Detection of bacteria and enteric viruses from river and estuarine sediment

Abstract

River and estuarine sediment is suggested to play an important role in transmission of microbes in the water environment. However, although effective methods to recover bacteria from sediment are available, preparation methods for viruses, especially using molecular detection methods, are still under development. In this study, preparation methods for viruses in sediment were evaluated by qPCR methods. Thirty-six sediment samples were collected from the Takagi River and the Matsushima Bay receiving the Takagi River from December 2007 to May 2008 and tested for fecal coliforms, Bacteroides spp., human adenoviruses and Cryptosporidium spp. As the results, recovery rate of a preparation method for RNA viruses was low (Geometric mean: 3.3%, n=11), while that for DNA viruses was relatively high and stable (Geometric mean: 37%, n=6). The detection rate was the highest for fecal coliforms (92%, 33/36), followed by Bacteroides spp. (61%, 22/36). Human adenoviruses and Cryptosporidium spp. were not detected partly due to the limited sediment volume (0.5 g) applicable to the DNA extraction kit. Although the high positive rates of fecal coliforms and Bacteroides showed that the preparation methods for fecal indicator bacteria were applicable for environmental application, it was recommended that more effective methods for enteric viruses and protozoa be developed for direct monitoring of pathogens in sediment.