Weather factors, soil microbiome, and bacteria-fungi interactions as drivers of the epiphytic phyllosphere communities of romaine lettuce

Authors: Brandl, Maria; MAMMEL, MARK - Food And Drug Administration(FDA); Simko, Ivan; RICHTER, TAYLOR - Food And Drug Administration(FDA); GEBRU, SOLOMON - Food And Drug Administration(FDA); LEONARD, SUSAN - Food And Drug Administration(FDA)

Submitted to: Food Microbiology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/7/2023
Publication Date: 3/13/2023
Citation: Brandl, M., Mammel, M., Simko, I., Richter, T., Gebru, S., Leonard, S. 2023. Weather factors, soil microbiome, and bacteria-fungi interactions as drivers of the epiphytic phyllosphere communities of romaine lettuce. Food Microbiology. 113. Article 104260. https://doi.org/10.1016/j.fm.2023.104260.
DOI: https://doi.org/10.1016/j.fm.2023.104260

Interpretive Summary: Lettuce is associated with recurrent outbreaks of Shiga toxin-producing E. coli (STEC) infections following seasonal trends. We investigated two romaine lettuce cultivars, which differ in shelf life and were planted at two different locations in the Salinas Valley, California, for their leaf microbiome prior to harvest in late-spring and -fall. No significant difference was observed in the leaf microbiome of the two cultivars. However, harvest season and field location were significant factors in the bacterial and fungal/oomycete community compositions of the leaves. The relative abundance of fungal vs bacterial members in the microbiome was 3.79x higher in fall-harvested lettuce than spring and the fall mycobiome comprised several lettuce pathogens. The Pseudomonadaceae and Erwiniaceae dominated the leaf bacterial communities by the end of both seasons. The ratio of Pseudomonadaceae to that of Enterobacteriaceae was greater in the fall than spring and was negatively correlated with solar radiation intensity, evapotranspiration, and wind speed. The latter weather factors showed lower daily averages in late fall, thus supporting the greater relative abundance of the Pseudomonadaceae on the lettuce leaves during that period. Surface soil next to the lettuce plants harbored bacterial communities that were more diverse than those on leaves and did not differ by cultivar. A large proportion of the leaf bacterial species were shared with those in soil, indicating microbiome transmission from the soil surface to the canopy. Our findings shed light on bacterial and fungal communities of lettuce leaves and the various abiotic factors affecting their composition.

Technical Abstract: Lettuce is associated with seasonal outbreaks of Shiga toxin-producing Escherichia coli infections. Previously, we investigated the leaf microbiome of two lettuce cultivars after processing and during storage (Leonard et al 2021). Sampling the same experimental crops, we here characterized the lettuce phyllosphere bacterial, fungal, and oomycete communities at harvest in late-spring and -fall in California using metagenomics. Harvest season and field type, but not cultivar, significantly influenced the microbiome composition of leaves and surface soil near plants. Phyllosphere and soil microbiome compositions were correlated with specific weather factors. The relative abundance of Enterobacteriaceae, but not E. coli, was enriched on leaves (5.2%) compared to soil (0.4%) and correlated positively with minimum air temperature and wind speed. Co-occurrence networks revealed seasonal trends in fungi-bacteria interactions on leaves. These associations represented 39%-44% of the correlations between species. All significant E. coli co-occurrences with fungi were positive, while all negative associations were with bacteria. A large proportion of the leaf bacterial species was shared with those in soil, indicating microbiome transmission from the soil surface to the canopy. Our findings provide new insight into factors that shape lettuce microbial communities and the microbial context of foodborne pathogen immigration events in the lettuce phyllosphere.