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United States Department of Agriculture

Agricultural Research Service

Research Project: SYSTEMATIC BIOLOGY OF INVASIVE AND EMERGING PLANT PATHOGENIC FUNGI
2012 Annual Report


1a.Objectives (from AD-416):
Characterize and analyze phylogenetic relationships for important disease-causing basidiomycetes with emphasis on smut and bunt fungi on cultivated grains and turf grasses, and rust fungi as pathogens of crops. Characterize and analyze phylogenetic relationships of ascomycetous pathogens based on morphological and molecular characteristics with emphasis on canker and related anthracnose fungi causing diseases of tree fruit crops and forest trees.


1b.Approach (from AD-416):
Smut and bunt fungi associated with turf grasses, cultivated grains, and weedy plants in the genera Tilletia, Ustilago, and Urocystis will be collected, cultured and characterized with morphological and molecular data. A wide range of rusts on weedy and crop plant hosts will be collected and characterized with DNA sequence data in order to determine both higher-level relationships and species relationships. Taxon-specific PCR primers will be developed for genes of interest when necessary. For both rusts and smuts PCR will be performed to amplify ribosomal and protein-coding genes, including ITS, LSU, SSU, EF1-alpha, and RNA polymerase gene regions. Species concepts will be defined based on multi-gene phylogenetic trees and morphological data when possible. Fungal pathogens of tropical hosts will be characterized with molecular data and ribosomal gene regions will be used to determine their relationships. Sequence data will be used to develop rapid methods for identification and correlated with morphological data when available. Diaporthalean taxa, including Diaporthe-Phomopsis and Valsa-Cytospora and taxa in the Nectria family of the Hypocreales will be collected and characterized morphologically. PCR will be performed to amplify ribosomal and protein-coding genes, including ITS, LSU, SSU, EF1-alpha, and RNA polymerase gene regions. Species concepts will be defined based on multi-gene phylogenetic trees in combination with morphological data. 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.


3.Progress Report:
This is the final report documenting progress for Project 1275-22000-245-00D, Systematic Biology of Invasive and Emerging Plant Pathogenic Fungi, which terminated April 2012, and continues as Project 1275-22000-279-00D, Systematics and Diagnostics of Emerging and Quarantine-Significant Plant Pathogenic Fungi. Substantial results were realized for both objectives over the five years of the project. Under Objective 1, Japanese apple rust was documented for the first time in the U.S. Bunt and rust fungi parasitizing switchgrass were discovered in the southeastern U.S. in varieties being grown for biofuel. Two new species of bunt fungi were described from turfgrass in the Pacific Northwest. Puccinia kuehnii, the destructive orange rust pathogen of sugarcane, was discovered for the first time in the Western Hemisphere in Florida and has since been found to be widespread in Central America, necessitating a change in cultivars grown in those areas. A diagnostic assay was developed and the relationships of orange rust to brown rust and other rust diseases of grasses were determined. Rust fungi on chickpeas, Potentilla, and an environmentally sensitive sandwort were characterized. Under Objective 2, research was completed on Nectria a large group of hardwood tree pathogens that resulted in a monographic account of this genus. Within the genus Neonectria that includes the beech bark canker fungus, it was determined that four different genera exist that differ biologically. The fungi that cause diseases on hardwood trees in temperate regions are distinct from those in the tropics that live on dead woody tissues. These are different from the fungi that cause root and rhizome rots. Illustrations, descriptions and DNA sequences were provided for these fungi. Research was also completed on several genera of fungi important as pathogens of hardwood trees, shrubs, and rosaceous fruit crops. These genera were described and illustrated and DNA sequence data were analyzed to determine the relationships among them. The overall impact of this work is to enable pathologists and plant quarantine officials to accurately identify pathogens and potentially invasive members of these groups and to identify host associations and distribution allowing better prediction of pathogen behavior when introduced into new environments.


4.Accomplishments
1. A new fungal pathogen discovered that controls Japanese stiltgrass. Japanese stiltgrass is an invasive weed from Asia that outcompetes and replaces native grasses. A previously unknown fungus was discovered to kill Japanese stiltgrass. Scientists in Beltsville named, described, and compared the microscopic features of this fungus with other known fungi. In addition, portions of the DNA of the fungus were sequenced and compared with other similar fungi. Using the information now available for this fungus, plant pathologists and conservation biologists can conduct the research to determine if this fungus will be useful and safe to apply in the field for the control of Japanese stiltgrass without the use of harmful chemicals.

2. Grassland morels were discovered and determined to give advantage to invasive cheat grass. Morels are highly prized edible fruiting bodies of fungi that develop in temperate and boreal forests following fire and other disturbances. They are not known to develop in dry places where trees do not grow. In this study two species of morels were isolated from cheatgrass in dryland regions in the western United States. Cheatgrass is an invasive plant that greatly increases the risk of fire. Scientists in Beltsville identified the species using DNA sequence data. The isolates of the morels were determined to increase growth, reproduction, and seed thermotolerance. This information will be useful to researchers and land managers in determining fire tolerance and potential for increased growth of cheatgrass in areas where these fungi are present.


Review Publications
Mejia, L.C., Rossman, A.Y., Castlebury, L.A., Yang, Z.L., White, J. 2012. Occultocarpon, a new monotypic genus of Gnomoniaceae on Alnus nepalensis from China. Fungal Diversity. 52:99-105.

Beirn, L., Moy, M., Meyer, W., Clarke, B., Crouch, J. 2011. Molecular analysis of turfgrass rusts reveals the widespread distribution of Puccinia coronata as a pathogen of Kentucky Bluegrass in the United States. Plant Disease. 95:1547-1557.

Baynes, M., Newcombe, G., Dixon, L., Castlebury, L., O Donnell, K. 2011. A novel plant-fungal mutualism associated with fire. Fungal Biology. 116:133-144.

Yun, H.Y., Minnis, A.M., Kim, Y.H., Castlebury, L.A., Aime, M.C. 2011. The rust genus Frommeëlla revisited: a later synonym of Phragmidium after all. Mycologia. 103(6):1451-1463.

Kruys, A., Castlebury, L.A. 2012. Molecular phylogeny of Sydowiellaceae, resolving the position of Cainiella. Mycologia. 104(2):419-426.

Crous, P.W., Pereira, O.L., Alfenas, A.C., Alfenas, R.F., Rossman, A.Y., Groenewald, J.Z., Minnis, A.M. 2011. What is Scirrhia? IMA Fungus. 2(2):127-133.

Rossman, A.Y., Melgar, J.C., Walker, D.M., Gonzales, A., Ramirez, T., Rivera, J.M. 2012. First report of Dolabra nepheliae associated with corky bark disease of Rambutan and Pulasan in Honduras. Plant Disease. 96:765.

Deadman, M.I., Al-Sadi, A.M., Al-Maqbali, Y.M., Farr, D.F., Aime, M.C. 2012. Additions to the rust fungi (Pucciniales) from northern Oman. Sydowia. 63(2):155-168.

Hirooka, Y., Rossman, A.Y., Samuels, G.J., Lechat, C., Chaverri, P. 2012. A monograph of Allantonectria, Nectria, and Pleonectria (Nectriaceae, Hypocreales, Ascomycota) and their pycnidial, sporodochial, and synnematous anamorphs. Studies in Mycology. 71:1-210.

Bennett, C., Aime, M.C., Newcombe, G. 2011. Molecular and pathogenic variation within Melampsora on Salix in western North America reveals numerous cryptic species. Mycologia. 103(5):1004-1018.

Last Modified: 7/25/2014
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