SGER: Detection of Trout Species by PCR Amplification of DNA from Stream Water

University Of Montana, Missoula MT

Investigators

Abstract

Describing and understanding the distribution of fishes across whole river basins is a central issue in landscape ecology, population biology, and invasive species research. The PI proposes to develop methods to detect aquatic species by PCR amplification of DNA from cellular materials in stream water. The project focuses on determining the presence or absence of salmonid fishes (trout and char) in streams by amplification of species-specific DNA sequences from cells shed by fish into the water. The particle concentration and assay sensitivity required for this work appear feasible based upon recent use of filtration and PCR methods to detect protozoan parasites (giardia, cryptosporidia) in public drinking water. However, the extreme dilution of biotic materials in clear mountain streams may be problematical because the quantity, fate and condition of cellular debris shed by fish into the water are unknown. In addition, the optimal methods to separate these materials from plankton, algae, and decaying plant materials that may compete with salmonid DNA in assays and may inhibit PCR also need to be developed. The proximate goal is to develop a procedure to detect fish in remote and inaccessible streams, without resorting to laborious and inefficient field methods. Applications of the methods developed will have much greater range, however, as the results will suggest modifications for assays of many other aquatic species.