About

Marc A. Cubeta is a professor in the Department of Entomology and Plant Pathology and serves as the Associate Director of the Center for Integrated Fungal Research at North Carolina State University. His research focuses on fungi's complex relationships with the environment, animals, insects, plants, and microbes, aiming to understand the ecological factors and population processes that enable fungi to cause disease and survive without a host. His work emphasizes species concepts, genome organization, evolution, and population genetics within plant microbial interactions, providing foundational knowledge for disease management and beneficial microorganism promotion. His laboratory primarily investigates the soil fungus Rhizoctonia solani, revealing it as a species complex with significant implications for agriculture and ecology, and has contributed to methods for identifying beneficial and pathogenic fungi affecting plants and animals. Additionally, his research includes bioinformatics, genomics, diagnostics, metabolomics, and microbiome resources to understand nuclear genome dynamics in fungi. Cubeta also teaches courses on fungal diversity and biology, integrating traditional and online formats, and has authored numerous publications and secured grants to advance understanding of soil fungi, microbial interactions, and plant resilience.

Research topics

• Biology
• Botany
• Genetics
• Demography
• Evolutionary biology

Selected publications

• A phylogenetic study of the Cantharellales supports recognition of four families and independent gains of biotrophic nutritional modes

  American Journal of Botany · 2025-06-01 · 1 citations

  articleOpen access

  PREMISE: The agaricomycete order Cantharellales contains approximately 1000 species of fungi characterized by diverse morphological forms, ecological guilds, and nutritional modes. Examples include coralloid lichens that form symbioses with unicellular green algae, bulbil-forming lichenicolous species, corticioid free-living fungi that degrade dead sources of organic carbon, pathogens that cause plant disease, orchid root endosymbionts, and ectomycorrhizal fungi including popular edible mushrooms. However, evolutionary relationships in the Cantharellales remain poorly understood due to conflicting estimates based on ribosomal DNA loci. METHODS: We constructed a five-gene phylogeny of the Cantharellales using data from 301 specimens to evaluate family-level relationships. We used penalized likelihood to estimate divergence times and ancestral state reconstruction to test the hypothesis of multiple independent origins of biotrophic ecologies in the order and whether those transitions are younger than the divergence times of associated plant or lichen hosts. RESULTS: Four monophyletic families were recovered with strong support: Botryobasidiaceae, Ceratobasidiaceae, Hydnaceae s.l., and Tulasnellaceae, with Hydnaceae containing the greatest species richness and morphological diversity. Our results suggest the Cantharellales diverged during the Carboniferous period with subsequent diversification following the Permian-Triassic extinction. Ancestral state reconstruction supports a saprotrophic most recent common ancestor with at least three transitions to an ectomycorrhizal ecology, multiple transitions to a lichenicolous habit with one or more subsequent transitions to mutualistic nutritional modes, four transitions to an orchid mycorrhizal ecology, and two transitions to a lichenized lifestyle. CONCLUSIONS: This study represents the first comprehensive examination of the evolution of form and function across this ecologically and morphologically diverse order of fungi.

  PublisherOA PDFDOI

• Stability of the Wheat Seed Mycobiome Across North Carolina’s Longitudinal Gradient

  bioRxiv (Cold Spring Harbor Laboratory) · 2024-02-23

  preprintOpen accessSenior author

  ABSTRACT Improving wheat yield and performance involves selecting varieties that are well adapted for a regional area. Although host genotype and environment are major factors that impact crop performance and resilience, less is known about the relative contribution and occurrence of wheat seed endophytic fungal communities across spatial and temporal scales. An increased understanding of composition and assembly of beneficial endophytic fungal communities across regional scales provides valuable insight into the stability of the endophytic seed mycobiome. Our aim in this study was to examine the relative contribution and impact of latitude and longitude gradients within North Carolina (NC) on wheat seed fungal community structure of two regionally adapted soft red winter wheat cultivars, Hilliard and USG 3640. We examined the endophytic wheat seed microbiome of the two winter wheat cultivars planted in official variety trials at five geographic locations across NC in 2021 and two geographic locations in 2022. ITS1 sequence-based analysis of surface disinfested wheat seeds was conducted to determine alpha and beta diversity. Species richness is influenced by geographical location, however wheat seed mycobiome community structure is stable across cultivars and years. Latitude and longitude contributed to the observed variation in wheat seed mycobiome structure, in addition to yield, seed moisture, and leaf nutrients. When surveying taxa present within all cultivars, geographical sites and years, Alternaria and Epicoccum spp. exhibited high relative abundance in the wheat seed mycobiome. Our results provide a comprehensive catalog of core fungal taxa well-adapted to diverse environments and conserved across wheat cultivars.

  PublisherOA PDFDOI

• A synergistic culture dependent and independent approach reveals a conserved wheat seed mycobiome

  bioRxiv (Cold Spring Harbor Laboratory) · 2024-02-23 · 2 citations

  preprintOpen accessSenior author

  ABSTRACT The occurrence of pathogenic fungal taxa associated with wheat ( Triticum aestivum L.) seeds is well studied, but less is known about non-pathogenic taxa of the wheat seed mycobiome. The goal of our research is to characterize wheat seed fungal endophyte diversity with a synergistic culture dependent and independent experimental approach. Four publicly available winter wheat cultivars developed in the southeastern United States with varying phenotypic and disease resistance traits were examined over a period of two years: Catawba, Hilliard, Shirley, and USG 3640. Our culture dependent methods involving two nutrient media generated 645 fungal isolates representing twelve genera sampled from multiple cultivars. Metabarcoding analysis identified a broader range of fungal taxa and a greater number of unique sequences than culture dependent methods. When examining fungal diversity across cultivars and years, richness decreased in 2021 for both culture dependent and independent approaches. However, wheat seed fungal community structure was stable across cultivars and years. Our results highlight the importance of combining culture independent and dependent methods to capture and establish a diverse endophytic fungal catalog associated with the wheat seed and highlight areas where future culture dependent efforts can focus their efforts.

  PublisherOA PDFDOI

• Influence of fungicide selection and application timing on take‐all root rot management under field and greenhouse conditions

  Crop Forage & Turfgrass Management · 2023-11-22 · 3 citations

  article

  Abstract Take‐all root rot (TARR) is a detrimental disease of ultradwarf bermudagrass ( Cynodon dactylon × Cynodon transvaalensis ; UDB) putting greens frequently diagnosed where warm‐season grasses are grown. Since this disease is largely aggregated and variable under field conditions, field research is difficult and often yields inconsistent results. Multiple pathogens have only recently been associated with this disease, so practical management solutions such as fungicide efficacy and fungicide application timing have not been thoroughly investigated. Therefore, the objectives of this research were to determine the influence of fungicide selection and fungicide application timing on take‐all root rot management under field and greenhouse conditions. In general, fungicides from the quinone outside inhibitor and/or demethylation inhibitor chemical classes provided the greatest reduction in take‐all root rot severity. Fungicide applications that were made when soil temperatures were between 77–86°F provided the greatest disease suppression. The in vivo greenhouse method developed in this research proved to be an efficient and consistent method to evaluate management practices such as fungicide efficacy on take‐all root rot. This research improves our understanding of fungicide efficacy and fungicide application timing for take‐all root rot management on ultradwarf bermudagrass.

  PublisherDOI

• <scp>PacBio</scp> high‐throughput multi‐locus sequencing reveals high genetic diversity in mushroom‐forming fungi

  Molecular Ecology Resources · 2023-10-30 · 13 citations

  articleOpen access

  Multi-locus sequence data are widely used in fungal systematic and taxonomic studies to delimit species and infer evolutionary relationships. We developed and assessed the efficacy of a multi-locus pooled sequencing method using PacBio long-read high-throughput sequencing. Samples included fresh and dried voucher specimens, cultures and archival DNA extracts of Agaricomycetes with an emphasis on the order Cantharellales. Of the 283 specimens sequenced, 93.6% successfully amplified at one or more loci with a mean of 3.3 loci amplified. Our method recovered multiple sequence variants representing alleles of rDNA loci and single copy protein-coding genes rpb1, rpb2 and tef1. Within-sample genetic variation differed by locus and taxonomic group, with the greatest genetic divergence observed among sequence variants of rpb2 and tef1 from corticioid Cantharellales. Our method is a cost-effective approach for generating accurate multi-locus sequence data coupled with recovery of alleles from polymorphic samples and multi-organism specimens. These results have important implications for understanding intra-individual genomic variation among genetic loci commonly used in species delimitation of fungi.

  PublisherOA PDFDOI

• Degradation of imidacloprid by <i>Phanerodontia chrysosporium</i> on wood chips for stormwater treatment

  Environmental Science Water Research & Technology · 2023-01-01 · 3 citations

  article

  The white-rot fungus Phanerodontia chrysosporium degraded more than 50% of imidacloprid in synthetic stormwater in one week, demonstrating the potential of fungal bioremediation for improved contaminant removal in stormwater infrastructure.

  PublisherDOI

• Additional file 1 of Comparative genomic analysis reveals contraction of gene families with putative roles in pathogenesis in the fungal boxwood pathogens Calonectria henricotiae and C. pseudonaviculata

  Figshare · 2022-01-01

  datasetOpen access

  Additional file 1: Genome metadata for the boxwood blight pathogens Calonectria henricotiae and C. pseudonaviculata, and 22 fungal taxa in the Nectriaceae.

  PublisherDOI

• 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 · 2022-06-21 · 11 citations

  articleOpen access

  BACKGROUND: Boxwood blight disease caused by Calonectria henricotiae and C. pseudonaviculata is of ecological and economic significance in cultivated and native ecosystems worldwide. Prior research has focused on understanding the population genetic and genomic diversity of C. henricotiae and C. pseudonaviculata, but gene family evolution in the context of host adaptation, plant pathogenesis, and trophic lifestyle is poorly understood. This study applied bioinformatic and phylogenetic methods to examine gene family evolution in C. henricotiae, C. pseudonaviculata and 22 related fungi in the Nectriaceae that vary in pathogenic and saprobic (apathogenic) lifestyles. RESULTS: A total of 19,750 gene families were identified in the 24 genomes, of which 422 were rapidly evolving. Among the six Calonectria species, C. henricotiae and C. pseudonaviculata were the only species to experience high levels of rapid contraction of pathogenesis-related gene families (89% and 78%, respectively). In contrast, saprobic species Calonectria multiphialidica and C. naviculata, two of the closest known relatives of C. henricotiae and C. pseudonaviculata, showed rapid expansion of pathogenesis-related gene families. CONCLUSIONS: Our results provide novel insight into gene family evolution within C. henricotiae and C. pseudonaviculata and suggest gene family contraction may have contributed to limited host-range expansion of these pathogens within the plant family Buxaceae.

  PublisherOA PDFDOI

• Additional file 3 of Comparative genomic analysis reveals contraction of gene families with putative roles in pathogenesis in the fungal boxwood pathogens Calonectria henricotiae and C. pseudonaviculata

  Figshare · 2022-01-01

  datasetOpen access

  Additional file 3. Gene gains and losses identified by CAFE for rapidly evolving gene families in the boxwood blight pathogens Calonectria henricotiae and C. pseudonaviculata, and 22 fungal taxa in the Nectriaceae.

  PublisherDOI

• Additional file 7 of Comparative genomic analysis reveals contraction of gene families with putative roles in pathogenesis in the fungal boxwood pathogens Calonectria henricotiae and C. pseudonaviculata

  Figshare · 2022-01-01

  datasetOpen access

  Additional file 7. COG and Pfam annotations and e-values for each protein sequence within rapidly evolving gene families of the boxwood blight pathogens Calonectria henricotiae and C. pseudonaviculata, and 22 fungal taxa in the Nectriaceae.

  PublisherDOI

Recent grants

• Research and Educational Use of North Carolina State University Mycological Herbarium Through Improved Computerization and Internet Presence

  NSF · $252k · 2009–2013

Frequent coauthors

• Larry F. Grand

  North Carolina State University

  65 shared

• Meghan A. McCormick

  Louisiana State University

  65 shared

• B. R. Cody

  23 shared

• Nicholas LeBlanc

  United States Department of Agriculture

  19 shared

• Rytas Vilgalys

  Duke University

  18 shared

• Linda M. Kohn

  Umeå University

  16 shared

• Yatika Kohli

  Mediprobe Research (Canada)

  16 shared

• Jo Anne Crouch

  Agricultural Research Service

  14 shared

Labs

• Structural Pest Management Training & Research FacilityPI

Education

• Ph.D., Entomology

  University of California, Davis

  1994

• M.S., Entomology

  University of California, Davis

  1991

• B.S., Entomology

  University of California, Davis

  1988