Fig. 8

Seasonality of EcO157 survival and core microbiomes on lettuce stored in MAP. a Heatmap table of the difference in EcO157 population size [ΔLog(CFU/g)] between either mid- or endpoint of storage at 6 °C and immediately after inoculation. The ten values representing lowest survival (green; nearly all of which, spring samples) and highest survival (brown; all of which, fall samples) out of all inoculated samples across the five experiments (n = 49) are listed. Values in blue font indicate those for samples most significantly associated with highest EcO157 survival also by RP analysis (Fig. 7). b Histogram of LDA scores computed using LEfSe analysis for taxa that discriminate between lettuce microbiomes supporting higher and lower survival of EcO157 during cold storage (biomarkers with LDA value ≥ 2.0 depicted). c NMDS plot illustrating spring and fall bacterial community structure on lettuce from conventional (C) and experimental (E) fields across the five harvests stored at 6 °C. The metagenomes associated with fall and spring harvests, including inoculated and noninoculated samples, were statistically different (PERMANOVA, P = 0.0001). d Progression of core and noncore (NC) microbiomes on spring and fall lettuce from pre-storage to end of storage at 6 °C and 24 °C. For 6 °C storage, relative abundance (RA) of each taxa was averaged over mid- and endpoint samples. RA shown for Erwiniaceae (Erw), Pseudomonadaceae (Pseud); Enterobacteriaceae (Ent); Yersiniaceae (Yers); Propionibacteriaceae (Prop, Propionibacterium); and Rhodocyclaceae (Rhod, Dechlorosoma suillum). In the fall 24 °C-stored lettuce microbiome, Exiguobacterium sibiricum (Bacillales) was present at RA = 0.17% and is not depicted. Taxa RA was computed with EcO157 removed for determination of all core microbiomes