Bacterial community shifts of commercial apples, oranges, and peaches at different harvest points across multiple growing seasons

Authors: GOFORTH, MADISON - University Of Arizona; COOPER, MARGARETHE - University Of Arizona; OLIVER, ANDREW - Orise Fellow; PINZON, JANNETH - University Of California, Davis; SKOTS, MARIYA - University Of California, Davis; OBERGH, VICTORIA - University Of Arizona; SUSLOW, TREVOR - University Of California, Davis; FLORES, GILBERTO - California State University; Huynh, Steven; Parker, Craig; MACKELPRANG, RACHEL - California State University; COOPER, KERRY - University Of Arizona

Submitted to: PLOS ONE
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/4/2024
Publication Date: 4/16/2024
Citation: Goforth, M., Cooper, M.A., Oliver, A.S., Pinzon, J., Skots, M., Obergh, V., Suslow, T.V., Flores, G.E., Huynh, S., Parker, C.T., Mackelprang, R., Cooper, K.K. 2024. Bacterial community shifts of commercial apples, oranges, and peaches at different harvest points across multiple growing seasons. PLOS ONE. 19(4). Article e0297453. https://doi.org/10.1371/journal.pone.0297453.
DOI: https://doi.org/10.1371/journal.pone.0297453

Interpretive Summary: Assessing the microbes present on tree fruit surfaces (carpospheres) as the fruit enters postharvest processing could have useful applications, as these microbes could have a major influence on spoilage, food safety, verification of packing process controls, or other aspects of processing. The goal of this study was to establish a baseline profile of bacterial communities associated with apple (pome fruit), peach (stone fruit), and Navel orange (citrus fruit) at harvest. We found that commercial peaches had the greatest bacterial richness (a measure of the total number of bacterial species and their relative abundances) followed by oranges then apples. Time of harvest significantly changed bacterial diversity (a measure of the total number of bacterial species) in oranges and peaches, but not apples. Shifts in diversity varied by fruit type, where 70% of the variability in beta diversity on the apple carposphere was driven by the gain and loss of species (i.e., nestedness). The peach and orange carposphere bacterial community shifts were driven by nearly an even split between turnover (species replacement) and nestedness. We identified a small core microbiome for apples and peaches, and a relatively diverse core microbiome for oranges. Overall, our findings illustrate the importance of time of harvest on the dynamics of bacterial communities found on major commercial tree fruit suggesting that at each harvest the microbiome was mostly unique and thus there is a lack of microbial index for a particular fruit. We discuss the implications entering postharvest packing and processing.

Technical Abstract: Assessing the microbes present on tree fruit carpospheres as the fruit enters postharvest processing could have useful applications, as these microbes could have a major influence on spoilage, food safety, verification of packing process controls, or other aspects of processing. The goal of this study was to establish a baseline profile of bacterial communities associated with apple (pome fruit), peach (stone fruit), and Navel orange (citrus fruit) at harvest. We found that commercial peaches had the greatest bacterial richness followed by oranges then apples. Time of harvest significantly changed bacterial diversity in oranges and peaches, but not apples. Shifts in diversity varied by fruit type, where 70% of the variability in beta diversity on the apple carposphere was driven by the gain and loss of species (i.e., nestedness). The peach and orange carposphere bacterial community shifts were driven by nearly an even split between turnover (species replacement) and nestedness. We identified a small core microbiome for apples and peaches, and a relatively diverse core microbiome for oranges. Overall, our findings illustrate the important temporal dynamics of bacterial communities found on major commercial tree fruit, and we discuss their implications entering postharvest packing and processing.