Microbiomes of soils and leafy vegetables in urban agriculture systems reflect crop management and local environmental conditions

ABSTRACT Soil and plant microbiomes influence crop quality and preharvest food safety, yet these processes have been largely unexplored in urban agriculture environments. Here, we investigated how the microbiota of soil and leafy greens (e.g., kale, lettuce, chard, and cabbage) interact with site-specific management practices and environmental conditions across seven urban agriculture sites in the greater Washington, DC, area. Samples of leaf tissue ( n = 92), rhizosphere soil ( n = 92), and “native” or bulk soil ( n = 39) were collected and analyzed with 16S rRNA gene and ITS2 genomic region amplicon sequencing. Microbial community composition varied significantly across sites for all sample types, as influenced by irrigation water source (i.e., municipal vs natural water), crop type, soil pH, soil moisture content, and climatic conditions (i.e., rainfall, temperature). Rhizosphere soils harbored the most bacterial taxa known to respond to organic inputs (e.g., Massilia and various members of Firmicutes and Verrucomicrobiota ), whereas fungal networks dominated by saprotrophic members of Ascomycota were more stable in the bulk soils. Source-tracking analysis indicated that the phyllosphere microbiota, although variable and transient in composition, were largely derived from the rhizosphere soil. Notably, leafy greens at some sites were enriched with taxa associated with biocontrol potential (e.g., Lactobacillaceae ). Moreover, machine learning models yielded strong performance in predicting specific production sites based on the bacterial communities in the rhizosphere and phyllosphere, suggesting possible microbiome-based applications for food traceability. Collectively, these findings demonstrate how local environments and crop management practices shape preharvest leafy green microbiomes in urban production. IMPORTANCE Urban farming and gardening are rapidly expanding to support local communities and enhance food security, yet these small-scale food systems are often established in uniquely developed landscapes and with resource-dependent operations. This study shows that complex site-specific factors influence the soil and leafy green microbiomes in urban agriculture systems. Our findings have important implications for future efforts in targeted farm management to enhance sustainable production and preharvest food safety.