M Jongman1, L Chidamba1, L Korsten1. 1. Department of Plant and Soil Sciences, University of Pretoria, P/Bag X20 Hatfield, Pretoria, South Africa.
Abstract
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.
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.