Fruit surface microbiomes are gaining increasing interest due to the relative ease in community profiling via Next-Generation Sequencing and postulated benefits of native microbiome competition with and biocontrol of fruit pathogens. This thesis is separated into two parts. The first, is a literature review on the assembly and function of fruit microbiomes. Many field and postharvest treatments affect fruit microbiomes, but that it is difficult to glean functional shifts associated with compositional ones. In the second part, we investigated the effects of the ethylene inhibitor aminoethoxyvinylglycine and low-oxygen controlled atmosphere (CA) storage on the apple microbiome. Microbiome shifts that occur as a result of long-term CA storage are associated with decreased abundance in pathways using oxygen as a reactant, linking potential functional microbiome changes to selection pressures.