Plant Pathology Department



Ashley Stengel

Kimberly M. Stanke

Amanda C. Quattrone

Joshua R. Herr

Date of this Version



Stengel A, Stanke KM, Quattrone AC and Herr JR (2022) Improving Taxonomic Delimitation of Fungal Species in the Age of Genomics and Phenomics. Front. Microbiol. 13:847067.

doi: 10.3389/fmicb.2022.847067


Copyright © 2022 Stengel, Stanke, Quattrone and Herr. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY).


Species concepts have long provided a source of debate among biologists. These lively debates have been important for reaching consensus on how to communicate across scientific disciplines and for advancing innovative strategies to study evolution, population biology, ecology, natural history, and disease epidemiology. Species concepts are also important for evaluating variability and diversity among communities, understanding biogeographical distributions, and identifying causal agents of disease across animal and plant hosts. While there have been many attempts to address the concept of species in the fungi, there are several concepts that have made taxonomic delimitation especially challenging. In this review we discuss these major challenges and describe methodological approaches that show promise for resolving ambiguity in fungal taxonomy by improving discrimination of genetic and functional traits. We highlight the relevance of eco-evolutionary theory used in conjunction with integrative taxonomy approaches to improve the understanding of interactions between environment, ecology, and evolution that give rise to distinct species boundaries. Beyond recent advances in genomic and phenomic methods, bioinformatics tools and modeling approaches enable researchers to test hypothesis and expand our knowledge of fungal biodiversity. Looking to the future, the pairing of integrative taxonomy approaches with multi-locus genomic sequencing and phenomic techniques, such as transcriptomics and proteomics, holds great potential to resolve many unknowns in fungal taxonomic classification.