Chapter 2. Cataloging Strains: Isolation and Identification of Invasive Fungi on Citrus limon

This project was sponsored by Counter Culture Labs and conducted in the San Francisco Bay Area. For questions and information on the project, please contact Louis Huang at


An unknown mold on a Citrus limon tree was isolated and identified using standard microbiology protocols: streaking, microscopy, and DNA barcoding. This was done to identify invasive mold that was hindering the growth of C. limon fruit and to catalog its relationship with other similar fungal species. The method details an efficient and cost-effective way to isolate and identify a wild-type organism.


The isolation and identification of a wild-type organism infecting C. limon was conducted. Due to its characteristics of phenotype and growth behavior—an earthy-colored fuzzy organism growing on expiring fruit—the targeted organism was presumed to be a mold. Using a combination of streaking, microscopy, and DNA barcoding, the strain of invasive mold was identified.  The barcode sequence was matched with other genetically similar strains and cataloged in a phylogenetic tree.

The streaking method isolates a pure strain microorganism from a diverse population. Microscopy, as applied in this experiment, is the use of microscopes to classify the genus of the organism, also known as taxonomy. The method of DNA barcoding, also a taxonomic indicator, ...

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