Microbial Source Tracking and Its Potential to Assist Edna Assay for Asian Carp Monitoring

The study is to develop a genetic-based method that can complement the current surveillance methods for Asian carps (AC), an invasive fish species of many water bodies in the U.S.  We propose to determine the relative abundance of AC through the quantification of the microbial populations unique to the AC gut microbiota in a manner similar to microbial source tracking.  Microbial source tracking is based on the concept that microbes from a polluted site can be traced to an animal, and thus indicating the origin of fecal contamination.  This approach has been successfully applied to identify the sources (e.g. human, cow, swine, and water fowl) of fecal contamination in rivers, lakes, and drinking water distribution systems.  Similarly, key microbial populations can be identified in the fecal matter of AC, which can then be used for the development of a genetic-based method to detect the presence of AC in water bodies. To do so, differences in the gut flora between indigenous planktivorous gizzard shad (GZSD) and silver carp (SVCP) (an invasive Asian carp) obtained from the middle region of the Mississippi river basin were investigated using 16S rRNA gene pyrosequencing. Unique and shared OTUs and OTUs with different abundances in each gut type were also identified with three OTUs from the order Bacteroidales, the genus Bacillariophyta, and the genus Clostridium found to have significantly higher (14.1%-22.7%) abundances in GZSD hindgut than in SVCP hindgut samples. These differences were presumably caused by the differences in the types of food sources ingested, the gut morphology and digestion, and the physiological behavior between GZSD and SVCP.  The unique populations identified can further be used as biomarkders for the monitoring of SVCP populations by developing specific quatitative PCR based on these biomarkers.  These biomarkers will be validated, and if successuful, can be used to complement the eDNA assay currently used.