A Polyphasic Taxonomy Approach in the Identification of a New Strain of Penicillium thymicola

Abstract

Fungal taxonomy has been a consistent challenge in mycology for many decades. This is partly the result of phenotypic instability of fungi across different environments and generations, wherein a species may alter their morphology and secondary metabolite profile in response to their growth conditions. Thus, the use of a polyphasic approach to fungal taxonomy can be used to ensure the proper categorisation of fungal species. The polyphasic approach to fungal taxonomy applies a combination of taxonomic techniques in the identification of a fungal species, including macro- and micromorphological characteristics, phylogenetics and genetic barcoding, and secondary metabolite expression. Presented in this thesis is a polyphasic approach to taxonomize a newly isolated strain of Penicillium thymicola, isolated as an actinomycete culture contaminant in a chemical biology research laboratory. Throughout the analysis, the isolated strain is compared with a previously characterized strain of P. thymicola, DAOMC 180753. In our approach, three different fungal taxonomy techniques are applied to compare the two P. thymicola strains to each other and to the previously established P. thymicola type strain description. The fungal strains’ macro- and micromorphological phenotypes were analyzed on six different media types, a phylogenetic analysis was performed using accepted Penicillium sp. barcode gene sequences, and their metabolomic profiles were characterised via UPLC-HRMS. Based on these investigations, it was determined that the newly isolated strain was, in fact, a strain of P. thymicola. However, the previously characterised strain DAOMC 180753 diverged from the official species description in both the morphological and metabolomic analyses, which were the result of either strain degeneration or species misidentification.