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Entomology and Plant Pathology

Dr. Stephen Marek, Associate Professor

B.S. Biology, University of Missouri, 1990

B.S. Biochemistry, University of Missouri, 1990

M.S. Agronomy, University of Missouri, 1994

Ph.D. Plant Pathology, University of California-Davis, 2001

Room/Lab 311D/318/324 NRC



PLP/BOT 3553     Fungi: Myths and More
PLP/BOT 5104     Mycology

Research: Biology and Functional Genomics of Plant Pathogenic Fungi


Switchgrass (Panicum virgatum) is a native tallgrass prairie species that has been developed as biomass feedstock crop for cellulosic biofuels. Its perennial growth habit and widely adapted ecotypes make it promisingly sustainable bioenergy crop that does not compete with food and feed supplies. Numerous diseases affect switchgrass. One of the most prevalent and potentially detrimental is rust caused by Puccinia emaculata. This obligate parasite produces repeating urediniospores and resting teliospores on switchgrass and presumably undergoes sexual recombination on some alternate host. We are collaborating with researchers in the NSF-EPSCoR Bioenergy program to develop identifying DNA barcodes and attempt to identify the alternate host of P. emaculata. In a separate USDA-NIFA-AFRI Sustainable Bioenergy project with researchers at Virginia Tech and Iowa State University, we will attempt to molecularly characterize the races and virulence factors of P. emaculata, as well as, help identify rust-resistant switchgrass germplasm.


Agrobacterium-mediated T-DNA tagging of genes involved in virulence and morphogenesis of fungi infecting Medicago spp. Numerous mutants of M. truncatula are available. Phoma medicaginis causes leaf spot and spring black stem and reproduces asexually, forming conidia in pycnidia. A T-DNA-tagged library of over 1000 transformants has been generated and numerous interesting mutant phenotypes in morphogenesis have been observed. Green and red fluorescent transformants are being used to dissect the cellular interactions of the fungus with Medicago. Leptosphaerulina trifolii causes Lepto leaf spot and reproduces sexually, forming ascospores in pseudothecia. This fungus is closely related to Phoma medicaginis and provides a valuable system for comparing their respective reproductive and pathogenic life styles.


Phymatotrichopsis Root Rot (a.k.a cotton root rot, Texas root rot, Phymatotrichum root rot or Ozonium root rot) is caused by the fungus Phymatotrichopsis omnivora, notorious soilborne fungus inhabiting the alkaline calcareous soils of the southwestern US and northern Mexico. It has broad host range of over 2000 dicot hosts and severely affects cotton, alfalfa, and numerous fruit and nut trees. In collaborations with the Noble Foundation (Ardmore, OK) and University of Oklahoma, (Norman, OK), we have used Medicago spp. (especially M. truncatula) as model hosts to better understand the host-pathogen interaction of this economically important disease and sequence the genome of the causal fungus. A long term goal is to identify resistant germplasm in Medicago.

Molecular characterization of the host-pathogen interaction. The Medicago host plant-side of the interaction is under study in the labs of Rick Dixon, Joe Bouton, Kiran Mysore, Rao Uppalapati, Lloyd Sumner and Carolyn Young at the Noble Foundation. Areas under study include the screening of Medicago germplasm for resistance, microarray analysis of plant gene expression during infection by P. omnivora, and antifungal phytochemicals. The fungal-side of the interaction is under study in our lab at OSU. We are characterizing ESTs from fungus during host plant infection and key life stages such as sclerotia, mycelial strand and sporemat formation. We hope to genetically transform P. omnivora in order to functionally characterize candidate virulence genes.

Genomic and EST sequencing of Phymatotrichopsis omnivora. Bruce Roe's Lab at the University of Oklahoma has been performed using a whole genome shotgun and paired end sequencing approaches, combining next generation pyrosequencing data with traditional Sanger sequencing. ESTs (cDNA libraries) and BAC library clones are also being sequenced to aid annotation and assembly. The P. omnivora sequence data can be searched using BLAST.

Phylogenetics, population genetics and development of diagnostic tools for the casual fungus, Phymatotrichopsis omnivora (synonym Phymatotrichum omnivorum). Isolates of P. omnivora have been collected throughout its natural range in the southwestern US and are being genotyped in collaboration with Carla Garzón. We hope to better understand the population genetics of this fungus in order to possibly identify races and/or the presence of genetic recombination between genotypes. Species- and genotype-specific markers are being developed improve diagnosis in collaborations with Carla Garzón, Francisco Ochoa-Corona and Carolyn Young.


Assessing the efficacy of the silicon supplementation in the control of important fungal pathogens of greenhouse ornamental crops, a collaboration with Sophia Kamenidou and Todd Cavins in the Horticulture and Landscape Architecture (now at Sun Gro Horticulture). We are examining how silicon protects floricultural crop plants grown in soilless peat mixes from Botrytis blight (gray mold), powdery mildew and Phytophthora root rot.


Molecular characterization of the rhizosphere fungi of tallgrass prairies and of the host-pathogen interaction of ectotrophic root fungi with turfgrasses are collaborations with Nathan Walker in Plant Pathology. In order to understand the impacts of indigenous soilborne fungi on native and introduced grasses, we are following the population dynamics of fungi inside the roots of grasses using molecular barcoding and metagenomic analyses. Most of the collections are being made from keystone grass species at the Nature Conservancy's Tallgrass Prairie Preserve, in order to best approximate a pristine rhizosphere, untouched by modern agriculture. To better understand spring dead spot of bermudagrass, the causal fungus Ophiosphaerella herpotricha has been transformed to express GFP and is being used to study its interaction with Cynodon spp.

Laboratory Personnel and Graduate Students:

Kihyuck Choi, pursuing a PhD in Plant Pathology
Research: Confirming T-DNA-tagged mutants of Phoma medicaginis through Agrotransformation-mediated genetic complementations and knock-outs and assessing gene expression by RT-PCR.


Gabriela Orquera, pursuing a MS in Plant Pathology

Research:  Switchgrass rust population biology, DNA barcodes for identification and phylogenetics of Puccinia emaculata, cDNA libraries for RNA-Seq, and SSRs for population biology.


Former Laboratory Personnel:

Madhavi Dhulipala, MS Student in Plant Pathology
Research: Foliar pathosystems for Medicago truncatula, T-DNA tagged (insertional mutagenesis using Agrobacterium-mediated transformation) library of Phoma medicaginis, characterization of the virulence and morphogenesis of generated mutants, cytology of the interaction of P. medicaginis and the closely related Leptosphaerulina trifolii with Medicago spp. Currently mentoring up-and-coming fungal geneticist, Revah Sambaraju in British Columbia.


(James is the one not wearing a hat)
James N. Enis, Research Specialist (2003-2005)
Research: construction binary vectors for Agrobacterium-mediated transformation of fungi, TAIL-PCR, amplification of phylogenetic genes from fungi, methodical record keeping.
Currently: Teaching science at Tulsa Community College.


Sandrine Casanova, Technical Paraprofessional (2005-2006)
Research: dogged transformation of recalcitrant fungi, amplification of Medicago truncatula mutants, phylogeographic study of Phymatotrichopsis omnivora .
Currently: A fitness instructor, Health Manager and proud mom in Lyon, France.


Victor Hernandez-Gordillo (2006)
Research: testing binary vectors for Agrobacterium-mediated transformation of fungi, cDNA libraries.
Currently: pursuing a PhD at Purdue University.


Jenny Stacey, INBRE intern (summer 2006)
Research: characterization of melanization and virulence of insertional mutants of Phoma medicaginis.
Currently: pursuing her BS in biology in Oklahoma City.


Dr. Tim Samuels, Post Doctoral Fellow, 2006-2007 Research: Transcriptome characterization and protoplast transformation of Phymatotichopsis omnivora. Constructed numerous cDNA libraries of P. omnivora during various developmental and parasitic stages and initiated the construction of novel P. omnivora-specific transformation vectors.
Currently: Working as a Senior Molecular Genetic Specialist in the Department of Plant and Soil Sciences at OSU.


Dr. Carrie Smith, Postdoctoral Fellow (2008-2009)
Research: Construction and validation of Agrotransformation vectors and signature-tagged ESTs for Phymatotrichopsis omnivora. Characterization and identification of T-DNA tagged genes in Phoma medicaginis.  Currently:  Working as the Biological Safety Officer of the University of Wisconsin.


Ian Moncrief, MS in Plant Pathology, 2006-2010
Research: Molecular karyotyping of Phymatotrichopsis omnivora isolates and used RT-qPCR to follow the expression of candidate virulence genes during infection of host plant roots. Currently: Pursuing a PhD in Plant Pathology at OSU with Jacque Fletcher in NIMFFAB.


Sophia Kamenidou, MS (2005) and PhD (2009) in Plant Science (Advisors: Todd Cavins, SunGro Horticulture and Mike Smith, HLA, respectively)
Research: Silicon supplementation of greenhouse floricultural crops for disease suppression of Botrytis blight, powdery mildew and Phytophthora root rot. Agrotransformed Botrytis cinerea to express GFP and DsRed to study the cytology of silicon-induced resistance.
Currently: Living in the Los Angeles area, working at the University of California, Riverside, proud mother of twins(!). 

Hourly Technicians:

Richard Muller, BS in Microbiology (with Walker Lab)
Sibo Hlatywayo, BS student in Chemical Engineering
Myla Mirdo, BS in Microbiology (with Walker Lab)
Cody Key, pre-Pharm-BS student in Microbiology
Gayan Herath, MS in environmental engineering
Jennifer Nguyen, BS in chemical engineering and BA in music
Jillian Prather, BS student in biochemistry and molecular biology, predental
Samantha Sanders, BS student in biochemistry and molecular biology, prenursing

Photo from lab party for Sandrine and Victor

Recent Publications:

Click here for a complete PDF list of my publications.

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