Research in the wine industry has previously characterized many aspects of the wine making process from soil fertility to the community of microbes in must and wine, but the epiphytic bacterial and fungal communities have not been studied throughout grape development. This project aims to investigate the epiphytic grape microbiome to better understand its role in disease and grape development, and the effects of terroir on the microbiome, by examining the epiphytic microbiome of developing and sour rot infected grapes in New York and Tasmania. Sour rot is characterized by a distinct vinegar smell that is caused by the combination of Drosophila spp., fermentative yeasts, the acetic acid producing bacteria Acetobacter and Gluconobacter. Total DNA was extracted from rinsate berry samples, and the bacterial 16S ribosomal RNA (rRNA) and fungal internal transcribed spacer (ITS) regions were amplified for Illumina sequencing. The tool Quantitative Insights into Microbial Ecology (Qiime) was used to quality filter the sequences and identify the operational taxonomic units (OTUs) present in each sample. The taxonomies of these OTUs were assigned using the Greengenes and Unite databases. Statistical analysis was done in Statistical Analysis of Metagenomic Profiles (STAMP), and hierarchical clustering and data visualizations were done in R. Sour rot infected grapes were found to have large communities of acetic acid producing bacteria in both terroirs, however the typical fermentative yeasts were not present in large quantities in New York. In general, when microbes known to cause sour rot were present on symptomatic grapes, they were also present on asymptomatic grapes, supporting an active role for Drosophila spp. in the disease complex, rather than simply acting as a vector. The core epiphytic microbiome remained relatively consistent throughout development but varied dramatically by terroir and year.

Library of Congress Subject Headings

Grapes--Diseases and pests; Microbial genomics; Microorganisms

Publication Date


Document Type


Student Type


Degree Name

Bioinformatics (MS)

Department, Program, or Center

Thomas H. Gosnell School of Life Sciences (COS)


Michael Osier

Advisor/Committee Member

Lance Cadle-Davidson

Advisor/Committee Member

Jeffrey Lodge


RIT – Main Campus

Plan Codes