Jongman M, Chidamba L, Korsten L
Department of Plant and Soil Sciences, University of Pretoria, P/Bag X20 Hatfield, Pretoria, South Africa.
J Appl Microbiol. 2017 Oct;123(4):1043-1053. doi: 10.1111/jam.13558.
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.
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.
Water sources quality used for irrigation greatly influences the microbial dynamics of the irrigated crop.
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.
采用焦磷酸测序法研究灌溉水微生物质量对商业农场、小规模农场以及家庭菜园生产的绿叶蔬菜的影响。
利用细菌16S rDNA的V1 - V3高变区的下一代测序分析来比较灌溉水源和绿叶蔬菜上的细菌多样性。在所有分析的样本（12个）中，发现变形菌门（64.5%）、γ-变形菌纲（56.6%）和气单胞菌属（14.4%）占主导地位。在所检测样本中检测到的所有大肠杆菌序列中，来自一个商业农场的生菜（16.3%）所含序列比来自小规模农场（1.3%）或家庭菜园（1.9%）的卷心菜更多。在小规模农场的灌溉水（4.6%）和卷心菜（1.3%）样本中均检测到了大肠杆菌序列。商业农场A的井水样本中未检测到沙门氏菌属，但在其蓄水池水中检测到了沙门氏菌属（<1%）。小规模农场的河水（<1%）和卷心菜（1.9%）样本中存在沙门氏菌序列，但在一个商业农场或家庭菜园的卷心菜样本中未检测到。
用于灌溉的水源质量极大地影响了灌溉作物的微生物动态。
通过焦磷酸测序法描述了灌溉水和绿叶蔬菜上的微生物群落，并揭示了不同生产系统中潜在和机会性病原菌的流行情况。
