Projection range of eDNA analysis in marshes: a suggestion from the Siberian salamander (Salamandrella keyserlingii) inhabiting the Kushiro marsh, Japan.

Daiki Takeshita,Kousuke Ikeda,Maslin Osathanunkul,Toshifumi Minamoto,Shigeharu Terui,Takashi Mitsuzuka

doi:10.7717/peerj.9764

Abstract

BackgroundFreshwater ecosystems are rapidly declining. The Siberian salamander (Salamandrella keyserlingii) which inhabits the Kushiro marsh in Hokkaido, Japan has lost some habitat due to human activity. There are many challenges associated with conventional monitoring methods, including cost, the need for specialist personnel, environmental impact, and ability to detect the presence of this species; thus, we investigated the feasibility of using environmental DNA (eDNA) analysis to detect its presence and identify its breeding grounds.MethodsWe performed tank experiments to confirm eDNA emission from egg sacs, larvae, and adult Siberian salamanders in the water. We also performed water sampling and visual observation of egg sacs in the Kushiro marsh during the end of the breeding season and the larval season.ResultsThe tank experiments found eDNA emission from all growth stages. It also implied concentrated emissions just after spawning and after hatching, and limited emissions during the incubation phase in egg sacs. We also detected eDNA in the field, likely reflecting the distribution of egg sacs or larvae. Combining this data with visual observations, it was determined that the eDNA results from the field were best explained by the number of egg sacs within 7–10 m of the sampling point.ConclusionsThe results of this investigation show that the breeding sites and habitats of marshland species can successfully be monitored using eDNA analysis. They also suggest that the eDNA results from the marshes may reflect the biomass that is in close range to the sampling point. These results support the increased use of eDNA analysis in marshes and provide knowledge that could improve the interpretation of future results.

Highlights

Freshwater ecosystems, provide habitat for at least 126,000 known species of mollusks, insects, fishes, reptiles, mammals, and plants (Balian et al, 2008), and are rapidly declining worldwide
We detected environmental DNA (eDNA) in the field, likely reflecting the distribution of egg sacs or larvae. Combining this data with visual observations, it was determined that the eDNA results from the field were best explained by the number of egg sacs within 7–10 m of the sampling point
The amount of eDNA detected in the negative controls was less than one-tenth of that found in other samples on the same sampling date (Table S2)

Summary

Introduction

Freshwater ecosystems, provide habitat for at least 126,000 known species of mollusks, insects, fishes, reptiles, mammals, and plants (Balian et al, 2008), and are rapidly declining worldwide. Freshwater ecosystems are strongly affected by habitat modification, fragmentation, and destruction; invasive species; overfishing; pollution; forestry practices; disease; and climate change (Grooten & Almond, 2018). In many cases, these combined threats have led to catastrophic declines in freshwater biodiversity (Collen et al, 2014; Cumberlidge et al, 2009). Environmental DNA (eDNA) analysis has been proven to be an effective tool to monitor species It allows for the estimation of the presence/absence (Ficetola et al., 2008), distribution (Thomsen et al, 2012), and biomass (Takahara et al, 2012) of target species via analysis of DNA found in the environment through water sampling, DNA extraction, and molecular biological methods such as PCR and next-generation sequencing. There are many challenges associated with conventional monitoring methods, including cost, the need for specialist personnel, environmental impact, and ability to detect the presence of this species; we investigated the feasibility of using environmental DNA (eDNA)

Methods

Results

Discussion

Conclusion