Quandt, C. Alisha

Research

research overview

Dr. Quandt's lab studies fungal evolutionary biology - especially the evolution of host association, the evolution of pathogenicity/ parasitism, and how fungi interact with other microorganisms. Phylogenetics, genomics, metagenomics, transcriptomics, and molecular community ecology are tools that the Quandt lab are currently using to address these larger interests in fungal biology.

keywords

Fungal genomics, Phylogenetics, Phylogenomics, Comparative Genomics, Fungal-microbial interactions

Publications

selected publications

chapter
- Metabolic Constraints and Dependencies Between “Uncultivable” Fungi and Their Hosts. 33-57. 2024
- Phylogenetic Advances in Leotiomycetes, an Understudied Clade of Taxonomically and Ecologically Diverse Fungi. 284-294. 2021
journal article
- Classes and phyla of the kingdom Fungi. Fungal Diversity. 2024
- The power of citizen science to advance fungal conservation. Conservation Letters. 2024
- Patterns recovered in phylogenomic analysis of Candida auris and close relatives implicate broad environmental flexibility in Candida/Clavispora clade yeasts. Microbial Genomics. 2024
- Biological knowledge shortfalls impede conservation efforts in poorly studied taxa-A case study of Laboulbeniomycetes. Journal of Biogeography. 29-39. 2024
- Heritable differences in abundance of bacterial rhizosphere taxa are correlated with fungal necrotrophic pathogen resistance. Molecular Ecology. 2024
- Recent fieldwork and fungarium studies double known diversity of Chlorosplenium and improve understanding of species distributions.. Mycologia. 993-1018. 2024
- Mr. Toad's wild fungi: Fungal isolate diversity on Colorado boreal toads and their capacity for pathogen inhibition. Fungal Ecology. 2023
- A review of the taxonomic diversity, host-parasite interactions, and experimental research on chytrids that parasitize diatoms. Frontiers in Microbiology. 2023
- Five new species of Gloeandromyces (Fungi, Laboulbeniales) from tropical American bat flies (Diptera, Streblidae), revealed by morphology and phylogenetic reconstruction. Mycologia. 714-737. 2023
- A combined microscopy and single-cell sequencing approach reveals the ecology, morphology, and phylogeny of uncultured lineages of zoosporic fungi. mBio. 2023
- Evaluating the diversity of the enigmatic fungal phylum Cryptomycota across habitats using 18S rRNA metabarcoding. Fungal Ecology. 2023
- Comparative genomics and phylogenomic investigation of the class Geoglossomycetes provide insights into ecological specialization and the systematics of Pezizomycotina. Mycologia. 499-512. 2023
- Hyperparasitic fungi—definitions, diversity, ecology, and research 2023
- Global consortium for the classification of fungi and fungus-like taxa. Mycosphere Online: Journal of Fungal Biology. 1960-2012. 2023
- Two new species of Phaeohelotium (Leotiomycetes: Helotiaceae) from Chile and their putative ectomycorrhizal status.. Fungal Systematics and Evolution. 231-249. 2022
- Diploid-dominant life cycles characterize the early evolution of Fungi. Proceedings of the National Academy of Sciences of USA. 2022
- Protocol for single-cell isolation and genome amplification of environmental microbial eukaryotes for genomic analysis. STAR Protocols. 2022
- Improving Fungal Cultivability for Natural Products Discovery. Frontiers in Microbiology. 2021
- A single-cell genomics pipeline for environmental microbial eukaryotes. iScience. 2021
- A growing pandemic: A review of Nosemaparasites in globally distributed domesticated and native bees. PLoS Pathogens. 2020
- Revisiting the aquatic phycomycete biota of the Douglas Lake region since the time of Dogma and Sparrow 2020
- Fungi in the Marine Environment: Open Questions and Unsolved Problems. mBio. 2019
- Chromosome rearrangements shape the diversification of secondary metabolism in the cyclosporin producing fungus Tolypocladium inflatum. BMC Genomics. 2019
- Leveraging single-cell genomics to expand the fungal tree of life. Nature Microbiology. 1417-1428. 2018
- Harnessing the power of phylogenomics to disentangle the directionality and signatures of interkingdom host jumping in the parasitic fungal genus Tolypocladium. Mycologia. 104-117. 2018
- A phylogenetically-based nomenclature for Cordycipitaceae (Hypocreales). IMA Fungus: the global mycological journal. 335-353. 2017
- The genome of an intranuclear parasite, Paramicrosporidium saccamoebae, reveals alternative adaptations to obligate intracellular parasitism. eLife. 2017
- Morphological, molecular, and ultrastructural characterization of Rozella rhizoclosmatii, a new species in Cryptomycota. Fungal Biology. 1-10. 2017
- Ectomycorrhizal ecology is imprinted in the genome of the dominant symbiotic fungus Cenococcum geophilum. Nature Communications. 2016
- Fine-scale spatial genetic structure of a fungal parasite of coffee scale insects. Journal of Invertebrate Pathology. 34-41. 2016
- Differential Expression of Genes Involved in Host Recognition, Attachment, and Degradation in the Mycoparasite Tolypocladium ophioglossoides. G3: Genes, Genomes, Genetics. 731-741. 2016
- New 1F1N Species Combinations in Ophiocordycipitaceae (Hypocreales). IMA Fungus: the global mycological journal. 357-362. 2015
- Metagenome sequence of Elaphomyces granulatus from sporocarp tissue reveals Ascomycota ectomycorrhizal fingerprints of genome expansion and a Proteobacteria-rich microbiome. Environmental Microbiology. 2952-2968. 2015
- The genome of the truffle-parasite Tolypocladium ophioglossoides and the evolution of antifungal peptaibiotics. BMC Genomics. 2015
- Phylogenetic-based nomenclatural proposals for Ophiocordycipitaceae (Hypocreales) with new combinations in Tolypocladium. IMA Fungus: the global mycological journal. 121-134. 2014
- The phylogenetic placement of hypocrealean insect pathogens in the genus Polycephalomyces: An application of One Fungus One Name. Fungal Biology. 611-622. 2013
- The Genome of Tolypocladium inflatum: Evolution, Organization, and Expression of the Cyclosporin Biosynthetic Gene Cluster. PLoS Genetics. 2013
- Draft Genome Sequence of the Cyclosporin Producing Fungus Tolypocladium inflatum Reveals Complex Patterns of Secondary Metabolite Evolution and Expression. PLoS Genetics. 2013
- Phylogenetic placement of the ectomycorrhizal genus Cenococcum in Gloniaceae (Dothideomycetes). Mycologia. 758-765. 2012
- A class-wide phylogenetic assessment of Dothideomycetes. Studies in Mycology. 1-15. 2009

Teaching

courses taught

EBIO 3400 - Microbiology
Primary Instructor - Spring 2018 / Spring 2019 / Spring 2020 / Spring 2022 / Spring 2024
Surveys distinguishing characteristics of microorganisms based on structural-functional relationships, taxonomy, growth and physical-chemical agents of control including antibiotics, metabolism and genetics. Introduces applied microbiology emphasizing infectious diseases, basic concepts of immunology and microbial ecology. Uses animals and/or animal tissues. Recommended prerequisites: EBIO 1210 and EBIO 1220 and EBIO 1230 and EBIO 1240 (minimum grade C-).
EBIO 4460 - Special Topics
Primary Instructor - Fall 2018 / Fall 2019 / Fall 2021 / Fall 2022 / Fall 2023
Familiarizes students with specialized areas of biology. May be repeated up to 15 total credit hours. Recommended prerequisites: EBIO 1210 and EBIO 1220 and EBIO 1230 and EBIO 1240 (minimum grade C-). Same as EBIO 5460.
EBIO 4620 - Mycology: the Biology of Fungi
Primary Instructor - Fall 2024
A broad taxonomic and biological survey of fungi. This is an upper division lecture, field, and lab-based course designed for biology majors interested in microbial science. Field and Laboratory components include two lab practicals in which students identify macro- and micro- fungi, preparation of a fungal specimen collection, and the use of light microscopy for identification and visualization of fungal structures. Formerly offered as a special topics course. Recommended prerequisites: EBIO 2070 and EBIO 3080.
EBIO 4870 - Independent Research: Upper Division
Primary Instructor - Fall 2018 / Spring 2019 / Fall 2019 / Spring 2020 / Spring 2024
May be repeated up to 6 total credit hours.
EBIO 5460 - Special Topics
Primary Instructor - Fall 2018 / Fall 2019 / Fall 2021 / Fall 2022 / Fall 2023
Familiarizes students with specialized areas of biology. May be repeated up to 9 total credit hours. Same as EBIO 4460.
EBIO 6300 - Seminar in Organismic Biology
Primary Instructor - Spring 2022 / Fall 2023 / Fall 2024
May be repeated up to 7 total credit hours.

Background

education and training

Ph.D., Oregon State University 2014
B.S., University of South Carolina - Columbia 2006

awards and honors

Alexopoulos Prize, conferred by Mycological Society of America, 2024

International Activities

geographic focus

Belgium Country
Brazil Country
Germany Country
Mozambique Country
Norway Country
Panama Country
Peru Country
Portugal Country
Thailand Country
United Kingdom Country

Other Profiles

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Positions

Research Areas

Research

research overview

keywords

Publications

selected publications

chapter

journal article

Teaching

courses taught

Background

education and training

awards and honors

International Activities

geographic focus

Other Profiles

ORCID iD

Google Scholar

ResearchGate