Bacteria Associated with Tomato Microbiomes: Ripe vs. Unripe

Introduction: The majority of tomatoes that have been implicated in Salmonella outbreaks associated with Virginia grown tomatoes were harvested when they were green (a common agricultural practice). Enhanced understanding of bacteria associated with tomato microbiomes may shed light on how pathogens such as Salmonella become associated with the fruits and result in foodborne outbreaks. Different stages of ripening may harbor distinct microbial communities that play currently un-described, yet significant roles in plant responses to introduction and persistence of human pathogens on tomato surfaces.

Purpose: The purpose of this study is to describe microbial communities associated with tomato fruits at mature green and red ripe stages to better understand microbial dynamics of different ripening stages that may be significant to food safety.

Methods: Green and red tomatoes were aseptically collected in the summer of 2014 from the Agricultural Research Station in Painter, Virginia. Culture-independent DNA was extracted from washes of fruit surfaces. PCR amplicons of V1-V3 region of 16S rRNA gene were used to characterize bacterial communities associated with green and red fruits. Bioinformatic analyses were performed using QIIME.

Results: Ripe and unripe tomato surfaces supported distinct microbial communities in principal coordinates analyses (P < 0.001). Red ripe tomatoes supported a higher relative abundance of Enterobacteriaceae (P = 0.001) and unripe tomatoes demonstrated higher incidences of certain taxa including; Sphingomonas (P = 0.036), Pseudomonadaceae (P = 0.036), and Rhizobiaceae (P = 0.036).

Significance: These data will contribute to an improved understanding of food safety risks correlated with ripening dynamics and improved recommendations for agricultural practices associated with harvest of tomato at specific stages of maturity.