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A 16S ribosomal DNA clone library from Zhenjiang municipal sewage was established by PCR using suitable primers. The total of 100 clones was selected by plasmid extraction and PCR identification. 31 clones were obtained and sequenced. From the DNA databases all sequences had above 94% similarity to reference sequences of the closest related organisms. The sequences analysis indicated that there were identified as Arcobacter sp., Fusobacterium necrophorum, anaerobic bacterium and Clostridium sp., Acinetobacter sp. and Comamonas sp. in the municipal sewage. And Arcobacter sp. predominates in the study, constituting 83.9% of the 31 clones. The results also showed that these bacteria were almost pathogenic organisms. Use of this molecular method establishes the rapid detection of bacterial different from those isolated and identified by traditional cultures. The bacteria detection in Zhenjiang municipal sewage provides reference for the deep study of pathogenic organisms and the assessment of sewage discharge security.