungivorous nematode and a fungus within the endophytic community of Bromus tectorum. Fungal Ecology. 5:610-623.

Walker, D., Castlebury, L.A., Rossman, A.Y., White, J. 2012. New molecular markers for fungal phylogenetics: Two genes for species level systematics in the Sordariomycetes (Ascomycota). Molecular Phylogenetics and Evolution. 64:500-512.

Walker, D.M., Castlebury, L.A., Rossman, A.Y., Mejía, L.C., White, J.F. 2012. Phylogeny and taxonomy of Ophiognomonia (Gnomoniaceae, Diaporthales), including twenty-five new species in this highly diverse genus. Fungal Diversity. 57:85-147.

Rajeshkumar, K.C., Rossman, A.Y. 2013. Taiwanascus samuelsii sp. nov., an addition to Niessliaceae from the Western Ghats, Kerala, India. IMA Fungus. 4(1):1-4.

Walker, D.M., Rossman, A.Y., Adams, G.C., Longa, C.M., Maresi, G. 2012. Valsalnicola D. Walker & Rossman, gen. nov. Persoonia: Molecular Phylogeny and Evolution of Fungi. 29:148-149.

Minnis, A.M., Rossman, A.Y., Kleczewski, N.M., Flory, L.S. 2012. Bipolaris microstegii Minnis, Rossman, Kleczewki & S.L. Flory, sp. nov. Persoonia: Molecular Phylogeny and Evolution of Fungi. 29:150-151.

Cariello, P.F., Wickes, B.L., Sutton, D.A., Castlebury, L.A., Levitz, S.M., Finberg, R.W., Thompson, E.H., Daly, J.S. 2013. Phomopsis bougainvilleicola prepatellar bursitis in a renal transplant recipient. Journal of Clinical Microbiology. 51(2):692-695.

Bruckart, W.L., Eskandari, F., Berner, D.K., Aime, M.C. 2012. Comparison of Puccinia acroptili from Eurasia and the USA. Botany. 90:465-471.

Herrera, C.S., Rossman, A.Y., Samuels, G.J., Lechat, C., Chaverri, P. 2013. Revision of the Genus Corallomycetella with Corallonectria gen. nov. for C. jatrophae (Nectriaceae, Hypocreales). Mycosystema. 32(3):518-544.

Bruckart, W.L., Eskandari, F., Coombs, E.M., Rossman, A.Y., Palm, M.E. 2013. First report of Pilidium concavum causing leaf necrosis on Fallopia japonica in the United States. Plant Disease. 97(1):146.

Hirooka, Y., Rossman, A.Y., Zhuang, W., Salgado-Salazar, C., Chaverri, P. 2013. Species delimitation for Neonectria coccinea group including the causal agents of beech bark disease in Asia, Europe, and North America. Mycosystema. 32:485-517.

Last Modified: 9/10/2014
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