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Marc Cubeta

Professor, Soil Mycology and Plant Disease Ecology

Ecology and population genetics of soil fungi

Partners Building III 225



My laboratory is interested in understanding the ecology and population biology of soil fungi that cause plant disease. The ultimate goal of my research program is to generate science-based knowledge to develop improved disease management approaches that reduce economic losses to plant disease while promoting increased plant health and productivity. For many years, we have studied the soil fungus Rhizoctonia solani, which is an economically important pathogen of species of agricultural and forestry crops throughout the world. The fungus also infects non-cultivated species of plants in natural ecosystems and is of ecological importance as a recycler of soil nutrients. Research conducted in my laboratory has provided a conceptual framework for identifying species of Rhizoctonia fungi to better define populations and understand their evolutionary history and plant disease ecology. Current research in my lab is focused on the use of “omic”-based methods to better understand the genetic basis of how Rhizoctonia solani produces microsclerotia, structures that promote long-term survival of the fungus in soil in absence of a plant host. More recently we have been involved in the study of Rhizoctonia fungi and soil microbial communities associated with terrestrial species of orchids, cacao, and wheat. Information generated from collaborative research studies is being used to better understand the interaction of soil chemical factors and microbial communities for developing improved approaches to conserve terrestrial orchid species and to manage diseases of cacao and wheat.


PP222 Kingdom of Fungi (fall and spring) – This course provides an overview of the diversity of fungi and their ecological, economic and historical impact on the environment and society. The fall course is a taught in a traditional classroom setting (face-to-face) and supplemented with the examination and discussion of fungal specimens. For the spring course, lectures, course content and discussions are presented and delivered in an online, distance education format.

PP575 Introduction to Mycology (fall, odd years) – This course provides a synthesis and survey of organisms in the Kingdom Fungi. Lectures focus on providing a comprehensive understanding of the biology, diversity, ecology, phylogeny, systematics, and taxonomy of fungi. The laboratory component of this course complement the lectures and involve characterizing, culturing and identifying fungi sampled from diverse ecological habitats.


Selected Peer-Reviewed Publications (last 10 years):


Becker L.E. and Cubeta M.A. 2020. Evaluation of calibrachoa cultivars for black root rot resistance, 2019. Plant Disease Management Reports 14: OT013.

Flemming, A., Phillips, M., Shea, E.K., Bolton, A., Lincoln, C., Green, K.E., Mast, A., and Cubeta, M.A. 2020. Using Digital Natural History Collections in K-12 STEM Education. Journal of Museum Education (Accepted, pending revision).


Cullen, M., Jacob, M.E., Vanderschel, I.Q., Cotter, H.V.T., Cornish, V., Cubeta M.A., Carbone, I., and Gilger, B.C. 2019. Relationship of multi-locus DNA sequence analysis, anti-fungal agent susceptibility and equine fungal keratitis outcome. PLoS One, Mar 28;14(3):e0214214. doi:10.1371/journal.pone.0214214. eCollection 2019.

Green, K.E., Roller, C., and Cubeta, M.A. 2019. A plethora of fungi: developing mycological educational resources for biology and environmental science teachers and students. Science Activities ISSN: 0036-8121 (Print) 1940-1302 (Online)

Koehler, A.M., Larkin, M.T., Rogers, L.W., Carbone, I., Cubeta, M.A., and Shew, H.D. 2019. Identification and characterization of Septoria steviae as the causal agent of Septoria leaf spot disease of stevia in North Carolina. Mycologia, 111:3, 456-465, DOI: 10.1080/00275514.2019.1584503.

Salgado-Salazar, C., Shishkoff, N., LeBlanc, N., Ismaiel, A.A., Collins, M.D., Cubeta, M.A., and Crouch, J.A. 2019. Coccinonectria pachysandricola, causal agent of a new foliar blight disease of Sarcococca hookeriana. Plant Disease 103(4):1337-1346.


Lookabaugh, E.C., Kerns, J.P., Shew, B.B, and Cubeta, M.A. 2018. Fitness attributes of Pythium aphanidermatum with dual resistance to mefenoxam and fenamidone. Plant Disease 102(10).

Miller, M.E., Shishkoff, N. and Cubeta, M.A. 2018. Thermal sensitivity of Calonectria henricotiae and Calonectria pseudonaviculata conidia and microsclerotia. Mycologia 110 (3): 546-558, doi:10.1080/002755514.2018.1465778.


Burchhardt, K.M., Miller, M.E., Cline, W.O., and Cubeta, M.A. 2017. Fine-scale genetic structure and reproductive biology of the blueberry pathogen Monilinia vaccinii-corymbosi. Phytopathology 107:231-239.

Duckworth, O.W., Andrews, M.Y., Cubeta, M.A., Grunden, A.M., and Ojiambo, P. 2017. Revisiting graduate student training to address agricultural and environmental societal challenges. Agric. Environ. Lett. 2:170019, doi:10.2134/ael2017.06.0019.


Cubeta, M.A., Mozley, S.E., and Porter, D. 2016. Laboratory Exercises with Zoosporic Fungi. In Plant Pathology Laboratory Exercises and Concepts. CRC Press, eds. Trigiano and Windham, pp. 99-110.

Gonzalez, D, Rodriguez-Carres, M., Boekhout, T., Stalper, J., Kurame, E.E., Nakatani, A.K., Vilgalys, R., and Cubeta, M.A. 2016. Phylogenetic relationships of Rhizoctonia fungi within the Cantharellales. Fungal Biology 120:603-619.

Pettersson, M., Frampton, J., Rönnberg, J., Shew, H.D., Benson, D.M., Kohlway, W.H., Escanferla, M.E., and Cubeta, M.A. 2016. Increased diversity of Phytophthora Species in Fraser fir Christmas Tree Plantations in the Southern Appalachians. Scandinavian Journal of Forestry


Burchhardt, K.M. and Cubeta, M.A. 2015. Population dynamics of the blueberry pathogen Monilinia vaccinii-corymbosi in the United States. Phytopathology 105:1-9 (selected as Editor’s pick for June).

Chamoun, R., Samsatly, J., Pakala, S., Cubeta, M.A., and Jabaji, S. 2015. Suppression subtractive hybridization and comparative expression of a pore-forming toxin and glycosyl hydrolase genes in Rhizoctonia solani during potato sprout infection. Molecular Genetics and Genomics: DOI: 10.1007/s00438-014-0962-x.

Gkarmiri, K., Finlay, R.D., Alström, S., Thomas, E., Cubeta, M.A., and Högberg, N. 2015. Transcriptomic analyses of changes in gene expression in the fungal pathogen Rhizoctonia solani AG-3 in response to the bacterial antagonists Serratia proteamaculans and Serratia plymuthica. BMC Genomics 16:630 DOI 10.1186/s12864-015-1758-z.

Jr-Hau Jiang, J-H., Lee, Y-I., Cubeta, M.A., and Chen, L-C. 2015. Characterization and colonization of endomycorrhizal Rhizoctonia fungi in the medicinal herb Anoectochilus formosanus (Orchidaceae). Mycorrhizae DOI 10.1007/s00572-014-0616-1.

Mothapo, N.V. Chen, H., Cubeta, M.A., Grossman, J.M., Fuller, F, and Shi, W. 2015. Phylogenetic, taxonomic and functional diversity of fungal denitrifiers and associated N2O production efficacy. Soil Biology & Biochemistry 83:160-175.


Bazzle, L., Cubeta, M.A., Marks, S.L., and Dorman, D.C. 2014. Feasibility of flotation concentration of fungal spores as a method to identify toxigenic mushrooms. Vet Med Res Reports. (In Press).

Burchhardt, K.M. and Cubeta, M.A. 2014. Population dynamics of the blueberry pathogen Monilinia vaccinii-corymbosi in the United States. Phytopathology 104: (Accepted, manuscript number PHYTO-03-14-0074-R).

Chamoun, R., Samsatly, J., Pakala, S., Cubeta, M.A., and Suha Jabaji, S. 2014. Suppression subtractive hybridization and comparative expression of a pore-forming toxin and glycosyl hydrolase genes in Rhizoctonia solani during potato sprout infection. Molecular Genetics and Genomics: (Accepted, manuscript number MGAG-D-14-00189).

Jr-Hau Jiang, J-H., Lee, Y-I., Cubeta, M.A., and Chen, L-C. 2014. Characterization and colonization of endomycorrhizal Rhizoctonia fungi in the medicinal herb Anoectochilus formosanus(Orchidaceae). Mycorrhizae. (Accepted, manuscript number MCOR-D-14-00082).

Losada, L., Pakala, S.B., Fedorova, N.D., Joardar, V., Shabalina. S., Hostetler, J., Pakala, S., Zafar, N., Thomas, E.T., Rodriguez-Carres, M., Dean R.A., Vilgalys, R.J., Nierman, W.C., and Cubeta, M.A.2014. Mobile intron-like elements and novel mitochondrial genome expansion in the soil fungus and potato pathogen Rhizoctonia solani. FEMS Letters 350:1-11 (DOI: 10.1111/1574-6968.12387).


Bartz, F.E., Danehower, D.A., Glassbrook, N., and Cubeta, M.A. 2013. Modulation of the phenylacetic acid metabolic complex by quinic acid alters the disease-causing activity of Rhizoctonia solani on tomato. Phytochemistry 75:

Ferrucho, R.L., Garcia-Dominguez, C., Ramirez-Escobar, U.M., McDonald, B. A., Cubeta, M.A., and P.C. Ceresini, P.C. 2013. The population genetic structure of Rhizoctonia solani AG-3PT from potatoes in the Colombian Andes. Phytopathology 103:862-869.

McCormick, M.A., Grand, L.F., Post, J.B., and Cubeta, M.A. 2013. Phylogenetic relatedness and phenotypic characterization of Fomes fasciatus and Fomes fomentarius sampled from the United States. Mycologia 105(6):1524-1535.

McCormick, M.A., Cubeta, M.A., and Grand, L.F. 2013. Geography and hosts of the wood decay fungi Fomes fasciatus and Fomes fomentarius in the United States. North American Fungi 8(2):1-53. doi:10.2509/naf2013.008.002.

Mothapo, N.V, Chen, H., Cubeta, M.A., and Shi, W. 2013. Nitrous oxide producing activity of diverse fungi from distinct agroecosystems. Soil Biology & Biochemistry 66:94-101.

Skamnaki, V., Peumans, W., Kantsadi, A., Cubeta, M.A., Plas, K., Pakala, S., Zographos, S., Smagghe, G., Nierman, W.C., Van Damme, E., and Leonidas, D. 2013. Structural analysis of the Rhizoctonia solani agglutinin reveals an unusual dimeric assembly. FEBS Journal 280:1750-1763.


Bartz, F.E., Danehower, D.A., Glassbrook, N., and Cubeta, M.A. 2012. Elucidating the role of phenylacetic acid and hydroxy- and methoxy- phenylacetic acid derivatives in the pathogenic activity of Rhizoctonia solani AG-3. Mycologia 104:793-803.

Burchhardt, K. and Cubeta, M.A. 2012. Microsatellite marker development for the plant pathogenic fungus Monilinia vaccinii-corymbosi. Molecular Ecology Resources 12:72-74.

Mozley, S.E., Porter, D, and Cubeta, M.A. 2012. Concepts and Laboratory Exercises with Zoosporic Fungi. In Plant Pathology Laboratory Exercises and Concepts. CRC Press, eds. Trigiano and Windham, pp. 91-98.

Samuels, G., Ismaiel, A., McMahon, P., Guest, D., Rosmana, A., Junaid, M., Rodriguez-Carres, M., and Cubeta, M.A. 2012. Vascular streak dieback of cacao in Southeast Asia and Melanesia: in planta detection of the pathogen and a new taxonomy. Fungal Biology 116(1):11-23.

Thomas, E., Pakala, S., Fedorova, N. D., Nierman, W. C., and Cubeta, M. A. 2012. Triallelic SNP-mediated genotyping of regenerated protoplasts of the heterokaryotic fungus Rhizoctonia solani. Journal of Biotechnology 158:144-150. 


Aliferis, K.A., Jabaji, S., and Cubeta, M.A. 2011. Chemotaxonomy of fungi in the Rhizoctonia solani species complex using GC/MS metabolic profiling. Metabolomics (30 July), pp 1-11, doi:10.1007/s11306-011-0340-1.

Copes, W., Rodriguez-Carres, M., Toda, T., Rinehart, T.A., and Cubeta, M.A. 2011. Seasonal prevalence of species of binucleate Rhizoctonia fungi in growing medium, leaf litter, and stems of container grown azalea. Plant Dis. 95:705-711. 

Kaye, A.C., Moyer, J.W., Parks, E.J., Carbone, I., and Cubeta, M.A. 2011. Population genetic analysis of Tomato spotted wilt virus on peanut in North Carolina and Virginia. Phytopathology 110:147-153.

Toda, T., Strausbaugh, C., Rodriguez-Carres, M., and Cubeta, M.A. 2011. Characterization of a basidiomycete fungus from sugarbeet. Mycologia 104:70-78.

Woodhall, J.W., Webb, K.M., Harper, G., Peters, J.C., Rodriguez-Carres, M., and Cubeta, M.A. 2011. First report of a new binucleate Rhizoctonia in UK potato tubers. New Disease Reports23:31 [doi:10.5197/j.2044-0588.2011.023.031].

Yin, J., Koné, D., Rodriguez-Carres, M. Cubeta, M.A., Burpee, L.L., Fonash, E.G. Csinos, A.S., and Ji, P. 2011. First report of root rot caused by binucleate Rhizoctonia anastomosis group F on Musa spp. Plant Disease 94:490.



BS, Plant Pathology, North Carolina State University (1980)
MS, Plant Pathology, University of Illinois (1983)
Ph.D, Plant and Soil Science, University of Delaware (1991)