The increase of the burden on environment caused by development and climate change has affected wild species habitat. To make effective strategy to conserve freshwater ecosystem and biodiversity, knowing a species distribution or total biomass in large area can be important information. For this aim, monitoring method is usually based on visual detection, counting or trapping; however, these traditional monitoring methods have difficulties of time consuming, monetary and human costs. Furthermore, these methods have been applied limitedly to qualitative information such as exist or absent research, and it is difficult to estimate potential biomass through the upstream and the downstream of rivers. These days, environmental DNA (eDNA) analysis has been known as novel molecular technique and it can lead to the solution of these problems. eDNA means the DNA which can be extracted from environment such as water bodies, and it originates from animal metabolite like the feces, saliva or skin cells. It enables to detect the presence of species specific base sequence of DNA, and can be expected to have considerable advantage to estimate the presence and population of a species. eDNA study has been promoted in experimental aquarium and closed water area such as pond, lake, and small lagoon. From these studies, it is revealed that eDNA is degraded by bacteria or DNAase in water bodies, and collapsed by UV, chemical substances and there is a positive correlation between the number of eDNA copies and biomass or density of individuals. On the other hand, eDNA study in a river is limited because its various environment and physical condition and the effect of advective diffusion make it complicated. Moreover, the studies are mostly focused on specific rare species or important species for fishery resources; however estimating the mass of the bottom of ecological pyramid (i.e. algae, primary producer and aquatic invertebrates, primary consumer) is a key to comprehensively understand and manage a river ecosystem.
In this study, we applied an eDNA approach to invertebrates and revealed longitudinal and seasonal profiles of the eDNA in the Hirose River, Japan. For this aim, we conducted sampling and quantitated the mass of eDNA using qPCR. We sampled 2L of stream water at three reaches of up-, middle- and downstream whose land uses consist of different properties (i.e., forested, agricultural, and urbanized) once per a month along the river through August to December 2015. As the primers for PCR, we focused on the detection of mitochondrial DNA, cytochrome b gene, which is able to detect universal gene area for almost all invertebrate species. Using the result, we can assess the river environment to discuss river design in the future and to consider the relationship between flood and environment. Furthermore, it is indicated that eDNA also can extend the possibility of continual survey to evaluate wasted water and land use change.