Commercial washing and storage over shelf life impact bacterial communities more than the fungal communities on baby spinach

Many types of minimally processed fresh produce, including baby spinach, are sensitive to microbial spoilage and other defects that influence quality and consumer acceptance. However, there is limited understanding of how various growing, processing, and storage practices can influence the composition of bacterial and fungal communities on leafy greens, including the proliferation of spoilage microorganisms. Baby spinach samples obtained from a single supply chain at various stages of the produce supply chain (i.e., after harvest and after commercial washing, packaging, and storage) over 1 year were analyzed using 16S ribosomal RNA and internal transcribed spacer amplicon sequencing to assess changes in the bacterial and fungal microbiota. Our data showed that there were significant differences in the bacterial and fungal community composition of Harvest samples associated with (i) the geographic area where the spinach was grown and (ii) seasonality (i.e., time since the start of the growing season). After commercial washing and during storage, Pseudomonas spp. dominated the bacterial community (>60% average relative abundance [RA], compared to 8.62% average RA on Harvest samples). Analysis at the amplicon sequence variant (ASV) level revealed that the RA of 39 out of 868 Pseudomonas ASVs significantly increased over shelf life, indicating that only select taxa from a particular genus might drive spoilage. Four of the top five fungal genera maintained a high RA across harvest, washing, and postharvest storage, except for one genus ( Vishniacozyma ) that was only represented among the top five in samples after washing. Our data could be used to inform more targeted quality management practices. IMPORTANCE While spoilage of leafy greens can be influenced by a variety of factors, the limited understanding of how microbial communities change throughout the various stages of the produce supply chain remains a barrier to identifying factors that drive baby spinach spoilage. Additionally, many studies focus solely on the bacterial community, leaving gaps in understanding how the fungal community is impacted by processing and storage conditions. The findings of this study deepen our understanding of how the bacterial and fungal communities on baby spinach are influenced by both (i) preharvest factors (i.e., growing region and seasonality) and (ii) postharvest factors (i.e., commercial washing/packaging and storage over shelf life). This research deepens our understanding of the variation of the microbial composition of leafy greens and specifically suggests the potential value of spoilage mitigation efforts that target specific Pseudomonas taxa.