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Bacterial biomes and potential human pathogens in irrigation water and leafy greens from different production systems described using pyrosequencing

Jongman, M., Chidamba, L., Korsten, L.
Journal of applied microbiology 2017 v.123 no.4 pp. 1043-1053
Aeromonas, Escherichia, Salmonella, animal pathogens, cabbage, commercial farms, ecosystems, gardens, high-throughput nucleotide sequencing, irrigated farming, irrigation, irrigation water, lettuce, microbiological quality, production technology, ribosomal DNA, river water, secondary infection
AIMS: To investigate the influence of irrigation water microbial quality on leafy green vegetables produced in commercial and small‐scale farms as well as homestead gardens using pyrosequencing. METHODS AND RESULTS: Next generation sequencing analysis of the V1–V3 hypervariable region of bacterial 16S rDNA was used to compare bacterial diversity in irrigation water sources and on leafy vegetables. In all samples (12) analysed, the phylum Proteobacteria (64·5%), class Gammaproteobacteria (56·6%) and genus Aeromonas (14·4%) were found to be dominant. Of the total Escherichia sequences detected in tested samples, lettuce (16·3%) from the one commercial farm harboured more sequences than cabbage from the small‐scale farm (1·3%) or homestead gardens (1·9%). Escherichia sequences were detected in both irrigation water (4·6%) and on cabbage (1·3%) samples from the small‐scale farm. The genus Salmonella was absent in borehole water but was detected in the holding dam water (<1%) from commercial farm A. Salmonella sequences were present in river water (<1%) and on cabbages (1·9%) from the small‐scale farm but were not detected on cabbage samples from the one commercial farm or the homestead gardens. CONCLUSION: Water sources quality used for irrigation greatly influences the microbial dynamics of the irrigated crop. SIGNIFICANCE AND IMPACT OF THE STUDY: Microbial biomes in irrigation water and on leafy greens were described with pyrosequencing and revealed insights into prevalence of potential and opportunistic pathogens across different production systems.