Skip to main content
Think and Do The Extraordinary
Support the Unit

Marc Cubeta

Professor and Associate Director, Center for Integrated Fungal Research

Ecology and population genetics of beneficial and plant pathogenic soil fungi

Partners Building III 225



Fungi have evolved complex relationships with the environment, animals, insects, plants and microbes, that have ultimately contributed to their success in space and time. My research aims to gain better insight into the ecological factors and population processes that have contributed to the ability of fungi to cause disease and survive in the absence of a host; this requires a comprehensive understanding of species concepts, genome organization, evolution, and population genetics in the context of plant microbial interactions. This is critical for establishing a foundation of fundamental knowledge that can be translated for the practical management of disease causing fungi and the promotion of beneficial microorganisms that address societal grand challenges. Research in my laboratory has focused primarily on understanding the disease ecology, genome organization, soil microbiome, population biology, and systematics of the soil fungus Rhizoctonia solani, an economically important pathogen of a wide array of cultivated and native species of plants. Our research has revealed that R. solani is not a single species, but a species complex that represents an early diverging assemblage of fungi that may have given rise to the mushroom forming fungi. These results have provided a conceptual framework for delineating species, examining the genetic diversity and structure of field populations, determining the occurrence and transmission of fungal viruses, and identifying two previously undescribed Rhizoctonia 1) the disease-causing species of Rhizoctonia on agricultural plants and 2) beneficial species of Rhizoctonia on orchids. In addition to Rhizoctonia fungi, research from my lab has contributed to the development of methods for identifying other species of beneficial and disease-causing fungi of plants and more recently animals. My laboratory has also provided valuable bioinformatics, genomic, diagnostic, metabolomic, and microbiome resources for scientists interested in understanding the complex dynamics of different nuclear genomes in Rhizoctonia and other plant/soil associated beneficial and disease-causing fungi. This information has provided foundational knowledge that is key to conducting comparative studies that address fundamental research questions related to host plant adaptation in relation to nuclear genome heterogeneity.


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. 2024. Leveraging the wheat seed mycobiome for a climate resilient future. Environmental Microbiology Reports (Accepted, manuscript number EMIR-2024-0051).

Becker, L.E. and Cubeta, M.A. 2024. Multigenerational drought reveals a stable wheat seed fungal community. Phytobiomes

Doydora, S.A., Baars, O., Cubeta, M.A., Barlaz, M.A., and Duckworth, O.W. 2024. Using Mn-oxidizing fungi to recover metals from electronic waste. Minerals 14(1), 111;

Roberts, D., Thomas, J.,  Salmon, J., Cubeta, M.A., Stapelmann, K., and Gilger, B.C. 2024. Cold atmospheric plasma inactivates Aspergillus flavus and Fusarium keratoplasticum biofilms and conidia in vitro. Journal of Medical Microbiology (In Press).

Stephens, C.M, Gannon, T.. Thiessen, L.D., Cubeta, M.A.,  and Kerns, J.P. 2024. Influence of fungicide selection, application timing, and manganese application on take-all root rot management under field and greenhouse conditions. Crop, Forage, & Turfgrass Management 10(1);


French, K.S., Chukwuma, E., Linshitz, I., Duckworth, O.W., Cubeta, M.A., and Baars, O. 2023.  Degradation and production of siderophores by the plant endophyte fungus Drechslera biseptata.Environmental Microbiology Reports; 16 e13234,

Roberts, D. Salmon, J., Cubeta, M.A., and Gilger, B.C. 2023.  Phase-dependent differential in vitro and ex vivo susceptibility of Aspergillus flavus and Fusarium keratoplasticum to azole antifungals. Journal of Fungi 9(10), 966;

Sweenie, R.A., Looney, B.P., Ke, Y-H., Rojas, A., Cubeta, M.A., Langer, G.J., Vilgalys, R., and Matheny, P.B. 2023. A PacBio high-throughput multi-locus sequencing method for fungal systematics and species delimitation. Molecular Ecology Resources 24(1);

Weaver, L.M., Alexander, N.L., Cubeta, M.A., Knappe, D., and Aziz, T.N. 2023. Degradation of imidacloprid by Phanerodontia chrysosporium on wood chips for stormwater treatment. Royal Society of Chemistry Environmental Science: Water Research & Technology 9:3333-3343.


Rogers, L.W., Koehler, A.M., Cubeta. M.A., Crouch, J.A., and LeBlanc, N.R. 2022 Comparative genomic analysis reveals contraction of gene families with putative roles in pathogenesis in the fungal boxwood pathogens Calonectria henricotiae and C. pseudonaviculata. BMC Ecology and Evolution 22(1), https;//

Stephens, C.M, Gannon, T.. Thiessen, L.D., Cubeta, M.A.,  and Kerns, J.P. 2022. In vitro fungicide sensitivity and effect of organic matter concentration on fungicide bioavailability. Plant Health Progress doi

Stephens, C.M, Sit, T., Cubeta, M.A., Gannon, T. and Kerns, J.P. 2022. Characterization and aggressiveness of take-all root rot pathogens isolated from symptomatic bermudagrass putting greens. Phytopathology 111,


Becker, L.E., Adhikari, U., Mays, T., Shishkoff, N., Crouch, J.A. and Cubeta, M.A. 2021. Evaluation of boxwood cultivars for resistance to boxwood blight. Plant Disease Management Reports 15: OT008.

LeBlanc, N., Cubeta, M.A., and Crouch, J. 2021. Population genomics trace clonal diversification and intercontinental migration of an emerging fungal disease of boxwood. Phytopathology 111(1):184-193, Invited submission for Special Population Focus Issus, Population Genomic and Phylogenomic Enabled Advances to Increase Insight Into Pathogen Biology and Epidemiology.


Nowicki, M., Hadziabdic, D., Trigiano, R.N., Boggess, S.L., Kanetis, L., Wadl, P.A., Ojiambo, P., Cubeta, M.A., Spring, O., Thines, M., Runge, F., and Scheffler, B.E. 2021. ‘Jumping Jack’: Genomic microsatellites underscore the distinctiveness of closely related Pseudoperonospora cubensis and Pseudoperonospora humuli and provide new insights into their evolutionary past.
Frontiers in Microbiology

Shishkoff, N. Miller, M.E., and Cubeta, M.A. 2021. Rooting response of healthy boxwood cultivars to hot water treatment and thermal inactivation of Calonectria henricotiae and C. pseudonaviculata in diseased boxwood tissue. Journal of Environmental Horticulture 39(1):1-10,

Stalpers, J., Redhead, S.A., Rossman, A., Crouch, J.A., Cubeta, M.A., Kirschner, R., Langer, G.J., Larsson, K-H., Mack, J., Marvanova, L., May, T.W., Norvell, L.L., Oberwinkler, F., Roberts, P., Rajchenberg, R., Seifert, K.A., and Thorn, R.G. 2021. Competing sexual-asexual generic names in the Agaricomycotina (Basidiomycota) with recommendations for use. IMA Fungus 12:22

Yow, A., Zhang, Y., Bansal, K, Maren, N., Eacker, S.M., Sullivan, S., Liachko, I., Cubeta, M.A., Rollins, J.A., and Ashrafi, H.. 2021. Genome sequence of Monilinia vaccini-corymbosi sheds light on mummy berry disease infection of blueberry and mating type. Genes Genomes Genetics 11(2),


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

Castroagudín, V.L., Weiland, J.E., Baysal-Gurel, F., Cubeta, M.A., Daughtrey, M, Gauthier, N.W., LaMondia, J., Luster, D.G., Hand, F.P., Shishkoff, N., Williams-Woodward, J., Yang, X., LeBlanc, N., and  Crouch, J.A. 2020. One clonal lineage of Calonectria pseudonaviculata is primarily responsible for the boxwood blight epidemic in the United States. Phytopathology 110(11):1845-1853. Cited as Editor’s pick for November.

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, doi 10.1080/10598650.2020.1833296.  

Roberts, D., Cotter, H.V., Cubeta, M.A., and Gilger, B.C. 2020. In vitro susceptibility of Aspergillus and Fusarium associated with equine keratitis to new antifungal drugs. Veterinary Ophthalmology (


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.

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.

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 56(2):52-62

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.

Miller, M.E., Norris, R. and Cubeta, M.A. 2015. Evaluation of boxwood cultivars for resistance to boxwood blight. Plant Disease Management Reports 10:OT009.

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.J, 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 2015(6):1-9, doi

Cubeta, M.A., Thomas, E., Dean, R.A., Jabaji, S., Neate, S.M., Tavantzis, S., Toda, T., Vilgalys, R., Bharathan, N., Fedorova-Abrams, N., Pakala, S., Zafar, N., Joardar, V., Losada, L., and Nierman, W.C. 2014. Draft Genome Sequences of the Plant Pathogenic Fungus Rhizoctonia solani Anastomosis Group 3 Strain Rhs1AP. Genome Announc. 2(5):e1072-14. doi:10.1128/genomeA.01072-14.

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., Dykstra, M., 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 Microbiology Letters 350:1-11 (DOI: 10.1111/1574-6968.12387). Cited as one of 10 articles to exemplify visualization in microbiology.


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