Profiling bacterial communities of irrigation water and leafy green vegetables produced by small‑scale farms and sold in informal settlements in South Africa

Morogo is an African indigenous term used for leafy green vegetables harvested in the wild or cultivated in small-scale farms and consumed by the local populations of the region. Small-scale farmers have gained recognition as important suppliers of morogo to informal settlements. In commercial production systems, leafy green vegetables have increasingly been reported as associated with foodborne pathogens and disease outbreaks. Little is known of the presence of these organisms on leafy green vegetables in the informal unregulated food systems. This study aimed to profile bacterial communities in irrigation water (flooding and overhead irrigation water) and leafy green vegetables (Brassica rapa L. chinensis and Brassica rapa varieties of morogo) to establish the natural bacterial flora at the water-fresh produce interface from five small-scale farms in two provinces in South Africa. Illumina MiSeq high-throughput sequencing showed that each farm exhibited a unique bacterial community composition, with an overall high relative abundance of Proteobacteria, Firmicutes and Actinobacteria, including prominent families such as Burkholderiaceae (48%), Enterobacteriaceae (34%), Bacillales Family XII (8%), Rhodobacteraceae (3%), Micrococcaceae (1.98%) and Pseudomonadaceae (1.79%). Specific Enterobacteriaceae Serratia, Enterobacter, Salmonella, Shigella, Escherichia coli, Buchnera, Citrobacter, Klebsiella and Proteus were identified, in addition to unique communities associated with plant or irrigation water source. These findings suggest that the edible plant microbiome can play an important role as transient contributor to the human gut and has the potential to affect overall health

Profiling bacterial communities of irrigation water and leafy green vegetables produced by small-scale farms and sold in informal settlements in South Africa

AVAILABILITY OF DATA AND MATERIALS : Sequence data are available at NCBI-SRA under submission numbers SUB12270895 and SUB12272756 for BioProject number PRJNA900001.ADDITIONAL FILE 1: TABLE S1. Samples analysed for bacterial community characterisation. TABLE S2. Taxonomic breakdown of core bacterial taxa present in flooding irrigation water. TABLE S3. Bacterial families that are associated with isolation and outbreaks in South Africa.Morogo is an African indigenous term used for leafy green vegetables harvested in the wild or cultivated in small-scale farms and consumed by the local populations of the region. Small-scale farmers have gained recognition as important suppliers of morogo to informal settlements. In commercial production systems, leafy green vegetables have increasingly been reported as associated with foodborne pathogens and disease outbreaks. Little is known of the presence of these organisms on leafy green vegetables in the informal unregulated food systems. This study aimed to profile bacterial communities in irrigation water (flooding and overhead irrigation water) and leafy green vegetables (Brassica rapa L. chinensis and Brassica rapa varieties of morogo) to establish the natural bacterial flora at the water-fresh produce interface from five small-scale farms in two provinces in South Africa. Illumina MiSeq high-throughput sequencing showed that each farm exhibited a unique bacterial community composition, with an overall high relative abundance of Proteobacteria, Firmicutes and Actinobacteria, including prominent families such as Burkholderiaceae (48%), Enterobacteriaceae (34%), Bacillales Family XII (8%), Rhodobacteraceae (3%), Micrococcaceae (1.98%) and Pseudomonadaceae (1.79%). Specific Enterobacteriaceae Serratia, Enterobacter, Salmonella, Shigella, Escherichia coli, Buchnera, Citrobacter, Klebsiella and Proteus were identified, in addition to unique communities associated with plant or irrigation water source. These findings suggest that the edible plant microbiome can play an important role as transient contributor to the human gut and has the potential to affect overall health.The Water Research Commission (WRC) for the funded project “Measurement of water pollution determining the sources and changes of microbial contamination and impact on food safety from farming to retail level for fresh vegetables”, the Department of Science and Innovation (DSI)—National Research Foundation (NRF) Centre of Excellence in Food Security, the Partnerships for Enhanced Engagement in Research (PEER) USAID/DST funded project “Characterizing and tracking of antimicrobial resistance in the water-plant-food public health interface” and in part by the NRF of South Africa.https://cabiagbio.biomedcentral.comhj2023Plant Production and Soil Scienc